DNA Replication and Irreducible Complexity

[Laurence A. Moran]

DNA Replication and "Irreducible Complexity"

Julie Thomas said,

"I'd like to add to Behe's hypothesis of IC and ultimately use
my reply to the IC critic's points about DNA replication to work
through these ideas. In the past, I have noted that there are
several layers of IC. In talking about DNA replication, I want
to propose three such layers. This discussion will repeat several
of the points above, however, they will now be placed in a
particular context. Let's consider the three layers.

1. Thematic IC - In this case, we are talking about IC themes
regardless of the specific players. This type of IC is more general
and theoretical. For example, the replication of DNA itself
(regardless of the specific players) is a candidate. We will see
that various activities must work together to replicate DNA: the
origin of replication; a factor that binds to the origin; a
helicase that unwinds the DNA; single-stranded binding proteins
that stabilize the ssDNA; a factor that lies down primer; a
polymerase that synthesizes the DNA using one strand as a template;
a topoisomerase the removes the strain that results from unwinding
the DNA; and a ligase the joins fragments together. It is hard to
imagine DNA replication occurring without all these *activities*.
Remove any, and no effective DNA replication occurs. Thus, the
general process of DNA replication is thematically IC."

Let me begin by saying that I appreciate what Julie is trying to do here.
She is trying to focus the discussion and prevent us from wandering off or
gettng involved in flame wars over terminology. She has taken care to
distinguish between "thematic", "systematic" and "molecular" irreducible
complexity in her essay. I will try and do the same.

Julie says that "It is hard to imagine DNA replication occurring without
all these *activities*." This is not correct. I don't have much difficulty
imagining such a situation. But I don't have to "imagine" because there
are known examples of DNA replication that do not require all these
activities.

In this case Julie is confusing thematic DNA replication and a particular
systematic version - namely the replication of large chromosomes. I assume
that what she really means is that she can't imagine how modern, large
bacterial chromosomes can be replicated without these activities. But that's
a different kettle of fish entirely. What we are concerned about is how the
modern system came to be (evolution or de novo design). In that case the
ability to "imagine" or demonstrate that simpler systems will work is highly
relevant.

Julie's lack of imagination may lead her to conclude that DNA replication
was designed by aliens but the rest of us need not be bound by her
limitations. In the postings that follow I will be examining the "alien
design" model that Julie proposes. By "alien design" I mean the thesis
that the modern form of DNA replication in bacteria could only have arisen
by instantaneous creation de novo. The "aliens" who created such a system
could be one or more supernatural beings (i.e. gods or godesses) but I
assume that Julie does not want to restrict her proposal to such entities
since that brings religion into the discussion and Julie has taken great
care to avoid this.

"Evidence" for Julie's alien design model is based largely on negative
inference as many others have pointed out. She suggests that some systems
are so complicated and interconnected that it would be impossible to
imagine or reconstruct a natural explanation involving evolution from a
primitive ancestor. But the absence of evidence is not evidence of absence.
This is a point that Julie consistently tries to obfuscate.

Julie and her like-minded friends are fond of the term "irreducible
complexity". This is a rhetorical device that is designed to convert the
absence of evidence into something positive that is subject to scientific
analysis (i.e. that the system will not work if any part is removed). We
are not fooled by this cheap trick. The fundamental point is that alien design
proponents are basing their argument entirely on the lack of hard proof of
natural causes. Lacking such proof they assume the existence of aliens who
must have done the deed.

There is, of course, no proof that such aliens exist or that they existed in
the past. The assumption of "designers" is something that they bring to
the table from outside of science. At least that's how it appears to this
observer. On the other hand, there are times when Julie almost seems to be
offering irreducible complexity as proof of the existence of aliens. This
is nothing more than the argument from design dressed up for the 90's.

It's an old argument. Here's what Clarence Darrow had to say about it sixty-
seven years ago (1932),

"To discover that certain forms and formations are adjusted for
certain action has nothing to do with design. None of these
developments are perfect, or anywhere near so. All of them,
including the eye, are botchwork that any good mechanic would
be ashamed to make. All of them need constant readjustment, are
always out of order, and are entirely too complicated for
dependable work. They are not made for any purpose; they simply
grew out of needs and adaptations; in other words, they happened.
Just as God must have happened, if he exists at all."

I will be returning to this theme many times in the next few days. It's
not good enough to claim that a system is simply "irreducibly complex" if
you are trying to prove that intelligent aliens exist. You also have to
show that the system is well designed, so well designed that there had
to be aliens behind it.

Larry Moran

[Peter Nyikos]

CC: Julie and Laurence, because the automatic moderator of talk.origins
has been especially quirky of late, kicking back posts
apparently at random even when the address talk-o...@moderators.uu.net
is used.

What's talk.philosophy.humanism doing up there? Are you a
member of the Humanist Society, Dr. Moran?

lam...@bioinfo.med.utoronto.ca (Laurence A. Moran) writes:

[disarming opening spiel deleted to get down to the brass tacks
of this particular post:]

>Julie says that "It is hard to imagine DNA replication occurring without
>all these *activities*." This is not correct. I don't have much difficulty
>imagining such a situation. But I don't have to "imagine" because there
>are known examples of DNA replication that do not require all these
>activities.

Viral ones?

>In this case Julie is confusing thematic DNA replication and a particular
>systematic version - namely the replication of large chromosomes. I assume
>that what she really means is that she can't imagine how modern, large
>bacterial chromosomes can be replicated without these activities. But that's
>a different kettle of fish entirely.

But worth addressing also.

> What we are concerned about is how the
>modern system came to be (evolution or de novo design). In that case the
>ability to "imagine" or demonstrate that simpler systems will work is highly
>relevant.

Sure. But those are different systems, with fewer parts, and the challenge
is in showing how to get from there to replication of modern, large
bacterial chromosomes.

>Julie's lack of imagination may lead her to conclude that DNA replication
>was designed by aliens but the rest of us need not be bound by her
>limitations.

Nor is she bound by those Strawwoman Julie limitations.

> In the postings that follow I will be examining the "alien
>design" model that Julie proposes. By "alien design" I mean the thesis
>that the modern form of DNA replication in bacteria could only have arisen
>by instantaneous creation de novo.

More Strawwoman Julie stuff. In the first place, "de novo" traditionally
means the creation of matter from nothing; that is not at all
necessary to contemplate at this stage. Secondly, "instantaneous"
is either an enormous hyperbole or another strawman creation
of yours. Thirdly, Julie never claimed intelligent
design of these systems is the ONLY reasonable hypothesis,
only that she suspects it is the BEST hypothesis.

> The "aliens" who created such a system
>could be one or more supernatural beings (i.e. gods or godesses) but I
>assume that Julie does not want to restrict her proposal to such entities
>since that brings religion into the discussion and Julie has taken great
>care to avoid this.

So why don't you mention the other alternative, namely production
of prokaryotes in a laboratory by an alien species that has
a simpler cellular replication method of its own, to avoid
infinite regresses?

>"Evidence" for Julie's alien design model is based largely on negative
>inference as many others have pointed out.

Correction: as many other philosopher-wannabes, arguing in an
intensely personalist mode, have claimed.

A more objective treatment would say that she poses a challenge
to everyone to come up with an explanation of the kind that
she is characterized as being unable to imagine:

>She suggests that some systems
>are so complicated and interconnected that it would be impossible to
>imagine or reconstruct a natural explanation involving evolution from a
>primitive ancestor.

She has some candidates for such roles, yes, and the months-long
example of the bacterial flagellum has demonstrated the reluctance
of everyone else to even try to come up with such natural
explanations. Instead we've seen flights of fancy like the
highly fictitious [and entertaining if one does not take
it too seriously] evolution of a mousetrap which others, including
Howard Hershey and myself, have brought crashing to earth.

> But the absence of evidence is not evidence of absence.
>This is a point that Julie consistently tries to obfuscate.

How utterly stereotyped your treatment of Strawwoman Julie is!
I've come to expect much better of you, Dr. Moran. One
would hope that your own hostile reception by the likes
of Steve LaBonne, Matt Wiener, and Wade Hines and, more
recently, Mike Noren, would have taught you to be a little
more circumspect in your criticism of others.

>Julie and her like-minded friends are fond of the term "irreducible
>complexity". This is a rhetorical device that is designed to convert the
>absence of evidence into something positive that is subject to scientific
>analysis (i.e. that the system will not work if any part is removed).

What's with the "rhetorical device" spiel? Take it out, and
you have a perfectly reasonable description of a perfectly
reasonable concept.

>We are not fooled by this cheap trick.

Worse and worse. You sound as propagandistic as an announcer for the defunct
Soviet news agency Tass.

>The fundamental point is that alien design
>proponents are basing their argument entirely on the lack of hard proof of
>natural causes.

I note the Strawwoman Julie implicit in "hard proof" when you
have not even established the existence of a plausible scenario
for getting from there to here.

> Lacking such proof they assume the existence of aliens who
>must have done the deed.

It must really be fun to knock down one straw woman after another.
When will you ever get around to talking about the scientific
aspects of Julie's writing--or to any aspects of Julie's writing,
for that matter?

>There is, of course, no proof that such aliens exist or that they existed in
>the past.

If there were, we wouldn't be having this discussion, would we now?
Julie's case would have been closed and we could all be talking
about something else.

>The assumption of "designers" is something that they bring to
>the table from outside of science.

What table? The humanist table?

> At least that's how it appears to this
>observer. On the other hand, there are times when Julie almost seems to be
>offering irreducible complexity as proof of the existence of aliens. This
>is nothing more than the argument from design dressed up for the 90's.

And you are using stereotyped arguments against it without
even trying to dress them up for the 90's:

>It's an old argument. Here's what Clarence Darrow had to say about it sixty-
>seven years ago (1932),

Gee, Clarence Darrow. What were his scientific credentials?
What were his philosophical credentials?

> "To discover that certain forms and formations are adjusted for
> certain action has nothing to do with design.

"has nothing to do with"--typical either/or thinking. Even
atheist Dawkins, in _The Blind Watchmaker_, had more respect
for Paley than this.

>None of these
> developments are perfect, or anywhere near so. All of them,
> including the eye, are botchwork that any good mechanic would
> be ashamed to make.

Hume's old argument in _Dialogues Concerning Natural Religion_, dressed
down for the 1930's.

> All of them need constant readjustment, are
> always out of order, and are entirely too complicated for
> dependable work. They are not made for any purpose; they simply
> grew out of needs and adaptations; in other words, they happened.
> Just as God must have happened, if he exists at all."

If this is as sophisticated as your arguments are going to
get, Dr. Moran, you might as well return to your long vacation
from talk.origins. Whatever made you end it, anyway?

>I will be returning to this theme many times in the next few days.

I'm burning with anticipation. Not.

> It's
>not good enough to claim that a system is simply "irreducibly complex" if
>you are trying to prove that intelligent aliens exist. You also have to
>show that the system is well designed, so well designed that there had
>to be aliens behind it.

For someone who berated Julie for laying down "ground rules", you
certainly lay down some demanding ones yourself.

I for one have rejected YOUR ground rules from the beginning,
being familiar with the Francis Crick-Leslie Orgel theory of
directed panspermy. Until YOU can find someone producing a living
cell that has a better DNA replication system than the existing
one, you have no reason to believe that an alien intelligent
species, with our level of intelligence, could have come up
with a better system that actually WORKS.

Peter Nyikos -- standard disclaimer --
Professor, Dept. of Mathematics
University of South Carolina
Columbia, SC 29208

[Julie Thomas]

In his reply to my article on IC and DNA replication, Larry Moran says:

>Julie Thomas said,

> "I'd like to add to Behe's hypothesis of IC and ultimately use
> my reply to the IC critic's points about DNA replication to work
> through these ideas. In the past, I have noted that there are
> several layers of IC. In talking about DNA replication, I want
> to propose three such layers. This discussion will repeat several
> of the points above, however, they will now be placed in a
> particular context. Let's consider the three layers.

> 1. Thematic IC - In this case, we are talking about IC themes
> regardless of the specific players. This type of IC is more general
> and theoretical. For example, the replication of DNA itself
> (regardless of the specific players) is a candidate. We will see
> that various activities must work together to replicate DNA: the
> origin of replication; a factor that binds to the origin; a
> helicase that unwinds the DNA; single-stranded binding proteins
> that stabilize the ssDNA; a factor that lies down primer; a
> polymerase that synthesizes the DNA using one strand as a
> template; a topoisomerase the removes the strain that results from

> unwinding the DNA; and a ligase the joins fragments together. It is

> hard to imagine DNA replication occurring without all these

> *activities*. Remove any, and no effective DNA replication occurs.

> Thus, the general process of DNA replication is thematically IC."

Larry replies:

>Let me begin by saying that I appreciate what Julie is trying to do
>here. She is trying to focus the discussion and prevent us from
>wandering off or gettng involved in flame wars over terminology. She
>has taken care to distinguish between "thematic", "systematic" and
>"molecular" irreducible complexity in her essay. I will try and do the
>same.

>Julie says that "It is hard to imagine DNA replication occurring without

>all these *activities*." This is not correct. I don't have much difficulty
>imagining such a situation. But I don't have to "imagine" because there
are known examples of DNA replication that do not require all these
activities.

I'll be looking forward to these known examples of DNA as I suspect I
know what you are talking about. But I do concede that I ought not
have used the "imagination" test as the issues really do not revolve
around the things people can imagine. So let me rephrase my claim:

> "We will see
> that various activities must work together to replicate DNA: the
> origin of replication; a factor that binds to the origin; a
> helicase that unwinds the DNA; single-stranded binding proteins
> that stabilize the ssDNA; a factor that lies down primer; a
> polymerase that synthesizes the DNA using one strand as a
> template; a topoisomerase the removes the strain that results from

> unwinding the DNA; and a ligase the joins fragments together. The
> evidence strongly suggests that DNA replication does not, and
> probably cannot, occur without all these *activities*. Remove any,

> and no effective DNA replication occurs. Thus, the general process of
> DNA replication is thematically IC."

Larry said:

>In this case Julie is confusing thematic DNA replication and a particular
>systematic version - namely the replication of large chromosomes.

Not quite. You are correct in that I have focused attention on the
replication of chromosomes and this is thus a systematic perspective.
However, the systems themselves revolve around the same theme thus
this is perhaps better referred to as thematic-systematic IC. However, I
will still hold to the strictly thematic claim (tentatively, of course) until
there is evidence suggesting otherwise.

>I assume that what she really means is that she can't imagine how
>modern, large bacterial chromosomes can be replicated without these
>activities.

Well, in the abstract I clearly said:

"Bacterial chromosomal DNA replication is then considered from these
various perspectives of IC."

As for the adjective "modern," it tends to bias the discussion as it
implies bacterial chromosomal replication was at one time different in
the past. But there is no evidence for this assumption.

As for not being able to imagination, it's really a case where there is no
evidence that bacterial chromosomes can be replicated without these
general activities. Furthermore, I would add that there is no evidence
to suggest cells can exist without chromosomes.

>But that's a different kettle of fish entirely. What we are concerned

>about is how the modern system came to be (evolution or de novo
>design). In that case the ability to "imagine" or demonstrate that
>simpler systems will work is highly relevant.

I do not think the ability to imagine is relevant. However,
demonstration of a simpler system might be very relevant.

>Julie's lack of imagination may lead her to conclude that DNA
>replication was designed by aliens but the rest of us need not be bound
>by her limitations.

First of all, I did not conclude that "DNA replication was designed by
aliens." I simply outlined the IC nature of DNA replication which in turn
strongly suggests the system was designed. The identity of the designer
is a separate issue.

As for my limitations, yes, I attempted to limit myself with the
evidence.

>In the postings that follow I will be examining the "alien design" model
>that Julie proposes.

Where did I say anything about aliens?

>By "alien design" I mean the thesis that the modern form of DNA
>replication in bacteria could only have arisen by instantaneous creation
>de novo.

Then why do you call this "alien design" rather than "design" or
"intelligent design?" It looks like to are trying to label my position as
something that stems from a UFO nut. Above you noted:

"She is trying to focus the discussion and prevent us from wandering off
or gettng involved in flame wars over terminology."

But you don't seem to helping matters with terms like "alien."

More importantly, if this is the thesis you are going to write about,
I hope you didn't put too much effort into it yet as you are barking up
the wrong tree. My thesis was simply that bacterial chromosomal DNA
replication is IC. This thesis does not require me to posit that the
process arose by "instantaneous creation de novo" (although IC is not
inconsistent with this claim). IC may also entail the creation of a mosaic
analogous (but superior) to the workings of molecular biologists.

>The "aliens" who created such a system could be one or more
>supernatural beings (i.e. gods or godesses) but I assume that Julie does
>not want to restrict her proposal to such entities since that brings
>religion into the discussion and Julie has taken great care to avoid this.

I still don't understand why you think the term "aliens" is required.
Intelligence is a far better term as it is more neutral.

>"Evidence" for Julie's alien design model is based largely on negative
>inference as many others have pointed out.

To point out something is to specify something that objectively exists.
Others have not "pointed out" anything other than to draw attention to
their perceptions of things.

>She suggests that some systems are so complicated and interconnected
>that it would be impossible to imagine or reconstruct a natural
>explanation involving evolution from a primitive ancestor.

Where did I suggest this? In fact, I just did a word search of my entire
50 page article and not once did the word "impossible" appear. I'm
sorry Larry, but you have simply put words in my mouth and thus your
characterization of my article is seriously flawed. After all, I've always
admitted that someone can "imagine" a natural explanation involving
evolution from a primitive ancestor. So what? What matters is
whether this imagination is a fantasy or reflective of reality.

>But the absence of evidence is not evidence of absence. This is a point
>that Julie consistently tries to obfuscate.

Instead of accusing me of obfuscation, why not simply consider the
possibility that we may not be communicating effectively.

First, the claim, "the absence of evidence is not evidence of absence." Is
this an absolute truth that is always true? Often times in science,
the absence of evidence is interpreted as evidence of absence. After all,
if there was absence, we would expect no evidence. For example, if
there is no evidence that gene X is part of the process of DNA
replication, scientists don't continue trying to find where gene X fits into
DNA replication because they view this absence of replicating activity
for gene X to mean gene X is not part of DNA replication. They wouldn't
claim this with certainty, but they would probably argue it is a
reasonable, yet tentative, inference

Now, if you claim DNA replication evolved from a primitive ancestor
along Darwinian lines, I simply note there is no evidence for this claim
(or at the very most, the evidence is very weak). If, as I believe, design
is a better explanation for the IC nature of DNA replication, I *then*
consider your absence of evidence and say "no wonder there is no
evidence; y'all are pursuing a dead end." Thus, the failure of Darwinism
is *supporting* evidence.

I think there is much confusion concerning this topic. My major
intention in focusing on IC is not to come up with an anti-darwinian
argument. I don't need that. When it comes to DNA replication or the
bacterial flagellum (and many other things to come), I am simply not
convinced that Darwinism has anything to do with their origin. But I
am still quite interested in their origin. Should I wait, and hope, that
someday folks like Paul Myers will come up with a story that will
probably only convince those hoping to be convinced? Nah. Thus, I
look for alternative explanations that *I* find far more intellectually
satisfying. And, as I see it, Michael Behe has given me the key. So I
begin to look afresh at these systems with Behe's key and it generates
new insights and new lines of inquiry. Put simply, it's a way to
interpret data and do science under a design paradigm. That's why I
said to Paul that "Ill go my way and y'all go yours." Would you be
another one who is bothered by that?

>Julie and her like-minded friends are fond of the term "irreducible
>complexity".

It's not a matter of being fond of a term. It's matter of
exploring the utility of a fresh concept.

>This is a rhetorical device that is designed to convert the absence of
>evidence into something positive that is subject to scientific analysis

>(i.e. that the system will not work if any part is removed). We

>are not fooled by this cheap trick.

Rhetorical device? Cheap trick? Could you be a tad more insulting?

Look, when you say the "absence of evidence," I must ask, "evidence for
what?" The term "absence of evidence" is meaningless by itself. Now,
did I argue there was an absence of evidence for the IC nature of DNA
replication? Nope. I argued that DNA replication *is* IC.

Now I assume you mean "absence of evidence" for a Darwinian origin to
DNA replication. Well, yes, this is *also* true. But there is no
conversion going on. Absence of evidence for a Darwinian origin simply
means I have no good reason to think a Darwinian origin is part of the
true explanation. I then simply approach the topic differently and
explore a concept so that it is subject to scientific analysis. At the very
least, it is fun! Then I look over at you and see you struggling to come
up with even a just-so story. I see folks getting emotional and wanting
to talk instead about invisible pink unicorns. Etc. One example of this
strangeness may not be all that significant, but if the same dynamic
holds in the analysis of system after system after system (even allowing
for some vague just-so stories), I'm going to start to *really* believe
there is a reason for this dynamic.

>The fundamental point is that alien design proponents are basing their

>argument entirely on the lack of hard proof of natural causes. Lacking

>such proof they assume the existence of aliens who must have done the
>deed.

It would be polite if you would refrain from labeling me an "alien design
proponent." I have gone to great lengths to refrain from speculating
about the designer(s).

More importantly, you completely misunderstand my position. It has
nothing to do with "hard proof" or the lack of it. In fact, a desire for
"hard proof" is not scientific.

>There is, of course, no proof that such aliens exist or that they existed
>in the past.

Again, what does proof have to do with science. There is likewise no
proof that life ever existed on Mars, but scientists and engineers plan on
looking for it (or its traces).

>The assumption of "designers" is something that they bring to
>the table from outside of science.

Nope. It is something that is inferred, as the best explanation, from the
data. Science often infers the unseen to explain what is seen.

>At least that's how it appears to this observer.

That's fair. But since you also seem to think I appear to be arguing for
alien designers because you can't show it is possible that DNA
replication evolved, perhaps you should question your perceptions.

>On the other hand, there are times when Julie almost seems to be
>offering irreducible complexity as proof of the existence of aliens. This
>is nothing more than the argument from design dressed up for the 90's.

Oh please. If you interpret my articles as one big "Argument From
Design," you will continually be clueless about my writings.

>It's an old argument. Here's what Clarence Darrow had to say about it
>sixty-seven years ago (1932),

> "To discover that certain forms and formations are adjusted for
> certain action has nothing to do with design.

How did Darrow know this? He has simply confused his opinions with a
statement of fact.

>None of these developments are perfect, or anywhere near so.

Duh. Is this relevant? Er, no. My car is not perfect either. So it has
nothing to do with design, right?

>All of them, including the eye, are botchwork that any good mechanic
>would be ashamed to make.

Yeah, right. Find me one good mechanic who can make an eye.
Darrow's arrogance is astounding.

>All of them need constant readjustment, are always out of order, and
>are entirely too complicated for dependable work.

So Darrow admits he was incapable of doing anything dependable? Is
this his excuse for losing the case? ;)

>They are not made for any purpose; they simply grew out of needs and
>adaptations; in other words, they happened.

Such faith! Of course, there is no evidence for thinking Darrow's faith
has anything to do with the origin of DNA replication.

>Just as God must have happened, if he exists at all."

"God" grew out of needs and adaptations?? Was this all supposed to be
a serious argument of some sort?

>I will be returning to this theme many times in the next few days.

I'll be here (although other obligations may prevent prompt replies).
BTW, I'm still waiting for that evidence that the bacterial
flagellum evolved from a "primitive secretory apparatus."

>It's not good enough to claim that a system is simply "irreducibly
>complex" if you are trying to prove that intelligent aliens exist.

Says who? You? The Gang?

>You also have to show that the system is well designed, so well
>designed that there had to be aliens behind it.

You confuse science with philosophy. Scientific explanations do not
entail "had to be" claims. That's much too certain.

As far as determining if something is "well-designed," that's a subjective
point that depends on knowledge of the designer('s) intentions and
one's taste. But if you think it is relevant, you should probably start by
defining what you consider a "good design."

[Richard Harter]

lam...@bioinfo.med.utoronto.ca (Laurence A. Moran) wrote:

[snip]

Bravo! Double bravo!! It is such a delight to see such a clearly
written and informative article appearing like a jewel in the midst of
the dung heap of clap trap and snidery.

Richard Harter, c...@tiac.net, The Concord Research Institute
URL = http://www.tiac.net/users/cri, phone = 1-508-369-3911
Men were designed for short, nasty, brutal lives.
WOmen are designed for long, miserable ones.

[Laurence A. Moran]

The Origin of Replication

Julie Thomas claims that DNA replication is a alien designed system based on
the fact that it is so complex that it couldn't have arisen by natural causes.

One of the components she discusses is the origin of replication. I'd like
to correct some of the errors in her essay and then present some additional
information that she left out.

Julie says,

"The origin of replication (often called the DnaA box) is a
specific set of nucleotide sequence crucial for the initiation
of DNA replication. From a thematic IC perspective, the origin
appears crucial on bacterial cells. Let's consider it in detail
as it has been described in various species of bacteria who
last shared a common ancestor 1.2 billion years ago."

All modern species of bacteria have a specific site(s) on each of their
chromosomes where DNA replication is initiated. This site is called the
origin of replication. There are quite a few different kinds of origins,
the one found on most large chromosomes is called oriC. The E. coli origin
is an example. Other types of origins are often found on plasmids,
including those large plasmids that we now recognize as separate chromosomes.
OriT is the origin of DNA replication site on F-plasmids in E. coli. DNA
replication begins at this site during conjugative transfer even when the
plasmid is part of the main chromosome.

From a thematic IC perspective, one or more origins of replication seems
to be a ubiquitous component of DNA replication of large bacterial
chromosomes. However, there are different kinds of origins employing different
strategies of initiation. When Julie refers to "it" she means a specific
origin (i.e. systematic IC) in certain bacteria. The "it" appears to be oriC.

The generic oriC consists of a region that is recognized by the DNA-binding
protein DnaA. Specific binding sites are called DnaA boxes. Strictly speaking,
the DnaA box is only one part of one type of origin. Many distantly related
bacteria have this kind of origin - an oriC sequence. OriC is usually located
in the vicinity of the dnaA gene (more about that later). This is the gene
that encodes DnaA, the protein that plays a key role in initiation at oriC
regions. Many lines of evidence indicate that all bacteria share a common
ancestor that lived about two billion years ago. Thus, the oriC type of
initiation must be at least that old. If aliens made it then they must have
done it at that time. If it evolved then it must have evolved before then.

Eukaryotic chromosomes have multiple origins of replication even when the
chromosomes are smaller than typical bacterial chromosomes. Since all
available evidence indicates that eukaryotes and prokaryotes share a
common ancestor this means that it is impossible to tell which condition
(unique or multiple origins) is primitive and which is derived. It is
reasonable to propose that multiple origins were present in primitive
cells and the presence of unique origins in modern bacteria is the result
of evolution that eliminated all but one site as the genomes were stream-
lined. This is not an important point but it illustrates how easy it is
to be led astray by assuming that bacteria are "primitive". We must try
and avoid such thinking wherever possible.

DNA replication in eukaryotes need not even occur at a specific site. In
other words there may not be an origin. This is particularly true of
multicellular animals when DNA is dividing rapidly. In such cases initiation
occurs randomly at many sites on the chromosome (DePamphilis, 1993). These
examples demonstrate that an origin of replication is not an absolute
requirement for DNA replication in all cases. In other words origins are not
IC components in some cells. The non-origin examples suggest that primitive
DNA replication systems could have managed without a specific origin.

There are other examples of DNA replication in the absence of an origin.
Replication can begin at the ends of linear chromosomes. The extant examples
are confined to viral, bacteriophage and linear plasmid DNA's (Salas, 1991)
where proteins that bind to the ends of DNA are required. The primitive
ancestral cell may have contained multiple linear chromosomes that were
replicated in this manner before the evolution of internal origins of
replication. In other words, it is possible that the last common ancestor
of all life had chromosomes were replicated from their ends. Internal
(multiple?) origins evolved later according to this hypothesis.

In many cases the origin of DNA replication in eukaryotes, plasmids, and
viruses is associated with transcription initiation (Heintz et al., 1992;
Benbow et al., 1992). Often specific transcription factors are required
and they serve a dual role as enhancers of transcription and initiation
of DNA replication. (More about this in another article when I discuss
DnaA and the origin of origins.)

Now, back to Julie's description of oriC. Remember that she is claiming
that the DNA replication system in bacteria is designed by aliens because
there is no possible way it could have evolved from a more primitive
system. She says,

"The sequence in question extends about 240 nucleotides.
Essentially what we have are three AT-rich 13mers at one
end (left) that are then followed by at least four 9mers.
Two of the 9mers are separated by about 180bp. These two
(R1 and R4) are inverted repeats and show very strong
sequence conservation - TTATCCACA. The other two 9mers
lie between R1 and R4 and also show strong sequence conservation.

The replication origin works as follows. Several molecules
of DnaA (see below) bind to the 9mers. This is followed by
the melting of the AT-rich 13mers. This then allows DnaB
(see below) to bind to and initiate replication by unwinding
DNA further. Thus, the strong sequence conservation of the
9mers reflects its role as a binding site for DnaA. The
interactions between DnaA and oriC (and DnaB) represent
systematic IC."

This is basically correct but I'd like to clarify a few points so that
readers don't get the wrong impression. The actual structure of the generic
oriC region is much more sloppy than Julie suggests. She is making the common
error of assuming that E. coli is the paradigm for all bacteria but in
this case the E. coli oriC is the exception. We should avoid the impression
that the organization of this region is highly structured. Julie is
describing systemic IC (E. coli) but implying that it is thematic (all
bacteria).

In many bacteria there are two or three separate regions that contain DnaA
binding sites (DnaA boxes). The important one is near the dnaA promoter
(promoters are sites where RNA synthesis begins when the gene is transcribed).
There can be as many as eight DnaA boxes in a region or as few as two. In
most species of bacteria there are no obvious AT-rich sequences. It is rare
to find direct AT-rich repeats such as those at the E. coli origin so we can
safely assume that the E. coli sequence is derived and does not represent the
primitive origin organization. OriC in E. coli is not located in the promoter
region of the dnaA gene. There is good evidence that its present location
is due to a 40kb chromosomal inversion that "flipped" part of the chromosome
with oriC at one end. If we were to restrict our attention to E. coli we
would not recognize that most oriC origins are associated with dnaA (see
Yoshikawa and Ogasawara [1991] for a discussion of the evolution of oriC
sequences).

The complete genome of Mycoplasma genetalium was searched for oriC sequences
and DnaA boxes and none were found (Fraser et al., 1995). I believe that
the related species, Mycoplasma pneumoniae also lacks a recognizable oriC
(Himmelrich et al., 1997). The complete genome sequence of M. pneumoniae
was searched. This suggests that these organism may use another kind of
origin. However, it is more likely that they have DnaA boxes that have
diverged from the consensus sequence that we recognize in other species.
We just don't recognize the DnaA boxes in these species.

Both mycoplasma species have dnaA genes and there is some evidence that
DNA replication begins near these genes. There are also no oriC sequences in
the genome of Methanococcus jannaschii (Bult et al., 1996). M. jannaschii
is an archaebacterium - I think that Julie's alien design hypothesis assumes
that the aliens designed archaebacteria separately.

So, the minimal (IC) oriC origin consists of several DnaA boxes. AT-rich
repeats are not necessary. The DnaA box sequence is not as strictly defined
as Julie implies. The binding sites for DnaA match a CONSENSUS sequence
that varies somewhat from species to species. In general, a seven out of
nine match to the consensus sequence is more than sufficient for binding.

Let's look at the sequence of DnaA boxes. I apologize for belaboring this
point but Julie seems to think that this is a very important issue. I'll
quote from her essay later on to show you where we disagree.

There are five DnaA boxes at the oriC of enteric bacteria - species that
include E. coli and its relatives. The boxes are named R1-R5 and six
different species have been examined. In the list below I will use upper
case letters (i.e. T) when the nucleotide in all six species is the same
and lower case letters (i.e. t) when there are differences.

R1 TTATCCACA
R2 TTATaCACA
R3 TTATCCaAA
R4 TTATCCACA
R5 TCATTCACA

This is fairly typical of DNA binding sites. The protein binds to a set of
similar sequences that conform to a consensus - in this case the consensus
sequence is TTATCCACA which is the sequence Julie refers to in her essay.
Note that it is not necessary that every nucleotide conform to the
consensus in order to achieve binding.

Messer and Weigel (1997) review the extensive literature data on DnaA
binding. Adding in other DnaA binding sites and studies of DnaA binding
in vitro yields a stringent consensus binding site of TT(A/T)TNCACA where
(A/T) means that either A or T will work at that position and "N" means that
any base pair will do. There is good evidence that the real binding sequence
is even more relaxed - T(T/C)(A/T)T(A/C)CA(C/A)A. The important point is
that in enteric bacteria DnaA binds to a family of sequences defined by a
roughly 7/9 match to a consensus sequence.

A lot of work has been done on the role of DnaA and the DnaA boxes. A good
summary can be found in Langer et al. (1996). It turns out that you can
make small sequence alterations to each of the five sites without affecting
the initiation of DNA replication and you can even combine mutations to
three of the sites without effect. What this says is that the exact sequence
isn't very important as long as it resembles the consensus binding site.
If you delete one of the sites or completely scramble the sequence then
the origin doesn't work as well as the wild type oriC.

In mycobacteria (Mycobacterium smegmatis, M. leprae, M. tuberculosis) the
consensus binding site is (C/T)T(A/G)TCC(A/C)CA (Salazar et. al., 1996).
This is significantly different from the consensus sequence of the site in
enteric bacteria. It suggests that mycobacterial DnaA has evolved a slightly
different binding mode from that in E. coli. In other words, the two types
of bacteria show co-evolution of DnaA and boxA from a common ancestor.
The binding site in Streptomyces lividans has a G in the third position
like many of the sites in mycobacteria. The streptomyces and mycobacteria
both belong to the "High G+C Gram Positive" group of bacteria. The
substitution of G for A at the third position in this group could be due
to selection for higher G+C content in the genome.

Pseudomonads (Pseudomona aeruginosa, P. putida) seem to require a DnaA
binding site that corresponds very closely to the sequence TTATCCACA that
Julie refers to (Smith et al., 1991). This is a much more stringent
requirement than we see in the enteric bacteria (pseudomonads are related
to E. coli but not as closely as other enterics). It looks like the
pseudomonads and enterics have evolved separately from a common ancestor
and each group now has its own specific DnaA + boxA interactions. The
E. coli boxA sequences are too sloppy for pseudomonad DnaA and the
pseudomonad boxA sequences are too restrictive for E. coli DnaA to bind
effectively. The oriC origin from pseudomonads will not work in E. coli
and vice versa (see Smith et al., 1991).

Incidently, the swapping experiments quoted above don't work because of
mixing of DnaA proteins from one species and binding sites from another.
However, it is possible to dispense with oriC altogether. In E. coli
you can substitute oriP2, oriR1 or oriF and the chromosome will be
replicated. These origins don't use DnaA. In Bacillus subtilis you can
delete oriC and replace it with an unrelated origin from a B. natto
plasmid (Anwarul et al., 1997). DnaA is not required in this construct
and the chromosome is replicated although partition is inefficient.
These experiments demonstrate that oriC is not specifically part of an
IC system, although some form of DNA binding protein and binding site is.

Now it's time to see what Julie says about DnaA and its binding site,

"A molecular IC perspective would take into account the strong
sequence conservation found among the 9mers. Could these 9mers
be built up one gradual nucleotide at a time? This seems
unlikely given the strong sequence conservation which suggests
all 9 are needed to be functional. That is, what good is the
5mer that supposedly led to the 9mer? At this point, a critic
of IC might claim that I am employing 'the fallacy of believing
that is now must always have been so.'"

It is quite clear from reading the literature that "all 9" base pairs are
not needed for binding. It is quite clear that in many cases you need
only a 7/9 match to a consensus sequence that is itself somewhat sloppy.
It is not difficult to imagine a primitive DnaA that interacted with
9bp of DNA but only five of these needed to be specific base pairs. In fact,
the mycobacterial site is not far off this imaginary ancestral site.

Julie, you are employing that fallacy of believing that what is now in E.
coli must always have been so in all ancestral species of bacteria.

"Now, I'm not saying this state 'must always have been so'. In
my original article on IC DNA replication, I clearly said:

'it's hard to see how this conserved sequence was built
one little nucleotide at a time'

The critic of IC may claim that once upon a time a bacterial
origin was made up of one 5mer (or something like that), but,
let's be blunt -> there is no evidence for such a claim (making
it look awfully ad hoc)."

It is not hard to see how this "conserved" (sic) sequence evolved from a less
stringent specific binding site. Imagine that the ancestral DnaA protein
bound DNA non-specifically, contacting a region of about 9bp (proteins
are actually much bigger than this and can interact with larger regions
of DNA). There might have been mutations that enhanced the strength of
binding and these were selected because they enabled DnaA to do its thing
much better. For example, replacement of a particular amino acid side chain
could have led to tighter binding to sequences that ended in CA. (Side
chains such as lysine or arginine can interact with two adjacent base
pairs to confer specificity.) This wouldn't be much of a restriction since
CA sequences will occur every sixteen base pairs on average.

Now suppose that a second mutation in dnaA led to enhanced binding at sites
that had CA at the end and a preference for TT in the first two positions.
The protein could still bind sequences such as NNNNNNNCA but it bound more
tightly to sequences such as TTNNNNNCA. There was selection for the better
binding sites at certain positions in the chromosome where DnaA binding did
its thing. We now have a DNA binding protein that shows strong preference for
TTNNNNNCA sites. Like most DNA binding proteins it will bind other related
sites so there is no magical requirement for alien designers who create
a primitive IC system. Weak binding sites can evolve into stronger ones.
Do I have to continue? Can you see how easy it is to build up a binding
site a few base pairs at a time? Do you understand that there is evidence
to support this speculation?

"In fact, the simpler ori story has some strange features. Let's
think it through. The conservation tells us that you don't mess
with these ori sequences most likely because such messing is
deleterious. But to get to this point, the ori must not have been
that important because, after all, you had to mess with it to get
to the actual state we see today. In other words, if we could study
the ancestor origin, we wouldn't expect to find strong sequence
conservation. Otherwise, we couldn't get to the 9mer. For example,
say we found a conserved 5mer in these ancestors. We wouldn't
expect it to become a 9mer if it was functionally constrained
anymore than we expect our current 9mers to have become 12 mers
in the last 1.2 billion years."

Julie, your reasoning is flawed here. I think you got off track because
you assume that the modern DnaA protein can only bind to a specific 9mer.
Now that you know that such interactions are sloppy does the evolution
story make more sense to you? Now that you know that "messing" with the
BoxA sequences has little effect will you modify your conclusion?

The 5mer in ancestral cells may have worked well enough back in the days
when you only needed to synthesize DNA every week or so and it didn't matter
much if some mistakes were made. It need not have been "constrained", just
as the modern sequences are not as constrained as you imagine.

"Of course, one might argue that the original 5mer was seen by
some proto-DnaA protein (see below) and the relationship was
sloppy."

Yes, that's a good argument. Don't forget that the modern relationship is
also sloppy.

"Sloppiness meant "room for improvement" and the ability to be
messed with (unlike conservation). We can then wave our hands
and claim they "co-evolved" to arrive at the 9mer state."

I think "wave our hands" is too dismissive here. I hope I have convinced
you that there's a little more than hand waving involved.

"And once it was found, it was "locked in" for over a billion
years of microbial evolution involving several lineages in
different environments.

No, not "locked in" for a billion years. In fact different species of
bacteria have different DnaA boxes suggesting that each has chosen a
different pathway of evolution. The data says that there was a lot of
evolution over the past billion years. I suppose that your alien design model
would postulate something different. Perhaps the aliens created many different
designs in order to see which one would win out in the end? Maybe Earth is
just a giant test tube where a bunch of alien graduate students are doing
in vitro mutagenesis and evolution on a big scale?

There's no reason to believe that any of these modern pathways are better
or worse than any others. The evolution that took place involved both random
genetic drift and natural selection.

"But that's an uncanny story. For it clearly suggests the 9mer
state is optimal."

That's your strawman "Darwinist" talking. No one claims that the modern
situation is optimal or that each specific step had to confer selective
advantage. Perhaps it's just an accident that one species has a more
stringent consensus sequence than another. Besides, you're basing your
strawman argument on false information.

"How? First, we don't see any pre-9mer states, suggesting a huge
disadvantage compared to the 9mer state (those that had it are
gone)."

Actually we see a variety of states corresponding to 6-mers, 7-mers and
8-mers. All of these might be better than the primitive state of 5-mers
and 4-mers.

"Secondly, the 9mer state has persisted for a very, very long time
in very different lineages (eg., Micrococcus luteus, Bacillus
subtilis, Mycoplasma capricolum, Pseudomonas putida, and E. coli)."

We disagree on the facts here. Please post your evidence that the same
stringent 9 base pair sequence is required in all of these species. I've
given you my references (see below), now give me yours.

"And it hasn't been "improved" while these species evolved. Now
that's quite a pattern. The lack of pre-9mer states suggest
(at least to me) that such a transformation entailed a quantum
jump, not a gradual transformation. Yet the quantum jump
was into an optimal state. And in my opinion, that pattern
(quantum jump to optimal state) is quite suggestive of design."

The pattern is quite suggestive of evolution. You think it's design
because you have your facts wrong. I don't think that you have deliberately
misrepresented the data - I suspect that you are only seeing what you
want to see.

Let's summarize what we have learned about origins. What I've tried to
do is organize this description in a logical manner and discuss each of
Julie's points. Sometimes this means that I have re-arranged paragraphs
from her original posting in order to place them in a more appropriate
context. I do not intend to misrepresent Julie by doing this and if she
feels that I have done so I apologize in advance.

Julie described the oriC origin as follows,

"The replication origin works as follows. Several molecules of
DnaA (see below) bind to the 9mers. This is followed by the
melting of the AT-rich 13mers. This then allows DnaB(see below)
to bind and initiate replication by unwinding the DNA further.
Thus, the strong sequence conservation of the 9mers reflects
its role as a binding site for DnaA. The interactions between
DnaA and the oriC (and DnaB) represent systematic IC."

We have seen that the binding of DnaA to several binding sites is,
indeed, a fundamental property of this type of origin. The "AT-rich
13mers" are a derived feature found only in enteric bacteria. It is likely
that DnaA binding leads to local unwinding of DNA as Julie says. There
is reasonable conservation of DnaA binding sites (DnaA boxes) in different
species of bacteria but there is also plenty of evidence of considerable
evolution from a common ancestral sequence that is more sloppy. DnaA
interacts with helicase but so do a number of other DNA binding proteins
that can (partially) substitute for DnaA. (More on this later.)

"To sum up, the following features of the DnaA box appear to be
essential as determined by mutagenesis studies and/or comparative
analyses: 1. At least four 9mers positioned within a stretch of
180 bp; 2. Two 9mers must lie at each end of the 180 bp stretch;
3. The sequence of the 9mer; 4. Three AT-rich 13 mers upstream
of the 9mers. This is the molecular-thematic IC among bacteria
that has existed for at least 1.2 billion years [1,2]."

Julie is describing the E. coli oriC and not the generic version. All four
of her features are non-essential when we look at typical bacterial oriC
regions.

1. There can be anywhere from two to nine DnaA boxes and they can
be spread out over shorter or longer distances than what we
see in E. coli.
2. It is not necessary to have two DnaA boxes at each end of a
180bp region.
3. The sequence of the DnaA box is not nearly as conserved as Julie
claims.
4. Three AT-rich 13mers are not necessary.

Recall that Julie defined "systematic IC" as follows,

"Systematic IC - In this case, we are talking about the actual
system with clear reference to the specific players in the system.
Now we are not talking about "a helicase," we are talking about
DnaB. We are no longer talking merely about a generic "origin
of replication," we are talking about OriC. Etc. While a discussion
of thematic IC are more general (and thus more vulnerable to
typical Darwinian "just-so" responses), systematic IC discussions
are more precise and scientific and entail data."

What I've tried to do in this posting is clarify the difference between
thematic and systematic IC with respect to replication origins. I've
shown that Julie confused the two in her original essay - although she
sometimes gets it right. She focused her attention on a particular origin,
namely oriC. In fact, she referred mainly to the E. coli version of this
origin. There is a generic oriC in bacteria and it is not as rigidly
structured as Julie implies. The essence of oriC is a bunch of DnaA binding
sites located near the promoter of the dnaA gene itself. All other variants
seem to be derived from the primitive generic form.

I agree with Julie that discussions such as this require reference to the
scientific literature and data. I have done my best to provide this.

The next step is to see if we can come up with a reasonable explanation
of oriC origins based on evolution from something that could have existed
in the primitive ancestors of modern bacteria. We already know that Julie's
explanation is that these origins were designed by aliens and couldn't have
arisen naturally. Any "reasonable explanation" will, of course, be
speculative. The reader will have to decide for themselves whether the
evolution model or the alien design model offer the most reasonable
explanation of the data.

Larry Moran

REFERENCES

Anwarul, K.M. et al. (1997) Supression of Initiation Defects of Chromosome
Replication in Bacillus subtilis dnaA and oriC-Deleted Mutants by
Integration of a Plasmid Replicon into the Chromosomes.
J. Bacteriol. 179, 2494-2502.

Benbow, R.M., Zhao, J. and Larson, D.D. (1992) On the Nature of DNA
Replication in Eukaryotes. BioEssays 14, 661-670.

DePamphilus, M.L. (1993) Origins of DNA Replication in Metazoan Chromosomes.
J. Biol. Chem. 268, 1-4.

Fraser, C.M. t al. (1995) The Minimal Gene Complement of Mycoplasma
genetalium. Science 270, 397-403.

Heintz, N.H., Dailey, L., Held, P. and Heintz, N. (1992) Eukaryotic
replication origins as promoters of bidirectional DAN synthesis.
Trends in Genetics 8, 376-381.

Messer, W. and Weigel, C. (1997) DnaA initiator - also a transcription
factor. Molec. Microbiol. 24, 1-6.

Salas, M. (1991) Protein-Priming of DNA Replication.
Ann. Rev. Biochem. 60, 39-71.

Salazar, L. et al. (1996) Organization of the origins of replication of the
chromosomes of Mycobacterium smegmatis, Mycobacterium leprae and
Mycobacterium tuberculosis and isolation of a functional origin from
M. smegmatis. Molec. Microbiol. 20, 283-293.

Smith, D.W., Yee, T.W., Baird, C. and Krishnapillai, V. (1991) Pseudomonad
replication origins: a paradigm for bacterial origins?
Molec. Microbiol. 5, 2581-2587.

Yoshikawa, H. and Ogasawara, N. (1991) Structure and function of DnaA and
the DnaA-box in eubacteria: evolutionary relationships of bacterial
replication origins. Molec. Microbiol. 5, 2589-2597.

[Matt Silberstein]

In talk.origins iz...@cleveland.Freenet.Edu (Julie Thomas) wrote:

[snip]

>
>First of all, I did not conclude that "DNA replication was designed by
>aliens." I simply outlined the IC nature of DNA replication which in turn
>strongly suggests the system was designed. The identity of the designer
>is a separate issue.
>

As I see it the chain of logic is this. IC systems are less likely to
have evolved than non-IC systems. Therefore some entity wanted the
system to exist. But we don't know anything else about that entity. Is
that correct?

>As for my limitations, yes, I attempted to limit myself with the
>evidence.
>

And the evidence for intention is?

>>In the postings that follow I will be examining the "alien design" model
>>that Julie proposes.
>
>Where did I say anything about aliens?
>

Actually it is Peter who has suggested aliens. You have not put any
meaning to your designer.

>More importantly, if this is the thesis you are going to write about,
>I hope you didn't put too much effort into it yet as you are barking up
>the wrong tree. My thesis was simply that bacterial chromosomal DNA
>replication is IC. This thesis does not require me to posit that the
>process arose by "instantaneous creation de novo" (although IC is not
>inconsistent with this claim). IC may also entail the creation of a mosaic
>analogous (but superior) to the workings of molecular biologists.
>

So you don't have any propose mechanism. For instance, it is possible
that different IC systems have considerably different designers? Or
one designer and multiple implementors. Or multiple designers and a
single implementor?

>>The "aliens" who created such a system could be one or more
>>supernatural beings (i.e. gods or godesses) but I assume that Julie does
>>not want to restrict her proposal to such entities since that brings
>>religion into the discussion and Julie has taken great care to avoid this.
>
>I still don't understand why you think the term "aliens" is required.
>Intelligence is a far better term as it is more neutral.
>

More neutral? We have significant disagreement about how this term
"intelligence" applies to people. There are quite good arguments that
the there are really multiple kinds of intelligence, but you apply it
to some entity that you can't make any other claim about. This does
not make sense to me. Where is your evidence for intelligence?

[snip]

>
>I think there is much confusion concerning this topic. My major
>intention in focusing on IC is not to come up with an anti-darwinian
>argument. I don't need that. When it comes to DNA replication or the
>bacterial flagellum (and many other things to come), I am simply not
>convinced that Darwinism has anything to do with their origin. But I
>am still quite interested in their origin. Should I wait, and hope, that
>someday folks like Paul Myers will come up with a story that will
>probably only convince those hoping to be convinced? Nah. Thus, I
>look for alternative explanations that *I* find far more intellectually
>satisfying. And, as I see it, Michael Behe has given me the key. So I
>begin to look afresh at these systems with Behe's key and it generates
>new insights and new lines of inquiry. Put simply, it's a way to
>interpret data and do science under a design paradigm. That's why I
>said to Paul that "Ill go my way and y'all go yours." Would you be
>another one who is bothered by that?
>

This brings up an interesting side thread. You find it more satisfying
to propose an undefined intentional intelligent entity with unknown
abilities. I wonder if you could try to explain how that is
satisfying to you? For me that seems the height of unsatisfactory
explanation.

[snip]

>>It's not good enough to claim that a system is simply "irreducibly
>>complex" if you are trying to prove that intelligent aliens exist.
>
>Says who? You? The Gang?
>
>>You also have to show that the system is well designed, so well
>>designed that there had to be aliens behind it.
>
>You confuse science with philosophy. Scientific explanations do not
>entail "had to be" claims. That's much too certain.
>
>As far as determining if something is "well-designed," that's a subjective
>point that depends on knowledge of the designer('s) intentions and
>one's taste. But if you think it is relevant, you should probably start by
>defining what you consider a "good design."

Now wait a second. You claim the ability to detect intentions. Are you
saying that you can detect that they exist but not what they are?
Maybe the designer intended things to be quite different and is
incompetent in execution. That would also fit your argument and the
data.

Matt Silberstein
----------------------------------------------

CAUCHON. And you, and not the Church, are to be the judge?

JOAN. What other judgment can I judge by but my own?

_Saint Joan_ by GBS, Scene VI

[Laurence A. Moran]

Do you claim that every example of DNA replication requires the following?

1. an origin of replication
2. a factor that binds to the origin
3. helicase
4. single-stranded DNA binding protein
5. a factor that synthesizes a primer
6. DNA polymerase
7. topoisomerase
8. ligase

Or are you restricitng your claim to the replication of large bacterial
chromsomes? Please clarify your claim - I don't want to waste time
discussing this with you if I have misunderstood your claim.

>>I assume that what she really means is that she can't imagine how
>>modern, large bacterial chromosomes can be replicated without these
>>activities.
>
>Well, in the abstract I clearly said:
>
>"Bacterial chromosomal DNA replication is then considered from these
>various perspectives of IC."

I take that to mean that you are making a general claim but that you
are only discussing the evidence that bacterial chromosomal DNA
replication satisfies the criteria. Please indicate whether you are
making the general claim or not.

>As for the adjective "modern," it tends to bias the discussion as it
>implies bacterial chromosomal replication was at one time different in
>the past. But there is no evidence for this assumption.

No such assumption is implied. I use the word "modern" in order to make
it clear that we are looking at species that are alive today and not
species that existed in the past. If we could examine DNA replication
in extinct organisms I would use the word "extinct". Would it be better
if I used the word "extant" instead of "modern"? I'm happy to do this.

Our goal is to try and understand how the present form of DNA replication
can to be. Did it evolve or was it designed by someone/something?

>As for not being able to imagination, it's really a case where there is no
>evidence that bacterial chromosomes can be replicated without these
>general activities. Furthermore, I would add that there is no evidence
>to suggest cells can exist without chromosomes.

All of these activities are used in the replication of bacterial chromosomes
in extant species. In your essay you make a number of additional claims that
are more open to dispute and I will try and cover these later. What I will
be looking for is evidence that the eight activities may not have been
essential in the past. I will also be looking for natural explanations
that can account for what we see today. You, on the other hand, are in a
much better position. You get to take pot shots at my explanations without
having to come up with evidence to support your design model. Perhaps
you could try and explain why you believe in design - is there some
scientific evidence to support the idea that designers exist?

>>But that's a different kettle of fish entirely. What we are concerned
>>about is how the modern system came to be (evolution or de novo
>>design). In that case the ability to "imagine" or demonstrate that
>>simpler systems will work is highly relevant.
>
>I do not think the ability to imagine is relevant. However,
>demonstration of a simpler system might be very relevant.

I'm interested in your design model. Do you simply "imagine" that
designers exist or is there evidence? Remember that you don't think
the ability to "imagine" is relevant so let's see how you can explain
"intelligent design" without using imagination.

>>Julie's lack of imagination may lead her to conclude that DNA
>>replication was designed by aliens but the rest of us need not be bound
>>by her limitations.
>
>First of all, I did not conclude that "DNA replication was designed by
>aliens." I simply outlined the IC nature of DNA replication which in turn
>strongly suggests the system was designed. The identity of the designer
>is a separate issue.
>
>As for my limitations, yes, I attempted to limit myself with the
>evidence.

First of all, you need to stop beating around the bush. The only reason
for claiming IC is to support the idea that the system was designed. The
only reason for wanting a system to be designed is that it fits in with
your belief in a "designer". If all you want to say is that DNA replication
looks complicated then there is no disagreement. But you want much more
than that - you want to convince us that it could not have evolved. Since
it could not have evolved, according to you, then the competing hypothesis
must be correct. But you won't come out of the closet and tell us what
the competing hypothesis is. Why?

If the identity of the "designer" is a separate issue then let's use a
neutral term. I suggested "aliens" to emphasize that it isn't humans. If
you have a better idea then let's hear it.

>>In the postings that follow I will be examining the "alien design" model
>>that Julie proposes.
>
>Where did I say anything about aliens?

You didn't. Is reading comprehension a problem for you? (see below)

>>By "alien design" I mean the thesis that the modern form of DNA
>>replication in bacteria could only have arisen by instantaneous creation
>>de novo.
>
>Then why do you call this "alien design" rather than "design" or
>"intelligent design?" It looks like to are trying to label my position as
>something that stems from a UFO nut. Above you noted:

Richard Dawkins claims that evolution can design natural systems and I
tend to agree with him on this point. You are attempting to exclude this
possibility. This means that "design" is inappropriate. I suppose that
"intelligent design" would be acceptable as long as everyone understands
that it means either supernatural beings or intelligent beings from
another planet. After all, we don't want to exclude the possibility that
it could have been aliens, do we? That would be unscientific since there
is no evidence that it wasn't the scientific officer of a UFO.

>"She is trying to focus the discussion and prevent us from wandering off
>or gettng involved in flame wars over terminology."
>
>But you don't seem to helping matters with terms like "alien."

I admit that the use of "alien" was partially motivated by your use of
the term "Darwinist". A term that I find very offensive since it implies
a strawman version of evolution. If you start being more considerate
then I will too.

>More importantly, if this is the thesis you are going to write about,
>I hope you didn't put too much effort into it yet as you are barking up
>the wrong tree. My thesis was simply that bacterial chromosomal DNA
>replication is IC. This thesis does not require me to posit that the
>process arose by "instantaneous creation de novo" (although IC is not
>inconsistent with this claim). IC may also entail the creation of a mosaic
>analogous (but superior) to the workings of molecular biologists.

Come on, Julie. Give us a little credit - we are not idiots. What's the
real reason for claimimg that a system is irreducibly complex? Are you
just playing rhetorical games or is there a bigger stake? If the process
didn't evolve then what is your explanation? Would "slow and steady
creation from pre-existing components" be a satisfactory substitute?
I think not.

>>She suggests that some systems are so complicated and interconnected
>>that it would be impossible to imagine or reconstruct a natural
>>explanation involving evolution from a primitive ancestor.
>
>Where did I suggest this? In fact, I just did a word search of my entire
>50 page article and not once did the word "impossible" appear. I'm
>sorry Larry, but you have simply put words in my mouth and thus your
>characterization of my article is seriously flawed.

Excuuuuse me. In the opening paragraphs of your essay you said,

"Recall that Darwin said,

'If it could be shown that any complex organ existed
which could not possibly have been formed by numerous,
successive, slight modifications, my theory would
absolutely break down.'

IC appears to get close to the heart of this challenge since
an IC system is a very good candidate system for something
that cannot be formed "by numerous, successive, slight
modifications." I should, however, point out that IC is more
than an anti-Darwinian argument. IC is also characteristic
of design."

I stand by my statement. If you want to deny that that's what you mean
then please clarify.

> After all, I've always
>admitted that someone can "imagine" a natural explanation involving
>evolution from a primitive ancestor. So what? What matters is
>whether this imagination is a fantasy or reflective of reality.

If you want to get picky then the onus is on you to conform to Darwin's
challenge. You must show that a complex system could not possibly have
arisen by evolution. In other words you must show that it is impossible
for it to have evolved.

I'm actually letting you off the hook. You have suggested that there is
no natural explanation for DNA replication as we know it and I will
attempt to provide one. This involves "imagination" or "speculation"
that is reasonable. Will you accept it or would you rather try and
live up to Darwin's challenge?

>>But the absence of evidence is not evidence of absence. This is a point
>>that Julie consistently tries to obfuscate.
>
>Instead of accusing me of obfuscation, why not simply consider the
>possibility that we may not be communicating effectively.
>
>First, the claim, "the absence of evidence is not evidence of absence." Is
>this an absolute truth that is always true?

It's true in this context. You have two choices, Julie. You can be satisfied
with pointing out the difficulties of explaining DNA replication by
natural means in which case we can discuss possibilities. Or you can attempt
to *prove* that it is impossible. If you want to attempt the latter then
be my guest - so far you haven't even come close. All you have done is
point to lack of hard evidence for evolution.

>Now, if you claim DNA replication evolved from a primitive ancestor
>along Darwinian lines, I simply note there is no evidence for this claim
>(or at the very most, the evidence is very weak). If, as I believe, design
>is a better explanation for the IC nature of DNA replication, I *then*
>consider your absence of evidence and say "no wonder there is no
>evidence; y'all are pursuing a dead end." Thus, the failure of Darwinism
>is *supporting* evidence.

I look at the data and see several possible explanations that are consistent
with evolution. Then I look for evidence of design and designers and see
none. The lack of evidence of intelligent designers must mean that there
aren't any, right? I then consider your absence of evidence and conclude
that you are playing with an empty deck. The failure of designism then
becomes supporting evidence for evolution.

If you find this charicature offensive then you will be taking the first
step to understanding how I feel about your logic. Why not cut to the chase
and stop playing silly semantic games?

>I think there is much confusion concerning this topic. My major
>intention in focusing on IC is not to come up with an anti-darwinian
>argument. I don't need that.

I really have to get me one of Irony-O-Meter thingies. I wonder if they
have models with log scales?

>>Julie and her like-minded friends are fond of the term "irreducible
>>complexity".
>
>It's not a matter of being fond of a term. It's matter of
>exploring the utility of a fresh concept.

The concept is very old. Do you really expect us to believe that you
never thought of it before the term "irreducible complexity" was
popularized?

>>This is a rhetorical device that is designed to convert the absence of
>>evidence into something positive that is subject to scientific analysis
>>(i.e. that the system will not work if any part is removed). We
>>are not fooled by this cheap trick.
>
>Rhetorical device? Cheap trick? Could you be a tad more insulting?

No, I think that did the trick. Could you try being a bit more honest?

>Look, when you say the "absence of evidence," I must ask, "evidence for
>what?" The term "absence of evidence" is meaningless by itself. Now,
>did I argue there was an absence of evidence for the IC nature of DNA
>replication? Nope. I argued that DNA replication *is* IC.

Maybe a log scale Irony-O-Meter won't be good enough.

>>The fundamental point is that alien design proponents are basing their
>>argument entirely on the lack of hard proof of natural causes. Lacking
>>such proof they assume the existence of aliens who must have done the
>>deed.
>
>It would be polite if you would refrain from labeling me an "alien design
>proponent." I have gone to great lengths to refrain from speculating
>about the designer(s).

I will call you an "intelligent design proponent". OK? You will agree
to refrain from calling me a Darwinist. Agreed?

>>On the other hand, there are times when Julie almost seems to be
>>offering irreducible complexity as proof of the existence of aliens. This
>>is nothing more than the argument from design dressed up for the 90's.
>
>Oh please. If you interpret my articles as one big "Argument From
>Design," you will continually be clueless about my writings.

I don't think so. If you continue to deny your real motives you will only
be fooling yourself. Maybe you are foooling yourself.

Larry Moran

[Christopher J. Carrell]

Richard Harter wrote:
>
> lam...@bioinfo.med.utoronto.ca (Laurence A. Moran) wrote:
>
> [snip]
>
> Bravo! Double bravo!! It is such a delight to see such a clearly
> written and informative article appearing like a jewel in the midst of
> the dung heap of clap trap and snidery.

My only complaint is with the first sentence...

"Julie Thomas claims that DNA replication is a alien designed system
based on the fact that it is so complex that it couldn't have arisen
by natural causes."

... and the word "alien", which is used several times. I find it a
little vague as to what that means, and some people with private
meanings of that word will claim that the entire piece can be
ignored. Too bad, as it's as worthy a piece as has ever been
written here.

Other than that point of clarity, no problems here.

Chris

--
Chris Carrell - Replace each _dot_ with . if you want to email me
They say the meek shall inherit
Because they stay up late and change the will. - Heywood Banks

[George Acton]

In article <5rrp51$4...@alexander.INS.CWRU.Edu>,

iz...@cleveland.Freenet.Edu (Julie Thomas) wrote:
>
>
> In his reply to my article on IC and DNA replication, Larry Moran says:
>

...

> >In this case Julie is confusing thematic DNA replication and a particular
> >systematic version - namely the replication of large chromosomes.
>
> Not quite. You are correct in that I have focused attention on the
> replication of chromosomes and this is thus a systematic perspective.
> However, the systems themselves revolve around the same theme thus
> this is perhaps better referred to as thematic-systematic IC. However, I
> will still hold to the strictly thematic claim (tentatively, of course) until
> there is evidence suggesting otherwise.

Unless you're using the term for purely incantatory effect, it might be
helpful if you explained how your definition of "irreducible complexity"
differs from Behe's. Behe defines it as a property of a "system" and
the system either has it or not, based on his usage.
This might require you to go to the inconvenience of reading his book,
since you claimed a few weeks ago that you hadn't read "Darwin's Black Box"
and didn't intend to unless you "ran across" it. I'd be happy to look up
the publication information for you, if you're interested.
It might also help if you stated its relation to the question of
whether a system is "designed". Behe concedes somewhere that there is a
possibility that an "irreducibly complex" system arose by evolution. He
seems also to leave open the possibility that a system with redundant parts
might have been designed. IOW, there's no relationship of logical
implication between the two concepts. Given this situation, it's
reasonable to ask why he couldn't directly examine the question of evolution
vs. design without the intermediary concept.
At any rate, I'm trying to understand the difference between thematic
and systematic IC. Into which category should I place the genes for the
bones of the inner ear?

...

> ... My major

> intention in focusing on IC is not to come up with an anti-darwinian

> argument. I don't need that. When it comes to DNA replication or the
> bacterial flagellum (and many other things to come), I am simply not
> convinced that Darwinism has anything to do with their origin. But I
> am still quite interested in their origin. Should I wait, and hope, that
> someday folks like Paul Myers will come up with a story that will
> probably only convince those hoping to be convinced? Nah. Thus, I
> look for alternative explanations that *I* find far more intellectually
> satisfying. And, as I see it, Michael Behe has given me the key. So I
> begin to look afresh at these systems with Behe's key and it generates
> new insights and new lines of inquiry.

Could you indicate one "new insight" or "new line of inquiry"? As
several people have pointed out, the only experiment suggested by the
concept of "irreducible complexity" (sensu Behe) is a knockout preparation
in which a gene is disabled and the phenotypic effects observed. But
people have been doing this for years.

> >Julie and her like-minded friends are fond of the term "irreducible
>
> >complexity".
>
> It's not a matter of being fond of a term. It's matter of
> exploring the utility of a fresh concept.

But focus groups show it's not as popular as the "new, improved" theory
of Universal Gravitation or "Quanta Work Good like Neat Physics Should",
the campaign that Chiat-Day did for the U. of Heidelberg.

> >This is a rhetorical device that is designed to convert the absence of
> >evidence into something positive that is subject to scientific analysis
> >(i.e. that the system will not work if any part is removed). We
> >are not fooled by this cheap trick.
>
> Rhetorical device? Cheap trick? Could you be a tad more insulting?

It's no more insulting than "just so stories" or "closed minds" or
"dead end". But don't worry about it. You're simply followng the
rule that the nicer the "anti-Darwinians" are at the beginning, the
underlying hostility emerges after they stay a while.

> Now I assume you mean "absence of evidence" for a Darwinian origin to
> DNA replication. Well, yes, this is *also* true.

The "absence of evidence" holds for a theory of design as well. But
there's no reason to believe that a naturalistic explanation is impossible.
If a lack of detail means a "just so story", shouldn't "Design Theory" be
held to the same standard of precision? Shouldn't it make predictions,
suggest experiments to determine the number of steps involved in the
"design", provide estimates of how many separate "design events" there
were, und so weiter?
Indeed, "design theory" should pass more stringent tests, since the
theistic variant requires a violation of fundamental laws of chemistry
and physics. Obviously, the "design" is going to have to be translated
into a physical realization, a process occasionally referred to as
"creation".

> >It's an old argument. Here's what Clarence Darrow had to say about it
> >sixty-seven years ago (1932),
>
>

> ...

>
> >All of them need constant readjustment, are always out of order, and
> >are entirely too complicated for dependable work.
>
> So Darrow admits he was incapable of doing anything dependable? Is
> this his excuse for losing the case? ;)
>

Some people think his losing was due to a characteristic Christian
hatred of science, scholarship and education. But that's neither
here nor there. You certainly have the right and privilege of being a
pom-pom girl for the intellectual prowess of the Tennessee Legislature.
--George Acton

[Wade Hines]

Peter Nyikos <nyi...@math.SC.EDU> writes:

>More Strawwoman Julie stuff. In the first place, "de novo" traditionally
>means the creation of matter from nothing; that is not at all
>necessary to contemplate at this stage. Secondly, "instantaneous"

Totally false. This is a biological/biochemical discussion and the use
of "de novo" is not as you suggest. Perhaps you mean "ex nilo".

>is either an enormous hyperbole or another strawman creation
>of yours. Thirdly, Julie never claimed intelligent
>design of these systems is the ONLY reasonable hypothesis,
>only that she suspects it is the BEST hypothesis.

Who is playing with straw?

[Wade Hines]

Peter Nyikos <nyi...@math.SC.EDU> writes:

>lam...@bioinfo.med.utoronto.ca (Laurence A. Moran) writes:

>> But the absence of evidence is not evidence of absence.
>>This is a point that Julie consistently tries to obfuscate.

>How utterly stereotyped your treatment of Strawwoman Julie is!

You haven't read much of Julie's posts have you?

>I've come to expect much better of you, Dr. Moran. One
>would hope that your own hostile reception by the likes
>of Steve LaBonne, Matt Wiener, and Wade Hines and, more
>recently, Mike Noren, would have taught you to be a little
>more circumspect in your criticism of others.

Have I savaged Moran? Look, I omitted the Dr. part. Is he
offended? Have I attacked his positions without any deference
to his stature in biology? Yes. Does he care? Maybe alittle?
Do I care? Not noticably.
Does Peter have an intellectual point to make? Seemingly not.

[George Acton]

[howard hershey]

Peter Nyikos wrote:
>
> CC: Julie and Laurence, because the automatic moderator of talk.origins
> has been especially quirky of late, kicking back posts
> apparently at random even when the address talk-o...@moderators.uu.net
> is used.
>
> What's talk.philosophy.humanism doing up there? Are you a
> member of the Humanist Society, Dr. Moran?
>
> lam...@bioinfo.med.utoronto.ca (Laurence A. Moran) writes:
>
> [disarming opening spiel deleted to get down to the brass tacks
> of this particular post:]
>
> >Julie says that "It is hard to imagine DNA replication occurring without
> >all these *activities*." This is not correct. I don't have much difficulty
> >imagining such a situation. But I don't have to "imagine" because there
> >are known examples of DNA replication that do not require all these
> >activities.
>
> Viral ones?

Yes. And viral ones show that DNA is not the only possible genetic
material.

>
> >In this case Julie is confusing thematic DNA replication and a particular
> >systematic version - namely the replication of large chromosomes. I assume
> >that what she really means is that she can't imagine how modern, large
> >bacterial chromosomes can be replicated without these activities. But that's
> >a different kettle of fish entirely.
>
> But worth addressing also.

Yes. If certain features had not been 'invented', we would not have
modern, large chromosomes. Since the general idea of evolution of
complex genomes is that there were simpler, smaller genomes initially,
the use of simpler, smaller genomes observable in the present is a
logical source of ideas for past simpler systems since we *know* that
these ideas are compatible with existence as, at the very least, a
lifestyle where the environment is relatively rich. It grounds the
necessarily speculative pathway in reality. We don't need to 'invent'
magical compounds for alternate genetic materials. We *know* that RNA
can be used as a genetic material. We do not need to assume that
genomes must always be dsDNA. We *know* that ssDNA can be used. We do
not need to assume that primase activity must always be modified RNA
transcription. We *know* that alternate mechanisms for priming DNA
replication exist.

Of course, modern large chromosomes do exist in the one trial we know
about. So that process could have been 'directed' invisibly by an IPU.
What we need to try to do is put some meat on the bones of the possible
mechanisms by which this could be accomplished, and, as scientists, we
are limited to looking for mechanisms compatible with natural law rather
than being able to simply say that it was accomplished by magic by our
dear old IPU.

>
> > What we are concerned about is how the
> >modern system came to be (evolution or de novo design). In that case the
> >ability to "imagine" or demonstrate that simpler systems will work is highly
> >relevant.
>
> Sure. But those are different systems, with fewer parts, and the challenge
> is in showing how to get from there to replication of modern, large
> bacterial chromosomes.

Absolutely. That is why it is important to note that some systems serve
other functions, like RNA transcription.

>
> >Julie's lack of imagination may lead her to conclude that DNA replication
> >was designed by aliens but the rest of us need not be bound by her
> >limitations.
>
> Nor is she bound by those Strawwoman Julie limitations.
>
> > In the postings that follow I will be examining the "alien
> >design" model that Julie proposes. By "alien design" I mean the thesis
> >that the modern form of DNA replication in bacteria could only have arisen
> >by instantaneous creation de novo.
>
> More Strawwoman Julie stuff. In the first place, "de novo" traditionally
> means the creation of matter from nothing; that is not at all
> necessary to contemplate at this stage. Secondly, "instantaneous"
> is either an enormous hyperbole or another strawman creation
> of yours. Thirdly, Julie never claimed intelligent
> design of these systems is the ONLY reasonable hypothesis,
> only that she suspects it is the BEST hypothesis.

But isn't *de novo* and *instantaneous* (at least in geological terms)
exactly what IC systems predict if one excludes the stepwise with
utterly useless intermediates explanation? Julie, of course, never
discusses *any* model for the 'invention', 'creation', or 'evolution' of
any of the present-day systems she describes in detail. I consider that
rather a fault when one is arguing about how 'systems' are 'invented',
'created', or 'evolved'. Sort of like completely ignoring even
imperfect historical evidence and concluding that *computers* were
always a vital component of the economy on the basis of their current
role and complete integration into the economy. Remove computers (say
in the year 2000) and the economy 'collapses' (runs so inefficiently
that it cannot be claimed to function effectively).

>
> > The "aliens" who created such a system
> >could be one or more supernatural beings (i.e. gods or godesses) but I
> >assume that Julie does not want to restrict her proposal to such entities
> >since that brings religion into the discussion and Julie has taken great
> >care to avoid this.
>
> So why don't you mention the other alternative, namely production
> of prokaryotes in a laboratory by an alien species that has
> a simpler cellular replication method of its own, to avoid
> infinite regresses?

Infinite regress is limited by the Big Bang unless one starts
postulating alternate-universe travels. Even that simpler model simply
begs the question and leaves no room for the Great Invisible Nudger.

>
> >"Evidence" for Julie's alien design model is based largely on negative
> >inference as many others have pointed out.
>
> Correction: as many other philosopher-wannabes, arguing in an
> intensely personalist mode, have claimed.
>
> A more objective treatment would say that she poses a challenge
> to everyone to come up with an explanation of the kind that
> she is characterized as being unable to imagine:

And sketchy models have been presented. Now it is her and your turn to
present an equally sketchy model congruent with the evidence and supply
evidence that your model is consistent with the way the world works
today. Physical evidence for there being 'intelligent designers and
implementers' at the appropriate times would be nice. Otherwise, said
designer is hard to distinguish from an IPU, a solution which is
'logically' but trivially possible.

>
> >She suggests that some systems
> >are so complicated and interconnected that it would be impossible to
> >imagine or reconstruct a natural explanation involving evolution from a
> >primitive ancestor.
>
> She has some candidates for such roles, yes, and the months-long
> example of the bacterial flagellum has demonstrated the reluctance
> of everyone else to even try to come up with such natural
> explanations. Instead we've seen flights of fancy like the
> highly fictitious [and entertaining if one does not take
> it too seriously] evolution of a mousetrap which others, including
> Howard Hershey and myself, have brought crashing to earth.

As well as less trivial possibilities such as DNA replication being
derived from a modification of RNA transcription and posts that cite
homologies of flagellar 'rivet' proteins with type III protein secretory
systems (the homologies extend to function). These systems are often
transmitted horizontally on plasmids. and flagellins with other secreted
pillins. Certainly not a complete story. But certainly pointing to a
mechanism. And your and Julie's equally sketchy model for how the
present IC system arose is... accomplished invisibly by an invisible
intelligent entity? BTW, the ref. is Van Gijsegem, et. al. Mol. Micro.
15 (1995) 1095. References cited therein are also of interest.

>
> > But the absence of evidence is not evidence of absence.
> >This is a point that Julie consistently tries to obfuscate.
>
> How utterly stereotyped your treatment of Strawwoman Julie is!
> I've come to expect much better of you, Dr. Moran. One
> would hope that your own hostile reception by the likes
> of Steve LaBonne, Matt Wiener, and Wade Hines and, more
> recently, Mike Noren, would have taught you to be a little
> more circumspect in your criticism of others.
>
> >Julie and her like-minded friends are fond of the term "irreducible
> >complexity". This is a rhetorical device that is designed to convert the
> >absence of evidence into something positive that is subject to scientific
> >analysis (i.e. that the system will not work if any part is removed).
>
> What's with the "rhetorical device" spiel? Take it out, and
> you have a perfectly reasonable description of a perfectly
> reasonable concept.

I have been trying to get someone (you ar Julie) to make some sort of
explicit potentially testable statement based on the concept of IC
(IC-ness implies either relatively instantaneous creation as a unit or
stepwise creation with utterly useless intermediates). So far I haven't
seen any serious reply or alternative predictions. Maybe IC-ness
doesn't have any implications? Maybe IC-ness is compatible with any
natural law mechanism as well as an IPU mechanism?

>
> >We are not fooled by this cheap trick.
>
> Worse and worse. You sound as propagandistic as an announcer for the defunct
> Soviet news agency Tass.
>
> >The fundamental point is that alien design
> >proponents are basing their argument entirely on the lack of hard proof of
> >natural causes.
>
> I note the Strawwoman Julie implicit in "hard proof" when you
> have not even established the existence of a plausible scenario
> for getting from there to here.

And you have one? Why didn't you say so? How does it differ from the
IPU explanation?

>
> > Lacking such proof they assume the existence of aliens who
> >must have done the deed.
>
> It must really be fun to knock down one straw woman after another.
> When will you ever get around to talking about the scientific
> aspects of Julie's writing--or to any aspects of Julie's writing,
> for that matter?

Actually, I agree. Julie did not specify that aliens did it. She did
not even try to explain any alternative explanations about how the IC
systems she described arose. Yet she asserts that something called an
'intelligent design' explanation was more likely than natural law
mechanisms without explaining how the two differ.

>
> >There is, of course, no proof that such aliens exist or that they existed in
> >the past.
>
> If there were, we wouldn't be having this discussion, would we now?
> Julie's case would have been closed and we could all be talking
> about something else.

Quite right. If she had some evidence to support her alternative, she
would have presented it.

>
> >The assumption of "designers" is something that they bring to
> >the table from outside of science.
>
> What table? The humanist table?

The one where Occam's razor carves the meal. And where immaterial
supernatural meals are considered indigestible until they become
material and natural.
>
[snip]

>
> > It's
> >not good enough to claim that a system is simply "irreducibly complex" if
> >you are trying to prove that intelligent aliens exist. You also have to
> >show that the system is well designed, so well designed that there had
> >to be aliens behind it.
>
> For someone who berated Julie for laying down "ground rules", you
> certainly lay down some demanding ones yourself.
>
> I for one have rejected YOUR ground rules from the beginning,
> being familiar with the Francis Crick-Leslie Orgel theory of
> directed panspermy. Until YOU can find someone producing a living
> cell that has a better DNA replication system than the existing
> one, you have no reason to believe that an alien intelligent
> species, with our level of intelligence, could have come up
> with a better system that actually WORKS.

In simpler systems of artificial selection, where selection is used to
blindly select a protein with a certain activity, different trials can
produce quite different proteins with the same functional activity.
Some of these are quite different than the ones nature has been
restricted to by the force of common history. There are also examples
*in nature* of independent solution to a particular enzymatic problem.
Each shows signs of historical derivation from different sources. But
DNA replication (of complex organism's large genomes opnly) all use
basically the same system (an n of 1) and represents a case where there
is no information about alternatives in nature. Even moderately
intelligent naked apes certainly *can* imagine simpler or more optimally
designed systems than the Rube Goldberg mechanism actually used. Any
*omnipotent* designer certainly could have implemented such systems. So
what inferences can you draw?

[Laurence A. Moran]

Julie Thomas says,
>Larry Moran says,
>>Julie Thomas says,

In an earlier posting I asked Julie two relatively simple questions that
could easily have been answered "yes" or "no". The purpose of the question
was to narrow our discussion of DNA replication. I wanted to know what
kind of IC claim Julie was making. Here's the first question.

>>Do you claim that every example of DNA replication requires the
>>following?

>> 1. an origin of replication
>> 2. a factor that binds to the origin
>> 3. helicase
>> 4. single-stranded DNA binding protein
>> 5. a factor that synthesizes a primer
>> 6. DNA polymerase
>> 7. topoisomerase
>> 8. ligase

Julie's reponse follows,

>You forgot one:

> 9. DNA sufficient to code for cellular life.

>Also, since we are talking about thematic IC, keep in mind that
>these are simply activities, not specific enzymes. For example, a
>helicase or unwinding activity is needed, not necessarily the enzyme
>called helicase.

Did you forget the question Julie? Do you really think that it was
extremely important to add DNA to the list?

I'm well aware of the distinction between an activity, a general name for
an enzyme, and the name of a specific enzyme. Items 3 to 6 are all general
names of activities and not specific enzymes from a particular species.
One gets the strong impression that you are avoiding the question.

Here's the second question.

>>Or are you restricting your claim to the replication of large bacterial
>>chromosomes?

>"Large bacterial chromosomes" is needlessly redundant as all bacterial
>chromosomes are large. My claim is restricted to DNA molecules
>sufficient, and perhaps, necessary for cellular life. And since bacteria
>are the simplest cellular forms we can study they seem to nicely satisfy
>the needs of my empirically inquiring mind. ;)

Yep, I really do think that you forgot the first question. Either that, or
you think this is an answer - I don't know which possibility is more
scary.

Your gratuitous comment about "large bacterial chromosomes" is quite
interesting. As I'm sure you know (NOT) there are many bacterial
chromosomes that are smaller than some plasmids and some bacteriophage
genomes. Do you mean to exclude these small chromosomes - they are
essential for life.

Have we made any progress here? I don't think so. Julie now claims that
the eight activities are required for the replication of DNA molecules
that are "sufficient, and perhaps, necessary for cellular life". Unless
she objects I will interpret her "answers" as follows. No, she does not
require all eight activities in order to replicate every kind of DNA. All
eigh activities are required in order to replicate bacterial chromosomes,
where "chromosome" means non-dispensable DNA.

>>>>I assume that what she really means is that she can't imagine how
>>>>modern, large bacterial chromosomes can be replicated without these
>>>>activities.
>>

>>>Well, in the abstract I clearly said:
>>
>>>"Bacterial chromosomal DNA replication is then considered from these
>>>various perspectives of IC."

>>I take that to mean that you are making a general claim but that you
>>are only discussing the evidence that bacterial chromosomal DNA
>>replication satisfies the criteria. Please indicate whether you are
>>making the general claim or not.

>Yes, I was discussing only the evidence that bacterial chromosomal DNA
>replication satisfies the criteria of IC.

We all know that, Julie. The question is whether you think that *ALL* DNA
replication is IC and requires the eight activities or whether you want
to restrict your claim to the example you discussed. I really do think you
have a problem in reading comprehension.

>If you think there is a non-IC
>form of DNA replication that is also relevant to the origin of bacterial
>chromosomal DNA replication, I'm all ears.

Julie, Julie, Julie. You're the one making the claims around here. Is
there, in your opinion, a non-IC form of DNA replication? That's really
the question that I asked before and you skated around it. You should know
the answer since you must be an expert on DNA replication. How do I know
that you are an expert on DNA replication, you might ask? Because only an
expert would presume to know the entire literature on DNA replication and
you would have to be familiar with the entire literature in order to make
believable claims about what is NOT known. You made lots of such claims in
your essay.

>>Our goal is to try and understand how the present form of DNA
>>replication can to be. Did it evolve or was it designed by
>>someone/something?

>These are not mutually exclusive categories.

I understand the modern religious position on this matter, Julie. No need
to get picky. Modern religious people accept that evolution can occur
but they often postulate some intervention by their deities. So it is
possible to have design AND evolution if one is religious. Except for
the Old Earth Creationist fringe the "all design" model is dead.

Non-religious people don't have a design model that involves intelligent
beings. In their case evolution excludes design. I fall into this catagory
of people but I'll try and remember that I'm discussing this with someone
who does not share my viewpoint.

>>In your essay you make a number of additional claims that
>>are more open to dispute and I will try and cover these later.

>Well, I'm still waiting.

How long did it take you to do the research to prepare your essay, Julie?
Well, it takes longer for me to correct it because I have to actually
read the papers than you conveniently ignored. Then I have to figure out
how to explain your misconceptions to the readers of talk.origins while
keeping the posting to less than 5000 lines. It's going to take a bit of
time. Are you in a hurry?

>>What I will be looking for is evidence that the eight activities may not
>>have been essential in the past.

>Great. Let's have it.

I assume that you already have it since you are an expert on DNA
replication (NOT).

When I mentioned similar evidence on the evolution of flagella you
dismissed it with a comment such as "I already know all about that". I
suspect that you will try the same trick here. It won't wash, Julie. If
you already know about serious objections to your hypotheses then you
should have addressed them in your essay. So let me ask you a direct
question. Is there any evidence against your IC hypothesis that you
deliberately left out of your essay in order to make your case look
stronger than it should?

>>You, on the other hand, are in a much better position. You get to take
>>pot shots at my explanations without having to come up with evidence
>>to support your design model.

>That's an odd perception. As I see it, I'm the only one who has taken
>the time to gather the evidence to support *my* position while others
>have been taking "pot shots." If you have another explanation for the
>origin of bacterial DNA replication (and don't forget the flagellum) I'd
>be happy to look at it. At the very least, it will help me understand
>what type of explanation you find intellectually satisfying.

And what exactly is *your* position, Julie? You know, the one you were
gathering evidence to support? Was it an explanation for the origin
of bacterial DNA replication that you were proposing? Of course it was.
Your explanation is intelligent design. (In most other parts of your
response to me you claim that you only wanted to show that DNA replication
was IC but here you slip up.)

You know, it's been a few hours since I've read your essay and I've
forgotten some of your evidence. Be a good sport and remind us. What was
your very best piece of evidence that DNA replication was intelligently
designed?

The type of explanation that I find intellectually satisfying is one
based on natural causes (i.e. evolution). I do not find it intelectually
satisfying to invoke intelligent designers every time I run into
something complicated.

>>Perhaps you could try and explain why you believe in design - is there
>>some scientific evidence to support the idea that designers exist?

>As I see it, there is plenty of scientific evidence to support the idea
>of design. Whether the designers exist is another question.

Are you a lawyer? You would probably make a good one since you are often
able to argue both sides of an issue simultaneously. Take these sentences
for example. If we accept them at face value then you admit that evolution
can produce design; or at least something other than designers can produce
design. But read what you say later on,

>>Richard Dawkins claims that evolution can design natural systems and
>>I tend to agree with him on this point.

>That's like saying the wind designed the surface of those rocks. In my
>opinion, it's a huge quivocation. Evolution designs nothing. Things
>simply evolve so that they looked designed.

Here's a direct question, Julie.

Can you have design in the absence of a designer?

This is not a hard question. A simple "Yes" or "No" will do. I reserve the
right to follow up on your answer. Meanwhile, I'll give odds of three to
one that Julie avoids answering the question.

>>I'm interested in your design model. Do you simply "imagine" that
>>designers exist or is there evidence?

>I simply infer that certain things have been designed. And there is no
>need for imagination when it comes to connecting IC and intelligence.

I'm afraid you lost me there, Julie. My imagination isn't good enough
to fathom your meaning. Please tell me about the connection between IC
and intelligence. While you're at it, here's another simple question,

Is every IC system designed?

>>Remember that you don't think the ability to "imagine" is relevant so
>>let's see how you can explain "intelligent design" without using
>>imagination.

>I have experienced countless IC entities that are the products of
>designers.

I assume that you are referring to mechanical things like pocket watches
and IBM PC Jrs. In this sentence you seem to be making connections between
"design", "designers" and "IC". I am anxiously awaiting the answers to my
questions. Here's another.

In your mind, do IC entities imply designers?

>>The only reason for claiming IC is to support the idea that the system
>>was designed.

>As I just said:

>"I simply outlined the IC nature of DNA replication which in turn
>strongly suggests the system was designed."

>>The only reason for wanting a system to be designed is that it fits in

>>with your belief in a "designer".

>Oh please. Not another person who wants to argue with me by relying
>on some stereotype. I don't "want" any system to be designed. I'm
>trying to determine, out of deep and sincere curisity, what *has* been
>designed to my own satisfaction. Maybe nothing has been designed.
>Who knows? But the evidence is pretty convincing *to me*. So I
>explore it.

Oh please. Not another religious person who pretends to just be just
sincerely "curious" about how life was created! If you do not believe
in a "designer" then this would be a good time to let us in on the troll.
Yes, it's a stereotype. But if it quacks like a duck ....

Oh, and you might want to re-read some of your "quacks" (comments) that
follow. Pay close attention to the ones where you tell us how lack of
evidence for evolution fits so nicely into your pre-conceived beliefs.
Do a word search on "intellectually satisfying".

When are you going to tell us about this evidence of design?

>>If all you want to say is that DNA replication looks complicated then
>>there is no disagreement. But you want much more than that - you
>>want to convince us that it could not have evolved.

[snip]

>For the umpteenth time, I have never claimed that things "could not
>have evolved." Hell, Tim showed how a mousetrap "could have
>evolved." Do you think I am so stupid I would believe and defend a
>claim that said X (where X can be anything) is *impossible*?

I don't believe you. It sure looks to this observer as though your main
intent is to prove that DNA replication is IC. What that means is that
it would be *impossiblBe* for it to have evolved. It must have been
designed. Oh, you can wiggle and squirm and claim that you never used
the word "impossible" and that you are just trying to satisfy your
"intellectual curiosity" but I don't buy it. You can prove me wrong by
answering the following questions,

Can you have design in the absence of a designer?
Is every IC system designed?
In your mind, do IC entities imply designers?

>>Since it could not have evolved, according to you, then the competing
>>hypothesis must be correct.

>I never said anything could not have evolved.

[howard hershey]

But organisms can certainly live without *large* chromosomes.
_Tetrahymena_ and other ciliates have a *functional* nucleus which is
composed of gene-sized (or several genes) subunits with short
non-templated telomeric ends. They can live for many thousands of
generations using only this chromosome, which is highly amplified and
does not even undergo mitosis but segregates via simple fission. And
this genome is larger than an average bacteria's. It seems perfectly
*feasible* that the current status of bacterial chromosomes is not the
ancestral one. And if small chromosome subunits are feasible, it is
reasonable to consider other mechanisms than the current one as being
possible for DNA replication. Mechanisms that work well with smaller
genomes and polyploidy. It is absurd to look at the current structure
of a complex system and *assume* that that was the way it always was.
It would be like looking at the dependence of the current economy on
computers (the present economy and computers may be IC, and we might be
able to test it in the year 2000) and assuming that the economy always
used computers because computers are so fully integrated and necessary
in the present system. But if you rule out even considering simpler
systems in the past, you are cooking the books and saying that we can't
use any analogies to any simpler economies seen in the present as models
for how an economy could have 'evolved' to its present state without
computers. Since, unlike the economy example, biochemistry's fossils
are only visible and written in present organisms, that essentially
rules out any possible evidence to resolve the problem one way or the
other. OTOH, if I can make a reasonable hypothesis congruent with
natural law mechanisms and points to feasible steps and requires certain
properties (similarity to transcriptional processes, for example) of the
proposed intermediates, that remains better than a hypothesis which
assumes either *ex nihilo* or near instantaneous 'creation' of complex
structures by an invisible intellignece/implementor or the step-wise
'construction' of complex structures with every possible intermediate
being totally inutile, but preserved by some unknown mechanism.

>
> >But that's a different kettle of fish entirely. What we are concerned
> >about is how the modern system came to be (evolution or de novo
> >design). In that case the ability to "imagine" or demonstrate that
> >simpler systems will work is highly relevant.
>
> I do not think the ability to imagine is relevant. However,
> demonstration of a simpler system might be very relevant.

But you insist that that system be bacterial, that the genome be dsDNA,
that the chromosome structure be identical to the present structure,
right?

>
> >Julie's lack of imagination may lead her to conclude that DNA
> >replication was designed by aliens but the rest of us need not be bound
> >by her limitations.
>
> First of all, I did not conclude that "DNA replication was designed by
> aliens." I simply outlined the IC nature of DNA replication which in turn
> strongly suggests the system was designed. The identity of the designer
> is a separate issue.

And I outlined some criteria for how an IC system can be created: All
at once in a sudden process that instantaneously produces a functional
system, or stepwise with all possible intermediates being utterly
useless until all parts exist. If you have another alternative let me
know.

>
> As for my limitations, yes, I attempted to limit myself with the
> evidence.
>
> >In the postings that follow I will be examining the "alien design" model
> >that Julie proposes.
>
> Where did I say anything about aliens?

Just a term for the invisible implementor of the design.

>
> >By "alien design" I mean the thesis that the modern form of DNA
> >replication in bacteria could only have arisen by instantaneous creation
> >de novo.
>
> Then why do you call this "alien design" rather than "design" or
> "intelligent design?" It looks like to are trying to label my position as
> something that stems from a UFO nut. Above you noted:

Would 'implementation by an invisible implementor of design by an
invisible designer' make you look less like a UFO nut? Shouldn't you be
focusing on these features of your alternative hypotheses? You can't
make an argument for any mechanism of
'construction'/'creation'/'evolution', which are by nature historical,
by focusing entirely on a present system.

>
> "She is trying to focus the discussion and prevent us from wandering off
> or gettng involved in flame wars over terminology."
>
> But you don't seem to helping matters with terms like "alien."
>
> More importantly, if this is the thesis you are going to write about,
> I hope you didn't put too much effort into it yet as you are barking up
> the wrong tree. My thesis was simply that bacterial chromosomal DNA
> replication is IC. This thesis does not require me to posit that the
> process arose by "instantaneous creation de novo" (although IC is not
> inconsistent with this claim). IC may also entail the creation of a mosaic
> analogous (but superior) to the workings of molecular biologists.

Create useless 'subsystems' and then put them together? They *would*
have to be utterly useless if IC has any real meaning wrt the
'creation'/'construction' of the system.

>
> >The "aliens" who created such a system could be one or more
> >supernatural beings (i.e. gods or godesses) but I assume that Julie does
> >not want to restrict her proposal to such entities since that brings
> >religion into the discussion and Julie has taken great care to avoid this.
>
> I still don't understand why you think the term "aliens" is required.
> Intelligence is a far better term as it is more neutral.

And 'invisible' intelligence and implementor is more accurate.

>
> >"Evidence" for Julie's alien design model is based largely on negative
> >inference as many others have pointed out.
>
> To point out something is to specify something that objectively exists.
> Others have not "pointed out" anything other than to draw attention to
> their perceptions of things.
>
> >She suggests that some systems are so complicated and interconnected
> >that it would be impossible to imagine or reconstruct a natural
> >explanation involving evolution from a primitive ancestor.
>
> Where did I suggest this? In fact, I just did a word search of my entire
> 50 page article and not once did the word "impossible" appear. I'm
> sorry Larry, but you have simply put words in my mouth and thus your
> characterization of my article is seriously flawed. After all, I've always
> admitted that someone can "imagine" a natural explanation involving
> evolution from a primitive ancestor. So what? What matters is
> whether this imagination is a fantasy or reflective of reality.

Also true (even more so) for models that propose 'invisible'
intelligences and mechanisms that have never been observed
(instantaneous creation and/or persistent inutility). The existence of
organisms with small chromosomes and non-DNA genomes and different modes
of priming and simpler replication machinery show that such methods are
compatible with duplicating genomes. Proposing that intermediates have
*some* kind of utility is merely saying that natural selection (a
mechanism which *can* be observed today) existed in the past.

>
> >But the absence of evidence is not evidence of absence. This is a point
> >that Julie consistently tries to obfuscate.
>
> Instead of accusing me of obfuscation, why not simply consider the
> possibility that we may not be communicating effectively.
>
> First, the claim, "the absence of evidence is not evidence of absence." Is
> this an absolute truth that is always true? Often times in science,
> the absence of evidence is interpreted as evidence of absence. After all,
> if there was absence, we would expect no evidence. For example, if
> there is no evidence that gene X is part of the process of DNA
> replication, scientists don't continue trying to find where gene X fits into
> DNA replication because they view this absence of replicating activity
> for gene X to mean gene X is not part of DNA replication. They wouldn't
> claim this with certainty, but they would probably argue it is a
> reasonable, yet tentative, inference
>
> Now, if you claim DNA replication evolved from a primitive ancestor
> along Darwinian lines, I simply note there is no evidence for this claim
> (or at the very most, the evidence is very weak).

To say that there is *no* evidence which supports the existence of
alternative mechanisms for genome replication is overstating the case
considerably. Your assertion is that earlier systems could not use any
of these alternatives.

> If, as I believe, design
> is a better explanation for the IC nature of DNA replication, I *then*
> consider your absence of evidence and say "no wonder there is no
> evidence; y'all are pursuing a dead end."

And then you need to show how your models fit the data and known laws of
nature better.

> Thus, the failure of Darwinism
> is *supporting* evidence.

Even if both systems were equally sketchy in that neither had any
supporting evidence, how can you twist that into a failure of
Darwinism? That would merely be an unproven case with no evidence. IC,
as Behe points out, does not rule out *indirect evolution* (whatever he
meant by that). Certainly you are not claiming to have any direct
evidence for the posited intelligent implementor?

>
> I think there is much confusion concerning this topic. My major
> intention in focusing on IC is not to come up with an anti-darwinian
> argument. I don't need that. When it comes to DNA replication or the
> bacterial flagellum (and many other things to come), I am simply not
> convinced that Darwinism has anything to do with their origin. But I
> am still quite interested in their origin.

Then why don't you start making a specific proposal for *how* they were
'created'/'implemented'/'whatever'?

> Should I wait, and hope, that
> someday folks like Paul Myers will come up with a story that will
> probably only convince those hoping to be convinced? Nah. Thus, I
> look for alternative explanations that *I* find far more intellectually
> satisfying. And, as I see it, Michael Behe has given me the key. So I
> begin to look afresh at these systems with Behe's key and it generates
> new insights and new lines of inquiry.

Such as? One can clearly ignore comparisons and similarities and
patterns and simply choose to focus on a single system and how it works.

> Put simply, it's a way to
> interpret data and do science under a design paradigm. That's why I
> said to Paul that "Ill go my way and y'all go yours." Would you be
> another one who is bothered by that?
>
> >Julie and her like-minded friends are fond of the term "irreducible
> >complexity".
>
> It's not a matter of being fond of a term. It's matter of
> exploring the utility of a fresh concept.

So how are you going to explore how these systems arise? I know you can
explore any system without asking how it arose.

>
> >This is a rhetorical device that is designed to convert the absence of
> >evidence into something positive that is subject to scientific analysis
> >(i.e. that the system will not work if any part is removed). We
> >are not fooled by this cheap trick.
>
> Rhetorical device? Cheap trick? Could you be a tad more insulting?

Yes. But that was adequate.

>
> Look, when you say the "absence of evidence," I must ask, "evidence for
> what?" The term "absence of evidence" is meaningless by itself. Now,
> did I argue there was an absence of evidence for the IC nature of DNA
> replication? Nope. I argued that DNA replication *is* IC.
>
> Now I assume you mean "absence of evidence" for a Darwinian origin to
> DNA replication.

Actually, for any model. The Darwinian explanation(s) have much more
evidence than any specific alternative(s) you have presented (since you
have not presented any).

> Well, yes, this is *also* true. But there is no
> conversion going on. Absence of evidence for a Darwinian origin simply
> means I have no good reason to think a Darwinian origin is part of the
> true explanation. I then simply approach the topic differently and
> explore a concept so that it is subject to scientific analysis. At the very
> least, it is fun! Then I look over at you and see you struggling to come
> up with even a just-so story.

Any just-so story *must* be compatible with the evidence. The real
problem is narrowing down the options. I have already ruled out the IPU
explanation as a useful scientific description.

> I see folks getting emotional and wanting
> to talk instead about invisible pink unicorns. Etc. One example of this
> strangeness may not be all that significant, but if the same dynamic
> holds in the analysis of system after system after system (even allowing
> for some vague just-so stories), I'm going to start to *really* believe
> there is a reason for this dynamic.

If I keep looking at protozoa and jellyfish lineages, I can find all the
examples I want of lineages without much of a fossil record.

>
> >The fundamental point is that alien design proponents are basing their
> >argument entirely on the lack of hard proof of natural causes. Lacking
> >such proof they assume the existence of aliens who must have done the
> >deed.
>
> It would be polite if you would refrain from labeling me an "alien design
> proponent." I have gone to great lengths to refrain from speculating
> about the designer(s).

And *how* you think the IC system arose. Strange if you are arguing for
a specific scientific model of how systems arise. Not strange if you
have absolutely no supporting evidence for any necessary feature of your
model: 'the invisible implementor', systems that arise at once or
stepwise with useless intermediate stages, etc.

>
> More importantly, you completely misunderstand my position. It has
> nothing to do with "hard proof" or the lack of it. In fact, a desire for
> "hard proof" is not scientific.

Supporting evidence would be nice.

>
> >There is, of course, no proof that such aliens exist or that they existed
> >in the past.
>
> Again, what does proof have to do with science. There is likewise no
> proof that life ever existed on Mars, but scientists and engineers plan on
> looking for it (or its traces).

So how are you going to look for traces of the 'invisible implementor'?
That depends upon where, when, and how you think the action took place,
doesn't it?

>
> >The assumption of "designers" is something that they bring to
> >the table from outside of science.
>
> Nope. It is something that is inferred, as the best explanation, from the
> data. Science often infers the unseen to explain what is seen.

So what specifically do you infer about how the IC systems were
implemented?

>
> >At least that's how it appears to this observer.
>
> That's fair. But since you also seem to think I appear to be arguing for
> alien designers because you can't show it is possible that DNA
> replication evolved, perhaps you should question your perceptions.
>
> >On the other hand, there are times when Julie almost seems to be
> >offering irreducible complexity as proof of the existence of aliens. This
> >is nothing more than the argument from design dressed up for the 90's.
>
> Oh please. If you interpret my articles as one big "Argument From
> Design," you will continually be clueless about my writings.

[snip]

>
> I'll be here (although other obligations may prevent prompt replies).
> BTW, I'm still waiting for that evidence that the bacterial
> flagellum evolved from a "primitive secretory apparatus."

It could, of course, be the other way around for the current Type III
secretory systems. But since these are simpler systems with a
'function' that is clearly related to the function of the homologous
proteins in the flagellar 'system', namely protein secretion, it does
provide a possible role for an intermediate stage. Since these genes
appear often on plasmids, this opens up a considerable role for
'horizontal' transfer bringing it into cells with other 'parts' of the
'system' which are serving other functions (like pillins). This is a
just-so story compatible with observed evidence which does not require
the importation of 'invisible implementors'. It is very sketchy, but
the 'invisible implementor' has no, zero, nada, supporting evidence.

>
> >It's not good enough to claim that a system is simply "irreducibly
> >complex" if you are trying to prove that intelligent aliens exist.
>
> Says who? You? The Gang?

Says Brother Occam.

>
> >You also have to show that the system is well designed, so well
> >designed that there had to be aliens behind it.
>
> You confuse science with philosophy. Scientific explanations do not
> entail "had to be" claims. That's much too certain.
>
> As far as determining if something is "well-designed," that's a subjective
> point that depends on knowledge of the designer('s) intentions and
> one's taste. But if you think it is relevant, you should probably start by
> defining what you consider a "good design."

What does the design tell *you* about the invisible designer's and the
implementor's mechanisms and tastes? Nothing? Just that it is design?

[Julie Thomas]

In a previous article, lam...@bioinfo.med.utoronto.ca (Laurence A. Moran) says:

I'd like to begin first by thanking Larry Moran for an excellent reply
concerning the bacterial origin of replication. I would like to reply
in turn. A word of warning, however. I wrote this reply Sunday
evening after a Saturday night of very little sleep so I hope it
isn't too confusing.

>The Origin of Replication

>Julie Thomas claims that DNA replication is a alien designed system
>based on the fact that it is so complex that it couldn't have arisen by
>natural causes.

Unfortunately, this statement tended to detract from an otherwise good
article. The problem is that I have never claimed that DNA replication
is an "alien designed system" Neither have I ever claimed that DNA
replication is so "complex that it couldn't have arisen by natural causes."
This is most unfortunate as Larry is well aware of this. What's worse, it
suggests that Larry's entire article is simply a response to a strawman
argument.

>One of the components she discusses is the origin of replication. I'd like
>to correct some of the errors in her essay and then present some
>additional information that she left out.

And I'd like to do likewise with Larry's article. ;)

Julie says,

"The origin of replication (often called the DnaA box) is a
specific set of nucleotide sequence crucial for the initiation
of DNA replication. From a thematic IC perspective, the origin
appears crucial on bacterial cells. Let's consider it in detail
as it has been described in various species of bacteria who
last shared a common ancestor 1.2 billion years ago."

>All modern species of bacteria have a specific site(s) on each of their
>chromosomes where DNA replication is initiated. This site is called the
>origin of replication. There are quite a few different kinds of origins,
>the one found on most large chromosomes is called oriC. The E. coli
>origin is an example. Other types of origins are often found on

>plasmids,including those large plasmids that we now recognize as

>separate chromosomes. OriT is the origin of DNA replication site on F-
>plasmids in E. coli. DNA replication begins at this site during
>conjugative transfer even when the plasmid is part of the main
>chromosome.

This is all true, but apart from presenting general background info for
the reader, it is not very relevant to IC. Thematic IC simply states that
some origin sequence is needed and all of these origins underscore that
point. And from a systematic IC perspective, none of these origins helps
to explain the existence of OriC (the bacterial chromosome origin).

>From a thematic IC perspective, one or more origins of replication
>seems to be a ubiquitous component of DNA replication of large
>bacterial chromosomes. However, there are different kinds of origins
>employing different strategies of initiation. When Julie refers to "it" she
>means a specific origin (i.e. systematic IC) in certain bacteria. The "it"
>appears to be oriC.

This is true. It is important that the reader keep in mind that my
article attempts to address bacterial DNA replication from all three IC
perspectives.

>Eukaryotic chromosomes have multiple origins of replication

>chromosomes are smaller than typical bacterial chromosomes. Since all
>available evidence indicates that eukaryotes and prokaryotes share a
>common ancestor this means that it is impossible to tell which
>condition (unique or multiple origins) is primitive and which is
>derived.

I simply do not agree "all available evidence indicates that eukaryotes
and prokaryotes share a common ancestor." Just for starters, we've
already seen that there is little or no sequence homology between the
two (bacteria and eukaryotes) when it comes the DNA replication
machinery (btw, ditto for the flagella). Thus, there is little-to-no
reason to think the eukaryotic process tells us anything about the
prokaryotic lineage.

>It is reasonable to propose that multiple origins were present in
>primitive cells and the presence of unique origins in modern bacteria is
>the result of evolution that eliminated all but one site as the genomes
>were stream-lined.

Why propose multiple origins were present in the putative ancestors of
bacteria? As for genomic streamlining, this notion received much
impetus from the lack of mRNA introns in bacteria. However, the
evidence indicates that introns are probably recent (Palmer and
Logsdon, 1991). Thus, Larry uses the concept of streamlining in this
context in a manner that appears somewhat ad hoc.

>This is not an important point but it illustrates how easy it is to be led
>astray by assuming that bacteria are "primitive". We must try and
>avoid such thinking wherever possible.

Larry is correct that we should not think of bacteria as "primitive."
However, bacteria do indeed represent the simplest of cells and this is
quite relevant to IC.

>DNA replication in eukaryotes need not even occur at a specific site. In
>other words there may not be an origin. This is particularly true of
>multicellular animals when DNA is dividing rapidly. In such cases
>initiation occurs randomly at many sites on the chromosome
>(DePamphilis, 1993). These examples demonstrate that an origin of
>replication is not an absolute requirement for DNA replication in all
>cases. In other words origins are not IC components in some cells. The
>non-origin examples suggest that primitive DNA replication systems
>could have managed without a specific origin.

This is a good point. Thus, DNA replication, from a purely thematic IC
perspective, might not entail some specified origin sequence. I'll have
to return to this later when discussing eucaryotic DNA replication.
However, in the case of bacterial chromosomal DNA replication, such
specified sequences are required. And since this feature is shared by
all bacteria, it is more than systematic. Thus, the specified origin site is
thematically IC in the case of bacterial DNA replication. On the other
hand, one could describe it simply as an example of thematic-systematic
IC.

>There are other examples of DNA replication in the absence of an
>origin. Replication can begin at the ends of linear chromosomes. The
>extant examples are confined to viral, bacteriophage and linear plasmid
>DNA's (Salas, 1991) where proteins that bind to the ends of DNA are
>required.

But as I have explained in my original article, none of this is clearly
relevant to bacterial DNA replication as viruses and linear plasmids
(which probably evolved from viruses) are likely to be more recent than
bacterial cells.

>The primitive ancestral cell may have contained multiple linear
>chromosomes that were replicated in this manner before the evolution
>of internal origins of replication. In other words, it is possible that the
>last common ancestor of all life had chromosomes were replicated from
>their ends. Internal (multiple?) origins evolved later according to this
>hypothesis.

Yet this speculation is based entirely on viral sequence analysis As
was originally noted above, we shouldn't think of bacteria as being
"primitive" but this hypothesis seems to make just that mistake in
thinking of viruses as "primitive." In fact, this is even more relevant
when we consider that viruses typically show a much higher mutation
rate. Thus, this hypothesis could very well be reading relatively recent,
highly streamlined processes into the distant past.

>Now, back to Julie's description of oriC. Remember that she is claiming
>that the DNA replication system in bacteria is designed by aliens
>because there is no possible way it could have evolved from a more
>primitive system. She says,

>"The sequence in question extends about 240 nucleotides.
>Essentially what we have are three AT-rich 13mers at one
>end (left) that are then followed by at least four 9mers.
>Two of the 9mers are separated by about 180bp. These two (R1 and
>R4) are inverted repeats and show very strong sequence conservation -
>TTATCCACA. The other two 9mers lie between R1 and R4 and also
>show strong sequence conservation.

>The replication origin works as follows. Several molecules
>of DnaA (see below) bind to the 9mers. This is followed by
>the melting of the AT-rich 13mers. This then allows DnaB
>(see below) to bind to and initiate replication by unwinding
>DNA further. Thus, the strong sequence conservation of the
>9mers reflects its role as a binding site for DnaA. The
>interactions between DnaA and oriC (and DnaB) represent
>systematic IC."

>This is basically correct but I'd like to clarify a few points so that
>readers don't get the wrong impression. The actual structure of the
>generic oriC region is much more sloppy than Julie suggests.

But much less sloppy than Larry suggests.

>She is making the common error of assuming that E. coli is the
>paradigm for all bacteria but in this case the E. coli oriC is the
>exception. We should avoid the impression that the organization of this
>region is highly structured. Julie is describing systemic IC (E. coli) but
>implying that it is thematic (all bacteria).

Actually, I was using one of Larry's references:

Smith, D.W., Yee, T.W., Baird, C. and Krishnapillai, V. (1991)
Pseudomonad replication origins: a paradigm for bacterial origins?
Molec. Microbiol. 5, 2581-2587.

In this article, the authors compare the origins from E. coli, two
Pseudomonads, and B. subtilis (the latter is very distantly related to the
former two). They conclude:

"Comparisons between these three classes of bacterial origins indicate
that the fundamental features of a primary bacterial origin are as
follows: (i) at least four 9-mer DnaA-binding sites are present; (ii) two
of these (R1 and R4) are separated by close to 180 bp; (iii) these two are
inverted repeats; (iv) two or more additional 9-mer DnaA sites are
present between the R1 and R4 sites; and (v) three 13bp to 16 bp AT-
rich direct repeats are found adjacent to the R1 site but not within the
R1-R4 region."

>In many bacteria there are two or three separate regions that contain
>DnaA binding sites (DnaA boxes). The important one is near the dnaA
>promoter (promoters are sites where RNA synthesis begins when the
>gene is transcribed). There can be as many as eight DnaA boxes in a
>region or as few as two.

So even if Smith et al. are wrong, we still seem to need at least two
DnaA boxes.

>In most species of bacteria there are no obvious AT-rich sequences. It
>is rare to find direct AT-rich repeats such as those at the E. coli origin
>so we can safely assume that the E. coli sequence is derived and does
>not represent the primitive origin organization.

AT-rich repeats are not restricted to E. coli. They exist in the
pseudomonads (Smith et al., 1991) although the conservation between
repeats is not as strong as in E. coli. Perhaps a better way of describing
the origin is that the DnaA boxes are found in AT-rich regions. A
comparison with E.coli, the pseudomonads, and B. subtilis shows a 50-60
bp region adjacent to DnaAboxes that is 72-82% AT (Yoshikawa and
Ogasawara, 1991).

>The complete genome of Mycoplasma genetalium was searched for oriC
>sequences and DnaA boxes and none were found (Fraser et al., 1995). I
>believe that the related species, Mycoplasma pneumoniae also lacks a
>recognizable oriC (Himmelrich et al., 1997). The complete genome
>sequence of M. pneumoniae was searched. This suggests that these
>organism may use another kind of origin. However, it is more likely
>that they have DnaA boxes that have diverged from the consensus
>sequence that we recognize in other species. We just don't recognize
>the DnaA boxes in these species. Both mycoplasma species have dnaA
>genes and there is some evidence that DNA replication begins near
>these genes.

I agree it is more likely the DnaA boxes in these species have diverged.
Not only do the DnaA genes suggest this, but also DnaA boxes have been
found in other mycoplasma (Dybvig and Voelker, 1996). However, this
would not challenge IC as there is a significant difference between
gradually evolving an IC system and an IC system that gradually
evolves.

>There are also no oriC sequences in the genome of Methanococcus
>jannaschii (Bult et al., 1996). M. jannaschii is an archaebacterium - I
>think that Julie's alien design hypothesis assumes that the aliens
>designed archaebacteria separately.

I have no "alien design" hypothesis, but I do indeed think it irrelevant
to refer to archaebacterial features as they are so different and I am not
convinced they shared a common ancestor with eubacteria.

>So, the minimal (IC) oriC origin consists of several DnaA boxes. AT-rich
>repeats are not necessary.

AT-rich regions do seem important.

>The DnaA box sequence is not as strictly defined as Julie implies. The
>binding sites for DnaA match a CONSENSUS sequence that varies
>somewhat from species to species. In general, a seven out of nine
>match to the consensus sequence is more than sufficient for binding.

And this, IMO, is very strong sequence conservation. Let's not forget
that this sequence probably arose 1-2 billion years ago. If we consider
the various distantly related lineages that demonstrate it, that amounts
to several billion years of microbial evolution where a 7/9 match
occurs.

>Let's look at the sequence of DnaA boxes. I apologize for belaboring this
>point but Julie seems to think that this is a very important issue. I'll

>quote from her essay later on to show you where we disagree.(p10).

>There are five DnaA boxes at the oriC of enteric bacteria - species that
>include E. coli and its relatives. The boxes are named R1-R5 and six
>different species have been examined. In the list below I will use
>upper case letters (i.e. T) when the nucleotide in all six species is the
>same and lower case letters (i.e. t) when there are differences.
> R1 TTATCCACA
> R2 TTATaCACA
> R3 TTATCCaAA
> R4 TTATCCACA
> R5 TCATTCACA

>This is fairly typical of DNA binding sites. The protein binds to a set of
>similar sequences that conform to a consensus - in this case the
>consensus sequence is TTATCCACA which is the sequence Julie refers to
>in her essay.

And note that R1 and R4 conform perfectly to the consensus and these
were the two boxes I initially singled out.

>Note that it is not necessary that every nucleotide conform to the
>consensus in order to achieve binding.

Yes, but note also how tight the consensus is. Furthermore, this
interpretation would be stronger if all bacteria had only one DnaA box.
Multiple boxes translate as redundancy which in turn translates as
more tolerance for variation in individual boxes.

>Messer and Weigel (1997) review the extensive literature data on
>DnaA binding. Adding in other DnaA binding sites and studies of DnaA
>binding in vitro yields a stringent consensus binding site of
>TT(A/T)TNCACA where (A/T) means that either A or T will work at
>that position and "N" means that any base pair will do.

And this supports my point as I never said the 9-mer was invariant.
I said it showed "strong sequence conservation" and built from there.

>There is good evidence that the real binding sequence is even more
>relaxed - T(T/C)(A/T)T(A/C)CA(C/A)A.

What is this good evidence?

>The important point is that in enteric bacteria DnaA binds to a family

>of sequences defined by a roughly 7/9 match to a consensus sequence.

Actually, it's a 7.5/9 match, as G/C doesn't work in the third position.
Furthermore, Larry gives the impression that the consensus sequence is
more restricted than it is. This strong consensus extends well beyond
the enterics. As Larry himself noted:

"Pseudomonads (Pseudomona aeruginosa, P. putida) seem to require a
DnaA binding site that corresponds very closely to the sequence
TTATCCACA that Julie refers to (Smith et al., 1991)."

Also, the same consensus is seen in B. subtilis, and Miccrococcus luteus
(Yoshikawa and Ogasawara, 1991). M.luteus also contains consensus
sequences (in three boxes) that differ in only one position:
TTGTCCACA(Yoshikawa and Ogasawara, 1991). The A->G change at the
third position is not surprising given that it's chromosome is 75% GC rich.
In fact, given the strong mutational pressure towards GC, it is even
more remarkable that the 7th and 9th position remain A. Mycoplasma
capricolum also has E. coli-like consensus sequences that differ by only
one nucleotide (Yoshikawa and Ogasawara, 1991).

>A lot of work has been done on the role of DnaA and the DnaA boxes. A
>good summary can be found in Langer et al. (1996). It turns out that
>you can make small sequence alterations to each of the five sites
>without affecting the initiation of DNA replication and you can even
combine mutations to three of the sites without effect.

Which is consistent with the need for two DnaA boxes. Although, again,
my case does not depend on absolute invariance of sequence.

>What this says is that the exact sequence isn't very important as long
>as it resembles the consensus binding site.

Yes, but it should strongly resemble it. Also, keep in mind that the
redundant box function (> 2) may allow for some sequence variation.

>If you delete one of the sites or completely scramble the sequence then
>the origin doesn't work as well as the wild type oriC. In mycobacteria
>(Mycobacterium smegmatis, M. leprae, M. tuberculosis) the consensus
>binding site is (C/T)T(A/G)TCC(A/C)CA (Salazar et. al., 1996). This is
>significantly different from the consensus sequence of the site in
>enteric bacteria.

And many other bacteria distant from E. coli. And I don't think it's that
significantly different as it is still a 7.5/9 match.

>However, it is possible to dispense with oriC altogether. In E. coli you
>can substitute oriP2, oriR1 or oriF and the chromosome will be
>replicated. These origins don't use DnaA. In Bacillus subtilis you can
>delete oriC and replace it with an unrelated origin from a B. natto
>plasmid (Anwarul et al., 1997). DnaA is not required in this construct
>and the chromosome is replicated although partition is inefficient.
>These experiments demonstrate that oriC is not specifically part of an
>IC system, although some form of DNA binding protein and binding site
>is.

Larry confuses systematic IC with thematic IC at this point. The
different origin strategies (as Larry mentions) underscore that a DNA
binding protein and binding site is needed (thematic IC). But they are
not relevant to OriC from a systematic perspective unless these other
origins can be shown to predate oriC and have given rise to oriC.

>Now it's time to see what Julie says about DnaA and its binding site,

>"A molecular IC perspective would take into account the strong
>sequence conservation found among the 9mers. Could these 9mers
>be built up one gradual nucleotide at a time? This seems
>unlikely given the strong sequence conservation which suggests
>all 9 are needed to be functional. That is, what good is the
>5mer that supposedly led to the 9mer? At this point, a critic
>of IC might claim that I am employing 'the fallacy of believing
>that is now must always have been so.'"

>It is quite clear from reading the literature that "all 9" base pairs are
>not needed for binding.

I do concede this point. This part of my article was written earlier
when it was still in the "reply to X" form.

>It is quite clear that in many cases you need only a 7/9 match to a
>consensus sequence that is itself somewhat sloppy.

You need "only"? Sorry, but that's strong sequence conservation given
we're looking at the products of billions of years of microbial evolution.

>It is not difficult to imagine a primitive DnaA that interacted with 9bp
>of DNA but only five of these needed to be specific base pairs.

It's not difficult to imagine a primitive DnaA that interacted with DNA
anyway you wanted it to interact.

>In fact, the mycobacterial site is not far off this imaginary ancestral
>site.

It's a 7.5/9 match. Besides, are you arguing that the mycobacterial site
is the most primitive?

>Julie, you are employing that fallacy of believing that what is now in E

>coli must always have been so in all ancestral species of bacteria.

This is simply not true. My discussion of the oriC comes from
comparative studies of E. coli, P. putida, P. aeruginosa, B. subtilis, M.
luteus, and M. capricolum.

I said:

> "Now, I'm not saying this state 'must always have been so'. In
> my original article on IC DNA replication, I clearly said:

> 'it's hard to see how this conserved sequence was built
> one little nucleotide at a time'

> The critic of IC may claim that once upon a time a bacterial
> origin was made up of one 5mer (or something like that), but,
> let's be blunt -> there is no evidence for such a claim (making
> it look awfully ad hoc)."

Larry replied:

>It is not hard to see how this "conserved" (sic) sequence evolved from a
>less stringent specific binding site. Imagine that the ancestral DnaA
>protein bound DNA non-specifically, contacting a region of about 9bp
>(proteins are actually much bigger than this and can interact with
>larger regions of DNA). There might have been mutations that
>enhanced the strength of binding and these were selected because they
>enabled DnaA to do its thing much better. For example, replacement of
>a particular amino acid side chain could have led to tighter binding to
>sequences that ended in CA. (Side chains such as lysine or arginine can
>interact with two adjacent base pairs to confer specificity.) This
>wouldn't be much of a restriction since CA sequences will occur every
>sixteen base pairs on average.

Before getting to the main point, there are problems with this
explanation. Larry appears to be describing molecular tinkering, which
is plausible once a system is up-and-running, but not so obviously
plausible in talking about the origin of the system. Specifically, Larry
seems to be reading modern capabilities back into the distant past. For
example, Larry imagines an ancestral DnaA protein that binds non-
specifically to a 9bp region. Non-specific binding tends to occur only
when protein concentrations are high relative to DNA. Could the
ancestor carry this out? Invoking mutations essentially presumes DNA
replication (the source of mutations) was up and running already.
Focusing only on the DNA-binding property of DnaA is insufficient as
DnaA functions as a replication initiator because it also carries out other
activities. Were they already functioning? And there is not a shred of
evidence to think the ancestor of DnaA bound nonspecificly to a 9bp
region.

>Now suppose that a second mutation in dnaA led to enhanced binding
>at sites that had CA at the end and a preference for TT in the first two
>positions. The protein could still bind sequences such as NNNNNNNCA
>but it bound more tightly to sequences such as TTNNNNNCA. There was
>selection for the better binding sites at certain positions in the
>chromosome where DnaA binding did its thing. We now have a DNA
>binding protein that shows strong preference for TTNNNNNCA sites.
>Like most DNA binding proteins it will bind other related sites so there
>is no magical requirement for alien designers who create a primitive IC
>system. Weak binding sites can evolve into stronger ones. Do I have to
>continue? Can you see how easy it is to build up a binding site a few
>base pairs at a time? Do you understand that there is evidence to
>support this speculation?

Larry describes the construction of a binding site, but it misses my
whole point as I was talking about a highly *conserved* binding site.
Let's see why this is relevant.

We start with the binding site NNNNNNNNN. Larry imagines a mutation
in the DnaA ancestor so that NNNNNNNCA is now recognized
preferentially. Next, another mutation occurs so that TTNNNNNCA is
preferentially recognized. From there another mutation in the proto-
DnaA could occur causing it to prefer,say, TTNNNNACA. Etc. Ultimately, we
reach the TTATCCACA consensus site and Larry states:

"Weak binding sites can evolve into stronger ones. Do I have to
continue?"

But it's not a question of coming up with a stronger binding site, it's a
question explaining the origin of this particular conserved site. Larry's
explanation posits the existence of bacteria that possessed a DnaA-like
protein that bound to NNNNNNNNN, others that bound to NNNNNNNCA,
and others that bound to TTNNNNNCA, and others that bound to
TTNNNNACA, etc. There is no evidence that a DnaA-like protein could
bind to such relaxed sequences, but what is more relevant is that it
would mean the lineages of *all* these bacteria, representing these
intermediate stages, went extinct except for the one that stumbled upon
the TTATCCACA consensus sequence (or we have some amazing convergence
occurring).

What's even more relevant yet is that Larry's explanation is also
consistent with the following scenario:

NNNNNNNNN -> CANNNNNNN-> CANNNGGNN -> CANNNTTNN-> etc.

and

NNNNNNNNN -> NNNGCNNNN-> NNNGCNNAA-> TNNGCNNAA -> etc.

and

Etc.

That is, what Larry fails to mention is that there are millions of possible
ways a weak binding site can become a strong binding site through co-
evolution. But where are they? Are we to believe that none of these were
explored by the bacteria not evolving towards the TTATCCACA
consensus sequence? Why? It seems clear to me that Larry's
hypothesis entails a countless number of variants lurching towards a
"strong" DnaA binding site. But then all these other variants must have
gone extinct because they are not represented by extant species.
That's quite an impressive bottleneck!

To put it another way, Larry starts with NNNNNNNNN and reaches
specifically for TTATTCACA. But there is nothing in Larry's explanation
which causes us to believe different consensus sequences would not be
found by different DnaA-like proteins mutating in different directions.
Larry's case would be much stronger if bacteria did not show thematic-
systematic IC with this origin. That is, if oriC and DnaA were simply one
among *many* origin sequences and origin binding proteins used by
bacterial chromosomes from various species, the co-evolution story
would be better supported.

I said:

> "In fact, the simpler ori story has some strange features. Let's
>think it through. The conservation tells us that you don't mess with
>these ori sequences most likely because such messing is deleterious.
>But to get to this point, the ori must not have been that important
>because, after all, you had to mess with it to get to the actual state we
>see today. In other words, if we could study the ancestor origin, we
>wouldn't expect to find strong sequence conservation. Otherwise, we
>couldn't get to the 9mer. For example, say we found a conserved 5mer
>in these ancestors. We wouldn't expect it to become a 9mer if it was
>functionally constrained anymore than we expect our current 9mers to
>have become 12 mers in the last 1.2 billion years."

Larry replied:

>Julie, your reasoning is flawed here. I think you got off track because
>you assume that the modern DnaA protein can only bind to a specific
>9mer. Now that you know that such interactions are sloppy does the
>evolution story make more sense to you? Now that you know that
>"messing" with the BoxA sequences has little effect will you modify
>your conclusion?

I don't think my reasoning is flawed. Say we went back in time and
found primitive bacteria with the following origin sequence:
TTATCNNNN. Would you predict this sequence to be strongly conserved
if you went looking in other bacteria also lurching towards a better DNA
replication strategy? Wouldn't your same co-evolution scenario predict
NNNGAATTN, NNACCTCNN, etc. sequences used in other lineages
reflecting the different directions that the pre-DnaA was evolving? Or is
the TTTATCNNNN sequence so special that all the other routes went
extinct? This does not seem reasonable to me. I can easily imagine
hundreds of different sloppy Dna-like proteins co-evolving with their
respective binding sites in hundreds of different directions all binding
to DNA with not significantly different affinities. Yet when one lineage
reaches the particular solution of TTATTCACA, all the rest (perhaps
millions) disappeared (or they all rushed to converge on this same
solution).

>The 5mer in ancestral cells may have worked well enough back in the
>days when you only needed to synthesize DNA every week or so and it
>didn't matter much if some mistakes were made.

In this case, the mistake would be failure to initiate DNA replication.
And if organisms only replicated their DNA every week, this would be
very risky especially when the environment became chaotic. As I see
it, if something didn't replicate that often, it would be even more
important to replicate properly *when* they replicated.

>It need not have been "constrained", just as the modern sequences are
>not as constrained as you imagine.

The modern sequences are strongly conserved across distant lineages.
And if the primitive sequences were not strongly conserved, where are
their modern representatives? Where are the dozens of analogs of
DnaA?

> "Of course, one might argue that the original 5mer was seen by
> some proto-DnaA protein (see below) and the relationship was
> sloppy."

>Yes, that's a good argument. Don't forget that the modern relationship
>is also sloppy.

I don't think 7.5/9 is very sloppy.

>>"Sloppiness meant "room for improvement" and the ability to be
>>messed with (unlike conservation). We can then wave our hands
>>and claim they "co-evolved" to arrive at the 9mer state."

>I think "wave our hands" is too dismissive here. I hope I have
>convinced you that there's a little more than hand waving involved.

While I truly appreciate you explaining your reasoning, I must confess
that at most, I see a little more than hand-waving. No offense intended,
as I'm sure you view my reasoning in an even less favorable way.

>> "And once it was found, it was "locked in" for over a billion
>> years of microbial evolution involving several lineages in
>> different environments.

>No, not "locked in" for a billion years.

Sure it is. This is seen when the same consensus sequence is seen in
bacteria who last shared a common ancestor over a billion years ago.

>In fact different species of bacteria have different DnaA boxes
>suggesting that each has chosen a different pathway of evolution.

Yes, some species have strayed somewhat from the the consensus and a
few seem to have replaced it with something else.

>The data says that there was a lot of evolution over the past billion
>years.

Yet the consensus remains in very distantly related bacteria.

>I suppose that your alien design model would postulate something
>different. Perhaps the aliens created many different designs in order to
>see which one would win out in the end? Maybe Earth is just a giant
>test tube where a bunch of alien graduate students are doing in vitro
>mutagenesis and evolution on a big scale?

I have never asserted that aliens created anything so why do you insist
on misrepresenting me?

The design model, however, is (IMO) more consistent with this pattern.
If OriC is indeed part of thematic-systematic IC, it is reasonable to
assume it was designed de novo As such, it would have probably been
the TTATCCACA sequence (or something close). This would explain why
we don't see any evidence of pre-TTATCCACA origins (which should
have been quite numerous in the past if they existed). That the
TTATCCACA consensus has persisted for so long and in so many lineages
may be due to the molecular IC nature of DnaA box/DnaA interactions.

>There's no reason to believe that any of these modern pathways are
>better or worse than any others. The evolution that took place involved
>both random genetic drift and natural selection.

Drift doesn't explain strong sequence conservation across long
phylogenetic distances. Selection would explain preservation of the
consensus, but not it's origin (IMO).

>>"But that's an uncanny story. For it clearly suggests the 9mer state
>>is optimal."

>That's your strawman "Darwinist" talking.

Like believing in alien designers proving Darwinian evolution is
impossible?

>No one claims that the
>modern situation is optimal or that each specific step had to confer
>selective advantage.

So what happened to all the other origins and pre-DnaA proteins?

>Perhaps it's just an accident that one species has a more stringent
>consensus sequence than another.

I don't find accidents to be a better explanation than design.

>Besides, you're basing your strawman argument on false information.

I don't think so.

>>"How? First, we don't see any pre-9mer states, suggesting a huge

>>disadvantage compared to the 9mer state (those that had it are
>>gone)."

>Actually we see a variety of states corresponding to 6-mers, 7-mers
>and 8-mers. All of these might be better than the primitive state of 5-
>mersand 4-mers.

We see some and they probably evolved *since* the 9mer state.

>>"Secondly, the 9mer state has persisted for a very, very long time
>>in very different lineages (eg., Micrococcus luteus, Bacillus subtilis,
>>Mycoplasma capricolum, Pseudomonas putida, and E. coli)."

>We disagree on the facts here. Please post your evidence that the same
>stringent 9 base pair sequence is required in all of these species. I've
>given you my references (see below), now give me yours.

But it's in one of *your* references!

Yoshikawa, H. and Ogasawara, N. (1991) Structure and function of DnaA
and the DnaA-box in eubacteria: evolutionary relationships of bacterial
replication origins. Molec. Microbiol. 5, 2589-2597.

See Table 2.

>>"And it hasn't been "improved" while these species evolved. Now
>>that's quite a pattern. The lack of pre-9mer states suggest (at least
>>to me) that such a transformation entailed a quantum
>>jump, not a gradual transformation. Yet the quantum jump
>>was into an optimal state. And in my opinion, that pattern
>>(quantum jump to optimal state) is quite suggestive of design."

>The pattern is quite suggestive of evolution.

Perhaps guided evolution where NNNNNNNNN was specifically pushed
towards the TTATCCACA consensus. Such guided evolution would
probably have happened rapidly as there are no obvious
representatives of the intermediates in this *particular* route. Then
again, in this context, positing evolution is not needed. Once the
TTATCCACA consensus appears, it remains strongly conserved among
various lineages over a billion or so years. As I said, it's quite
suggestive of design.

>Julie described the oriC origin as follows,

>>"The replication origin works as follows. Several molecules of
>>DnaA (see below) bind to the 9mers. This is followed by the
>>melting of the AT-rich 13mers. This then allows DnaB(see below)
>>to bind and initiate replication by unwinding the DNA further.
>>Thus, the strong sequence conservation of the 9mers reflects
>>its role as a binding site for DnaA. The interactions between
>>DnaA and the oriC (and DnaB) represent systematic IC."

>We have seen that the binding of DnaA to several binding sites is,
>indeed, a fundamental property of this type of origin. The "AT-rich
>13mers" are a derived feature found only in enteric bacteria.

But AT rich regions, adjacent to the DnaA box, are not found only in
enteric bacteria.

>It is likely that DnaA binding leads to local unwinding of DNA as Julie
>says. There is reasonable conservation of DnaA binding sites (DnaA
>boxes) in different species of bacteria but there is also plenty of
>evidence of considerable evolution from a common ancestral sequence
>that is more sloppy.

There is strong sequence conservation in the DnaA binding sites of very
different bacteria. Some straying from this consensus occurs.

>DnaA interacts with helicase but so do a number of other DNA binding
>proteins that can (partially) substitute for DnaA. (More on this later.)

I'll be looking forward to this.

>>"To sum up, the following features of the DnaA box appear to be
>>essential as determined by mutagenesis studies and/or comparative
>>analyses: 1. At least four 9mers positioned within a stretch of
>>180 bp; 2. Two 9mers must lie at each end of the 180 bp stretch;
>>3. The sequence of the 9mer; 4. Three AT-rich 13 mers upstream
>>of the 9mers. This is the molecular-thematic IC among bacteria
>>that has existed for at least 1.2 billion years [1,2]."

>Julie is describing the E. coli oriC and not the generic version. All four
>of her features are non-essential when we look at typical bacterial oriC
>regions.

>1. There can be anywhere from two to nine DnaA boxes and they can
>be spread out over shorter or longer distances than what we
>see in E. coli.
>2. It is not necessary to have two DnaA boxes at each end of a180bp
>region.
>3. The sequence of the DnaA box is not nearly as conserved as Julie
>claims.
>4. Three AT-rich 13mers are not necessary.

Again, from Smith et al.:

"Comparisons between these three classes of bacterial origins indicate
that the fundamental features of a primary bacterial origin are as
follows: (i) at least four 9-mer DnaA-binding sites are present; (ii) two
of these (R1 and R4) are separated by close to 180 bp; (iii) these two are
inverted repeats; (iv) two or more additional 9-mer DnaA sites are
present between the R1 and R4 sites; and (v) three 13bp to 16 bp AT-
rich direct repeats are found adjacent to the R1 site but not within the
R1-R4 region."

Of course, I'm more than happy to modify their claim.

>Recall that Julie defined "systematic IC" as follows,

>>"Systematic IC - In this case, we are talking about the actual
>>system with clear reference to the specific players in the system.
>>Now we are not talking about "a helicase," we are talking about
>>DnaB. We are no longer talking merely about a generic "origin
>>of replication," we are talking about OriC. Etc. While a discussion
>>of thematic IC are more general (and thus more vulnerable

>>typical Darwinian "just-so" responses), systematic IC discussions
>>are more precise and scientific and entail data."

>What I've tried to do in this posting is clarify the difference between
>thematic and systematic IC with respect to replication origins. I'v

>shown that Julie confused the two in her original essay - although she
>sometimes gets it right.

I could say the same about Larry.

>She focused her attention on a particular origin, namely oriC.

A very old, widespread, and strongly conserved origin.

>In fact, she referred mainly to the E. coli version of this origin.

Nope. I was using two of Larry's references that entailed comparative
analysis beyond E. coli.

>There is a generic oriC in bacteria and it is not as rigidly
>structured as Julie implies.

But far more structured than Larry implies.

>The essence of oriC is a bunch of DnaA binding sites located near the
>promoter of the dnaA gene itself. All other variants seem to be derived
>from the primitive generic form.

As if it is no problem coming up with a bunch of conserved sequences.

>I agree with Julie that discussions such as this require reference to the
>scientific literature and data. I have done my best to provide this.

And Larry has done an excellent job except for his misrepresentations
of my position.

>The next step is to see if we can come up with a reasonable explanation
>of oriC origins based on evolution from something that could have
>existed in the primitive ancestors of modern bacteria.

Let me guess? Transcription?

>We already know that Julie's explanation is that these origins were
>designed by aliens and couldn't have arisen naturally.

This is not my explanation.

>Any "reasonable explanation" will, of course, be speculative. The reader
>will have to decide for themselves whether the evolution model or the
>alien design model offer the most reasonable explanation of the data.

Apart from the word "alien," this is well-stated.

>REFERENCES

[snip]

Smith, D.W., Yee, T.W., Baird, C. and Krishnapillai, V. (1991) Pseudomonad replication origins: a paradigm for bacterial origins?
Molec. Microbiol. 5, 2581-2587.

Yoshikawa, H. and Ogasawara, N. (1991) Structure and function of DnaA and the DnaA-box in eubacteria: evolutionary relationships of bacterial.
Molec. Microbiol. 5, 2589-2597.

[PZ Myers]

In article <5s3b05$7...@alexander.INS.CWRU.Edu>, iz...@cleveland.Freenet.Edu
(Julie Thomas) wrote:

> In a previous article, lam...@bioinfo.med.utoronto.ca (Laurence A.
Moran) says:
>
> I'd like to begin first by thanking Larry Moran for an excellent reply
> concerning the bacterial origin of replication. I would like to reply
> in turn. A word of warning, however. I wrote this reply Sunday
> evening after a Saturday night of very little sleep so I hope it
> isn't too confusing.
>
> >The Origin of Replication
>
> >Julie Thomas claims that DNA replication is a alien designed system
> >based on the fact that it is so complex that it couldn't have arisen by
> >natural causes.
>
> Unfortunately, this statement tended to detract from an otherwise good
> article. The problem is that I have never claimed that DNA replication
> is an "alien designed system" Neither have I ever claimed that DNA
> replication is so "complex that it couldn't have arisen by natural causes."
> This is most unfortunate as Larry is well aware of this. What's worse, it
> suggests that Larry's entire article is simply a response to a strawman
> argument.

Oh, please, please, clarify *exactly* what you are arguing about! You sound
just like Nyikos -- every time someone tries to grapple with your point,
you dismiss their every effort with a cry of "Strawman!"

--
Paul Z. Myers
http://fishnet.bio.temple.edu/

[Christopher J. Carrell]

PZ Myers wrote:
>
> In article <5s3b05$7...@alexander.INS.CWRU.Edu>, iz...@cleveland.Freenet.Edu
> (Julie Thomas) wrote:
>

> > In a previous article, lam...@bioinfo.med.utoronto.ca (Laurence A.
> Moran) says:
> >
> > I'd like to begin first by thanking Larry Moran for an excellent reply
> > concerning the bacterial origin of replication. I would like to reply
> > in turn. A word of warning, however. I wrote this reply Sunday
> > evening after a Saturday night of very little sleep so I hope it
> > isn't too confusing.
> >
> > >The Origin of Replication
> >
> > >Julie Thomas claims that DNA replication is a alien designed system
> > >based on the fact that it is so complex that it couldn't have arisen by
> > >natural causes.
> >
> > Unfortunately, this statement tended to detract from an otherwise good
> > article. The problem is that I have never claimed that DNA replication
> > is an "alien designed system" Neither have I ever claimed that DNA
> > replication is so "complex that it couldn't have arisen by natural causes."
> > This is most unfortunate as Larry is well aware of this. What's worse, it
> > suggests that Larry's entire article is simply a response to a strawman
> > argument.
>

> Oh, please, please, clarify *exactly* what you are arguing about! You sound
> just like Nyikos -- every time someone tries to grapple with your point,
> you dismiss their every effort with a cry of "Strawman!"

Y'know, I predicted that response, somewhat, just because of
the presence of the word "alien" and its connotations...

----repost---
From <5ru6oc$a...@snews2.zippo.com>...

My only complaint is with the first sentence...

"Julie Thomas claims that DNA replication is a alien designed system

based on the fact that it is so complex that it couldn't have arisen
by natural causes."

... and the word "alien", which is used several times. I find it a

little vague as to what that means, and some people with private
meanings of that word will claim that the entire piece can be
ignored. Too bad, as it's as worthy a piece as has ever been
written here.

----end repost---

Of course, it still hasn't been clarified what "alien" means.
First the "design theorists" refuse to make themselves clear
on any point, then they perform a rhetorical cheap shot by
whining "Strawman" whenever someone tries to penetrate whatever
their point is. I guess by using the Instant Strawman Dismissal
Tactic, they can just go on being vague without having to
take responsibility for their ideas.

[Michael L. Siemon]

In article <5s3gav$r...@snews1.zippo.com>, "Christopher J. Carrell"
<"cjcmeow"@super.zippo.com (wilhelp)> wrote:

+My only complaint is with the first sentence...
+
+"Julie Thomas claims that DNA replication is a alien designed system
+based on the fact that it is so complex that it couldn't have arisen
+by natural causes."
+
+... and the word "alien", which is used several times. I find it a
+little vague as to what that means...

Larry was quite clear and explicit about this (though Julie was
of course miffed :-)). If Julie is criticizing the standard natural
law (i.e. evolutionary) hypotheses in favor of "design" then she
*must* have in mind an agency of this design (actually, she's being
equivocal about this, too -- Larry has subsequently tried to get
her to state yes or no as to whether "design" needs to have an
agent. Her writings *suggest* very strongly that she *wants° to
have a divine agent, but she has never admitted this.)

Larry used "alien" specifically to include divine or other non-
terrestrial intelligences as the agent of "intelligent design."
Protesting the usage *because* it includes the (generaly laughable
and disregarded) case of space aliens doing the designing is *not*
a good rhetorical move -- it simply suggests Julie has ignored
that possiblity and REALLY REALLY does want a specific designer
that she has been totally mealy-mouthed about mentioning, presumably
because she has exactly zero justification for her preferred designer.

NOTE: my comments are those of a Christian, who sees JHWH as the
designer -- but is entirely content to accept that design as being
carried out through an entirely natural evolutionary process, and
hence an advocate of "if you can't explain it by natural law, you
can't explain it and probably should shut up about 'other' causes."
--
Michael L. Siemon m...@panix.com

"Green is the night, green kindled and apparelled.
It is she that walks among astronomers."
-- Wallace Stevens

[Tim Ikeda]

FWIW:

"Alien designer" = Any agent of external, and "purposeful"
directed change in a organism.

Nominally, this could refer to humans for their attempts at genetic
engineering. However, in the context of ID and the early development
of life on earth, I would understand this definition to refer
primarily to any entity or directive force that operated with
external plans (ie. plans made outside or independently of the system
in question). The influence of forethought in modifications would be
expected.

Thus, "alien" could refer to God, little green things from Beta Centauri
and their ilk. This is not a perjorative but a means of naming a
_nonhuman_ agent.

There is one possibility that doesn't quite fit well under this
umbrella. An alternative explanation could be the existence of
"unintelligent influences" along the lines of Rupert Sheldrake's
"Morphic fields". This influence would passively direct an organism's
development via physical interactions that are not currently known.
Thus this mechanism would be a previously undescribed but otherwise
"natural" phenomenon. Of course, if this option was considered, one
couldn't describe the influence as "intelligent design".

Personally, I do not see direct evidence of either option...

Regards, Tim Ikeda (ti...@mendel.berkeley.edu)

[Christopher J. Carrell]

Michael L. Siemon wrote:
>
> In article <5s3gav$r...@snews1.zippo.com>, "Christopher J. Carrell"
> <"cjcmeow"@super.zippo.com (wilhelp)> wrote:
>
> +My only complaint is with the first sentence...
> +

> +"Julie Thomas claims that DNA replication is a alien designed system
> +based on the fact that it is so complex that it couldn't have arisen

> +by natural causes."
> +
> +... and the word "alien", which is used several times. I find it a
> +little vague as to what that means...
>
> Larry was quite clear and explicit about this (though Julie was
> of course miffed :-)).

I noticed.

> If Julie is criticizing the standard natural
> law (i.e. evolutionary) hypotheses in favor of "design" then she
> *must* have in mind an agency of this design (actually, she's being
> equivocal about this, too -- Larry has subsequently tried to get
> her to state yes or no as to whether "design" needs to have an
> agent. Her writings *suggest* very strongly that she *wants° to
> have a divine agent, but she has never admitted this.)

I suspect that the strawman protests are because the "alien"
(broad usage) agent is merely strongly suggested rather than
explicitly stated.

> Larry used "alien" specifically to include divine or other non-
> terrestrial intelligences as the agent of "intelligent design."

I also interpreted it as that general definition. I did know, however,
that others might think of something else when they see the
word "alien". (X-Files connotations and all that.) And as it
turns out, I'm going through a round of gratuitous self-
congratulations about that because I was right. =]

At any rate, it should be emphasized that Larry's article made the
issues very clear.

> Protesting the usage *because* it includes the (generaly laughable
> and disregarded) case of space aliens doing the designing is *not*
> a good rhetorical move

As a rhetorical move, I do rather dislike it as well. Smacks of
obfuscation.

> -- it simply suggests Julie has ignored
> that possiblity and REALLY REALLY does want a specific designer
> that she has been totally mealy-mouthed about mentioning, presumably
> because she has exactly zero justification for her preferred designer.
>
> NOTE: my comments are those of a Christian, who sees JHWH as the
> designer -- but is entirely content to accept that design as being
> carried out through an entirely natural evolutionary process, and
> hence an advocate of "if you can't explain it by natural law, you
> can't explain it and probably should shut up about 'other' causes."

Concur.

Chris

--
Chris Carrell

[Wade Hines]

iz...@cleveland.Freenet.Edu (Julie Thomas) writes:

>This is all true, but apart from presenting general background info for
>the reader, it is not very relevant to IC. Thematic IC simply states that
>some origin sequence is needed and all of these origins underscore that
>point. And from a systematic IC perspective, none of these origins helps
>to explain the existence of OriC (the bacterial chromosome origin).

I'm at quite a loss as to how to process this. The grammer is fine
and so is the spelling but there's something else missing ....

Let me try to see if I get the logic.
Origins of replication need origins of replication? or replication
needs an origins or replication needs a unique origins?

Do multiple sites of origins work but having a unique site works better?

There are multiple different sequences that can function as an
origin of replication. You suggest this is irrelevent.

Something called thematic IC "states" that some origin is needed.
What is it about thematic IC that prohibits multiple origins from
existing? Do these IC concepts require a designer? Do we know enough
about a designer to know that they would only design in one origin?

Given that multiple types of origins of replication exist, what
specifically about OriC is so necessary to explain other than that
some type of origin is needed as things that aren't begun don't
get finished.

And I can't recall if you've commented on
de Massy B; Fayet O; Kogoma T.
Multiple origin usage for DNA replication in sdrA(rnh) mutants of
Escherichia coli K-12. Initiation in the absence of oriC.
Journal of Molecular Biology, 1984 Sep 15, 178(2):227-36.

Not only does replication work in the absense of oriC, it appeared
to work from 4 different alternative sites.

So I'm confused about the requirement for oriC, the requirement
for a unique site, and so many many other things? Why is Weld
trying to be ambassador to Mexico? Is the battle with Helms a
ticket to differentiate himself from old school republicans?
Does he think that win or loose this will help him with the
Latino vote and therefor give him a big margin in CA, TX and FL
in his presidential campaigns? If true, why would Clinton give
him such an express ticket to the White House?

Only answe what you can.

[Paul J. Gans]

Richard Harter (c...@tiac.net) wrote:
: lam...@bioinfo.med.utoronto.ca (Laurence A. Moran) wrote:
:
:
: [snip]
:
: Bravo! Double bravo!! It is such a delight to see such a clearly
: written and informative article appearing like a jewel in the midst of
: the dung heap of clap trap and snidery.

While I fully agree with your huzzahs, I am curious about
clap traps. Are they irreducible?

----- Paul J. Gans [ga...@scholar.chem.nyu.edu]

[mel turner]

In article <5s5159$fv4$2...@news.nyu.edu>, ga...@SCHOLAR.CHEM.NYU.EDU says...

>
>Richard Harter (c...@tiac.net) wrote:
>: lam...@bioinfo.med.utoronto.ca (Laurence A. Moran) wrote:
>:
>: [snip]
>:
>: Bravo! Double bravo!! It is such a delight to see such a clearly
>: written and informative article appearing like a jewel in the midst of
>: the dung heap of clap trap and snidery.
>
>While I fully agree with your huzzahs, I am curious about
>clap traps. Are they irreducible?

It's a plausible apprehension...

cheers

[Peter Nyikos]

m...@panix.com (Michael L. Siemon) writes:

>In article <5s3gav$r...@snews1.zippo.com>, "Christopher J. Carrell"
><"cjcmeow"@super.zippo.com (wilhelp)> wrote:

>+My only complaint is with the first sentence...
>+

>+"Julie Thomas claims that DNA replication is a alien designed system
>+based on the fact that it is so complex that it couldn't have arisen

>+by natural causes."
>+
>+... and the word "alien", which is used several times. I find it a
>+little vague as to what that means...

>Larry was quite clear and explicit about this (though Julie was

>of course miffed :-)). If Julie is criticizing the standard natural

>law (i.e. evolutionary) hypotheses in favor of "design"

The two are not mutually exclusive, as is clear from what comes next:

then she
>*must* have in mind an agency of this design (actually, she's being
>equivocal about this, too -- Larry has subsequently tried to get
>her to state yes or no as to whether "design" needs to have an
>agent. Her writings *suggest* very strongly that she *wants to
>have a divine agent, but she has never admitted this.)

>Larry used "alien" specifically to include divine or other non-

>terrestrial intelligences as the agent of "intelligent design."

Which is a highly nonstandard way of using it, hence Julie
can well be mystified.

>Protesting the usage *because* it includes the (generaly laughable
>and disregarded) case of space aliens doing the designing

"space aliens" probably means B-flick aliens; otherwise there
is nothing laughable about the idea, as I've indicated in
my own followup to Carrell.

> is *not*
>a good rhetorical move -- it simply suggests Julie has ignored

>that possiblity and REALLY REALLY does want a specific designer
>that she has been totally mealy-mouthed about mentioning,

Reading way way too much into what Julie has written, though
not as egregiously as the thing Paul Myers loved to see
Laurence write.

>presumably
>because she has exactly zero justification for her preferred designer.

>NOTE: my comments are those of a Christian, who sees JHWH as the
>designer

...even though, by your own admission, you have zero justification
for it. This is NOT what a real Christian would say, IMO, since
it flies in the face of a great deal of Christian and even
Biblical tradition, such as in _Hebrews_.

> -- but is entirely content to accept that design as being
>carried out through an entirely natural evolutionary process,

So am I, but I'm keeping my mind open about various
alternatives. You are not.

>and
>hence an advocate of "if you can't explain it by natural law, you
>can't explain it

So you don't believe in an actual "JHWH" [sic] at all?

> and probably should shut up about 'other' causes."

So you think your so-called JHWH is explainable by natural law?
Or simply another name for it?

[Michael L. Siemon]

I wrote:

+> >NOTE: my comments are those of a Christian, who sees JHWH as the
+> >designer

and Peter appears to have written

+> ...even though, by your own admission, you have zero justification
+> for it. This is NOT what a real Christian would say, IMO, since
+> it flies in the face of a great deal of Christian and even
+> Biblical tradition, such as in _Hebrews_.

Dear Peter. Always misreading, always twisting the world into the
pattern he *wants* it to take -- and always being frustrated in his
efforts, by the sheer perversity of things.

I said that Julie has no justification (she has certainly *given*
none) for her rejection of evolutionary explanations. I implied,
perhaps, that I see nothing in biology that can seriously be argued
as "justification" for believing that JHWH (or any deity else) has
left traces in the record. As to the word "justification" -- its
most common meaning in Christian discourse has essentially NOTHING
to do with natural philosophy in any of its branches.

I have no problem "flying in the face of a great deal of Christian
and even Biblical tradition" -- at least I understand and take my
place *within* those traditions. In any case "Biblical tradition" is
an oxymoron here. I will only point out that the vast bulk of the
Bible (including the epistle to the Hebrews, by the way) makes NO
claim of direct revelation from God. Very little in the Bible does
so. One of these few spots occurs in the Book of Isaiah, where the
prophet relays something perhaps closer to the truth of God's place
in causation than the Peters or Julies of this world much like to
hear:

"My thoughts are not your thoughts,
my ways not your ways -- it is YHWH who speaks.
Yes, the heavens are as high above earth
as my ways are above your ways,
my thoughts above your thoughts." (55:6...)

That pretty much accuses those who want to drag in God as a petty
explanation for what THEY don't understand in biology as blaspheming.
Of course, Isaiah's -- and presumably JHWH's :-) -- concern in the
passage has little or nothing to do with biology. But then, there is
*NOTHING* in scripture that tells us a damned thing about the relation
of God to nature, with the possible exception of Genesis 1:11, 1:20
and 1:24, all completely compatible with WHATEVER abiogenetic and
evolutionary explanations we can manage to develop. Only an overarching
faith in God as the Creator of all things, visible and invisible remains
as the "content" of Christian belief in this matter.

Now, how would Peter suggest one go about producing a "justification"
for this belief? What evidence could possibly deny it? It is a way of
*looking* at the world, and one might adduce causes or personal history
to "explain" why one *does* look at the world this way. But there is
no foothold in all this for *any* kind of critical, public "debate."
You either look at the world this way or you don't. "Techniques" to
"persuade" people into such a way of looking are as old as propaganda
for the faith. But all claims I have ever seen to base the belief on
"reasonable" justification are bogus. And the propaganda techniques
have a dubious record, so I look at them with a rather cold eye.

In article <5s5tqi$5...@snews1.zippo.com>, "Christopher J. Carrell"
<"cjcmeow"@super.zippo.com (wilhelp)> wrote:

+This post by Michael vindicates my accusation that you
+deliberately slandered me. I demand an apology and a retraction.

I would suggest you just forget it, and ignore Peter. He *will*
slander people, and he *won't* admit it or apologize -- so drop it.

[Peter Nyikos]

"Christopher J. Carrell" <"cjcmeow"@super.zippo.com (wilhelp)> writes:

>PZ Myers wrote:
>>
>> In article <5s3b05$7...@alexander.INS.CWRU.Edu>, iz...@cleveland.Freenet.Edu
>> (Julie Thomas) wrote:
>>

>> > In a previous article, lam...@bioinfo.med.utoronto.ca (Laurence A.
>> Moran) says:
>> >
>> > I'd like to begin first by thanking Larry Moran for an excellent reply
>> > concerning the bacterial origin of replication. I would like to reply
>> > in turn. A word of warning, however. I wrote this reply Sunday
>> > evening after a Saturday night of very little sleep so I hope it
>> > isn't too confusing.
>> >
>> > >The Origin of Replication
>> >
>> > >Julie Thomas claims that DNA replication is a alien designed system
>> > >based on the fact that it is so complex that it couldn't have arisen by
>> > >natural causes.

This grotesque misrepresentation is the same kind of thing
we've been seeing from Behe's detractors about Behe time and
time again. They even copy from each other, as Doolittle
did off Orr. See "Doolittle tries to critique Behe", posted
earlier today.

>> > Unfortunately, this statement tended to detract from an otherwise good
>> > article. The problem is that I have never claimed that DNA replication
>> > is an "alien designed system" Neither have I ever claimed that DNA
>> > replication is so "complex that it couldn't have arisen by natural causes."
>> > This is most unfortunate as Larry is well aware of this. What's worse, it
>> > suggests that Larry's entire article is simply a response to a strawman
>> > argument.
>>

>> Oh, please, please, clarify *exactly* what you are arguing about! You sound
>> just like Nyikos -- every time someone tries to grapple with your point,
>> you dismiss their every effort with a cry of "Strawman!"

Wrong. She only dismisses egregious misrepresentations with that
cry, just as I do.

Myers is a hate-driven propagandist who misrepresents allies
as trying to grapple with substantive points when they are
just misrepresenting people in the same old ways time and time
and time again, and are impervious to correction.

>Y'know, I predicted that response, somewhat, just because of
>the presence of the word "alien" and its connotations...

>----repost---
>From <5ru6oc$a...@snews2.zippo.com>...

>My only complaint is with the first sentence...

>"Julie Thomas claims that DNA replication is a alien designed system

>based on the fact that it is so complex that it couldn't have arisen
>by natural causes."

>... and the word "alien", which is used several times. I find it a

>little vague as to what that means, and some people with private
>meanings of that word will claim that the entire piece can be
>ignored. Too bad, as it's as worthy a piece as has ever been
>written here.

>----end repost---

>Of course, it still hasn't been clarified what "alien" means.

I've done it many times. I do believe Carrell is deliberately
lying here. Just look at all the commentaries I have done
in the past concerning the following quote:

An honest man, armed with all the knowledge available
to us now, could only state that in some sense, the
origin of life seems at the moment to be almost a miracle,
so many are the conditions which would have had to have
been satisfied to get it going.
--Nobel Laureate Francis Crick, _Life Itself_,
Simon and Schuster, 1981, p. 88.

The most oft-repeated commentary I made was:

Lest creationists make too much of this, it should
be pointed out that the whole thrust of Crick's book is that
we DO NOT KNOW how likely the spontaneous production of life
is. A large part of the book is taken up by one possible
origin of life on earth, "directed panspermy" whereby it
arose elsewhere and was sent here via a space probe carrying
prokaryotes and possibly very primitive eukaryotes. He doesn't claim
this is more likely or less likely than life arising here spontaneously,
precisely because he doesn't know what the odds are.

So, the "aliens" I have been considering as a possible
explanation for things like the bacterial flagellum
would have been an intelligent species that arose
on another planet and sent prokaryotes here roughly 3.5 billion
years ago.

[Christopher J. Carrell]

Peter Nyikos wrote:
>
> m...@panix.com (Michael L. Siemon) writes:
>

> >In article <5s3gav$r...@snews1.zippo.com>, "Christopher J. Carrell"
> ><"cjcmeow"@super.zippo.com (wilhelp)> wrote:
>
> >+My only complaint is with the first sentence...
> >+
> >+"Julie Thomas claims that DNA replication is a alien designed system
> >+based on the fact that it is so complex that it couldn't have arisen

> >+by natural causes."
> >+
> >+... and the word "alien", which is used several times. I find it a
> >+little vague as to what that means...
>
> >Larry was quite clear and explicit about this (though Julie was
> >of course miffed :-)). If Julie is criticizing the standard natural
> >law (i.e. evolutionary) hypotheses in favor of "design"
>
> The two are not mutually exclusive, as is clear from what comes next:
>
> then she
> >*must* have in mind an agency of this design (actually, she's being
> >equivocal about this, too -- Larry has subsequently tried to get
> >her to state yes or no as to whether "design" needs to have an
> >agent. Her writings *suggest* very strongly that she *wants to
> >have a divine agent, but she has never admitted this.)
>
> >Larry used "alien" specifically to include divine or other non-
> >terrestrial intelligences as the agent of "intelligent design."
>
> Which is a highly nonstandard way of using it, hence Julie
> can well be mystified.

How is this nonstandard? It is exactly how I was thinking about it
before Michael's response here. But as I had also said, there would
be others who would not be so clear. Care to take a guess as to
who I thought that would be? Hmmmmmm?

> >Protesting the usage *because* it includes the (generaly laughable
> >and disregarded) case of space aliens doing the designing
>
> "space aliens" probably means B-flick aliens; otherwise there
> is nothing laughable about the idea, as I've indicated in
> my own followup to Carrell.

Nice strawman definition.

> > is *not*
> >a good rhetorical move -- it simply suggests Julie has ignored
> >that possiblity and REALLY REALLY does want a specific designer
> >that she has been totally mealy-mouthed about mentioning,
>
> Reading way way too much into what Julie has written, though
> not as egregiously as the thing Paul Myers loved to see
> Laurence write.
>
> >presumably
> >because she has exactly zero justification for her preferred designer.
>

> >NOTE: my comments are those of a Christian, who sees JHWH as the

> >designer

>
> ...even though, by your own admission, you have zero justification

> for it. This is NOT what a real Christian would say, IMO, since

> it flies in the face of a great deal of Christian and even

> Biblical tradition, such as in _Hebrews_.

Who are you to decide who is a Real Christian? Does this fit
in with your tactic of ascribing to dishonesty what should be
ascribed to less nefarious motivations, such as ignorance?

This post by Michael vindicates my accusation that you

deliberately slandered me. I demand an apology and a retraction.

Chris

--
Chris Carrell - Replace each _dot_ with . if you want to email me

[Christopher J. Carrell]

Peter Nyikos wrote:
>
> "Christopher J. Carrell" <"cjcmeow"@super.zippo.com (wilhelp)> writes:
[snip]

>
> >Of course, it still hasn't been clarified what "alien" means.
>
> I've done it many times. I do believe Carrell is deliberately
> lying here.

This is outright slander. Retract this statement immediately.

Larry Moran merely asked me if I had missed the clarification. I
said that I had. (That was in private.) Michael Siemon asked the
same in public. Yet what I ascribe to not having time to read
500+ line posts, and what they ascribe to having missed something
that was said, Peter ascribes it to outright dishonesty. This is
the mark of a malicious individual who would much rather carry
forth a personal vendetta aginst those who prove him wrong.

So you'll probably make some kind of backpedal, "Didn't you see the
equivocation words, 'I believe'? You are being a Below-10-IQ
Simulation again, and you're being thoroughly deceitful."
So what? Your above words are an accusation of lying on my part.
You really are a lowlife.

> Just look at all the commentaries I have done
> in the past concerning the following quote:
>
> An honest man, armed with all the knowledge available
> to us now, could only state that in some sense, the
> origin of life seems at the moment to be almost a miracle,
> so many are the conditions which would have had to have
> been satisfied to get it going.
> --Nobel Laureate Francis Crick, _Life Itself_,
> Simon and Schuster, 1981, p. 88.
>
> The most oft-repeated commentary I made was:
>
> Lest creationists make too much of this, it should
> be pointed out that the whole thrust of Crick's book is that
> we DO NOT KNOW how likely the spontaneous production of life
> is. A large part of the book is taken up by one possible
> origin of life on earth, "directed panspermy" whereby it
> arose elsewhere and was sent here via a space probe carrying
> prokaryotes and possibly very primitive eukaryotes. He doesn't claim
> this is more likely or less likely than life arising here spontaneously,
> precisely because he doesn't know what the odds are.
>
> So, the "aliens" I have been considering as a possible
> explanation for things like the bacterial flagellum
> would have been an intelligent species that arose
> on another planet and sent prokaryotes here roughly 3.5 billion
> years ago.

Which there is still zero evidence for. This means that ...
you said something with zero evidence behind it. If I said something
with zero evidence behind it, you'd say I was deliberately lying.

Again, retract your slander, with a full apology. Your harassment
campaign is quite unwelcome.

[Michael L. Siemon]

In article <5s7nmm$n...@bcarh8ab.bnr.ca>, "Stephen Watson"
<swa...@nortel.ca> wrote:

+Peter, could you be more specific as to the problems you see in
+Michael's position vis-a-vis Christian tradition? Which bits
+(i.e. chap & vs) of _Hebrews_ is he in conflict with?

I don't know what Peter has in mind -- there is some standard
doxologizing at the beginning of Hebrews, by way of quoting some
psalms, that might be marginally relevant. But the only passage
in Hebrews that I know of which bears on the issue is 11.3

"It is by faith that we understand that the world was
created by one word from God..."

which, so far as I can tell, is exactly *my* position, so that
it rather undermines Peter's accusation against me. Now, that
sentence goes on to say

"... so that no apparent cause can account for the
things we can see."

which Peter may be reading in a rather twisted fashion. It must,
obviously, be read in light of the first clause and hence must
be a strong *disjunction* of God's creation from the realm of
discourse of apparent (i.e., observable) cause and effect. That
is precisely why I suggest that Christians shut up about the
matter, when the discussion is about nature (cosmology or biology.)
The "account" that the author of Hebrews has in mind is an account
in the realm of sin and providence and divine love, where we have
(a limited, "as in a glass darkly" :-)) understanding *by faith*
of the mind and ways of God (about which I quoted Isaiah quoting
God in my last note. :-))

After my first mention of this (that Peter was so upset by), I
conceived a notion to write an essay "on God and Cause" that I've
sketched out a bit, and may send off to soc.religion.christian if
it ever comes together. The current draft is organized around a
discussion by Karl Barth (with whom, when matters of vocabulary
and tendency are pruned, I seem to share an agreement on these
matters.) I guess if Barth was "neo-Orthodox", I am neo-neo-
Orthodox, or maybe (given that I challenge Barth's word games,
and am rather free with usages from mulitple ages of tradition)
I am post-neo-0rthodox.

[Laurence A. Moran]

What Happens at Origins of DNA Replication?
Laurence A. Moran

Here's a short summary of what happens at DNA replication origins in
prokaryotes. The emphasis is on oriC, the usual origin in bacterial
chromosomes.

The protein DnaA binds to multiple binding sites (BoxA) in a short
stretch of DNA called oriC. In some cases the proteins bind
independently while in others binding is co-operative. Co-operative
binding means that when one molecule of DnaA is bound it makes it
easier for nearby proteins to bind to their sites. It all depends on the
number of BoxA sequences, how close they are to each other, and how
good the binding sites are (i.e. how closely they match the consensus
binding sequence). The exact mode of binding varies from species to
species. This variation on a theme is made possible because DnaA can
bind to a large number of slightly different BoxA sequences and the
protein has the property of forming aggregates with itself. This latter
property is quite common among DNA binding proteins.

Bound DnaA molecules associate with each other creating a complex
where the DNA is wrapped around the outside of a protein core.
Additional unbound DnaA molecules join this complex along with a
protein called HU. HU is the common DNA packaging protein in
bacteria. The complex may have about 20-40 DnaA proteins and several
hundred base pairs of DNA. It has been hard to pin down the exact
number of proteins, probably because it doesn't matter very much. As
long as there are a bunch of proteins it will work.

For those of you who know about nucleosomes you can think of the
DnaA/BoxA complex as a large nucleosome-like structure that is not as
highly organized as a nucleosome.

The build up of the DnaA complex induces local unwinding of DNA in
an adjacent region that is considered to be part of the origin sequence.
Sometimes the unwound region is localized to obvious A/T-rich
stretches of DNA but not always. If there is "pressure" to unwind DNA
then it will occur at the least stable region and this happens to be
sequences that are rich in A's and T's. We don't know exactly how
local unwinding occurs but the net effect is to create a replication
bubble where DNA replication can begin.

One of the factors that contribute to DNA unwinding is the DnaA
complex itself as you might well imagine once you understand how the
complex is formed. It turns out that when you wrap DNA around a
protein core you create supercoils much like the supercoils in the phone
cord that accumulate when you aren't looking. In the case of DNA the
"tension" in such supercoils can be relieved by unwinding a bit of
DNA. Local unwinding is also assisted by common enzymes called
topoisomerases. These are enzymes that alter the topology of DNA by
creating or removing supercoils. There are several different
topoisomerases in bacteria and any of them can contribute at the
replication origin. Topoisomerases pump in supercoils that help the
local unwinding at the replication origin. They do the same thing for
transcription and other processes.

In fact, transcription is probably necessary at most origins. Many (all?)
chromosomal DNA initiation events are coupled to transcription of
nearby genes. Transcription helps to unwind the DNA and the RNA
that is made can serve as a primer to get DNA replication started. The
association between transcription and DNA replication initiation is
probably very ancient since all kinds of different origins use it. It turns
out that DnaA is a transcription initiation factor suggesting, that its
role in DNA replication evolved from a more primitive role in transcription.
One of the genes regulated by DnaA in the dnaA gene itself and most
origins of replication in bacteria are located beside the dnaA gene
promoter where there is a BoxA sequence used for transcription.

Helicases are enzymes that unwind DNA directly. The replication
helicase is called DnaB/C (two different polypeptide subunits derived
from the dnaB and dnaC genes). DnaB/C binds to the locally unwound
region at oriC. This interaction is stimulated by the DnaA complex
because the helicase has an affinity for DnaA. Perhaps this is why
DnaA was chosen over other transcription factors to be the primary site
of DNA replication initiation in bacterial chromosomes. Once the
helicase enters the small unwound region it extends it in both directions
and this eventually disrupts the DnaA-BoxA complex causing it to fall
apart.

One can imagine that the DnaB/C helicase has a general affinity for
other proteins and that's why it became the main DNA replication
helicase. Originally it triggered the start of DNA replication at many
different sites by gobbing on to any old DNA bound protein. DnaA just
happened to be a more compatible protein than the dozens of other
DNA binding proteins in the cell so it was used more frequently. Over
the course of millions of years there was selection for tighter interaction
between DnaA and DnaB/C until this became the preferred way of
starting DNA replication in the cell. However, even now, it is possible
to delete the dnaA gene and substitute another origin with a different
binding protein and the helicase will use it.

There are lots of things going on at oriC. The DnaA complex seems to
act like a "magnet" attracting all sorts of different characters.
Transcription of short pieces of DNA is induced by RNA polymerase;
topoisomerases do their thing; and helicase tries to join the party. Lots
of ATP is hydrolyzed during this party activity since almost all of the
characters use up energy. Somehow, as the activity dies down and the
smoke clears, we are left with a replication bubble.

We don't know who is mainly responsible for unwinding DNA at oriC.
We know that DnaA started it all but probably didn't do the actual
deed. At some kinds of origins it seems that transcription is the main
culprit and at others it's the topoisomerases. At oriC it looks like the
helicase gets most of the blame but everyone at the party is guilty to
some extent. One gets the general impression of a rather sloppy and
confusing whirlwind of activity with lots of wasted energy but it gets
the job done eventually. Perhaps in a few hundred million years
bacteria will have evolved a simpler, more sophisticated method but this
one will have to do for now.

In any case, we are left with an "open complex" containing two
helicases bound at each end of the bubble. The single-stranded regions
are coated with single-stranded DNA binding protein, called "SSB" in
E. coli. There are lots and lots of molecules of SSB inside the cell and
it latches on to any exposed single-stranded DNA that it bumps into.
There's nothing special about this particular site as far as SSB is
concerned. SSB also works at sites of DNA repair and recombination.
The next step is the formation of the DNA replication complex or
"replisome".

Several proteins including primase (DnaG) bind to helicase when there
is enough room in the replication bubble. Recall that DnaB/C is a rather
sticky protein. The DnaB/C + DnaG structure is called the primosome
- it appears to be a discrete entity that can be used in other forms of
initiation. A bunch of other proteins sometimes assist in the formation
of the primosome at oriC.

Next DNA polymerase joins the primosome in the pre-initiation
complex. DNA polymerase is a large and complex enzyme and it is
assembled stepwise by co-operative binding to the unwound DNA and
the primosome. The exact order of assembly needn't concern us. It's
sufficient to understand that DNA polymerase binds to the primosome
and the completed complex at each fork is called the replisome. There
will be two replisomes at each oriC-type origin, one at each end of the
replication bubble.

There are quite a few other ways of starting DNA replication. We don't
have time to cover them all but it's worth mentioning a few examples
because they help us understand the strategy behind the initiation
events. This, in turn, suggests how the present initiation scheme might
have evolved from a much simpler one.

Single-stranded DNA doesn't need complicated origins in order to be
converted into double-stranded DNA. For example, on the single-strand
chromosome of bacteriophage phi-X174 the primosome binds directly to
DNA and makes a small primer. This primer is then extended by a
single DNA polymerase molecule until the entire strand is copied.

There's another very common form of DNA replication called "rolling
circle replication". It usually works on double-stranded circular DNA.
Replication begins when one of the strands is "nicked" or cut. Then
DNA polymerase binds to the site of the nick and starts to add DNA to
one of the ends of the nicked strand. In this way the original strand
serves as the primer and the "origin" consists of a nick site.

As DNA synthesis proceeds, a single strand of DNA is displaced and
this single strand gets longer and longer as the DNA polymerase moves
around the circle. In fact. the polymerase can go around the
chromosome several times making a single strand tail that can be
several times longer than the length of the entire circular DNA. That's
why it is called "rolling circle" replication.

This mode of replication doesn't use complicated origins and specific
initiator proteins such as DnaA. Primases and helicases are not
necessary. There is no complicated replication fork and no need to
assemble bidirectional forks at an origin.

The rolling circle mode of replication is used during the replication of
some bacteriophage genomes where the long tails of DNA are chopped
into pieces that are just large enough to be stuffed into a 'phage head.
Often the single-stranded region is converted to double-stranded DNA
before packaging using the same sort of tricks that phi-X174 uses.

Rolling circle is also used during conjugation in many species of
bacteria. Here the long single-stranded DNA is passed into another
bacterium where it is subsequently copied to produce double-stranded
DNA that can recombine with the recipient. The entire bacterial
chromosome can be replicated in this manner. In E. coli the
chromosome can be replicated by a rolling circle mechanism that begins
with a nick at oriT and in Streptomyces the replication of the
chromsomal DNA starts at an SCP1 origin of replication. These origins
can also be found on plasmids.

Another variation of DNA replication initiation involves the formation
of D-loops. RNA polymerase makes a little piece of RNA by
transcribing a short stretch of DNA and this primer is extended by one
of the DNA polymerases, displacing a single strand. The mechanism is
similar to rolling circle except that there was no nick and continued
synthesis creates a D-loop and not a single-stranded tail. (The "D" in
D-loop is supposed to represent the shape of the region.)

D-loops can get very large but eventually a primosome binding site is
uncovered as replication proceeds. The primosome binds and makes a
short primer on the single-strand side of the D-loop. When this happens
a replisome is assembled and both strands of the DNA are copied from
this point onward.

D-loop replication initiation doesn't require a specific origin of
replication. It's a transcription promoter that does the job. No specific
initiator protein such as DnaA is required.

The D-loop mechanism is used in the replication of many plasmids
including some that are quite large. It is also used to replicate
mitochondrial DNA. Mitochondrial genomes are the reduced remnants
of an ancient bacterial genome. It would be interesting to know wether
the extinct bacterial ancestor replicated its genome this way or whether
the D-loop mechanism was adopted later. Incidently, in mitochondria
the D-loop forms in the D-region of the genome. There are no genes in
this region. It is possible that mutations occur more frequently in the D-
region because it is single-stranded for much of the time. The DNA
sequence of the D-region is often used to construct phylogenetic trees of
closely related species or populations. For example, the tree that
suggests that we are all descendants of a mitochondrial African "Eve"
used D-region sequences.

What these examples illustrate, of course, is that there are many ways
of making DNA that do not involve the oriC mechanism. We can't say
which mechanism is the most primitive. However, assuming that the
simpler systems arose first we could envisage a primitive replication
system in which DNA polymerase acts randomly at any available nicks
and starts making DNA by a rolling circle mechanism. The single-
stranded tails are copied by making use of random primers that are
floating around (i.e. mRNAs). This mode of replication was probably
not very efficient but it worked well enough to get by in a world where
the competition was no better.

[Laurence A. Moran]

Julie Thomas says,
>Larry Moran says,
>>Julie Thomas says,

>>Since it could not have evolved, according to you, then the competing
>>hypothesis must be correct.

>I never said anything could not have evolved.

Picky, picky, picky. Maybe you never actually wrote those words but here's
what you claimed in your essay in the section on origins of replication.

a) It is "unlikely" that the 9mer DnaA box could have been
built up one nucleotide at at time.
b) Phylogenetic information from the non-core oriC sequences
"would not mean that the core evolved. It would simply help
us pinpoint when the core was designed."
c) "The critic of IC may claim that once upon a time a bacterial

origin was made up of one 5mer (or something like that), but,

let's be blunt, there is no evidence for such a claim (making

it look awfully ad hoc)."

d) "The lack of pre-9mer states suggest (at least to me) that

such a transformation entailed a quantum jump, not a gradual

transformation. And in my opinion, that pattern (quantum
jump) is quite suggestive of design."
e) You have a discussion about why it would be "selectively
disadvantageous" to evolve a protein like DnaA.
f) You point out that there are several ATP consuming steps in
DNA replication and say, "This makes it hard to envision the
gradualistic evolution of DNA replication."
g) You point out that the sequence of the Mycoplasma DnaA protein
doesn't fit into a phylogenetic tree where it should. You
say, "A molecular IC interpretation avoids the problem of
trying to fit these proteins in scheme that shows a common
ancestor."

I haven't bothered to flip through the remainder of your essay.

You are making the case that DNA replication could not have evolved.
Therefore it had to be designed. Designed things need designers just
as Paley claimed two hundred years ago.

I don't know why you insist on denying the obvious. Who are you trying
to fool?

>>But you won't come out of the closet and tell us what the competing
>>hypothesis is. Why?

>[scratches head]. As I said:

>"I simply outlined the IC nature of DNA replication which in turn
>strongly suggests the system was designed."

[scratches head]

The competing hypothesis is that the system was designed, right? Is every
IC system designed? Can you have design in the absence of a designer?

In your mind, do IC entities imply designers?

Why don't you come out of the closet and tell us about your intelligent
design model? You seem to think that if you can cast doubt on evolution
then this is support for your model but how are we to know if you won't
tell us about it? What are you afraid of, Julie?

>>I admit that the use of "alien" was partially motivated by your use of
>>the term "Darwinist". A term that I find very offensive since it implies
>>a strawman version of evolution. If you start being more considerate
>>then I will too.

>I'm truly sorry. I didn't realize you were offended by the term
>"Darwinist." But how shall I refer to your position? I don't want to
>refer to you as an "evolutionist" because that makes it seem like I am
>anti-evolution (and I am not).

Damn! There goes my brand-new Irony-O-Meter. I'll have to ask the store
if I can have my money back.

"Evolutionist" would be fine by me. I'm happy to be called an
evolutionist. You'll simply have to live with any semantic problems that
this creates for you. Frankly, I don't see why you prefer "Darwinist" -
your writings suggest that you actually believe that your strawman version
of evolution is the one we all believe in. So "evolutionist" should be the
same thing if I interpret you correctly. Are you an anti-Darwinist? Is
that why you wanted to refer to your strawman critics as "Darwinists"?
Do *you* see a difference between a Darwinist and an evolutionist?

>>Come on, Julie. Give us a little credit - we are not idiots. What's the

>>real reason for claiming that a system is irreducibly complex?
>For the third time:

>"I simply outlined the IC nature of DNA replication which in turn
>strongly suggests the system was designed."

>>Are you just playing rhetorical games or is there a bigger stake?

>Well, I suppose that a desire to know what's the truth about our
>reality is a "bigger stake."

>>If the process didn't evolve then what is your explanation?

>If it didn't evolve, then it was mostly likely designed.

So it's "truth" we're after, is it? You have almost come clean here - one
more little step and we'll be able to see what this bigger stake is
... this "truth about our reality". Here's the key question,

Can you have design in the absence of a designer?

Several postings ago I summarized Julie's hypothesis like this,

>>>She suggests that some systems are so complicated and
>>>interconnected that it would be impossible to imagine or reconstruct
>>>a natural explanation involving evolution from a primitive ancestor.

There followed bit of back and forth where Julie complains that I am
putting words in her mouth. Apparently there is something in my summary
that she doesn't want to openly admit. Maybe it's just the word
"impossible", I dunno.

Anyway, Julie now offers an alternate version of the introduction to her
essay where she discusses Darwin's quotation - the one where he says

"If it could be shown that any complex organ existed which could not
possibly have been formed by numerous, successive, slight modifications,

my theory would absolutely break down." Julie says,

>In my opinion, there are several IC systems which lack evidence of
>Darwin's mode of transformation, and in fact, appear unlikely to have
>originated in this wy.

Would this be a good summary of what you are trying to say?

Julie says that IC systems are very unlikely to have evolved.

Would that make you more comfortable than my previous summary of your
position? You don't say that it's "impossible" just "unlikely". How
unlikely, Julie? Is there less than a 1% chance that an IC system
could have evolved? Is it *possible* that an IC system could have
evolved? How?

>I should, however, point out that IC is

>more than a problem for Darwinism. IC is also characteristic of design
>(although design need not entail IC) and is very similar to the concept
>Paley employed in his analysis of a watch (although Behe has more
>rigorously defined this in his book). Thus, a Darwinian explanation of a
>systemm is not a refutation of design. It is merely an alternative
>explanation.

Would this be an accurate summary of your position?

Julie says that IC systems suggest design. This line of reasoning
is similar to the arguments that Paley used to demonstrate
that a watch was designed. Paley then goes on to suggest that
the design of natural systems suggests a watchmaker (God) but
Julie doesn't take that step with her natural system.

>Now, can we get beyond this notion that I am claiming "some systems

>are so complicated and interconnected that it would be impossible to
>imagine or reconstruct a natural explanation involving evolution from a

>primitive ancestor?" Because....I'm not.

You haven't convinced me.

>>You have suggested that there is no natural explanation for DNA
>>replication as we know it and I will attempt to provide one.

>I do not suggest that there is "no natural explanation for DNA
>replication."

I gave you a quotation from your essay. Here it is again,

"This makes it hard to envision the gradualistic evolution
of DNA replication."

I must have misunderstood. I guess you only meant to eliminate
"gradualistic evolution" as a natural explanation. There must be other
natural explanations of DNA replication that you prefer. Either
that or you just told a fib. Please let me know what "natural explanation"
you are intending to include.

>>>Now, if you claim DNA replication evolved from a primitive ancestor
>>>along Darwinian lines, I simply note there is no evidence for this

>>>claim (or at the very most, the evidence is very weak). If, as I

>>>believe, design is a better explanation for the IC nature of DNA
>>>replication, I *then* consider your absence of evidence and say "no

>>>wonder there is no evidence; y'all are pursuing a dead end." Thus, the

>>>failure of Darwinism is *supporting* evidence.

>>I look at the data and see several possible explanations that are

>>consistent with evolution. Then I look for evidence of design and

>>designers and see none. The lack of evidence of intelligent designers
>>must mean that there aren't any, right? I then consider your absence
>>of evidence and conclude that you are playing with an emptyeck. The
>>failure of designism then becomes suorting evidence for evolution.>I can
respect this except for one claim - "lack of evidence MUST mean
>there aren't any." I make no "must" claims. In my case, lack of
>evidence for your claims is simply consistent with what I believe. Also,
>I didn't quite accurately convey the essence of my thoughts when I
>said, "no wonder there is no evidence; y'all are pursuing a dead end" I
>should rephrase that thought as follows:

>"hmm, that there is no evidence tends to confirm what I suspected; y'all

>are pursuing a dead end."

I'm curious about your statement that "lack of evidence for your claims
is simply consistent with what I believe". You seem to "believe" in
something that doesn't involve evolution. So when someone fails to come
up with an evolutionary explanation you are quite satisfied because you
suspected all along that evolution wasn't the answer. So what do you
"believe"?

Do you think it possible that your search for IC and design is motivated
by your "beliefs" and not by a real search for the truth? Is it possible
that you already "believe" that you know the truth and you are simply
looking for pseudo-scientific proof that will make you feel good?

>I think there is much confusion concerning this topic. My major
>intention in focusing on IC is not to come up with an anti-darwinian
>argument. I don't need that. When it comes to DNA replication or the
>bacterial flagellum (and many other things to come), I am simply not
>convinced that Darwinism has anything to do with their origin. But I

>am still quite interested in their origin. Should I wait, and hope, that

>someday folks like Paul Myers will come up with a story that will
>probably only convince those hoping to be convinced? Nah. Thus, I
>look for alternative explanations that *I* find far more intellectually
>satisfying. And, as I see it, Michael Behe has given me the key. So I
>begin to look afresh at these systems with Behe's key and it generates

>new insights and new lines of inquiry. Put simply, it's a way to

>interpret data and do science under a design paradigm. That's why I
>said to Paul that "Ill go my way and y'all go yours."

In referring to your ideas in the future would it be fair to paraphrase
as follows?

Julie is not convinced that evolution has anything to do with
the creation of a DNA replication system. She finds intelligent
design far more intellectually satisfying.

>>>>This is a rhetorical device that is designed to convert the absence of
>>>>evidence into something positive that is subject to scientific
>>>>analysis (i.e. that the system will not work if any part is removed).
>>>>We are not fooled by this cheap trick.
>>
>>>Rhetorical device? Cheap trick? Could you be a tad more insulting?

>>No, I think that did the trick. Could you try being a bit more honest?

>My, so now I am dishonest? We've only had two or three exchanges
>and you've already launched some serious ad hominems.

Yep, and there's more in this posting. I think that you are deliberately
pretending to "do science" when what you are actually doing is promoting
religion. I don't have a problem with religion but I do have a problem
with hypocrisy.

Here's another example of hypocrisy,

>Now I assume you mean "absence of evidence" for a Darwinian origin

>to DNA replication. Well, yes, this is *also* true. But there is no

>conversion going on. Absence of evidence for a Darwinian origin simply
>means I have no good reason to think a Darwinian origin is part of the
>true explanation. I then simply approach the topic differently and
>explore a concept so that it is subject to scientific analysis. At the
>very least, it is fun! Then I look over at you and see you struggling to

>come up with even a just-so story. I see folks getting emotional and

>wanting to talk instead about invisible pink unicorns. Etc. One example
>of this strangeness may not be all that significant, but if the same
>dynamic holds in the analysis of system after system after system (even
>allowing for some vague just-so stories), I'm going to start to *really*
>believe there is a reason for this dynamic.

Here's Julie's closing statement in the most recent posting. I'll let
her have the last word.

>>>>On the other hand, there are times when Julie almost seems to be
>>>>offering irreducible complexity as proof of the existence of aliens.
>>>>This is nothing more than the argument from design dressed up for
>>>>the 90's.

>>>Oh please. If you interpret my articles as one big "Argument From
>>>Design," you will continually be clueless about my writings.

>>I don't think so. If you continue to deny your real motives you will
>>only be fooling yourself. Maybe you are fooling yourself.

>Look Larry, I really wish you'd get to those articles outlining the
>evidence for your interpretations of the origin of bacterial DNA
>replication and the bacterial flagellum. As it stands, I'm starting to
>suspect that I'm wasting my time with you. I mean, why argue about
>something like bacterial DNA replication with someone who apparently
>has everything figured out to the point where he thinks he knows my
>"real motives" better than I do?

>You need to consider something, Larry. When you dismiss my claims
>about myself, it looks bad from where I sit. It looks like you are
>ignoring what doesn't seem to fit into some preconceived pattern that
>you have about people. It looks like you need to view me in a
>particular manner, and if I, who knows myself *far* better than you do,
>deny this, you then follow with a "you're fooling yourself claim." It's
>one nice, tidy, internally consistent view that exists only in your head.
>And after you have done this, you are *now* going to explain the
>evidence that bacterial DNA replication arose by "natural means?" But
>don't y'see, you've already conveyed to me that you are one who seems
>to have a need to fit things into preconceived patterns.

>So please, just get to the evidence for your claims about bacterial DNA
>replication and the bacterial flagellum. You probably could have had
>them written and posted by now if it wasn't for this exchange.

Larry Moran

[Richard Harter]

ga...@SCHOLAR.CHEM.NYU.EDU (Paul J. Gans) wrote:

>Richard Harter (c...@tiac.net) wrote:
>: lam...@bioinfo.med.utoronto.ca (Laurence A. Moran) wrote:
>:
>:
>: [snip]
>:
>: Bravo! Double bravo!! It is such a delight to see such a clearly
>: written and informative article appearing like a jewel in the midst of
>: the dung heap of clap trap and snidery.

>While I fully agree with your huzzahs, I am curious about
>clap traps. Are they irreducible?

Ineluctable. They're found by them at ic conferences.

Richard Harter, c...@tiac.net, The Concord Research Institute
URL = http://www.tiac.net/users/cri, phone = 1-508-369-3911
Men were designed for short, nasty, brutal lives.
WOmen are designed for long, miserable ones.

[Laurence A. Moran]

DNA as a Player in Irreducibly Complex DNA Replication

Julie Thomas begins her description of bacterial DNA replication with DNA.
Originally I was not planning on addressing this section of her
essay since I felt that it was pretty trivial. Now I think that I can make
a few points that relate to other issues. All of Julie's comments will be
indented and enclosed by quotation marks, like this,

"The first actual player in DNA replication is DNA itself.
DNA is needed to provide the template sequence. That is, DNA
replication is not the synthesis of DNA de novo. Instead, it
is simply the duplication of pre-existing DNA."

This is good. I'll accept that you need to have some DNA to begin with
if you're going to "replicate" DNA.

"The DNA component of DNA replication is clearly an ingredient
in thematic IC. All procaryotic cells (in fact, all cells) have
DNA genomes that are crucial in DNA replication. There are
viruses that have RNA genomes (most are single-stranded), but
these are probably not relevant since viruses have very small
genomes (unable to support cellular existence) and viruses most
likely evolved *from* cellular organisms."

We agree, mostly. Modern (extant?) bacteria have DNA genomes. DNA genomes
are a crucial component of DNA replication. It's very hard to imagine
why you would want to have a DNA replication machinery if you didn't
have any DNA. If you take away the DNA then you don't have anything
to replicate. This doesn't seem like a very profound observation.

"Thus, any attempt to discredit the IC status of DNA replication
must account for the existence of DNA without reference to the
replication machinery. The commonly proposed solution to this
problem is to invoke RNA as the original nucleic acid and then
assume that the RNA synthesis machinery was transformed into
DNA synthesis machinery."

Now you are on to something entirely different. You are imagining that
your opponents will disagree with you and you want to convince them that
they are wrong before you even hear what they have to say. The easiest
way to deal with this, of course, is to make up a straw man argument that
you think you can defeat. From now on whenever anyone questions
whether DNA is really IC you can tell them you have already dealt with
that objection.

Pretty clever, Julie. But I've seen one too many of these tricks before.
Your straw man argument is that RNA synthesis machinery was transformed
into DNA synthesis machinery. I don't know of any evolutionist who
proposes this. In any case, it has more to do with the origin of
the machinery than the origin of DNA. But let's see where you are going.
I've already been there, Julie. (-:

"The evidence behind the "RNA first" view remains unconvincing
and there are many problems with it. It is beyond the scope of
this article to extensively critique the hypothetical RNA World,
however, let us consider just a few of the problems. While some
RNA has limited catalytic activity associated with cutting and
pasting oligonucleotides, it doesn't have sufficient catalytic
power to synthesize the ribonucleotides themselves. Thus, an RNA
first view still doesn't explain the existence of RNA - it merely
assumes it. However, to pursue this discussion further than this
would take us down a tangent that gets too far away from a
discussion of IC. I will simply point out, for now, that the
reason (IMO) the "RNA first" hypothesis is currently popular is
simply because it is perceived to solve the dilemma of DNA's
existence."

The reasons why the "RNA World" is currently popular are complex and
not all of them are scientific. It's true that the RNA World idea is a
convenient way to get around "proteins first" and the problems that raises
in explaining the genetic code. In any case, I share your skepticism.

"So let us assume the existence of the hypothetical cellular
organism with an RNA genome. How did it give rise to a DNA
genome? First, deoxyribonucleotides had to be synthesized
via metabolic pathways. The nucleotides of RNA differ from
DNA in two main respects: DNA uses thymine in place of uracil
as a nitrogenous base and the ribose sugar of DNA is lacking
an OH group at the 2' position."

OK, let's assume that your evolutionist opponents propose that DNA is
derived from RNA (evolutionarily speaking). It's not terribly relevant to
the discussion about DNA replication machinery, but responding to your
comments may be fun and educational for both of us.

First, let's talk about thymidine since it comes up again shortly. As I'm
sure you know, thymidylate (dTMP) is made from uridylate (dUMP). The
difference is a single methyl group that is added at the 5-position of the
uracil moiety. Thymidine could easily be called 5-methyluridine. Uracil
obviously came first and a single enzyme, thymidylate synthase, is all
that's required to convert it to thymine. This isn't an unusual reaction.

There are lot's of different kinds of similar modifications in bacterial
and eukaryotic cells. For example, both adenine and cytosine can also be
methylated. There are also many examples of thymine in RNA's - every
single tRNA for example has ribothymidne.

Julie, you will certainly have come accross the classic explanation for why
thymidine replaced uracil in primitive DNA. It's in most of the best
textbooks. What do you think of that explanation? Why didn't you mention
it in your essay?

"What selective pressure would drive this synthetic change?"

Perhaps none. Why would there have to be selective pressure driving this
change (from RNA to DNA)? It could have been simply an accident or a
fluke that happened to get locked in as cells evolved.

"Darwinists typically cite that DNA is a more stable molecule,
thus the selective pressure seems clear (however, this doesn't
explain thymine instead of uracil)."

I don't know too many "Darwinists" who resemble your caricature.
Perhaps you would be kind enough to provide an example of one who
makes such a claim? Maybe you are referring to the fact that double-
stranded DNA is more stable than single-stranded RNA? If so, you and
your strawman Darwinist friends are comparing apples and oranges.
Actually, double-stranded RNA is at least as stable as double-stranded
DNA. I agree with you that stability arguments cannot provide enough
selective pressure to drive the switch from RNA to DNA.

Here would have been a good time to mention the classic argument for the
replacement of uracil by thymine. It makes a lot of sense to me. Do you
have several good arguments against it or just one? (The one I'm referring
to is ignorance.)

"But such an answer skips over the intermediate changes and
simply focuses on the start and end states. What would
these intermediate states involve?"

I don't know, but I suspect that you are about to make up a story about it.

"First, we'd have to change the proteins that can then change
the synthetic pathways to synthesize deoxyribonucleotides (or
we'd have to add to these pathways). As evidence of this
transformation, one could point out that deoxyribonucleotides
are indeed synthesized as modified ribonucleotides."

Julie, do you have any idea what's involved here? Did you bother to check
a biochemistry textbook to see how the synthetic pathways might have
been changed? Let me tell you about it.

In most species all four deoxyribonucleoside diphosphates are synthesized
from their corresponding ribonucleoside diphosphates by a single enzyme
called ribonucleotide reductase. In some species it's the ribonucleoside
triphosphates that are the substrate. That's it. One single enzyme is all
it takes to make deoxynucleotides from their ribonucleotides. This looks
like evolution to me but it's possible that the intelligent designer who
created the irreducibly complex DNA replication system just happened to
choose this way of making DNA from ribonucleotides. Anything is possible
when it comes to intelligent designers.

If I ever get the chance I'd like to ask the intelligent designer why she
choose to convert the diphosphates in some species and the triphosphates
in others. Why didn't she design a system that acted on the
unphosphorylated nucleosides? Oh, and while I had her attention, I'd ask
why the regulation of ribonucleotide reductase is so baroque. It's a little
bit different in every species and involves a panoply of factors. This
makes it a pain to teach or write about. Why didn't the intelligent
designer just design it correctly in the first place?

"But a purely function perspective also accounts for this
observation, without reference to such evolutionary assumptions,
as cells continuously need massive amounts of ribonucleotides
(to transcribe tRNAs, rRNAs, snRNAs, and mRNAs) while their
need for deoxyribonucleotides are limited to replication,
repair, and recombination. Thus, from a purely functional
perspective, one would expect cellular machinery to be primarily
geared to make ribonucleotides."

Let's see if I understand you correctly. You claim that cells need more
RNA than DNA. That's correct. Therefore, cells should be geared to make
ribonucleotides. OK. Therefore any intelligent designer would probably
have created cells that make DNA from ribonucleotides. Is that what you
meant to say? Guess one can't argue against that kind of logic.

BTW Julie, if you have the phone number of the intelligent designer could
you give her a call and ask her why she made DNA in the first place?
Inquiring minds want to know.

"Nevertheless, it is important to note that there is no
selective pressure behind this synthetic change unless it
occured almost instantaneously *and* almost immediately gave
rise to a DNA genome."

No selective pressure that I can see either. I'm anxiously awaiting the
result of your phone call to find out the answer. The proponents of
intelligent design obviously see some reason why DNA is better designed
than (double-stranded) RNA. Perhaps some of them could tell us about the
presumed advantages. Meanwhile, no respectable evolutionist would suggest
that the invention of ribonucleotide reductase gave rise instantly to a
DNA genome.

"Ignoring the enzymatic changes that would have to occur so
that suddenly, deoxyribonucleotides are being made."

Strawman alert!!!

"These would only be used if the RNA synthesis machinery had
no specificity in incorporating the nucleotides. That is, if
the RNA synthesis machinery had evolved to show preference for
ribonucleotides, we'd have to wait for this specificity to relax
in order for the deoxyribonucleotides to be used. But then the
machinery needed to make deoxyribonucleotides would be useless
and acquire mutations at the rate of a pseudogene."

What's wrong with the "RNA synthesis" machinery showing preference
for ribonucleotides but able to use deoxyribonucleotides? Your imagination
works well when you need to come up with a story to bolster your case
but it seems to fail you when you need to consider alternatives. Isn't
this strange?

"But what if no such specificity existed from the start? Then
we'd have another problem. The strands that would be synthesized
would be a random mixture of ribonucleotides and deoxy-
ribonucleotides. A Darwinist might claim this is a "more stable"
molecule than the RNA genome (without evidence), but such
purported stability comes at a price."

I dunno 'bout Darwinists but this evolutionist refrains from making such
claims. If it existed, the mixture may have been more stable, less stable,
or about the same.

Julie, what is it that you are doing here? To me it looks very much like
you are constructing ad hoc arguments against evolution. You seem to be
trying to convince us that DNA is IC by claiming that it couldn't have
evolved from RNA. Elsewhere, in your other postings, you deny that you are
pursuing this strategy. What gives?

"RNA-first people like to point to the catalytic ability of RNA
as an important process in these ancient cells that supposedly
once existed. But once you start randomly adding deoxynucleotides
to your RNA, you're likely to lose that catalytic activity of RNA
(as the 2' OH group on the ribose is the heart of RNA's catalytic
ability). Thus, it seems likely that these deoxyribonucleotides
would be initially deleterious."

The 2'-OH group is used in some cases but not others. You are probably
thinking of group II intron splicing. What about group I introns, the
peptidyl transferase reaction, and RNAse P activity? Do these activities
require a 2'-OH at the "heart"? Julie, it is one thing to make up
"just-so" stories to bolster your case but it is quite another to base
those stories on misinformation.

"Much more could be said about making DNA without DNA (see
below). But even at this point, we can see that the IC status
of DNA is not easy to deny."

I'd like to know why you think that DNA looks designed. What's so
special about DNA? Why wouldn't double-stranded RNA have worked just
as well?

I also recommend that you re-read what you have written in your essay.
It is full of various "just so" stories that claim to exclude the
possibility of evolution. Often your "just so" stories attempt to
refute a strawman argument that you have constructed. How are your
"just so" stories any different from those of the evolutionists you
criticize? Please don't try and pretend that your stories are more
scientific. I don't see any evidence of that.

Larry Moran

[Laurence A. Moran]

The Origin of Replication

In article <5s3b05$7...@alexander.INS.CWRU.Edu>

iz...@cleveland.Freenet.Edu (Julie Thomas) writes:
>
>In a previous article, lam...@bioinfo.med.utoronto.ca
(Laurence A. Moran) says:

>>Eukaryotic chromosomes have multiple origins of replication
>>chromosomes are smaller than typical bacterial chromosomes. Since all
>>available evidence indicates that eukaryotes and prokaryotes share a
>>common ancestor this means that it is impossible to tell which
>>condition (unique or multiple origins) is primitive and which is
>>derived.
>
>I simply do not agree "all available evidence indicates that eukaryotes
>and prokaryotes share a common ancestor." Just for starters, we've
>already seen that there is little or no sequence homology between the
>two (bacteria and eukaryotes) when it comes the DNA replication
>machinery (btw, ditto for the flagella). Thus, there is little-to-no
>reason to think the eukaryotic process tells us anything about the
>prokaryotic lineage.

When I said "all available evidence" I meant the sequences of those
genes that are homologous. That, plus the extraordinary number of other
shared characters such as the genetic code etc. By "all available
evidence" I did NOT mean those situations where there is no evidence.
That would have been silly.

Julie, in order for your position to be defensible it is not sufficient
to simply point to a few genes that are not shared by eukaryotes and
prokaryotes. You also have to explain away all the data that contradicts
your ideas.

>Why propose multiple origins were present in the putative ancestors of
>bacteria? As for genomic streamlining, this notion received much
>impetus from the lack of mRNA introns in bacteria. However, the
>evidence indicates that introns are probably recent (Palmer and
>Logsdon, 1991). Thus, Larry uses the concept of streamlining in this
>context in a manner that appears somewhat ad hoc.

The point about suggesting multiple origins in the primitive ancestor
was to emphasize that we should not assume that the bacterial mechanism
is necessarily primitive. I thought you understood that?

Introns are recent - we agree. However, the origin of introns has nothing
to do with whether bacterial genomes are compact. I did not create an
"ad hoc" argument. Instead I relied on the data from genome sequencing
projects. This data shows that bacterial genomes in general have much
less "extra" DNA than eukaryotic genomes. Bacterial genes are close
together and eukaryotic genes are much farther apart. The data suggests
that there has been selection in bacteria for compact genomes, operons
etc. You may disagree with the conclusion but you can't dispute the
data. Maybe you don't know very much about genomes?

>>There are other examples of DNA replication in the absence of an
>>origin. Replication can begin at the ends of linear chromosomes. The
>>extant examples are confined to viral, bacteriophage and linear plasmid
>>DNA's (Salas, 1991) where proteins that bind to the ends of DNA are
>>required.
>
>But as I have explained in my original article, none of this is clearly
>relevant to bacterial DNA replication as viruses and linear plasmids
>(which probably evolved from viruses) are likely to be more recent than
>bacterial cells.

Do you mean to say that all viruses and plasmids have arisen since the
time of the last common ancestor of all bacteria? How do you know this?

Assumming that you are correct, then how do you explain the DNA
replication mechanisms in plasmids and viruses? After all, your claim is
that some intelligent designer created DNA replication in the bacterial
ancestor. Did viruses and plasmids then evolve their own independent
mechanism because the "created" one wasn't good enough? Or, did the
intelligenet designer make separate mechanisms for every kind of virus
and plasmid?

You can't have it both ways. If viruses and plasmids pre-date the last
common ancestor of all life then we would expect to find them in all
living organisms, and we do. In that case, it is powerful evidence that
ancestral organisms used a variety of different ways of synthesizing DNA
and the modern mechanisms of chromosomal replication have evolved from
simpler mechanisms. The viruses and plasmids then represent independent
lines of evolution from the primitive condition as do the various
mechanisms used in eukaryotes.

If viruses and plasmids arose after the last common ancestor then you
have some explaining to do. Your hypothesis is that the bacterial mode
of DNA replication was designed by "intelligent designers". In order for
us to believe that this is an example of intelligent design we have to
accept that it is a pretty good way of making DNA. (Either that, or the
designers weren't particularly intelligent.) Presumably all other forms of
DNA replication came later, according to your suggestion. Do you want to
propose that each and every variation seen in viruses and plasmids is
another example of intelligent design? If so, why are they better than
the mechanism "created" for replicating bacterial chromsomes? What is the
evidence for intelligent design in these other systems?

>>She is making the common error of assuming that E. coli is the
>>paradigm for all bacteria but in this case the E. coli oriC is the
>>exception. We should avoid the impression that the organization of this
>>region is highly structured. Julie is describing systemic IC (E. coli) but
>>implying that it is thematic (all bacteria).
>
>Actually, I was using one of Larry's references:
>
>Smith, D.W., Yee, T.W., Baird, C. and Krishnapillai, V. (1991)
>Pseudomonad replication origins: a paradigm for bacterial origins?
>Molec. Microbiol. 5, 2581-2587.

Good. I'm glad you read this paper. It will make my discussion much
easier. Please let me know when you have read the other references that
I gave you. I suggest that you refrain from posting until you catch
up on your reading.

I concede that you considered the replication origins in species other
that E. coli although you tended to emphasize E. coli and its relatives
to the exclusion of more distantly related species. In some cases the
authors of the few older papers you relied on made the same mistake.

>In this article, the authors compare the origins from E. coli, two
>Pseudomonads, and B. subtilis (the latter is very distantly related to the
>former two). They conclude:
>
>"Comparisons between these three classes of bacterial origins indicate
>that the fundamental features of a primary bacterial origin are as
>follows: (i) at least four 9-mer DnaA-binding sites are present; (ii) two
>of these (R1 and R4) are separated by close to 180 bp; (iii) these two are
>inverted repeats; (iv) two or more additional 9-mer DnaA sites are
>present between the R1 and R4 sites; and (v) three 13bp to 16 bp AT-
>rich direct repeats are found adjacent to the R1 site but not within the
>R1-R4 region."

We are examining the irreducibly complex nature of DNA replication
origins in bacteria - all bacteria. You made the claim that all oriC
sequences have certain features. This defines the irreducibly complex
nature of oriC's. I am challenging your claim by pointing out that many
oriC sequences in different species do not have the features you claim to
be irreducibly complex.

I gave you a number of recent references to support my statements but here
you rely on a six year old paper that you have already read.

Let's briefly cover the features that you think are irreducibly complex.

i) at least four DnaA binding sites: Perhaps this is true although there
are some potential origins that have fewer. In any case we are agreed
that oriC sequences need a bunch of DnaA binding sites.

ii) two DnaA binding sites are separated by 180bp: I gave you some
counter-examples

iii) these two are inverted repeats: I gave you examples of oriC
sequences where all of the DnaA binding sites have the same
orientation

iv) two or more DnaA binding sites are located between the two that are
separated by 180bp: Lots of counter-examples.

v) three 13-16bp AT-rich repeats are found at one end of the cluster
of binding sites: not true of many oriC sequences

Let's look at the paper that I know you have read and see if the last
feature is even true there. I'm going to give you the sequences of the
three 13bp "repeats" from the Pseudomonas sequences. These sequences
are in the paper that you read. Smith et al. looked at three different
species. They use an upper case letter when the same nucleotide is
found in all three and a lower case letter when the nucleotide occurs
in only two species. "N" means that no two species agree.

gatgNgGgaNtAc
gaAgagaNaTNTN
gAANNNgTtatta

I leave it to each reader to decide whether they see three 13bp direct
repeats here and whether they are particulary AT-rich. Do you see them,
Julie? Does this look like irreducible complexity to you?

When you're done figuring this out try looking at the three Mycobacterial
sequences, the Mycoplasma species, and the Micrococcus luteum genome.
I gave you the references. Do you see AT-rich direct repeats? I didn't
think so. Face it, Julie, you made a mistake. The oriC origin is not as
irreducibly complex as you make out.

>>In many bacteria there are two or three separate regions that contain
>>DnaA binding sites (DnaA boxes). The important one is near the dnaA
>>promoter (promoters are sites where RNA synthesis begins when the
>>gene is transcribed). There can be as many as eight DnaA boxes in a
>>region or as few as two.
>
>So even if Smith et al. are wrong, we still seem to need at least two
>DnaA boxes.

Smith et al. are wrong. You are wrong. They have an excuse because they
published their paper six years ago. Yes, we still seem to need at
least two DnaA binding sites. That's about all you can salvage from
your original irreducibly complex oriC.

>>The complete genome of Mycoplasma genetalium was searched for oriC
>>sequences and DnaA boxes and none were found (Fraser et al., 1995). I

>>There are also no oriC sequences in the genome of Methanococcus
>>jannaschii (Bult et al., 1996). M. jannaschii is an archaebacterium - I
>>think that Julie's alien design hypothesis assumes that the aliens
>>designed archaebacteria separately.
>
>I have no "alien design" hypothesis, but I do indeed think it irrelevant
>to refer to archaebacterial features as they are so different and I am not

>convinced they shared a common ancestor with eubacteria.

Do you think that archaebacteria were created separately by the
intelligent designer? I do wish you would tell us more about your theory.

>>The DnaA box sequence is not as strictly defined as Julie implies. The
>>binding sites for DnaA match a CONSENSUS sequence that varies
>>somewhat from species to species. In general, a seven out of nine
>>match to the consensus sequence is more than sufficient for binding.
>
>And this, IMO, is very strong sequence conservation. Let's not forget
>that this sequence probably arose 1-2 billion years ago. If we consider
>the various distantly related lineages that demonstrate it, that amounts
>to several billion years of microbial evolution where a 7/9 match
>occurs.

A little earlier in this article [snipped] you agreed that there were
no obvious DnaA binding sites in the Mycoplasma genomes. I suggested that
this was because the consensus binding site in these species was quite
different. In other words, it had diverged so much from the common
ancestor that we don't recognize it. You agreed.

So why are you still harping about strong binding site sequence
conservation?

>>Messer and Weigel (1997) review the extensive literature data on
>>DnaA binding. Adding in other DnaA binding sites and studies of DnaA
>>binding in vitro yields a stringent consensus binding site of
>>TT(A/T)TNCACA where (A/T) means that either A or T will work at
>>that position and "N" means that any base pair will do.
>
>And this supports my point as I never said the 9-mer was invariant.
>I said it showed "strong sequence conservation" and built from there.

You're not listening, Julie. This is the consensus binding site in
E. coli. The one that the E. coli DnaA protein prefers to bind to.
In most cases the E. coli protein will bind quite nicely to anything
that approximates this sequence. The consensus sequence is 7.5bp in
length. The actual binding sites may match only six of these.

"Strong sequence conservation" refers to whether different species use
the same consensus sequence or one that is different. We have already
seen that the consensus sequence in other species is different. In
Mycoplasma it may be very different. You are using the term "consensus
sequence" to refer to your hypothetical ideal sequence and not to
the real consensus sequences in each species. This is confusing.

>>There is good evidence that the real binding sequence is even more
>>relaxed - T(T/C)(A/T)T(A/C)CA(C/A)A.
>
>What is this good evidence?

Read the papers - it's good intellectual stimulation.

>>A lot of work has been done on the role of DnaA and the DnaA boxes. A
>>good summary can be found in Langer et al. (1996). It turns out that
>>you can make small sequence alterations to each of the five sites
>>without affecting the initiation of DNA replication and you can even
>>combine mutations to three of the sites without effect.

[snip]

>>If you delete one of the sites or completely scramble the sequence then
>>the origin doesn't work as well as the wild type oriC. In mycobacteria
>>(Mycobacterium smegmatis, M. leprae, M. tuberculosis) the consensus
>>binding site is (C/T)T(A/G)TCC(A/C)CA (Salazar et. al., 1996). This is
>>significantly different from the consensus sequence of the site in
>>enteric bacteria.
>
>And many other bacteria distant from E. coli. And I don't think it's that
>significantly different as it is still a 7.5/9 match.

Here's the E. coli consensus: T T(T/A)CNC A CA
Here's the Mycobacterial consensus: (C/T)T(A/G)TCC(A/C)CA

By my count only four of the nine positions are completely "conserved".
You could make the case that there are three more "half-conserved"
sites but that still doesn't get us to 7.5/9. Please explain your
calculation.

You need to appreciate that what we are looking at here is an indirect
measure of the conservation of DnaA itself. As DnaA evolved from a common
ancestor it acquired mutations that altered its interaction with DNA. In
most cases this resulted in an increase in specificity compared to the
presumed ancestral binding site. Different evolving lineages acquired
different amino acid substitutions in the recognition domain. Then there
was selection for changes in the binding site sequences. Since the
interaction between DnaA and the binding sites is always a bit sloppy,
there was never a time when mutations destroyed the interactions entirely.

We know from the data that DnaA is not a particularly highly conserved
protein. The most distantly related bacteria show only 25% sequence
identity and this is barely above the lower limits for demonstrating
homology. If DnaA was designed by an intelligent designer then the
original design must not have been very good.

>>It is quite clear that in many cases you need only a 7/9 match to a
>>consensus sequence that is itself somewhat sloppy.
>
>You need "only"? Sorry, but that's strong sequence conservation given
>we're looking at the products of billions of years of microbial evolution.

You are still confused about the meanings of "consensus sequence" for a
particular DnaA in one species and the "conservation" of binding sites.
I hope I have helped to clear this up.

>Before getting to the main point, there are problems with this
>explanation. Larry appears to be describing molecular tinkering, which
>is plausible once a system is up-and-running, but not so obviously
>plausible in talking about the origin of the system. Specifically, Larry
>seems to be reading modern capabilities back into the distant past. For
>example, Larry imagines an ancestral DnaA protein that binds non-
>specifically to a 9bp region. Non-specific binding tends to occur only
>when protein concentrations are high relative to DNA.

Let's take your last point first - the one about non-specific binding.

Take a single molecule of SSB or histone and add it to a test tube full
of DNA. Will it bind? Of course it will. You don't know what you are
talking about, Julie. Here's another example. There are about ten
molecules of lac repressor in an E. coli cell. Lac repressor binds very
tightly to binding sites near the lac operon. In fact it's one of the
best of the proteins that bind specifically. Nevertheless, where are most
of the lac repressor proteins found? Nine of them are bound non-
specifically to DNA at any instant. You do not need high concentrations
of protein to bind non specifically. (Not that this is important
anyway.)

Other examples of proteins that bind to DNA non-specifically include
RNA polymerase, DNA polymerase, helicases, some topoisomerases, and
some DNAses. None of these are present at high concentrations.

The other point requires that you put on your thinking cap and try and
purge your mind of some of your biases. I'm discussing only one particular
aspect of your irreducibly complex system. I am indeed assuming that DNA
replication is "up and running" using some ancestral form of initiation.
What I'm trying to do here is show you that the oriC type of initiation
could have evolved later. It is not necessary to postulate that the
whole thing was intelligently created all at once. Later on I hope to
address the evolutionary origin of the rest of the DNA replication
machinery, having established that the primitive system didn't need
DnaA and oriC. Do you understand?

>Could the
>ancestor carry this out? Invoking mutations essentially presumes DNA
>replication (the source of mutations) was up and running already.
>Focusing only on the DNA-binding property of DnaA is insufficient as
>DnaA functions as a replication initiator because it also carries out other
>activities. Were they already functioning? And there is not a shred of
>evidence to think the ancestor of DnaA bound nonspecificly to a 9bp
>region.

As you well know, Julie, my reference to the possible evolution of a
specific DNA binding sequence was in response to your claim that it
couldn't have happened. For some reason you seem determined to convince
yourself that it was impossible for DnaA to have evolved. Why? Do you
know something I don't?

>Larry describes the construction of a binding site, but it misses my
>whole point as I was talking about a highly *conserved* binding site.
>Let's see why this is relevant.

We have established that the binding site is not particularly highly
conserved. But let's see where Julie is leading us anyway ....

>We start with the binding site NNNNNNNNN. Larry imagines a mutation
>in the DnaA ancestor so that NNNNNNNCA is now recognized
>preferentially. Next, another mutation occurs so that TTNNNNNCA is
>preferentially recognized. From there another mutation in the proto-
>DnaA could occur causing it to prefer,say, TTNNNNACA. Etc. Ultimately, we
>reach the TTATCCACA consensus site and Larry states:
>
>"Weak binding sites can evolve into stronger ones. Do I have to
>continue?"
>
>But it's not a question of coming up with a stronger binding site, it's a
>question explaining the origin of this particular conserved site. Larry's
>explanation posits the existence of bacteria that possessed a DnaA-like
>protein that bound to NNNNNNNNN, others that bound to NNNNNNNCA,
>and others that bound to TTNNNNNCA, and others that bound to
>TTNNNNACA, etc. There is no evidence that a DnaA-like protein could
>bind to such relaxed sequences, but what is more relevant is that it
>would mean the lineages of *all* these bacteria, representing these
>intermediate stages, went extinct except for the one that stumbled upon
>the TTATCCACA consensus sequence (or we have some amazing convergence
>occurring).

I imagine that the last common ancestor of all bacteria had a DnaA-like
protein that recognized something like (A/T)TNNNCNCA and all modern
species have evolved variations over the past several billion years.
The steps before the last common ancestor of all bacteria are gone
forever - all those species that were on paths to other kinds of primitive
consensus sequences left no descendants. There's probably nothing
special about this particular sequence. If we replay the tape of life
there may be a different initiator protein and a different binding
site.

I suspect that you are not trying very hard to understand the evolutionary
argument, Julie. You seem to be going far out of your way to construct
bizarre arguments against evolution. I don't know why you are so fixated
on the idea that DnaA could not have evolved. Do you?

I suppose it's possible that you just don't understand evolution and
biochemistry but somehow I get the feeling that there's more to it
than that.

>What's even more relevant yet is that Larry's explanation is also
>consistent with the following scenario:
>
>NNNNNNNNN -> CANNNNNNN-> CANNNGGNN -> CANNNTTNN-> etc.
>and
>NNNNNNNNN -> NNNGCNNNN-> NNNGCNNAA-> TNNGCNNAA -> etc.
>and
>Etc.
>
>That is, what Larry fails to mention is that there are millions of possible
>ways a weak binding site can become a strong binding site through co-
>evolution. But where are they? Are we to believe that none of these were
>explored by the bacteria not evolving towards the TTATCCACA
>consensus sequence? Why? It seems clear to me that Larry's
>hypothesis entails a countless number of variants lurching towards a
>"strong" DnaA binding site. But then all these other variants must have
>gone extinct because they are not represented by extant species.
>That's quite an impressive bottleneck!

For someone who claims to accept evolution you sure do a good imitation
of an anti-evolutionist. Read the FAQ on "Transitional Fossils" for a
general rebuttal of your objection.

>To put it another way, Larry starts with NNNNNNNNN and reaches
>specifically for TTATTCACA. But there is nothing in Larry's explanation
>which causes us to believe different consensus sequences would not be
>found by different DnaA-like proteins mutating in different directions.

This is correct. There are lots of other initiator proteins that bind
to different consensus sequences. These proteins are used in viral and
plasmid DNA replication.

>Larry's case would be much stronger if bacteria did not show thematic-
>systematic IC with this origin. That is, if oriC and DnaA were simply one
>among *many* origin sequences and origin binding proteins used by
>bacterial chromosomes from various species, the co-evolution story
>would be better supported.

Would this really make a difference to you? Wouldn't you just argue that
there are now several irreducibly complex DNA replication systems? Also,
I think that every time we come up with a transitional you will simply
point to two more gaps.

>I don't think my reasoning is flawed. Say we went back in time and
>found primitive bacteria with the following origin sequence:
>TTATCNNNN. Would you predict this sequence to be strongly conserved
>if you went looking in other bacteria also lurching towards a better DNA
>replication strategy? Wouldn't your same co-evolution scenario predict
>NNNGAATTN, NNACCTCNN, etc. sequences used in other lineages
>reflecting the different directions that the pre-DnaA was evolving?

We are talking about changes to the preferred binding sequence that
take place at the rate of about one base pair in several million
years. Each step might have conferred selective advantage in which
case it would have become fixed in the population quite quickly. It
might even have become fixed in many populations/species depending
on how common genetic exchanges were in the past.

Even if drift were the only possibility it is quite possible that only
one allele (mutation) became fixed in the population. Once this happens
the next mutation to the dnaA gene will build on the survivor. Thus,
within a single lineage we expect to see directional change.

If we could go back in time before the last common ancestor of all modern
bacteria then we might well see that different species had different
DnaA proteins that bound to very different sequences. Just as today we
see a similar variety of binding sites that evolved from the ancestor.

It does look as though the last common ancestor of all modern bacteria
represented a bottleneck. I can't think of any other way of interpreting
the data. We know that there must have been plenty of evolution before
this bottleneck because we have the data from gene families. This data
tells us that there are families of genes whose last common gene ancestor
pre-dates the last common species ancestor by millions of years.

Julie, I'm sure you have another explanation for all of this. Care to
share it with us?

>Or is
>the TTTATCNNNN sequence so special that all the other routes went
>extinct? This does not seem reasonable to me.

Not special. But the other possible variations of the crude ancestral
binding site (eg. (A/T)TNNNCNCA ) would have disappeared when their
lineages lost out in the big lottery.

>I can easily imagine
>hundreds of different sloppy Dna-like proteins co-evolving with their
>respective binding sites in hundreds of different directions all binding
>to DNA with not significantly different affinities. Yet when one lineage
>reaches the particular solution of TTATTCACA, all the rest (perhaps
>millions) disappeared (or they all rushed to converge on this same
>solution).

Glad to see your imagination working again. You need to get into the
habit of keeping to the known facts if you want it to be useful.

>>The 5mer in ancestral cells may have worked well enough back in the
>>days when you only needed to synthesize DNA every week or so and it
>>didn't matter much if some mistakes were made.
>
>In this case, the mistake would be failure to initiate DNA replication.
>And if organisms only replicated their DNA every week, this would be
>very risky especially when the environment became chaotic. As I see
>it, if something didn't replicate that often, it would be even more
>important to replicate properly *when* they replicated.

You aren't one of those people who think that all modern bacteria
divide every twenty minutes, are you?

In one of the references that I gave you the authors talk about species
of modern bacteria that only divide every two weeks. Did you read it?
Many soil bacteria divide about once a week and bacteria that live in
rocks have generation times measured in years.

E. coli replicates its DNA about once every 12-18 hours inside your
intestines. Outside in the real world the bacterium may only divide
every few days. In real life E. coli doesn't divide as rapidly as
it does in the laboratory during exponential growth for a few hours in
rich media. Think about it. There's only one way of getting rid of all
those bacteria that are growing in your intestines. If E. coli was really
this prolific in nature then we would be in deep shit! (pun intended)

It's quite reasonable to imagine that primitve bacteria divided every
week or so. What was your point?

>>It need not have been "constrained", just as the modern sequences are
>>not as constrained as you imagine.
>
>The modern sequences are strongly conserved across distant lineages.
>And if the primitive sequences were not strongly conserved, where are
>their modern representatives?

Have you tried looking in the papers I gave you?

> Where are the dozens of analogs of DnaA?

Ditto.

>>>"Sloppiness meant "room for improvement" and the ability to be
>>>messed with (unlike conservation). We can then wave our hands
>>>and claim they "co-evolved" to arrive at the 9mer state."
>
>>I think "wave our hands" is too dismissive here. I hope I have
>>convinced you that there's a little more than hand waving involved.
>
>While I truly appreciate you explaining your reasoning, I must confess
>that at most, I see a little more than hand-waving. No offense intended,
>as I'm sure you view my reasoning in an even less favorable way.

Let's just agree to wave at each other and hope that the readers of
talk.origins will be entertained by our antics. (-:

>>> "And once it was found, it was "locked in" for over a billion
>>> years of microbial evolution involving several lineages in
>>> different environments.
>
>>No, not "locked in" for a billion years.
>
>Sure it is. This is seen when the same consensus sequence is seen in
>bacteria who last shared a common ancestor over a billion years ago.

This isn't hand waving on your part, Julie. It is deliberately ignoring
the facts. I have explained this to you twice now and given you all
the key papers to read. There's nothing more I can do. Modern bacteria
do not all contain the same DnaA protein that binds to the same consensus
sequence. Live with it.

>>In fact different species of bacteria have different DnaA boxes
>>suggesting that each has chosen a different pathway of evolution.
>
>Yes, some species have strayed somewhat from the the consensus and a
>few seem to have replaced it with something else.

I give up! You can't even hold an idea in your head for five lines!

>>I suppose that your alien design model would postulate something
>>different. Perhaps the aliens created many different designs in order to
>>see which one would win out in the end? Maybe Earth is just a giant
>>test tube where a bunch of alien graduate students are doing in vitro
>>mutagenesis and evolution on a big scale?
>
>I have never asserted that aliens created anything so why do you insist
>on misrepresenting me?

We have covered this ground elsewhere. Substitute "intelligent designers"
for "aliens" then address the point.

>>>"But that's an uncanny story. For it clearly suggests the 9mer state
>>>is optimal."
>
>>That's your strawman "Darwinist" talking.
>
>Like believing in alien designers proving Darwinian evolution is
>impossible?

You got it.

>>No one claims that the
>>modern situation is optimal or that each specific step had to confer
>>selective advantage.
>
>So what happened to all the other origins and pre-DnaA proteins?

See above. Read the papers. Read the talk.origins FAQ's that discuss the
standard Creationist complaints about the lack of transistional fossils.

>>Perhaps it's just an accident that one species has a more stringent
>>consensus sequence than another.
>
>I don't find accidents to be a better explanation than design.

"Accidents" are an integral part of modern evolutionary theory. If we see
something that looks sloppy and non-optimal then we can account for it
by evolution since Rube Goldberg-type systems are what we expect. Modern
evolutionists do not postulate that everything is an adaptation.

Those who believe in intelligent design have a problem that needs to be
addressed. How do you get sloppy Rube Goldberg-like systems? When do you
plan to start with the explanations?

>>>"Secondly, the 9mer state has persisted for a very, very long time
>>>in very different lineages (eg., Micrococcus luteus, Bacillus subtilis,
>>>Mycoplasma capricolum, Pseudomonas putida, and E. coli)."
>
>>We disagree on the facts here. Please post your evidence that the same
>>stringent 9 base pair sequence is required in all of these species. I've
>>given you my references (see below), now give me yours.
>
>But it's in one of *your* references!
>
>Yoshikawa, H. and Ogasawara, N. (1991) Structure and function of DnaA
>and the DnaA-box in eubacteria: evolutionary relationships of bacterial
>replication origins. Molec. Microbiol. 5, 2589-2597.
>
>See Table 2.

For the benefit if those who haven't the time to look up all of these
papers, the Table that Julie is referring to lists the number of DnaA
potential binding sites at various potential origins. The number varies
from one to eight. There are three columns "0", "1" and "2". The legend
states "Numbers of TTATCCACA (0), and sequences one base different from
it (1) are listed. In some cases (M. capricolum C and L, and E. coli L),
numbers of sequences two bases different from the consensus (2) are also
listed."

Unfortunately, the authors are using the word "consensus" here in a very
misleading way to describe a global consensus of the sort that Julie
claims is the ancestral binding site. In the text of the paper the authors
are more careful. They discuss the "E. coli-like consensus" and the
Micrococcus-like consensus making it clear that they appreciate that
different species may have different consensus binding sites. They point
out that none of the Mycoplasma binding sites correspond to the TTATCCACA
sequence, suggesting that the Mycoplasma DnaA may recognize a different
consensus sequence. Yoshikawa and Ogasawara focus their attention on
the E. coli, Pseudomonad, and B. subtilis binding sites since others were
not well characterized in 1991. They discuss the in vitro binding studies
and conclude that for these species,

"It is difficult therefore, to define the DnaA-box apart from
the fact that (i) TTATCCACA is stronger in binding DnaA protein
regardless of its location relative to other boxes, and (ii) the
4th, 7th and 8th positions of the 9-mers are highly conserved
and may play important roles in binding DnaA protein."

I stand by my statement. The same 9bp sequence is not used in all species.
Instead there are different consensus sequences in different species as
the authors of this paper point out. The ancestral binding site was
probably much less well defined than the modern sites.

Julie, when do you think you will get around to reading the other papers?

Concerning another point. Now that I know you have read this paper I draw
your attention to page 2594 where the authors discuss the Micrococcus
luteus origin and say,

"No obvious AT-rich repeats were observed, although the DnaA-
box regions, particularly regions adjacent to the DnaA-boxes,
are relatively high in AT content (about 40%) for this
organism."

Even if you haven't read any other papers do you still maintain that
13bp AT-rich direct repeats are an irreducibly complex component of
oriC replication origins?

Now back to the discussion of "highly conserved" DnaA binding sites.
Here's what Julie thinks.

>>>"And it hasn't been "improved" while these species evolved. Now

>>>that's quite a pattern. The lack of pre-9mer states suggest (at least

>>>to me) that such a transformation entailed a quantum

>>>jump, not a gradual transformation. Yet the quantum jump

>>>was into an optimal state. And in my opinion, that pattern
>>>(quantum jump to optimal state) is quite suggestive of design."

I maintain that Julie's impression of design is based on an inadequate
understanding of the data.

>>The pattern is quite suggestive of evolution.
>
>Perhaps guided evolution where NNNNNNNNN was specifically pushed
>towards the TTATCCACA consensus. Such guided evolution would
>probably have happened rapidly as there are no obvious
>representatives of the intermediates in this *particular* route. Then
>again, in this context, positing evolution is not needed. Once the
>TTATCCACA consensus appears, it remains strongly conserved among
>various lineages over a billion or so years. As I said, it's quite
>suggestive of design.

Is "guided evolution" a euphemism for "intelligent design"?

I maintain that Julie hasn't read the papers carefully if she thinks that
every species uses TTATCCACA. The "intermediates" between the ancestral
sequence and Julie's imagined endpoint are with us today.

>>>"The replication origin works as follows. Several molecules of
>>>DnaA (see below) bind to the 9mers. This is followed by the
>>>melting of the AT-rich 13mers. This then allows DnaB(see below)
>>>to bind and initiate replication by unwinding the DNA further.
>>>Thus, the strong sequence conservation of the 9mers reflects
>>>its role as a binding site for DnaA. The interactions between
>>>DnaA and the oriC (and DnaB) represent systematic IC."
>
>>We have seen that the binding of DnaA to several binding sites is,
>>indeed, a fundamental property of this type of origin. The "AT-rich
>>13mers" are a derived feature found only in enteric bacteria.
>
>But AT rich regions, adjacent to the DnaA box, are not found only in
>enteric bacteria.

You concede that 13mer repeats are not an irreducibly complex component
of oriC regions in spite of what you said in your essay. Now, all you have
to do is read the papers carefully to see that even unusually AT-rich
regions aren't ubiquitous.

>>It is likely that DnaA binding leads to local unwinding of DNA as Julie
>>says. There is reasonable conservation of DnaA binding sites (DnaA
>>boxes) in different species of bacteria but there is also plenty of
>>evidence of considerable evolution from a common ancestral sequence
>>that is more sloppy.
>
>There is strong sequence conservation in the DnaA binding sites of very
>different bacteria. Some straying from this consensus occurs.

Change "strong" to "significant" and we can agree.

>>The essence of oriC is a bunch of DnaA binding sites located near the
>>promoter of the dnaA gene itself. All other variants seem to be derived
>>from the primitive generic form.
>
>As if it is no problem coming up with a bunch of conserved sequences.

That's not the point, Julie, and you know it. The point was to clarify
the exact nature of the irreducibly complex oriC region. Now that we
have reduced it to its essence we can proceed with the next step, which
is to explain how a bunch of DnaA binding sites came to be used as a
replication origin. We had to remove the extraneous garbage first because
you were pretending that all modern origins had much more structure
(i.e. design) than they really do.

>>The next step is to see if we can come up with a reasonable explanation
>>of oriC origins based on evolution from something that could have
>>existed in the primitive ancestors of modern bacteria.
>
>Let me guess? Transcription?

Right. You don't have to guess, Julie, because you have at least read
some of the papers that discuss this point. One wonders why you didn't
address this explanation in your original essay. Were you hoping that
no one else would take the time to do the research?

>>We already know that Julie's explanation is that these origins were
>>designed by aliens and couldn't have arisen naturally.
>
>This is not my explanation.

This is a quibble, and you know it. I shouldn't have let my cynicism
get the best of me when I referred to "alien design" because it just
gave you an opportunity to cop out. If I say "designed by intelligent
designers" will you stick to your denial?

>>Any "reasonable explanation" will, of course, be speculative. The reader
>>will have to decide for themselves whether the evolution model or the
>>alien design model offer the most reasonable explanation of the data.
>
>Apart from the word "alien," this is well-stated.

Good. When are we going to hear about your "reasonable explanation"
based on the actions of intelligent designers? Please don't post any
more examples of supposedly irreducibly complex systems until you
finish the job here.

Larry Moran

[Laurence A. Moran]

[Vladimir Svetlov]

I missed the 50 pages long article about aliens designing replication?!!
Good. Cause them did not. Cause there is no evidence for them aliens except
recurrent anal bleeding of my cousine Billy-Joe in Dickson Co., TN.
Seriously, dudes, how many more loonies would bring forward their
bewilderment with modern cellular machines and claim that someone just have
to create it (apparently, using Lewin's Genes VI as a manual)? Lawrence
Moran did a good job pointing out problems in the latest installment in a
series "I-Just-Don't-Get-It-Must-Be-Aliens". Too good, it seems, since the
author of those fifty pages is more familiar with design of cars than the
replicative machinery. Did you ever got her to explain what kind of
evidence she was looking for that bacterial chromosomes were at any time
different from what they are now ? What a lovely argument by itself... Even
in a modern system in order to replicate one has to provide a polymerase
(single polypeptide of <90 KD would do) and a helicase. Primase apparently
was not needed as long as the tRNA was around and one can get a distortion
amounting to quasi-open complex by binding a small (<20 kD) protein. Big
deal. Can't we show these lunatics a mol. biology textbook without them
freaking out and forming a cult of Chtulu, the Sole Creator of the DnaJ and
DnaK, the One Maker of Okasaki fragments...
Now go away.
Regards,
V.

[Julie Thomas]

In a previous article, m...@panix.com (Michael L. Siemon) says:

>I said that Julie has no justification (she has certainly *given*
>none) for her rejection of evolutionary explanations.

What an odd way of seeing things. I need justification for not thinking
bacterial DNA replication and/or flagella evolved? Michael has it
backwards. If he thinks I am obligated to believe such things, he
should at least try to convince me.

[howard hershey]

Julie Thomas wrote:
>
> In a previous article, lam...@bioinfo.med.utoronto.ca (Laurence A. Moran) says:
>
> I'd like to begin first by thanking Larry Moran for an excellent reply
> concerning the bacterial origin of replication.

So would I, despite my massive cutting of it to save band width. I
didn't really have time to look up that stuff.

> I would like to reply
> in turn. A word of warning, however. I wrote this reply Sunday
> evening after a Saturday night of very little sleep so I hope it
> isn't too confusing.

Don't worry, Julie. To us you are an intellectual marvel, a Newton
among the usual run of anti-evolutionary posters. It can truely be
stated that you stand on the shoulders of midgets. :-)

>
> >The Origin of Replication
>
> >Julie Thomas claims that DNA replication is a alien designed system
> >based on the fact that it is so complex that it couldn't have arisen by
> >natural causes.
>
> Unfortunately, this statement tended to detract from an otherwise good
> article. The problem is that I have never claimed that DNA replication
> is an "alien designed system" Neither have I ever claimed that DNA
> replication is so "complex that it couldn't have arisen by natural causes."
> This is most unfortunate as Larry is well aware of this. What's worse, it
> suggests that Larry's entire article is simply a response to a strawman
> argument.

Julie merely claims that *present-day* DNA replication in *present-day*
eubacteria represents an IC system as defined by Behe (knock-out one
part and the system collapses) and the equivalent negative statement by
Julie (if there exists a complementary activity that can replace the
knocked out activity, the system is not IC). She asserts (going far
beyond the data) that the IC-ness of DNA replication has a sufficient
number of fully integrated and mutually dependent parts that it is
unlikely to have arisen (directly?) stepwise by Darwinian (natural law)
mechanisms (which requires, typically, that the intermediate steps have
*some* functional utility, but most certainly that they cannot be
detrimental) but more likely requires intelligent design created by some
apparently invisible intelligent designer and implemented by an
apparently invisible design implementor (who does not act via natural
law mechanisms seen in action in the present).

She is most reluctant to discuss what IC-ness actually implies as
alternative mechanism: Either one fell swoop creation *de novo* by the
invisible implementor of design (as opposed to, say, horizontal transfer
from another source, which is a natural law mechanism) or stepwise
creation of utterly useless intermediates which are somehow invisibly
protected from loss by natural law mechanisms working in organisms
today. More often she hints at a supernaturally 'guided' evolution,
which is not hinted at or implied by IC-ness, but which certainly *can*
be made compatibile with any natural law mechanism one chooses or even
random mechanism, as it is little more than the IPU solution. The Great
Invisible Implementor of Design - Yahoo. It positively makes one GIIDY
with delight.

>
> >One of the components she discusses is the origin of replication. I'd like
> >to correct some of the errors in her essay and then present some
> >additional information that she left out.

But right off the bat, we have a problem. OriC and DnaA do not meet
either criteria for being part of an IC system.
>
[snip huge chunk showing that there is a wider range of possibilities in
OriC than Julie presented, implying that there is no single 'optimal'
design in nature, but merely a range of designs, equally utilitarian.
Also skip discussion of the lack of need for oriC-like mechanisms in
other organisms than eubacteria.]

>
> >However, it is possible to dispense with oriC altogether. In E. coli you
> >can substitute oriP2, oriR1 or oriF and the chromosome will be
> >replicated. These origins don't use DnaA. In Bacillus subtilis you can
> >delete oriC and replace it with an unrelated origin from a B. natto
> >plasmid (Anwarul et al., 1997). DnaA is not required in this construct
> >and the chromosome is replicated although partition is inefficient.
> >These experiments demonstrate that oriC is not specifically part of an
> >IC system, although some form of DNA binding protein and binding site
> >is.

Thus, one can knock out the parts and the 'system' does not collapse
because other elements (which are not simple duplications of the
original activity) can complement the missing activity. Isn't that how
one objectively determines the IC-ness of the 'parts' of a 'system'?

>
> Larry confuses systematic IC with thematic IC at this point. The
> different origin strategies (as Larry mentions) underscore that a DNA
> binding protein and binding site is needed (thematic IC).

I am deeply troubled by this use of 'thematic IC'. It merely is a
statement that the tests one has proposed to determine IC-ness are
irrelevant to some predetermined assumption of what is required. Knock
out the genes and the system still functions because some other element
complements the knocked out activity. The 'parts' are *still* IC, but
now they are IC *because* there is complementing activity replacing the
knocked-out activity. It is hard to beat that kind of funhouse logic.

> But they are
> not relevant to OriC from a systematic perspective unless these other
> origins can be shown to predate oriC and have given rise to oriC.

And this rather defeats the claim that IC-ness is objectively determined
by examining the *present-day* system. You would be better off by
jumping off this sinking ship, Julie. OriC and DnaA are not part of the
IC-ness of DNA replication, if IC-ness is to mean anything. There are
simply too many alternative mechanisms available, including all those
viral and eucaryotic systems that you ignore that provide 'reasonable'
stepwise (with useful intermediates) models for the step-wise evolution
and integration of these particular parts.

[snip discussion of how an initial low degree of specificity of protein
to a sequence can become more specific if there is selective pressure
for it, along with Julie's strange idea that the particular end result
was somehow teleologically ordained by design.]

> Yes, some species have strayed somewhat from the the consensus and a
> few seem to have replaced it with something else.
>
> >The data says that there was a lot of evolution over the past billion
> >years.
>
> Yet the consensus remains in very distantly related bacteria.

Which likely means that the oriC/dnaA system may well have evolved for
other functions *before* being recruited to a function in DNA
replication, just as other individual activities can be recruited as
complementing activity when the oriC/dnaA is knocked out. It likely
already had the affinity for at least the core sequence before it was
recruited.

>
> >I suppose that your alien design model would postulate something
> >different. Perhaps the aliens created many different designs in order to
> >see which one would win out in the end? Maybe Earth is just a giant
> >test tube where a bunch of alien graduate students are doing in vitro
> >mutagenesis and evolution on a big scale?
>
> I have never asserted that aliens created anything so why do you insist
> on misrepresenting me?

You certainly *are* implying 'intelligent design' which implies an
intelligent designer and someone/thing that implemented that design.
[snip]

> >There's no reason to believe that any of these modern pathways are
> >better or worse than any others. The evolution that took place involved
> >both random genetic drift and natural selection.
>
> Drift doesn't explain strong sequence conservation across long
> phylogenetic distances. Selection would explain preservation of the
> consensus, but not it's origin (IMO).

Both its origin (which may indeed be quite early) *and* its conservation
can be explained by selection.

[snip]

[Julie Thomas]

In a previous article, lam...@bioinfo.med.utoronto.ca (Laurence A. Moran) says:

Larry originally said:

>>Since it could not have evolved, according to you, then the competing
>>hypothesis must be correct.

So I replied:

>I never said anything could not have evolved.

Larry then replies:

>Picky, picky, picky. Maybe you never actually wrote those words but
>here's what you claimed in your essay in the section on origins of
>replication.

> a) It is "unlikely" that the 9mer DnaA box could have been
> built up one nucleotide at at time.
> b) Phylogenetic information from the non-core oriC sequences
> "would not mean that the core evolved. It would simply help
> us pinpoint when the core was designed."
> c) "The critic of IC may claim that once upon a time a bacterial
> origin was made up of one 5mer (or something like that),

> but,let's be blunt, there is no evidence for such a claim (making

> it look awfully ad hoc)."
> d) "The lack of pre-9mer states suggest (at least to me) that
> such a transformation entailed a quantum jump, not a

> gradualtransformation. And in my opinion, that pattern

> (quantum jump) is quite suggestive of design."
> e) You have a discussion about why it would be
> "selectively disadvantageous" to evolve a protein like DnaA.
> f) You point out that there are several ATP consuming steps
> in DNA replication and say, "This makes it hard to envision the
> gradualistic evolution of DNA replication."
> g) You point out that the sequence of the Mycoplasma DnaA
> protein doesn't fit into a phylogenetic tree where it should. You
> say, "A molecular IC interpretation avoids the problem of trying
> to fit these proteins in scheme that shows a common
> ancestor."

Hmmm. In an attempt to show that I have claimed "[DNA replication]
could not have evolved, [thus] the competing hypothesis must be true,"
Larry finds several claims that all fail to support his claim about
my claims. How interesting.

Larry then adds:

>I haven't bothered to flip through the remainder of your essay.
>You are making the case that DNA replication could not have evolved.

I am mystified by Larry's insistence that I am making the case that
DNA replication "could not have evolved." Apparently, Larry confuses
the fact that I *do* not think DNA replication evolved means I think it
"could not" have evolved. But that's sloppy thinking. For example, if
someone does not think there was life on Mars it doesn't mean they
think life could not have existed on Mars. Those are two very different
claims. Furthermore, just because I do not think DNA replication
evolved does not mean I think DNA replication *must* have been
designed.

Larry's confusion appears to stem (IMHO) from a desire to attribute
certainty to my beliefs. This could be due to his belief that he knows
me better than I know myself.

Of course, it is possible that Larry may be projecting his attitudes upon
me (projection is a common phenomenon with people who think they
know a person (or a group) better than the person or group know
themselves). That is, perhaps he is the one who believes "design could
not have occurred thus the evolution of DNA replication must have
occurred" and thus attributes this type of logic to me. After all, it
explains (to me) why it seems he is readily convinced by evidence for his
views that is weakly suggestive at best. Furthermore, I can easily say
that DNA replication could have very well evolved. It doesn't make
much difference in the scheme of things to me. Can Larry as easily say
that DNA replication could have very well been designed? Would it
make a difference in the scheme of things for him?

>Therefore it had to be designed.

I never said it "had" to be designed. Again, Larry needs to recast my
position before dealing with it.

>Designed things need designers just as Paley claimed two hundred
>years ago.

Sure, designed things need designers. That's pretty obvious to me. Of
course, as I have said before, things might look designed but not truly
be designed. I've also then addressed this point.

>I don't know why you insist on denying the obvious.

It's obvious *to Larry* (and I suspect other like-minded folks). Of
course, what *would* be obvious to truly objective folks would be the
actual claim where I said "X could not have evolved, thus it must have
been designed." But I have not claimed this for the simple reason that
it is not my belief. Larry has, however, created an internally consistent
view in his mind. From where he sits, it's "obvious" I believe what he
thinks I believe. Of course, when I deny it for the simple reason that it
is not true, I'm *really* (sneaking person that I am) "denying the
obvious." But it just doesn't even seem to occur to Larry that he could
just be plain wrong and that other people may think in ways that don't
conform to tidy little stereotypes.

>Who are you trying to fool?

Obviously, I cannot fool a man who knows me better than I know
myself.

Larry asks:

>>But you won't come out of the closet and tell us what the competing
>>hypothesis is. Why?

I replied:

>[scratches head]. As I said:
>"I simply outlined the IC nature of DNA replication which in turn
>strongly suggests the system was designed."

Larry replied:

>[scratches head]

>The competing hypothesis is that the system was designed, right?

Sure. But you then think I mistake this competing hypothesis for a
certain belief.

>Is every IC system designed?

Not necessarily. Michael Behe explains this in his book.

>Can you have design in the absence of a designer?

I don't think so. But you can have things that look designed without a
designer. Certain IC systems might very well be an example of this.

>In your mind, do IC entities imply designers?

Sure - but note the word "imply." Experience has taught me that IC
entities typically have designers. Thus, I find intelligence to be the best
explanation when it comes to IC. Of course, if there is powerful
evidence to the contrary, I can abandon intelligent causation as the best
explanation in the case under question.

>Why don't you come out of the closet and tell us about your intelligent
>design model?

I already have. I suspect you were not paying attention because you
were preoccupied with what you think is "obvious."

>You seem to think that if you can cast doubt on evolution
>then this is support for your model but how are we to know if you
>won't tell us about it?

Since intelligence is easily capable of generating IC systems, and IC
systems are known to have been generated by intelligence, I find
intelligence to be the best explanation in the case of IC. But what I find
is purely "tentative." For example, if a powerful evolutionary
explanation is made for an IC system (that goes beyond the "could have
happened" world), I find intelligent causation to be in a weaker position
(it may be merely an alternative, but not clearly the best explanation).

>What are you afraid of, Julie?

Nuclear war.

>>>I admit that the use of "alien" was partially motivated by your use of
>>>the term "Darwinist". A term that I find very offensive since it
>>>implies a strawman version of evolution. If you start being more
>>>considerate then I will too.

>>I'm truly sorry. I didn't realize you were offended by the term
>>"Darwinist." But how shall I refer to your position? I don't want to
>>refer to you as an "evolutionist" because that makes it seem like I am
>>anti-evolution (and I am not).

>Damn! There goes my brand-new Irony-O-Meter. I'll have to ask the
>store if I can have my money back.

Hey, if you didn't rely so much on stereotypes, you might save yourself
some money.

>"Evolutionist" would be fine by me. I'm happy to be called an
>evolutionist. You'll simply have to live with any semantic problems
>that this creates for you.

Or I could quit bothering with you. That seems to be a more attractive
choice.

>Frankly, I don't see why you prefer "Darwinist" - your writings suggest
>that you actually believe that your strawman version of evolution is
>the one we all believe in.

Imagine that. Perhaps you can tell us in what way your evolutionary
descriptions (so far) are not Darwinian.

>So "evolutionist" should be the same thing if I interpret you correctly.
>Are you an anti-Darwinist?

Nope.

>Is that why you wanted to refer to your strawman critics as
>"Darwinists"? Do *you* see a difference between a Darwinist and an
>evolutionist?

Sure. All Darwinists are evolutionists but not all evolutionists are
Darwinists.

Larry said:

>>Come on, Julie. Give us a little credit - we are not idiots. What's the
>>real reason for claiming that a system is irreducibly complex?

I replied:

>For the third time:
>"I simply outlined the IC nature of DNA replication which in turn
>strongly suggests the system was designed."

Larry asked:

>>Are you just playing rhetorical games or is there a bigger stake?

I replied:

>Well, I suppose that a desire to know what's the truth about our
>reality is a "bigger stake."

Larry asked:

>>If the process didn't evolve then what is your explanation?

So I replied:

>If it didn't evolve, then it was mostly likely designed.

Larry replies:

>So it's "truth" we're after, is it?

Sure. I have no desire to believe something that is false. Do you?

>You have almost come clean here - one more little step and we'll be

>able to see what this bigger stake is this "truth about our reality".

I know. It's so "obvious."

Larry asks:

>Here's the key question,

> Can you have design in the absence of a designer?

I don't think so. Of course, I could be wrong.

Larry then says:

>Several postings ago I summarized Julie's hypothesis like this,

>>>She suggests that some systems are so complicated and
>>>interconnected that it would be impossible to imagine or reconstruct
>>>a natural explanation involving evolution from a primitive ancestor.

Yes, and this was an erroneous summarization. But you still seem to
need to cling to it.

Larry said:

>There followed bit of back and forth where Julie complains that I am
>putting words in her mouth.

Which, of course, was true.

>Apparently there is something in my summary that she doesn't want
>to openly admit.

Er, it's just simply false that I ever claimed it was impossible to imagine

or reconstruct a natural explanation involving evolution from a

primitive ancestor. Even on a trivial point like this, Larry can't admit
he is wrong. And that says something to me when we discuss other
more substantial and controversial issues.

>Maybe it's just the word"impossible",

Maybe it's the whole darn claim.

>I dunno.

Not surprised.

>Anyway, Julie now offers an alternate version of the introduction to
>her essay where she discusses Darwin's quotation - the one where he
>says "If it could be shown that any complex organ existed which could
>not possibly have been formed by numerous, successive, slight
>modifications, my theory would absolutely break down."

Indeed. I'm one who thinks it is more important to clarify and modify
(even admitting error) rather than dogmatically defend something in a
Battle of the Egos.

I said:

>In my opinion, there are several IC systems which lack evidence of
>Darwin's mode of transformation, and in fact, appear unlikely to have

>originated in this way.

Larry replies:

>Would this be a good summary of what you are trying to say?

If you want a summary, it is:

In my opinion, there are several IC systems which lack convincing

evidence of Darwin's mode of transformation, and in fact, appear

unlikely to have originated in this way. When this is coupled with my
common experience where IC is tied to intelligent design (intelligence
easily generates IC and IC usually stems from intelligence), I find
intelligent design to be the best explanation for the IC systems in
question. Thus, I seek to explore the natural world from the
perspective of a design paradigm and invite others, hopefully with open
minds, to look on and enjoy.

>Julie says that IC systems are very unlikely to have evolved.

No, I said that's my opinion. You keep reading certainty into my claims.

>Would that make you more comfortable than my previous summary of
>your position?

Of course I would be more comfortable if your summary of my position
was even a little more accurate than your initial summary.

>You don't say that it's "impossible" just "unlikely". How
>unlikely, Julie?

Er, how likely was it that DNA replication evolved? We're in the same
boat.

>Is there less than a 1% chance that an IC system could have evolved?

I can't quantify this judgement. Is there a 99% chance DNA replication
evolved? Is there a 1% chance an IC system could have been designed?

>Is it *possible* that an IC system could have evolved?

Sure.

>How?

Read Behe's book.

I said:

>I should, however, point out that IC ismore than a problem for

>Darwinism. IC is also characteristic of design (although design need not
>entail IC) and is very similar to the concept Paley employed in his
>analysis of a watch (although Behe has more rigorously defined this in

>his book). Thus, a Darwinian explanation of system is not a refutation

>of design. It is merely an alternative explanation.

Larry replies:

>Would this be an accurate summary of your position?

> Julie says that IC systems suggest design. This line of reasoning
> is similar to the arguments that Paley used to demonstrate
> that a watch was designed. Paley then goes on to suggest that
> the design of natural systems suggests a watchmaker (God) but
> Julie doesn't take that step with her natural system.

If you want. Although I think the summary I provided is much clearer.

I said:

>Now, can we get beyond this notion that I am claiming "some systems
>are so complicated and interconnected that it would be impossible to
>imagine or reconstruct a natural explanation involving evolution from a
>primitive ancestor?" Because....I'm not.

Larry replies:

>You haven't convinced me.

Well, I suppose it is an exercise in futility in trying to convince someone
who thinks he knows me better than I know myself. Oh, well. I'll just
keep this in mind when you are also not convinced about more substantial
and controversial points I raise.

Larry said:

>>You have suggested that there is no natural explanation for DNA
>>replication as we know it and I will attempt to provide one.

I replied:

>I do not suggest that there is "no natural explanation for DNA
>replication."

Larry replied:

I gave you a quotation from your essay. Here it is again,

"This makes it hard to envision the gradualistic evolution
of DNA replication."

How does one get from "it is hard to envision the gradualistic evolution
of DNA replication" to "there is no natural explanation for DNA
replication?"

Perhaps Larry can fill in the gap.

I personally think the gap-filling goes like this. I make a tentative
claim about my perceptions of the world and Larry reads a certain
claim about the world. Could this be because Larry is reading my words
through the filter of his stereotype? It seems most likely (although I
must confess that I can't quantify this judgment).

>I must have misunderstood. I guess you only meant to eliminate
>"gradualistic evolution" as a natural explanation. There must be other
>natural explanations of DNA replication that you prefer. Either
>that or you just told a fib. Please let me know what "natural
>explanation" you are intending to include.

I just told a fib? Fits with the dishonest person you think I am, right?
Either that or you are simply confusing yourself with your stereotypes..
Go back and fill in the gap, Larry.

I said:

>>>Now, if you claim DNA replication evolved from a primitive ancestor
>>>along Darwinian lines, I simply note there is no evidence for this
>>>claim (or at the very most, the evidence is very weak). If, as I
>>>believe, design is a better explanation for the IC nature of DNA
>>>replication, I *then* consider your absence of evidence and say "no
>>>wonder there is no evidence; y'all are pursuing a dead end." Thus,
>>>the failure of Darwinism is *supporting* evidence.

Larry replied:

>>I look at the data and see several possible explanations that are
>>consistent with evolution. Then I look for evidence of design and
>>designers and see none. The lack of evidence of intelligent designers
>>must mean that there aren't any, right? I then consider your absence
>>of evidence and conclude that you are playing with an emptyeck. The
>>failure of designism then becomes suorting evidence for evolution.

So I said:

>I can respect this except for one claim - "lack of evidence MUST mean
>there aren't any." I make no "must" claims. In my case, lack of
>evidence for your claims is simply consistent with what I believe.
>Also, I didn't quite accurately convey the essence of my thoughts when
>I said, "no wonder there is no evidence; y'all are pursuing a dead end"
>I should rephrase that thought as follows:

>"hmm, that there is no evidence tends to confirm what I suspected;
>y'all are pursuing a dead end."

Larry replied:

>I'm curious about your statement that "lack of evidence for your claims
>is simply consistent with what I believe".

Y'know, it's no wonder you keep getting confused about my beliefs. It
looks to me like you are almost obsessed with reading between the lines
and thus don't pay much attention to reading the lines that are there.
Let me satisfy your curiosity. What I believe (due to experience) is that
IC systems are likely to reflect design. If that is the case, then I don't
expect there to be convincing evidence for a gradualistic/Darwinian
mode of origin for the IC system in question. Or, I predict a lack of
evidence. Thus, "lack of evidence for [such] claims is simply consistent

with what I believe".

>You seem to "believe" in something that doesn't involve evolution.

Sure. The origin of DNA replication and the bacterial flagellum (and
many others processes and structures).

>So when someone fails to come up with an evolutionary explanation
>you are quite satisfied because you suspected all along that evolution
>wasn't the answer. So what do you "believe"?

IC systems most likely reflect design.

>Do you think it possible that your search for IC and design is motivated
>by your "beliefs" and not by a real search for the truth?

Anything is possible, but I know myself pretty darn well (far better
than you do). Me thinks you're barking up the wrong tree.

>Is it possible that you already "believe" that you know the truth and
>you are simply looking for pseudo-scientific proof that will make you
>feel good?

Quite doubtful. I've spent so much of my intellectual life shying away
from "I know the truth" claims and I am not one who looks for ways
to make myself "feel good" with beliefs. Is it possible that you may
have been projecting when you asked this question?

I said:

>I think there is much confusion concerning this topic. My major
>intention in focusing on IC is not to come up with an anti-darwinian
>argument. I don't need that. When it comes to DNA replication or the
>bacterial flagellum (and many other things to come), I am simply not
>convinced that Darwinism has anything to do with their origin. But I
>am still quite interested in their origin. Should I wait, and hope, that
>someday folks like Paul Myers will come up with a story that will
>probably only convince those hoping to be convinced? Nah. Thus, I
>look for alternative explanations that *I* find far more intellectually
>satisfying. And, as I see it, Michael Behe has given me the key. So I
>begin to look afresh at these systems with Behe's key and it generates
>new insights and new lines of inquiry. Put simply, it's a way to
>interpret data and do science under a design paradigm. That's why I
>said to Paul that "Ill go my way and y'all go yours."

Larry asks:

>In referring to your ideas in the future would it be fair to paraphrase
>as follows?

Gee. You're really struggling with this, aren't ya?

> Julie is not convinced that evolution has anything to do with
> the creation of a DNA replication system. She finds intelligent
> design far more intellectually satisfying.

If you need the paraphrase, it would be better to replace "a DNA
replication system" with "the historical origin of the replication of
bacterial chromosomes."

Larry claimed:

>>>>This is a rhetorical device that is designed to convert the absence of
>>>>evidence into something positive that is subject to scientific
>>>>analysis (i.e. that the system will not work if any part is removed).

>>>>We are not fooled by this cheap trick.

I replied:

>>>Rhetorical device? Cheap trick? Could you be a tad more insulting?

Larry replied:

>>No, I think that did the trick. Could you try being a bit more honest?

So I said:

>My, so now I am dishonest? We've only had two or three exchanges
>and you've already launched some serious ad hominems.

Larry admits:

>Yep, and there's more in this posting.

Nice guy that Larry.

>I think that you are deliberately pretending to "do science" when what
>you are actually doing is promoting religion.

Of course you do. It's obvious to me that you are enslaved by this
stereotype. It's quite a pity though. You might find the world of people
a more interesting place if you let others simply be themselves.

>I don't have a problem with religion but I do have a problem
>with hypocrisy.

This is good. I'm now a dishonest, lying, hypocrite. Hmmm. I'll bet
that's not a novel way for Larry to look at those who don't agree with
him on these issues. ;)

>Here's another example of hypocrisy,

...in Larry's mind.

>Now I assume you mean "absence of evidence" for a Darwinian origin
>to DNA replication. Well, yes, this is *also* true. But there is no
>conversion going on. Absence of evidence for a Darwinian origin
>simply means I have no good reason to think a Darwinian origin is part
>of the true explanation. I then simply approach the topic differently
>and explore a concept so that it is subject to scientific analysis. At the
>very least, it is fun! Then I look over at you and see you struggling to
>come up with even a just-so story. I see folks getting emotional and
>wanting to talk instead about invisible pink unicorns. Etc. One
>example of this strangeness may not be all that significant, but if the
>same dynamic holds in the analysis of system after system after
>system (even allowing for some vague just-so stories), I'm going to
>start to *really* believe there is a reason for this dynamic.

Hey, I like that. ;)

[PZ Myers]

In article <5sdtku$6...@alexander.INS.CWRU.Edu>, iz...@cleveland.Freenet.Edu
(Julie Thomas) wrote:

Moran isn't the only one who is mystified, then. Let's assume you aren't
just playing word games here, and that you really concede that evolution
is not only possible, but that ic systems can evolve. You also concede that
a designer is not a *necessary* explanation for ic systems.

What is your evidence that there was an "intelligent designer"?

Your argument for a designer seems to have vanished, so I have no idea
why you brought it up in the first place.

As for your question about whether Larry could agree that replication
_could_ have been designed -- he probably could, with no problem. I know
I have no problem with the idea that there is a possibility that it
_could_ have happened. There is a huge difference between acknowledging
a possibility in the absence of evidence against it, and arguing that
it *did* happen in the absence of evidence for it. You and Nyikos have
been busy doing the latter, at great length.

[Julie Thomas]

In a previous article, gac...@softdisk.com () says:

>For Ms. Thomas to refer to herself as an "evolutionist" is certainly an
>unconventional use of the word. It usually implies acceptance of the
>notion of "common descent". But she has stated that she does not accept

>that eukaryotes and prokaryotes share a common ancestor.

But what if I believed that gene frequencies change in populations
over time? Most biology texts define evolution in this way.

In fact, what if I go much further than this and believe that while
bacteria and eucaryotes do not share a common ancestor, all bacteria
do share a common ancestor?

[Julie Thomas]

[I've previously posted a long reply to Larry's critique of my discussion
of the origin of replication in bacteria and IC. But I'd like to add a few
more things. However, I should mention that it continues to fascinate
me that so many of my critics (and some are getting just plain mean)
labor under this notion that I am out to prove evolution couldn't happen
(or even that I think evolution couldn't happen). But as I have made
clear several times, this is not the case. Once again, I am of the opinion
that people can look at the same data and see something entirely
different. When I see IC, I see design as the best explanation. Thus, the
purpose of my articles is to clarify to others, and myself, how science
can be viewed and conducted under a design paradigm. Not
surprisingly, however, this tends to upset some people.]

Metazoans and Origin of Replications

Larry said:

>DNA replication in eukaryotes need not even occur at a specific site. In
>other words there may not be an origin. This is particularly true of
>multicellular animals when DNA is dividing rapidly. In such cases
>initiation occurs randomly at many sites on the chromosome
>(DePamphilis, 1993). These examples demonstrate that an origin of
>replication is not an absolute requirement for DNA replication in all
>cases.

This is all true, but I'm afraid that Larry gives the false impression that
metazoans lack origins. In the paper cited by Larry, the author
summarizes some nice work done on the dihydrofolate reductase gene
locus from Chinese hamster ovary. This has led to the identification of a
specific site, 500-2000 bp in size, that appears to be involved in the
initiation of DNA replication. The site is called the origin of bidirectional
replication (OBR). Yet, as Larry notes, when cells are rapidly dividing,
the initiation of DNA replication appears to occur at random sites.
DePamphilis reconciles these two seemingly contradictory lines of
evidence with a model that suggests there are many initiation sites in
metazoan DNA but chromosome structure typically suppresses their
activity and facilitates the OBR.

Up to this point, there is not much cause for us to disagree. But Larry
then proceeds to interpret this data in two ways.

>In other words origins are not IC components in some cells.

I admit that this is what the metazoan data suggests. However, given
that origins are IC in so many other creatures (bacteria, yeast, slime
mold, protozoans), we have to ask two very relevant questions:

1. Why is this?

Why is it that metazoan cells that divide rapidly do not seem to need
origins (when it appears single-celled organisms need them)?
DePamphilis notes that such promiscuous selection of initiation sites
seem to be specific to embryos undergoing rapid cleavage. This, IMO,
is quite relevant as the cells of such embryos are usually packed with
proteins and mRNA that make transcription unnecessary for the first
few rounds of cell division. Thus, these cells probably don't use specific
origins because the chromosomal structure of these cells, along with a
higher concentration of proteins used to replicate DNA, bypasses this
requirement. In other words, the rapidly dividing embryonic cells of
certain metazoans may reflect specialization. This then takes us to the
next question:

2. Is this relevant to the historical origin of DNA replication? Larry
thinks it is as he claims:

>The non-origin examples suggest that primitive DNA replication
>systems could have managed without a specific origin.

I will credit Larry for positing this in a tentative fashion. However, I
find it is be weakly suggestive at best. That rapidly dividing cells from
metazoan embryos get by without origins doesn't seem to be good
reason to think a primitive unicellular creature could pull off the same
feat. There is no reason to think such a primitive cell would reflect the
intracellular conditions of a metazoan egg (or embryonic cell) that are
responsible for promiscuous initiation. Thus, in considering the origin of
DNA replication, I still fail to see the evidence that clearly shows an
origin of replication sequence was not needed.

Was I mistakenly restricting myself to the E. coli origin?

Larry said:

>She is making the common error of assuming that E. coli is the
>paradigm for all bacteria but in this case the E. coli oriC is the
>exception. We should avoid the impression that the organization of this
>region is highly structured. Julie is describing systemic IC (E. coli) but
>implying that it is thematic (all bacteria).

I have already shown that I was not making this "common error" but
was instead relying on two of the papers cited by Larry that make
comparative analyses including the pseudomonads and B. subtilis. Had
I been describing E. coli, I would have included the GATC sites that are
part of the E. coli origin and are methylated. But this *is* a feature that
(so far) seems to be restricted to E. coli.

Are there AT rich sequences near/in the origin?

Larry claimed:

>In most species of bacteria there are no obvious AT-rich sequences. It
>is rare to find direct AT-rich repeats such as those at the E. coli origin
>so we can safely assume that the E. coli sequence is derived and does
>not represent the primitive origin organization.

I originally identified the origin to include AT-rich repeats. I was
relying on Smith, D.W., Yee, T.W., Baird, C. and Krishnapillai, V. (1991)

Pseudomonad replication origins: a paradigm for bacterial origins?
Molec. Microbiol. 5, 2581-2587.

In this article, the authors compared the origins from E. coli, two

Pseudomonads, and B. subtilis (the latter is very distantly related to the
former two). They conclude:

"Comparisons between these three classes of bacterial origins indicate
that the fundamental features of a primary bacterial origin are as
follows: (i) at least four 9-mer DnaA-binding sites are present; (ii) two
of these (R1 and R4) are separated by close to 180 bp; (iii) these two are
inverted repeats; (iv) two or more additional 9-mer DnaA sites are
present between the R1 and R4 sites; and (v) three 13bp to 16 bp AT-
rich direct repeats are found adjacent to the R1 site but not within the
R1-R4 region."

But I also added:

"Perhaps a better way of describing the origin is that the DnaA boxes are found in AT-rich regions. A comparison with E.coli, the
pseudomonads, and B. subtilis shows a 50-60 bp region adjacent to
DnaAboxes that is 72-82% AT (Yoshikawa and Ogasawara, 1991)."

To further support this claim, in another paper cited by Larry, the
mycobacterial origins are also adjacent to an AT rich region:

"In the region just downstream of dnaA, the 165 bp segment that
contains the seven DnaA boxes is bounded by AT-rich regions and, by
analogy with the replication origins of other bacteria, the binding of
DnaA protein to these DnaA boxes would lead to DNA strand separation
and formation of the primosome in the 45bp AT-rich region just
downstream, which is probably the site at which chromosomal
replication initiates."

[Salazar, L. et al. (1996) Organization of the origins of replication of the
chromosomes of Mycobacterium smegmatis, Mycobacterium leprae and
Mycobacterium tuberculosis and isolation of a functional origin from
M. smegmatis. Molec. Microbiol. 20, 283-293.]

Deviating from the consensus?

Larry said:

>Let's look at the sequence of DnaA boxes. I apologize for belaboring this
>point but Julie seems to think that this is a very important issue. I'll
>quote from her essay later on to show you where we disagree.(p10).
>There are five DnaA boxes at the oriC of enteric bacteria - species that
>include E. coli and its relatives. The boxes are named R1-R5 and six
>different species have been examined. In the list below I will use
>upper case letters (i.e. T) when the nucleotide in all six species is the
>same and lower case letters (i.e. t) when there are differences.
> R1 TTATCCACA
> R2 TTATaCACA
> R3 TTATCCaAA
> R4 TTATCCACA
> R5 TCATTCACA

>This is fairly typical of DNA binding sites. The protein binds to a set of
>similar sequences that conform to a consensus - in this case the
>consensus sequence is TTATCCACA which is the sequence Julie refers to
>in her essay. Note that it is not necessary that every nucleotide
>conform to the consensus in order to achieve binding.

I replied:

"Yes, but note also how tight the consensus is. Furthermore, this
interpretation would be stronger if all bacteria had only one DnaA box.
Multiple boxes translate as redundancy which in turn translates as
more tolerance for variation in individual boxes."

I should also point out that there is evidence to support this
interpretation. In the mycobacteria paper cited above, the authors note:

"It has been shown, however, that B. subtilis DnaA protein will bind to
DnaA boxes that differ from the consensus at two positions only when
they are located adjacent to a consensus sequence."

This is an important point to keep in mind when talking about
sloppiness. After all, DnaA bends DNA when bound and this
conformational change, coupled with DnaA-DnaA protein interactions
after binding, suggests once a primary DnaA box is bound with a DnaA
monomer, it can then nucleate a complex that, in turn, is able to bind
DnaA boxes with relaxed sequence.

Larry also said:

>Messer and Weigel (1997) review the extensive literature data on
>DnaA binding. Adding in other DnaA binding sites and studies of DnaA
>binding in vitro yields a stringent consensus binding site of
>TT(A/T)TNCACA where (A/T) means that either A or T will work at
>that position and "N" means that any base pair will do.

I replied:

"And this supports my point as I never said the 9-mer was invariant.
I said it showed "strong sequence conservation" and built from there."

After looking at the paper that defines this consensus (Shaper, S. and
Messer, W. 1995. Interaction of the initiator protein DnaA of
Escherichia coli with its DNA target. JBC 270: 17622-17626), I am quite
satisfied. These investigators used DNA fragments containing single
DnaA boxes and determined this consensus. However, there are some
very interesting results not mentioned by Larry.

1. Slight deviation from consensus results in a dramatic loss in specific
binding so that binding becomes essentially non-specific. Three
examples stand out. Recall the consensus I cited: TTATCCACA.
However, when the sequence is altered by one nucleotide, as in
TTATCCAAA, TCATTCACA, and TTTTCCACA, all specific binding is lost.
Specific binding was measured with gel shift assays and the authors
show the results of two of these variants - you can't even see a shifted
band! (all the DnaA protein is bound up in a nonspecific competitor).

2. It appears that the R1 and R4 boxes, separately, along with 6 bp of
naturally flanking sequence on each side, bound the DNA with an
affinity that was only two-fold lower than seen when the entire oriC
segment was used. This further underscores my point about reading
too much sloppiness into the DnaA box sequences as other DnaA boxes
may play secondary roles that depend on the tight interactions with the
one or two primary DnaA boxes.

3. The investigators also showed that the DnaA binds specifically only
to double-stranded DNA. In fact, they replaced the thymines in the R4
sequence with (deoxy)uracil (TTATCCACA -> UUAUCCACA) on one
strand and found no specific binding. Thus, DnaA doesn't specifically
bind to the consensus when it is represented as a DNA/RNA hybrid
(which will probably become relevant later).

Of course, it will be very interesting to conduct similar studies with
DnaA boxes/DnaA from other bacteria, but these results do tend to
support my contention about the importance of this consensus.

However, Larry also added:

>There is good evidence that the real binding sequence is even more
>relaxed - T(T/C)(A/T)T(A/C)CA(C/A)A.

The good evidence in this case stems from Dnase I footprinting studies,
but I don't think that constitutes good evidence. High concentrations of
loosely bound proteins can provide the same footprint as low
concentrations of tightly bound protein. This is because a loosely bound
protein can interfere with Dnase I activity in a way that is
indistinsguishable from a tightly bound protein. A better measure of
binding, IMO, is the gel shift data. And this relaxed consensus was not
seen under those conditions.

Larry says:

>If you delete one of the sites or completely scramble the sequence then
>the origin doesn't work as well as the wild type oriC. In mycobacteria
>(Mycobacterium smegmatis, M. leprae, M. tuberculosis) the consensus
>binding site is (C/T)T(A/G)TCC(A/C)CA (Salazar et. al., 1996). This is
>significantly different from the consensus sequence of the site in
>enteric bacteria.

I think I know why Larry thinks this is so significantly different.

In the mycobacteria, there are up to 10 putative Dna boxes (maybe more).
The authors identify 3 that are upstream of the DnaA gene and
7 downstream of the gene. The sequence from three species
(Mycobacterium smegmatis, M. leprae, M. tuberculosis) was also aligned.
Thus, if you were to compare the 1st DnaA box of all three species, for
example, the DnaA boxes would indeed look like sloppy versions of
TTATCCACA (and of each other):

M. smeg: ATGTGCAGA
M. tub: CTGTGCACA
M. lep: CTGTGGACA

But what is relevant to this design theorist is not to compare sequences
found in homologous positions, but that each species has at least two
DnaA boxes that conform nicely to the E. coli consensus (TTATCCACA):

M smeg

Box 8 2
Seq. TTCTCCACA CTCTCCACA
Conf to consensus (8/9) (7/9)

M. tub

Box 5 8
Seq TCATCCACA CTGTCCACA
Conf to consensus (8/9) (7/9)

M .lep.

Box 8 6
Seq. CTGTCCACA TTATCCACA
Conf. to consensus (7/9) (9/9)

Notice that box 6 in M. lep conforms *perfectly* to the E. coli consensus.
Box 5 in M. tub differs by one nucleotide (T->C at position 2). And box 8
in M. smeg likewise differs by only nucleotide (A->C at position 3). The
remaining boxes all differ by two nucleotides and all are restricted to
the three nucleotides at the 5' end. This would give us a consensus
sequence of YY(A/G/C)TTCACA (Y=pyrimidine). And if we considered
only the individual boxes with the strongest conservation, the consensus
sequence would be TY(A/C)TCCACA.

What interests me most, however, is how IC has enabled me to view
this data differently so that I notice something missed by Larry and the
authors of this paper - the fact the M. lep has a sequence that perfectly
matches TTATCCACA. The authors seem to overlook this because they
are more interested in boiling the 6th box down to a consensus
sequence (and the 6th box in the other two species deviates by two and
three nucs). The same reason also seems to explain why they don't pay
much attention to the box sequence that varies by only one nucleotide.
This would also enable me to predict that homologous DnaA boxes in
different species are not similarly important.

As a design theorist employing IC, I would propose that at least two
DnaA boxes are needed in the origin that conform closely to the
TTATCCACA consensus sequence from E. coli (and seen in several other
species). These I would term the primary DnaA boxes (analogous to R1
and R4 in E. coli). Secondary DnaA boxes may also be needed, but their
number and sequence deviation can vary. I would predict that the two
sites from each species identified above constitute such primary boxes
and knockout experiments and gel shift analyses could support this
hypothesis. In contrast, I don't see anything in Larry's "sloppy
interaction" hypothesis that would lead to this prediction.

Of course, I can imagine the knee-jerk responses these claims will elicit
on this board. Yet, through all the rhetoric, it is merely my simple hope
that some open-minded readers will catch a glimpse of how we can
indeed see things differently (and thus focus differently) and such
diversity of perception may actually help us to better scientifically
understand our world than attempts to force all the data into one
monolithic viewpoint.

[PZ Myers]

In article <5sdu5e$9...@alexander.INS.CWRU.Edu>, iz...@cleveland.Freenet.Edu
(Julie Thomas) wrote:

> [I've previously posted a long reply to Larry's critique of my discussion
> of the origin of replication in bacteria and IC. But I'd like to add a few
> more things. However, I should mention that it continues to fascinate
> me that so many of my critics (and some are getting just plain mean)

Name some of these "mean" guys. I've seen nothing but respect for your
efforts, while many have deplored your misinterpretations. If you want to
see mean, look at how your pal Nyikos talks about just about everyone in
this newsgroup. Do you really think you have had even a fraction of that
malice directed at you?

> labor under this notion that I am out to prove evolution couldn't happen
> (or even that I think evolution couldn't happen). But as I have made
> clear several times, this is not the case. Once again, I am of the opinion
> that people can look at the same data and see something entirely
> different. When I see IC, I see design as the best explanation. Thus, the
> purpose of my articles is to clarify to others, and myself, how science
> can be viewed and conducted under a design paradigm. Not
> surprisingly, however, this tends to upset some people.]

This is a bit of rhetoric -- blaming the fact of opposition on an emotional
response, that those who disagree are "upset". This is not the case. You
have received a number of calm and rational replies that disagree strongly
with you. This is not a matter of being "upset".

There is opposition to this nonsense because you have not presented a
scrap of evidence for your "design paradigm". You have not presented
support for the idea, but I had thought that your ic arguments were an
attempt to show that natural mechanisms were incapable of explaining
certain phenomena, so that "design" was a viable explanation by default.
Now you claim this is not the case -- ic systems *can* evolve.

So far, then, "design" looks like wishful thinking with no evidence.
That's not science.
[snip]

[John Mazor]

To Julie Thomas:

Let me say up front that the discussions of cellular structures, chemistry,
etc. are well over my head. I cannot begin to assess the validity of the
arguments of you or your critics in this area.

However, I cannot help but notice a few irritating patterns I see in your
postings.

First, you spend a lot of time trying to defend a claim that your various
assertions, theories, etc. are proposed here merely in some spirit of
disinterested, scientific inquiry. Quite frankly, I don't give a damn
whether you offer these as an amusing exercise in scientific method or a
religious crusade. Your arguments stand or fall on their merits.

Second, despite careful reading of various threads, I'm still not sure
what, if anything you A.) Believe, and B.) Admit to believing, which in
this instance is not a trivial difference. I'm not trying to be cute here.
At various times you seem to be saying:

1. "I'm not claiming that I'm right, only that you (are) (may be)
wrong."
and elsewhere,
2. "I'm not claiming that you're wrong, only that I (am) (may be)
right."

You really do play word games, and that diminishes your credibility. E.g.,

> I am mystified by Larry's insistence that I am making the case that
> DNA replication "could not have evolved." Apparently, Larry confuses
> the fact that I *do* not think DNA replication evolved means I think it
> "could not" have evolved. But that's sloppy thinking. For example, if
> someone does not think there was life on Mars it doesn't mean they
> think life could not have existed on Mars. Those are two very different
> claims.

Other than in an obscure theoretical sense, what difference does it make if
you "think evolution could have evolved but it didn't" vs. "think evolution
couldn't have evolved"? Either way, you would put a stake through the
heart of evolution theory. The murder victim doesn't much care whether it
was a knife or a gun that done him in. You, on the other hand, spend an
inordinate amount of time trying to catch your critics on minor points like
the above.

> Furthermore, just because I do not think DNA replication
> evolved does not mean I think DNA replication *must* have been
> designed.

More word games. Okay, I give up. If DNA replication didn't evolve and it
wasn't the product of design, what is the other possibility? Random
instantaneous creation? And how does one test for that (or for design)?

> Of course, it is possible that Larry may be projecting his attitudes upon

> me

You seem to use that accusation a lot. Need I spell out the implications
of that thought?

Having now spent even more time re-reading your posts (including your
rejoinders to Moran's attempts to summarize your views), let me see if I
have it right:

1. Julie *thinks* evolution can't explain certain IC systems, although she
dutifully admits that she may be wrong and will change this view if anyone
presents convincing proof otherwise.

2. She *thinks* design is the best explanation for these same IC
phenomena, although although she dutifully admits that she may be wrong and
will change this view if anyone presents convincing proof otherwise.

3. She *thinks* that design is the result of a designer, although she
dutifully admits that she may be wrong and will change this view if anyone
presents convincing proof otherwise. (N.B. - Yes, I'm taking the liberty
in these first three items of equating her statements such as "implies,"
"suggests," etc. with "Julie thinks that." Please don't bother pointing
out any hairsplitting differences between the two.)

4. None of the above statements is meant to categorically rule out any
competing hypothesis (and although it is only by implication, I presume she
dutifully admits that she may be wrong and will change this view if anyone
presents convincing proof otherwise).

5. The assertions made in this NG do not necessarily reflect the *beliefs*
of Julie Thomas (although I do not recall seeing any statement explicitly
*affirming* that she does not believe in any of them, and if it's pointed
out where I'm wrong, I will cheerfully change my belief on her beliefs).

6. The net result of items 1-5 is that arguing with Julie is like trying
to nail Jell-o to the wall, but okay, some of us will deal with that as
best we can. (Others will interpret 1-5 as a lack of commitment on Julie's
part to her various assertions and dismiss her, but she'll have to deal
with that as best she can.)

Okay, we all understand now that your assertions are offered in the true
scientific spirit, and that you claim to hold no special attachment to
them. Fine. Now stop spending so much time on trivial points and focus on
more substantive items, lest we get the impression that you're more
interested in verbal sparring and dodging the issues. (And please, no
whining that "he started it.")

[John Mazor]

Julie Thomas <iz...@cleveland.Freenet.Edu> wrote in article
<5se2ff$l...@alexander.INS.CWRU.Edu>...

More cutesy word games and verbal judo. Answer the (implied) question.

[George Acton]

Julie Thomas wrote:
>
> In a previous article, hi...@cgl.ucsf.EDU (Wade Hines) says:
>
>
> The article that Wade cites was one of the first indications that E. coli
> has an alternative system of DNA replication. This system is fairly well-
> understood and is called constitutive stable DNA replication (cSDR). It is
> a system that is normally repressed but can be activated under extreme
> conditions. It shares many of the actual players used by the oriC
> system, but also shows some significant differences. But does it help us
> explain the origin of the irreducibly complex oriC system? Unlikely.
> Does it damage my case about IC and bacterial chromsosomal DNA
> replication? I don't think so. Here are some of my reasons.
>
You're just playing definitional games. If a "system" is something that
carries out a physiological function, the "system for initiating DNA
replication" clearly isn't "irreducibly complex", since it has a backup
sustem and doesn't meet Behe's definition for irreducible complexity.
Only if you arbitrarily modify the conditions by adding the proviso
"but not under conditions of stress" does it become "IC". And that
depends on what is "stress", which might well have been the standard
conditions at one time. It appears to be a pathetically ad hoc way
of getting the desired result. And it conceptually infects the whole
argument about replication, since if the "initiation" subsystem isn't
"IC", the whole "replication" system can't be IC, according to Behe.
Of course Behe doesn't take the definition any more seriously than
you do. In an interview he went off about how each and every factor
of the clotting system is itself "irreducibly complex", which is
totally incoherent with his repeated verbal formula, the mousetrap
claptrap, etc.
Although you claimed not to have read his book, you appear to be
defending his concept of "IC", without coming up with a definition
that makes any more sense than his.
--George Acton

[Wade Hines]

iz...@cleveland.Freenet.Edu (Julie Thomas) writes:

>I am mystified by Larry's insistence that I am making the case that
>DNA replication "could not have evolved." Apparently, Larry confuses
>the fact that I *do* not think DNA replication evolved means I think it
>"could not" have evolved. But that's sloppy thinking. For example, if
>someone does not think there was life on Mars it doesn't mean they
>think life could not have existed on Mars. Those are two very different
>claims. Furthermore, just because I do not think DNA replication
>evolved does not mean I think DNA replication *must* have been
>designed.

>Larry's confusion appears to stem (IMHO) from a desire to attribute
>certainty to my beliefs. This could be due to his belief that he knows
>me better than I know myself.

I think there are far better explainations.
1.) Julie has not been clear.
2.) Julie is currently allied with Behe who is quite clear
about his religous bias. Maybe it's 'guilt' by association.
Be it known, that there's nothing to be ashamed of.
3.) Julie writes things between the lines that Larry is quite
capable of reading, but don't lend themselves to recapitulation.

Mostly, I stick with number 1.

But let's look back at this new revelation of Julies.
She may be saying that she thinks DNA replication could have
evolved, but didn't. She isn't being very clear about why she
thinks it could have evovled or what 'could have' evolved means.
Maybe she's holding out for some one is a google line like
her mentor. This could all be cleared up so easily if Julie would
choose to be clear and forthright in her response.

Dna replication is:
a.) quite easily evolvable but it was designed first.
b.) no so easy, but given a half a billion years, could well have evolved.
c.) may have evovled in a much simpler system, but what we see now
is the product of 3 1/2 billion years of refinement of a very
critical system.
d.) probably more subject to horizontal transfer than any other
system so the record is just to muddled to sort out. Simply don't know.
e.) hard to imagine evolving as doing so seems quite implossible.

That covers quite a range but I'm sure doesn't capture your beliefs.
Why don't you be clear. You could do it in far less bandwidth than
is required for you to dance around Larry.

>Of course, it is possible that Larry may be projecting his attitudes upon
>me (projection is a common phenomenon with people who think they
>know a person (or a group) better than the person or group know
>themselves).

That may be. It is also common when a void is left by one who plays
so coy with their position that one can only guess.

> That is, perhaps he is the one who believes "design could
>not have occurred thus the evolution of DNA replication must have
>occurred" and thus attributes this type of logic to me.

Oh no. I'll assure you that this isn't Larry's belief. I'll wager
heavily that Larry can say that could have been designed is an
open possibility that is effectively impossible to rule out.

I'll also suppose that he has a bias toward evolved based on the
fact that it could be ruled out and yet the data seem to fit it
so much more closely.

It's the difference between a tight fit and a loose fit Julie.
Was designed to be how it is, is a loose fit. Exceedingly loose
as there's no real way to not fit. But that's not at all like
could not have been designed.

I really do wonder where you get such an opinion from. I've
not seen it around here.

>After all, it
>explains (to me) why it seems he is readily convinced by evidence for his
>views that is weakly suggestive at best.

This last characterization is one subjective opinion, at best. It's also
predicated on some very dubious reasoning suggesting that Larry thinks
replication could not have been designed. The evidence for that, is
so weak as to not even come close to being suggestive, in my opinion.

>Furthermore, I can easily say
>that DNA replication could have very well evolved. It doesn't make
>much difference in the scheme of things to me. Can Larry as easily say
>that DNA replication could have very well been designed? Would it
>make a difference in the scheme of things for him?

I'll wait to see if Larry responds. Meanwhile, what does Julie say
as opposed to what she could say.

Can we go with "weakly suggestive" with an "at best" qualifier to
say you see some weakly suggestive evidence that DNA replication
evolved but that the evidence is subject to alternative explainations
that make you reluctant to hang your hat on the suggestiveness
of the evidence? That wording is so awkward. Why don't you clean
it up with what you should say, rather than dance about what you
might say.

[Mark Isaak]

In article <5se2ff$l...@alexander.INS.CWRU.Edu>,

Julie Thomas <iz...@cleveland.Freenet.Edu> wrote:
>In a previous article, m...@panix.com (Michael L. Siemon) says:
>
>>I said that Julie has no justification (she has certainly *given*
>>none) for her rejection of evolutionary explanations.
>
>What an odd way of seeing things. I need justification for not thinking
>bacterial DNA replication and/or flagella evolved? Michael has it
>backwards. If he thinks I am obligated to believe such things, he
>should at least try to convince me.

Michael Siemon did not say you have no justification and need one; he said
you have no justification. To all appearances, he is right.

Please limit your arguing to what people actually say. Your posts are
wordy enough as it is.
--
Mark Isaak at...@best.com http://www.best.com/~atta
"To undeceive men is to offend them." - Queen Christina of Sweden

[Matt Silberstein]

In talk.origins iz...@cleveland.Freenet.Edu (Julie Thomas) wrote:

>
[snip]

> Experience has taught me that IC
>entities typically have designers.

This line may be the heart of the whole issue. Could you expand a bit
on what leads you to this? For instance, it is certainly not true that
all human designed systems are IC. I have no idea what "percentage" of
human designed systems are IC, I would not even know how to estimate
this number. But I can certainly come up with innumerable non-IC human
designed systems. So what else do you mean? You certainly can't be
arguing that all undesigned systems are non-IC? How would you go about
showing this. The very systems under discussion have there "designed"
nature disputed. So, from experience we know that there are non-IC
systems which are human designed and non-IC systems which are not
"human designed". Whether these non-IC systems are "not human"
designed we don't know. Then we have human designed IC systems and
disputed systems. It can't make any rule with this experience.

>Thus, I find intelligence to be the best
>explanation when it comes to IC. Of course, if there is powerful
>evidence to the contrary, I can abandon intelligent causation as the best
>explanation in the case under question.
>

What is the "powerful evidence" that tells you that intelligence is
the best explanation?

>>Why don't you come out of the closet and tell us about your intelligent
>>design model?
>
>I already have. I suspect you were not paying attention because you
>were preoccupied with what you think is "obvious."
>
>>You seem to think that if you can cast doubt on evolution
>>then this is support for your model but how are we to know if you
>>won't tell us about it?
>
>Since intelligence is easily capable of generating IC systems, and IC
>systems are known to have been generated by intelligence, I find
>intelligence to be the best explanation in the case of IC.

But intelligence is easily capable of generating non-IC systems as
well. Doesn't this show that intelligence was behind the non-IC
biological systems as well?

[snip]

>If you want a summary, it is:
>
>In my opinion, there are several IC systems which lack convincing
>evidence of Darwin's mode of transformation, and in fact, appear
>unlikely to have originated in this way. When this is coupled with my
>common experience where IC is tied to intelligent design (intelligence
>easily generates IC and IC usually stems from intelligence), I find
>intelligent design to be the best explanation for the IC systems in
>question. Thus, I seek to explore the natural world from the
>perspective of a design paradigm and invite others, hopefully with open
>minds, to look on and enjoy.
>

Again, that parenthetical remark seems to assume the conclusion. If we
assume that IC usually stems from intelligence, then an IC system
implies intelligence. If you don't have any support for that
assumption then you have no argument. And since that assumption is the
very question at hand, you can't use the same evidence that is under
discussion to support your assumption.

[snip]

Matt Silberstein
----------------------------------------------

CAUCHON. And you, and not the Church, are to be the judge?

JOAN. What other judgment can I judge by but my own?

_Saint Joan_ by GBS, Scene VI

[Wade Hines]

iz...@cleveland.Freenet.Edu (Julie Thomas) writes:
>In a previous article, hi...@cgl.ucsf.EDU (Wade Hines) says:

>Wade asked:

>>And I can't recall if you've commented on

>> de Massy B; Fayet O; Kogoma T.
>> Multiple origin usage for DNA replication in sdrA(rnh) mutants of
>> Escherichia coli K-12. Initiation in the absence of oriC.
>> Journal of Molecular Biology, 1984 Sep 15, 178(2):227-36.

>>Not only does replication work in the absense of oriC, it appeared
>>to work from 4 different alternative sites.

>Wade has left out a lot of relevant material as far as this system relates
>to the oriC system and its IC role.

Excuse me for interrupting. I wrote a relatively short sentence which
detailed exactly what was relevent to IC. This is why we asked for
definitions before. Definitions of parts and systems and functions.

You defined OriC as a part of the system of DNA replication with
the function of replicating DNA and the specific function of OriC
as the origin of replication.

The definition of IC states that if one can remove any part
and still have function, the system is not IC. Thus, if removing
the part OriC does not stop function - replication of DNA - then
DNA replication is not IC. But I see below that you bring up
"thematic IC" again. Let's here you out, even if I made the
only point from the paper that seem relevent to IC as Behe and
his local advocate Peter define it.

>Let's see if this paper is indeed
>relevant to my article (although I will be brief for lack of time).
<<< thanks for being brief. i tried to be >>>

>The article that Wade cites was one of the first indications that E. coli
>has an alternative system of DNA replication. This system is fairly well-
>understood and is called constitutive stable DNA replication (cSDR). It is
>a system that is normally repressed but can be activated under extreme
>conditions. It shares many of the actual players used by the oriC
>system, but also shows some significant differences. But does it help us
>explain the origin of the irreducibly complex oriC system?

I'm confused again. Two different systems. Same function. Some shared
players. I know something about DNA replication but can't quite handle
all the taxonomy of assigning system and part definitions. It seems
so arbitrary to me. Maybe that's why a dummy like me needs some
better definitions.

>Unlikely.
>Does it damage my case about IC and bacterial chromsosomal DNA
>replication? I don't think so. Here are some of my reasons.

>1. First, even the cSDR system employ specific origins (called oriK).
>Thus, it doesn't damage my thematic IC claims about the need for
>an origin.

When parts become generics, the notion of IC, now called 'thematic IC'
looses even the illusion of significance.

>2. The cSDR system does not employ DnaA. But I never claimed that
>DnaA is part of purely thematic IC, only a factor (acting in trans) that
>interacts with the origin to initiate replication.

Maybe you should explain your lingo to Peter who may want to defend you.
"acting in trans" is a rather essoteric genetics notion which
differentiates gene products from gene sites. Gene sites are places
where the functional activity is the DNA itself, a recognition sequence
or motif. Trans acting factors are most commonly proteins but can
also be RNA. This bit of obscura however barely seems relevent and
I'm frankly at a loss as to why you mention the trans acting part
at all.

>And cSDR has such a
>factor - RecA. OriC replication does not need RecA. Thus, here is yet
>another example of something I talked about in my article - a different
>system is not necessarily simpler (and thus less IC).

This is where people get so confused by you Julie. You seem to be
conflating simpler and IC. Let's use the whole words. You seem to
be conflating simpler and Irreducibly Complex. You can't just parse
this into two words and it's the irreducibly part that is being
addressed, not the complex part.

So what we have in a cartoonish sketch is some DNA replication
machinery that has in one part a site on the DNA which can be bound
by a protein in such a way that the remainder of the DNA replication
machinary can get in there and do the dirty deed. The fact is that
there are multiple DNA binding proteins. Proteins which also have
the abilility to bind co-operatively are likewise quite common.
These don't appear to be terribly rare functions and so are not
that unlikely to have evolved. The fact that the remainder of the
DNA replication machinary can work off different origination
complexes makes this a very reducible system, if still a complex
one.

Complexity does tend to create the illusion of unlikely to have
evolved but I'm sure Julie will acknowledge the problem with such
a simple minded conclusion.

>3. From a systematic IC perspective, oriK/RecA are able to complement
>OriC/DnaA activity. But is this relevant? Recall that in my essay,
>complementation by itself is not sufficient.

Is this another component of the ad hoc definition of 'thematic IC'
or was there some special logic behind this that did not completely
immasculate the concept of IC regarding the appearance of needing
a designer. The availability of subsystems for recruitment into
more complex systems goes directly toward the essence of the
IC arguement about 'difficult to imagine having evolved'.

>And in this case, there are
>several significant facts which cause me to doubt the significance of the
>oriK/RecA system when it comes to the origin of the IC oriC/DnaA
>system:

>a. The oriK/RecA system was identified not in wild-type cells, but in
>mutant cells lacking RNase H activity (which, BTW, don't grow in rich
>media). RNase H is a nuclease that degrades ssRNA when it is bound to
>ssDNA. If cSDR was the original replication system, one needs to
>explain away RNase H activity which itself appears to be quite ancient.

There is little reason to suppose that either currently observed system
was the original given so many many billions of generations with
which to optimize, but this is rather obvious.

Even if one supposes a 'much more like' cSDR system billions of
years ago, one wouldn't expect the retention of all factors required
to allow this putative ancestor to function in a world where it
is no longer the mainstay. This is also rather obvious.

At the top of this post, you suggested I left out many details
of relevance. I saw no need to set up the straw men you are setting
up just so I could know them down.

>b. The oriK/RecA may well be more recent. So far, this system has only
>been identified in E. coli, in contrast to the oriC system which has been
>seen in several distantly related species.

>c. As a continuation of point b., the oriK/RecA system may serve as a
>back-up system that only functions sufficiently as a short-term solution.
>This hypothesis is supported by the fact that the oriC system is so
>strongly conserved. If the oriK system could effectively replace the oriC
>system as a long-term, or even, primary system, we would expect to see
>many species of bacteria using this system as their primary system.

Firstly, let's clear up that there was no claim about oriK as the
original system. Rather the claim is that an alternative site of
the origin of replication works with the rest of the DNA replication
machinary. This makes oriC and DNA replication non-IC by the
definition put forth by Behe and as advocated by Nyikos. Other,
weaker definitions of IC such as that put forth by Julie have
been repeatedly criticized as being 'strawman IC' definitions
as they are so easily derived or identified in systems where
evolution is strongly evidenced.

My second point will be made in a pointed extraction retitled
"Julie: when did it evolve?"

>4. Of course, even if cSDR represents the original method of bacterial
>chromosome replication, it doesn't do anything but change the actual
>players in the IC system. Instead of oriC, we have oriK. Instead of
>DnaA, we have RecA. What's more, the oriK system appears to involve a
>far more complex method of priming involving all the factors in the
>primosome (priA, DnaT, etc.) which, contrary to my original article, don't
>seem to be needed by the oriC system. So it would be like jumping out
>of the frying pan and into the fire.

Despite the touching use of colloquialisms, it's more like a death
knell for those who would use IC as an arguement against evolutionary
origins. We have evidence of modularity to these IC systems where
wholesale substitution of one subsystem with another retains the
overall function --- in this case DNA replication. Thus we don't
have to justify a system of two dozen players springin forth fully
formed as athena from the head of zeus. We get subsystems with
indepent functions learning how to co-operate in a synergistic
fashion. Excuse the anthropomorphic usage of 'learning'. I hope
it doesn't confuse anyone.

[Doug Quarnstrom]

Julie Thomas (iz...@cleveland.Freenet.Edu) wrote:

: clear several times, this is not the case. Once again, I am of the opinion

: that people can look at the same data and see something entirely
: different.

This statement is too obvious to deny. This does not mean that multiple
explanations are plausible.

:When I see IC, I see design as the best explanation. Thus, the

: purpose of my articles is to clarify to others, and myself, how science
: can be viewed and conducted under a design paradigm.

Any supernatural design paradigm is antithetical to the scientific
process, because it undermines the assumptions with which science
works. And given that the "god did it" explanation is utterly
indistinguishable from a merely unexplained natural phenomenon,
the whole "design" paradigm is utterly unproductive of meaningful
answers in the realm of science.

:Not

: surprisingly, however, this tends to upset some people.]

Not surprising, because of its general incomprehensibility to
those who seek scientific explanations of phenomena.

Now, if you can makes some comments about the natural limits
of the designer and his place in the natural universe, you
MIGHT be able to test hypothesis about the interaction
of said designer with the design. Barring that, there is
no way to distinguish between something that is a naturally
ocurring event we do not understand and an artifact that
cannot be explained through natural processes alone...

doug

[Doug Quarnstrom]

PZ Myers (my...@netaxs.com) wrote:
: As for your question about whether Larry could agree that replication

: _could_ have been designed -- he probably could, with no problem.

Obviously it COULD have, and in fact, some form likely will. Scientists
are actively trying to create new kinds of self-replicating molecules
according to scientific american.

:I know

: I have no problem with the idea that there is a possibility that it
: _could_ have happened. There is a huge difference between acknowledging
: a possibility in the absence of evidence against it, and arguing that
: it *did* happen in the absence of evidence for it. You and Nyikos have
: been busy doing the latter, at great length.

Especially given the conundrum that a current lack of explanation can
never be accepted as a good argument that a designer was necessary.

doug

[Wade Hines]

"John Mazor" <maz...@erols.com> writes:

>To Julie Thomas:

>Let me say up front that the discussions of cellular structures, chemistry,
>etc. are well over my head. I cannot begin to assess the validity of the
>arguments of you or your critics in this area.

>However, I cannot help but notice a few irritating patterns I see in your
>postings.

>First, you spend a lot of time trying to defend a claim that your various
>assertions, theories, etc. are proposed here merely in some spirit of
>disinterested, scientific inquiry. Quite frankly, I don't give a damn
>whether you offer these as an amusing exercise in scientific method or a
>religious crusade. Your arguments stand or fall on their merits.

>Second, despite careful reading of various threads, I'm still not sure
>what, if anything you A.) Believe, and B.) Admit to believing, which in
>this instance is not a trivial difference. I'm not trying to be cute here.
> At various times you seem to be saying:

> 1. "I'm not claiming that I'm right, only that you (are) (may be)
>wrong."
> and elsewhere,
> 2. "I'm not claiming that you're wrong, only that I (am) (may be)
>right."

These are both valid equivocation consistent with open mindedness.
As paraphrased. If one places strong emphasis on the "are" in each
sentence above, implying definative belief, we are simply left wtih
"I'm not sure". That would be fine if it were't contrasted by so
many examples of 'as I have shown before, ...', which together with
the claims of openmindedness present a conflict.

The conflict is not however, evident in statements 1 and 2.

>You really do play word games, and that diminishes your credibility. E.g.,

>> I am mystified by Larry's insistence that I am making the case that

>> DNA replication "could not have evolved." Apparently, Larry confuses
>> the fact that I *do* not think DNA replication evolved means I think it
>> "could not" have evolved. But that's sloppy thinking. For example, if
>> someone does not think there was life on Mars it doesn't mean they
>> think life could not have existed on Mars. Those are two very different
>> claims.

The above is a strawman and there are word games but ...

>Other than in an obscure theoretical sense, what difference does it make if
>you "think evolution could have evolved but it didn't" vs. "think evolution
>couldn't have evolved"? Either way, you would put a stake through the
>heart of evolution theory.

... this is bullshit. There are lots of things that could have
happened that you don't believe did happen. Julie is under no
obligation to believe anything did or didn't happen. Statements about
could or could not are of a different sort.

>The murder victim doesn't much care whether it
>was a knife or a gun that done him in. You, on the other hand, spend an
>inordinate amount of time trying to catch your critics on minor points like
>the above.

It may be that the murder victim may not care regardless, as caring
may be limited to those who are alive.

>> Furthermore, just because I do not think DNA replication
>> evolved does not mean I think DNA replication *must* have been
>> designed.

This is an odd statement in light of the posting where Julie
tried to show that IC was evidence for design. It frankly is
contradictory unless she is speaking purely hypothetically
right now but that hypothetical does invalidate her supposed
evidence for design. In using *must* we have some room for
rhetorical maneuvering which may be all that Julie is doing now.
I think this is your complaint but you make it weakly.

>More word games. Okay, I give up. If DNA replication didn't evolve and it
>wasn't the product of design, what is the other possibility? Random
>instantaneous creation? And how does one test for that (or for design)?

It's the player to be named later which is intentially left vague.
There's some serious 'have your cake and eat it too' going on with Julie.

>>Of course, it is possible that Larry may be projecting his attitudes upon
>> me

Rather the reverse if you look at the part of Julie's post where she
sugests that Larry thinks DNA replication could not have been
designed despite zero evidence to suggest that opinion in anyone.
Many have in fact confirmed that the design hypothesis, in its
wonderfull flexibility, fits all data unless Julie means something
far more specific aobut design than she has yet detailed.

>You seem to use that accusation a lot. Need I spell out the implications
>of that thought?

>Having now spent even more time re-reading your posts (including your
>rejoinders to Moran's attempts to summarize your views), let me see if I
>have it right:

>1. Julie *thinks* evolution can't explain certain IC systems, although she
>dutifully admits that she may be wrong and will change this view if anyone
>presents convincing proof otherwise.

>2. She *thinks* design is the best explanation for these same IC
>phenomena, although although she dutifully admits that she may be wrong and
>will change this view if anyone presents convincing proof otherwise.

I'm curious as to whether is this is the case or if Julie's just having
a vit of fun with a novel way of looking at things.(and exposing those
who think they know more than they do).

>3. She *thinks* that design is the result of a designer, although she
>dutifully admits that she may be wrong and will change this view if anyone
>presents convincing proof otherwise. (N.B. - Yes, I'm taking the liberty
>in these first three items of equating her statements such as "implies,"
>"suggests," etc. with "Julie thinks that." Please don't bother pointing
>out any hairsplitting differences between the two.)

>4. None of the above statements is meant to categorically rule out any
>competing hypothesis (and although it is only by implication, I presume she
>dutifully admits that she may be wrong and will change this view if anyone
>presents convincing proof otherwise).

The record is rather conflicting on point 4. Some dubious reasoning
regarding either/or thinking has been presented but it has at times
been wrapped in fuzz making it hard to see what Julie means.

>5. The assertions made in this NG do not necessarily reflect the *beliefs*
>of Julie Thomas (although I do not recall seeing any statement explicitly
>*affirming* that she does not believe in any of them, and if it's pointed
>out where I'm wrong, I will cheerfully change my belief on her beliefs).

I couldn't think of a much less important topic than your beliefs
of her beliefs other than my impression of the importance of your
belief on her beliefs.

>6. The net result of items 1-5 is that arguing with Julie is like trying
>to nail Jell-o to the wall, but okay, some of us will deal with that as
>best we can. (Others will interpret 1-5 as a lack of commitment on Julie's
>part to her various assertions and dismiss her, but she'll have to deal
>with that as best she can.)

I have an alternative impression which I suspect others share.
There are real flaws and dubious tactics in some of Julies posts,
but she also presents some real arguments as well which is such a
refreshing change that many will put up with the doublespeak.

>Okay, we all understand now that your assertions are offered in the true
>scientific spirit, and that you claim to hold no special attachment to
>them. Fine. Now stop spending so much time on trivial points and focus on
>more substantive items, lest we get the impression that you're more
>interested in verbal sparring and dodging the issues. (And please, no
>whining that "he started it.")

Such evasiveness actually helps focus her antagonists on real
issues, even if it sidetracks some.

[Wade Hines]

iz...@cleveland.Freenet.Edu (Julie Thomas) writes:

>b. The oriK/RecA may well be more recent. So far, this system has only
>been identified in E. coli, in contrast to the oriC system which has been
>seen in several distantly related species.

In this little peice of a much longer post, you've proposed a
'just so' story for the existence of oriK as an alternative
origin of replication for E. coli. As I understand your stated
positions, you tend to favor the explaination of a designer
and independent design of at least two kingdoms.

Are you here supposing the evolution of oriK by those sorts of
mechanisms that the standard textbooks seem to favor?

This poses quite interesting questions about why this sub
system earns the favour of your supposing it evolved whilst
earlier systems do not.

The most obvious answer is, you can easily see how standard
mechanisms of evolution could give rise to oriK/RecA in a
functioning E.coli population but find it harder to justify
for a proto-prokaryote. Is that what's going on?

[Julie Thomas]

In a previous article, hi...@cgl.ucsf.EDU (Wade Hines) says:

Wade asked:

>And I can't recall if you've commented on

> de Massy B; Fayet O; Kogoma T.
> Multiple origin usage for DNA replication in sdrA(rnh) mutants of
> Escherichia coli K-12. Initiation in the absence of oriC.
> Journal of Molecular Biology, 1984 Sep 15, 178(2):227-36.

>Not only does replication work in the absense of oriC, it appeared
>to work from 4 different alternative sites.

Wade has left out a lot of relevant material as far as this system relates

to the oriC system and its IC role. Let's see if this paper is indeed

relevant to my article (although I will be brief for lack of time).

The article that Wade cites was one of the first indications that E. coli

has an alternative system of DNA replication. This system is fairly well-
understood and is called constitutive stable DNA replication (cSDR). It is
a system that is normally repressed but can be activated under extreme
conditions. It shares many of the actual players used by the oriC
system, but also shows some significant differences. But does it help us

explain the origin of the irreducibly complex oriC system? Unlikely.

Does it damage my case about IC and bacterial chromsosomal DNA
replication? I don't think so. Here are some of my reasons.

1. First, even the cSDR system employ specific origins (called oriK).
Thus, it doesn't damage my thematic IC claims about the need for
an origin.

2. The cSDR system does not employ DnaA. But I never claimed that

DnaA is part of purely thematic IC, only a factor (acting in trans) that

interacts with the origin to initiate replication. And cSDR has such a

factor - RecA. OriC replication does not need RecA. Thus, here is yet
another example of something I talked about in my article - a different
system is not necessarily simpler (and thus less IC).

3. From a systematic IC perspective, oriK/RecA are able to complement

OriC/DnaA activity. But is this relevant? Recall that in my essay,

complementation by itself is not sufficient. And in this case, there are

several significant facts which cause me to doubt the significance of the
oriK/RecA system when it comes to the origin of the IC oriC/DnaA
system:

a. The oriK/RecA system was identified not in wild-type cells, but in
mutant cells lacking RNase H activity (which, BTW, don't grow in rich
media). RNase H is a nuclease that degrades ssRNA when it is bound to
ssDNA. If cSDR was the original replication system, one needs to
explain away RNase H activity which itself appears to be quite ancient.

b. The oriK/RecA may well be more recent. So far, this system has only

been identified in E. coli, in contrast to the oriC system which has been
seen in several distantly related species.

c. As a continuation of point b., the oriK/RecA system may serve as a

back-up system that only functions sufficiently as a short-term solution.
This hypothesis is supported by the fact that the oriC system is so
strongly conserved. If the oriK system could effectively replace the oriC
system as a long-term, or even, primary system, we would expect to see
many species of bacteria using this system as their primary system.

4. Of course, even if cSDR represents the original method of bacterial

[Doug Quarnstrom]

George Acton (gac...@softdisk.com) wrote:
: Julie Thomas wrote:
: > ...

: > So I said:
: >
: > >My, so now I am dishonest? We've only had two or three exchanges
: > >and you've already launched some serious ad hominems.

: >
: Aren't youre repeated digs about "closed minds" ad hominem?

That is one of the defining characteristics of ad hominem. Nobody
is ever guilty of it in their own eyes.

doug

[Peter Nyikos]

my...@netaxs.com (PZ Myers) writes:

>In article <5sdu5e$9...@alexander.INS.CWRU.Edu>, iz...@cleveland.Freenet.Edu
>(Julie Thomas) wrote:

>> [I've previously posted a long reply to Larry's critique of my discussion
>> of the origin of replication in bacteria and IC. But I'd like to add a few
>> more things. However, I should mention that it continues to fascinate
>> me that so many of my critics (and some are getting just plain mean)

>Name some of these "mean" guys. I've seen nothing but respect for your

>efforts, while many have deplored your misinterpretations.

Typical Myers. "deplored your misrepresentations" is playing
fast and loose with the facts. In reality, both Moran and
Myers have been incredibly mean to Julie, as well as having egregiously
misrepresented her. To top it all off, Myers does not name
a single alleged misrepresentation by Julie. Not one.

> If you want to
>see mean, look at how your pal Nyikos talks about just about everyone in
>this newsgroup. Do you really think you have had even a fraction of that
>malice directed at you?

She has had far, far more malice than that directed at her from
Moran alone. I
post what I do not out of malice, but out of a sense of justice
and fairness and a realization that Myers and others trample
on the most elementary canons of both, then play "blame the
victim" when I call them on it.

>> labor under this notion that I am out to prove evolution couldn't happen
>> (or even that I think evolution couldn't happen). But as I have made
>> clear several times, this is not the case. Once again, I am of the opinion
>> that people can look at the same data and see something entirely
>> different. When I see IC, I see design as the best explanation. Thus, the
>> purpose of my articles is to clarify to others, and myself, how science
>> can be viewed and conducted under a design paradigm. Not
>> surprisingly, however, this tends to upset some people.]

>This is a bit of rhetoric -- blaming the fact of opposition on an emotional

>response, that those who disagree are "upset".

In the first place, it is just plain one-sided to claim that
Julie is blaming the fact of opposition on emotion; secondly, Myers
himself has all but admitted repeatedly that he is upset with
Julie's unwillingness to abandon her design hypotheses.

Thirdly, Myers continues to obfuscate in a way that has
become commonplace with him, trying to characterize all
the people arrayed against Julie as merely "disagree[ing]"
with her instead of doing what they are actually doing,
which is [collectively speaking] using one dirty debating
trick after another against her in addition to registering
disagreement [and almost nothing in the way of substantive
arguments, except for Howard Hershey and Larry Moran].

> This is not the case. You
>have received a number of calm and rational replies that disagree strongly
>with you.

And a far greater number of attacks whose rational component
is minimal. Matt Silberstein may have been "calm" when
he accused Julie of `asserting that she has overthrown science'--
he can well afford to be calm, seeing the army of people
on his side--but he certainly was not being rational when
he said it, he was not being rational when he repeatedly went through
the motions of justifying it, and he certainly was not being
rational when he claimed that I would keep on getting this
`explanations' if I kept after him about this incident.

> This is not a matter of being "upset".

So Myers claims. But Moran's relentless interrogation of
Julie strongly suggests otherwise in his case, and Myers's
behavior also strongly suggests major upset.

>There is opposition to this nonsense because you have not presented a
>scrap of evidence for your "design paradigm".

The same Usenet yahoo code that Moran employs: "evidence" where
opponents are concerned is code for "proof so airtight, even
I am forced to either acknowledge it or delete it from my
replies".

>You have not presented
>support for the idea,

"support" of course is used the same way as "evidence".

> but I had thought that your ic arguments were an
>attempt to show that natural mechanisms were incapable of explaining
>certain phenomena, so that "design" was a viable explanation by default.

Julie's numerous clarifications that she merely thinks design
is the *best* explanation have all gone down Myers's memory
hole, probably because they just don't fit in with Moran's
KGB-style interrogation strategy, which Myers is only too
happy to play along with.

>Now you claim this is not the case -- ic systems *can* evolve.

She never denied the possibility that some might. Neither
did Behe, of course.

>So far, then, "design" looks like wishful thinking with no evidence.
>That's not science.

So far, everything Myers has posted in response to Julie looks
like wishful thinking, and Myers has presented less than
a hundredth the evidence Julie has. That's not science,
that's propaganda and polemics.

But then, Myers never was keen on presenting much science
in the first place. I suspect the reason is that he
shares his netaxs.com account with one or more other people
with very little aptitude for the kind of science discussed here,
and it would stick out too much like a sore thumb if he
were to post a lot of science himself.

By the way, I apologize most abjectly for suggesting that the
other people were children of his. I have no reason to think
that, and I have made it my policy never to say negative
things about specific people who have not identified themselves
as posting to Usenet. I very much regret this departure
from this policy and hope I never forget myself in this way
again.

Peter Nyikos -- standard disclaimer --

[Peter Nyikos]

CC: Julie, because the semantic dispute here comes up quite often,
in many guises.

iz...@cleveland.Freenet.Edu (Julie Thomas) writes:

>In a previous article, gac...@softdisk.com () says:

>>For Ms. Thomas to refer to herself as an "evolutionist" is certainly an
>>unconventional use of the word. It usually implies acceptance of the
>>notion of "common descent". But she has stated that she does not accept
>>that eukaryotes and prokaryotes share a common ancestor.

>But what if I believed that gene frequencies change in populations
>over time? Most biology texts define evolution in this way.

So does the talk.origins FAQ. So does Paul Myers. He has even
given the standard U. of Ediacara response to my claims that
this definition, while standard, is not helpful for elucidating
the creationist-evolutionist split in talk.origins, since
almost all creationists will admit that gene frequencies DO
change in populations over time--the ones who know enough about
genetics to understand the issue, that is.

The standard U. of Ediacara reply is that we must not allow
a debate to "dictate" the definitions scientists must use.

This standard reply is given in response to many kinds of
criticisms, such as my criticism of the way cladistics
defines "X is more closely related to Y than to Z". Actually
the cladistic "definition" has nothing to do with science
and everything to do with cladistic dogma vis a vis more
traditional systematists, who would say Archaeopteryx was
more closely related to Confuciusornis than it was to
modern hummingbirds,
even though the cladists would say just the opposite.

>In fact, what if I go much further than this and believe that while
>bacteria and eucaryotes do not share a common ancestor, all bacteria
>do share a common ancestor?

Then you would be doing exactly what I have done in the past!
Whether this makes you or me evolutionists is a matter of
semantics more than anything else.

Peter Nyikos -- standard disclaimer --

Professor, Dept. of Mathematics
University of South Carolina
Columbia, SC 29208

[Peter Nyikos]

George Acton <gac...@softdisk.com> writes:

>Julie Thomas wrote:
>> ...

>> So I said:
>>
>> >My, so now I am dishonest? We've only had two or three exchanges
>> >and you've already launched some serious ad hominems.
>>

>Aren't youre repeated digs about "closed minds" ad hominem?

Sure, but she has ample evidence for it, especially where
you and your fan Paul Myers are concerned. And the evidence
in Moran's case is already quite impressive, especially
where his assessment of Julie's motives is concerned.

Moran, on the other hand, made charges of dishonesty and
hypocrisy as part of a general pattern of KGB-style
interrogation whose purpose was to get Julie to confess
to having the motives Moran is baselessly imputing to her.
He has NO evidence that she is dishonest, and hasn't even
pretended to present any AFAIK.

> Not
>to mention the repeated claims to "seeking truth" with the
>innuendo that other people aren't.

The innuendo is your inference. Normal people don't take
such responses to loaded questions and innuendo that way. She was subjected
to massive innuendo--REAL, blatant innuendo--by Moran that
she has a religious agenda, and she was just defending herself
against that.

But you just ate up all THAT innuendo, didn't you?

[Peter Nyikos]

Though I have severely curtailed my responses to Matt, in this
case I think others might benefit from the correction I make
to something he says.

mat...@ix.netcom.com (Matt Silberstein) writes:

>In talk.origins iz...@cleveland.Freenet.Edu (Julie Thomas) wrote:

>>
>[snip]

>> Experience has taught me that IC
>>entities typically have designers.

>This line may be the heart of the whole issue. Could you expand a bit

>on what leads you to this?

What follows is a typical example of confusing a statement with
its converse.

> For instance, it is certainly not true that
>all human designed systems are IC. I have no idea what "percentage" of
>human designed systems are IC, I would not even know how to estimate
>this number. But I can certainly come up with innumerable non-IC human
>designed systems. So what else do you mean?

The obvious. She did not say that "...designed systems are
typically IC"; she said the converse.

As the Mad Hatter says in _Through the Looking Glass_ [not the
whole title, but I don't have the book in front of me]
you might as well say "I see what I eat" is the same as
"I eat what I see".

Converse, inverse, contrapositive: these concepts and their
proper use were taught in my high school geometry class already.
Have times changed?

Peter Nyikos -- standard disclaimer --

[Peter Nyikos]

"John Mazor" <maz...@erols.com> writes:

>To Julie Thomas:

>Let me say up front that the discussions of cellular structures, chemistry,
>etc. are well over my head. I cannot begin to assess the validity of the
>arguments of you or your critics in this area.

>However, I cannot help but notice a few irritating patterns I see in your
>postings.

Irritating? Do you think she should roll over and play dead
when being misrepresented? Seems to me you are playing a game
of blame-the-victim:

>First, you spend a lot of time trying to defend a claim that your various
>assertions, theories, etc. are proposed here merely in some spirit of
>disinterested, scientific inquiry.

That is because of relentless interrogation, accompanied by
numerous accusations, designed to create the impression that
she has a completely different motive.

> Quite frankly, I don't give a damn
>whether you offer these as an amusing exercise in scientific method or a
>religious crusade. Your arguments stand or fall on their merits.

Then say so upfront, and leave off the "irritating patterns"
preliminaries. As it is, it looks like you are playing
"good cop" to just about everyone else's "bad cop".

>Second, despite careful reading of various threads, I'm still not sure
>what, if anything you A.) Believe, and B.) Admit to believing, which in
>this instance is not a trivial difference. I'm not trying to be cute here.
> At various times you seem to be saying:

> 1. "I'm not claiming that I'm right, only that you (are) (may be)
>wrong."
> and elsewhere,
> 2. "I'm not claiming that you're wrong, only that I (am) (may be)
>right."

Yup, and it's a case of "may be" in both cases. I'm amazed that
you haven't caught on to this by now.

Of course, it could be that you HAVE caught on but are
trying to engage in deliberate misdirection above.

>You really do play word games, and that diminishes your credibility.

Your failure to give credible evidence that she plays word games
diminishes YOUR credibility.

> E.g.,

>> I am mystified by Larry's insistence that I am making the case that
>> DNA replication "could not have evolved." Apparently, Larry confuses
>> the fact that I *do* not think DNA replication evolved means I think it
>> "could not" have evolved. But that's sloppy thinking. For example, if
>> someone does not think there was life on Mars it doesn't mean they
>> think life could not have existed on Mars. Those are two very different
>> claims.
>

>Other than in an obscure theoretical sense, what difference does it make if
>you "think evolution could have evolved but it didn't" vs. "think evolution
>couldn't have evolved"?

You are the one playing word games. A distinction of utmost
importance to anyone who aspires to becoming a scientist becomes
"an obscure theoretical" one. What are you, anyway? A high
school debater aspiring to be a politician?

You aren't even making sense. What do you mean by the word
string "evolution couldn't have evolved"? What does it
mean to claim that evolution evolved????

> Either way, you would put a stake through the
>heart of evolution theory.

Only the theory that the first Earth prokaryote is the
product of abiogenesis, which isn't really part of the theory
of evolution; it is merely an article of faith with many
of the people here.

> The murder victim doesn't much care whether it
>was a knife or a gun that done him in. You, on the other hand, spend an
>inordinate amount of time trying to catch your critics on minor points like
>the above.

She doesn't need to try. They have caught themselves, and she
is merely calling attention to that fact for the benefit of
people like you, who apparently still haven't caught on.

>> Furthermore, just because I do not think DNA replication
>> evolved does not mean I think DNA replication *must* have been
>> designed.

>More word games. Okay, I give up. If DNA replication didn't evolve and it

>wasn't the product of design, what is the other possibility?

YOU are the one playing word games, plastering over the distinction
between "did" and "must have" as if it never existed.

> Random
>instantaneous creation? And how does one test for that (or for design)?

Try: "One theory is that
the bacterial flagellum
and other systems Julie describes were designed by an
intelligent creature, or a team of them, in a lab
about 3.5 billion years ago,"

>> Of course, it is possible that Larry may be projecting his attitudes upon

>> me

>You seem to use that accusation a lot. Need I spell out the implications
>of that thought?

No. Larry comes across as someone with an axe to grind, as
his relentless interrogation of Julie should make it clear
to all but the densest person.

I think it is clear to you. Need I spell out the implications
of that thought?

>Having now spent even more time re-reading your posts (including your
>rejoinders to Moran's attempts to summarize your views),

You mean Moran's KGB-style explications of the things he wants
to get Julie to confess to.

> let me see if I
>have it right:

>1. Julie *thinks* evolution can't explain certain IC systems, although she
>dutifully admits that she may be wrong and will change this view if anyone
>presents convincing proof otherwise.

>2. She *thinks* design is the best explanation for these same IC
>phenomena, although although she dutifully admits that she may be wrong and
>will change this view if anyone presents convincing proof otherwise.

My, you certainly are able to make careful distinctions when
it suits you. Dare I suggest that you were being insincere
in your claim that the distinction you tried to paper over
was "obscure"?

Three more very carefully worded statements deleted.

>6. The net result of items 1-5 is that arguing with Julie is like trying
>to nail Jell-o to the wall,

No, trying to worm a confession out of Julie to something she
never subscribed to is like trying to nail Jell-O to the wall,
and for good reason.

>but okay, some of us will deal with that as
>best we can. (Others will interpret 1-5 as a lack of commitment on Julie's
>part to her various assertions and dismiss her, but she'll have to deal
>with that as best she can.)

Your complicity in these attempts to extract a confession
from Julie are duly noted.

>Okay, we all understand now that your assertions are offered in the true
>scientific spirit, and that you claim to hold no special attachment to
>them. Fine. Now stop spending so much time on trivial points and focus on
>more substantive items,

I see Julie's 2000+ line essay, prompted by earlier discussions
which you probably weren't privy to, means nothing to you.

lest we get the impression that you're more
>interested in verbal sparring and dodging the issues. (And please, no
>whining that "he started it.")

I doubt that she'll whine about that, especially since I am
relieving her of the temptation to do so by pointing out
that you are like all her other opponents: you criticize her
while handling her opponents with super kid gloves.

Heck, you haven't even admitted that Moran started it, even
though it should be crystal clear that this is exactly
what has happened.

You have already caught on to one U. of Ediacara principle: as long
as you don't explicitly admit that X did what you are criticizing
Y for, you will not be seen as implicitly criticizing X.

The default assumption, you see, is that it is not the behavior
you are crticizing, but Y. For all anyone can pin on you,
the behavior, were it to come from X, would be perfectly
acceptable to you.

[Peter Nyikos]

howard hershey <hers...@indiana.edu> writes:

>Julie Thomas wrote:

>> Larry confuses systematic IC with thematic IC at this point. The
>> different origin strategies (as Larry mentions) underscore that a DNA
>> binding protein and binding site is needed (thematic IC).

[snip Howard's response to this part]

>> But they are
>> not relevant to OriC from a systematic perspective unless these other
>> origins can be shown to predate oriC and have given rise to oriC.

>[...] OriC and DnaA are not part of the

>IC-ness of DNA replication, if IC-ness is to mean anything. There are
>simply too many alternative mechanisms available, including all those
>viral and eucaryotic systems

Huh? Are you suggesting they could have been part of the
eubacterial system at one time? or that they gave rise to it???

> that you ignore that provide 'reasonable'
>stepwise (with useful intermediates) models for the step-wise evolution
>and integration of these particular parts.

I thought viruses came from prokaryotes and eukaryotes, not vice
versa; and that YOU believe eukaryotes came from prokaryotes
and not vice versa.

Imagine my surprise. :-) You of all people, who castigated
Behe for supposedly putting grandchildren before their
grandparents.

>[snip discussion of how an initial low degree of specificity of protein
>to a sequence can become more specific if there is selective pressure
>for it, along with Julie's strange idea that the particular end result
>was somehow teleologically ordained by design.]

More Strawwoman Julie?

>> Yes, some species have strayed somewhat from the the consensus and a
>> few seem to have replaced it with something else.
>>
>> >The data says that there was a lot of evolution over the past billion
>> >years.
>>
>> Yet the consensus remains in very distantly related bacteria.

>Which likely means that the oriC/dnaA system may well have evolved for
>other functions

Got any guesses for what they might have been?

>> >I suppose that your alien design model would postulate something
>> >different. Perhaps the aliens created many different designs in order to
>> >see which one would win out in the end?

Maybe two or three, as in Crick and Orgel's directed panspermy. Why do
you make such a huge leap from what she actually wrote?

>> > Maybe Earth is just a giant
>> >test tube where a bunch of alien graduate students are doing in vitro
>> >mutagenesis and evolution on a big scale?

Maybe you will force me to keep mentioning that in my theory they did
their thing 3.5 billion years ago. Maybe you won't quit asking these smart
alecky questions until I've mentioned it a couple of hundred times.

>> I have never asserted that aliens created anything so why do you insist
>> on misrepresenting me?

>You certainly *are* implying 'intelligent design' which implies an
>intelligent designer and someone/thing that implemented that design.
>[snip]

Then don't use the word "aliens". It narrows things down to
the non-supernatural in most people's minds. Julie is trying
to keep all options open, as am I, although I'll stick to
my 3.5 bya theory for the next few months. Maybe the next
few years, unless y'all stop being coy about your REAL opinion
of the supernatural.

>> >There's no reason to believe that any of these modern pathways are
>> >better or worse than any others. The evolution that took place involved
>> >both random genetic drift and natural selection.
>>
>> Drift doesn't explain strong sequence conservation across long
>> phylogenetic distances. Selection would explain preservation of the
>> consensus, but not it's origin (IMO).

>Both its origin (which may indeed be quite early) *and* its conservation
>can be explained by selection.

An article of faith with you where its origin is concerned, but
without much evidence to support it, as the following quotes
indicate.

QUOTES OF THE WEEK

An honest man, armed with all the knowledge available
to us now, could only state that in some sense, the
origin of life seems at the moment to be almost a miracle,
so many are the conditions which would have had to have
been satisfied to get it going.
--Nobel Laureate Francis Crick, _Life Itself_,
Simon and Schuster, 1981, p. 88.

Scientists interested in the origins of life seem to
divide neatly into two classes. The first, usually
but not always molecular biologists, believe that
RNA must have been the first replicating molecule
and that chemists are exaggerating the difficulty
of nucleotide synthesis. ... The second group
of scientists is much more pessimistic. They believe
that the de novo appearance of oligonucleotides on
the primitive earth would have been a near miracle.
(The authors subscribe to this latter view). Time
will tell which is correct.
--G. F. Joyce and Leslie E. Orgel, "Prospects
for understanding the origin of the RNA
world," in: _The RNA World_, ed. R. F.
Gesteland and J. F. Atkins, Cold Spring
Harbor Press, 1993, p. 19.

Peter Nyikos -- standard disclaimer --

[Peter Nyikos]

at...@best.comNOSPAM (Mark Isaak) writes:

>In article <5se2ff$l...@alexander.INS.CWRU.Edu>,
>Julie Thomas <iz...@cleveland.Freenet.Edu> wrote:
>>In a previous article, m...@panix.com (Michael L. Siemon) says:
>>
>>>I said that Julie has no justification (she has certainly *given*
>>>none) for her rejection of evolutionary explanations.
>>
>>What an odd way of seeing things. I need justification for not thinking
>>bacterial DNA replication and/or flagella evolved? Michael has it
>>backwards. If he thinks I am obligated to believe such things, he
>>should at least try to convince me.

>Michael Siemon did not say you have no justification and need one; he said
>you have no justification. To all appearances, he is right.

>Please limit your arguing to what people actually say. Your posts are
>wordy enough as it is.

Get real, Mark. Are you seriously suggesting Michael Siemon
is NOT of the opinion that Julie needs to provide justification
for what she wrote?

If so, what do you make of "John Mazor" badgering Julie
to answer the (implied) question? Is he going to get an
e-mail from y'all not to give y'all's game away? or
an e-mail thanking him for playing "bad cop" to y'all's
"good cop"?

Oops, disregard those last two questions. Wade Hines and
Paul Gans just love to accuse me of being a conspiracy
theorist, and those two questions would set them drooling
worse than Pavlov's dogs, were I to really want you
to answer them.

Just answer my first two questions, please.

[howard hershey]

Julie Thomas wrote:
>
> In a previous article, hi...@cgl.ucsf.EDU (Wade Hines) says:
>
> Wade asked:
>
> >And I can't recall if you've commented on
>
> > de Massy B; Fayet O; Kogoma T.
> > Multiple origin usage for DNA replication in sdrA(rnh) mutants of
> > Escherichia coli K-12. Initiation in the absence of oriC.
> > Journal of Molecular Biology, 1984 Sep 15, 178(2):227-36.
>
> >Not only does replication work in the absense of oriC, it appeared
> >to work from 4 different alternative sites.
>
> Wade has left out a lot of relevant material as far as this system relates
> to the oriC system and its IC role. Let's see if this paper is indeed
> relevant to my article (although I will be brief for lack of time).
>
> The article that Wade cites was one of the first indications that E. coli
> has an alternative system of DNA replication. This system is fairly well-
> understood and is called constitutive stable DNA replication (cSDR). It is
> a system that is normally repressed but can be activated under extreme
> conditions. It shares many of the actual players used by the oriC
> system, but also shows some significant differences. But does it help us
> explain the origin of the irreducibly complex oriC system?

So now oriC is IC *despite* the fact that it can be knocked out and have
its 'function' complemented by another system? How *do* you determine
IC-ness?

> Unlikely.
> Does it damage my case about IC and bacterial chromsosomal DNA
> replication? I don't think so. Here are some of my reasons.
>
> 1. First, even the cSDR system employ specific origins (called oriK).
> Thus, it doesn't damage my thematic IC claims about the need for
> an origin.

Now Julie recognizes that the IC status (and all the probabilities that
derive from the idea that *current* IC-ness implies design) is
idiosyncratically determined. So she then shifts the goalpost to
'thematic IC-ness', but not in the correct thematic sense of "Does DNA
replication require an origin of replication like that in *eubacteria*?"
since she knows the answer to that question would not be congruent with
her perception of reality. Rather, she restricts the 'thematic sense'
to *current eubacteria (but clearly she is really working mostly with
gram-positive organisms, one gram-negative and mostly ignores the more
distantly related bacterial groups like spirochaetes)*. This is like
saying that there is a stringent consensus sequence for oriC in _E.
coli_ strains as a thematic sense of DNA origins. Because organisms
within a lineage resemble each other, it is not surprising that they
share common 'themes'.

>
> 2. The cSDR system does not employ DnaA. But I never claimed that
> DnaA is part of purely thematic IC, only a factor (acting in trans) that
> interacts with the origin to initiate replication. And cSDR has such a
> factor - RecA. OriC replication does not need RecA. Thus, here is yet
> another example of something I talked about in my article - a different
> system is not necessarily simpler (and thus less IC).

So there exist more than one example (probably independent) of proteins
(different) which bind to specific sites (different) which can be
*exploited* as an origin of replication under certain circumstances.
That makes *evolving* such systems seem soooooo dificult.

>
> 3. From a systematic IC perspective, oriK/RecA are able to complement
> OriC/DnaA activity. But is this relevant? Recall that in my essay,
> complementation by itself is not sufficient. And in this case, there are
> several significant facts which cause me to doubt the significance of the
> oriK/RecA system when it comes to the origin of the IC oriC/DnaA
> system:
>
> a. The oriK/RecA system was identified not in wild-type cells, but in
> mutant cells lacking RNase H activity (which, BTW, don't grow in rich
> media). RNase H is a nuclease that degrades ssRNA when it is bound to
> ssDNA. If cSDR was the original replication system, one needs to
> explain away RNase H activity which itself appears to be quite ancient.
>
> b. The oriK/RecA may well be more recent. So far, this system has only
> been identified in E. coli, in contrast to the oriC system which has been
> seen in several distantly related species.

Again, that's supposed to make producing such systems seem impossible by
any natural law mexhanisms? Then it is your claim that the
oriK/RecA/RNaseH also appeared by some unknown mechanism identical to
that that produced the oriC/DnaA system? You, of course, think the fact
that both DnaA and RecA bind to DNA sequences (although serving
different functions) to be irrelevant. Do you mean to imply that the
RecA 'function' does not exist in other species of bacteria? You might
need to change your post on recombination, since I thought that RecA was
part of an IC system there. Don't tell me (shock, shock) that a protein
can serve more than one function and emphasize one or the other
activity.

>
> c. As a continuation of point b., the oriK/RecA system may serve as a
> back-up system that only functions sufficiently as a short-term solution.

So what? OriK complements the oriC system, but probably is not derived
from the same ancestor but by an *independent* process *because* both
RecA and DnaA share a common function (with many other proteins to a
lesser extent) of binding DNA in such a way that DNA replication can
initiate in a nearby opening.

> This hypothesis is supported by the fact that the oriC system is so
> strongly conserved. If the oriK system could effectively replace the oriC
> system as a long-term, or even, primary system, we would expect to see
> many species of bacteria using this system as their primary system.

Not, of course, if RNaseH has a necessary utility in 'normal'
environments. In that case, oriK only replaces or suplements oriC when
RNaseH activity is low. The oriK system could only have replaced the
more ancient oriC if it worked *as well as* oriC in most environments.
The contingent fact of oriC being earlier works against its replacement
*even by an objectively superior system* if said superior system
requires passage through stages where it works worse than oriC.
Certainly there is no evidence that the OriC solution is optimal or
could only work if it is optimal.

>
> 4. Of course, even if cSDR represents the original method of bacterial
> chromosome replication, it doesn't do anything but change the actual
> players in the IC system. Instead of oriC, we have oriK. Instead of
> DnaA, we have RecA.

And we have more and more independently derived systems that all
function thematically by binding a DNA sequence and opening up a stretch
of DNA and (perhaps) having some affinity for some of the primosome
proteins so that they can assemble at a particular point. This 'theme'
appears to either be fairly easy to produce (which is certainly contrary
to the idea that such systems are so complex an example of IC-ness that
it is difficult to imagine how they could evolve).

> What's more, the oriK system appears to involve a
> far more complex method of priming involving all the factors in the
> primosome (priA, DnaT, etc.) which, contrary to my original article, don't
> seem to be needed by the oriC system. So it would be like jumping out
> of the frying pan and into the fire.

But, since all you have left is 'thematic' IC-ness (and that only if you
restrict yourself to the 'systematic' system of eubacteria rather than
to 'thematic' in the sense of what are the requirements for DNA
synthesis), why does this matter? Seems like the same notes being
played by a different instrument to me. Thus, there seems to be more
than one way to produce those notes.

[Michael L. Siemon]

In article <5sfvfm$4...@fcnews.fc.hp.com>, d...@hpfcla.fc.hp.com (Doug
Quarnstrom) wrote:

+George Acton (gac...@softdisk.com) wrote:

+: Aren't youre repeated digs about "closed minds" ad hominem?
+
+That is one of the defining characteristics of ad hominem. Nobody
+is ever guilty of it in their own eyes.

Sigh. In the *good* old days (of sophists hawking their wares in the
agora), those who used _argumentum ad hominem_, knew it, practiced it,
honed it and reveled in it (of course, they wouldn't admit it in COURT;
but there *are* professional courtesies, after all.)
--
Michael L. Siemon m...@panix.com

"Green is the night, green kindled and apparelled.
It is she that walks among astronomers."
-- Wallace Stevens

[Paul J. Gans]

Julie Thomas (iz...@cleveland.Freenet.Edu) wrote:
:
: [I've previously posted a long reply to Larry's critique of my discussion
: of the origin of replication in bacteria and IC. But I'd like to add a few
: more things. However, I should mention that it continues to fascinate
: me that so many of my critics (and some are getting just plain mean)

: labor under this notion that I am out to prove evolution couldn't happen

: (or even that I think evolution couldn't happen). But as I have made
: clear several times, this is not the case. Once again, I am of the opinion
: that people can look at the same data and see something entirely
: different. When I see IC, I see design as the best explanation. Thus, the
: purpose of my articles is to clarify to others, and myself, how science
: can be viewed and conducted under a design paradigm. Not
: surprisingly, however, this tends to upset some people.]

[rest deleted]

You are quite right. What you believe has no bearing here.

On the other hand "design" is not an explanation unless the
word means something. When you say, as you do above, "When I
see IC, I see design as the best explanation.", you must mean
something by "design".

Since you are rather intelligent, there are, it seems to me,
only two possibilities as to what you mean by "design". One
is that the designer (whom you admit must exist if there is
design) is "natural", i.e. came to be through the action of
evolution; the other possibility is that the designer is
supernatural.

As I've argued elsewhere, if the designer is "natural", then
your argument fails totally, since the "designer" is just
a natural way of producing the systems you feel are IC.
For instance, consider a virus whose action is to modify
the cellular DNA in some host. That's "natural". Changing
the virus to a macroscopic entity that injects some active
agent into a host and thereby changes the host's DNA is also a
"natural" process. Giving the macroscopic entity a brain changes
nothing. It is still all "natural" in the sense that all comes about
via evolution. I grant, of course, that in this case some
textbooks will have to be rewritten, but then, they are
always being rewritten anyway.

Further, if the designer is natural, all you are really doing
is introducing a novel pathway for the production of an "IC"
system. This is very interesting, but hardly a challenge for
evolution.

Thus the fundamental interest in "designed" systems is not
in "natural" designers, but in supernatural ones. I suspect
that you realize this. And I feel that it is just a bit
disingenuous of you to not face up to it. THIS is the
interesting case. Indeed, it is the *only* case, since as
I've show above, the case of a "natural" designer is not
a challege to evolution. This being so, it is hard to understand
why you keep running away from the idea of a supernatural
designer. Why not be out front with it? It is implicit in
what you are saying anyway.

------- Paul J. Gans [ga...@scholar.chem.nyu.edu]

[George Acton]

Julie Thomas wrote:
> ...
> So I said:
>
> >My, so now I am dishonest? We've only had two or three exchanges
> >and you've already launched some serious ad hominems.
>

Aren't youre repeated digs about "closed minds" ad hominem? Not

to mention the repeated claims to "seeking truth" with the
innuendo that other people aren't.

--George Acton

[Vladimir Svetlov]

In article <5se5bb$1...@alexander.INS.CWRU.Edu>, iz...@cleveland.Freenet.Edu
(Julie Thomas) wrote:

> In a previous article, hi...@cgl.ucsf.EDU (Wade Hines) says:
>
> Wade asked:
>
> >And I can't recall if you've commented on
>
> > de Massy B; Fayet O; Kogoma T.
> > Multiple origin usage for DNA replication in sdrA(rnh) mutants of
> > Escherichia coli K-12. Initiation in the absence of oriC.
> > Journal of Molecular Biology, 1984 Sep 15, 178(2):227-36.
>
> >Not only does replication work in the absense of oriC, it appeared
> >to work from 4 different alternative sites.
>
> Wade has left out a lot of relevant material as far as this system relates
> to the oriC system and its IC role. Let's see if this paper is indeed
> relevant to my article (although I will be brief for lack of time).
>
> The article that Wade cites was one of the first indications that E. coli
> has an alternative system of DNA replication. This system is fairly well-
> understood and is called constitutive stable DNA replication (cSDR). It is
> a system that is normally repressed but can be activated under extreme
> conditions. It shares many of the actual players used by the oriC
> system, but also shows some significant differences. But does it help us

> explain the origin of the irreducibly complex oriC system? Unlikely.

> Does it damage my case about IC and bacterial chromsosomal DNA
> replication? I don't think so. Here are some of my reasons.

My car mechanic can not design an eye, yeh, I know.

Julie, if any case at all, you have a case of indigestion of long words.
Can I ask you to give me your opinion on the following subjects, just to
test your thematic-systematic approach?

1. Phage (viral in general) replication system on average are "simpler"
than bacterial - could those evolve, or they still require a designer?

2. Transcription in eucarya - three polymerases by design?

3. Did the same or different tribes of aliens design transcription and
replication? Now, if they fight, which will win?

Any other proponents of the IC idea can also respond to this questionnaire.

Thank you for your time, the results will be tabulated and sent to all
participants with the next Hale-Bopp comet.

To everybody else trying to deal with this interstellar CIA-KGB conspiracy
to create a replication system - it is really an old delusion, called
uniformitarism, a rather stagnant approach to historical processes, when
the laws and relations between the objects existing now are declared to be
the only ones that can be known with certainty and thus the only ones that
should be universally applied.
I do not know why these particular group is so hang up on the replication;
may be because since they can say oriC and DnaK, they fancy themselves any
different from the simpler crowd, screaming here about evolution of an eye
or flight or whatever else strikes them as "irreducibly complex"...

Regards,
V.

[Peter Nyikos]

CC: Julie

iz...@cleveland.Freenet.Edu (Julie Thomas) writes:

>In a previous article, lam...@bioinfo.med.utoronto.ca (Laurence A. Moran) says:

Huge deletia here. It's obvious that Larry Moran has
made up his mind about Julie's motivations, and is playing the
role of KGB-style interrogator, trying to get Julie to
confess to a conviction that a supernatural designer is behind
everything.

Larry Moran has, I think, been avoiding me because I am more
accustomed to this kind of insincere in-fighting than Julie
is, and he still has high hopes of catching Julie in a trap.

>>Who are you trying to fool?

>Obviously, I cannot fool a man who knows me better than I know
>myself.

Nice sarcasm, Julie. I must say, Larry Moran seems to have
even more of a one track mind on this than most of Julie's
opponents, even Matt Silberstein, who apparently gave
up trying to make Julie break down and confess to creationist-like
motivations. Instead, he has come up with a step-by-step evolution
of a perfectly innocent and reasonable statement of Julie's
into a confession not only to being motivated to "overthrow
science", but to a belief that she has actually done that.

[...]

>>Is every IC system designed?

>Not necessarily. Michael Behe explains this in his book.

>>Can you have design in the absence of a designer?

>I don't think so. But you can have things that look designed without a
>designer. Certain IC systems might very well be an example of this.

Nice clarification, Julie. I have gone further and decided,
as long as I am on Usenet, not to call something "design"
unless I have a purposive and at least somewhat
intelligent designer (with some simple tools, a chimp might
do) in mind. Just too much room for misunderstanding otherwise.

Of course, there is ample room for misunderstanding no matter
how clear Julie and I are; as I said on the thread,
Peter's Clotting Description (was Mr. Ford's "precictions")
this KGB-style interrogation is apt to continue for the
foreseeable future, because I certainly don't confine my
"designer" to a supernatural one. You don't either, do you,
Julie?

>>Why don't you come out of the closet and tell us about your intelligent
>>design model?

>I already have. I suspect you were not paying attention because you
>were preoccupied with what you think is "obvious."

I've done it too, but Wade Hines, who may be really tight with
Larry Moran by now, ignored the obvious on that "Peter's..." thread:

==================== begin excerpt from reply to Hines

>How many have asked for some constraints on
> design or designer?

Plenty, and I have given plenty of them. Finally,
out of exasperation, I have even posted that Howard
Hershey apparently will not be satisfied with a
description along the lines, "One theory is that

the bacterial flagellum
and other systems Julie describes were designed by an
intelligent creature, or a team of them, in a lab

about 3.5 billion years ago," but will
not rest until the description includes a detailed
description of the workings of the brain of this
intelligent creature, so that all creativity, including
human creativity, can be reduced to microbiological
and biochemical phenomena.

People keep asking silly questions, like asking for direct evidence
of creatures that existed 3.5 billion years ago but
may long ago have become extinct, questions which
show no understanding of the basic fact repeatedly
emphasized by Francis Crick in respect to directed
panspermy: "Prokaryotes travel farther". They may
never have developed the capacity to send themselves
on such long interstellar voyages.

Mike S. and Michael Siemon [hmmm... interesting similarity]
have even suggested that this whole "alien intelligence"
bit is based on tabloid-style stories instead of serious
scientific hypotheses like the Crick-Orgel theory.

> Why does he think all the questions are coming?

Some of them, because of the scams I mention above. It's not
sincere questioning, it's KGB-style interrogation
in many key places.

And it will continue for the forseeable future. Hines ally Myers,
for instance, has utterly failed to meet Julie on
a scientific level, and continues to badger her the
same way he has badgered me.

> Could it just be because he's utterly failed to make a clear point?
>

Questions like this are part and parcel of these scams.
Nowhere in this post, except for that one "designer"
question, does Hines even attempt to get
specific, and for good reason: if he were to actually
mention some other specific questions, he would be undercutting
this general question of his.

=================== end of excerpt

>>You seem to think that if you can cast doubt on evolution
>>then this is support for your model but how are we to know if you
>>won't tell us about it?

>Since intelligence is easily capable of generating IC systems, and IC
>systems are known to have been generated by intelligence, I find

>intelligence to be the best explanation in the case of IC. But what I find
>is purely "tentative." For example, if a powerful evolutionary
>explanation is made for an IC system (that goes beyond the "could have
>happened" world), I find intelligent causation to be in a weaker position
>(it may be merely an alternative, but not clearly the best explanation).

>>What are you afraid of, Julie?

>Nuclear war.

Were Julie to break down and "confess" under this relentless
interrogation, Matt Silberstein would be able to cut a whole
chain of evolutionary steps out of this "demonstration"
that Julie claims to have "overthrown science" and thereby
making it at least halfway plausible.

>>>>I admit that the use of "alien" was partially motivated by your use of
>>>>the term "Darwinist". A term that I find very offensive since it
>>>>implies a strawman version of evolution. If you start being more
>>>>considerate then I will too.

>>>I'm truly sorry. I didn't realize you were offended by the term
>>>"Darwinist." But how shall I refer to your position? I don't want to
>>>refer to you as an "evolutionist" because that makes it seem like I am
>>>anti-evolution (and I am not).

>>Damn! There goes my brand-new Irony-O-Meter. I'll have to ask the
>>store if I can have my money back.

Under normal circumstances, this would be a mystifying statement
because there is nothing ironic about what Moran wrote. What
Moran wrote was probably insincere, because he probably has no inkling
of what Julie means by "Darwinist," and probably knows he
has no inkling, and so is premature, at best,
in talking about her implying a "strawman" version of evolution.

But I do believe, in the light of his KGB-style role-playing,
that Dr. Moran is accusing Julie of not noticing the
irony inherent in what she is saying. Of course, as an
experienced interrogator, he does not spell out just where
he believes the irony lies.

>Hey, if you didn't rely so much on stereotypes, you might save yourself
>some money.

Again, well said, Julie. But be careful: the more you resist
these interrogations, the more Dr. Moran's allies like Myers,
Carrell, Hines, and Siemon will be attacking you, and unless
you learn to roll over and play dead in the wake of massive
misrepresentation of you, you run the risk of being called
"beyond the pale" by self-appointed net.good-cop Chris Ho-Stuart,
because of the number of enemies you have made.

You see, Ho-Stuart's system of values makes no allowance
for the fact that you and I are terribly outnumbered, and only
counts the number of times we make negative comments about
others, and the number of people we make negative comments
about. It also makes almost no allowance as to whether the
negative comments are justified or not. Since our adversaries
have only you and me and a few creationists to contend
with, none of them will be seen by Ho-Stuart to be making as
many negative comments about as many people; hence they are
home free, no matter how unjustified their comments are
and how justified ours are.

It wouldn't be so bad if Ho-Stuart were isolated, but
his flaming of me has been enthusiastically quoted by
others in the past, including Mike Noren, as evidence
that I really *am* beyond the pale.

>>"Evolutionist" would be fine by me. I'm happy to be called an
>>evolutionist. You'll simply have to live with any semantic problems
>>that this creates for you.

>Or I could quit bothering with you. That seems to be a more attractive
>choice.

Oops, watch it, Julie. Myers and others are chomping at the
bit and straining on the leash, ready to pop into action were
you to cease bothering with the inimitable Dr. Moran.

>>Frankly, I don't see why you prefer "Darwinist" - your writings suggest
>>that you actually believe that your strawman version of evolution is
>>the one we all believe in.

>Imagine that. Perhaps you can tell us in what way your evolutionary
>descriptions (so far) are not Darwinian.

Perhaps he can, but it is the interrogator's prerogative not to
explain himself to the interrogated.

>>So "evolutionist" should be the same thing if I interpret you correctly.
>>Are you an anti-Darwinist?

>Nope.

>>Is that why you wanted to refer to your strawman critics as
>>"Darwinists"? Do *you* see a difference between a Darwinist and an
>>evolutionist?

>Sure. All Darwinists are evolutionists but not all evolutionists are
>Darwinists.

Careful, Julie. This kind of answer is perfectly acceptable if it
comes from U. of Ediacara types, but I expect Wade Hines and
Paul Myers and other U. of Ediacara types to attack you for merely answering
the question and failing to answer what they perceive to
be the intended question.

As you may have noticed by now, these people don't even care
if they are perceived as being obnoxious and insincere and even
dishonest. Their attitude is like that of "Boss" Tweed of
Tamanny Hall when confronted with an account of his wrongdoing;
he simply taunted, "What are you going to do about it?"

>Larry said:

>>>Come on, Julie. Give us a little credit - we are not idiots. What's the
>>>real reason for claiming that a system is irreducibly complex?

>I replied:

> >For the third time:
> >"I simply outlined the IC nature of DNA replication which in turn
> >strongly suggests the system was designed."

>Larry asked:

>>>Are you just playing rhetorical games or is there a bigger stake?

>I replied:

>>Well, I suppose that a desire to know what's the truth about our
>>reality is a "bigger stake."

>Larry asked:

>>>If the process didn't evolve then what is your explanation?

>So I replied:

>>If it didn't evolve, then it was mostly likely designed.

>Larry replies:

>>So it's "truth" we're after, is it?

>Sure. I have no desire to believe something that is false. Do you?

Nice comeback. And if Larry were sincere, I think he would
say, "I desire to believe in the Humanist Manifesto, even
if large parts of what it asserts are false."

>>You have almost come clean here - one more little step and we'll be
>>able to see what this bigger stake is this "truth about our reality".

>I know. It's so "obvious."

Again, a nice comeback.

[...]

>Larry then says:

>>Several postings ago I summarized Julie's hypothesis like this,

>>>>She suggests that some systems are so complicated and
>>>>interconnected that it would be impossible to imagine or reconstruct
>>>>a natural explanation involving evolution from a primitive ancestor.

>Yes, and this was an erroneous summarization. But you still seem to
>need to cling to it.

>Larry said:

>>There followed bit of back and forth where Julie complains that I am
>>putting words in her mouth.

>Which, of course, was true.

>>Apparently there is something in my summary that she doesn't want
>>to openly admit.

This is downright paranoid. I'm sorry, but after seeing so much
of this relentless interrogation, I am finally moved to use
the magic word that Wade Hines and Paul Gans love to use
at the drop of a hat.

>Er, it's just simply false that I ever claimed it was impossible to imagine
>or reconstruct a natural explanation involving evolution from a
>primitive ancestor. Even on a trivial point like this, Larry can't admit
>he is wrong. And that says something to me when we discuss other
>more substantial and controversial issues.

[lots deleted, to get to this beaut:]

>Larry replied:

>I gave you a quotation from your essay. Here it is again,
>
> "This makes it hard to envision the gradualistic evolution
> of DNA replication."

>How does one get from "it is hard to envision the gradualistic evolution
>of DNA replication" to "there is no natural explanation for DNA
>replication?"

>Perhaps Larry can fill in the gap.

It would be a cinch for Matt Silberstein to do so. :-)

>I personally think the gap-filling goes like this. I make a tentative
>claim about my perceptions of the world and Larry reads a certain
>claim about the world. Could this be because Larry is reading my words
>through the filter of his stereotype? It seems most likely (although I
>must confess that I can't quantify this judgment).

The same applies to Matt.

>>I must have misunderstood. I guess you only meant to eliminate
>>"gradualistic evolution" as a natural explanation. There must be other
>>natural explanations of DNA replication that you prefer. Either
>>that or you just told a fib. Please let me know what "natural
>>explanation" you are intending to include.

There are lots of them, but it's not the role of interrogators
to suggest them, hence Larry isn't proposing any of them
as possibilities.

>I just told a fib? Fits with the dishonest person you think I am, right?
>Either that or you are simply confusing yourself with your stereotypes..
>Go back and fill in the gap, Larry.

This isn't apt to go over too well, Julie. I think Larry was
fishing for another 2000+ line essay on the whole spectrum
of possible natural explanations in addition to the gradualistic
ones. ;-)

>>Do you think it possible that your search for IC and design is motivated
>>by your "beliefs" and not by a real search for the truth?

This kind of question is a staple of U. of Ediacara types
like Wade Hines ["Could it just be because..."] and
Chris Ho-Stuart and Paul Myers. I'm no longer surprised to see it coming
from Larry Moran.

>Anything is possible, but I know myself pretty darn well (far better
>than you do). Me thinks you're barking up the wrong tree.

Again, well said.

>>Is it possible that you already "believe" that you know the truth and
>>you are simply looking for pseudo-scientific proof that will make you
>>feel good?

>Quite doubtful. I've spent so much of my intellectual life shying away
>from "I know the truth" claims and I am not one who looks for ways
>to make myself "feel good" with beliefs. Is it possible that you may
>have been projecting when you asked this question?

I believe there is a good chance that Dr. Moran is a militant
atheist who "knows" there is no God and will not rest until
the design argument is dead and buried, even if it means
sacrificing the possibility that we are the product of
a direct panspermy event of the kind proposed by Nobel Laureate Francis
Crick and Leslie Orgel.

[...]

>>I think that you are deliberately pretending to "do science" when what
>>you are actually doing is promoting religion.

If Crick and Orgel [see Quotes of the Week below] were ever to
propose intelligent design for
the first prokaryotes, instead of those hypothesized aliens
simply taking bacteria from their environment without redesigning
them [what, no recombinant DNA even?], to the extent of inventing
the bacterial flagellum and the bacterial DNA rep system, would
Larry also say this about them?

He just might, at that. Their use of the word "miracle" in the
Quotes of the Week just might be enough to raise his hackles.

>Of course you do. It's obvious to me that you are enslaved by this
>stereotype. It's quite a pity though. You might find the world of people
>a more interesting place if you let others simply be themselves.

Touche.

>>I don't have a problem with religion but I do have a problem
>>with hypocrisy.

Except for his own. And I do believe that when Larry claims
he has no problem with religion, he really means that he
has no problem with people having blind faith, but when
they try to come up with rational arguments for it, he will
play good cop to all the "bad cops" who attack the other
kind for their "blind faith". I believe at least one of
the following is in the same boat: Howard Hershey, Michael Siemon,
Matt Silberstein.

>This is good. I'm now a dishonest, lying, hypocrite. Hmmm. I'll bet
>that's not a novel way for Larry to look at those who don't agree with
>him on these issues. ;)

I doubt that he looks at you that way. I think he is just
baiting you so you will eventually get to be "beyond the
pale" sensu Chris Ho-Stuart.

>>Here's another example of hypocrisy,

>...in Larry's mind.

I don't even see why he used the word.

>> I see folks getting emotional and
>>wanting to talk instead about invisible pink unicorns.

Specifically, Paul Myers, Wade Hines, Howard Hershey,
and Matt Silberstein. Anyone else I've missed?

>>>Etc. One
>>example of this strangeness may not be all that significant, but if the
>>same dynamic holds in the analysis of system after system after
>>system (even allowing for some vague just-so stories), I'm going to
>>start to *really* believe there is a reason for this dynamic.

I believe Moran is playing Mutt to Hershey's Jeff, just like Paul
Myers did on the thread, "Query on blood clotting and irreducible complexity".

================== begin excerpt from reply to Myers

>Why move from topic to topic?

To counteract people like Howard Hershey who play Mutt to Myers's
Jeff, pretending that Julie and my "God of the vanishing gaps" is restricted
to gaps that Julie and I have brought up to date.

> How about dealing with the many very substantial
>criticisms of your replication article that Moran has brought up,
>instead?

She has begun to do so with an article ten times as long
as the Myers article I am responding to.

> Never mind, I can answer my own question

Of course--Myers is too closed minded and fanatical to let
Julie answer the loaded questions he asks.

=========================== end of excerpt

By the way, Julie, do you have a clue as to what Myers had
in mind when talking about "very substantial criticisms"?
I've seen none in this post.

Peter Nyikos -- standard disclaimer --

Professor, Dept. of Mathematics
University of South Carolina
Columbia, SC 29208

[Peter Nyikos]

"John Mazor" <maz...@erols.com> indulges in more complicity
with Julie's interrogators:

>Julie Thomas <iz...@cleveland.Freenet.Edu> wrote in article
><5se2ff$l...@alexander.INS.CWRU.Edu>...
>>

>> In a previous article, m...@panix.com (Michael L. Siemon) says:
>>
>> >I said that Julie has no justification (she has certainly *given*
>> >none) for her rejection of evolutionary explanations.
>>
>> What an odd way of seeing things. I need justification for not thinking
>> bacterial DNA replication and/or flagella evolved? Michael has it
>> backwards. If he thinks I am obligated to believe such things, he
>> should at least try to convince me.

>More cutesy word games and verbal judo.

By Michael Siemon, talking about "rejection of evolutionary
explanations," as though Julie had been presented with evolutionary
explanations for the bacterial flagellum and DNA replication.

All I've seen is implicit assertions by Paul Myers that he has
evidence these things evolved by natural selection, but not
one iota of reasoning in support of this implicit assertion.

> Answer the (implied) question.

She has, with two posts of 1000+ lines each, as well as some
very long, highly substantive followups to Dr. Moran, as
well as a long article in "The Bacterial Flagellum and IC"
on Aug 3 in response to an extremely short and condescending
challenge by her chief interrogator of the moment, Laurence Moran.

You admitted that you couldn't assess the science involved.
So why are you asking her to answer the implied question?

[Doug Quarnstrom]

Julie Thomas (iz...@cleveland.Freenet.Edu) wrote:

: In a previous article, m...@panix.com (Michael L. Siemon) says:

: >I said that Julie has no justification (she has certainly *given*
: >none) for her rejection of evolutionary explanations.

: What an odd way of seeing things. I need justification for not thinking
: bacterial DNA replication and/or flagella evolved?

You need no justification whatsoever to believe whatever you wish to
believe.

:Michael has it

: backwards. If he thinks I am obligated to believe such things, he
: should at least try to convince me.

For anyone who does not recognize the inherent flaw in the "God did it"
argument, such convincing is likely not possible...

doug

[Matt Silberstein]

In talk.origins Peter Nyikos <nyi...@math.SC.EDU> wrote:

Peter wrote a comment on a Julie Thomas post responding to a post by
Laurence Moran. In that post Peter made comparisons to or statements
about:

Matt Silberstein,
Wade Hines,
Mike S.,
Michael Siemon,
Hines ally Myers,
Carrell,
net.good-cop Chris Ho-Stuart,
Mike Noren,
Paul Myers,
other U. of Ediacara types,
"Boss" Tweed of Tamanny Hall,
Howard Hershey,
and, of course, the KGB.

[howard hershey]

Julie Thomas wrote:
>
> [I've previously posted a long reply to Larry's critique of my discussion
> of the origin of replication in bacteria and IC. But I'd like to add a few
> more things. However, I should mention that it continues to fascinate
> me that so many of my critics (and some are getting just plain mean)
> labor under this notion that I am out to prove evolution couldn't happen
> (or even that I think evolution couldn't happen). But as I have made
> clear several times, this is not the case. Once again, I am of the opinion
> that people can look at the same data and see something entirely
> different. When I see IC, I see design as the best explanation.

Actually, you see 'thematic' IC (but limited to 'themes' seen in present
eubacteria, to the extent that we know them). Design accomplished by an
intelligent designer and his invisible assistant, the Grand Invisible
Implementor of Design - Yahoo (GIIDY) is simply inferred by
extrapolating way beyond the data. The inference amounts only to a claim
that sufficiently complex IC makes evolution *unlikly* and does *not*
rely on any independent evidence for GIIDY nor *even* independent
evidence for either of the two mechanisms that IC-ness implies that are
clearly contrary to evolutionary expectation: IC 'systems' can be
created in one fell swoop (because functional intermediate stages are
forbidden for non-evolutionary steps in IC creation and Behe argues
against horizontal transfer as a true non-evolutionary mechanism) or the
'system' is created stepwise with utterly useless intermediates.
Evolution implies intermediate stages with functionality of some sort.
Clearly, the more parts an IC system has, the less likely the second
possiblity is.
Somehow, they think history only requires an examination of the present
system, though I think they would recognize that it is silly to
determine the evolution of the IC present economy merely by looking at
IBM (or Apple) or even developed economies.
But more typically, one gets twaddle like 'guided evolution' which is
indistinguishable from 'evolution' except for the assertion that it was
'guided' and a few desultory comments using *a posteriori* calculations
of improbability or one gets twaddle about invisible aliens at the
initiation of life or one gets twaddle about invisible aliens that come
down three times (once for eubacteria, once for archae, once for
sucaryotes), except that they then use examples like clotting factors.

> Thus, the
> purpose of my articles is to clarify to others, and myself, how science
> can be viewed and conducted under a design paradigm. Not
> surprisingly, however, this tends to upset some people.]
>

> Metazoans and Origin of Replications
>
> Larry said:
>
> >DNA replication in eukaryotes need not even occur at a specific site. In
> >other words there may not be an origin. This is particularly true of
> >multicellular animals when DNA is dividing rapidly. In such cases
> >initiation occurs randomly at many sites on the chromosome
> >(DePamphilis, 1993). These examples demonstrate that an origin of
> >replication is not an absolute requirement for DNA replication in all
> >cases.

This goes to the heart of 'thematic' DNA replication. Does DNA
replication absolutely require an origin? The answer is no. Does DNA
replication require a eubacterial-like origin? The answer is no.
>
> This is all true, but I'm afraid that Larry gives the false impression that
> metazoans lack origins. In the paper cited by Larry, the author
> summarizes some nice work done on the dihydrofolate reductase gene
> locus from Chinese hamster ovary. This has led to the identification of a
> specific site, 500-2000 bp in size, that appears to be involved in the
> initiation of DNA replication. The site is called the origin of bidirectional
> replication (OBR). Yet, as Larry notes, when cells are rapidly dividing,
> the initiation of DNA replication appears to occur at random sites.
> DePamphilis reconciles these two seemingly contradictory lines of
> evidence with a model that suggests there are many initiation sites in
> metazoan DNA but chromosome structure typically suppresses their
> activity and facilitates the OBR.

Just as there are often alternative origins in eubacteria. The
important 'thematic' point is that DNA replication does not absolutely
require a specific origin. It is not only possible to 'imagine' DNA
replication without origins, it is possible to observe organisms in
which this happens. This does not require that the observed non-origin
'system' *be* an ancestral system for which we have no evidence. It
only means that such a non-origin containing 'system' can exist and that
it represents one *possible* route to a system with an origin. Out goes
the *impossibility* of a stepwise system from one without origins to one
with.
>
> Up to this point, there is not much cause for us to disagree. But Larry
> then proceeds to interpret this data in two ways.
>
> >In other words origins are not IC components in some cells.
>
> I admit that this is what the metazoan data suggests. However, given
> that origins are IC in so many other creatures (bacteria, yeast, slime
> mold, protozoans), we have to ask two very relevant questions:

And your task was to render all possible and reasonable stepwise
mechanisms with intermediates having function inviable. That failed.
Not only is it possible to have intermediate stages in a DNA replication
'system' without origins, they exist in the present.
>
> 1. Why is this?
>
> Why is it that metazoan cells that divide rapidly do not seem to need
> origins (when it appears single-celled organisms need them)?
> DePamphilis notes that such promiscuous selection of initiation sites
> seem to be specific to embryos undergoing rapid cleavage. This, IMO,
> is quite relevant as the cells of such embryos are usually packed with
> proteins and mRNA that make transcription unnecessary for the first
> few rounds of cell division. Thus, these cells probably don't use specific
> origins because the chromosomal structure of these cells, along with a
> higher concentration of proteins used to replicate DNA, bypasses this
> requirement. In other words, the rapidly dividing embryonic cells of
> certain metazoans may reflect specialization. This then takes us to the
> next question:

Knock out a part and the function (DNA replication) remains. Doesn't
that mean, in 'thematic' terms that origins are not IC parts of the
system? Every form of DNA replication is specialized in some way.
>
> 2. Is this relevant to the historical origin of DNA replication? Larry
> thinks it is as he claims:
>
> >The non-origin examples suggest that primitive DNA replication
> >systems could have managed without a specific origin.
>
> I will credit Larry for positing this in a tentative fashion. However, I
> find it is be weakly suggestive at best. That rapidly dividing cells from
> metazoan embryos get by without origins doesn't seem to be good
> reason to think a primitive unicellular creature could pull off the same
> feat. There is no reason to think such a primitive cell would reflect the
> intracellular conditions of a metazoan egg (or embryonic cell) that are
> responsible for promiscuous initiation. Thus, in considering the origin of
> DNA replication, I still fail to see the evidence that clearly shows an
> origin of replication sequence was not needed.

Modern parasites are often good clues to finding out which functions are
necessary for viability because they are simplified. Again, I don't
think Larry is claiming that the ur-organism in which DNA replication
developed would be exactly like a modern metazoan embryo. But the
existence of such embryos show that the ur-organism need not have an
origin. Lack of origins is consistent with viability. Intermediate
systems can be functional. The ur-organism, BTW, likely was a bit like
the macronucleus of _Tetrahymena_ with gene sized 'chromosomes'
replicating independently and with promiscuous fussion/fission cycles.
But that is speculative too.
>
> Was I mistakenly restricting myself to the E. coli origin?
>
> Larry said:
>
> >She is making the common error of assuming that E. coli is the
> >paradigm for all bacteria but in this case the E. coli oriC is the
> >exception. We should avoid the impression that the organization of this
> >region is highly structured. Julie is describing systemic IC (E. coli) but
> >implying that it is thematic (all bacteria).

Limiting the 'thematic' to any specific lineage (whether that be as
large as bacteria or as small as the Genus _Escherichia_) is allowing
one to pick and choose. 'Thematic' means broad concepts like 'DNA
replication' not 'DNA replication in eubacteria' or 'DNA replication in
_Escherichia coli_).
>
[snip rest, not because it is boring, but because I do not find it
surprising that an ancient origin initiator which works by recognizing
several sites rather than a single one would be evolutionarily conserved
once it arose (by historical contingency) and would tend to re-rat
rather than drift further away from the historical consensus sequence.
And I certainly see oriC and dnaA as an ancient system (perhaps
predating DNA replication itself!) which was co-opted into a DNA
replication origin 'function' early in the eubacterial lineage. That
doesn't mean that newer similar 'themed' systems cannot arise, just like
oriK/recA did, rendering _E. coli's_ oriC/dnaA system non-IC.]

[Matt Silberstein]

In talk.origins Peter Nyikos <nyi...@math.SC.EDU> wrote:

I suspect that you may have had exposure to selective deletion as
well. I tried to explore what Julie could have meant. You took a piece
from the middle of the post, did not bother to mark your snips, and
acted as though that was my entire post.

I am able to distinguish between "IC systems have designers" and "all
designed systems are IC". However, if the second phrase were true, it
would give some kind of support for the first. Now maybe after you
attempt to critique my intelligence and education you can respond to
the actual content of my post. What kind of experience do you think
Julie was talking about? What experience shows or suggests that IC
systems have designers?

[Peter Nyikos]

hi...@cgl.ucsf.EDU (Wade Hines) writes:

>iz...@cleveland.Freenet.Edu (Julie Thomas) writes:

>>I am mystified by Larry's insistence that I am making the case that
>>DNA replication "could not have evolved." Apparently, Larry confuses
>>the fact that I *do* not think DNA replication evolved means I think it
>>"could not" have evolved. But that's sloppy thinking. For example, if
>>someone does not think there was life on Mars it doesn't mean they
>>think life could not have existed on Mars. Those are two very different

>>claims. Furthermore, just because I do not think DNA replication

>>evolved does not mean I think DNA replication *must* have been
>>designed.

>>Larry's confusion appears to stem (IMHO) from a desire to attribute
>>certainty to my beliefs. This could be due to his belief that he knows

>>me better than I know myself.

>I think there are far better explainations.

I question your sincerity here.

>1.) Julie has not been clear.
>2.) Julie is currently allied with Behe who is quite clear
> about his religous bias.

Where? He is a Roman Catholic but that seems largely
irrelevant to what he says in _Darwin's Black Box_.

> Maybe it's 'guilt' by association.
> Be it known, that there's nothing to be ashamed of.

Not ashamed of indulging in guilt by association? That
certainly seems in line with the rest of your behavior here,
Wade.

>3.) Julie writes things between the lines that Larry is quite
> capable of reading, but don't lend themselves to recapitulation.

Larry Moran has a stereotype which he seems ready to stick
to come hell or high water. He is reading things into
Julie's writing, that's the bottom line. Your attempt
to take the blame off him is very slick, but nothing more.

>Mostly, I stick with number 1.

Of course, because that's your style. See my long reply to Julie
on this thread where I quote a claim by you about
me to this same effect, and my response to it.

>But let's look back at this new revelation of Julies.
>She may be saying that she thinks DNA replication could have
>evolved, but didn't. She isn't being very clear about why she
>thinks it could have evovled or what 'could have' evolved means.
>Maybe she's holding out for some one is a google line like
>her mentor.
^^^^^^^^^^^

Flattery will get you nowhere, Wade.

> This could all be cleared up so easily if Julie would
>choose to be clear and forthright in her response.

I can't speak for Julie, but I see you have left out the
"googol" part below:

>Dna replication is:
>a.) quite easily evolvable but it was designed first.
>b.) no so easy, but given a half a billion years, could well have evolved.
>c.) may have evovled in a much simpler system, but what we see now
> is the product of 3 1/2 billion years of refinement of a very
> critical system.
>d.) probably more subject to horizontal transfer than any other
> system so the record is just to muddled to sort out. Simply don't know.
>e.) hard to imagine evolving as doing so seems quite implossible.

"quite impossible" is ignoring the googol-year-expected waiting
time possibility. Or more simply, the "expected waiting time far greater
than the age of the universe" possibility.

>That covers quite a range but I'm sure doesn't capture your beliefs.
>Why don't you be clear. You could do it in far less bandwidth than
>is required for you to dance around Larry.

She isn't dancing around Larry, Larry is dancing around her,
trying to extract a confession out of her. He is trying
to get her to confess to a motivation that hasn't been
MY motivation for the last twenty years. And I'll gladly
write a long, heartfelt essay some time this year if you
don't believe ME.

[But not now--for one thing, I don't want to spoil y'all's
fun by making it possible for Julie to just say, "I am coming from
the same place Peter is."]

Are YOU trying to extract the same confession out of her? If
not, what's YOUR game? Are you trying to get her to claim,
"expected waiting time far greater than the age of the universe",
so y'all can start interrogating her about her estimates
for expected waiting time, while sitting on y'all's duffs
and refusing to give YOUR ideas about how it could have
happened in LESS time?

Why don't YOU try to be more clear with what you are up to?
Not to mention YOUR scenario for how these things could be
expected to evolve in less time?

Could it be that you perceive evasiveness to be a virtue
where you and your net.allies are concerned, but a vice
where your net.opponents are concerned?

>>Of course, it is possible that Larry may be projecting his attitudes upon

>>me (projection is a common phenomenon with people who think they
>>know a person (or a group) better than the person or group know
>>themselves).

>That may be. It is also common when a void is left by one who plays
>so coy with their position that one can only guess.

What's YOUR position on whether the universe was created
by a supernatural being or not? You've been very, very
coy about this one for a lot longer than Julie's been posting.

Could it be that...but I don't like repeating myself.

>> That is, perhaps he is the one who believes "design could
>>not have occurred thus the evolution of DNA replication must have
>>occurred" and thus attributes this type of logic to me.

>Oh no. I'll assure you that this isn't Larry's belief. I'll wager
>heavily that Larry can say that could have been designed is an
>open possibility that is effectively impossible to rule out.

Now that you, his net.mentor, :-)
have put this idea in his head, I think he'll seize on it,
yessiree.

>I'll also suppose that he has a bias toward evolved based on the
>fact that it could be ruled out and yet the data seem to fit it
>so much more closely.

Since the data do nothing of the sort, I think I would be
justified in interrogating you just as relentlessly about
your beliefs concering the supernatural as Moran has
Julie concerning her beliefs about evolution.

It is indeed lucky for you that I can't spare the time
for that kind of thing. If the ratios were reversed,
and our kind outnumbered your kind as badly as your
kind outnumbers ours in talk.origins, (mine and Julie's--creationists
are off in another world by themselves) you would have
been subjected to such relentless interrogation on this
score that you would probably have quit talk.origins
by now.

>It's the difference between a tight fit and a loose fit Julie.
>Was designed to be how it is, is a loose fit. Exceedingly loose
>as there's no real way to not fit.

This is sheer garbage where my small variation on the
Crick-Orgel directed panspermy theory is concerned.

> But that's not at all like
>could not have been designed.

All kinds of things could not have been designed by those
Crick-Orgel style aliens, including the minutiae of our
planet as the fundies think Genesis says happened.

>I really do wonder where you get such an opinion from. I've
>not seen it around here.

I wonder why you didn't talk about the tight fit evolutionary
theory makes with the bacterial flagellum and the DNA rep
systems.

Actually I don't. You are going on blind faith in natural
selection, hoping someone a hundred times smarter than
you comes up with an explanation as complete and intelligible as,

"One theory is that the bacterial flagellum
and other systems Julie describes were designed by an
intelligent creature, or a team of them, in a lab
about 3.5 billion years ago,"

as I put it to you in a post on the thread,

Peter's Clotting Description (was Mr. Ford's "precictions")

earlier today.

>>After all, it
>>explains (to me) why it seems he is readily convinced by evidence for his
>>views that is weakly suggestive at best.

>This last characterization is one subjective opinion, at best. It's also
>predicated on some very dubious reasoning suggesting that Larry thinks
>replication could not have been designed.

Don't be ridiculous. Julie doesn't reason the way she depicted a
Moran-style-Julie as reasoning.

The characterization is based on y'all's failure to come up
with a natural selection explanation; a failure even more
glaring in the case of the bacterial flagellum, since y'all
have had MONTHS of time in which to do so.

> The evidence for that, is
>so weak as to not even come close to being suggestive, in my opinion.

You just love strawmen, don't you? You love them so much,
you accused me of creating them, of course without an iota
of evidence.

But that's your style, accusing others of doing things
you and your cronies do all the time. Only I don't call
it "projection," which implies an element of misguided
sincerity. I call it "apparent insincerity and dishonesty."

>>Furthermore, I can easily say
>>that DNA replication could have very well evolved. It doesn't make
>>much difference in the scheme of things to me. Can Larry as easily say
>>that DNA replication could have very well been designed? Would it
>>make a difference in the scheme of things for him?

>I'll wait to see if Larry responds.

How would you respond to Julie's question, had she said "Wade"
instead of "Larry"?

No fair claiming she didn't ask you. *I* am asking you.

I already know Paul Myers's answer; his actions speak a lot
louder than his words, so much so that his real answer comes
through loud and clear. But you are a lot more coy
than Myers is.

>Can we go with "weakly suggestive" with an "at best" qualifier to
>say you see some weakly suggestive evidence that DNA replication
>evolved but that the evidence is subject to alternative explainations
>that make you reluctant to hang your hat on the suggestiveness
>of the evidence?

The hat is way too heavy for such a flimsy peg, is what
I would answer.

[George Acton]

Wade Hines wrote:

>
> "John Mazor" <maz...@erols.com> writes:
>
>
> >6. The net result of items 1-5 is that arguing with Julie is like trying
> >to nail Jell-o to the wall, but okay, some of us will deal with that as
> >best we can. (Others will interpret 1-5 as a lack of commitment on Julie's
> >part to her various assertions and dismiss her, but she'll have to deal
> >with that as best she can.)
>
> I have an alternative impression which I suspect others share.
> There are real flaws and dubious tactics in some of Julies posts,
> but she also presents some real arguments as well which is such a
> refreshing change that many will put up with the doublespeak.

She really has only one argument, which is "this system is very
complicated and complicated things always have designers. Therefore
I have falsified Darwinism and shown how narrow-minded it is to
dismiss the supernatural".

> >Okay, we all understand now that your assertions are offered in the true
> >scientific spirit, and that you claim to hold no special attachment to
> >them. Fine. Now stop spending so much time on trivial points and focus on
> >more substantive items, lest we get the impression that you're more
> >interested in verbal sparring and dodging the issues. (And please, no
> >whining that "he started it.")
>
> Such evasiveness actually helps focus her antagonists on real
> issues, even if it sidetracks some.

This is open to question. Her guidelines are standard Creationist --
"my beliefs are off limits, but let's discuss how science is wrong
about Darwinism and how closed-minded scientists are". She started
with several long attacks on Behe's critics, meanwhile avoiding any
defense of Behe by claiming she hadn't read his book. She said she
didn't expect to convince anyone, but that she was just sharing her
delight in exploring a marvelous new concept. The only thing that
might be disingenious is her expression of "surprise" that people were
bothered by her insults. I can't see any purpose for her postings
except to annoy, but don't plan on wasting a lot of time worrying
about where she's consciously mischievous. But there's nothing
overtly dishonest about any of this.
At least people have sharpened their forensic and apologetic
skills, and we've had the enjoyment of reading Laurence Moran's
excellent survey of DNA replication mechanisms. And Ms. Thomas
should be proud of the exceptional accomplishment of devising a new
Internet art-form: molecular spam.
--George Acton

[Julie Thomas]

My, my. What a flurry of replies. Who should I respond to? John?
Paul M.? Paul G.? Maybe Wade? Wade again? Paul M. again?
Vladimir (but which reply?)? How about Matt? Or maybe George (again,
which reply?)? Maybe Doug? I think Howard replied (judging from
a reply by Peter). And I bet Larry's workin' hard on a reply.
Is there a pattern here? :)

Anyway, after all that writing, after all those arguments, after
all those claims, something is missing. What was it? [thinks for
a moment]. Oh yeah, now I remember....no one has yet to explain
how the replication of the bacterial chromosome evolved in a
Darwinian fashion. But, by golly, I'm supposed to believe that,
right?

Of course, since there have been so many replies, I simply cannnot
answer all (or even most) of the points y'all bring up. But let's
take a look at a few. Since I have yet to respond to John, let's
take a looksie.

In a previous article, maz...@erols.com (John Mazor) says:

>To Julie Thomas:
>
>Let me say up front that the discussions of cellular structures, chemistry,
>etc. are well over my head. I cannot begin to assess the validity of the
>arguments of you or your critics in this area.

That's fine. But then why did John end his article with this?

"Now stop spending so much time on trivial points and focus on
more substantive items, lest we get the impression that you're more
interested in verbal sparring and dodging the issues."

Like a scolding father, John feels he is in a position to make demands
on me. Interesting. But I have spent a *great* deal of time on
substantive items. And if John (or anyone else) can't admit this,
I will not waste my time on such folks (since there are *so* many
of ya to choose from).

>However, I cannot help but notice a few irritating patterns I see in your
>postings.

Well, John's getting irritated. We better end it here for the sake of
his blood pressure. :)

(seriously, I have no interest in arguing with folks who are going to
get emotional).

[Julie Thomas]

In a previous article, my...@netaxs.com (PZ Myers) says:

>> I never said it "had" to be designed. Again, Larry needs to recast my
>> position before dealing with it.
>
>Moran isn't the only one who is mystified, then. Let's assume you aren't
>just playing word games here, and that you really concede that evolution
>is not only possible, but that ic systems can evolve. You also concede that
>a designer is not a *necessary* explanation for ic systems.

"Let's assume?" Note that Paul is attempting (in a back-handed way)
to imply I am merely out to play "word games." Thus, I will not
answer his questions. :(

>What is your evidence that there was an "intelligent designer"?
>
>Your argument for a designer seems to have vanished, so I have no idea
>why you brought it up in the first place.

Hmmm. Like Larry, Paul too thinks this is all about "an argument
for a designer."

[Michael L. Siemon]

In article <5se2ff$l...@alexander.INS.CWRU.Edu>,
iz...@cleveland.Freenet.Edu (Julie Thomas) wrote:

+In a previous article, m...@panix.com (Michael L. Siemon) says:
+
+>I said that Julie has no justification (she has certainly *given*
+>none) for her rejection of evolutionary explanations.
+
+What an odd way of seeing things. I need justification for not thinking
+bacterial DNA replication and/or flagella evolved? Michael has it
+backwards. If he thinks I am obligated to believe such things, he
+should at least try to convince me.

Julie,
You are under no obligation to me, or anyone, on USENET --
except insofar as your own ethical strictures might impose them on
you. I would *hope* that you feel some obligation, as a mature
human being, to deal honestly with others in an open forum that
imposes no constraints on you of itself. Honesty with others, in
a context of scientific and critical inquire, involves a *very*
serious component of self-criticism and self-examination to avoid
the mere mechanical repetition of favored stances.

You come across as intelligent (*extremely* refreshing in the general
mass of anti-evolutionists) and even well-informed (as far as I can judge
from the outside) in relevant and important fields of biology. In this,
I think you are *unique* in my 10 years of reading talk.origins. Pardon
me if I hold you to as high an ethical standard as you seem to aspire to
intellectually.

And yet, you *continually* follow the same *stupid* trajectory as the
moronic Creationists like ksjj and markh. When confronted with excellent
data on variation in bacterial reproduction origins and informed deduction
about probable ancestral versions very different from the "IC" systems you
are going on and on about, what do you do? You introduce totally irrelevant
and specious digs at abiogenesis. And your comment is either

a) Totally ignorant of the history of speculation from Oparin
to Miller-Urey, and of the complex criticial evaluation of
the assumptions and ideas behind these early efforts up to
current speculations -- *none* of which are taken as "truth"
and *none* of which are relevant to issues of the evolution
of current biochemical systems (bacterial or otherwise, and
"thematic" versus "systemic" pulls no irons out of the fire
on this.)
or b) Devious as all hell.

If you are ignorant, fine -- just don't go around making ringing state-
ments reeking with comtempt about things you are not in a position to
judge. If not, there is a clanging alarm bell about your honesty that is
going to ring in my mind, and that of most other interested readers.

Your evasions of questions addressed to you, by people who have taken
the trouble to take *you* seriously enough to look carefully at what you
write, is even worse. You have made *one* move in a critical game, by
urging a critique of standard theory. No problem. *Now* you must subject
yourself to the *equivalent* critique -- and answer it honestly, or you
have forgone any claim to be answered as to your own questions. You *may*
not dodge questions and *at the same time* regard *your* questions as
being of any moment. Or else you are a fraud.

The only "obligations" here are ones that you have to impose on yourself.
But if you do not show any signs of accepting such a discipline, you also
forgo any respect (and deserve no answers) from your readers.

[John Mazor]

Julie Thomas <iz...@cleveland.Freenet.Edu> wrote in article

<5sgvqb$i...@alexander.INS.CWRU.Edu>...

>
>
> "Now stop spending so much time on trivial points and focus on
> more substantive items, lest we get the impression that you're more
> interested in verbal sparring and dodging the issues."
>
> Like a scolding father, John feels he is in a position to make demands
> on me.

And like the precocious child, you think that people will forever be
mesmerized by your charming qualities (which, BTW, you do have). As long
as you continue to waste your time (and ours) by cheap tricks (as in the
above, where you dodged the point and tried to turn it into a teenager's
"you can't control me" fight), then you do yourself a disservice.

> But I have spent a *great* deal of time on
> substantive items. And if John (or anyone else) can't admit this,
> I will not waste my time on such folks (since there are *so* many
> of ya to choose from).

I never said you haven't spent a great deal of time on substantive issues.
You're reading far too much into what I said to think you know what I
believe. (Oops! I'm starting to sound like Julie. So-o-o sorry!)

> >However, I cannot help but notice a few irritating patterns I see in
your
> >postings.
>
> Well, John's getting irritated. We better end it here for the sake of
> his blood pressure. :)

Is this all you have to say? I make numerous comments about how you
present your points (and fail to do so), chide you for playing word games,
etc. etc. etc., and you choose *this* to comment on???

Julie, this is precisely the kind of elusiveness that I and many others
find so "irritating" about you. You obviously have a good mind. Use it
for more than scoring meaningless points in meaningless sorties.

> (seriously, I have no interest in arguing with folks who are going to
> get emotional).

Hoo, boy! Then I hope you never get crossways with Peter! (Fat chance,
considering the mail these two have floated.)

[PZ Myers]

In article <5sh0u1$j...@alexander.INS.CWRU.Edu>, iz...@cleveland.Freenet.Edu
(Julie Thomas) wrote:

> In a previous article, my...@netaxs.com (PZ Myers) says:
>
> >> I never said it "had" to be designed. Again, Larry needs to recast my
> >> position before dealing with it.
> >
> >Moran isn't the only one who is mystified, then. Let's assume you aren't
> >just playing word games here, and that you really concede that evolution
> >is not only possible, but that ic systems can evolve. You also concede that
> >a designer is not a *necessary* explanation for ic systems.
>
> "Let's assume?" Note that Paul is attempting (in a back-handed way)
> to imply I am merely out to play "word games." Thus, I will not
> answer his questions. :(

You have been very vague about precisely what you are trying to prove
lately -- that's why I said "let's assume...". I am *trying* to give you
the benefit of the doubt. That was not a back-handed comment at all --
I am sincerely trying to understand your point.

>
> >What is your evidence that there was an "intelligent designer"?
> >
> >Your argument for a designer seems to have vanished, so I have no idea
> >why you brought it up in the first place.
>
> Hmmm. Like Larry, Paul too thinks this is all about "an argument
> for a designer."

No, as I said above, I'm mystified now. I'm thoroughly confused. You've
posted thousands of lines of text, but your point is unclear. I thought
this discussion was all about ic and design, but apparently it is not. It
would help if you would say *succinctly* what the topic of all your postings
was supposed to be.

As you note, I'm not the only one who thought your discussion was directed
towards "intelligent design". I suppose it is possible that we are all
merely stupid, but you might want to consider the possibility that *YOU*
have been less than straightforward in defining your intent. The fact that
you now choose to duck the questions doesn't encourage much confidence in
you, either.

--
Paul Z. Myers
http://fishnet.bio.temple.edu/

[PZ Myers]

In article <5sgvqb$i...@alexander.INS.CWRU.Edu>, iz...@cleveland.Freenet.Edu
(Julie Thomas) wrote:

> My, my. What a flurry of replies. Who should I respond to? John?
> Paul M.? Paul G.? Maybe Wade? Wade again? Paul M. again?
> Vladimir (but which reply?)? How about Matt? Or maybe George (again,
> which reply?)? Maybe Doug? I think Howard replied (judging from
> a reply by Peter). And I bet Larry's workin' hard on a reply.
> Is there a pattern here? :)

Are you this naive? Of course there is a pattern here. People who frequent
and post to this newsgroup are interested in problems of evolutionary
origins, and tend to respond to issues in evolution. Why are you acting
surprised? Were you hoping that we would all just ignore you?

>
> Anyway, after all that writing, after all those arguments, after
> all those claims, something is missing. What was it? [thinks for
> a moment]. Oh yeah, now I remember....no one has yet to explain
> how the replication of the bacterial chromosome evolved in a
> Darwinian fashion. But, by golly, I'm supposed to believe that,
> right?

Yes, it has been explained that you have been misled or misleading (the
requirements for replication are not as stringent as you claimed), and
that you have been pursuing a red herring -- the modern bacterial
replication system is not a good model for the early replication system.
As one example, the maintenance of long chromosomes is not a constraint
that would have been present in the early replicators. You've also been
given citations that show sequence homology between the various components
you've listed, and the pattern of descent with modification that can
be inferred from that. It is rather troubling that you can pretend that
there were no replies of any substance, but I suppose that does save
you the difficulty of addressing any of those replies in an equally
substantive way, doesn't it?

>
> Of course, since there have been so many replies, I simply cannnot
> answer all (or even most) of the points y'all bring up. But let's
> take a look at a few. Since I have yet to respond to John, let's
> take a looksie.
>
> In a previous article, maz...@erols.com (John Mazor) says:
>
> >To Julie Thomas:
> >
> >Let me say up front that the discussions of cellular structures, chemistry,
> >etc. are well over my head. I cannot begin to assess the validity of the
> >arguments of you or your critics in this area.
>
> That's fine. But then why did John end his article with this?
>

> "Now stop spending so much time on trivial points and focus on
> more substantive items, lest we get the impression that you're more
> interested in verbal sparring and dodging the issues."
>
> Like a scolding father, John feels he is in a position to make demands

> on me. Interesting. But I have spent a *great* deal of time on

> substantive items. And if John (or anyone else) can't admit this,
> I will not waste my time on such folks (since there are *so* many
> of ya to choose from).
>

> >However, I cannot help but notice a few irritating patterns I see in your
> >postings.
>
> Well, John's getting irritated. We better end it here for the sake of
> his blood pressure. :)
>

> (seriously, I have no interest in arguing with folks who are going to
> get emotional).

<sarcasm>Great response. You sure clobbered him in the war of
wits!</sarcasm> You just chopped off everything in the middle, ignoring it
totally,
and used one mild comment to excuse yourself from answering anything. I
notice you did exactly the same thing in a reply to me today -- you ducked
the question altogether. Is this your new strategy? It puts you in the
same league as karl and markh...I thought you were smarter than that.

But perhaps you are just getting *irritated* and *upset* at all these people
who have been trying to poke holes in your pet theories. Take a posting
break, and come back when you've recovered your equilibrium and are willing
to address content again, OK?

[PZ Myers]

In article <hines.8...@cgl.ucsf.edu>, hi...@cgl.ucsf.EDU (Wade Hines)
wrote:

> iz...@cleveland.Freenet.Edu (Julie Thomas) writes:
>
> >My, my. What a flurry of replies. Who should I respond to? John?
> >Paul M.? Paul G.? Maybe Wade? Wade again? Paul M. again?
> >Vladimir (but which reply?)? How about Matt? Or maybe George (again,
> >which reply?)? Maybe Doug? I think Howard replied (judging from
> >a reply by Peter). And I bet Larry's workin' hard on a reply.
> >Is there a pattern here? :)
>

> It appears that the pattern will be to post and run away.
> Maybe you should make direct replies to those whom you were directly
> replying to. Any comments of special merit in other replies can be
> tagged in. Keeps things from exploding.
>
> Or you could post and run away. Whatever suits you best.

Wade, you completely missed the point of the message. *Julie* is supposed
to post, and *we* are supposed to run away...at least, I think that is
what she would prefer.

[Julie Thomas]

In a previous article, hi...@cgl.ucsf.EDU (Wade Hines) says:

>iz...@cleveland.Freenet.Edu (Julie Thomas) writes:
>
>>My, my. What a flurry of replies. Who should I respond to? John?
>>Paul M.? Paul G.? Maybe Wade? Wade again? Paul M. again?
>>Vladimir (but which reply?)? How about Matt? Or maybe George (again,
>>which reply?)? Maybe Doug? I think Howard replied (judging from
>>a reply by Peter). And I bet Larry's workin' hard on a reply.
>>Is there a pattern here? :)
>
>It appears that the pattern will be to post and run away.

Almost. The pattern I saw developing has just been actualized by
your response - so many people would reply that it would become simply
too time-consuming to respond to all. Thus, when I don't respond,
I'd be accused of "running away." Just as I figured.

>Maybe you should make direct replies to those whom you were directly
>replying to. Any comments of special merit in other replies can be
>tagged in. Keeps things from exploding.

Like I haven't been making direct replies for the past 3-4 months.

>Or you could post and run away. Whatever suits you best.

See what I mean?

[Mark Isaak]

[Most names removed to concentrate on the principles, not the people.]

In article <1997080822...@milo.math.sc.edu>,
Peter Nyikos <nyi...@math.SC.EDU> wrote:
>at...@best.comNOSPAM (Mark Isaak) writes:
>>[Person A] did not say you have no justification and need one; he said
>>you have no justification. To all appearances, he is right.
>
>Get real, Mark. Are you seriously suggesting [person A]
>is NOT of the opinion that [person B] needs to provide justification
>for what she wrote?

Yes.

>If so, what do you make of [person C] badgering [person B]

>to answer the (implied) question?

If person B wants anyone else to accept, or even understand, her views,
she will need to define her terms.

A person is always welcome to believe whatever crap the person wants to
believe. If, however, the person wants anyone else to accept the same
belief, that person had better justify the belief somehow. And, to return
to the specific belief under consideration, nobody has yet supplied an
iota of justification for *any* beliefs concerning whatever it is that the
string of characters "design" refers to.

I'm glad that reciting the mantra "design" makes some people happy, but
don't expect *me* to use it for no reason.
--
Mark Isaak at...@best.com http://www.best.com/~atta
"To undeceive men is to offend them." - Queen Christina of Sweden

[Julie Thomas]

In a previous article, at...@best.comNOSPAM (Mark Isaak) says:

>In article <5se2ff$l...@alexander.INS.CWRU.Edu>,

>Julie Thomas <iz...@cleveland.Freenet.Edu> wrote:
>>In a previous article, m...@panix.com (Michael L. Siemon) says:
>>
>>>I said that Julie has no justification (she has certainly *given*

>>>none) for her rejection of evolutionary explanations.
>>

>>What an odd way of seeing things. I need justification for not thinking

>>bacterial DNA replication and/or flagella evolved? Michael has it

>>backwards. If he thinks I am obligated to believe such things, he

>>should at least try to convince me.
>

>Michael Siemon did not say you have no justification and need one; he said

>you have no justification. To all appearances, he is right.

Well, if I don't need a justification, does it mean anything that you
think I have no justification??

[Laurence A. Moran]

In article <5sicri$7...@alexander.INS.CWRU.Edu> iz...@cleveland.Freenet.Edu
(Julie Thomas) writes:
>
>In a previous article, sve...@oncology.wisc.edu (Vladimir Svetlov) says:

>>I missed the 50 pages long article about aliens designing replication?!!
>>Good. Cause them did not. Cause there is no evidence for them aliens except
>>recurrent anal bleeding of my cousine Billy-Joe in Dickson Co., TN.
>>Seriously, dudes, how many more loonies would bring forward their
>>bewilderment with modern cellular machines and claim that someone just have
>>to create it (apparently, using Lewin's Genes VI as a manual)?
>
>Hmmm. So now I am also a loonie? I suspect that Larry may have
>labeled my postion as "alien design" hoping someone like Vladimir
>would take it and run.
>
>What's interesting is that Vladimir admits not reading my article,
>but feels free to comment on it. Even to the point of claiming I
>used Lewin's text as a manual. Of course, I did not. So how is it
>that Vladimir could make such an erroneous claim (yet seem fairly
>confident that it is correct)?

Probably because he's an idiot. Julie, you don't have to respond to every
kook that comes out of the woodwork.

> I think it has to do with pack-mentality.
>Vladimir gets his info from second-hand sources and trusts those sources
>because he is part of the pack. I recall Myers making a claim that
>my article was derived from textbooks. Moran labels my position
>as "alien design." Then along comes Vladimir, probably having read
>Moran and Myers, and voila, he speaks erroneously. Of course, I could
>ignore this. But then someone else will come along and build on
>Vladimir's misconceptions. And round and round it goes.

Go ahead and ignore Vladimir. It won't matter one wit to most of us. In
fact we'd be glad to help you ignore people like him. If you want, we
can create a whole new thread called "Vladimir's Misconceptions" and
then we'll all put it in our KILL files. OK?

There are others in my KILL file already.

Larry Moran

[Mark Isaak]

In article <5sibpe$4...@alexander.INS.CWRU.Edu>,

Julie Thomas <iz...@cleveland.Freenet.Edu> wrote:
>Well, if I don't need a justification, does it mean anything that you
>think I have no justification??

To you, I don't know. To me, yes, it does matter. If you are never going
to explain what "design" means when you use the word, then I can skip all
your posts as utterly pointless.

[Wade Hines]

iz...@cleveland.Freenet.Edu (Julie Thomas) writes:

>My, my. What a flurry of replies. Who should I respond to? John?
>Paul M.? Paul G.? Maybe Wade? Wade again? Paul M. again?
>Vladimir (but which reply?)? How about Matt? Or maybe George (again,
>which reply?)? Maybe Doug? I think Howard replied (judging from
>a reply by Peter). And I bet Larry's workin' hard on a reply.
>Is there a pattern here? :)

It appears that the pattern will be to post and run away.

Maybe you should make direct replies to those whom you were directly
replying to. Any comments of special merit in other replies can be
tagged in. Keeps things from exploding.

Or you could post and run away. Whatever suits you best.

[Julie Thomas]

In a previous article, my...@netaxs.com (PZ Myers) says:

>In article <5sgvqb$i...@alexander.INS.CWRU.Edu>, iz...@cleveland.Freenet.Edu
>(Julie Thomas) wrote:
>

>> My, my. What a flurry of replies. Who should I respond to? John?
>> Paul M.? Paul G.? Maybe Wade? Wade again? Paul M. again?
>> Vladimir (but which reply?)? How about Matt? Or maybe George (again,
>> which reply?)? Maybe Doug? I think Howard replied (judging from
>> a reply by Peter). And I bet Larry's workin' hard on a reply.
>> Is there a pattern here? :)
>

>Are you this naive? Of course there is a pattern here. People who frequent
>and post to this newsgroup are interested in problems of evolutionary
>origins, and tend to respond to issues in evolution. Why are you acting
>surprised? Were you hoping that we would all just ignore you?

Sorry, but I saw very little in that last flurry of replies that had
to do with evolution. The only one I recall was Wade's, and I have
already replied to that. Others may have brought up isolated points
here and there, but from where I sit, they appear to be situated in a
context of ridicule, personal attacks, and/or attempts to misrepresent
my position. If y'can't talk about "issues in evolution" without
resorting to such tactics, that's not my problem.

Of course, when it comes to pack mentality, I probably am naive.
I've never been much for joining a pack. In fact, on several occasions
in the past, I've walked into arguments where one person was arguing
with four or five. If the one person is arguing a point I agree with,
I'll join in. If the five are arguing a point I agree with, I
let it alone as I think it is just plain mean to gang up. But that's
just me I suppose. Y'do what y'want. There's safety in dem der numbers
(although why one would choose comfort over a challenge is something
I don't understand very well).

>> Anyway, after all that writing, after all those arguments, after
>> all those claims, something is missing. What was it? [thinks for
>> a moment]. Oh yeah, now I remember....no one has yet to explain
>> how the replication of the bacterial chromosome evolved in a
>> Darwinian fashion. But, by golly, I'm supposed to believe that,
>> right?
>
>Yes, it has been explained that you have been misled or misleading (the
>requirements for replication are not as stringent as you claimed),

This is merely your opinion (and that it might be backed up by the
pack means nothing to me). And the bias beind your opinion is
rather clear to me. When Larry misled folks into thinking I claimed
DNA replication could not have occurred, not a peep from Paul. When
Larry claimed I was arguing that aliens designed DNA replication, not
a peep from Paul. Shall I continue? Thus, I simply do not recognize
Paul's position as one that can make even a semi-objective judgment
about what consitutes "misleading."

As for the scientific claims, I have *already* dealt with all those
"explanations." But that's not going to matter when I'm interacting
with such a biased man.

and
>that you have been pursuing a red herring -- the modern bacterial
>replication system is not a good model for the early replication system.

Says who? You? The pack? I realize this may be *your* assumption,
but I don't see the validity in it except that you *need* it.

Furthermore, you and others apparently think modern viral systems
are good models for the early replication system. Isn't that odd?

>As one example, the maintenance of long chromosomes is not a constraint
>that would have been present in the early replicators.

How do you know? Are you thinking of those modern viral systems?

You've also been
>given citations that show sequence homology between the various components
>you've listed, and the pattern of descent with modification that can
>be inferred from that.

Yes, and I have shown that those sequence homologies fail to damage
my claims about IC.

It is rather troubling that you can pretend that
>there were no replies of any substance, but I suppose that does save
>you the difficulty of addressing any of those replies in an equally
>substantive way, doesn't it?

Er, I said:

> Anyway, after all that writing, after all those arguments, after
>> all those claims, something is missing. What was it? [thinks for
>> a moment]. Oh yeah, now I remember....no one has yet to explain
>> how the replication of the bacterial chromosome evolved in a
>> Darwinian fashion.

And it was clear I was talking about the last flurry of replies. Now,
it is rather troubling that Paul can pretend that there were such
replies that outlined this phenomenon. And since Paul wants to be
my mentor, perhaps he can *specifically* point out where someone
explained how the replication of the bacterial chromosome evolved in
a Darwinian fashion."

>> Of course, since there have been so many replies, I simply cannnot

No, I said I will not argue with someone who appears to be getting emotional.
If y'all can't make a point without getting irritated, that's not my
problem.

I
>notice you did exactly the same thing in a reply to me today -- you ducked
>the question altogether. Is this your new strategy? It puts you in the
>same league as karl and markh...I thought you were smarter than that.

If you can't reply to me without misrepresenting me, it's not my problem.

>But perhaps you are just getting *irritated* and *upset* at all these people
>who have been trying to poke holes in your pet theories.

I'm not the one who claimed to be irritated (you are mistaking me for
John and Howard).

Take a posting
>break, and come back when you've recovered your equilibrium and are willing
>to address content again, OK?

Me thinks you might again be confusing me with your stubborn and misguided
female graduate student.

[Julie Thomas]

In a previous article, hi...@cgl.ucsf.EDU (Wade Hines) says:

>iz...@cleveland.Freenet.Edu (Julie Thomas) writes:
>
>>I am mystified by Larry's insistence that I am making the case that
>>DNA replication "could not have evolved." Apparently, Larry confuses
>>the fact that I *do* not think DNA replication evolved means I think it
>>"could not" have evolved. But that's sloppy thinking. For example, if
>>someone does not think there was life on Mars it doesn't mean they
>>think life could not have existed on Mars. Those are two very different
>>claims. Furthermore, just because I do not think DNA replication
>>evolved does not mean I think DNA replication *must* have been
>>designed.
>
>>Larry's confusion appears to stem (IMHO) from a desire to attribute
>>certainty to my beliefs. This could be due to his belief that he knows
>>me better than I know myself.
>
>I think there are far better explainations.

>1.) Julie has not been clear.
>2.) Julie is currently allied with Behe who is quite clear

> about his religous bias. Maybe it's 'guilt' by association.

> Be it known, that there's nothing to be ashamed of.

>3.) Julie writes things between the lines that Larry is quite
> capable of reading, but don't lend themselves to recapitulation.
>

>Mostly, I stick with number 1.

Hmmm. Since Wade sticks with number 1, why did he even mention numbers
2 and 3? I suspect he is trying to poison the well by putting out
images/perceptions, but refusing to take responsibility for the images/
perceptions he helps to create. Thus, I see no reason to acknowledge
this type of subtle attack with a further reply.

[Julie Thomas]

In a previous article, gac...@softdisk.com (George Acton) says:

> Although you claimed not to have read his book, you appear to be
>defending his concept of "IC", without coming up with a definition
>that makes any more sense than his.

Tell me George, by noting that I "claimed not to have read [Behe's]
book," are you trying to imply that I was being less than honest?

[George Acton]

Julie Thomas wrote:
>
> In a previous article, hi...@cgl.ucsf.EDU (Wade Hines) says:
>
>

> >You defined OriC as a part of the system of DNA replication with
> >the function of replicating DNA and the specific function of OriC
> >as the origin of replication.
>
> As do most scientists.
>
> >The definition of IC states that if one can remove any part
> >and still have function, the system is not IC.
>
> No. That part is then not a component of the IC system. I've already
> covered this.
>
> >Thus, if removing the part OriC does not stop function - replication
> >of DNA - then DNA replication is not IC.
>
> No, then OriC would not be an actual player in the IC system of DNA
> replication.
>
You're using a definition of "IC" that's totally at variance with
Behe's. According to him, it's a property of a "system" such that
every "part" is necessary for "function". As he uses the term,
it's a binary property of the system -- either there or not. This
carries out the metaphor of the watch or mousetrap, and relates
to common-sense notions of "design".
You're perfectly free to use any terms you want to, but it
would be less confusing to readers if you suppled a definition
for your version. It would also clear up "thematic" and "systematic"
IC. As it is, they appear to be as meaningful as "thematic phlogiston"
and "systematic luminiferous ether".
--George Acton

[Julie Thomas]

In a previous article, hi...@cgl.ucsf.EDU (Wade Hines) says:

>>>And I can't recall if you've commented on

>>> de Massy B; Fayet O; Kogoma T.
>>> Multiple origin usage for DNA replication in sdrA(rnh) mutants of
>>> Escherichia coli K-12. Initiation in the absence of oriC.
>>> Journal of Molecular Biology, 1984 Sep 15, 178(2):227-36.

>>>Not only does replication work in the absense of oriC, it appeared
>>>to work from 4 different alternative sites.

>>Wade has left out a lot of relevant material as far as this system
>>relates to the oriC system and its IC role.

>Excuse me for interrupting. I wrote a relatively short sentence which
>detailed exactly what was relevent to IC. This is why we asked for
>definitions before. Definitions of parts and systems and functions.

And you left out a lot of material that I find relevant. If you had read
my article on DNA replication and IC, you might have realized this.

>You defined OriC as a part of the system of DNA replication with
>the function of replicating DNA and the specific function of OriC
>as the origin of replication.

As do most scientists.

>The definition of IC states that if one can remove any part
>and still have function, the system is not IC.

No. That part is then not a component of the IC system. I've already
covered this.

>Thus, if removing the part OriC does not stop function - replication of
>DNA - then DNA replication is not IC.

No, then OriC would not be an actual player in the IC system of DNA
replication.

>But I see below that you bring up "thematic IC" again. Let's here you
>out, even if I made the only point from the paper that seem relevent to
>IC as Behe and his local advocate Peter define it.

And it ignored just about everything I wrote about IC in my DNA rep
article. If you are going to ask *me* a question, why are you surprised
when I answer using the notions *I* have outlined previously??

>Let's see if this paper is indeed relevant to my article (although I will
>be brief for lack of time).

See? As I said, was it relevant to *my* article?

<<< thanks for being brief. i tried to be >>>

>>The article that Wade cites was one of the first indications that E. coli
>>has an alternative system of DNA replication. This system is fairly
>>well-understood and is called constitutive stable DNA replication
>>(cSDR). It is a system that is normally repressed but can be activated
>>under extreme conditions. It shares many of the actual players used
>>by the oriC system, but also shows some significant differences. But
>>does it help us explain the origin of the irreducibly complex oriC
>>system?

>I'm confused again. Two different systems. Same function. Some shared
>players. I know something about DNA replication but can't quite handle
>all the taxonomy of assigning system and part definitions. It seems
>so arbitrary to me. Maybe that's why a dummy like me needs some
>better definitions.

Read my article.

>>Unlikely. Does it damage my case about IC and bacterial
>>chromsosomal DNA replication? I don't think so. Here are some of
>>my reasons.

>>1. First, even the cSDR system employ specific origins (called oriK).
>>Thus, it doesn't damage my thematic IC claims about the need for
>>an origin.

>When parts become generics, the notion of IC, now called 'thematic IC'
>looses even the illusion of significance.

Those are your perceptions, not mine. For example, I suspect that
thematic IC will become very helpful to me when I discuss eucaryotic
DNA replication.

>>2. The cSDR system does not employ DnaA. But I never claimed that
>>DnaA is part of purely thematic IC, only a factor (acting in trans) that
>>interacts with the origin to initiate replication.

>Maybe you should explain your lingo to Peter who may want to defend
>you.

Hmmm. Wade only has about a dozen folks on this board who would
probably rush quickly to "defend" him, yet I get the odd feeling it
bothers him if just one other person "defends" me. Or maybe it's
supposed to be a subtle dig at Peter. I don't know.

>"acting in trans" is a rather essoteric genetics notion which
>differentiates gene products from gene sites. Gene sites are places
>where the functional activity is the DNA itself, a recognition sequence
>or motif. Trans acting factors are most commonly proteins but can
>also be RNA. This bit of obscura however barely seems relevent and
>I'm frankly at a loss as to why you mention the trans acting part
>at all.

Let's see. First he says:

"Maybe that's why a dummy like me needs some better definitions."

{although I don't think Wade is a "dummy."}

but now he complains when he gets one? Sorry for trying to be more
precise.

>>And cSDR has such a factor - RecA. OriC replication does not need
>>RecA. Thus, here is yet another example of something I talked about
>>in my article - a different system is not necessarily simpler (and thus
>>less IC).

>This is where people get so confused by you Julie. You seem to be
>conflating simpler and IC. Let's use the whole words. You seem to
>be conflating simpler and Irreducibly Complex. You can't just parse
>this into two words and it's the irreducibly part that is being
>addressed, not the complex part.

And this is why I don't understand your confusion. One of the ways to
"attack" an IC system is to try to break it down into simpler systems
(that's why I said *less* IC). Thus, a simpler system is one step in an
attempt to reduce the IC system to something that is not IC. It's such a
common "attack" (but not the only type) that I fail to understand your
confusion. My point was to address *this* line of attack (explained in
my DNA rep article).

>So what we have in a cartoonish sketch is some DNA replication
>machinery that has in one part a site on the DNA which can be bound
>by a protein in such a way that the remainder of the DNA replication
>machinary can get in there and do the dirty deed.

But not just any ol' site or protein. If that was true, you'd be in a better
position.

>The fact is that there are multiple DNA binding proteins.

So? Do they explain DnaA's interaction with oriC? As explained in my
article, I do not think "similar activity", in-of-itself, is relevant. If you
think it is, explain. IMO, there's much more work to be done if y'wanna
challenge IC.

>Proteins which also have the abilility to bind co-operatively are
>likewise quite common.

So? I suppose if someone wants to believe DNA replication evolved via
a Darwinian mode, the mere fact of DNA-binding proteins would become
an understandably handy theme in a just-so story. But I need more
than that.

>These don't appear to be terribly rare functions and so are not
>that unlikely to have evolved.

You've not shown that the intiation of bacterial chromosome replication
is likely. In fact, if this explanation was so likely, why the strong
conservation of the oriC/DnaA type of initiation? Your explanation
suggests to me that various lineages would have found various solutions
and we'd therefore see all kinds of bacteria using very different modes
of chromosomal replication initiation. But we don't. Thus, it looks an
awful lot like an unlikely solution (but then what would be so unlikely
about it given your description of common binding protein?). Either that,
or something even more unlikely happened - all the critters who found
different modes of replicating their chromosomes disappeared. Now, if
we're looking at something that was designed and has evolved since the
design event, the pattern makes more sense (at least to me).

>The fact that the remainder of the DNA replication machinary can work
>off different origination complexes makes this a very reducible system,
>if still a complex one.

Nope. At the most it would mean a specific initation mechanism was
not part of the IC system (which doesn't mean the rest is "very
reducible). But I don't think you've even gotten this far.

BTW, always keep in mind that I chose DNA replication *because* it was
vulnerable to these types of responses. Now, if y'got problems handling
this one, there's plenty more that's gonna be much harder.

>Complexity does tend to create the illusion of unlikely to have
>evolved but I'm sure Julie will acknowledge the problem with such
>a simple minded conclusion.

No one is arguing about mere complexity.

>>3. From a systematic IC perspective, oriK/RecA are able to
>>complement OriC/DnaA activity. But is this relevant? Recall that in
>>my essay, complementation by itself is not sufficient.

>Is this another component of the ad hoc definition of 'thematic IC'
>or was there some special logic behind this that did not completely
>immasculate the concept of IC regarding the appearance of needing
>a designer.

It was clearly spelled out in my DNA rep article.

>The availability of subsystems for recruitment into more complex
>systems goes directly toward the essence of the IC arguement about
>'difficult to imagine having evolved'.

First of all, you are responding to me and I do not think the essence of
the "IC argument" is that it means something "is difficult to imagine
having evolved." One thing seems clear to me. Y'all have no difficulty
when it comes to imagining things.

Secondly, the cSDR system is not truly a subsystem that is recruited into
a larger system. It is more properly thought of as an alternative
system that works under specific conditions.

Thirdly, the alternative system goes nowhere if it appeared *after* the
IC system in question.

Fourth, the alternative system seems itself to be quite IC.

Fifth, the alternative system doesn't appear to account for the commonly used
system.

>>And in this case, there are several significant facts which cause me to
>>doubt the significance of the oriK/RecA system when it comes to the
>>origin of the IC oriC/DnaA system:

>>a. The oriK/RecA system was identified not in wild-type cells, but in
>>mutant cells lacking RNase H activity (which, BTW, don't grow in rich
>>media). RNase H is a nuclease that degrades ssRNA when it is bound
>>to ssDNA. If cSDR was the original replication system, one needs to
>>explain away RNase H activity which itself appears to be quite ancient.

>There is little reason to suppose that either currently observed system
>was the original given so many many billions of generations with
>which to optimize, but this is rather obvious.

Nevertheless, we can make judgments about the relative age of systems
based upon their distribution. In this case, the oriC/DnaA system has
been found in many species that are distantly related and this leads
scientists to conclude it appeared well over a billion years ago. The
cSDR system so far has only been identified in E. coli, thus it could very
well be a more recent adaptation. If this turns out to be true, the cSDR
system itself doesn't explain the origin of the oriC/DnaA system.
However, as you say......

>Even if one supposes a 'much more like' cSDR system billions of
>years ago, one wouldn't expect the retention of all factors required
>to allow this putative ancestor to function in a world where it
>is no longer the mainstay. This is also rather obvious.

As it stands, this would mean that E. coli alone retained it and everyone
else disposed of it. A more parsimonious explanation would be to
propose that E. coli obtained it at a later date.

>At the top of this post, you suggested I left out many details
>of relevance. I saw no need to set up the straw men you are setting
>up just so I could know them down.

As it appears to me, you've done nothing but claim we can't use the
data from living systems to opine on the origin of systems except when
it comes to finding facts that can be fitted into a vague just-so story
that happens to support your position. How convenient.

>>b. The oriK/RecA may well be more recent. So far, this system has
>>only been identified in E. coli, in contrast to the oriC system which has
>>been seen in several distantly related species.

>>c. As a continuation of point b., the oriK/RecA system may serve as a
>>back-up system that only functions sufficiently as a short-term
>>solution. This hypothesis is supported by the fact that the oriC system
>>is so strongly conserved. If the oriK system could effectively replace
>>the oriC system as a long-term, or even, primary system, we would
>>expect to see many species of bacteria using this system as their
>>primary system.

>Firstly, let's clear up that there was no claim about oriK as the
>original system. Rather the claim is that an alternative site of
>the origin of replication works with the rest of the DNA replication
>machinary. This makes oriC and DNA replication non-IC by the
>definition put forth by Behe and as advocated by Nyikos.

No it doesn't.

First, oriC can only be replaced under *certain* conditions. You thus
need to show these conditions are relevant.

Secondly, even if oriC is displaced from the IC system, this doesn't mean
DNA replication is not IC. You confuse the role of one component for the
whole system itself.

Thirdly, you are arguing with me and not Peter or Behe. And I have
argued that the mere example of similar activity is *not* sufficient for
displacing an actual player from an IC system.

>Other, weaker definitions of IC such as that put forth by Julie have
>been repeatedly criticized as being 'strawman IC' definitions
>as they are so easily derived or identified in systems where
>evolution is strongly evidenced.

The evolution of bacterial chromsomal replication is "strongly
evidenced?" Why not back up that claim?

>>4. Of course, even if cSDR represents the original method of bacterial
>>chromosome replication, it doesn't do anything but change the actual
>>players in the IC system. Instead of oriC, we have oriK. Instead of
>>DnaA, we have RecA. What's more, the oriK system appears to involve
>>a far more complex method of priming involving all the factors in the
>>primosome (priA, DnaT, etc.) which, contrary to my original article,
>>don't seem to be needed by the oriC system. So it would be like
>>jumping out of the frying pan and into the fire.

>Despite the touching use of colloquialisms, it's more like a death
>knell for those who would use IC as an arguement against evolutionary
>origins.

I see. When you invoke another IC system to explain an IC system,.
that's a death knell for IC.

>We have evidence of modularity to these IC systems where
>wholesale substitution of one subsystem with another retains the
>overall function --- in this case DNA replication.

Yet both systems remain IC. And the cSDR system could very well have
appeared after the oriC/DnaA system meaning it would be irrelevant to
the origin of the oriC/DnaA system.

>Thus we don't have to justify a system of two dozen players springin
>forth fully formed as athena from the head of zeus.

Really? You replace oriC with oriK, DnaA with RecA, and DnaG with
DnaT, PriA, PriB, etc. and you think you've gotten away from IC??

>We get subsystems with indepent functions learning how to co-operate
>in a synergistic fashion.

Where? And of course, in the meantime, there's no DNA replication.
If only there was some evidence that unicellular creatures can exist
without DNA. But alas, we can always imagine such an entity.

[Julie Thomas]

In a previous article, sve...@oncology.wisc.edu (Vladimir Svetlov) says:

>I missed the 50 pages long article about aliens designing replication?!!
>Good. Cause them did not. Cause there is no evidence for them aliens except
>recurrent anal bleeding of my cousine Billy-Joe in Dickson Co., TN.
>Seriously, dudes, how many more loonies would bring forward their
>bewilderment with modern cellular machines and claim that someone just have
>to create it (apparently, using Lewin's Genes VI as a manual)?

Hmmm. So now I am also a loonie? I suspect that Larry may have
labeled my postion as "alien design" hoping someone like Vladimir
would take it and run.

What's interesting is that Vladimir admits not reading my article,
but feels free to comment on it. Even to the point of claiming I
used Lewin's text as a manual. Of course, I did not. So how is it
that Vladimir could make such an erroneous claim (yet seem fairly

confident that it is correct)? I think it has to do with pack-mentality.

Vladimir gets his info from second-hand sources and trusts those sources
because he is part of the pack. I recall Myers making a claim that
my article was derived from textbooks. Moran labels my position
as "alien design." Then along comes Vladimir, probably having read
Moran and Myers, and voila, he speaks erroneously. Of course, I could
ignore this. But then someone else will come along and build on
Vladimir's misconceptions. And round and round it goes.

> Lawrence Moran did a good job pointing out problems in the latest
>installment in a series "I-Just-Don't-Get-It-Must-Be-Aliens".

This is Vladimir's opinion. Of course, I've already responded to
this good job. I admit, however, that Larry did do a good job of
misrepresenting me. Vladimir's opinions are good evidence of this.

[PZ Myers]

In article <5sih8s$l...@alexander.INS.CWRU.Edu>, iz...@cleveland.Freenet.Edu
(Julie Thomas) wrote:

> In a previous article, hi...@cgl.ucsf.EDU (Wade Hines) says:
>

You really are pushing pathetic excuses in an attempt to dodge questions
today, aren't you?

Hines is not trying to poison the well, he's trying to understand what
you are up to. In recent posts, you've said that everyone's attempts
to encapsulate your arguments are strawmen, but you haven't gone on
to tell us what your arguments are *really* about. Instead of just
making this list of people you won't reply to anymore, how about
clearing up the misconceptions and telling us what your central thesis
actually is?

[PZ Myers]

In article <5siios$r...@alexander.INS.CWRU.Edu>, iz...@cleveland.Freenet.Edu
(Julie Thomas) wrote:

> In a previous article, my...@netaxs.com (PZ Myers) says:
>
>
> >As for your question about whether Larry could agree that replication
> >_could_ have been designed -- he probably could, with no problem.
>
> Please Paul, you're sounding like the Borg. Let Larry answer the questions
> addressed to Larry.

I would NEVER attempt to speak for Moran -- he's got his own definite
and strongly held opinions. That's why I stuffed in that very tentative
"probably".

>
> >I know I have no problem with the idea that there is a possibility that it
> >_could_ have happened.
>
> Fine. And I have said I have no problem with the idea that there is a
> possibility that DNA replication (or the flagella) _could_ have evolved.
> But this doesn't stop the pack from agreeing that I claim such things
> could not have happened. So why can't I turn your perceptions of me
> around and apply them to you? If I were to misrepresent your position
> as one which argued design could not have happened therefore evolution
> must have occured, you'd probably squeal awful loud. Yet when Larry
> (and others) does the same thing with my position, there is not a peep
> from you. Are you starting to understand the impression you are making
> on me? Don't y'see the double standard?

Nope. Not yet. That's because I and others have clearly said that we don't
think that design is impossible, but that we certainly haven't seen any
evidence for it. In your case, I can only now see that you don't regard
an evolutionary explanation as impossible...but instead I'm left in total
confusion about the point of those thousands of lines on the sophistication
of various systems that you posted. I'm trying not to misrepresent you,
but you aren't helping much. What is your position? What is the evidence
for your position?

[PZ Myers]

In article <5si99a$p...@alexander.INS.CWRU.Edu>, iz...@cleveland.Freenet.Edu
(Julie Thomas) wrote:

> In a previous article, hi...@cgl.ucsf.EDU (Wade Hines) says:
>
> >iz...@cleveland.Freenet.Edu (Julie Thomas) writes:
> >

> >>My, my. What a flurry of replies. Who should I respond to? John?
> >>Paul M.? Paul G.? Maybe Wade? Wade again? Paul M. again?
> >>Vladimir (but which reply?)? How about Matt? Or maybe George (again,
> >>which reply?)? Maybe Doug? I think Howard replied (judging from
> >>a reply by Peter). And I bet Larry's workin' hard on a reply.
> >>Is there a pattern here? :)
> >

> >It appears that the pattern will be to post and run away.
>

> Almost. The pattern I saw developing has just been actualized by
> your response - so many people would reply that it would become simply
> too time-consuming to respond to all. Thus, when I don't respond,
> I'd be accused of "running away." Just as I figured.

Nope. Nobody would have any problem with you just focusing on one
set of messages and doing your best to address that limited problem.
But let's see what you did with the recent set of replies -- you said
one person was getting "emotional", apparently because he called something
irritating, so you said you would not bother with him; you got huffy
at one comment I made ("let's assume you aren't playing word games") and
used that as an excuse to refuse to answer my questions. You didn't try
at all to answer anything. Instead, you chose to find excuses to not
answer.

How about just totally ignoring me, Acton, Silberstein, just about
everyone, and just addressing Moran? He seems to have made the most
thorough and detailed critique, so I'm sure that in the process of
replying to him you would also cover everyone else's complaints. Or if
you'd rather, pick anyone else's posts and deal with them one at a time.
But please don't waste your time whining about so-and-so being too mean,
so you won't talk to him anymore.

>
> >Maybe you should make direct replies to those whom you were directly
> >replying to. Any comments of special merit in other replies can be
> >tagged in. Keeps things from exploding.
>

> Like I haven't been making direct replies for the past 3-4 months.
>

> >Or you could post and run away. Whatever suits you best.
>

> See what I mean?

[PZ Myers]

In article <5sij0i$r...@alexander.INS.CWRU.Edu>, iz...@cleveland.Freenet.Edu
(Julie Thomas) wrote:

> In a previous article, at...@best.comNOSPAM (Mark Isaak) says:
>
> >In article <5sibpe$4...@alexander.INS.CWRU.Edu>,
> >Julie Thomas <iz...@cleveland.Freenet.Edu> wrote:
> >>Well, if I don't need a justification, does it mean anything that you
> >>think I have no justification??
> >
> >To you, I don't know. To me, yes, it does matter. If you are never going
> >to explain what "design" means when you use the word, then I can skip all
> >your posts as utterly pointless.
>

> Well then skip them for cripes sake.

Is this an admission that you aren't going to explain what "design" means?

> But I bet you can't skip 'em
> for long. ;)