Behe's Black Box: A review

[howard hershey]

The following is my personal review of Michael Behe's book "Darwin's
Black Box". I make no claim that it is the best of reviews (I am sure
there are confusing parts and I wrote it as I read and did not do much
going back), but I think that I mention a few things that differ from
other reviews I have seen. I certainly apologize for the length. If
you are unwilling or unable to read the entire thing, the gist of my
review is summarized in the first paragraph. I wrote this to assure
Peter that I have indeed read Behe's book. I also now know where Peter
got all his quotes for his alien hypothesis.

Although I will occassionally resort to scattershot comments on
particular ideas, there will be a few common threads running throughout
this review: First, Behe misunderstands the requirements of a 'good'
scientific theory and insists that evolution meet requirements that *no*
scientific theory can meet. Second, Behe has a double standard for
evidence, requiring evidence by the ton in exquisite detail for
evolution by natural selection for any system *he* chooses, but
apparently (because I saw none) requiring no evidence at all that
explicitly favors the logical implications one can draw from his
alternative explanations (when he even proposes an alternative). Third,
he violates his own statement in the preface (p. ix) ("Still, the point
remains that understanding the origin of something is different from
understanding its day-to-day workings.") by continually describing the
day-to-day workings of *a* 'current' system as if that were sufficient
evidence in itself to justify a particular mechanism for its origin.
Fourth, he clearly has a very rigid definition of 'function' that fails
to countenance secondary activities or variation in activity and
otherwise presents activities in the narrowest possible way, never
noting that the *activity* described (sometimes even the enzymes
themselves) can be used in many places and 'systems' besides the one
described. Behe has never heard of exadaption, apparently, or the
acquisition of emergent properties as a secondary consequence of
development for another property.

We can start with his disingeuous definition of evolution as a "process
whereby life arose from non-living matter and subsequently developed
entirely by natural means." (p. xi). That's his *entire* definition! The
first part (which confounds abiogenesis and evolution) is contradicted
by the very person he wants to displace in the Pantheon of Biology -
Darwin - and for exactly the reason that one might expect from a
scientist of Darwin's caliber. With respect to the evolution of the eye,
Darwin said "How a nerve comes to be sensitive to light hardly concerns
us more than how life itself originated." Darwin meant by this that it
is idle to speculate in the absence of evidence, and at the time, there
was no evidence that he could use to explain the molecular workings of
vision or the mechanisms of abiogenesis of life. As more evidence
accumulates one can, and should, readdress such problems and test
whether they remain compatible with current understanding (theory) to
the extent that the new evidence permits. Abiogenesis is clearly an
area where much more evidence is needed. But the work so far has not
presented any evidence that 'kills' the possibility of a natural
mechanism of *some* sort. This is clearly an area where the question of
'is the evidence compatible with the way we think nature works' should
regularly be re-visited. But the pre-biotic changes leading to life are
not really evolution. Evolution is a theory of life and how life
works. Life is, in fact, a prerequisite for evolution.
One should always *develop* theory by first looking at those examples
where there is the best available evidence and then test that theory by
seeing whether or not it is consistent with new evidence to the extent
that evidence exists. This is what Darwin did for evolution; he
accumulated mounds of evidence for common descent (and Behe claims to
accept common descent, so this rather crucial feature of evolution not
mentioned in his definition doesn't seem to bother him) and provided a
natural law mechanism (natural selection) by which it could occur.
Natural selection, of course, *is* and *was* observable. There is no
question but that natural selection happens in nature. The only possible
question is whether the changes that produced common descent are
congruent with natural selection (and several additional natural law
mechanisms - neutral drift, horizontal transfer, etc. - that have also
been shown to occur in nature) or instead *require* or are *better
explained* by an alternative mechanism. But it apparently is this
feature (invocation of natural law explanation) of Darwin's idea that
Behe objects to. It is the idea that common descent does occur congruent
with (note that 'congruent with' does not *exclude* the possibility that
evolution is divinely guided; it does limit the range of mechanisms that
the Divine used to those that have some actual supporting evidence; the
naturalism of science is not philosophical Naturalism, despite Behe's
disingenuous definition) natural law mechanism and natural selection in
particular that Behe finds objectionable. Behe *wishes* to find, at some
level of analysis, that evolution cannot be made congruent with any
natural law mechanism (not just any *known* natural law mechanism, but
the more absolutist *any* natural law mechanism). That is the whole
point of this odd definition.
Indeed, although he fuzzes over the idea of natural selection working to
produce changed morphology, he is quite insistent that "Although
Darwin's mechanism - natural selection working on variation - might
explain many things, however, I do not believe it explains molecular
life." (p.5) I find this passing strange, given that some of the *very
best* evidence for natural selection working on variation is at the
molecular level, both in the natural and artificial evolution of
viruses, bacteria, yeast and in antibiotic and other resistances. I
presume he meant that he cannot see how natural selection (or any
natural law mechanism) can generate the IC-ness he sees in certain
biochemical pathways. But, in science, such inability of a current
theory to explain (be congruent with) an event *requires* the
invocation of alternative explanations that *can* be seen to work in
some system or it provokes an 'I don't know' shrug. This is not what
Behe apparently wants: he wants us to accept the idea that, absent a
natural law explanation, one can invoke a supernatural explanation in
science. Make no mistake about it. Behe is not interested in an
alternative natural law explanation - even a natural law 'intelligent
designer', like space aliens (his odd definition of evolution makes this
perfectly clear); he wants a *supernatural* explanation. But a
*super*natural explanation is one that cannot be tested or analyzed in
any way by science and is not a scientific explanation. Supernatural
explanations are useless, unless the *supernatural* entity is posited to
work by natural law mechanism (is an IPU). At that point the
distinction between natural and supernatural becomes irrelevant. That,
of course, is why religious belief and science can co-exist.

On pages 13-15, Behe describes the difference between 'jumps' (changes
that can be observed in the present) and 'chasms'. He agrees that
natural selection is clearly a real mechanism for generating 'jumps',
i.e. natural selection is a real force in biological change. And he
describes 'chasms' that exist in the present. But he then describes the
difference between the two as if time played no role in creating a
'chasm' where there once was a merely a 'jump'. Indeed, he avoids
mentioning time as a mechanism for creating chasms in this entire
section. And he merely asks whether it is reasonable to think that
someone could leap a 'chasm' that exists right now. I found this section
strange for someone who claims to understand common descent. He
correctly points out that *one* way to provide evidence for a possible
way to diferentiate a 'chasm' is to look for possible intermediate
stages that exist in the present in one organism or another (as Darwin
did for the morphology of the eye).
But he incorrectly states that somehow this is the *best* evidence. The
*best* evidence for how a 'jump' actually *became* a 'chasm' would be
seen by looking at hard parts preserved in the fossil record in those
organisms with the largest and most complete fossil record. E.g., the
foramnifera. This is direct evidence. The second best evidence would
come from organisms with a less perfect or complete fossil record. If
there is no (or extremely limited) fossil record, as in the case of the
eye's morphology or, even more so in the case of biochemistry, you are
limited to the *indirect* evidence of currently extant variations that
can be shown to be compatible with life and function. This type of
evidence will *never* give you a direct and specific 'One True'
explanation. It can only give you 'More or Less Likely' explanations
that can either be 'compatible with' or 'incompatible with' a theory
(hopefully a theory which is also consistent with those cases where the
evidence is more direct). The evidence may be consistent with a number
of possible explanations. If one has a choice between an explanation
that is also consistent with cases where there is direct evidence and
one that has no supporting direct evidence (IC differs in the pattern of
appearance and I have seen no currently observable mechanism that has
been observed to produce systems by IC-specific mechanisms - namely all
at once or with utterly useless intermediate stages). Of course, if
what you are really interested in is implying that a supernatural entity
is involved in the difficult cases, you cannot possibly propose a
natural law mechanism.

Chapter 3. Cilia and Flagella

Clearly the problem here is Behe's insistance that every possible
intermediate must serve the *exact same function* as the end 'system'.
He ridicules the idea that tubulins might serve a useful structural
function before it acquired the end function of motility. Let us
imagine a bundle of tubulins serving a structural function at the cell
membrane, sticking out and causing a projection (but a static one) from
the cell surface. Let's call such a projection a microvillus (to choose
a name at random :-)). One of the consequences of these microvilli
would be an increase in the surface to volume ratio of the cell.
Surely, even Behe might be able to come up with a reasonable selective
environment where such microvilli might be favored, even if they could
not move at all. Now one, as Behe points out, might envision motor
molecules involved in transport along the axis of these fiber bundles
(for precisely the reasons one might expect microvilli to form in the
first place). Linking some of the bundles might allow some minor
movement of the microvilli at levels that would be insufficient to cause
cell motility. But movement, by creating microcurrents, might have uses
without being sufficient to move the organism. Under conditions that
select for more vigorous movement, you might well get the emergent
property of motility.
I have previously given a highly speculative, but similar, possible
pathway to produce flagella via non-motile, but still functional
intermediates.
Can I prove these scenarios? Nope. Are they totally out of line?
Well, if you look for evidence of these intermediate states, you need to
ask whether tubulins are involved in maintaining cell structure in
microvilli, whether pilins have utility, whether there are protein
transport pores, etc in current organisms. This, of course, is not
direct evidence. It is evidence like that that Darwin presented for the
eye. It is evocative, possible, and is congruent with natural law
mechanisms. But it is the only type of evidence that anyone has in
these cases.

Chapter 4. Clotting.

I presume that Behe's description of Doolittle's talk as "State of the
Art" was meant as a bit of humor. Clearly Behe knew, from the language
used, that this was not meant to be a formal scientific presentation. I
suspect he also knew that the yahoos who would drool over this book
would not know the difference, so that he could get away with a bit of
sarcasm over the language Doolittle used.
But the worst, most inadequate section in this entire book (there are
serious competitors) is ensconsed between pp. 93-96, where Behe tries to
explain what he finds wrong with evolution by domain shuffling and gene
duplication. It starts with his GIGO *a posteriori* calculation of the
improbability of gene shuffling. What anti-evolution book would be
complete without some sort of *a posteriori* improbability argument? In
addition, Behe makes his calculation using numbers that indicate a total
lack of familiarity with the ideas of 'gene families' and 'domains'.
But clearly Behe does (or should) know about these facts about the
genomes of organisms if he wants to comment intelligently instead of
simply making wild assertions without any evidence. I can only conclude
that the calculation is not serious.

Behe says, "The second question to consider is the implicit assumption
that a protein made from a duplicated gene would immediately have the
new, necessary properties. (p. 94)" The only person (quite literally)
making this assumption is Behe. This is often called a 'strawman'
argument. A simple gene duplication *can* be useful (or neutral or
detrimental) by itself (there are examples of each *in present-day
organisms*). A neutral duplication (which would be the most common
kind) would provide the *opportunity* for divergence and specialization
of the genes in different directions in a way that would not be possible
if there were only one gene and the different functions had to be
accomplished by its protein (again, there are examples of duplicated
isozymes with slightly different properties, including the beta
hemoglobins). A hybrid duplication product (by translocation or
transposition of a different group of domains) would not be a simple
duplication, of course, and *could* have significantly different
properties than its original (and, of course, would be selected for or
against on the basis of these properties). I find that most
undergraduates can understand the concept of duplication *and*
divergence. I wonder why Behe has problems? If he were an undergrad
with an undergrad's understanding of genetics, he would get a
gentleman's C (if I were in a generous mood). That this actually got
past the reviewers says something about them.

Behe then says that what is needed is "the putative route it took to
acquire a new function (p. 94)". Now, let's look at what evidence *can*
be found (until we make the time machine that will allow us to go back
and analyze real 'living fossils'). We often can say (because of
extensive sequence, functional, and structural similarities) that
present gene X and present gene Y are likely to heve diverged from a
hypothetical ancestral gene Z (rather than being independently created
from scratch). Let's say we have the sequences of X and Y and know the
functions (not function) that X and Y perform. If we have done enough
study, we know which parts of the sequence have an effect on specific
functions and which parts are relatively unimportant. We can see what
effect results from substituing particular amino acids. Now, how can we
determine, by logical inference, what the putative ancestor Z looks
like.

U Y X
\ \ /
\ Z
\ /
\/

First, we assume that the amino acids that are identical in both X and Y
probably were also present in Z (it is always possible, of course, that
an amino acid changed and changed back in one of the lineages). Then
comes the problems of places where there are differences between X and
Y. Did Z have the amino acid seen in X or did it have the amino acid
seen in Y? If we have a protein (U) which had an even earlier split;
that is, it split before Z was formed, we can sometimes make a
reasonable guess. If U has the same amino acid as X, then it is
*simpler* to assume that this is the ancestral amino acid and that Z is
the lineage with the changed amino acid. But one cannot exclude less
likely possibilities. Again, one has to consider the possibility of an
amino acid making more than one change. If we don't have protein U,
then it is a simple coin flip with the clear additional possiblity of
'neither of the above'. Now most of the observed changes seem to occur
in the regions of proteins that are selectively unimportant rather than
in the regions that are crucial for distinguishing the difference in
function between X and Y, but clearly, if X and Y differ in function,
some of those changes are important in the functional difference. But
the idea that a small number of changes lead to the functional
difference (and often in an additive way, but not uniformly additive,
some changes being more important than others) is a very important point
for analysing the feasibility of natural selection as a mechanism for
producing the often small functional difference between these proteins.
*The changes that determine functional differences are typically small
in number relative to the total number of changes or are produced
primarily by hybridization of functional subunits. To repeat, most
observed differences are neutral. Only a small number of discrete
events (which are often additive) are needed to produce the small change
in function seen in closely related genes.* I presume that Behe is not
arguing the fact that a protein's function is determined largely (if not
completly) by its sequence. It is perfectly clear that one can change a
sequence in a stepwise process and that proteins can exhibit more or
less and slightly to considerably different activity by such sequence
changes (the existence of 'leaky' mutations says so; only those fixated
on the idea that mutations only result in dramatic qualitative effects -
fully on or fully off - would think otherwise).

Can we use this type of information to determine what *the one true*
ancestral protein Z looked like and what every step and the order of
every step that led to the two current proteins X and Y was? Of course
not (absent our time machine). All we can do is give an approximation
of a possible ancestral protein Z *and* show that the observed rates of
change needed to produce either present gene from *any* reasonable
ancestor gene can be accomplished in the time available by using known
natural law mechanisms. That latter point, of course, is easy. Most of
the amino acid changes seen between two proteins which are suspected to
have been evolved by duplication (and divergence since that duplication
event) appear to be selectively neutral (and the timing of neutral
substitutions appears to average out over long time periods, providing a
clock for a particular protein). The rate of neutral substitution and
fixation of neutral changes is simply the rate of mutation at that
particular locus and that rate can be independently determined in the
present. The rate of fixation of a selectively favorable mutation is
very high relative to the rate of neutral fixation, so if the *observed*
rate of change in the proteins X and Y is equal to or less than the rate
of neutral fixation, there is clearly no problem in fixing in favorable
mutations. In fact, the rate of change observed in most proteins is
almost always *less* than the rate of neutral substitution by itself.
Thus, as in the present, the vast majority of selection events act as a
conservative force. There is nothing in the rates of substitution that
makes selection for new functionality (again, changing functionality can
easily and often be due to a single nucleotide change or other type of
single mutation) unlikely or impossible. The observed amount of change
is *congruent with* natural law mechanisms involving random change,
neutral drift, and selection. There is no need to invoke supernatural
mechanisms to change *any* best estimation of a pathway from ancestral
protein Z's sequence into that of proteins Y and Z. Unless, of course,
one has independent evidence that *all* the observed functionally
relevant changes had to occur in one fell swoop or independent evidence
that there could not be a protein Z to duplicate at the appropriate
time. Behe does make the *claim* that current IC-ness somehow requires
all the functionally relevant changes to occur in all the functionally
relevant proteins in one fell swoop, but the *evidence* shows that
neutral changes that do not affect function at all, which can be
observed by looking at proteins that serve identical functions in
different lineages, certainly do not occur all at once, but over time as
expected for organisms showing common descent. Perhaps he has some
reason to believe (some evidence) that the changes in the functionally
relevant sections of the 'system's' proteins occurred all at once? Such
evidence is not presented here. Note that I am specifically discussing
*how* you can get from an ancestral protein to current proteins using
natural law mechanisms and asking whether the observed differences
between the present proteins is *congruent with* their having occurred
through these known natural law mechanisms. I will discuss why this is
a different question than the question Behe *really* seems to be
interested in (despite the fact that it conforms to his definition of
evolution, which makes no requirement except compatibility with natural
law mechanism). Behe really wants to know *why* we have this particular
change? In one sense, this last is a potentially answerable question,
but a hard one to present evidence for or against. In another sense, it
is a theological question which is unanswerable by science.

Behe then says, "The third problem in the blood-coagulation scenario is
that it avoids the crucial issues of how much, how fast, when, and
where. (p. 94)" Apparently, Behe will not accept anything but the
report from the time machine. Are we supposed to invent the last common
ancestor and every creature in between so that we can measure their
internal fluid pressure and how this changed with every amino acid
difference? This is followed by the idiotic statement that "without
numbers, there is no science. (p. 95)" There is good science without
numbers (in any case, the programs that analyse sequence phylogenies
certainly are not numberless) and there is bad science with numbers
(Behe's GIGO calculation being a case in point).

But his last (and most serious) objection is that the system is IC, and
thus must be complete before selection can work. He then pretends that
Doolittle thinks the proto-thrombin and proto-plasminogen would be
hanging around *totally useless* until the entire system is assembled.
Actually, the total uselessness of any possible intermediate stages is a
requirement of IC systems; if IC is defined as Behe does, a functional
(any function) intermediate stage in an IC system is a contradiction in
terms. The evidence for this (particularly the idea that such
protoenzymes can only serve a function if it is the end function) is not
given. This again is an example of a functional intellectual rigidity
(anti-evolutionists apparently cannot think except in clear dichotomies;
the idea that there might be two or more functions and gradations
between them seems to be lacking) in that he can only imagine a protein
serving one function, and certainly cannot imagine a shift in functional
emphasis. So he then again repeats his GIGO calculations.

Now, if I may repeat a theme, what is the evidence that he presents that
a) shows that the natural law mechanism of duplication and divergence is
inadequate to explain the observed sequence differences, b) evidence
that the clotting system occurred in an IC-specific fashion (either all
at once or stepwise with completely useless intermediate stages). Given
his ridicule of the latter (stepwise) mechanism here (although he comes
back to it later) when he presents this as a strawman version of
Doolittle, I think he favors the first mechanism. Actually, however, he
doesn't present his alternative explanation and supporting evidence here
either. Where is his argument *for* IC-specific creation mechanisms and
supporting evidence?

Chpt. 5. Intracellular transport.

In this part, Behe confounds the issue by lumping together three
different transport mechanisms and treating them as if they were
inseparable. It ain't so. But actually all he does is present, yet
again, a vision of transport as being different for every single protein
transported or somehow mystically requiring that the end function must
always and forever be the sole function.
Every cell (from the ur-organism on) has the problem of selectively
transporting materials across the membrane. This is often accomplished
by active transport through transmembrane pores. Membranes naturally
tend to bleb off or invaginate because of their fluid nature and this
process can be facilitated and regulated by proteins (the feature of
vesicular transport).
Transducing signals across a membrane are so important that they takes
up a sizeable fraction of the genome, with many genes in the family of
transmembrane proteins.
Proteins also need to be transported across membranes. The first to do
so were undoubtedly digestive enzymes (it is not surprising that
clipping a leader sequence is involved in the activation of proteases
and in intracellular transport and that proteases are often used as
extracelluar regulatory proteins). But, as usual, the problem is that
all Behe does is describe the current system. He presents no evidence
that it occurred by sudden appearance (such evidence is not available,
AFAIK) and does nothing to add to our understanding of how it could have
occurred stepwise with useless intermediate stages. All he does is to
say that it is amazing and that he personally doesn't see how to
simplify it.
For the case of gated transport, Behe decides that this process requires
three components, a component with the signal (the amino terminal leader
sequence), the protein that binds the leader and transports it to the
active pore, and the pore itself. I see two as a possible initial
'system': the leader sequence containing protein and a pore protein that
both binds and transports the leader. The latter protein could easily
produce the two current systems and the initial system might arise from
earlier and generalized transport proteins (that can transport more than
proteins), or by the fusion of a membrane transport and clipping
enzyme. There are a lot of possibilities for accidental affinities to
lead to something favored. Once such a simple system appears, it seems
to get used over and over again by cells. I see the problem of too
ready dichotomization of function and assuming that current function
explains origin. This seems to be a recurring problem.

Chpt. 6. The Immunoglobins.

First, Behe does absolutely no comparative analysis (aside from
mentioning that sharks have an immune system), and this is a case where
there actually is some very interesting comparative analysis that could
actually tell you (if you accept the idea of common descent, as Behe
claims to do) where and when certain specific changes in the way
immunoglobins are structured and used in various different lineages.
Indeed, there is little comparative analysis in any of Behe's examples,
which is surprising if he really does understand what happens with
common descent. And the immune system might be a good system to look at
in terms of testing the ideas of IC-specific 'appearance' (to avoid the
term evolution) of 'systems'. As seems to be a common pattern, Behe
also seems to lump in the complement system into the mix to just make it
seem more complex. Apparently, I need to mention again, that no
IC-specific alternative explanation is given.

Chpt. 7. The AMP _de novo_ synthesis pathway.

This is perhaps Behe's most interesting chapter. In it, he accurately
points out that many metabolic pathways do not appear to be constructed
by the principles of rational design but rather construct their end
products by a round about Rube Goldberg mechanism. How do you get such
a system? One way, of course, is the IC way whereby it all appears at
once or appears stepwise with utterly useless intermediates (*and* there
may well be some truth to this last idea). The other way is the idea
that the intermediate stages served *some* useful purpose, but not
necessarily the end function. It is interesting, in this regard, that
enzymes often have secondary substrates that they can utilize to a
lesser extent than their primary target. These minor activities are
going on in your cells as we speak. So it is not, perhaps, surprising
that, say, the enzymes that transfer the amino group from glutamine to
target molecules all show common descent features. What differs in the
modern system is the relative specialization of target (although even in
present enzymes other targets can still be used - e.g. betagalactosidase
can cleave almost any beta galactoside linkage between two molecules).
What is needed to get from an enzyme which incidently adds an amino
group to the precursor leading to AMP as a minor secondary activity
(even if that newly made molecule is *utterly useless* garbage to the
cell, sometimes even if the garbage can build up to harmful levels
[note: current cells also make these minor 'garbage' compounds]) to
become transformed so that its primary purpose is forming that product
is duplication and specialization. That would only require some
selective reason to make more of a former 'garbage' molecule. Cells are
great recyclers and, even now, garbage compounds are sometimes used as
pigments or toxins. If useful enough, they sometimes become the main
event.
Also, the AMP pathway that Behe mentions is fed into at an intermediate
point by a histidine pathway, meaning that this pathway can easily be
broken down into two pathways. But I agree with Behe that the general
idea of evolving steps backwards from the forward pathway is far too
simplistic. I would imagine that each metabolic pathway will have its
own unique history involving various amounts of specialization of minor
secondary reactions and chance encounters with horizontal transfer of
enzymes that utilize minor products. This seems to be a situation where
the ideas of IC-ness (useless side products hanging around indefinitely
because of the usefulness of the primary product *until* some second
event makes or converts that formerly useless side product into
something useful) might even have some utility. I do not, however,
think that this is what Behe has in mind for the concept of IC. This
is, after all, a natural law mechanism, and that is what he defines as
all that is wrong with evolution.

Chpt. 8. Behe and the sequencing problem

After a brief discussion of abiogenesis, where the complaint is made
that all scientists do is look at the niggling details (can amino acids
be made under relevant conditions) followed by more niggling details
based on the findings of the former research (assuming we do have a
reasonable source of amino acids, can we construct proteins), Behe goes
on to what I regard as the more interesting idea of explaining why
sequencing does not help explain IC systems. Complaints about the
status of abiogenesis research are a dime a dozen, and the best do not
come from the camp of those who reject the possibility of abiogenesis.
So his ideas on abiogenesis can be easily ignored, but not necessarily
because they are wrong. Because they are presented better by others.
What I see in Behe's discussion of sequencing is a failure to fully
differentiate between the words 'how' and the teleological (and
theological) notion of 'why' an event occurred. Science, of course, is
most interested in the former and tends to avoid the latter.

Here, and in several other places, Behe clearly points out that he
thinks sequencing *can* show relatedness of proteins and can show and
support the ideas of common descent at the molecular level. I found
this puzzling at first, since common descent *is* evidence of evolution
(but not of a particular mechanism). Indeed, it was the crucial feature
that Darwin needed to show happened (common descent rather than *ex
nihilo* creation) and the one part of his work that essentially all
biologists accepted (his mechanism, natural selection, was not as widely
accepted at the time). Then I remembered that Behe's definition of
evolution was a very strange one. Something is not *evolution* in
Behe's view *unless* it occurs by a natural law mechanism; indeed, his
definition of evolution mentions abiogenesis first and then the idea
that life must "subsequently develop entirely by natural means" (p.
xi). That's it. The entire definition of evolution (except for
abiogenesis) is "subsequently develop entirely by natural means". No
mention is made of common descent in this definition at all, just the
idea that subsequent development occurs by natural means. So let's take
an example of what sequencing shows and what it doesn't show. If we see
two protein sequences, say alpha-hemoglobin and beta-hemoglobin, and
look at their sequences we will see many similarities and some
differences. It is quite clear that these two genes did not evolve
independently. So the proposed 'common descent' model is that the
ancestral alpha-hemoglobin-like (because hagfish, which diverged early,
lack beta-globin) molecule duplicated and divergence of that duplicated
molecule produced the present observed sequence differences. Now let's
distinguish between *how* this could occur and *why* this did occur.
Science, of course, can merely show that the proposed process of *how*
this could occur is *compatible with* known natural law mechanisms in
this case. Absent the Handy Jim-Dandy Acme Time Machine the only
evidence we have is our knowledge of the way genetics and ecology
(including selection) works in the present and the observed differences
in the two molecules in various living organisms.
Behe presents no specific alternative mechanism for *how* this observed
event (production of beta-globin) occurred. The idea that it arose by
duplication and divergence of an ancient alpha-globin is certainly
compatible with observed events in the presence (gene duplications occur
in nature; point mutations occur in nature) and is also compatible with
the rate at which such mutational events occur in nature. Indeed, the
observed rate is slow enough, relative to the predicted rate of fixation
of random neutral events, that it is clear that there must be net
selection *against* change. Science has no problem explaining *how*
the observed differences could occur.
*Why* they occurred is a different question. Naturally, scientists tend
to supply the only known natural law mechanisms for why these particular
changes occurred. For those changes that are selectively neutral, the
mechanism of random fixation suffices. Nothing, obviously, will prevent
it from having occurred in the past, just as nothing prevents it today.
For those events that result in a *change* in function, we naturally
wish to apply the mechanism that deals with the way today's nature
treats random mutations that change a gene's function (we have no
evidence for teleologically directed mutation and Behe certainly does
not present such evidence, so unless Behe has evidence he isn't
presenting, we can, I think, agree that mutation - the source of
variation - is unpredictable or random in the scientific sense), namely
natural selection. Again, natural selection occurs. There is no reason
to believe that it did not occur in the past. The net observed changes
in the sequences of the two proteins (the difference between them)
certainly occurs slowly enough to be accounted for by of natural
selection for *some function in some particular environment*. Natural
selection is very rapid relative to neutral fixation and the observed
rate of differences between the sequences actually occurs *more slowly*
than this. In short, the available evidence is *compatible with* a role
for natural selection in those changes that affect function. But Behe
wants more. He wants to know what the specific selective pressures
where that led to the initial divergence.

By and large, *that* information is not available to anyone. We don't
know *for sure* what the ancestral organism was and what selective
pressure (the environmental conditions it was under) was working on that
organism. But we do know that selective pressures *can* lead to an
altered morphology by selecting for useful variants that occur by random
mutation (as in, e.g. the peppered moth) in those cases where the
selective pressures and organism are known, and can do so extremely
rapidly. We can often make reasonable inferences as to what selective
pressures *might* lead to a present function, e.g. if a duplication and
divergence or hybrid duplication by chance produces a product that
better controls clotting, it *will* be selected for in particular
organisms with particular selective environments. But, until our time
machine is made, such proposals must remain merely reasonable inferences
or possiblities congruent with known natural law mechanism (or just-so
stories, if you like). This, of course, is why these models are usually
mentioned in the discussion sections of papers. Behe's 'solution' is
that certain such changes (even though the changes themselves are
*consistent with* the rates of known natural law mechanisms involving
chance and neutral fixation and selection and often show clear signs of
the *how* mechanisms of duplication and divergence) requires some
unknown, unspecified, and never seen mechanism that differs from known
natural law mechanisms (or, he would prefer, *any* natural law
mechanism). He requires either effectively instantaneous construction
or requires useless intermediate stages (because a true IC system can
have no useful intermediate). No such mechanism has been seen in the
way that present-day organisms work. Not for Behe the possibility of
intermediate stages serving different functions (much as the Calvin
cycle can be used for either electrons from photons or electrons from
chemistry). Where is his presentation of a system that he *knows*, by
the evidence and not by postulation from the current system, was either
created essentially instantaneously (rather than a system he presumes
must have been created instantaneously to perform its *current*
function) or which has evidence of 'systems' that are there but *not
yet* serving a useful function (as opposed to secondarily having lost
utility). These are the types of systems that IC-ness infers. The
inference of all parts of a system having been created at the same time
can use sequence homology, but one must be sure to post the error bars.
The key number is 100 million years, which is the time it takes to get
100% substitution of amino acids in a peptide where the amino acids are
essentially all selectively neutral.

Chapter 9 and 10. Intelligent design.

Let's just say that I am still looking for a definition of 'design' that
doesn't amount to "If it looks like an artifact produced by a human (but
not so complicated that one cannot distinguish it from randomness), it's
designed." Some, of course, require that anything that was 'designed'
must have a 'designer'. That still leaves the question of whether life
(or any subcomponents) is designed in either sense. Life is certainly
as complicated as a watch. But that is not a sure sign of design. The
analogy with human-designed products breaks down with living systems
*because* living systems have a mechanism that permits the appearance of
design by self-reproduction of favorable variants and a mechanism
(mutation) that ensures the continual production of variants (favorable,
unfavorable, and neutral). As Behe rightly points out (p. 202),
scientists are now using this 'blind process' to produce new
biochemicals *because* we are too ignorant to purposely and
intentionally 'design' the optimal biochemicals. Computer programers
are using genetic algorithms for the same reason. I.e., nature's blind
mechanism is *still* smarter than we are in many cases. Of course, _S.
aureus_ resistance to vancomycin is telling us the same thing.

BTW, I also have problems with the METHINKSITISAWEASEL analogy as well,
many of the same ones that Behe mentions. But my complaint is that it
is a poor analogy of evolution *because* the intermediate stages have no
utility at all. Although I think that one *can* have an enzyme that
produces a useless byproduct which is kept merely because there is no
way to get rid of it without losing the utility of the primary product,
I do think that most stages in the development of a system will have
*some* functional utility. But that utility may have little to do with
the final function.
The attempts to deal with the appearance of imperfection (less than
optimal) in design (pp. 222-225) that is, in fact obvious in living
system's apparent 'design' at all levels of analysis amounts to "Who
knows what evil lurks in the mind of the Designer." The reply to the
argument of 'vestigiality' at the molecular level (pseudogenes) is
extremely weak (pp. 225-227). To try to argue that pseudogenes serve
useful functions is, with rare exception, totally without support and
amounts to wishful thinking. To then to go on to say that there is no
known mechanism by which pseudogenes can be produced beggars belief!
Then he presents his wild unsupported idea of genes present from the
start of life, about which the less said the better (pp. 227-228).
Perhaps the weakest section (pp. 230-231) is when Behe talks about how
'intelligent design' will lead to new types of research, a section which
is contradicted on p.251, where it is made explicit that his feeling is
that IC would probably lead to a state of no research, because no one
has a clue as to how or why an intelligent designer works or decides not
to work and let things procede by natural law mechanism. Once you
fixate upon *the* irrevokable function of a current 'system',
determining IC-ness is simple. Determining which IC systems could not
have evolved, howver, remains difficult.

Ch. 11. Philosophy.

I'm no philosopher, but I thought this was pretty darn simplistic.
Especially when he defines supernatural as being the equivalent of
'higher intelligence' (p.239) as a way of refuting Richard Dickerson's
restatement of Occam's razor. Higher intelligences (and also not so
high intelligences, from ants to jackasses) can be either natural or
supernatural. The natural ones can be dealt with in science because
they and their consequences have the potential for being observed and
tested. Higher intelligences that are invisible and unseen are either
supernatural or the functional equivalent of supernatural (functional
equivalents like space aliens at least have the potential to become
visible whereas truely supernatural beings don't).

But I'm bored and I no longer see the point of this book. By this time,
Behe is talking as if he has actually shown some evidence that some
system somewhere arose in an IC-specific fashion and is thus, definitely
IC in origin as well as in present incarnation. You would think he
would have informed his readers of these findings.

[PZ Myers]

In article <340AE3...@indiana.edu>, howard hershey
<hers...@indiana.edu> wrote:

I commend you for actually making your way through the entire book.
Of course, you are aware that even though you did actually read it,
because you are critical you obviously have made a strawman interpretation
of the content -- the true meaning of the book is a platonic ideal
that you have missed (hey, I just wanted to be the first to shout
"Strawman!", 'cause I know you'll hear a lot of that in short order).

One serious question. You've pretty well trashed it, chapter by chapter.
Is there *any* value to reading this book? I've actually been considering
reading it myself (at the end of the semester, not now!), on the
principle that it seems to be the focal point for a lot of creationist
nonsense, and that I have read a few of Behe's papers, and he can
raise some reasonable and valid objections to adaptationist arguments.
So what's the bottom line? You clearly dislike the book, but is there
any nugget of merit that would justify a biologist reading it?

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

[Laurence A. Moran]

In article <340AE3...@indiana.edu>
howard hershey <hers...@indiana.edu> writes:

>The following is my personal review of Michael Behe's book "Darwin's
>Black Box".

Thank you very, very much. I enjoyed your review. Don't think I'll buy the
book though - you ruined the ending. (-:

Larry Moran

[Sherilyn]

Sorry, I just couldn't resist it. :)

In article <340AE3...@indiana.edu>, howard hershey

<hers...@indiana.edu> writes

>The following is my personal review of Michael Behe's book "Darwin's
>Black Box".

...
--
Sherilyn
For the Snark was a Boojum, you see.

[howard hershey]

PZ Myers wrote:
>
> In article <340AE3...@indiana.edu>, howard hershey

> <hers...@indiana.edu> wrote:
>
[snip]

>
> I commend you for actually making your way through the entire book.
> Of course, you are aware that even though you did actually read it,
> because you are critical you obviously have made a strawman interpretation
> of the content -- the true meaning of the book is a platonic ideal
> that you have missed (hey, I just wanted to be the first to shout
> "Strawman!", 'cause I know you'll hear a lot of that in short order).
>
> One serious question. You've pretty well trashed it, chapter by chapter.
> Is there *any* value to reading this book? I've actually been considering
> reading it myself (at the end of the semester, not now!), on the
> principle that it seems to be the focal point for a lot of creationist
> nonsense, and that I have read a few of Behe's papers, and he can
> raise some reasonable and valid objections to adaptationist arguments.
> So what's the bottom line? You clearly dislike the book, but is there
> any nugget of merit that would justify a biologist reading it?
>

Depends. The book is clearly aimed at a different audience than
professional biologists or biochemists. Indeed, anyone who can read a
bichemistry of molecular biology text without blanching will find parts
of it annoyingly condescending (how often do you need to read the aside
to the reader telling him or her that she is probably too dumb to
understand all this complexity?). I found his descriptions a strange
mixture of dumbing down and refusing to make the obvious simplifying
statements that can clarify an biochemical pathway (for example, he does
not present the clotting mechanism as a system that largely acts as
modifiers and regulators of the activity of its core feature: cleavage
of fibrinogen to fibrin). I can certainly understand this as a
rhetorical device, but not from someone who is trying to be objective.
Presenting it as if all the parts were equally important conflates his
argument.
Some of the reasonable objections are there (and I hope that I pointed
out where I thought he might be correct in his critiques) but couched in
a way that seems to imply that science really should be able to tell
exactly what selective forces were acting on the particular organism
step-by-step rather than merely make reasonable inferences for
*possible* slective pressures.
The worst part of the book was not so much what was in it, but what was
not. No serious analysis of the implications of IC was presented
(IC-ness *means* that no intermediate stage with any utility can exist
or it means nothing). Nor did he actually present his best shot at
proving that *any* system he deems IC actually *did*, in fact, 'develop'
(to avoid the term 'evolve') in an IC-specific fashion.
In another post (Julie and DNA IC), I will present some specific ideas
for how one *could* go about doing this in a way that has the potential
of convincing scientists. (Why do I bother telling IC-biologists their
job?)

[howard hershey]

Sherilyn wrote:
>
> Sorry, I just couldn't resist it. :)
>

> In article <340AE3...@indiana.edu>, howard hershey

> <hers...@indiana.edu> writes

> >The following is my personal review of Michael Behe's book "Darwin's
> >Black Box".

> ...
> --
> Sherilyn
> For the Snark was a Boojum, you see.

Looks like I'm in good company. :-) :-)
But I was really waiting for the real Julie thing, not this pale
imitation. :-)

[Ed. Stoebenau]

On 1 Sep 1997 18:07:20 -0400, my...@netaxs.com (PZ Myers) wrote:

<snip>

>Is there *any* value to reading this book? I've actually been considering
>reading it myself (at the end of the semester, not now!), on the
>principle that it seems to be the focal point for a lot of creationist
>nonsense, and that I have read a few of Behe's papers, and he can
>raise some reasonable and valid objections to adaptationist arguments.

No, the reason you gave is really the only one to read it: it is and
will stay popular with creationists. Behe's book is a confusing and
confused one. And, given some of the philosophers he apparently
conversed with during writing it (Van Inwagen and Plantinga), his
philosophical sections are quite lame. One case in point. He says
that if we were to make life in the laboratory, this would be evidence
for design, from the inductive argument that all life which we knew
how it has arisen, has been designed, therefore, it is probable that
all life arose from design. This ignores the main point: naturalism
vs supernaturalism in abiogenesis. Because, if life were to be formed
in the laboratory, we would more realistically use the argument that
all life we know how it arisen arose by asupernatural means,
therefore, it is probable that all life arose by asupernatural means.

--
a #143
Just my four half cents worth Standard disclaimer
Ed. Stoebenau esto...@vt.edu

[George Acton]

Awesome, but did you actually finish it? It was once said that
only six men per generation read Erasmus Darwin's _Loves of the
Flowers+_ (sorry girls, just repeating). You may be in an
equally elite group.
--George Acton

[Bruce Salem]

In article <340BDB...@indiana.edu>,

howard hershey <hers...@indiana.edu> wrote:
> No serious analysis of the implications of IC was presented
>(IC-ness *means* that no intermediate stage with any utility can exist
>or it means nothing). Nor did he actually present his best shot at
>proving that *any* system he deems IC actually *did*, in fact, 'develop'
>(to avoid the term 'evolve') in an IC-specific fashion.

But this is an old strawman often raised by the Creationists, that
Greek Math Professor lied to us, it is just the same old same-old crap
that structures can't transition and retain function. They can and must.
And, If I read the replies from that self-same Greek Math Professor from the
Bible Thumping South, the case of the jaw bones of reptiles being able to
serve their dual function of sound conduction and structural support is
in direct opposition to the idea of IC.

Bruce Salem

--
!! Just my opinions, maybe not those of my sponsor. !!

[hamilton]

Ed. Stoebenau wrote:

<snip, talking about Behe's final chapter>

> One case in point. He says
> that if we were to make life in the laboratory, this would be evidence
> for design, from the inductive argument that all life which we knew
> how it has arisen, has been designed, therefore, it is probable that
> all life arose from design. This ignores the main point: naturalism
> vs supernaturalism in abiogenesis. Because, if life were to be formed
> in the laboratory, we would more realistically use the argument that
> all life we know how it arisen arose by asupernatural means,
> therefore, it is probable that all life arose by asupernatural means.

Hmmm. If the origin of life is reproduced in the lab, it would be
asupernatural yet designed. **PROOF THAT ALIENS EXIST!!!** Alert Julie
Thomas immediately!

UnALTERED reproduction and DISSEMINATION of this MATERIAL is ENCOURAGED

Tracy P. Hamilton

[Peter Nyikos]

sa...@pangea.Stanford.EDU (Bruce Salem) writes:

>In article <340BDB...@indiana.edu>,
>howard hershey <hers...@indiana.edu> wrote:
>> No serious analysis of the implications of IC was presented
>>(IC-ness *means* that no intermediate stage with any utility can exist
>>or it means nothing).

Hershey propagandizes here, throwing scientific caution to the
winds. I'll have a lot more to say about his review tomorrow.

>> Nor did he actually present his best shot at
>>proving that *any* system he deems IC actually *did*, in fact, 'develop'
>>(to avoid the term 'evolve') in an IC-specific fashion.

Whatever "IC-specific" means.

> But this is an old strawman often raised by the Creationists, that
>Greek Math Professor lied to us, it is just the same old same-old crap
>that structures can't transition and retain function.

Bruce is slandering me here. And not for the first time, either.
He has done it on this very subject at least twice before,
and been corrected both times.

> They can and must.
>And, If I read the replies from that self-same Greek Math Professor from the
>Bible Thumping South, the case of the jaw bones of reptiles being able to
>serve their dual function of sound conduction and structural support is
>in direct opposition to the idea of IC.

You did not read the replies with anything resembling understanding.

By the way, my name isn't Greek. Nikos is Greek. Nyikos is not.

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

[howard hershey]

Peter Nyikos wrote:
>
> sa...@pangea.Stanford.EDU (Bruce Salem) writes:
>
> >In article <340BDB...@indiana.edu>,
> >howard hershey <hers...@indiana.edu> wrote:
> >> No serious analysis of the implications of IC was presented
> >>(IC-ness *means* that no intermediate stage with any utility can exist
> >>or it means nothing).
>
> Hershey propagandizes here, throwing scientific caution to the
> winds. I'll have a lot more to say about his review tomorrow.

The whole idea of IC-ness is that all the parts are necessary or there
can be no function, is it not? If there are subsystems that serve a
useful function, that rather defeats the idea that all parts are
necessary for function.

>
> >> Nor did he actually present his best shot at
> >>proving that *any* system he deems IC actually *did*, in fact, 'develop'
> >>(to avoid the term 'evolve') in an IC-specific fashion.
>
> Whatever "IC-specific" means.
>

It means a 'system', which, *because no intermediate stage in its
development can have any useful function*, either develops all at once
or develops stepwise with utterly useless intermediate stages.
Evolution requires intermediate stages and (with some relatively minor
exceptions) requires that they serve *some* useful function.

[Julie Thomas]

In a previous article, nyi...@math.SC.EDU (Peter Nyikos) says:

>howard hershey <hers...@indiana.edu> writes:

>>The following is my personal review of Michael Behe's book "Darwin's
>>Black Box". I make no claim that it is the best of reviews (I am sure
>>there are confusing parts and I wrote it as I read and did not do much
>>going back), but I think that I mention a few things that differ from
>>other reviews I have seen.

Peter said:

>Good start. And I should add, you've come up with a much
>better review than any I've seen before--not that it's hard
>to come up with a better review; it's hard to come up with
>worse ones than the published ones and still get published
>in places like _American Scientist_.

I haven't seen Howard's reply. Perhaps someone can e-mail it to
me. I recently read Dorit's review, however. I doubt I'll
have time to critique it, but he did make a good point:

"Any one of us can come up with multiple, plausible stories
concerning the evolution of any given biological feature."

Note that he admits that *ANY* biological system can be accounted
for by such story-telling. As I've always said, they tell us
more about a person's ability to imagine than the natural world.

"But plausibility is about the weakest criterion one can apply
to an evolutionary hypothesis."

I should put the above two sentences in my sig-file as many
around here seem to think plausible stories are all that needed.
This is why as I am consistently portrayed as one who argues
"evolution can't happen" as those plausible stories are ONLY
effective in reply to such a position. When folks argue
with me, it would be prudent for them to do so with the foreknowledge
that Dorit and I concur.

But Dorit adds something else. Don't want to quote him out
of context. :)

"Evolutionary biology may finally be coming of age because we are
moving away from particularistic, speculative scenarios - the
just-so stories. The rigorous testing of evolutionary hypotheses
depends on the use of comparative data, on an understanding of
mechanism and, increasingly, on the experimental manipulation
of components of the system."

There are quite a few interesting things to say about this. First,
it seems like Dorit is admitting that "up to now," evolutionary
hypotheses have been barely more than weak just-so stories. But
I would bet if we could go back in time, and argue with the Larry
Morans and Howard Hersheys of 30-40 years ago, they wouldn't be
even slightly more tentative than the modern Howards and Larrys.
But if evolutionary biology is coming of age only today,
what would explain the same degree of assuredness?

Secondly, some folks have accused me of using insults when I point
out the just-so story nature of so many evolutionary explanations.
But it should be clear from Dorit's use that this term was not invented
by me and has been a long-time problem for evolutionary explanations
that is usually swept under the rug. The question is whether a
Darwinian explanation can ever truly get away from a just-so story.
I don't think it can. I think they are inherent in Darwinism.
This doesn't mean all evolutionary explanation have to involve them.
From the analyses Dorit cites, one can reach a decent interpretation
outlining evolutionary *relationships*. But when Darwinism is then
employed to explain the origin of the relationships, the just-so
mindset re-surfaces. Those just-so stories then mean something to
folks who can't accept intelligent designers because they show
a plausible way something that "looks designed" could come about without
an intelligent designer. But as Dorit says, this is the weakest criterion
we can apply. Yet it is exactly at this point that the debate about
design occurs.

Darwinists need to realize that just-so stories have long given
rise to skepticism from people from all sorts of different background
beliefs. They are ususally quick to blame those background beliefs
for the skepticism. But they never seem to realize the just-so
element of their belief naturally arouses skepticism regardless of
background beliefs. Dorit essentially admits this and does so probably
because he thinks we are finally about to abandon those just-so stories.
We should be so lucky.

Thirdly, Dorit fails to consider that one might build a case for
intelligent design as the best explanation *because* of the comparative
data, considerations of mechanisms, and what we know from experimentally
manipulating systems. After all, this is exactly what I am doing in
my discussion of oriC and DNA replication. And guess what? It looks
like all these analyses simply mean that the just-so stories have
now simply extended into the molecular realm.

>This first post handles your preamble in detail, and provides just
>a few comments about the rest.

I certainly apologize for the length. If
>>you are unwilling or unable to read the entire thing, the gist of my
>>review is summarized in the first paragraph. I wrote this to assure
>>Peter that I have indeed read Behe's book. I also now know where Peter
>>got all his quotes for his alien hypothesis.

>Are you referring to the solitary Orgel quote? The Crick quote
>comes from my having read Crick in the original, and you won't
>find it anywhere in Behe's book. In fact I read the Crick book
>_Life Itself_ before I ever heard of Behe.

Indeed. The search for ETI has also been around in scientific circles
long before Behe's book.

>>Although I will occassionally resort to scattershot comments on
>>particular ideas, there will be a few common threads running throughout
>>this review: First, Behe misunderstands the requirements of a 'good'
>>scientific theory and insists that evolution meet requirements that *no*
>>scientific theory can meet.

>Which ones?

>> Second, Behe has a double standard for
>>evidence, requiring evidence by the ton in exquisite detail for
>>evolution by natural selection for any system *he* chooses, but
>>apparently (because I saw none) requiring no evidence at all that
>>explicitly favors the logical implications one can draw from his
>>alternative explanations (when he even proposes an alternative).

>I'm not following this.

I didn't get the impression that Behe was invoking a double-standard.
To me, it look more like "if you talk the talk, walk the walk."
Darwinism has been around for over a century and supposedly makes
sense of all biology. There are Darwinian apologists (like Dawkins)
who make huge claims about its utility. Behe essentially highlights
how the talk is far ahead of the science.

>> Third,
>>he violates his own statement in the preface (p. ix) ("Still, the point
>>remains that understanding the origin of something is different from
>>understanding its day-to-day workings.") by continually describing the
>>day-to-day workings of *a* 'current' system as if that were sufficient
>>evidence in itself to justify a particular mechanism for its origin.

>That's your inference. You aren't suggesting he shouldn't have
>described the day-to-day workings of various systems, do you?

I think Howard is suggesting that Behe should have considered
the hypothetical ancestral states. Of course, to do this,
he would have to describe the day-to-day workings of other systems.
However, I don't think Behe wrote his book as the "final word."
I think he wrote it as a "first step" and by introducing the concept
of IC, he has opened the door for folks like me to analyze IC
systems WITH Howard's concern in mind. Besides, don't forget that
Howard uses the day-to-day workings of modern viral systems to
explain DNA replication in the purported ancestors of bacteria.
I hope he's not suggesting a double standard here. ;)

>>Fourth, he clearly has a very rigid definition of 'function' that fails
>>to countenance secondary activities or variation in activity and
>>otherwise presents activities in the narrowest possible way, never
>>noting that the *activity* described (sometimes even the enzymes
>>themselves) can be used in many places and 'systems' besides the one
>>described.

>You seem to be criticizing Behe for not blatantly asserting, without
>a scrap of evidence, that the activities he describes can be
>used elsewhere. Because that's all you've been doing, AFAIK.

If Behe had done what Howard wants, his book would have been
1000 pages. He drew the line by introducing the concept with
preliminary considerations.

BTW, I have already taken Howard's concerns into consideration
and argued that the mere existence of similar activites is
not sufficient to displace an actual player from an IC system
(see my original article on DNA replication and IC).

>> Behe has never heard of exadaption, apparently, or the
>>acquisition of emergent properties as a secondary consequence of
>>development for another property.

>He has, but when Julie challenged people for specific examples,
>she got none. And you aren't giving any here, except for
>individual parts, with no clue as to how they coalesced,
>as in the bacterial flagellum.

Exactly. You can't just wave your hands and act as if these *are*
relevant to the system in question. You need evidence to show they
*were* involved. My continual analysis of DNA replication shows
why such explanations, by themselves, fail. Anyone could say, for
example, that DnaA protein was originally a transcription factor
that became a replication initiating protein because it makes
for a plausible just-so story. But is there evidence to think this
is true? That's the question.

>>We can start with his disingeuous definition of evolution as a "process
>>whereby life arose from non-living matter and subsequently developed
>>entirely by natural means." (p. xi). That's his *entire* definition! The
>>first part (which confounds abiogenesis and evolution)

>As does Paul Gans. As do those people who think I am a creationist
>because I don't accept abiogenesis.

Yes, it is *very* common for those who deny abiogenesis to be
lumped with those who deny evolution. Howard's attempt to label
Behe as disingenious fails to consider these dynamics. It would
be nice to hear Howard and others explicitly proclaim that
all the evidence for evolution is not evidence for abiogenesis.

Well, it's late and I gotta go. Just some observations from a sleepy
brain. ;)

[Matt Silberstein]

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

[snip]

>
>But Dorit adds something else. Don't want to quote him out
>of context. :)
>
>"Evolutionary biology may finally be coming of age because we are
>moving away from particularistic, speculative scenarios - the
>just-so stories. The rigorous testing of evolutionary hypotheses
>depends on the use of comparative data, on an understanding of
>mechanism and, increasingly, on the experimental manipulation
>of components of the system."
>
>There are quite a few interesting things to say about this. First,
>it seems like Dorit is admitting that "up to now," evolutionary
>hypotheses have been barely more than weak just-so stories.

That is some tortured logic to get this conclusion from that quote.
First, the words "barely" and "weak" are entirely unjustified by the
quote. Second, the quote does not imply that just-so stories are
useless nor that evolution only consisted of such stories. What is
states clearly is that the science is moving from that to other
methods. IOW, the mix of methods is changing for the better.

So what do you offer us in exchange? Do you offer a detailed
description of the mechanisms you propose? No. Do you offer an
experimental design to determine those mechanisms? No. Do you at least
offer an detailed story of how those mechanisms could have operated?
No. In fact, you offer no story and no proposed mechanisms. All you
give us is some anthropomorphic category of "entity" that you assert
could have performed some unevidenced, unspecified, and undescribed
action at some unknown time and place.

[snip]

>
>>> Second, Behe has a double standard for
>>>evidence, requiring evidence by the ton in exquisite detail for
>>>evolution by natural selection for any system *he* chooses, but
>>>apparently (because I saw none) requiring no evidence at all that
>>>explicitly favors the logical implications one can draw from his
>>>alternative explanations (when he even proposes an alternative).
>
>>I'm not following this.
>
>I didn't get the impression that Behe was invoking a double-standard.
>To me, it look more like "if you talk the talk, walk the walk."
>Darwinism has been around for over a century and supposedly makes
>sense of all biology. There are Darwinian apologists (like Dawkins)
>who make huge claims about its utility. Behe essentially highlights
>how the talk is far ahead of the science.
>

I guess I must have missed all that evidence *for* some intelligent
designer. And all that evidence that show the steps from design to
implementation. And all that evidence for intelligence. Hey I even
missed all that evidence that speaks to purpose and intension.

>>> Third,
>>>he violates his own statement in the preface (p. ix) ("Still, the point
>>>remains that understanding the origin of something is different from
>>>understanding its day-to-day workings.") by continually describing the
>>>day-to-day workings of *a* 'current' system as if that were sufficient
>>>evidence in itself to justify a particular mechanism for its origin.
>
>>That's your inference. You aren't suggesting he shouldn't have
>>described the day-to-day workings of various systems, do you?
>
>I think Howard is suggesting that Behe should have considered
>the hypothetical ancestral states. Of course, to do this,
>he would have to describe the day-to-day workings of other systems.
>However, I don't think Behe wrote his book as the "final word."
>I think he wrote it as a "first step" and by introducing the concept
>of IC, he has opened the door for folks like me to analyze IC
>systems WITH Howard's concern in mind. Besides, don't forget that
>Howard uses the day-to-day workings of modern viral systems to
>explain DNA replication in the purported ancestors of bacteria.
>I hope he's not suggesting a double standard here. ;)
>

The standard in question is Behe's, not Howard's. Howard could violate
that standard since he has not proposed it. OTOH, Behe explicitly
presents the standard and then does not violate it. Regardless of why
he does so, he did so. Did he, in his book, explain (and apologize
for) this violation of his own explicit standard?

[snip]

>
>>>We can start with his disingeuous definition of evolution as a "process
>>>whereby life arose from non-living matter and subsequently developed
>>>entirely by natural means." (p. xi). That's his *entire* definition! The
>>>first part (which confounds abiogenesis and evolution)
>
>>As does Paul Gans. As do those people who think I am a creationist
>>because I don't accept abiogenesis.
>
>Yes, it is *very* common for those who deny abiogenesis to be
>lumped with those who deny evolution. Howard's attempt to label
>Behe as disingenious fails to consider these dynamics.

No, the definition is wrong. It would be nice to hear Julie and other
explicitly proclaim that evolution is not a "process whereby life

arose from non-living matter and subsequently developed entirely by
natural means".

>It would

>be nice to hear Howard and others explicitly proclaim that
>all the evidence for evolution is not evidence for abiogenesis.
>

I would rather make the stronger statement that abiogenesis and
evolution are distinctly different subjects. It is possible, but
certainly not necessary, that some evidence for one is evidence for
the other. It is also possible, but not necessary, that some of the
mechanisms that operated in one operated in the other.

>Well, it's late and I gotta go. Just some observations from a sleepy
>brain. ;)
>
>

Matt Silberstein
-----------------------------
The opinions expressed in this post reflect those of the Walt
Disney Corp. Which might come as a surprise to them.

[Wade Hines]

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

>I haven't seen Howard's reply. Perhaps someone can e-mail it to
>me. I recently read Dorit's review, however. I doubt I'll
>have time to critique it, but he did make a good point:

>"Any one of us can come up with multiple, plausible stories
>concerning the evolution of any given biological feature."

>Note that he admits that *ANY* biological system can be accounted
>for by such story-telling. As I've always said, they tell us
>more about a person's ability to imagine than the natural world.

And what, to flush things out, does the lack of an ability to
suggest a story for how something evolved mean?

Is it a case of no, or almost no support for evolutino from a
'just so' story but big damage to evolutinary theory from the
lack of such stories? I don't want to just read that into your
position but ... to tell the truth, that's what I think you and
others are trying to say.

>"But plausibility is about the weakest criterion one can apply
>to an evolutionary hypothesis."

Same question as above. We know that 'truth is stranger than
fiction' as common observation such that plausibility is a poor
substitute for evidence but to complete the picture, is the lack
of plausibility then to be taken as evidence against? That
just doesn't seem to add up.

>I should put the above two sentences in my sig-file as many
>around here seem to think plausible stories are all that needed.

This may be the horse after teh cart. There's a fellow around
this newsgroup who tries to make much out of the lack of
stories that he considers plausible. Even if one factors out
the issues surrounding his lack of training by which to adequately
judge plausibility, the main push for plausible stories seems
to be from taunting from the design advocate side. So please
don't confuse this with people confusing stories with proof.

>This is why as I am consistently portrayed as one who argues
>"evolution can't happen" as those plausible stories are ONLY
>effective in reply to such a position. When folks argue
>with me, it would be prudent for them to do so with the foreknowledge
>that Dorit and I concur.

I'ld like some more foreknowledge about what the lack of plausible
stories means. Just to round out the picture you see.

>But Dorit adds something else. Don't want to quote him out
>of context. :)

>"Evolutionary biology may finally be coming of age because we are
>moving away from particularistic, speculative scenarios - the
>just-so stories. The rigorous testing of evolutionary hypotheses
>depends on the use of comparative data, on an understanding of
>mechanism and, increasingly, on the experimental manipulation
>of components of the system."

>There are quite a few interesting things to say about this. First,
>it seems like Dorit is admitting that "up to now," evolutionary
>hypotheses have been barely more than weak just-so stories. But

No. Coming of age is more a matter of adding more meaty details.
The difference between pi is about 22/7 and the expanded taylor series.

>I would bet if we could go back in time, and argue with the Larry
>Morans and Howard Hersheys of 30-40 years ago, they wouldn't be
>even slightly more tentative than the modern Howards and Larrys.
>But if evolutionary biology is coming of age only today,
>what would explain the same degree of assuredness?

When did physics "come of age" or chemistry? You are playing
word games in a rather shameless way.

>Secondly, some folks have accused me of using insults when I point
>out the just-so story nature of so many evolutionary explanations.
>But it should be clear from Dorit's use that this term was not invented
>by me and has been a long-time problem for evolutionary explanations
>that is usually swept under the rug. The question is whether a
>Darwinian explanation can ever truly get away from a just-so story.
>I don't think it can. I think they are inherent in Darwinism.

Think again. Some just so stories have very specific requirements
on sequence homology data. In other words, tehy are testable.
The same can be said of pjust so stories predicting transitional
fossiles which may at some point be discovered, or alternative
transitions might be found to rule a particular just so story
out. But this is so basic, you know this quite well, so you must
have meant something else. I just can't figure out what it was.

>This doesn't mean all evolutionary explanation have to involve them.
>From the analyses Dorit cites, one can reach a decent interpretation
>outlining evolutionary *relationships*. But when Darwinism is then
>employed to explain the origin of the relationships, the just-so
>mindset re-surfaces. Those just-so stories then mean something to
>folks who can't accept intelligent designers because they show
>a plausible way something that "looks designed" could come about without
>an intelligent designer. But as Dorit says, this is the weakest criterion
>we can apply. Yet it is exactly at this point that the debate about
>design occurs.

What an interesting juxtaposition. We have "looks designed" and what
I suppose results from a _plausible_ just so story, which we might
call "looks evolved". The looks evolved is being dismissed for the
poor evidenciary relationship between its looks and its actual
history. What, one wonders, is the analogue to "looks designed"?

>Darwinists need to realize that just-so stories have long given
>rise to skepticism from people from all sorts of different background
>beliefs. They are ususally quick to blame those background beliefs

How backwards! Just so stories should not "give rise" to skepticism,
they just shouldn't go very far to alleviate it as "truth is
stranger than fiction", right? Your rhetorical manuevering attempts
to say that evolutionary theory has been nothing more than
just so stories, leveraging your own interpretation of "coming
of age" to support this assertion. That's how it reads. Surely
you won't stand and defend such a position and will claim I
misrepresent you, so take this is my feeble attempt to clarify
your point as there may be others with such low reading
comprehension skills as mine who would likewise misunderstand.
But then, what is your point if it isn't that evolutionary
theory is principly supported by (just so stories) unworthy
support? Are you denying the existence of strong support?
Do you think that because populist "understanding" of eovolution
is a bundle of plausible just so stories that the scientific
theory can be conflated with with these same stories?

>for the skepticism. But they never seem to realize the just-so
>element of their belief naturally arouses skepticism regardless of
>background beliefs. Dorit essentially admits this and does so probably
>because he thinks we are finally about to abandon those just-so stories.

Let's remember that next time you accuse others of trying to read
too much into what you write. I again complain about your
misrepresentation of just so stories actively promoting
skepticism rather than being a weak justification for abandoning
skepticism. I'ld almost suggest that you are too smart to make
such a mistake on accident.

>We should be so lucky.

But then Gould would have to take up writing romance novels.

>Thirdly, Dorit fails to consider that one might build a case for
>intelligent design as the best explanation *because* of the comparative
>data, considerations of mechanisms, and what we know from experimentally
>manipulating systems. After all, this is exactly what I am doing in
>my discussion of oriC and DNA replication. And guess what? It looks

Whoops there goes another irony-o-meter.
The double standard you take to 'looks evolved' and 'looks designed'
with respect to biological systems is so hard for me to understand.
There must be something in your philosphy of science or perhaps
just philosophy that I'm missing because from where I sit, the
contrasted standard screams out its irrational inconsistency.

[howard hershey]

Peter Nyikos wrote:
>
> howard hershey <hers...@indiana.edu> writes:
>
[snip]

>
> >Although I will occassionally resort to scattershot comments on
> >particular ideas, there will be a few common threads running throughout
> >this review: First, Behe misunderstands the requirements of a 'good'
> >scientific theory and insists that evolution meet requirements that *no*
> >scientific theory can meet.
>

> Which ones?

No scientific theory *must* be able to provide non-existent evidence for
every single case chosen. Science works by extrapolating from the best
understood (most evidence) cases to the less well understood (less
evidence) ones, not the other way around. An explanation only needs to
be *compatible with* whatever evidence actually does exist; it is not
compelled to invent non-existent evidence. It is perfectly permissible
to use reasonable inferences derived from a scientific theory's
mechanisms as long as those inferences are treated with the
tentativeness that they deserve and as long as it is all *congruent
with* known mechanisms and the body of evidence in other systems. It is
the burden of those that oppose a particular well-supported theory with
observable mechanisms to present examples which compel one to reject the
standard mechanism *because* the example is incompatible with some
feature of the mechanism.

>
> > Second, Behe has a double standard for
> >evidence, requiring evidence by the ton in exquisite detail for
> >evolution by natural selection for any system *he* chooses, but
> >apparently (because I saw none) requiring no evidence at all that
> >explicitly favors the logical implications one can draw from his
> >alternative explanations (when he even proposes an alternative).
>

> I'm not following this.

Where is his evidence that a single system *did* (rather than *could
have* in his dreams) evolve in one fell swoop. (In another thread,
which was labelled 'Testing IC candidates' or something like that, I
indicated how one could explicitly go about doing this. I didn't see
anyone commenting on that post, though, so I am asking if anyone saw
it. To provide an example that supports the one-fell-swoop version of
IC, one must have a rooted tree so one can say x system evolved within
such and such million, or tens of millions, or billions of years
(between this time when no organism had the system and some later time
when all did, unless lost by secondary processes). Then one can add
evidence that supports a shorter time from sequence data.) This then
(if such a system actually exists, which I doubt) would be support *for*
the idea of essentially simultaneous creation of all parts of the
system. If, OTOH, the evidence indicates that the system's parts did
not appear simultaneously, this would be evidence *for* one of the two
stepwise mechanisms (either with useless intermediate stages, as would
be expected for an IC system, or via stages having some utility, as
would be expected for evolution). To distinguish between IC's
expectation of inutility of intermediate stages and evolution's
expectation that intermediate stages are useful, one needs to turn to a
statistical analysis of 3 or more stepped metabolic pathways.
I certainly would expect that there are many systems where there is
insufficient evidence to resolve the mode of appearance (including the
bacterial flagella and OriC/DnaA). But if Behe or Julie or Peter can
present an example which *supports* the *necessity* to invoke a
non-Darwinian mechanism (Darwinian mechanisms, at least, are known to
exist and are compatible with the observed rates of change, contrary to
Behe's GIGO *a posteriori* argument), I have not seen it presented
either here nor in Behe's book.

>
> > Third,
> >he violates his own statement in the preface (p. ix) ("Still, the point
> >remains that understanding the origin of something is different from
> >understanding its day-to-day workings.") by continually describing the
> >day-to-day workings of *a* 'current' system as if that were sufficient
> >evidence in itself to justify a particular mechanism for its origin.
>

> That's your inference. You aren't suggesting he shouldn't have
> described the day-to-day workings of various systems, do you?

No. I am suggesting that that is insufficient to either support a new
mechanism or to argue effectively against an old one.

>
> >Fourth, he clearly has a very rigid definition of 'function' that fails
> >to countenance secondary activities or variation in activity and
> >otherwise presents activities in the narrowest possible way, never
> >noting that the *activity* described (sometimes even the enzymes
> >themselves) can be used in many places and 'systems' besides the one
> >described.
>

> You seem to be criticizing Behe for not blatantly asserting, without
> a scrap of evidence, that the activities he describes can be
> used elsewhere. Because that's all you've been doing, AFAIK.

No. I am criticising him for blatantly asserting that the end function
he describes is the 1) the only function the present system can serve,
or 2) the only function that any possible intermediate can serve.

>
> > Behe has never heard of exadaption, apparently, or the
> >acquisition of emergent properties as a secondary consequence of
> >development for another property.
>

> He has, but when Julie challenged people for specific examples,
> she got none. And you aren't giving any here, except for
> individual parts, with no clue as to how they coalesced,
> as in the bacterial flagellum.

Back to a system for which there is no *evidence* to support any of the
alternatives. Mine (stepwise with useful intermediate stages) is
certainly as good as yours, and has the advantage of occuring by
mechanisms that can and have been seen in nature. AFAIK, no one has
'seen' any evidence *for* an 'intelligent designer' that might have
actually existed at the right time.

>
> >We can start with his disingeuous definition of evolution as a "process
> >whereby life arose from non-living matter and subsequently developed
> >entirely by natural means." (p. xi). That's his *entire* definition! The
> >first part (which confounds abiogenesis and evolution)
>

> As does Paul Gans. As do those people who think I am a creationist
> because I don't accept abiogenesis.
>

> >is contradicted
> >by the very person he wants to displace in the Pantheon of Biology -
> >Darwin - and for exactly the reason that one might expect from a
> >scientist of Darwin's caliber.
>

> Different meanings of the same word. I do agree Behe needs to
> pay closer attention to semantics.

I suspect that he has been paying more attention to semantics than to
evidence or clear thinking about the implications of IC-ness.

>
> > With respect to the evolution of the eye,
> >Darwin said "How a nerve comes to be sensitive to light hardly concerns
> >us more than how life itself originated." Darwin meant by this that it
> >is idle to speculate in the absence of evidence,
>

> Are you reading something into Darwin that isn't there?

>
> > and at the time, there
> >was no evidence that he could use to explain the molecular workings of
> >vision or the mechanisms of abiogenesis of life. As more evidence
> >accumulates one can, and should, readdress such problems and test
> >whether they remain compatible with current understanding (theory) to
> >the extent that the new evidence permits. Abiogenesis is clearly an
> >area where much more evidence is needed. But the work so far has not
> >presented any evidence that 'kills' the possibility of a natural
> >mechanism of *some* sort.
>

> I'm reminded of the vaudeville act where a man leads an
> elephant into an office and the boss tells him to "get the
> elephant out of here," and the man says, "what elephant?"
>
> What cilium? :-)
>
> What bacterial flagellum? :-)
>
> What protein transport mechanism? :-)

All of which occurred *sometime* in a span of considerable length. The
crucial evidence will be evidence of a system of n parts where all n
parts occurred in a relatively short time. I.e., where are the putative
God-directed gene(s) which appears too rapidly to be accounted for by
any know natural law mechanism. Most of them can be accounted for by
drift alone. A lot can happen in a billion years. Unless you start
specifying how (what order, what timing) was involved in the appearance
of your system, you are not differentiating between your mechanism and
evolution on the basis of evidence, but only on the basis of ignorance
(in the non-pejoritive sense of simply not knowing).

> >This is clearly an area where the question of
> >'is the evidence compatible with the way we think nature works' should
> >regularly be re-visited. But the pre-biotic changes leading to life are
> >not really evolution.
>

> Depends on how you define "life". Some people consider a self-replicating
> ribozyme, assuming such things are even possible, to be life. At the
> opposite extreme, one might only use "life" to refer to prokaryotes
> and above--from the simplest complete-genome living things today,
> on up.

There is certain to be a gray area where the ur-organism exhibits some
features that will lead to selection and evolution like all present day
life. There will be other features of abiogenesis which will simply be
inorganic chemistry, geology and physics. But evolution is a process,
not an organism. The process certainly occurs in living organisms and
only rarely and sporodically in non-living chemistry. The minimal
requirements for evolution include semi-accurate replication of a genome
and the idea that the specific genome affects its chance for further
replication.
>
> >... This is what Darwin did for evolution; he

> >accumulated mounds of evidence for common descent (and Behe claims to
> >accept common descent,
>

> Does he, or does he simply say that he doesn't reject it? There's
> a big difference.

>
> >Natural selection, of course, *is* and *was* observable. There is no
> >question but that natural selection happens in nature. The only possible
> >question is whether the changes that produced common descent are
> >congruent with natural selection (and several additional natural law
> >mechanisms - neutral drift, horizontal transfer, etc. - that have also
> >been shown to occur in nature) or instead *require* or are *better
> >explained* by an alternative mechanism. But it apparently is this
> >feature (invocation of natural law explanation) of Darwin's idea that
> >Behe objects to. It is the idea that common descent does occur congruent
> >with (note that 'congruent with' does not *exclude* the possibility that
> >evolution is divinely guided; it does limit the range of mechanisms that
> >the Divine used to those that have some actual supporting evidence; the
> >naturalism of science is not philosophical Naturalism, despite Behe's
> >disingenuous definition) natural law mechanism and natural selection in
> >particular that Behe finds objectionable. Behe *wishes* to find, at some
> >level of analysis, that evolution cannot be made congruent with any
> >natural law mechanism (not just any *known* natural law mechanism, but
> >the more absolutist *any* natural law mechanism).
>

> You were doing fine until that last sentence. You need to
> get clear about whether intelligent aliens that arose on
> another planet 3.5+ billion years ago, producing living
> things in a lab from nonliving things, would constitute
> a "natural law mechanism" or not. If you claim they do,
> then your last sentence is incorrect.

Reread Behe's definition of evolution (ignoring the abiogenesis bit):
"and subsequently developed entirely by natural means." Unless Behe is
against the idea that organisms 'developed' or changed over time, it
sure seems to me that his objection is against the idea that the
'development' could occur 'entirely by natural means'. That *you* think
that Behe is talking about real naturalistic aliens (who are still
indistinguishable from supernatural beings in terms of actual evidence,
AFAIK) is your problem.

>
> >Indeed, although he fuzzes over the idea of natural selection working to
> >produce changed morphology, he is quite insistent that "Although
> >Darwin's mechanism - natural selection working on variation - might
> >explain many things, however, I do not believe it explains molecular
> >life." (p.5) I find this passing strange, given that some of the *very
> >best* evidence for natural selection working on variation is at the
> >molecular level,
>

> Now YOU are confusing abiogenesis with evolution. Without
> molecular life, there is no life.

Read it again and in context. He was not discussing abiogenesis. He
was discussing evolution, and, in particular, Darwin's mechanism -
natural selection working on variation.
>
> >[...] I presume he meant that he cannot see how natural selection (or any

> >natural law mechanism) can generate the IC-ness he sees in certain
> >biochemical pathways. But, in science, such inability of a current
> >theory to explain (be congruent with) an event *requires* the
> >invocation of alternative explanations that *can* be seen to work in
> >some system
>

> And Behe does that in Chapter 11, when discussing Crick.

When and where have the aliens been observed? Rosswell, NM? In what
system can we observe alien production at work in the same way as one
can find a system where natural selection can be seen to work?

>
> >or it provokes an 'I don't know' shrug. This is not what
> >Behe apparently wants: he wants us to accept the idea that, absent a
> >natural law explanation, one can invoke a supernatural explanation in
> >science.
>

> "in science"? No. What you should have written instead is,
> "absent an explanation of how it could have arisen without
> design, one can invoke the explanation that it was designed,
> in science."

I take it you mean 'without intelligent design' in the first clause. In
that case, one, at minimum, has to have some ideas about the intelligent
designer. Otherwise, one could just as well argue, "absent an
explanation of how an intelligent designer works nor any evidence for
such a designer, one can invoke the explanation that there is no such
thing, in science" Really, Peter, "absent an explanation of how it
could have arisen (with or without design)" is not positive, direct
evidence for a designer. It is a statement of ignorance of any real
explanation, period.
>
> And one can, because one is not committed to postulating
> a *supernatural* designer.

Your natural designer has all the features of a supernatural designer.
No evidence for their existence, invisibility, beyond current human
capabilities, etc.

>
> > Make no mistake about it. Behe is not interested in an
> >alternative natural law explanation - even a natural law 'intelligent
> >designer', like space aliens (his odd definition of evolution makes this
> >perfectly clear); he wants a *supernatural* explanation.
>

> That's your inference, not supported by any explicit statements
> by Behe to that effect.

Except his definition of evolution (and general acceptance of common
descent) makes clear that his objection is to natural law mechanisms for
the development (common descent?) of organisms.

>
> > But a
> >*super*natural explanation is one that cannot be tested or analyzed in
> >any way by science and is not a scientific explanation.
>

> This isn't a science newsgroup; this is talk.origins. Behe's
> book isn't exclusively science; some of it is philosophical.

>
> > Supernatural
> >explanations are useless, unless the *supernatural* entity is posited to
> >work by natural law mechanism (is an IPU).
>

> Invisible pink unicorns are not assumed to work by natural law
> mechanisms, are they?

They always work invisibly. So they seem to work by natural law
mechanisms, all the better to fool us.

>
> >On pages 13-15, Behe describes the difference between 'jumps' (changes
> >that can be observed in the present) and 'chasms'. He agrees that
> >natural selection is clearly a real mechanism for generating 'jumps',
> >i.e. natural selection is a real force in biological change. And he
> >describes 'chasms' that exist in the present. But he then describes the
> >difference between the two as if time played no role in creating a
> >'chasm' where there once was a merely a 'jump'.
>

> Incorrect. Read p. 15 again. He does say that this is where
> Darwin invokes skepticism, but he explicitly describes what you
> claim he doesn't.

>
> >But he incorrectly states that somehow this is the *best* evidence. The
> >*best* evidence for how a 'jump' actually *became* a 'chasm' would be
> >seen by looking at hard parts preserved in the fossil record in those
> >organisms with the largest and most complete fossil record. E.g., the
> >foramnifera.
>

> He's looking at the whole tree of life, and seeing huge chasms there.
> I happen to believe they are bridgeable, but you don't bridge them by looking
> just at forams and then waving your hands.

No. You do it by extrapolating the mechanisms that work best from cases
with the most evidence to those with less evidence and asking whether
the less good evidence that exists there is *congruent with* the way the
mechanism works where the evidence is best. It only has to be congruent
with the evidence to the extent that evidence exists. If little
evidence exists, there may be other alternative mechanisms that work.
But if those alternatives *only* seem to work in cases where there is
little or no evidence, only fools would regard that as evidence that
these mechanisms are likely to be the correct answer. Even worse would
be mechanisms for which there is no support in any presently observable
system. Again, natural selection *can* be observed to have an effect on
morphology of organisms. The intelligent designer of any biochemical
system in nature is a pure hypothetical without evidentiary grounding.
>
[snip rest].

[Wade Hines]

"John Mazor" <maz...@erols.com> writes:

><hines.8...@cgl.ucsf.edu>...

>> What an interesting juxtaposition. We have "looks designed" and what
>> I suppose results from a _plausible_ just so story, which we might
>> call "looks evolved". The looks evolved is being dismissed for the
>> poor evidenciary relationship between its looks and its actual
>> history. What, one wonders, is the analogue to "looks designed"?
>>

>Here you have put your finger on what, IMHO, is the largest gap in Julie's
>exposition. All the talk about nature of the designers, Julie's motives,
>etc. is off-center.

Perhaps but consider: Julie demonstrates fair detailed knowledge of
biochemistry establishing herself as an expert in comparision to the
general population. Julie say "it looks designed to me". Given her
expertise her opinion weighs in as worthy of note and actually demands
consideration. On her half, she basically accuses scientists in general
of toeing the line to the dominate paradigm as her excuse for why
"they" don't see thinks like she does. Explaining why Julie doesn't
see things like other scientists may indeed be explainable through
understanding her initial bias, just as Julie attempts to ascribe
the opinions of other scientists to their 'conformist' bias. (Also
note I think that there are enough with 'nonconformist' biases
in science to seek out real flaws as attention to the controversy
over the Hubble constant will attest)

>It's one thing to assert (paraphrasing) that "Based on the following
>observations and analysis, I don't think that evolution does a really good
>job of explaining certain phenomena I see." It's quite another to try to
>support, let alone prove, the alternative theory that it must (or even
>might) have been by (intelligent) design. The same lack of knowledge, gaps
>in the record, etc. that might support criticisms of evolution theory (as
>Julie criticizes it) seem to work equally against trying to build a case
>for the existence of intelligent design.

>All other questions, including politics, religion, etc., are quibbles
>compared to this massive lacuna in the heart of Julie's expostion.

[Bruce Salem]

In article <1997090316...@milo.math.sc.edu>,

Peter Nyikos <nyi...@math.SC.EDU> wrote:
>sa...@pangea.Stanford.EDU (Bruce Salem) writes:
>

>> But this is an old strawman often raised by the Creationists, that
>>Greek Math Professor lied to us, it is just the same old same-old crap
>>that structures can't transition and retain function.
>
>Bruce is slandering me here. And not for the first time, either.
>He has done it on this very subject at least twice before,
>and been corrected both times.

>[...]

>By the way, my name isn't Greek. Nikos is Greek. Nyikos is not.

Someone wrote to me via e-mail and said that Peter Nyikos
amazes him by being able to post thousands of lines of reply a day
to talk.origins and another biology group. So there is no reference
to him in this reply as he is not Greek, but he found it. Now, I
wonder how I sould have slandered this person Peter Nyikos as I
did not describe him correctly. He is a Math Professor, so so his
.sig claims, but he is not Greek. It is like claiming that species
B is transitionional between A and C without getting the comparisons
correct.

In any case, Irreducible Complexity sounds like an old arguments
that structures cannot lose and acquire new functions and change while
doing so. I wonder if it is the same old rigged argument we get from
"philosophers" that nature is incapable of self-organizing or acquiring
complexity without the help of intelligence, and we know where that
leads to...

[John Mazor]

Wade Hines <hi...@cgl.ucsf.EDU> wrote in article
<hines.8...@cgl.ucsf.edu>...

> "John Mazor" <maz...@erols.com> writes:
>
> ><hines.8...@cgl.ucsf.edu>...
>

> >> What an interesting juxtaposition. We have "looks designed" and what
> >> I suppose results from a _plausible_ just so story, which we might
> >> call "looks evolved". The looks evolved is being dismissed for the
> >> poor evidenciary relationship between its looks and its actual
> >> history. What, one wonders, is the analogue to "looks designed"?
> >>
>

> >Here you have put your finger on what, IMHO, is the largest gap in
Julie's
> >exposition. All the talk about nature of the designers, Julie's
motives,
> >etc. is off-center.
>
> Perhaps but consider: Julie demonstrates fair detailed knowledge of
> biochemistry establishing herself as an expert in comparision to the
> general population. Julie say "it looks designed to me". Given her
> expertise her opinion weighs in as worthy of note and actually demands
> consideration. On her half, she basically accuses scientists in general
> of toeing the line to the dominate paradigm as her excuse for why
> "they" don't see thinks like she does. Explaining why Julie doesn't
> see things like other scientists may indeed be explainable through
> understanding her initial bias, just as Julie attempts to ascribe
> the opinions of other scientists to their 'conformist' bias. (Also
> note I think that there are enough with 'nonconformist' biases
> in science to seek out real flaws as attention to the controversy
> over the Hubble constant will attest)

(snip)

I pretty much ignored Julie's jabs at establishment conformity, on the
grounds that two wrongs don't make a right. However, I see your point, and
you are absolutely correct. Now if we could get both sides to stop relying
on characterizations of the other's mental flexibility or lack thereof.
(And to save at least one round of responses, it doesn't really matter who
"hit the other one back first." There's much bigger fish to fry here! For
example, I'm still waiting for someone to explain how we're supposed to
logically leap from "Evolution is dead!" (at least WRT IC artifacts such as
rotating flagellae) to "Long live the designer!" For me, Julie's
exposition is a non-starter unless she's got cards she ain't showing yet.
Being a stodgy conformist, I haven't yet abandoned my belief that merely
proving "not A" doesn't prove or necessarily even imply "then B".)

[Chris Carrell]

Bruce Salem wrote:
>
> In article <1997090316...@milo.math.sc.edu>,
> Peter Nyikos <nyi...@math.SC.EDU> wrote:
> >sa...@pangea.Stanford.EDU (Bruce Salem) writes:
> >
> >> But this is an old strawman often raised by the Creationists, that
> >>Greek Math Professor lied to us, it is just the same old same-old crap
> >>that structures can't transition and retain function.
> >
> >Bruce is slandering me here. And not for the first time, either.
> >He has done it on this very subject at least twice before,
> >and been corrected both times.
> >[...]
> >By the way, my name isn't Greek. Nikos is Greek. Nyikos is not.
>
> Someone wrote to me via e-mail and said that Peter Nyikos
> amazes him by being able to post thousands of lines of reply a day
> to talk.origins and another biology group. So there is no reference
> to him in this reply as he is not Greek, but he found it. Now, I
> wonder how I sould have slandered this person Peter Nyikos as I
> did not describe him correctly. He is a Math Professor, so so his
> .sig claims, but he is not Greek. It is like claiming that species
> B is transitionional between A and C without getting the comparisons
> correct.

Of course, his ancestry is about as relevant as, oh, my personality
traits that he has gone on and on about, usually in several
threads at once.

> In any case, Irreducible Complexity sounds like an old arguments
> that structures cannot lose and acquire new functions and change while
> doing so. I wonder if it is the same old rigged argument we get from
> "philosophers" that nature is incapable of self-organizing or acquiring
> complexity without the help of intelligence, and we know where that
> leads to...

Doesn't matter what the philosophers think, since the fact that
self-assembly exists is trivial. The mechanisms are fun to study,
though.

Chris

--
Chris Carrell
I em Cheff ooff Bork. Prepere-a tu be-a esseemileted.
Bork Bork Bork!

[PZ Myers]

In article <34101B...@super.zippo.com>, Chris Carrell
<cjc...@super.zippo.com> wrote:

And his math degree is about as relevant as his ancestry.

--
PZ Myers
http://fishnet.bio.temple.edu/

[Richard Keatinge]

In article <5ulg0b$r...@alexander.INS.CWRU.Edu>, Julie Thomas
<iz...@cleveland.Freenet.Edu> writes

>The question is whether a
>Darwinian explanation can ever truly get away from a just-so story.
>I don't think it can.

I agree. It may well be better to stick to "just-don't-know" stories
when we really don't have the relevant evidence. But, of course, this
leaves "gaps" of the unknown into which the desire for the Unknowable
(and much else) can be fitted.

>I think they are inherent in Darwinism.
>This doesn't mean all evolutionary explanation have to involve them.

Unless you can produce better evidence of how things actually did
evolve, they probably do.

I'd like to praise you at this point (and even Peter, although I do
think his rhetorical style unworthy of his no-doubt-enormous intellect)
for the hard work and thought that you have put into this argument. It
does make a change to meet someone with unorthodox ideas, brains, and
the willingness to use them.

I still think that you're outlining a research programme that is leading
only to a dead end.

--
Richard Keatinge

homepage http://www.keatinge.demon.co.uk

[Peter Nyikos]

Myers claimed on "Doolittle tries to critique Behe" that his joining
in rant-fests against me was "ancient history". I guess he figures
as long as he only follows up to one or a few ranters at a time,
it's perfectly OK.

my...@netaxs.com (PZ Myers) writes:

>In article <5uiqt8$ka0$1...@nntp.Stanford.EDU>, sa...@pangea.Stanford.EDU
>(Bruce Salem) wrote:

>> In article <340BDB...@indiana.edu>,
>> howard hershey <hers...@indiana.edu> wrote:
>> > No serious analysis of the implications of IC was presented
>> >(IC-ness *means* that no intermediate stage with any utility can exist

>> >or it means nothing). Nor did he actually present his best shot at

>> >proving that *any* system he deems IC actually *did*, in fact, 'develop'
>> >(to avoid the term 'evolve') in an IC-specific fashion.
>>

>> But this is an old strawman often raised by the Creationists, that
>> Greek Math Professor lied to us, it is just the same old same-old crap

>> that structures can't transition and retain function. They can and must.

>> And, If I read the replies from that self-same Greek Math Professor from the
>> Bible Thumping South, the case of the jaw bones of reptiles being able to
>> serve their dual function of sound conduction and structural support is
>> in direct opposition to the idea of IC.

>I *think* you are talking about Nyikos, but what makes you think he's
>Greek? The name sounds Slavic to me.

Wrong. Nothing Slavic about my name.

[Peter Nyikos]

howard hershey <hers...@indiana.edu> writes:

>Peter Nyikos wrote:
>>
>> sa...@pangea.Stanford.EDU (Bruce Salem) writes:
>>

>> >In article <340BDB...@indiana.edu>,
>> >howard hershey <hers...@indiana.edu> wrote:
>> >> No serious analysis of the implications of IC was presented
>> >>(IC-ness *means* that no intermediate stage with any utility can exist
>> >>or it means nothing).
>>

>> Hershey propagandizes here, throwing scientific caution to the
>> winds. I'll have a lot more to say about his review tomorrow.

Oops, too much else to take care of. It'll have to wait until
next week.

But you shouldn't mind, Howard. This will give you a chance
to get caught up on the thread,

Peter's Clotting Description (was Mr. Ford's "precictions")

>The whole idea of IC-ness is that all the parts are necessary or there
>can be no function, is it not?

Not the specified function. Some parts might be useful for
other functions elsewhere. But please note what he says on
p. 66 before concluding this wipes out his case.

>> >> Nor did he actually present his best shot at
>> >>proving that *any* system he deems IC actually *did*, in fact, 'develop'
>> >>(to avoid the term 'evolve') in an IC-specific fashion.
>>

>> Whatever "IC-specific" means.
>>
>It means a 'system', which, *because no intermediate stage in its
>development can have any useful function*, either develops all at once
>or develops stepwise with utterly useless intermediate stages.
>Evolution requires intermediate stages and (with some relatively minor
>exceptions) requires that they serve *some* useful function.

Yep, and that the transition from one step to the next be
relatively easy to understand.

Peter Nyikos -- standard disclaimer --

[Peter Nyikos]

George Acton <gac...@softdisk.com> writes:

Much ado about nothing. Behe's book is no more difficult than
the average book by Stephen Jay Gould, and somewhat shorter
than many of Gould's.

[howard hershey]

Mark Isaak wrote:
>
> Most of these ideas appear in Howard Hershey's review of _Darwin's Black
> Box_, but I thought it would be worthwhile to summarize them. I would
> appreciate comments from geneticists telling me if anything I say below is
> wrong, or if any of the methods are as unlikely as Behe seems to think
> they are.
>
> How to evolve irreducible complexity:
>
> Method 1: Duplication and variation.
>
> Some kinds of mutations can duplicate large segments of the genome,

or small ones

> leading to redundant copies of parts or even of entire systems. More
> nearly neutral mutations can then cause the redundant parts to specialize.

Let's say, less eventful point mutations.

But duplication need not be exact and it can lead directly to the
formation of a hybrid protein with different functionality.

> Two formerly identical parts can specialize divergently so that their new
> functions no longer overlap, and both would then be necessary. Other
> redundant parts will eventually be removed by random mutations.
>
> Method 2: Change of function.
>
> A system can gradually evolve to fulfill one function but gradually
> acquire a second function in the process. It can then specialize on the
> second function until the first function is no longer obvious. Parts can
> also serve more than one function and switch from one system to another.

AKA exadaption and/or emergent properties. Ideas also used in
morphological evolution.
>
> Method 3: Gradual change.
>
> Parts need not be integral. They can grow gradually from smaller parts,
> and two or more parts can grow more-or-less in unison. For example, a
> strong muscle needs a strong base to support it, but starting from a puny
> muscle and a really flimsy base, both can grow stronger together.

AKA coevolution.
>
> Method 4: Random assemblage.
>
> Duplication and variation will create several unused parts that hang
> around just because they're not hurting anything and because no deletion
> mutations have yet removed them. If enough such random parts exist, it's
> entirely possible that some of them may come together to do something
> useful.

Redundancy is useful. But one should point out that secondary
metabolites of an enzyme are hardly an unheard of property. As long as
the primary metabolite is needed and there is no pressure to lose the
secondary metabolite, you will have it.
>
> Any other methods I missed?

Horizontal transfer.
> --
> Mark Isaak at...@best.com http://www.best.com/~atta
> "To undeceive men is to offend them." - Queen Christina of Sweden

[howard hershey]

Wade Hines wrote:
>
> iz...@cleveland.Freenet.Edu (Julie Thomas) writes:
>
> >I haven't seen Howard's reply. Perhaps someone can e-mail it to
> >me. I recently read Dorit's review, however. I doubt I'll
> >have time to critique it, but he did make a good point:
>
> >"Any one of us can come up with multiple, plausible stories
> >concerning the evolution of any given biological feature."
>
> >Note that he admits that *ANY* biological system can be accounted
> >for by such story-telling. As I've always said, they tell us
> >more about a person's ability to imagine than the natural world.

Not if the stories have to be congruent with what we know about how
biological systems work. As I pointed out in my review, I think that
Behe is asking a different question than he thinks he is asking. Behe
is really asking "Why did this system evolve?" or more accurately "What
specific selective forces were involved in the evolution of this
system?" This last is potentially answerable by science, but in most
cases we do not have sufficient evidence to do more than provide some
reasonable inferences (a just-so story). Unfortunately, Behe also
confounds this with the more teleological (and ultimately unanswerable)
question which also reads "Why did this system evolve?" and answers that
in the same way that old Bill Paley does. The question Behe *claims* to
be asking, "*How* could this system evolve by natural law mechanisms?"
can often actually *be* answered. The observed changes in genes and
proteins that are required to produce the current differences from
reasonable ancestral forms (typically by duplication and divergence,
sometimes by scrambling of protein motifs, often with considerable
neutral drift) are *congruent with* the idea that these differences
arose by natural selection (acting primarily in a conservative fashion)
acting on random mutations (the only kind of mutation that we have ever
observed) of various kinds, from duplication to point mutation and
neutral drift by fixation of random mutations. The way that you
disprove the "How did this evolve?" question is by either presenting a
different observable and/or testable mechanism by which it could occur
or by presenting evidence that the observed differences are too great to
be accomplished in the time available by these *known* natural law
mechanisms. Answering this question does not require any attempt to
describe which specific selective forces were at work. All it asks is
whether the observed extent of changes can be due to known natural law
mechanisms or not. So far, the clear answer is yes, all of the observed
differences are within the range of changes over time that can be
explained by known natural law mechanisms. There is no reason to
propose unseen mechanisms.

The scientifically answerable part of the "Why did this evolve?"
question (what selective forces pushed the selected for 'parts' of the
change - much of the observed change typically appears to be due to
neutral drift) requires, as it does in the present, a knowledge of the
organism's selective environment relevant to this system. For fossil
organisms, one can often only make reasonable inferences (based on
homologies in living organisms and similarities to other systems and
based on the known functions - note plural - of these systems) as to
what selective forces *might* be at work (i.e., propose a reasonable
just-so story). But the same lack of knowledge afflicts the just-so
story of "it was invented all at once" or the just-so story of "it was
invented stepwise with useless intermediate stages" and those two
stories require the invention of new mechanisms that have never been
observed or requires supernatural mechanisms that also have never been
observed. In fact, these stories run contrary to known natural law
mechanisms.

The ultimate teleological "Why?" question, of course, is not a
scientific one.

>
> And what, to flush things out, does the lack of an ability to
> suggest a story for how something evolved mean?
>
> Is it a case of no, or almost no support for evolutino from a
> 'just so' story but big damage to evolutinary theory from the
> lack of such stories? I don't want to just read that into your
> position but ... to tell the truth, that's what I think you and
> others are trying to say.

It's a case of damned if you do and damned if you don't. That is why
most biologists dislike these stories and concentrate on the question of
whether the observed changes that did occur are consistent with their
happening by known natural law mechanisms.

IC will become relevant if (if ever; I personally consider it unlikely)
it presents evidence for a 'system' which appears to have 'appeared' in
an IC-specific fashion incompatible with known natural law mechanisms
(which require stepwise events with by-and-large intermediate utility
for any steps selected for). I have suggested approaches for doing so
in another thread. Different approaches for
IC-by-instantaneous-appearance and IC-by-useless-intermediate-stages.

[I have kept the rest of the discussion without further comment from me,
in case you have not already read it.]

[Julie Thomas]

In a previous article, maz...@erols.com (John Mazor) says:

>Wade Hines <hi...@cgl.ucsf.EDU> wrote in article
><hines.8...@cgl.ucsf.edu>...

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

(snip)

> >This doesn't mean all evolutionary explanation have to involve them.
> >From the analyses Dorit cites, one can reach a decent interpretation
> >outlining evolutionary *relationships*. But when Darwinism is then
> >employed to explain the origin of the relationships, the just-so
> >mindset re-surfaces. Those just-so stories then mean something to
> >folks who can't accept intelligent designers because they show
> >a plausible way something that "looks designed" could come about without
> >an intelligent designer. But as Dorit says, this is the weakest
criterion
> >we can apply. Yet it is exactly at this point that the debate about
> >design occurs.

>> What an interesting juxtaposition. We have "looks designed" and what
>> I suppose results from a _plausible_ just so story, which we might
>> call "looks evolved". The looks evolved is being dismissed for the
>> poor evidenciary relationship between its looks and its actual
>> history. What, one wonders, is the analogue to "looks designed"?

>Here you have put your finger on what, IMHO, is the largest gap in Julie's

>exposition. All the talk about nature of the designers, Julie's motives,
>etc. is off-center.

Almost. But in my discussion of the bacterial flagella and the oriC/
DNA replication, the pattern doesn't amount to "looks evolved."

>It's one thing to assert (paraphrasing) that "Based on the following
>observations and analysis, I don't think that evolution does a really good
>job of explaining certain phenomena I see." It's quite another to try to
>support, let alone prove, the alternative theory that it must (or even
>might) have been by (intelligent) design. The same lack of knowledge, gaps
>in the record, etc. that might support criticisms of evolution theory (as
>Julie criticizes it) seem to work equally against trying to build a case
>for the existence of intelligent design.

>All other questions, including politics, religion, etc., are quibbles
>compared to this massive lacuna in the heart of Julie's expostion.

Agreed. But as I noted, the hole will not be unplugged forever.
That ID model might very well take shape before your watching eyes.
Pieces and parts have been put together now for the last few months.
Scientific predictions have been made and supported. Mini-patterns
have begun to emerge. Flesh all this out and plug your hole,
and a viable alternative system may be born. ;)

--

Any one of us can come up with multiple, plausible stories concerning the

evolution of a given biological feature. But plausibility is about the
weakest crtierion one can apply to an evolutionary hypothesis.
- Robert Dorit, Biology Dept., Yale University

[Julie Thomas]

In a previous article, ric...@keatinge.demon.co.uk (Richard Keatinge) says:

>I'd like to praise you at this point (and even Peter, although I do
>think his rhetorical style unworthy of his no-doubt-enormous intellect)
>for the hard work and thought that you have put into this argument. It
>does make a change to meet someone with unorthodox ideas, brains, and
>the willingness to use them.

Why, thank you! As I see it, even if I am totally wrong, Darwinism
is better off with folks like me than without me. Any system of
belief does much better when it must compete for the best interpretation
of the data. Folks like me stimulate folks like Howard and Larry
to better define their position and actually look for ways to interpret
the data in ways no one has seriously thought of before. Look at it this
way. I bet Michael Behe's book alone will turn out to do more to get
Darwinian evolutionists to look for good evidence of how these molecular
features evolved than all the books of Gould and Dawkins' put together.
Ask yourself this. If it wasn't for me, would Larry Moran have written
and posted his article about the evolutionary origin of the oriC?
Nothing that detailed appears in the scientific literature.

Competition and diversity is the name of the game. I think reductionists
do themselves a disfavor in trying to restrict science to a monolithic
mindset that shares the same metaphysical assumptions and lumps ID
folks with the ICR.

>I still think that you're outlining a research programme that is leading
>only to a dead end.

Perhaps. But the only truly scientific way to find out is to walk
that road. And if it turns out to be dead end, I'll report back to
you. ;)
--

Any one of us can come up with multiple, plausible stories concerning the

[Bruce Salem]

In article <1997090522...@milo.math.sc.edu>,
Peter Nyikos <nyi...@math.SC.EDU> wrote:
>[...]

>>The whole idea of IC-ness is that all the parts are necessary or there
>>can be no function, is it not?
>
>Not the specified function. Some parts might be useful for
>other functions elsewhere. But please note what he says on
>p. 66 before concluding this wipes out his case.

[...]

Please produce a quote or explain what Behe is saying. This
sounds like waffeling.

Irreducable Complexity:

>>It means a 'system', which, *because no intermediate stage in its
>>development can have any useful function*, either develops all at once
>>or develops stepwise with utterly useless intermediate stages.
>>Evolution requires intermediate stages and (with some relatively minor
>>exceptions) requires that they serve *some* useful function.
>
>Yep, and that the transition from one step to the next be
>relatively easy to understand.

But clearly in the case of the reptilian jaw bones or the
heaart going from two to four chambers the intermediate stages are
functional. In choosing bacterial flagellia or something else one
can deal in mystery, fallacy by appeal to ignorance, and say that
there is a problem when the details are poorly understood and do
not challenge an explaination which works for cases where the
structural developments are well understood.

By the way, I bring up the chambers of the heart because of
an exhange that occured between myself and Julie Thomas a couple of
years ago. She raised the posited evolution of the four chambered heart
as problematic because there is no fossil history and because it
could be used to make the same kind of argument as IC, that possible
gradual intermediates cannot work, cannot be. I think that at the
time myself and others traced the anatomy of the eart in extant
reptiles and in the developing embryo which suggests
all of the intermediate stages including the formation of the
vertrical septum exist and its incompleness in some animals and as a defect
in animals, including Man, that normally have a divided ventricle. These
partial manifestations and intermediates clearly are not fatal, they
might be imperfect, and even morbid, in young children. But the transitional
features work quite well in many features. Even supposed tortion of the
atrial vessels can be understood from the developmental anatomy.

Prehaps the real problem is the underlying religious assumption
that perfection and completeness is to be found in Human and Animal
design, Because they are God's Creations, when biology clearly shows that
many features are imperfect and kludgy. I hope that Peter doesn't have
hemmaroids, to wit!

Bruce Salem

[Laurence A. Moran]

In article <5uqj97$f...@alexander.INS.CWRU.Edu> iz...@cleveland.Freenet.Edu

(Julie Thomas) writes:
>
>In a previous article, ric...@keatinge.demon.co.uk (Richard Keatinge) says:
>
>>I'd like to praise you at this point (and even Peter, although I do
>>think his rhetorical style unworthy of his no-doubt-enormous intellect)
>>for the hard work and thought that you have put into this argument. It
>>does make a change to meet someone with unorthodox ideas, brains, and
>>the willingness to use them.
>
>Why, thank you! As I see it, even if I am totally wrong, Darwinism
>is better off with folks like me than without me. Any system of
>belief does much better when it must compete for the best interpretation
>of the data. Folks like me stimulate folks like Howard and Larry
>to better define their position and actually look for ways to interpret
>the data in ways no one has seriously thought of before. Look at it this
>way. I bet Michael Behe's book alone will turn out to do more to get
>Darwinian evolutionists to look for good evidence of how these molecular
>features evolved than all the books of Gould and Dawkins' put together.
>Ask yourself this. If it wasn't for me, would Larry Moran have written
>and posted his article about the evolutionary origin of the oriC?
>Nothing that detailed appears in the scientific literature.

You are absolutely correct. I thank you as well.

The only reason I am discussing these issues with you is because you have
taken the time to read the literature and you don't automatically reject
rationality. This is what makes the discussion so much fun. I never would
have bothered to read half of those papers if you hadn't kicked sand in
our faces. I sincerely thank you for that.

Having said that, I think you overestimate Behe's book. Most of us have
not read the book and never will. The vast majority of biologists have
never heard of it. Gould and Dawkins, on the other hand, have been in
everybody's face at one time or another. They are stimulating thought in
a way that Behe never could. Gould and Dawkins are listened to and respected
because they know what they are talking about. Even if you don't like
what they are saying you can't really claim that they are ignorant.
(Well, some people like to claim that they are ignorant. It usually
reveals more about the claimer than the claimee.)

Larry Moran

[PZ Myers]

In article <340BDB...@indiana.edu>, howard hershey
<hers...@indiana.edu> wrote:

> PZ Myers wrote:
> >
> > In article <340AE3...@indiana.edu>, howard hershey
> > <hers...@indiana.edu> wrote:
> >
> [snip]
> >
> > I commend you for actually making your way through the entire book.
> > Of course, you are aware that even though you did actually read it,
> > because you are critical you obviously have made a strawman interpretation
> > of the content -- the true meaning of the book is a platonic ideal
> > that you have missed (hey, I just wanted to be the first to shout
> > "Strawman!", 'cause I know you'll hear a lot of that in short order).
> >
> > One serious question. You've pretty well trashed it, chapter by chapter.

> > Is there *any* value to reading this book? I've actually been considering
> > reading it myself (at the end of the semester, not now!), on the
> > principle that it seems to be the focal point for a lot of creationist
> > nonsense, and that I have read a few of Behe's papers, and he can
> > raise some reasonable and valid objections to adaptationist arguments.

> > So what's the bottom line? You clearly dislike the book, but is there
> > any nugget of merit that would justify a biologist reading it?
> >
> Depends.

That's an interesting answer, given that everything you say below is
essentially a condemnation of the book :-)

I will interpret your statement to mean, "the book is a hodge-podge
of badly supported ideological rhetoric with no scientific value, but
when you're shoveling out the stables, sometimes you've gotta look
at a little crap". Is that a fair assessment?

> The book is clearly aimed at a different audience than
> professional biologists or biochemists. Indeed, anyone who can read a
> bichemistry of molecular biology text without blanching will find parts
> of it annoyingly condescending (how often do you need to read the aside
> to the reader telling him or her that she is probably too dumb to
> understand all this complexity?). I found his descriptions a strange
> mixture of dumbing down and refusing to make the obvious simplifying
> statements that can clarify an biochemical pathway (for example, he does
> not present the clotting mechanism as a system that largely acts as
> modifiers and regulators of the activity of its core feature: cleavage
> of fibrinogen to fibrin). I can certainly understand this as a
> rhetorical device, but not from someone who is trying to be objective.
> Presenting it as if all the parts were equally important conflates his
> argument.
> Some of the reasonable objections are there (and I hope that I pointed
> out where I thought he might be correct in his critiques) but couched in
> a way that seems to imply that science really should be able to tell
> exactly what selective forces were acting on the particular organism
> step-by-step rather than merely make reasonable inferences for
> *possible* slective pressures.
> The worst part of the book was not so much what was in it, but what was
> not. No serious analysis of the implications of IC was presented

> (IC-ness *means* that no intermediate stage with any utility can exist

> or it means nothing). Nor did he actually present his best shot at

> proving that *any* system he deems IC actually *did*, in fact, 'develop'
> (to avoid the term 'evolve') in an IC-specific fashion.

> In another post (Julie and DNA IC), I will present some specific ideas
> for how one *could* go about doing this in a way that has the potential
> of convincing scientists. (Why do I bother telling IC-biologists their
> job?)
> > --
> > Paul Z. Myers
> > http://fishnet.bio.temple.edu/

[Matt Silberstein]

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

>
>In a previous article, ric...@keatinge.demon.co.uk (Richard Keatinge) says:
>
>>I'd like to praise you at this point (and even Peter, although I do
>>think his rhetorical style unworthy of his no-doubt-enormous intellect)
>>for the hard work and thought that you have put into this argument. It
>>does make a change to meet someone with unorthodox ideas, brains, and
>>the willingness to use them.
>
>Why, thank you! As I see it, even if I am totally wrong, Darwinism
>is better off with folks like me than without me. Any system of
>belief does much better when it must compete for the best interpretation
>of the data.

This is one of the delightful almost claims. "Darwinism" (or, more
correctly evolutionary biology) may be better off with folks like you,
but Darwinism is not a belief.

[snip]

[Steve Geller]

> Behe's book .... He [Behe] says

>that if we were to make life in the laboratory, this would be evidence
>for design, from the inductive argument that all life which we knew
>how it has arisen, has been designed, therefore, it is probable that
>all life arose from design.

This is an interesting idea. But I doubt it would put an end
to the creationist claims (nothing will).

If some lab could make life from non-living materials, this would
demonstrate that miracles are not required for life itself.

But this still leaves the problem of how life actually arose,
and how it came to be as we find it today. There's plenty of
"we don't know" there to put in God as a place-holder.

I'm still amazed that Behe and other "irreducible complexity"
enthusiasts do not find it far simpler to say that even if life arose
and evolved entirely by natural processes, those natural processes are
the Hand of God.

I think creationists dumb-down God too much. This is especially true
of "fringe creationists" like Behe.

[John Mazor]

Matt Silberstein <mat...@ix.netcom.com> wrote in article
<3413691e...@nntp.ix.netcom.com>...

> In talk.origins iz...@cleveland.Freenet.Edu (Julie Thomas) wrote:
>
> >
> >In a previous article, ric...@keatinge.demon.co.uk (Richard Keatinge)
says:
> >
> >>I'd like to praise you at this point (and even Peter, although I do
> >>think his rhetorical style unworthy of his no-doubt-enormous intellect)
> >>for the hard work and thought that you have put into this argument. It
> >>does make a change to meet someone with unorthodox ideas, brains, and
> >>the willingness to use them.
> >
> >Why, thank you! As I see it, even if I am totally wrong, Darwinism
> >is better off with folks like me than without me. Any system of
> >belief does much better when it must compete for the best interpretation
> >of the data.
>
> This is one of the delightful almost claims. "Darwinism" (or, more
> correctly evolutionary biology) may be better off with folks like you,
> but Darwinism is not a belief.
>
> [snip]
>

Ah, but the recursiveness of it! This means that Darwinism must compete in
a Darwinian fashion against rival interpretations.

[Julie Thomas]

In a previous article, mat...@ix.netcom.com (Matt Silberstein) says:

>
>In talk.origins iz...@cleveland.Freenet.Edu (Julie Thomas) wrote:
>
>>
>>In a previous article, ric...@keatinge.demon.co.uk (Richard Keatinge) says:
>>
>>>I'd like to praise you at this point (and even Peter, although I do
>>>think his rhetorical style unworthy of his no-doubt-enormous intellect)
>>>for the hard work and thought that you have put into this argument. It
>>>does make a change to meet someone with unorthodox ideas, brains, and
>>>the willingness to use them.
>>
>>Why, thank you! As I see it, even if I am totally wrong, Darwinism
>>is better off with folks like me than without me. Any system of
>>belief does much better when it must compete for the best interpretation
>>of the data.
>
>This is one of the delightful almost claims. "Darwinism" (or, more
>correctly evolutionary biology) may be better off with folks like you,
>but Darwinism is not a belief.

So you believe it is not a belief.
--

Any one of us can come up with multiple, plausible stories concerning the

evolution of a given biological feature. But plausibility is about the

weakest criterion one can apply to an evolutionary hypothesis.

[Julie Thomas]

In a previous article, maz...@erols.com (John Mazor) says:

>Matt Silberstein <mat...@ix.netcom.com> wrote in article
><3413691e...@nntp.ix.netcom.com>...

>> In talk.origins iz...@cleveland.Freenet.Edu (Julie Thomas) wrote:
>>
>> >
>> >In a previous article, ric...@keatinge.demon.co.uk (Richard Keatinge)
>says:
>> >
>> >>I'd like to praise you at this point (and even Peter, although I do
>> >>think his rhetorical style unworthy of his no-doubt-enormous intellect)
>> >>for the hard work and thought that you have put into this argument. It
>> >>does make a change to meet someone with unorthodox ideas, brains, and
>> >>the willingness to use them.
>> >
>> >Why, thank you! As I see it, even if I am totally wrong, Darwinism
>> >is better off with folks like me than without me. Any system of
>> >belief does much better when it must compete for the best interpretation
>> >of the data.
>>
>> This is one of the delightful almost claims. "Darwinism" (or, more
>> correctly evolutionary biology) may be better off with folks like you,
>> but Darwinism is not a belief.
>>

>> [snip]
>>
>Ah, but the recursiveness of it! This means that Darwinism must compete in
>a Darwinian fashion against rival interpretations.

Not quite. If Darwinism was to truly compete against us design folks
in a Darwinian fashion, they'd allow us to use our intelligence to
formulate arguments while the Darwinists would start randomly including
erroneous claims in their arguments. ;)

--

Any one of us can come up with multiple, plausible stories concerning the

evolution of a given biological feature. But plausibility is about the

weakest criterion one can apply to an evolutionary hypothesis.

[Wade Hines]

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

>In a previous article, maz...@erols.com (John Mazor) says:

>>Wade Hines <hi...@cgl.ucsf.EDU> wrote in article

>>> What an interesting juxtaposition. We have "looks designed" and what

>>> I suppose results from a _plausible_ just so story, which we might
>>> call "looks evolved". The looks evolved is being dismissed for the
>>> poor evidenciary relationship between its looks and its actual
>>> history. What, one wonders, is the analogue to "looks designed"?

>>Here you have put your finger on what, IMHO, is the largest gap in Julie's

>>exposition. All the talk about nature of the designers, Julie's motives,
>>etc. is off-center.

>Almost. But in my discussion of the bacterial flagella and the oriC/
>DNA replication, the pattern doesn't amount to "looks evolved."

You are ignoring the problem with your 'looks designed'.
This is your claim, and it's in the nature of a just so story, without
any implications for testablity or much of a story for that matter:
more of a just so cause I say so.

[Matt Silberstein]

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

>
>
>In a previous article, mat...@ix.netcom.com (Matt Silberstein) says:
>
>>
>>In talk.origins iz...@cleveland.Freenet.Edu (Julie Thomas) wrote:
>>
>>>
>>>In a previous article, ric...@keatinge.demon.co.uk (Richard Keatinge) says:
>>>
>>>>I'd like to praise you at this point (and even Peter, although I do
>>>>think his rhetorical style unworthy of his no-doubt-enormous intellect)
>>>>for the hard work and thought that you have put into this argument. It
>>>>does make a change to meet someone with unorthodox ideas, brains, and
>>>>the willingness to use them.
>>>
>>>Why, thank you! As I see it, even if I am totally wrong, Darwinism
>>>is better off with folks like me than without me. Any system of
>>>belief does much better when it must compete for the best interpretation
>>>of the data.
>>
>>This is one of the delightful almost claims. "Darwinism" (or, more
>>correctly evolutionary biology) may be better off with folks like you,
>>but Darwinism is not a belief.
>

>So you believe it is not a belief.
>

If you want to play the game of using private definitions, then I
suppose you can find such a definition to support your claim. But
"Darwinism" (or, more correctly, evolutionary biology) does not fit
the standard definition of belief. I do not believe in evolution or
Natural Selection. I accept that these are the best explanations for
the our observations. You, OTOH, seem to believe that IC systems are
the product of intelligence. Therefore you claim that when we see an
IC system, it must come from an intelligent entity. In all, I would
rather present a belief than a circular argument.

[Julie Thomas]

In a previous article, mat...@ix.netcom.com (Matt Silberstein) says:

>>>In talk.origins iz...@cleveland.Freenet.Edu (Julie Thomas) wrote:
>>>>
>>>>Why, thank you! As I see it, even if I am totally wrong, Darwinism
>>>>is better off with folks like me than without me. Any system of
>>>>belief does much better when it must compete for the best interpretation
>>>>of the data.
>>>
>>>This is one of the delightful almost claims. "Darwinism" (or, more
>>>correctly evolutionary biology) may be better off with folks like you,
>>>but Darwinism is not a belief.
>>
>>So you believe it is not a belief.
>>
>If you want to play the game of using private definitions, then I
>suppose you can find such a definition to support your claim.

What private defintions? You believe Darwinism is not belief, right?
Or don't you believe this?

But
>"Darwinism" (or, more correctly, evolutionary biology) does not fit
>the standard definition of belief. I do not believe in evolution or
>Natural Selection. I accept that these are the best explanations for
>the our observations.

So acceptance doesn't entail an element of belief?

You, OTOH, seem to believe that IC systems are
>the product of intelligence.

Not necessarily. I view them as good candidates for such things.

Therefore you claim that when we see an
>IC system, it must come from an intelligent entity.

For the umpteenth time, I make no "must" claims.

>In all, I would rather present a belief than a circular argument.

So you believe my belief is a circular argument? Maybe it's because
you believe I believe things I don't. ;)

[John Mazor]

Julie Thomas <iz...@cleveland.Freenet.Edu> wrote in article
<5uuntj$1...@alexander.INS.CWRU.Edu>...

>
> In a previous article, maz...@erols.com (John Mazor) says:

> >Matt Silberstein <mat...@ix.netcom.com> wrote in article
> ><3413691e...@nntp.ix.netcom.com>...

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

> >> >In a previous article, ric...@keatinge.demon.co.uk (Richard
Keatinge)
> >says:
> >> >
> >> >>I'd like to praise you at this point (and even Peter, although I do
> >> >>think his rhetorical style unworthy of his no-doubt-enormous
intellect)
> >> >>for the hard work and thought that you have put into this argument.
It
> >> >>does make a change to meet someone with unorthodox ideas, brains,
and
> >> >>the willingness to use them.
> >> >

> >> >Why, thank you! As I see it, even if I am totally wrong, Darwinism
> >> >is better off with folks like me than without me. Any system of
> >> >belief does much better when it must compete for the best
interpretation
> >> >of the data.
> >>
> >> This is one of the delightful almost claims. "Darwinism" (or, more
> >> correctly evolutionary biology) may be better off with folks like you,
> >> but Darwinism is not a belief.
> >>

> >> [snip]
> >>
> >Ah, but the recursiveness of it! This means that Darwinism must compete
in
> >a Darwinian fashion against rival interpretations.
>
> Not quite. If Darwinism was to truly compete against us design folks
> in a Darwinian fashion, they'd allow us to use our intelligence to
> formulate arguments while the Darwinists would start randomly including
> erroneous claims in their arguments. ;)
>

(snip)

What, you want Darwinian competition to be fair? Somebody better tell that
to the cuckoo bird! ;-)

[howard hershey]

Julie Thomas wrote:
>
> In a previous article, nyi...@math.SC.EDU (Peter Nyikos) says:
>
> >howard hershey <hers...@indiana.edu> writes:
>
[snip]

> "Any one of us can come up with multiple, plausible stories

> concerning the evolution of any given biological feature."
>
> Note that he admits that *ANY* biological system can be accounted
> for by such story-telling. As I've always said, they tell us
> more about a person's ability to imagine than the natural world.

Of course, the only difference between the scientific 'plausible'
stories and the intelligent design 'plausible' stories is that the
former is congruent with known natural mechanisms that can be observed
in the present while the latter requires mechanisms that no one has any
reason to suspect even existed at the time they would be required and
which certainly cannot be observed today in a way that could be
extrapolated back (unless you support the idea of time travel)

>
> "But plausibility is about the weakest criterion one can apply
> to an evolutionary hypothesis."

I agree entirely. This is why most scientists require speculation about
the specific selective forces that might have existed in the past that
could lead to system x as just that, speculation; and why there is
little talk about it in the journals. However, the mechanisms by which
any such system could have evolved is the same regardless of the
specific selective forces, and the present systems look like they
derived by common descent via neutral drift and selection. Obviously
you are proposing a different mechanism from any seen in the present.

>
> I should put the above two sentences in my sig-file as many
> around here seem to think plausible stories are all that needed.

> This is why as I am consistently portrayed as one who argues
> "evolution can't happen" as those plausible stories are ONLY
> effective in reply to such a position. When folks argue
> with me, it would be prudent for them to do so with the foreknowledge
> that Dorit and I concur.
>

> But Dorit adds something else. Don't want to quote him out
> of context. :)
>
> "Evolutionary biology may finally be coming of age because we are
> moving away from particularistic, speculative scenarios - the
> just-so stories. The rigorous testing of evolutionary hypotheses
> depends on the use of comparative data, on an understanding of
> mechanism and, increasingly, on the experimental manipulation
> of components of the system."

Quite right. Which is why I proposed my ways of testing whether any
system actually evolved (appeared) in a IC-specific fashion in another
thread. My problem is that the set of 'systems' that evolved in an
IC-specific fashion that can actually be seen in the evidence appears to
be a null set.

>
> There are quite a few interesting things to say about this. First,
> it seems like Dorit is admitting that "up to now," evolutionary
> hypotheses have been barely more than weak just-so stories. But

> I would bet if we could go back in time, and argue with the Larry
> Morans and Howard Hersheys of 30-40 years ago, they wouldn't be
> even slightly more tentative than the modern Howards and Larrys.
> But if evolutionary biology is coming of age only today,
> what would explain the same degree of assuredness?
>

> Secondly, some folks have accused me of using insults when I point
> out the just-so story nature of so many evolutionary explanations.

I don't. They are 'just-so' stories. But they are 'just-so' stories
that are constrained by known natural law mechanisms and are congruent
with the types of changes one might expect using those mechanisms.

> But it should be clear from Dorit's use that this term was not invented
> by me and has been a long-time problem for evolutionary explanations
> that is usually swept under the rug. The question is whether a
> Darwinian explanation can ever truly get away from a just-so story.
> I don't think it can. I think they are inherent in Darwinism.

> This doesn't mean all evolutionary explanation have to involve them.
> From the analyses Dorit cites, one can reach a decent interpretation
> outlining evolutionary *relationships*. But when Darwinism is then
> employed to explain the origin of the relationships, the just-so
> mindset re-surfaces. Those just-so stories then mean something to
> folks who can't accept intelligent designers because they show
> a plausible way something that "looks designed" could come about without
> an intelligent designer. But as Dorit says, this is the weakest criterion
> we can apply. Yet it is exactly at this point that the debate about
> design occurs.
>

> Darwinists need to realize that just-so stories have long given
> rise to skepticism from people from all sorts of different background
> beliefs. They are ususally quick to blame those background beliefs

> for the skepticism. But they never seem to realize the just-so
> element of their belief naturally arouses skepticism regardless of
> background beliefs. Dorit essentially admits this and does so probably
> because he thinks we are finally about to abandon those just-so stories.

> We should be so lucky.

And 'just-so' (or 'just-not-so') stories involving invisible
'intelligent designers' working by rules that cannot be observed also
give justifiable rise to skepticism (including the vast majority of
scientists).

>
> Thirdly, Dorit fails to consider that one might build a case for
> intelligent design as the best explanation *because* of the comparative
> data, considerations of mechanisms, and what we know from experimentally
> manipulating systems. After all, this is exactly what I am doing in
> my discussion of oriC and DNA replication. And guess what? It looks

> like all these analyses simply mean that the just-so stories have
> now simply extended into the molecular realm.

No. It means that one must use known mechanisms to try to explain the
past rather than invisible ones that literally could do or be anything
and everything. Success of a 'just-so' story in science (although all
are no more than 'just-so' stories) depends on the extent to which it is
grounded in evidence and known natural law mechanisms.
>
[snip]

> >>Although I will occassionally resort to scattershot comments on
> >>particular ideas, there will be a few common threads running throughout
> >>this review: First, Behe misunderstands the requirements of a 'good'
> >>scientific theory and insists that evolution meet requirements that *no*
> >>scientific theory can meet.
>
> >Which ones?

That it be able to explain any system, even if there is no evidence in a
particular system.
>
> >> Second, Behe has a double standard for
> >>evidence, requiring evidence by the ton in exquisite detail for
> >>evolution by natural selection for any system *he* chooses, but
> >>apparently (because I saw none) requiring no evidence at all that
> >>explicitly favors the logical implications one can draw from his
> >>alternative explanations (when he even proposes an alternative).
>
> I didn't get the impression that Behe was invoking a double-standard.
> To me, it look more like "if you talk the talk, walk the walk."
> Darwinism has been around for over a century and supposedly makes
> sense of all biology. There are Darwinian apologists (like Dawkins)
> who make huge claims about its utility. Behe essentially highlights
> how the talk is far ahead of the science.

Not in term of workable mechanisms. Determing the exact selective
forces acting in the invisible past may not ever be possible.
>
> >> Third,
> >>he violates his own statement in the preface (p. ix) ("Still, the point
> >>remains that understanding the origin of something is different from
> >>understanding its day-to-day workings.") by continually describing the
> >>day-to-day workings of *a* 'current' system as if that were sufficient
> >>evidence in itself to justify a particular mechanism for its origin.
>
> >That's your inference. You aren't suggesting he shouldn't have
> >described the day-to-day workings of various systems, do you?
>
> I think Howard is suggesting that Behe should have considered
> the hypothetical ancestral states. Of course, to do this,
> he would have to describe the day-to-day workings of other systems.

Not necessarily. If IC is correct in its implications about the origin
of systems, there is no function in any earlier system. The current
system is either created in one fell swoop or stepwise with useless
intermediates.

> However, I don't think Behe wrote his book as the "final word."
> I think he wrote it as a "first step" and by introducing the concept
> of IC, he has opened the door for folks like me to analyze IC
> systems WITH Howard's concern in mind.

Feel free to do so at any time.

> Besides, don't forget that
> Howard uses the day-to-day workings of modern viral systems to
> explain DNA replication in the purported ancestors of bacteria.
> I hope he's not suggesting a double standard here. ;)

Only to the extent that these systems show the range of variations in
mechanisms that is compatible with the function of replicating DNA.
>
> >>Fourth, he clearly has a very rigid definition of 'function' that fails
> >>to countenance secondary activities or variation in activity and
> >>otherwise presents activities in the narrowest possible way, never
> >>noting that the *activity* described (sometimes even the enzymes
> >>themselves) can be used in many places and 'systems' besides the one
> >>described.
>
> >You seem to be criticizing Behe for not blatantly asserting, without
> >a scrap of evidence, that the activities he describes can be
> >used elsewhere. Because that's all you've been doing, AFAIK.
>
> If Behe had done what Howard wants, his book would have been
> 1000 pages. He drew the line by introducing the concept with
> preliminary considerations.

As it is, he ignores the point except on p.64.
>
> BTW, I have already taken Howard's concerns into consideration
> and argued that the mere existence of similar activites is
> not sufficient to displace an actual player from an IC system
> (see my original article on DNA replication and IC).
>
> >> Behe has never heard of exadaption, apparently, or the
> >>acquisition of emergent properties as a secondary consequence of
> >>development for another property.
>
> >He has, but when Julie challenged people for specific examples,
> >she got none. And you aren't giving any here, except for
> >individual parts, with no clue as to how they coalesced,
> >as in the bacterial flagellum.
>
> Exactly. You can't just wave your hands and act as if these *are*
> relevant to the system in question. You need evidence to show they
> *were* involved. My continual analysis of DNA replication shows
> why such explanations, by themselves, fail. Anyone could say, for
> example, that DnaA protein was originally a transcription factor

It still *is* a transcription factor. That hardly takes imagination.

> that became a replication initiating protein because it makes
> for a plausible just-so story. But is there evidence to think this
> is true? That's the question.

The fact that dnaA still *is* a transcription factor doesn't count as
evidence? What, pray tell, would then?
>
> >>We can start with his disingeuous definition of evolution as a "process
> >>whereby life arose from non-living matter and subsequently developed
> >>entirely by natural means." (p. xi). That's his *entire* definition! The
> >>first part (which confounds abiogenesis and evolution)
>
> >As does Paul Gans. As do those people who think I am a creationist
> >because I don't accept abiogenesis.
>
> Yes, it is *very* common for those who deny abiogenesis to be
> lumped with those who deny evolution. Howard's attempt to label
> Behe as disingenious fails to consider these dynamics. It would
> be nice to hear Howard and others explicitly proclaim that
> all the evidence for evolution is not evidence for abiogenesis.
>
> Well, it's late and I gotta go. Just some observations from a sleepy
> brain. ;)
>

[Matt Silberstein]

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

>
>In a previous article, mat...@ix.netcom.com (Matt Silberstein) says:
>
>>>>In talk.origins iz...@cleveland.Freenet.Edu (Julie Thomas) wrote:
>>>>>
>>>>>Why, thank you! As I see it, even if I am totally wrong, Darwinism
>>>>>is better off with folks like me than without me. Any system of
>>>>>belief does much better when it must compete for the best interpretation
>>>>>of the data.
>>>>
>>>>This is one of the delightful almost claims. "Darwinism" (or, more
>>>>correctly evolutionary biology) may be better off with folks like you,
>>>>but Darwinism is not a belief.
>>>

>>>So you believe it is not a belief.
>>>
>>If you want to play the game of using private definitions, then I
>>suppose you can find such a definition to support your claim.
>
>What private defintions? You believe Darwinism is not belief, right?
>Or don't you believe this?
>

What do you mean by "belief" in this context? Are we talking about the
same "belief" as religious belief? If so, then I do not believe that
Darwinism is a belief, I have no beliefs about the question at all.
Nor do I believe, in the religious sense, in Darwinism.

> But
>>"Darwinism" (or, more correctly, evolutionary biology) does not fit
>>the standard definition of belief. I do not believe in evolution or
>>Natural Selection. I accept that these are the best explanations for
>>the our observations.
>
>So acceptance doesn't entail an element of belief?
>

Not in evolution nor in science. I have the same beliefs that one uses
to find one's shoes in the morning. I have the same beliefs in
naturalism that one uses to decide what to have for breakfast. I have
the same beliefs in science that one uses to read the newspaper. IOW,
I tend to believe that the same rules apply in roughly the same
manner. That is all.

> You, OTOH, seem to believe that IC systems are
>>the product of intelligence.
>
>Not necessarily. I view them as good candidates for such things.
>

You have made a somewhat stronger statement than "good candidates".
For instance, you seem to see it as a better candidate, a more
probable answer, than neo-darwinian evolution. And you made the
explicit statement that IC systems usually come from intelligence.
However, you have not presented any evidence to support this claim.
Not a bit. As I said before, we see for categories of systems. IC
system that people make. IC systems that people did not make. Non-IC
system that people make. And non-IC system that people did not make.
How have you been able to determine anything about the relative
prevalence of these categories?

> Therefore you claim that when we see an
>>IC system, it must come from an intelligent entity.
>
>For the umpteenth time, I make no "must" claims.
>

You are right and the "must" was unsupportable. So I will rephrase
that as:

Therefore you claim that when we see an IC system, it usually comes
from an intelligent entity.

>>In all, I would rather present a belief than a circular argument.
>
>So you believe my belief is a circular argument? Maybe it's because
>you believe I believe things I don't. ;)

You can play rhetorical games or you can deal with the issue. Your
claim was:

>"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),

So, while you are right on the point of "must", you have not answered
the primary question of the circular reasoning. How can you possible
justify the claim that "IC usually stems from intelligence"? Of
course, with this assumption, you reasoning follows. But this is just
assuming your conclusion.

[John Wilkins]

In article <5uffl9$m...@bioinfo.med.utoronto.ca>,
lam...@bioinfo.med.utoronto.ca (Laurence A. Moran) wrote:

| In article <340AE3...@indiana.edu>
| howard hershey <hers...@indiana.edu> writes:
|
| >The following is my personal review of Michael Behe's book "Darwin's
| >Black Box".
|
| Thank you very, very much. I enjoyed your review. Don't think I'll buy the
| book though - you ruined the ending. (-:

Don't worry. The movie script of the book has three different endings, and
they won't tell you which one will be used until they've done some audience
testing.

--
John Wilkins, Head of Communication Services, Walter and Eliza
Hall Institute of Medical Research, Melbourne, Australia
<http://www.wehi.edu.au/~wilkins><mailto:wil...@wehi.edu.au>
It is not enough to succeed. Friends must be seen to have failed. - Capote

[Michael S Agney]

Matt Silberstein (mat...@ix.netcom.com) wrote:
: In talk.origins iz...@cleveland.Freenet.Edu (Julie Thomas) wrote:

: >

: >In a previous article, ric...@keatinge.demon.co.uk (Richard Keatinge) says:
: >
: >>I'd like to praise you at this point (and even Peter, although I do
: >>think his rhetorical style unworthy of his no-doubt-enormous intellect)
: >>for the hard work and thought that you have put into this argument. It
: >>does make a change to meet someone with unorthodox ideas, brains, and
: >>the willingness to use them.

: >
: >Why, thank you! As I see it, even if I am totally wrong, Darwinism

: >is better off with folks like me than without me. Any system of
: >belief does much better when it must compete for the best interpretation
: >of the data.

: This is one of the delightful almost claims. "Darwinism" (or, more
: correctly evolutionary biology) may be better off with folks like you,
: but Darwinism is not a belief.

Whoa, there. Are you sure you aren't just jumping on a single word
in someone's post and blowing it out of all proportion to its importance
in the poster's argument?

If we replace 'system of belief' with 'systematization of knowledge', or
some other such phrase with a different load of metaphysical baggage,
Ms. Thomas's post makes its point just as clearly.

Mr. Silberstein, I think your 'religious-motivation-for-anti-evolution'
detector is registering a false positive. Turn down the gain a bit,
please.

--
Michael Agney

[Michael S Agney]

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

: In a previous article, mat...@ix.netcom.com (Matt Silberstein) says:

: >

: >In talk.origins iz...@cleveland.Freenet.Edu (Julie Thomas) wrote:
: >
: >>
: >>In a previous article, ric...@keatinge.demon.co.uk (Richard Keatinge) says:
: >>
: >>>I'd like to praise you at this point (and even Peter, although I do
: >>>think his rhetorical style unworthy of his no-doubt-enormous intellect)
: >>>for the hard work and thought that you have put into this argument. It
: >>>does make a change to meet someone with unorthodox ideas, brains, and
: >>>the willingness to use them.
: >>
: >>Why, thank you! As I see it, even if I am totally wrong, Darwinism
: >>is better off with folks like me than without me. Any system of
: >>belief does much better when it must compete for the best interpretation
: >>of the data.
: >
: >This is one of the delightful almost claims. "Darwinism" (or, more
: >correctly evolutionary biology) may be better off with folks like you,
: >but Darwinism is not a belief.

: So you believe it is not a belief.

(My apologies to Matt Silberstein re my other post on this thread. I was
the one going off half-cocked. The word 'belief' was relevant to Ms.
Thomas after all.)

Darwinism isn't a system of belief in itself. Rather, it is merely a
subcomponent of the general 'system of belief' which many (if not most
(if not all)) scientists subscribe to; namely, that the scientific method
(physical observation and theories derived from those observations) can be
used to discover approximately true statements about the world. (This is
to be distinguished from the rather stronger, and somewhat less justified,
belief that the scientific method can be used to discover _all_ true
statements about the world. This belief is sometimes known as
'scientism'. [*])

If you're not aware of it, I should warn you that calling Darwinism a
'system of belief' tends to set off warning bells among t.o. regulars. We
see all too many cases of religious fundamentalists claiming that
'evolution is a faith' as a first step to claiming that their own faith in
creation carries equal weight; if you don't wish for people to respond to
you as if they were debunking a fundamentalist, try to avoid such
infelicitous turns of phrase.

--
Michael Agney

(*) Much has been made by other t.o. regulars about an earlier post by you
in which you said you did not feel 'constrained by naturalism'. Would it
be reasonable to suppose that all you meant by that is that you reject
scientism?

[Peter Nyikos]

Matt indulges in what looks like a dishonest selective deletion.
He plays dumb about these, making it look like he has only
advanced in sophistication to tell the difference between
marked and unmarked deletia. If so, Paul Myers could
teach him a long lesson on the subject of dishonest marked
deletia.

mat...@ix.netcom.com (Matt Silberstein) writes:

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

>[snip]

======================= begin partial restoration

>>"But plausibility is about the weakest criterion one can apply
>>to an evolutionary hypothesis."

======================================== end of restoration

>>But Dorit adds something else. Don't want to quote him out
>>of context. :)
>>
>>"Evolutionary biology may finally be coming of age because we are
>>moving away from particularistic, speculative scenarios - the
>>just-so stories. The rigorous testing of evolutionary hypotheses
>>depends on the use of comparative data, on an understanding of
>>mechanism and, increasingly, on the experimental manipulation
>>of components of the system."
>>

>>There are quite a few interesting things to say about this. First,
>>it seems like Dorit is admitting that "up to now," evolutionary
>>hypotheses have been barely more than weak just-so stories.

>That is some tortured logic to get this conclusion from that quote.

She was getting it from other things Dorit wrote as well,
like the part you deleted and I partially restored.

>First, the words "barely" and "weak" are entirely unjustified by the
>quote.

Are you deliberately playing dumb? There wasn't even much
between the part I restored above, and where your snip
ended; in fact, what came in between was commentary about
the part I restored:

I should put the above two sentences in my sig-file as many
around here seem to think plausible stories are all that needed.
This is why as I am consistently portrayed as one who argues
"evolution can't happen" as those plausible stories are ONLY
effective in reply to such a position. When folks argue
with me, it would be prudent for them to do so with the foreknowledge
that Dorit and I concur.

[remainder flushed, to use a word Matt seems to have grown
increasingly fond of]

[Matt Silberstein]

In talk.origins mag...@winnie.fit.edu (Michael S Agney) wrote:

[snip]

>
>(My apologies to Matt Silberstein re my other post on this thread. I was
>the one going off half-cocked. The word 'belief' was relevant to Ms.
>Thomas after all.)
>

Apology accepted.

[snip]

[Matt Silberstein]

In talk.origins Peter Nyikos <nyi...@math.SC.EDU> wrote:

>Matt indulges in what looks like a dishonest selective deletion.

Peter, how can you detect the dishonesty in the deletion? For
instance, did I not mark the delete? Some people will do that. The
will even delete a single line from the middle of a paragraph and not
it. Or they will delete an explanation and complain because there was
no explanation. Do you know anyone who does this? And, as a bonus
question, have I ever accused you of dishonesty for doing the above?
(And for completeness I will explicitly state that you have done the
above style deletions.)

>He plays dumb about these, making it look like he has only
>advanced in sophistication to tell the difference between
>marked and unmarked deletia. If so, Paul Myers could
>teach him a long lesson on the subject of dishonest marked
>deletia.
>

But what about dishonest unmarked deletia? Doesn't that bother you at
all? And, again, how do you detect the dishonesty? What evidence and
rules do you use? You have made a clear and explicit accusation.
Please back it up.

Where have I used that word? (I did a DejaNews search. The only post
by me it showed with either flush or flushed was a response to a post
by Peter. Interestingly enough Peter's post did not show up in the
search, but many other Peter posts did. I do not think we should
consider DejaNews terribly reliable.)

But since we are on the subject of deletion, I wonder if you were
being dishonest in your deletion of my points? Actually, on second
thought, I don't really care. I would rather you respond to them.

[restored deletion]

So what do you offer us in exchange? Do you offer a detailed
description of the mechanisms you propose? No. Do you offer an
experimental design to determine those mechanisms? No. Do you at least
offer an detailed story of how those mechanisms could have operated?
No. In fact, you offer no story and no proposed mechanisms. All you
give us is some anthropomorphic category of "entity" that you assert
could have performed some unevidenced, unspecified, and undescribed
action at some unknown time and place.

[end restoration]

[restored deletion]

I guess I must have missed all that evidence *for* some intelligent
designer. And all that evidence that show the steps from design to
implementation. And all that evidence for intelligence. Hey I even
missed all that evidence that speaks to purpose and intension.

[end restoration]

[PZ Myers]

In article <3424c3a3...@nntp.ix.netcom.com>, mat...@ix.netcom.com
(Matt Silberstein) wrote:

>In talk.origins Peter Nyikos <nyi...@math.SC.EDU> wrote:
>
>>Matt indulges in what looks like a dishonest selective deletion.
>
>Peter, how can you detect the dishonesty in the deletion? For
>instance, did I not mark the delete? Some people will do that. The
>will even delete a single line from the middle of a paragraph and not
>it. Or they will delete an explanation and complain because there was
>no explanation. Do you know anyone who does this? And, as a bonus
>question, have I ever accused you of dishonesty for doing the above?
>(And for completeness I will explicitly state that you have done the
>above style deletions.)
>
>>He plays dumb about these, making it look like he has only
>>advanced in sophistication to tell the difference between
>>marked and unmarked deletia. If so, Paul Myers could
>>teach him a long lesson on the subject of dishonest marked
>>deletia.
>>
>But what about dishonest unmarked deletia? Doesn't that bother you at
>all? And, again, how do you detect the dishonesty? What evidence and
>rules do you use? You have made a clear and explicit accusation.
>Please back it up.

Another despicable Nyikos habit: criticize someone like Silberstein
by telling him how ghastly awful and nasty someone else (like me) is.
I seem to be seeing a lot of this lately, secondhand -- I'm not even
in these discussions, but my name just seems to bubble up in Nyikos'
posts, like a frothy little gobbet of phlegmy spit that he has to get
off his chest now and then.

Of course, it is nothing but a dirty debating trick, because:

a) it's irrelevant. I could be Satan incarnate and even the most
honest criticism of me does not necessarily apply to Silberstein.
So why bring me up?

b) it's an inarguable point from Silberstein's point of view. What can
he say--"I am not a liar like Myers"? That's making an unwarranted
insult against a third party not even in the discussion. And he has
no grounds to defend me -- maybe you're right, and I lie constantly.

c) it's cowardly. As Silberstein cannot be expected to defend me, and
as I'm not a participant in the discussion, it gives Nyikos the
opportunity to make as many extravagantly vicious accusations as
he wants (and boy, does he want to make lots of those!) with no
risk that somebody might actually call him on it -- and if they
do, he can sidetrack the whole discussion into one of those
lovely Nyikosian slander-fests that he is so darn good at.

Stay on topic, Peter...and obviously, the topic here is to harass and
insult Silberstein. Go ahead and accept as a given that I am the most
evil, vile, repulsive, depraved poster on talk.origins, but realize that
since *nobody* on this newsgroup blindly accepts my pernicious dictates,
you can't use my perversions as a tool to insult others.

[great gross dishonest deletion of all the elegant points that Peter
and Matt later made in the post, but at least I marked it.]

[George Acton]

iz...@cleveland.Freenet.Edu (Julie Thomas) wrote:
>
> ... As I see it, even if I am totally wrong, Darwinism

> is better off with folks like me than without me. Any system of
> belief does much better when it must compete for the best interpretation
> of the data.

You seem to be saying that even if your position is wrong it's still
respectable. But science doesn't work that way. The presumption is
that there is and was an actual physical reality and that things
happened one way. Either naturalism is correct and there were no
supernatural events, or it isn't, and your position wins. The
theory of combustion doesn't "do much better" if someone still advances
the phlogiston theory. Plate tectonics isn't better off because someone
still rejects it.

> Folks like me stimulate folks like Howard and Larry
> to better define their position and actually look for ways to interpret
> the data in ways no one has seriously thought of before.

Their philosophic position, naturalism, hasn't changed one iota.

> Look at it this
> way. I bet Michael Behe's book alone will turn out to do more to get
> Darwinian evolutionists to look for good evidence of how these molecular
> features evolved than all the books of Gould and Dawkins' put together.
> Ask yourself this.

I bet it won't. Take Behe's clotting chapter, which you avoided
discussing
for good reason. Do you think any serious researcher is going to take
seriously a chapter with the information of a 20 year old handout,
making
fun of a summary speech, citing a 10 year old review of DNA sequences
using an arrangement of the pathways rejected in a 5 year old general
review? As anyone who trudges through the book going to sigh with
relief with he reassures people that letting in a little supernaturalism
won't overwhelm science?

> If it wasn't for me, would Larry Moran have written
> and posted his article about the evolutionary origin of the oriC?
> Nothing that detailed appears in the scientific literature.

Ask Larry. I think he said he did all the reading for a graduate
seminar. And its posting here isn't publication in the scientific
literature. A handful of biochemists will look at it, and some people
may appreciate the cites. But nobody is going to do an experiment
based on it in order to prove or disprove "Design Theory".

> Competition and diversity is the name of the game.

In some fields. But in science finding out new facts about nature _is_
the game. If one theory is correct, diversity winds up in the history
of science books.

> I think reductionists
> do themselves a disfavor in trying to restrict science to a monolithic
> mindset that shares the same metaphysical assumptions and lumps ID
> folks with the ICR.

Most experiments designed according to reductionism have the potential
to raise questions about it, just as every examination of Jurassic
strata
has the possibility of turning up a human footprint. And you're welcome
to come up with an experiment based on metaphysical assumptions, but you
haven't proposed one. And some of the proof-of-principle experiments
are
the cheapest, like semi-conservation of DNA replication
(Meselson-Stahl?).
Considering the money TV preachers collect by stirring up hatred of
godless evolution, which must be orders of magnitude more than the total
spent on biochemical evolution, there would be no trouble getting a
grant.
If they would come up with 1%, it would fund a bigger place than the
Salk.
You're lumping yourself with the IRC with your accusatory tone,
assumption of moral superiority and innuendos that scientists are part
of
a closed-minded conspiracy. It appears that you want to raise the
relative
respectability of supernatural theories by attacking the good faith and
integrity of conventional science. If you believe in competition, why
not
compete cleanly on the merits rather than trying to feed buckshot to the
opponent's frog?

> >I still think that you're outlining a research programme that is leading
> >only to a dead end.
>
> Perhaps. But the only truly scientific way to find out is to walk
> that road. And if it turns out to be dead end, I'll report back to
> you. ;)

That's what Archimedes Plotonium says, too. If you're just going to
write up a complicated system and announce that it could have evolved
but looks more designed to you, and only publish it where a few
scientists
will read it, It's difficult to see what you will accomplish.
--George Acton

[John Mazor]

George Acton <gac...@softdisk.com> wrote in article
<341673...@softdisk.com>...

>
> iz...@cleveland.Freenet.Edu (Julie Thomas) wrote:
> >
> > ... As I see it, even if I am totally wrong, Darwinism
> > is better off with folks like me than without me. Any system of
> > belief does much better when it must compete for the best
interpretation
> > of the data.
>
> You seem to be saying that even if your position is wrong it's still
> respectable. But science doesn't work that way. The presumption is
> that there is and was an actual physical reality and that things
> happened one way. Either naturalism is correct and there were no
> supernatural events, or it isn't, and your position wins. The
> theory of combustion doesn't "do much better" if someone still advances
> the phlogiston theory. Plate tectonics isn't better off because someone
> still rejects it.

Right, but both are better off if someone disproves the challenging theory.
(That which does not kill it, makes it stronger.)

(snip)

Again, Julie has carefully avoided ascribing any charactertistics to the
putatyive designers. And the politics of this, as fascinating as I find
it, still is irrelevant to the scientific merits. I take no comfort in
arguments that attack an odd-ball hypothesis on these kinds of grounds,
especially when there seems to be an abundance of approaches to take with
arguments based on science and logic.

> > >I still think that you're outlining a research programme that is
leading
> > >only to a dead end.
> >
> > Perhaps. But the only truly scientific way to find out is to walk
> > that road. And if it turns out to be dead end, I'll report back to
> > you. ;)

*That* I'm anxiously awaiting.

[Matt Silberstein]

In talk.origins George Acton <gac...@softdisk.com> wrote:

>iz...@cleveland.Freenet.Edu (Julie Thomas) wrote:
>>
>> ... As I see it, even if I am totally wrong, Darwinism
>> is better off with folks like me than without me. Any system of
>> belief does much better when it must compete for the best interpretation
>> of the data.
>
>You seem to be saying that even if your position is wrong it's still
>respectable. But science doesn't work that way. The presumption is
>that there is and was an actual physical reality and that things
>happened one way. Either naturalism is correct and there were no
>supernatural events, or it isn't, and your position wins.

Sorry, but as used by science, naturalism does not deny the existence
of "supernatural event", it just rejects the use of them in the
development of explanations. It is possible that when someone claims
that God spoke to them and touched them He cured their cancer. But if
we can't verify the speaking and the touching and if this is a one
time only event there is not much we can do to put this into a theory.
It may or may not have occurred, but as such it is useless. Now if
there are many such reports and lots of cancer is being cured, then
the situation changes. Or if everybody in the football stadium hears
the voice and "photographs" the hand, then we have a different issue.

>
[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

[George Acton]

In article <3417b2a8...@nntp.ix.netcom.com>,

mat...@ix.netcom.com (Matt Silberstein) wrote:
>
> In talk.origins George Acton <gac...@softdisk.com> wrote:
>
> >iz...@cleveland.Freenet.Edu (Julie Thomas) wrote:
> >>
> >> ... As I see it, even if I am totally wrong,
> >> Darwinism is better off with folks like me than without me.
> >> Any system of belief does much better when it must compete for
> >> the best interpretation of the data.
> >
> >You seem to be saying that even if your position is wrong it's
> >still respectable. But science doesn't work that way. The
> >presumption is that there is and was an actual physical reality
> >and that things happened one way. Either naturalism is correct

> >and there were no supernatural events, or it isn't, and your .
> >position wins

>
> Sorry, but as used by science, naturalism does not deny the
> existence of "supernatural event", it just rejects the use of
> them in the development of explanations. It is possible that when
> someone claims that God spoke to them and touched them He cured
> their cancer. But if we can't verify the speaking and the touching
> and if this is a one time only event there is not much we can do
> to put this into a theory. It may or may not have occurred, but
> as such it is useless. Now if there are many such reports and lots
> of cancer is being cured, then the situation changes. Or if
> everybody in the football stadium hears the voice and "photographs"
> the hand, then we have a different issue.
>

Perhaps I didn't put it clearly. Your definition of naturalism is of
course correct. But in your example either the events occurred or they
did not. The way to decide is by collecting evidence. If one group
of people believe it happened and another believe it didn't, it is
still the case that one or the other is correct. One group isn't
necessarily "doing better" for the disagreement from the other group.
This is a lame analogy from democratic politics or the adversary
set-up of our legal system. It may be that one side is correct and the
other is just delaying recognition of the obvious facts. Often,
Julie Thomas's observation is correct, but there are many
counterexamples.
--George Acton

[Matt Silberstein]

In talk.origins George Acton <gac...@softdisk.com> wrote:

>In article <3417b2a8...@nntp.ix.netcom.com>,
[snip]

>Perhaps I didn't put it clearly. Your definition of naturalism is of
>course correct. But in your example either the events occurred or they
>did not. The way to decide is by collecting evidence.

You are now describing something entirely different. This is the
implementation, so to speak, of the intention, so to speak, of
naturalism. It is not, obviously, the necessary implementation. One
could, for instance, believe in the naturalist principles, but avoid
as much observation as possible. Or one could publish anything and not
have the peer-reviewed process. These different processes would lead
to quite different "sciences". We have developed a set of processes
that will help us mean our "true" purpose (or at least one more layer
in), to find out how the universe works and control it.

>If one group
>of people believe it happened and another believe it didn't, it is
>still the case that one or the other is correct. One group isn't
>necessarily "doing better" for the disagreement from the other group.
>This is a lame analogy from democratic politics or the adversary
>set-up of our legal system. It may be that one side is correct and the
>other is just delaying recognition of the obvious facts. Often,
>Julie Thomas's observation is correct, but there are many
>counterexamples.

There can be no counter examples to an observation. Observations,
evidence not commentary, stand by themselves. They are, to a large
extent, immune to theories.

[Peter Nyikos]

This is my second followup to Howard's long review, which is
indeed a lot more helpful than any other review I've read,
but which also has its share of misconceptions. A CC goes
to Howard because of the long delay.

howard hershey <hers...@indiana.edu> writes:

[deletia of long preamble, most of which was dealt with in my
first followup]

>Chapter 3. Cilia and Flagella

>Clearly the problem here is Behe's insistance that every possible
>intermediate must serve the *exact same function* as the end 'system'.

You are imagining things. And you backed down when I called
you on this point, on the thread,

Peter's Clotting Description (was Mr. Ford's "precictions")

==================================== begin excerpt from followup to you

>> >And he rejected this particular example as a possible explanation of
>> >cillia (far to quickly, IMHO, as I pointed out in my review, because he
>> >is stuck on the idea that the only possible 'function' of cillia is cell
>> >motility).

>> That's your inference. I don't get that from reading p. 66 at all.

>Read it again. He goes through an indirect process, but finds it full
>of holes and ultimately decides that cillia are IC that is unlikely to
>have evolved by this indirect process.

That's a completely different statement, one I'm not quarreling with.

============================== end of excerpt

>He ridicules the idea that tubulins might serve a useful structural
>function before it acquired the end function of motility.

He uses the word "microtubules," and he does nothing of the
sort. On p. 66 he explicitly points out their usefulness
as structural supports and also as "highways" on which
motor proteins travel.

Let us
>imagine a bundle of tubulins serving a structural function at the cell
>membrane, sticking out and causing a projection (but a static one) from
>the cell surface. Let's call such a projection a microvillus (to choose
>a name at random :-)). One of the consequences of these microvilli
>would be an increase in the surface to volume ratio of the cell.

Behe didn't go into that possibility, true, but then, he didn't
have your papers to clue him onto it. And what do you envision
as the utility of this increase?

>Surely, even Behe might be able to come up with a reasonable selective
>environment where such microvilli might be favored, even if they could
>not move at all.

Make that, "Surely, Behe can succeed where I have shown no inclination
to even try, and be able to come up with..."

> Now one, as Behe points out, might envision motor
>molecules involved in transport along the axis of these fiber bundles
>(for precisely the reasons one might expect microvilli to form in the
>first place).

This is the same song you were singing on that other thread,
about how the "pressures" [never named] that caused the
clotting mechanism to evolve to its present state are
the "same" ones which keep it at that state currently.
When we got into specifics, you clammed up.

> Linking some of the bundles might allow some minor
>movement of the microvilli at levels that would be insufficient to cause
>cell motility.

Why link them in the first place? Why would one bundle ten times as
thick do a better job than ten bundles of single tubules? and where does the
binder come from?

A protein that indiscriminately bound microtubules
together would disrupt the cell's shape--just
as a building's shape would be disrupted by
an erroneously placed cable that accidentally
pulled together girders supporting the building.
A linker that strengthened microtubule bundles
for structural supports would tend to make them
inflexible, unlike the flexible linker nexin.
--DBB, pp. 66-67

And how does linking them "allow motor movement" where none
occurred previously?

...even if [the incipient cilium] were at the
cell surface, the number of motor proteins would
probably not be enough to move the cilium.
--DBB, p. 67

> But movement, by creating microcurrents, might have uses
>without being sufficient to move the organism. Under conditions that
>select for more vigorous movement, you might well get the emergent
>property of motility.

And if the cell did move, it would be an unregulated
motion using energy and not corresponding to any need
of the cell.
--DBB, p. 67

Now, of course, you can imagine all kinds of regulator systems
that make the cilia beat in a coordinated way, etc. but you've
conveniently left out all mention of them.

>I have previously given a highly speculative, but similar, possible
>pathway

You haven't proposed a possible pathway above. You've proposed
a tiny fragment of a pathway, with maybe one percent of all
the required components.

> to produce flagella via non-motile, but still functional
>intermediates.

Ditto. You have not described the intermediates in the
kind of detail needed to explain such things as coordinated
motility.

>Can I prove these scenarios? Nope. Are they totally out of line?

Hard to tell until you start fleshing them out.

>Well, if you look for evidence of these intermediate states, you need to
>ask whether tubulins are involved in maintaining cell structure in
>microvilli, whether pilins have utility, whether there are protein
>transport pores, etc in current organisms.

Those aren't intermediate states; they are ingredients which
you propose bringing together from far-flung corners of the
genome. See that other thread for just how much dirt you
are sweeping under the rug here.

> This, of course, is not
>direct evidence. It is evidence like that that Darwin presented for the
>eye.

I'd like to think Darwin did a much more competent job than
you have.

Remainder deleted, to be dealt with in detail later.

[Peter Nyikos]

CC: Richard, because of the invitation below

Richard Keatinge <ric...@keatinge.demon.co.uk> writes:

>In article <5ulg0b$r...@alexander.INS.CWRU.Edu>, Julie Thomas
><iz...@cleveland.Freenet.Edu> writes

>>The question is whether a
>>Darwinian explanation can ever truly get away from a just-so story.
>>I don't think it can.

>I agree. It may well be better to stick to "just-don't-know" stories
>when we really don't have the relevant evidence. But, of course, this
>leaves "gaps" of the unknown into which the desire for the Unknowable
>(and much else) can be fitted.

On the other hand, you've dealt with the insistent claim
of creationists that it's impossible even in principle. And
in talk.origins, it's a big part of the battle right there.

>>I think they are inherent in Darwinism.
>>This doesn't mean all evolutionary explanation have to involve them.

>Unless you can produce better evidence of how things actually did
>evolve, they probably do.

Well, we do have transitional fossils in many parts of the
tree of life. Kathleen Hunt's Transitional Vertebrate Fossils
FAQ, for all its imperfections, points the way nicely.

>I'd like to praise you at this point (and even Peter, although I do
>think his rhetorical style unworthy of his no-doubt-enormous intellect)

I put my intellect to good use too, e.g. in such things as critiquing
Doolittle. And I'm not even paying back Doolittle in his
own coin--only a small piece of it.

>for the hard work and thought that you have put into this argument. It
>does make a change to meet someone with unorthodox ideas, brains, and
>the willingness to use them.

>I still think that you're outlining a research programme that is leading

>only to a dead end.

Well, let's see you argue against it on either of the "directed
panspermy" threads, or on "The Bacterial Flagellum and IC (really!)"
where I did a solidly on-topic post in followup to Silberstein
a short while ago, and intend to keep the thread focused
on the title topic from here on in.

[Peter Nyikos]

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

>Having said that, I think you overestimate Behe's book. Most of us have
>not read the book and never will.

But that doesn't stop Moran from reviewing it sight unseen:

> The vast majority of biologists have
>never heard of it. Gould and Dawkins, on the other hand, have been in
>everybody's face at one time or another.

They've been around a lot longer, and are not one whit more
competent than Behe, by all that I have seen.

And I wonder how many biologists have heard of a *given* randomly
selected Dawkins book or Gould book.

> They are stimulating thought in a way that Behe never could.

Sheer speculation.

> Gould and Dawkins are listened to and respected
>because they know what they are talking about.

Neither knows what he is talking about all the time. Gould
has yet to come clear on what HE means by "transitional".
Dawkins is hilariously incompetent at times--see the critique
of him by Behe on p. 221, and Behe didn't even pick the
best example. Had he picked the "virtual insects" that
Dawkins dotes on at great length in _The Blind Watchmaker_,
the results could have been absolutely mortifying to Dawkins.

> Even if you don't like
>what they are saying you can't really claim that they are ignorant.

They are at least as "ignorant" as Behe, by all that I have
seen.

>(Well, some people like to claim that they are ignorant. It usually
>reveals more about the claimer than the claimee.)

Just as Larry's misdirection about the word "ignorant" [note how
he is cagey enough not to *explicitly* apply it to Behe] reveals
even MORE about him than about these claimers.

[Peter Nyikos]

sge...@dsp.net (Steve Geller) writes:

>> Behe's book .... He [Behe] says
>>that if we were to make life in the laboratory, this would be evidence
>>for design, from the inductive argument that all life which we knew

>>how it has arisen, has been designed, therefore, it is probable that
>>all life arose from design.

He said that? On which page?

>If some lab could make life from non-living materials, this would
>demonstrate that miracles are not required for life itself.

>But this still leaves the problem of how life actually arose,
>and how it came to be as we find it today. There's plenty of
>"we don't know" there to put in God as a place-holder.

Very sensible. But now you undermine what you just wrote:

>I'm still amazed that Behe and other "irreducible complexity"
>enthusiasts do not find it far simpler to say that even if life arose
>and evolved entirely by natural processes, those natural processes are
>the Hand of God.

Are you saying you are amazed that Behe is not a pantheist?

>I think creationists dumb-down God too much.

It is the pantheists who dumb down God, at least the ones
who identify It with our universe and deny It awareness
of Its own existence.

[I restrict "It" to such "God"s. I use the traditional
"He" for God, but try to use it as little as I can. If
the pronoun "E" ever came into general use, I'd jump on it.]

> This is especially true
>of "fringe creationists" like Behe.

Actually, Behe isn't even a creationist in the usual sense of
the word.

[Peter Nyikos]

howard hershey <hers...@indiana.edu> writes:

[humongous snip]

>Quite right. Which is why I proposed my ways of testing whether any
>system actually evolved (appeared) in a IC-specific fashion in another
>thread.

Which other thread? If you ever cross Wade Hines, he'll
eat you alive for such vague references.

My problem is that the set of 'systems' that evolved in an
>IC-specific fashion that can actually be seen in the evidence appears to

>be a null set. ^^^^^^^^^^^^^^^^^^^^^^^^^

That's probably because it was rigged by you to be that way.
In other words, you've proposed a strawman category.

Now, if you'd just acknowledge that the bacterial flagellum
was designed rather than evolving in IC-specific fashion,
you'd save us all a lot of trouble.

Even if you were just to stick to this *issue* where the
bf is concerned, you would have saved me the trouble of
doing this followup. But you seem afraid to touch the
issue with a ten-foot pole in the last two months.

[Peter Nyikos]

my...@astro.ocis.templeNOSPM.edu (PZ Myers) writes:

[off topic, and completely off base tirade against me by Myers, deleted]

>Stay on topic, Peter

[off topic paranoia by Myers deleted]

Where is John Mazor when he is really needed? :-)

[Peter Nyikos]

mat...@ix.netcom.com (Matt Silberstein) writes:

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

>>
>>In a previous article, ric...@keatinge.demon.co.uk (Richard Keatinge) says:
>>

>>>I'd like to praise you at this point (and even Peter, although I do
>>>think his rhetorical style unworthy of his no-doubt-enormous intellect)

>>>for the hard work and thought that you have put into this argument. It
>>>does make a change to meet someone with unorthodox ideas, brains, and
>>>the willingness to use them.
>>

>>Why, thank you! As I see it, even if I am totally wrong, Darwinism

>>is better off with folks like me than without me. Any system of
>>belief does much better when it must compete for the best interpretation
>>of the data.

>This is one of the delightful almost claims. "Darwinism" (or, more

>correctly evolutionary biology) may be better off with folks like you,
>but Darwinism is not a belief.

It is in the hands of a great many people here, including
Silberstein himself, by all available evidence. See "Spotlight
on Silberstein" back in April for a post where Silberstein's
ineptitude at scientific thinking is written about in excruciating
detail.

[Matt Silberstein]

In talk.origins Peter Nyikos <nyi...@math.SC.EDU> wrote:

Peter, do you or don't you agree with Julie that "Darwinism" is a
system of belief?

[Peter Nyikos]

howard hershey <hers...@indiana.edu> writes:

>Wade Hines wrote:
>>
>> iz...@cleveland.Freenet.Edu (Julie Thomas) writes:
>>
>> >I haven't seen Howard's reply. Perhaps someone can e-mail it to
>> >me. I recently read Dorit's review, however. I doubt I'll
>> >have time to critique it, but he did make a good point:

>>
>> >"Any one of us can come up with multiple, plausible stories
>> >concerning the evolution of any given biological feature."
>>
>> >Note that he admits that *ANY* biological system can be accounted
>> >for by such story-telling. As I've always said, they tell us
>> >more about a person's ability to imagine than the natural world.

>Not if the stories have to be congruent with what we know about how
>biological systems work.

I agree with you on this one, Howard. Trouble is, you haven't
been trying for congurence. You are like the person who
constructs six points for a Star of David and then goes away,
deciding that he's made something congruent to it.

> As I pointed out in my review, I think that
>Behe is asking a different question than he thinks he is asking. Behe
>is really asking "Why did this system evolve?" or more accurately "What
>specific selective forces were involved in the evolution of this
>system?" This last is potentially answerable by science, but in most
>cases we do not have sufficient evidence to do more than provide some
>reasonable inferences (a just-so story).

So, when do you plan to write *your* scenario for bat
evolution? :)

> Unfortunately, Behe also
>confounds this with the more teleological (and ultimately unanswerable)
>question which also reads "Why did this system evolve?" and answers that
>in the same way that old Bill Paley does.

Does he? Or does he propose such things as *solutions* to
problems where nobody in the literature (that he was aware
of, anyway, and his reviewers aren't trying to make up
for that hole) has proposed even "just-so" stories for,
and where he hasn't a clue as to what one might go like?

Note, please, his reviewers, except for Keith Robison,
haven't lifted a finger to provide clues.

> The question Behe *claims* to
>be asking, "*How* could this system evolve by natural law mechanisms?"
>can often actually *be* answered.

So, when do you plan to write a REAL scenario for the evolution
of the flagellum or cilium?

The observed changes in genes and
>proteins that are required to produce the current differences from
>reasonable ancestral forms (typically by duplication and divergence,
>sometimes by scrambling of protein motifs, often with considerable
>neutral drift)

Or even deleterious drift, when piggybacked onto chromosomes
with highly advantageous alleles for other systems. A possibility
that never even entered your head when we discussed this very
issue on "Peter's Clotting Description (was Mr. Ford's "precictions")"

> are *congruent with*

Read: consistent with

> the idea that these differences
>arose by natural selection (acting primarily in a conservative fashion)
>acting on random mutations (the only kind of mutation that we have ever
>observed)

Look up the term "recombinant DNA".

>of various kinds, from duplication to point mutation and
>neutral drift by fixation of random mutations. The way that you
>disprove the "How did this evolve?" question is by either presenting a
>different observable and/or testable mechanism by which it could occur

Done by me for the bacterial flagellum.

>or by presenting evidence that the observed differences are too great to
>be accomplished in the time available by these *known* natural law
>mechanisms. Answering this question does not require any attempt to
>describe which specific selective forces were at work.

But unless you have a scenario in which you specify the selective
forces, you have done NOTHING to allay the suspicion that
a suspiciously gizmo-like contraption like the bacterial
flagellum is designed. The scenario doesn't have to divine
the selective forces that ACTUALLY produced it billions
of years ago (assuming they existed at all), but you have
to come up with SOME plausible selective forces.

> All it asks is
>whether the observed extent of changes can be due to known natural law
>mechanisms or not.

You are equivocating. "known natural law mechanisms" may take
100,000 billion years or more to come up with changes like the one
I postulated on that "Peter's..." thread the other day.

> So far, the clear answer is yes, all of the observed
>differences are within the range of changes over time that can be
>explained by known natural law mechanisms.

If you are lucky enough to hit on just the right sequence
of events, yes. Let's see you trim the odds on the
bacterial flagellum.

>The scientifically answerable part of the "Why did this evolve?"
>question (what selective forces pushed the selected for 'parts' of the
>change - much of the observed change typically appears to be due to
>neutral drift) requires, as it does in the present, a knowledge of the
>organism's selective environment relevant to this system.

To some extent. One can postulate various environments. If they
are realistic, you've done your job.

>just-so story). But the same lack of knowledge afflicts the just-so
>story of "it was invented all at once" or the just-so story of "it was
>invented stepwise with useless intermediate stages" and those two
>stories require the invention of new mechanisms that have never been
>observed or requires supernatural mechanisms that also have never been
>observed. In fact, these stories run contrary to known natural law
>mechanisms.

A demonstrable falsehood where my scenario for the design
of the bacterial flagellum is concerned. And Behe explicitly
considers such things on p. 249.

>The ultimate teleological "Why?" question, of course, is not a
>scientific one.

Whatever you mean by "ultimate". It's quite scientific to
ask about the possible motives of ETI designers.

>> And what, to flush things out, does the lack of an ability to
>> suggest a story for how something evolved mean?
>>
>> Is it a case of no, or almost no support for evolutino from a
>> 'just so' story but big damage to evolutinary theory from the
>> lack of such stories? I don't want to just read that into your
>> position but ... to tell the truth, that's what I think you and
>> others are trying to say.

>It's a case of damned if you do and damned if you don't.

I won't damn you if you do. I am very much in disagreement
with Julie on "just-so stories" as far as human understanding
goes. She (and Dorit) may have a point if one has a rather
narrow idea of what constitutes "science".

That is why
>most biologists dislike these stories

I suspect the real reason they dislike them is that they
are very poor at coming up with them. It took almost
a hundred years (AFAIK) for people to come up with even
*plausible* ideas about what the lifestyle
Deinotherium might have been, and they still haven't much
of a clue for Astrapotherium, AFAIK. And it's only
recently that the various competing ideas on the lifestyle
of Chalicotherium are anywhere near conforming to all
that we know about its skeleton.

Reference: Robert L. Carroll, _Vertebrate Paleontology and Evolution_.
Published in 1988 by W. H. Freeman and Co., New York.
ISBN 0-716-71822-7.

>> >"But plausibility is about the weakest criterion one can apply
>> >to an evolutionary hypothesis."
>>

>> Same question as above. We know that 'truth is stranger than
>> fiction' as common observation such that plausibility is a poor
>> substitute for evidence but to complete the picture, is the lack
>> of plausibility then to be taken as evidence against? That
>> just doesn't seem to add up.

It does to me. Plausibility is a poor substitute, all right,
but it IS the *only* substitute worthy of serious thought.
Truth may be "stranger" than fiction but once one has
a complete picture of the truth, it is also plausible.
One could hardly do science otherwise.

>> >I should put the above two sentences in my sig-file as many
>> >around here seem to think plausible stories are all that needed.
>>

>> This may be the horse after teh cart. There's a fellow around
>> this newsgroup who tries to make much out of the lack of
>> stories that he considers plausible.

Much more frequently, of stories that are even worthy of the name.
See my comments on the threads,
"A scenario for bat evolution?" and
"Evolution of the horse (Was: God has a bone to pick with Darwin)"

>> Even if one factors out
>> the issues surrounding his lack of training by which to adequately
>> judge plausibility,

How can you tell until you *do* come up with just-so stories
instead of just chapter titles for the book-long just-so-story
of how the genetic code came to be?

the main push for plausible stories seems
>> to be from taunting from the design advocate side.

Sure, other people in this newsgroup are content with blind faith.
See my post "Uncritical scientists (Was: God has a bone to pick with Darwin)"
where both of you (Hines and Hershey) are mentioned by name.

>> >This is why as I am consistently portrayed as one who argues
>> >"evolution can't happen" as those plausible stories are ONLY
>> >effective in reply to such a position. When folks argue
>> >with me, it would be prudent for them to do so with the foreknowledge
>> >that Dorit and I concur.
>>

>> I'ld like some more foreknowledge about what the lack of plausible
>> stories means. Just to round out the picture you see.

You have it from me. Check the directed panspermy threads.

>> >I would bet if we could go back in time, and argue with the Larry
>> >Morans and Howard Hersheys of 30-40 years ago, they wouldn't be
>> >even slightly more tentative than the modern Howards and Larrys.
>> >But if evolutionary biology is coming of age only today,
>> >what would explain the same degree of assuredness?
>>

>> When did physics "come of age" or chemistry? You are playing
>> word games in a rather shameless way.

Physics and inorganic chemistry came of age a long time ago, IMHO.
I'm not sure of organic chemsitry--you'd think organic chemists
would be breaking down the doors of NASA offices to get a Titan
(that's the moon of Saturn which may have hydrocarbon seas)
probe maximum priority.

Biochemistry? read _Darwin's Black Box_.

>> >Secondly, some folks have accused me of using insults when I point
>> >out the just-so story nature of so many evolutionary explanations.

>> >But it should be clear from Dorit's use that this term was not invented
>> >by me and has been a long-time problem for evolutionary explanations

>> >that is usually swept under the rug. The question is whether a

>> >Darwinian explanation can ever truly get away from a just-so story.

>> >I don't think it can. I think they are inherent in Darwinism.
>>
>> Think again. Some just so stories have very specific requirements
>> on sequence homology data. In other words, tehy are testable.

And Wade Hines, who penned the above lines, seems satisfied
with the laughably inadequate (and dubious in places)
testing that's been done on Doolittle-Feng.

>> The same can be said of pjust so stories predicting transitional
>> fossiles which may at some point be discovered,

None worthy of the name exist to my knowledge. What passes
for "predictions" most of the time is a bunch of discoveries
that are *consistent* with the general principle that intermediates
should exhibit structures in various stages of intermediacy.

The devil is in the details of that "various". If anyone
tried to predict what *Ambulocetus* would have looked
like before it was discovered, that person is probably
frustrated by how large the hind limbs and how small
the tail are. But I doubt that anyone had the courage
to disseminate such a prediction before the discovery was made.

>> or alternative
>> transitions might be found to rule a particular just so story
>> out.

Case in point.

Remainder deleted due to lack of time.

Peter Nyikos -- standard disclaimer --

[Peter Nyikos]

sa...@pangea.Stanford.EDU (Bruce Salem) writes:

>In article <1997090522...@milo.math.sc.edu>,
>Peter Nyikos <nyi...@math.SC.EDU> wrote:
>>[...]
>>>The whole idea of IC-ness is that all the parts are necessary or there
>>>can be no function, is it not?
>>
>>Not the specified function. Some parts might be useful for
>>other functions elsewhere. But please note what he says on
>>p. 66 before concluding this wipes out his case.
> [...]

> Please produce a quote or explain what Behe is saying. This
>sounds like waffeling.

Please get hold of the book. I'm not your personal typist. I have
enough trouble humoring you on the evolution of bats, whales,
and perissodactyls.

>Irreducable Complexity:

The following is not a definition, but a *hypothesis* which
holds in some cases but may fail in others, notably in systems
where autocatalycity exists.

>>>It means a 'system', which, *because no intermediate stage in its
>>>development can have any useful function*, either develops all at once
>>>or develops stepwise with utterly useless intermediate stages.
>>>Evolution requires intermediate stages and (with some relatively minor
>>>exceptions) requires that they serve *some* useful function.
>>
>>Yep, and that the transition from one step to the next be
>>relatively easy to understand.

> But clearly in the case of the reptilian jaw bones or the
>heaart going from two to four chambers the intermediate stages are
>functional.

Please try relating this oft-repeated mantra of yours to
the ongoing discussion.

> In choosing bacterial flagellia or something else one
>can deal in mystery, fallacy by appeal to ignorance, and say that
>there is a problem when the details are poorly understood and do
>not challenge an explaination which works for cases where the
>structural developments are well understood.

There IS no explanation that can be readily transferred
from one system to the other, because the structure
of the flagellum is a lot more artifact-like
than a heart, and its parts don't have nearly as much scope
for variety.

> By the way, I bring up the chambers of the heart because of
>an exhange that occured between myself and Julie Thomas a couple of
>years ago.

Where? I thought Julie was like a bolt out of the blue
in this newsgroup.

> She raised the posited evolution of the four chambered heart
>as problematic because there is no fossil history and because it
>could be used to make the same kind of argument as IC, that possible
>gradual intermediates cannot work, cannot be.

You wouldn't be making this up, would you? Like you made
up THE SAME DAMN STORY about me in the last few weeks,
but without being as specific?

You made up a tall tale about how I brought up `the misconception
of lethal intermediates' without specifying something as
specific as the heart, although you did make a big song
and dance around reptilian-to-mammalian jaw bones as though I had
disagreed with you on anything related to their evolution.

Or is it possible that all this time you have been laboring
under the delusion that Julie Thomas and I are one and the
same person?

> I think that at the
>time myself and others traced the anatomy of the eart in extant
>reptiles and in the developing embryo which suggests
>all of the intermediate stages including the formation of the
>vertrical septum exist and its incompleness in some animals and as a defect
>in animals, including Man, that normally have a divided ventricle.

Aren't you confusing the mammalian atria with the mammalian
ventricles?

> These
>partial manifestations and intermediates clearly are not fatal, they
>might be imperfect, and even morbid, in young children. But the transitional
>features work quite well in many features.

The partially divided atrium of the mammalian embryo isn't even homologous
to the partly divided ventricle of reptiles.

> Prehaps the real problem is the underlying religious assumption
>that perfection and completeness is to be found in Human and Animal
>design,

Maybe for fundamentalists, but certainly not for me and probably
not for Julie.

>Because they are God's Creations, when biology clearly shows that
>many features are imperfect and kludgy. I hope that Peter doesn't have
>hemmaroids, to wit!

I do. I even mentioned them to Keith "Justified and Ancient" Cochran
[whose posts once polluted talk.origins as well as talk.abortion]
after he offered to ransom an unborn baby from abortion if I would
submit to being fisted by him. His allies, who consitituted
the dominant clique in that newsgroup, and who probably gloated
over each and every fisting offer he made, and had only words
of approval for them if they commented at all, went into paroxysms
over how "tasteless" it was for me to mention the fact that
I have hemorrhoids in public.

That was in talk.abortion. The dominant clique in this
newsgroup is marginally better--but only marginally.

[Wade Hines]

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

I'll ignore the other points which I'll assert without proof
have rather simple standard answers and answer this one, out
of whimsey.

> And if the cell did move, it would be an unregulated
> motion using energy and not corresponding to any need
> of the cell.
> --DBB, p. 67

>Now, of course, you can imagine all kinds of regulator systems
>that make the cilia beat in a coordinated way, etc. but you've
>conveniently left out all mention of them.

I'm actually rather familiar with chemotaxis, at least as of about
6 years ago with respect to CheY, CheA and CheW but that's a rather
mature system. Let's address the quote of Behe.

In the first case, lets consider an ability to simply turn
motion on and off without an ability to direct it. Turn on motion
when food supplies are low and one stands a chance of moving to
where food supplies are higher. Even a random walk is better than
nothing and the first step to directed locomotion. Even a system
without an off switch has an advantage as it obviously depletes
its local enviroment and has to move on. So, I disagree with
"not corresponding to any need of the cell" and think that the
comment about unregulated is overblown. Regulated chemotaxis is
better, but even unregulated movement can be advantagous.

The rest of the deleted Behe quotes are likewise rather
empty on examination, even if they superficially sound good.
The embody a particularly disturbing level of off handed
dismissal of standard thinking on topics where it isn't clear
Behe has done any due dilligence despite his far reaching
comments about his take on the state of the scientific literature.

As his book is chock full of such statements, it simply is
not to be taken seriously.

[Wade Hines]

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

>howard hershey <hers...@indiana.edu> writes:

>[humongous snip]

>>Quite right. Which is why I proposed my ways of testing whether any

>>system actually evolved (appeared) in a IC-specific fashion in another
>>thread.

>Which other thread? If you ever cross Wade Hines, he'll

>eat you alive for such vague references.

Only if he make it a large (>20% ?) part of his posting with
more than half being nothing but personal attacks and claims
of his own glory. I think he's safe.

[howard hershey]

An increase in the surface to volume ratio. Same reason why there are
microvilli lining your small intestine (you didn't really think I chose
the name microvillus at random, did you?).

>
> >Surely, even Behe might be able to come up with a reasonable selective
> >environment where such microvilli might be favored, even if they could
> >not move at all.
>
> Make that, "Surely, Behe can succeed where I have shown no inclination
> to even try, and be able to come up with..."

Anybody with the slightest knowledge of physiology would understand the
advantage of increasing surface to volume ratio. The word microvilli
was a not too subtle hint.

> > Now one, as Behe points out, might envision motor
> >molecules involved in transport along the axis of these fiber bundles
> >(for precisely the reasons one might expect microvilli to form in the
> >first place).
>
> This is the same song you were singing on that other thread,
> about how the "pressures" [never named] that caused the
> clotting mechanism to evolve to its present state are
> the "same" ones which keep it at that state currently.
> When we got into specifics, you clammed up.

Better regulatory control of the primary reaction: thrombin cleaving
fibrinogen.

> > Linking some of the bundles might allow some minor
> >movement of the microvilli at levels that would be insufficient to cause
> >cell motility.
>
> Why link them in the first place? Why would one bundle ten times as
> thick do a better job than ten bundles of single tubules? and where does the
> binder come from?

Come on, Peter. The advantage of linkage is that it permits some
movement of the microvilli (but not necessarily motility of the
organism). The linker would be the last step in the process. The other
two parts serve functions without utility. All it would take is the
production of a two-headed binder with a flexible linker inbetween
them. A simple tandem duplication could do this.

>
> A protein that indiscriminately bound microtubules
> together would disrupt the cell's shape--just
> as a building's shape would be disrupted by
> an erroneously placed cable that accidentally
> pulled together girders supporting the building.
> A linker that strengthened microtubule bundles
> for structural supports would tend to make them
> inflexible, unlike the flexible linker nexin.
> --DBB, pp. 66-67
>
> And how does linking them "allow motor movement" where none
> occurred previously?

Once linked, the motor (nee transport molecule) would pull on one side
of the linked tubulins.

>
> ...even if [the incipient cilium] were at the
> cell surface, the number of motor proteins would
> probably not be enough to move the cilium.
> --DBB, p. 67
>
> > But movement, by creating microcurrents, might have uses
> >without being sufficient to move the organism. Under conditions that
> >select for more vigorous movement, you might well get the emergent
> >property of motility.
>
> And if the cell did move, it would be an unregulated
> motion using energy and not corresponding to any need
> of the cell.
> --DBB, p. 67
>
> Now, of course, you can imagine all kinds of regulator systems
> that make the cilia beat in a coordinated way, etc. but you've
> conveniently left out all mention of them.

Wade did that.

>
> >I have previously given a highly speculative, but similar, possible
> >pathway
>
> You haven't proposed a possible pathway above. You've proposed
> a tiny fragment of a pathway, with maybe one percent of all
> the required components.

The primary components (all three of them) are all accounted for. Only
the bit players remain. And your evidence that the cillia did not
appear this way, but rather by an IC-specific mechanism is...?

>
> > to produce flagella via non-motile, but still functional
> >intermediates.
>
> Ditto. You have not described the intermediates in the
> kind of detail needed to explain such things as coordinated
> motility.
>
> >Can I prove these scenarios? Nope. Are they totally out of line?
>
> Hard to tell until you start fleshing them out.

Just the way you have fleshed out the IC-specific mechanism by which
they arose?

>
> >Well, if you look for evidence of these intermediate states, you need to
> >ask whether tubulins are involved in maintaining cell structure in
> >microvilli, whether pilins have utility, whether there are protein
> >transport pores, etc in current organisms.
>
> Those aren't intermediate states; they are ingredients which
> you propose bringing together from far-flung corners of the
> genome. See that other thread for just how much dirt you
> are sweeping under the rug here.

And the evidence for an IC-specific mechanism is...?

[Peter Nyikos]

mat...@ix.netcom.com (Matt Silberstein) writes:

in back-and-forth with Julie, against whom he made what looks
like a suspiciously selective deletion earlier in this thread.

>>>This is one of the delightful almost claims. "Darwinism" (or, more
>>>correctly evolutionary biology) may be better off with folks like you,
>>>but Darwinism is not a belief.
>>

>>So you believe it is not a belief.
>>

>If you want to play the game of using private definitions, then I
>suppose you can find such a definition to support your claim. But
>"Darwinism" (or, more correctly, evolutionary biology) does not fit
>the standard definition of belief. I do not believe in evolution or
>Natural Selection. I accept that these are the best explanations for
>the our observations.

And, since you have shown yourself to lack the competence to
evaluate it, this "acceptance" is a belief in a pretty
strong sense of the word.

> You, OTOH, seem to believe that IC systems are
>the product of intelligence.

No, only that two of them are, and for reasons you can't
even begin to comprehend, by the looks of it.

> Therefore you claim that when we see an
>IC system, it must come from an intelligent entity.

Don't you ever get tired of "rhetorical excess" as to
what Julie has claimed?

Why don't you save us all a lot of trouble and mark your
"rhetorical excesses"? Because then we can ignore
them, confident that they bear NO resemblance to anything
Julie ever claimed.

It would be even more helpful if you skipped the "rhetorical
excesses" and told us what behavior they are the secret
codes for.

[Matt Silberstein]

In talk.origins Peter Nyikos <nyi...@math.SC.EDU> wrote:

>mat...@ix.netcom.com (Matt Silberstein) writes:
>
>in back-and-forth with Julie, against whom he made what looks
>like a suspiciously selective deletion earlier in this thread.
>

Again I ask what kind of standard you use. And are you merely saying
that I deleted deliberately rather than by accident? If not, what does
"selective" mean in this context. Finally, does this sudden appearance
of comments on my deletions have anything to do with my recent posts
that pointed out your unmarked deletions?

BTW, I have don't remember your responding to any of those comments. I
also want to point out that I just mentioned where you did not mark
the deletion. No judgements, no "suspicions", no "selective". Just the
objective comment.

>>>>This is one of the delightful almost claims. "Darwinism" (or, more
>>>>correctly evolutionary biology) may be better off with folks like you,
>>>>but Darwinism is not a belief.
>>>
>>>So you believe it is not a belief.
>>>
>>If you want to play the game of using private definitions, then I
>>suppose you can find such a definition to support your claim. But
>>"Darwinism" (or, more correctly, evolutionary biology) does not fit
>>the standard definition of belief. I do not believe in evolution or
>>Natural Selection. I accept that these are the best explanations for
>>the our observations.
>
>And, since you have shown yourself to lack the competence to
>evaluate it, this "acceptance" is a belief in a pretty
>strong sense of the word.
>

I am aware that you are convinced that you know everything about my
scientific competence. As I remember, it was a single phrase in one
post that showed you that I know nothing at all about science.

BTW, it is amusing to see how you are complaining about some lack on
my part, but you have no comments on Julie's rhetorical games.

>> You, OTOH, seem to believe that IC systems are
>>the product of intelligence.
>
>No, only that two of them are, and for reasons you can't
>even begin to comprehend, by the looks of it.
>

And for reasons that neither your nor Julie seem willing to discuss.
And your position in not the same as Julie. You need to stop thinking
of yourself as a pack, you have significant differences. Julie made
the explicit claim that IC systems usually come from intelligence so
the presences of IC means the system was probably designed. Not just
the two under consideration, but IC systems in general. I do not
remember your comment on the circular logic involved.

>> Therefore you claim that when we see an
>>IC system, it must come from an intelligent entity.
>
>Don't you ever get tired of "rhetorical excess" as to
>what Julie has claimed?
>

You are so right, it is not "must", it is just "usually". Here is the
quote in question:

JT> When this is coupled with my common experience where IC is tied
JT> to intelligent design (intelligence easily generates IC and IC
JT> usually stems from intelligence),

Now this seems like she is assuming the conclusion. It is possible
that she has some kind of support for this statement, but I can't see
how it could be. I have asked you both before, and I will ask again to
justify this seemingly circular logic.

>Why don't you save us all a lot of trouble and mark your
>"rhetorical excesses"?

Why don't you mark where you snip, Peter? Why don't you mark where you
snip out a single line from the middle of a paragraph? Or snip out an
explanatory paragraph and only leave in the opening? Why don't you
explain why the marked deletions made by others raise your suspicions,
but your own unmarked deletions does not bother you at all?

> Because then we can ignore
>them, confident that they bear NO resemblance to anything
>Julie ever claimed.
>

You know, if you commented on the circular logic it would be better
than trying to attack me with this game.

>It would be even more helpful if you skipped the "rhetorical
>excesses" and told us what behavior they are the secret
>codes for.

Matt Silberstein

[howard hershey]

Peter Nyikos wrote:
>
> howard hershey <hers...@indiana.edu> writes:
>
> >Wade Hines wrote:
> >>
> >> iz...@cleveland.Freenet.Edu (Julie Thomas) writes:
> >>

[snip]

>
> So, when do you plan to write *your* scenario for bat
> evolution? :)
>

First, I posit an intelligent alien race. The aliens sent the bats in a
sleeping berth looking for planets with sutible caves. This is
reasonable because 1) there are a lot of planet with potential aliens
and 2) if the aliens were intelligent enough they could easily build a
bat.

[howard hershey]

howard hershey wrote:
>
> Peter Nyikos wrote:
> >
> > howard hershey <hers...@indiana.edu> writes:
> >

[snip]

> >
> > Hard to tell until you start fleshing them out.
>
> Just the way you have fleshed out the IC-specific mechanism by which
> they arose?
> >

[snip]

I have to admit that the insistence that I flesh out my admitedly
simplistic and non-detailed (as befits the evidence) pathway to cillia
is somewhat amusing coming from someone whose response to the real
problems of abiogenesis is "First, we posit an alien..."

Reminds me of the economist trapped in a pit who suggested that he could
get out by positing a ladder.

[Julie Thomas]

In a previous article, hers...@indiana.edu (howard hershey) says:

>Wade Hines wrote:
>
>> iz...@cleveland.Freenet.Edu (Julie Thomas) writes:
>

> >I haven't seen Howard's reply. Perhaps someone can e-mail it to
> >me. I recently read Dorit's review, however. I doubt I'll
> >have time to critique it, but he did make a good point:
>
> >"Any one of us can come up with multiple, plausible stories
> >concerning the evolution of any given biological feature."
>
> >Note that he admits that *ANY* biological system can be accounted
> >for by such story-telling. As I've always said, they tell us
> >more about a person's ability to imagine than the natural world.

>Not if the stories have to be congruent with what we know about how
>biological systems work.

If only this were true. Are cells with RNA genomes congruent
with what we know about how biological systems work? Nope.
Are cells that replicate their DNA genomes for thousands, maybe
millions years, with a semi-functional R-loop mechanism congruent
with what we know about how biological systems work? Who knows?
These just-so storied almost invariably postulate hypothetical
creatures with imaginary systems which show only how the author
is creative at pasting together different features of modern systems.
It's the modern version of inventing unicorns and mermaids.
But we usually haven't the foggiest notion if these imaginary
entities could indeed exist in a way that is congruent with what
we know about how biological systems work. Everytime a just-so
story is told at the molecular level, we end up talking about a sloppy,
unregulated, simple system when what we known about how those biological
systems work doesn't seem to support such a sloppy, unregulated, simple state.
You yourself have invoked DNA polymerases that could only replicate
10-20 nucleotides in a tiny, little genome. But is this *life*?

>As I pointed out in my review, I think that
>Behe is asking a different question than he thinks he is asking. Behe
>is really asking "Why did this system evolve?" or more accurately "What
>specific selective forces were involved in the evolution of this
>system?"

Which is the milk of Darwinism! You seem to forget that Behe's
problem is with *Darwinian* evolution and not simply evolution itself.

>This last is potentially answerable by science, but in most
>cases we do not have sufficient evidence to do more than provide some
>reasonable inferences (a just-so story).

And as I said, it then looks like Darwinism and just-so stories are
joined at the hip. And whether or not they are "reasonable" is in the
eye of the beholder. Or shall we say it's "story-dependent?" ;)

>Unfortunately, Behe also
>confounds this with the more teleological (and ultimately unanswerable)
>question which also reads "Why did this system evolve?" and answers that

>in the same way that old Bill Paley does. The question Behe *claims* to

>be asking, "*How* could this system evolve by natural law mechanisms?"
>can often actually *be* answered.

Sure. As Dorit notes, "Anyone of us can come up with multiple,
plausible stories concerning the evolution of a given biological feature."
Big deal.

>The observed changes in genes and
>proteins that are required to produce the current differences from
>reasonable ancestral forms (typically by duplication and divergence,
>sometimes by scrambling of protein motifs, often with considerable

>neutral drift) are *congruent with* the idea that these differences

>arose by natural selection (acting primarily in a conservative fashion)
>acting on random mutations (the only kind of mutation that we have ever

>observed) of various kinds, from duplication to point mutation and

>neutral drift by fixation of random mutations.

As a criterion, congruency seems no better than plausibility. In fact,
what is the difference between the two?

Furthermore, I could likewise adopt such a standard. The notion that
certain IC systems are designed is congruent with the capabilities
of intelligence.

>The way that you
>disprove the "How did this evolve?" question is by either presenting a
>different observable and/or testable mechanism by which it could occur

Intelligent intervention qualifies.

>or by presenting evidence that the observed differences are too great to
>be accomplished in the time available by these *known* natural law
>mechanisms.

Sure. This would be very powerful evidence. But it is not needed.

>Answering this question does not require any attempt to

>describe which specific selective forces were at work. All it asks is

>whether the observed extent of changes can be due to known natural law
>mechanisms or not.

I see. So the design theorist must show that something CANNOT be due
to "natural law mechanisms." We're back to proving the impossible.
It doesn't matter (to me) if one can imagine just-so stories congruent with
"natural law mechanisms" that generate a system. It doesn't matter (to me)
if the system doesn't seem to violate any "natural law mechanisms." What
matters is whether the "natural law mechanism" is the *best* explanation.
Howard's whole argument appears to be a needlessly complicated way of saying,
"If an explanation doesn't violate natural law mechanisms, it *is* the best
explanation" and, BTW, I'm using the term "natural law mechanisms" to mean
nonintelligent intervention. But that's not an argument - it's an assertion.

>So far, the clear answer is yes, all of the observed
>differences are within the range of changes over time that can be

>explained by known natural law mechanisms. There is no reason to
>propose unseen mechanisms.

Sure there is. Just because it *can* be vaguely explained in such ways
doesn't mean it *best* accounts for the system.

Look. As I see it, the molecular world of life is loaded with things that
are quite unlike anything we see in the rest of nature. The closest
analog to these things are our machines. If one doesn't have an
aversion to proposing intelligent causation, one seeks to explore
these strange similarities without a need to force them into
a nonintelligent origin. Of course, I'm not saying that folks like
Howard are rationally obligated to agree. Howard is satisfied with
any explanation as long as it is congruent with "natural law mechanisms."
But I'm not. Because of my perceptions, because I "see" little machines,
I require something more than an explanation congruent with "natural
law mechanisms" to show that the analogy between molecular machines
and intelligently-derived machines is faulty at its very core.
As I have said again and again, we simply see the same data
differently. Thus, I'm more interested in determining if a truly
scientific approach under a design paradigm can be created that
interprets, and even illuminates, the workings and origin of these
machines. I'm not interested in convincing Howard or Larry or Matt, etc.,
to join me in my approach.

{snip}

>[I have kept the rest of the discussion without further comment from me,
>in case you have not already read it.]

This part contains Wade's replies to my observations.

> >"But plausibility is about the weakest criterion one can apply
> >to an evolutionary hypothesis."
>
>> Same question as above. We know that 'truth is stranger than
>> fiction' as common observation such that plausibility is a poor
>> substitute for evidence but to complete the picture, is the lack
>> of plausibility then to be taken as evidence against? That
>> just doesn't seem to add up.

Why not? It's very easy to come up with plausible stories about
something, especially if we're talking about history. Thus,
plausible stories don't amount to much, as Dorit notes. However,
it is much harder to show that a story is implausible because one
is swimming against the current of another's imagination. Thus,
if implausibility is shown, this means more.

Look at it this way. If I could show that it was plausible that
Jones murdered Smith, it wouldn't mean much (he was in town
when the murder happened). However, if I could show it was implausible
that Jones murdered Smith (he was not in town when the murder
happened), that would mean much more. And I'm not talking about a court
of law, I'm simply talking about one's curiosity concerning Jones' involvement.

>>>I should put the above two sentences in my sig-file as many
>>>around here seem to think plausible stories are all that needed.

Well, as y'all can see, I couldn't resist. ;)

>> This may be the horse after teh cart. There's a fellow around
>> this newsgroup who tries to make much out of the lack of

>> stories that he considers plausible. Even if one factors out

>> the issues surrounding his lack of training by which to adequately

>> judge plausibility, the main push for plausible stories seems
>> to be from taunting from the design advocate side. So please
>> don't confuse this with people confusing stories with proof.

I see. Since y'all run in a pack, you can't help but view the other
side this way, eh? ;)

>>>This is why as I am consistently portrayed as one who argues
>>>"evolution can't happen" as those plausible stories are ONLY
>>>effective in reply to such a position. When folks argue
>>>with me, it would be prudent for them to do so with the foreknowledge
>>>that Dorit and I concur.
>
>> I'ld like some more foreknowledge about what the lack of plausible
>> stories means. Just to round out the picture you see.

The lack of plausible stories can mean either one of two things:

1. A lack in the story-teller due to lack of imagination and/or lack
of understanding at the moment. In other words, "we don't know"
may mean nothing more than "we don't know."

2. The essence of the story is misguided, i.e., X didn't evolve.
If X didn't evolve, one might expect it would be hard to come up
with plausible stories, especially when they are so easy to invent.
(Note: X didn't evolve does not mean evolution never occurs).

Choosing between 1 and 2 is a judgment call, but if one's worldview
handicaps them into thinking #2 cannot be true, then there is no real
choice for them. As for me, I suspect it is because of #2. Thus,
I seek to flesh out an alternative approach. I may turn out to be
wrong. So what?

>>>But Dorit adds something else. Don't want to quote him out
>>>of context. :)
>
>>>"Evolutionary biology may finally be coming of age because we are
>>>moving away from particularistic, speculative scenarios - the
>>>just-so stories. The rigorous testing of evolutionary hypotheses
>>>depends on the use of comparative data, on an understanding of
>>>mechanism and, increasingly, on the experimental manipulation
>>>of components of the system."
>
>>>There are quite a few interesting things to say about this. First,
>>>it seems like Dorit is admitting that "up to now," evolutionary

>>>hypotheses have been barely more than weak just-so stories. But
>
> No. Coming of age is more a matter of adding more meaty details.
> The difference between pi is about 22/7 and the expanded taylor series.

Dorit doesn't impress me as one talking about some extra meaty details.
It's more like we might finally have a hotdog to go with our mustard.
But Dorit errs in equating an evolutionary view with a Darwinian
view. Comparative data and the experimental manipulation of systems
may give us reason to think something is related. And often it does.
But that doesn't mean Darwinism is at the core of the relationship.
To propose that, one ultimately has to fall back on a Darwinian
just-so story.

>>>I would bet if we could go back in time, and argue with the Larry
>>>Morans and Howard Hersheys of 30-40 years ago, they wouldn't be
>>>even slightly more tentative than the modern Howards and Larrys.
>>>But if evolutionary biology is coming of age only today,
>>>what would explain the same degree of assuredness?
>
>> When did physics "come of age" or chemistry? You are playing

>> word games in a rather shameless way.

You're entitled to your opinions concerning my shameless ways.

>>>Secondly, some folks have accused me of using insults when I point
>>>out the just-so story nature of so many evolutionary explanations.
>>>But it should be clear from Dorit's use that this term was not invented
>>>by me and has been a long-time problem for evolutionary explanations
>>>that is usually swept under the rug. The question is whether a
>>>Darwinian explanation can ever truly get away from a just-so story.
>>>I don't think it can. I think they are inherent in Darwinism.
>
> Think again.

You don't think there *has* been a problem with the just-so element of
Darwinism? If not, you're sounding to me like an apologist.

> Some just so stories have very specific requirements
> on sequence homology data. In other words, tehy are testable.

> The same can be said of pjust so stories predicting transitional

> fossiles which may at some point be discovered, or alternative

> transitions might be found to rule a particular just so story

> out. But this is so basic, you know this quite well, so you must
> have meant something else. I just can't figure out what it was.

I never said all just-so stories are equally bad. There are bad
ones. And really bad ones. ;)

> >This doesn't mean all evolutionary explanation have to involve them.

> >From the analyses Dorit cites, one can reach a decent interpretation
> >outlining evolutionary *relationships*. But when Darwinism is then
> >employed to explain the origin of the relationships, the just-so
> >mindset re-surfaces. Those just-so stories then mean something to
> >folks who can't accept intelligent designers because they show
> >a plausible way something that "looks designed" could come about without
> >an intelligent designer. But as Dorit says, this is the weakest criterion
> >we can apply. Yet it is exactly at this point that the debate about
> >design occurs.
>
> What an interesting juxtaposition. We have "looks designed" and what
> I suppose results from a _plausible_ just so story, which we might
> call "looks evolved". The looks evolved is being dismissed for the
> poor evidenciary relationship between its looks and its actual
> history. What, one wonders, is the analogue to "looks designed"?

Well, you've side-stepped my point. As for the "looks designed"
vs. "looks evolved" comparision, I don't dismiss the "looks evolved"
thingies because of the poor evidence. You seriously need to
consider that I don't think things like the bacterial flagella
"looks evolved." Things that look like they've evolved are things
I tend to think *did* evolve. If you've read some of my articles
about DNA replication, you don't see me claiming that *E. coli*
was "designed," *Pseudomonas putida* was "designed,' etc., now do you?
Instead, I show (and will show) that the pattern of "looks evolved"
leads to a "looks designed" event.

> >Darwinists need to realize that just-so stories have long given
> >rise to skepticism from people from all sorts of different background
> >beliefs. They are ususally quick to blame those background beliefs
>
> How backwards! Just so stories should not "give rise" to skepticism,
> they just shouldn't go very far to alleviate it as "truth is
> stranger than fiction", right?

What "should" happen is a matter of opinion. It's simply a fact
that just-so stories often *do* arouse skepticism.

> Your rhetorical manuevering attempts
> to say that evolutionary theory has been nothing more than
> just so stories, leveraging your own interpretation of "coming
> of age" to support this assertion.

There's a difference between "evolutionary theory" and particular
explanations that purport to explain a particular biological
feature.

> That's how it reads. Surely
> you won't stand and defend such a position and will claim I
> misrepresent you, so take this is my feeble attempt to clarify
> your point as there may be others with such low reading
> comprehension skills as mine who would likewise misunderstand.

If you were truly interested in merely clarifying, you wouldn't
put words in my mouth. You'd simply ask.

> But then, what is your point if it isn't that evolutionary
> theory is principly supported by (just so stories) unworthy
> support?

That particular evolutionary explanations, told through Darwinian
filters, have been little more than just-so stories for quite some
time. IMO, Dorit comes very close to admitting this probably because
he thinks its safe since now we can replace them in these "coming-of-age"
times. Dorit doesn't seem to realize that evidence that indicates
organisms A and B share a common ancestor doesn't automatically
mean that the events associated with the divergence and lineage-specific
transformations that led to organisms A and B had anything to do with
Darwinism.

> Are you denying the existence of strong support?

Of evolution? Not at all.

> Do you think that because populist "understanding" of eovolution
> is a bundle of plausible just so stories that the scientific
> theory can be conflated with with these same stories?

Popular understanding? I've learned some in the university and even encounter
them on this board from folks who would not like it if I said they
had a "populist understanding" of evolution.

> >for the skepticism. But they never seem to realize the just-so
> >element of their belief naturally arouses skepticism regardless of
> >background beliefs. Dorit essentially admits this and does so probably
> >because he thinks we are finally about to abandon those just-so stories.
>
> Let's remember that next time you accuse others of trying to read
> too much into what you write.

Let's not. Y'see, Dorit doesn't post on this board, otherwise, I'd
simply ask him. I do post on this board, so you have no excuse for
not asking me.

> I again complain about your
> misrepresentation of just so stories actively promoting
> skepticism rather than being a weak justification for abandoning
> skepticism. I'ld almost suggest that you are too smart to make
> such a mistake on accident.

You can complain all you want. I simply said they often arouse
skepticism, regardless of background beliefs. That's a fact.

> >We should be so lucky.
>
> But then Gould would have to take up writing romance novels.

Panda's In Paradise? Panda's In Heat?

> >Thirdly, Dorit fails to consider that one might build a case for
> >intelligent design as the best explanation *because* of the comparative
> >data, considerations of mechanisms, and what we know from experimentally
> >manipulating systems. After all, this is exactly what I am doing in
> >my discussion of oriC and DNA replication. And guess what? It looks
> >like all these analyses simply mean that the just-so stories have
> >now simply extended into the molecular realm.

> Whoops there goes another irony-o-meter.
> The double standard you take to 'looks evolved' and 'looks designed'
> with respect to biological systems is so hard for me to understand.

Because there is no double-standard. Not to mention that this paragraph
says nothing about 'looks evolved' and 'looks designed.'

> There must be something in your philosphy of science or perhaps
> just philosophy that I'm missing because from where I sit, the
> contrasted standard screams out its irrational inconsistency.

You shouldn't let those knee jerks take your eyes off the words. ;)
--

Any one of us can come up with multiple, plausible stories concerning the

evolution of a given biological feature. But plausibility is about the

weakest criterion one can apply to an evolutionary hypothesis.

- Robert Dorit, Biology Dept., Yale University

[Julie Thomas]

In a previous article, nyi...@math.SC.EDU (Peter Nyikos) says:

>This is my second followup to Howard's long review, which is
>indeed a lot more helpful than any other review I've read,
>but which also has its share of misconceptions. A CC goes
>to Howard because of the long delay.

I have several other projects going on right now, but I thought
I'd add a few comments at this time.

>howard hershey <hers...@indiana.edu> writes:

>[deletia of long preamble, most of which was dealt with in my
>first followup]

>Chapter 3. Cilia and Flagella

>>Let us
>>imagine a bundle of tubulins serving a structural function at the cell
>>membrane, sticking out and causing a projection (but a static one) from
>>the cell surface. Let's call such a projection a microvillus (to choose
>>a name at random :-)). One of the consequences of these microvilli
>>would be an increase in the surface to volume ratio of the cell.

>Behe didn't go into that possibility, true, but then, he didn't
>have your papers to clue him onto it. And what do you envision
>as the utility of this increase?

We're hip-deep in just-so land already. So we need to clear up some
stuff. First, microvilli clearly exist in multicellular organisms.
The are most commonly found lining the digestive tracts. But this
is all irrelevant as multicellular creatures arose after cilia.
Thus, Howard needs to cite some unicellular creatures that make
microvilli.

Secondly, most microvilli are made not using tubulin, but by using
actin. The actin filaments, in turn, are cross-linked by other
proteins to form a stiff, rigid structure that reinforces the
membrane. Again, this is irrelevant as Howard needs microvilli
constructed from tubulin (which is quite different, and as old, as
actin).

Of course, this leads to all sorts of other questions. Why
would an organism use microtubules instead of actin? Where did
the microtubules themselves come from considering that bacteria
have none?

>>Surely, even Behe might be able to come up with a reasonable selective
>>environment where such microvilli might be favored, even if they could
>>not move at all.

>Make that, "Surely, Behe can succeed where I have shown no inclination
>to even try, and be able to come up with..."

Indeed. Besides, would a "bundle of tubules" really provide such
support to a microvillus? In modern cells, even the actin filaments
must be cross-linked. It would seem that Howard also has to assume
some cross-linking from the start.

>> Now one, as Behe points out, might envision motor
>>molecules involved in transport along the axis of these fiber bundles
>>(for precisely the reasons one might expect microvilli to form in the
>>first place).

>This is the same song you were singing on that other thread,
>about how the "pressures" [never named] that caused the
>clotting mechanism to evolve to its present state are
>the "same" ones which keep it at that state currently.
>When we got into specifics, you clammed up.

It would help if Howard would be more specific. How can one argue
against something that his imagination envisions "might" happen.

>> Linking some of the bundles might allow some minor
>>movement of the microvilli at levels that would be insufficient to cause
>>cell motility.

>Why link them in the first place? Why would one bundle ten times as
>thick do a better job than ten bundles of single tubules? and where does the
>binder come from?

Furthermore, since the selective advantage is found in increasing surface-
to-volume ratios, what selective advantage is found in causing minor
movements?

> A protein that indiscriminately bound microtubules
> together would disrupt the cell's shape--just
> as a building's shape would be disrupted by
> an erroneously placed cable that accidentally
> pulled together girders supporting the building.
> A linker that strengthened microtubule bundles
> for structural supports would tend to make them
> inflexible, unlike the flexible linker nexin.
> --DBB, pp. 66-67

Indeed. You can't simply imagine linkers to make the microvillus
more stable without thinking about the side-effects elsewhere.
Those linkers better function specifically in the microvillus.
In real-life microvilli, the actin filaments are bound together
by either fascin or fimbrin. These are relatively small and
rigid connecting proteins which don't allow for much mobility.
It's for this reason that microvilli are relatively stable and
don't change their lengths or shape very much during the life of
a cell.

>And how does linking them "allow motor movement" where none
>occurred previously?

> ...even if [the incipient cilium] were at the
> cell surface, the number of motor proteins would
> probably not be enough to move the cilium.
> --DBB, p. 67

>> But movement, by creating microcurrents, might have uses
>>without being sufficient to move the organism. Under conditions that
>>select for more vigorous movement, you might well get the emergent
>>property of motility.

> And if the cell did move, it would be an unregulated
> motion using energy and not corresponding to any need
> of the cell.
--DBB, p. 67

Yep. If it started to move, it might move right out of a pool
of nutrients leaving the immobile cells at an advantage.

>Now, of course, you can imagine all kinds of regulator systems
>that make the cilia beat in a coordinated way, etc. but you've
>conveniently left out all mention of them.

Yep.

>>I have previously given a highly speculative, but similar, possible
>>pathway

>You haven't proposed a possible pathway above. You've proposed
>a tiny fragment of a pathway, with maybe one percent of all
>the required components.

Besides, I'm not impressed in the least with highly speculative
possible pathways!

>> to produce flagella via non-motile, but still functional
>>intermediates.

>Ditto. You have not described the intermediates in the
>kind of detail needed to explain such things as coordinated
>motility.

>>Can I prove these scenarios? Nope. Are they totally out of line?

>Hard to tell until you start fleshing them out.

I don't know if they are totally out of line. But I find them
totally unconvincing.

>>Well, if you look for evidence of these intermediate states, you need to
>>ask whether tubulins are involved in maintaining cell structure in
>>microvilli, whether pilins have utility, whether there are protein
>>transport pores, etc in current organisms.

>Those aren't intermediate states; they are ingredients which
>you propose bringing together from far-flung corners of the
>genome. See that other thread for just how much dirt you
>are sweeping under the rug here.

Here's the recipe for making a just-so story. First, survey
the biological world for structures/functions. Find those
that seem useful for coming up with a precursor to the system
in question and patch them together without much regard for
biochemical and/or genetic details. Place the patchwork in
an imaginary creature from the distant past which has conveniently
gone extinct. Invoke a vague selective pressure that selects
for the patchwork and then imagine it is plastic and amenable
to further selective modification that just happens to arive
at the system in question.

Well, in the meantime, let's see if Howard can come up with microvilli
from unicellular organisms that are supported by microtubules linked
by precursors to nexin. Furthermore, the distribution of such
microvilli should be at least as widespread as cilia themselves
if we are to believe they are older that cilia.

>> This, of course, is not
>>direct evidence. It is evidence like that that Darwin presented for the
>>eye.

>I'd like to think Darwin did a much more competent job than
>you have.

Charles was the father of the just-so story and the rest think
they need only mimic him. ;)

[George Acton]

In article <3419a87b...@nntp.ix.netcom.com>,

mat...@ix.netcom.com (Matt Silberstein) wrote:
>
> In talk.origins George Acton <gac...@softdisk.com> wrote:
>

> [snip]

>
> Often,
> >Julie Thomas's observation is correct, but there are many
> >counterexamples.
>
> There can be no counter examples to an observation. Observations,
> evidence not commentary, stand by themselves. They are, to a large
> extent, immune to theories.
>

You're reading something complex into some simple-minded comments of
mine. I plead innocent to doing philosophy.
The "observation" of Julie Thomas's that I meant was the her
assertion that "Design Theory" is valuable because of it's critique
of normal science (which she refers to by the term "Darwinism").
It doesn't refer to scientific data-collection.
Her point is that that even if incorrect, "Design Theory" is
somehow "respectable" because it keeps normal science honest and
therefore contributes to achieving ultimate truth. I merely pointed
out that historically, science doesn't always work this way. Often
the correct theory is completely accepted and the contribution of
erroneous theories appears to be nil. It is difficult to find any
contribution of the ether theory in Special or General Relativity,
for instance. Not only did the ether theory not prevail, but any
emotional attacks on Relativity as "just-so stories" or a form of
collective dishonesty appear mistaken in retrospect.
Ms. Thomas's posts have the accusatory implication that scientists
are morally derelict in their complacency about naturalism, and most
of the heated exchanges associated with her postings derive from
her innuendos, rather than the documentation she presented. I
merely noted that there are historical analogies in which one theory
prevailed and we don't respect the unsuccessful for making a
contribution to our final understanding. The ether theory was the
best people could come up with in its time, and it was testable. But
it wasn't needed to keep the Relativitists honest. People who pushed
it long after it was shown inadequate just made it look like "crank
science", which in that context it was.
--George Acton

[Peter Nyikos]

CC: Julie, because I am curious about the mammalian hearts bit,
and because I don't want her wasting any more time on what
look to me like trumped-up charges on Silberstein's part.

mat...@ix.netcom.com (Matt Silberstein) writes:

>In talk.origins Peter Nyikos <nyi...@math.SC.EDU> wrote:

>>mat...@ix.netcom.com (Matt Silberstein) writes:
>>
>>in back-and-forth with Julie, against whom he made what looks
>>like a suspiciously selective deletion earlier in this thread.
>>
>Again I ask what kind of standard you use. And are you merely saying
>that I deleted deliberately rather than by accident?

It *looks* that way to me, yes. And I was amused by Paul Myers's
off-the-wall tirade which COMPLETELY MISSED my point about
him being able to give you an extended lecture on the subject
of dishonest marked deletia.

Y'see, *he* caught *me* in what may well have looked to him like
a dishonest *marked* deletion on *my* part, and broke his
habit of never following up directly to me, probably because
he thought he had a chance to go for my net.jugular; for sure,
he played his chance to plausibly hit me to the hilt, just
as Clark Dorman has done more recently.

Myers's post, and my reply, are highly instructive already on this
subject, but I'm sure he could go a lot more deeply into
the topic with you in e-mail if you are interested.

But it's really amusing to see Paranoid Paul #1 guess that
my whole point was how "ghastly awful and nasty" he was,
whereas I wasn't even going to *hint* at how he capitalized
on my marked deletion, but only to let y'all know that
he knows what "dishonest marked deletia" are
all about. I believe you are hundreds of times more willing
to learn about the topic from him than from me.

If not, what does
>"selective" mean in this context. Finally, does this sudden appearance
>of comments on my deletions have anything to do with my recent posts
>that pointed out your unmarked deletions?

You mean the ones you did almost a month ago? Get real!

>BTW, I have don't remember your responding to any of those comments. I
>also want to point out that I just mentioned where you did not mark
>the deletion. No judgements, no "suspicions", no "selective". Just the
>objective comment.

Good, then there's no need for me to reply. Unmarked deletia,
in and of themselves, are not a cause for concern.

>>>>>This is one of the delightful almost claims. "Darwinism" (or, more
>>>>>correctly evolutionary biology) may be better off with folks like you,
>>>>>but Darwinism is not a belief.
>>>>
>>>>So you believe it is not a belief.
>>>>
>>>If you want to play the game of using private definitions, then I
>>>suppose you can find such a definition to support your claim. But
>>>"Darwinism" (or, more correctly, evolutionary biology) does not fit
>>>the standard definition of belief. I do not believe in evolution or
>>>Natural Selection. I accept that these are the best explanations for
>>>the our observations.
>>
>>And, since you have shown yourself to lack the competence to
>>evaluate it, this "acceptance" is a belief in a pretty
>>strong sense of the word.

>I am aware that you are convinced that you know everything about my
>scientific competence.

Skip the rhetorical excesses, Matt, and let the people out
there know what they are the secret code for.

> As I remember, it was a single phrase in one
>post that showed you that I know nothing at all about science.

On the contrary, it was your dogged defense of it, in the
face of repeated explanations on my part, that did the trick.
You even whined about how I kept going back to earlier
things you said and deleting all your (off-topic, as I
kept explaining) new points. Each time I did that, I
did it because my earlier explanations were inadequate,
and I kept coming up with new ways of getting my message
across--which were also inadequate.

>BTW, it is amusing to see how you are complaining about some lack on
>my part, but you have no comments on Julie's rhetorical games.

WHAT rhetorical games? Are you going to come up with
some trumped-up charges like the ones you came up with
about me playing some "plausible deniability" game,
just so you could strut your stuff for ~1000 lines
to show me how a real pro like you plays the game?

>>> You, OTOH, seem to believe that IC systems are
>>>the product of intelligence.
>>
>>No, only that two of them are, and for reasons you can't
>>even begin to comprehend, by the looks of it.
>>
>And for reasons that neither your nor Julie seem willing to discuss.

I can't discuss her private thoughts with anyone, since
I am not privy to them.

>And your position in not the same as Julie.

Of course not, and I HAVE been quite willing to discuss
MY reasons and have BEEN discussing them on the "directed
panspermy" threads, and yesterday I even brought the
bacterial flagellum "(really!)" thread back to topic to
discuss it with none other than one Matt Silberstein.

> You need to stop thinking
>of yourself as a pack, you have significant differences.

And I've pointed them out often enough, so your first
clause is a Pee Wee Hermanism.

> Julie made
>the explicit claim that IC systems usually come from intelligence

That's a subjective statement that I don't know how to
evaluate.

so
>the presences of IC means the system was probably designed. Not just
>the two under consideration, but IC systems in general. I do not
>remember your comment on the circular logic involved.

I took your "evidence" for the circular logic to be "rhetorical
excess", and was waiting for you to decode it. Which you have,
below, after a fashion.

>>> Therefore you claim that when we see an
>>>IC system, it must come from an intelligent entity.
>>
>>Don't you ever get tired of "rhetorical excess" as to
>>what Julie has claimed?
>>
>You are so right, it is not "must", it is just "usually". Here is the
>quote in question:

>JT> When this is coupled with my common experience where IC is tied
>JT> to intelligent design (intelligence easily generates IC and IC
>JT> usually stems from intelligence),

Well, that's her personal experience. Of all things Julie
talks about, I am least able to comment on her personal
experiences. It came as a remarkable piece of news to me
that Bruce Salem had encountered her before, talking about
the four-chambered mammalian heart.

Funny thing, though:
Bruce seems to have completely misunderstood what Julie
(if indeed it was the same Julie Thomas) was about. There
*is* quite an interesting riddle about how the foramen ovale
and related structures evolved in mammals, since they are NOT
homologous to any known structure in any other class of vertebrates.

>Now this seems like she is assuming the conclusion.

To me it seems like she is just elaborating on her personal
observations.

>>Why don't you save us all a lot of trouble and mark your
>>"rhetorical excesses"?

>Why don't you mark where you snip, Peter?

Because it's time consuming to do it every time, and because
it's strictly optional on Usenet. A person whose name
I've mentioned to you often enough, Keith Cochran, even
put in his "keywords" line for years, "do you think I
mark my deletions? dream on". Nobody, not even his
opponents, faulted him for it AFAIK. The guy is a scoundrel
who makes even *you* look good in comparison, but that wasn't
one of the things that made him that way.

>[...] Why don't you

>explain why the marked deletions made by others raise your suspicions,

Stop smuggling in words like "the". When I get suspicious,
I usually restore the suspicious deletion on the spot,
and let people see the devious comments that were made
plausible thru the deletion. That's exactly what I did with
you. Have you owned up to what your deletion was all about
like a responsible adult, or have you just continued the diversionary
tactics you and Myers initiated?

If I complained about every deletion you made, or even about
one-tenth of them, I'd be a laughingstock, and rightly so.

[Correction: if you suddenly start making a rash of selective
deletia, a la James Keegan, I just might start complaining
about one-tenth or so of your deletia.]

>> Because then we can ignore
>>them, confident that they bear NO resemblance to anything
>>Julie ever claimed.
>>
>You know, if you commented on the circular logic it would be better
>than trying to attack me with this game.

You know, this is not a game. I could not comment on your
"circular logic" idiocy/scam until you decoded it.

>>It would be even more helpful if you skipped the "rhetorical
>>excesses" and told us what behavior they are the secret
>>codes for.

Which you seem to have done, so NOW I have dealt with what
look to me like trumped-up charges of circular logic.

[Peter Nyikos]

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

>In a previous article, nyi...@math.SC.EDU (Peter Nyikos) says:

>>howard hershey <hers...@indiana.edu> writes:

>>[deletia of long preamble, most of which was dealt with in my
>>first followup]

>>Chapter 3. Cilia and Flagella

[...]

>Of course, this leads to all sorts of other questions. Why
>would an organism use microtubules instead of actin? Where did
>the microtubules themselves come from considering that bacteria
>have none?

Interesting. So cilia are confined to eukaryotes? No wonder
they call those protozoans "ciliates".

[Trivia: some ciliates actually have a slightly different
genetic code than we do. It took
me a while to make even Keith Robison appreciate the fact that the
problem of explaining how this could have happened
is fundamentally far more difficult than accounting for
the different genetic code in mitochondrie, but Keith finally
acknowledged the seriousness of the problem, and relayed
some good ideas on how it could have happened. ]

>>>Surely, even Behe might be able to come up with a reasonable selective
>>>environment where such microvilli might be favored, even if they could
>>>not move at all.

>>Make that, "Surely, Behe can succeed where I have shown no inclination
>>to even try, and be able to come up with..."

Howard's disinclination is very evident in two short posts
he did in response to tiny snippets from this post of mine
you are following up to. I think I've dealt with his
disinclination in a most fitting manner.

>Indeed. Besides, would a "bundle of tubules" really provide such
>support to a microvillus? In modern cells, even the actin filaments
>must be cross-linked. It would seem that Howard also has to assume
>some cross-linking from the start.

Thanks for pointing these details out, Julie.

[...]

>>> Linking some of the bundles might allow some minor
>>>movement of the microvilli at levels that would be insufficient to cause
>>>cell motility.

>>Why link them in the first place? Why would one bundle ten times as
>>thick do a better job than ten bundles of single tubules? and where does the
>>binder come from?

>Furthermore, since the selective advantage is found in increasing surface-
>to-volume ratios, what selective advantage is found in causing minor
>movements?

Not to mention the fact that linking them cuts down on the
surface-to-volume ratios. But don't expect Howard to
say, "after a while, this ratio got to be too much of
a good thing." I sense a profound disinclination on
his part to let himself be sucked into talking about
the specifics of what he pretentiously calls "just-so stories"--
which are little more than titles for stories.

[...]

>>>I have previously given a highly speculative, but similar, possible
>>>pathway

>>You haven't proposed a possible pathway above. You've proposed
>>a tiny fragment of a pathway, with maybe one percent of all
>>the required components.

>Besides, I'm not impressed in the least with highly speculative
>possible pathways!

Please, Julie, this is talk.origins, not some science newsgroup.
Howard and his kind are engaged in a bitter political battle
against creationists, who keep throwing out to them claims
that this or that thing "could not have evolved". Now, of
course, you may be unaware of the ferocity of this struggle
because these people bombard you with so much garbage, you
have no time (and neither do I, lately) to monitor activity on
threads you are not involved with. But try and show some
appreciation for at least the *concept* of doing speculative
scenarios, even though nobody has actually tried to give
any worthy of the name. [I aim to change that with my
scenario on bat evolution.]

>>> to produce flagella via non-motile, but still functional
>>>intermediates.

>>Ditto. You have not described the intermediates in the
>>kind of detail needed to explain such things as coordinated
>>motility.

>>>Can I prove these scenarios? Nope. Are they totally out of line?

>>Hard to tell until you start fleshing them out.

>I don't know if they are totally out of line. But I find them
>totally unconvincing.

That may be just because Howard is actually trying to
make a virtue out of NOT fleshing them out.

>>>Well, if you look for evidence of these intermediate states, you need to
>>>ask whether tubulins are involved in maintaining cell structure in
>>>microvilli, whether pilins have utility, whether there are protein
>>>transport pores, etc in current organisms.

>>Those aren't intermediate states; they are ingredients which
>>you propose bringing together from far-flung corners of the
>>genome. See that other thread for just how much dirt you
>>are sweeping under the rug here.

>Here's the recipe for making a just-so story. First, survey
>the biological world for structures/functions. Find those
>that seem useful for coming up with a precursor to the system
>in question and patch them together without much regard for
>biochemical and/or genetic details. Place the patchwork in
>an imaginary creature from the distant past which has conveniently
>gone extinct. Invoke a vague selective pressure that selects
>for the patchwork and then imagine it is plastic and amenable
>to further selective modification that just happens to arive
>at the system in question.

Well, that may be the recipe where biochemical systems are
concened, but it's a completely different story in the
large-scale world of skeletal and other anatomical structures,
where the stories can be a lot more realistic.

Not that there aren't some real stumpers out there. The
one about the foramen ovale and related structures of
the mammalian heart is a real poser. But don't give up--
it took me two years to finally think of a plausible
scenario for bat evolution.

>Well, in the meantime, let's see if Howard can come up with microvilli
>from unicellular organisms that are supported by microtubules linked
>by precursors to nexin. Furthermore, the distribution of such
>microvilli should be at least as widespread as cilia themselves
>if we are to believe they are older that cilia.

Are you kidding? Howard has burned his bridges behind him
with his snide remarks about aliens. :-)

He wouldn't dare risk postulating organisms for which there
is no direct evidence. :-)

[Note the smileys. AFAIK no one has ever accused Howard
of such anal-retentive qualities :-) as consistency.]

>>> This, of course, is not
>>>direct evidence. It is evidence like that that Darwin presented for the
>>>eye.

>>I'd like to think Darwin did a much more competent job than
>>you have.

>Charles was the father of the just-so story and the rest think
>they need only mimic him. ;)

Do they? or do they just give the titles and demand that
the reader fill in the story for themselves, the way
Wade Hines kept demanding I do wrt abiogenesis for most of 1996.

>Any one of us can come up with multiple, plausible stories concerning the
>evolution of a given biological feature. But plausibility is about the
>weakest criterion one can apply to an evolutionary hypothesis.
>- Robert Dorit, Biology Dept., Yale University

That's within science. In the big outside world these plausibility
arguments are very important politically.

[Peter Nyikos]

howard hershey <hers...@indiana.edu> writes:

>Peter Nyikos wrote:
>>
>> howard hershey <hers...@indiana.edu> writes:
>>
>> >Wade Hines wrote:
>> >>
>> >> iz...@cleveland.Freenet.Edu (Julie Thomas) writes:
>> >>

>[snip]

>>
>> So, when do you plan to write *your* scenario for bat
>> evolution? :)
>>

>First, I posit an intelligent alien race. The aliens sent the bats in a

>sleeping berth looking for planets with sutible caves. This is
>reasonable because 1) there are a lot of planet with potential aliens
>and 2) if the aliens were intelligent enough they could easily build a
>bat.

You are indulging in a One Shade of Gray Meltdown. Bats are
a problem, sure, but it is possible to come up with a plausible
*detailed* scenario just on the basis of orthodox Darwin-Spencer
mechanisms. You'll see that next week.

And I expect it
to inspire you to come up with a similarly plausible scenario
on the evolution of the bacterial flagellum. :-)

But seriously, I expect nothing of the sort. I expect you and
Wade Hines to go on playing the "Somedunce Kid" as far
as detailed scenarios go. As I said a couple of days ago:

====================== begin excerpt from post, names added in brackets

[Hines:]
>> It
>>>does involve assertions of plausibility of some steps which are
>>>are not (yet) confirmed by experiment.

[Nyikos:]
>>Also, as far as t.o. is concened, it involves assertion
>>of plausiblity of "after a whole bunch of steps, ribozymes
>>were all replaced by polypeptide enzymes" and similar
>>"now-you-see-it-now-you-don't" `steps'.

[Hines:]
>Magic shows are so boring when you know how they are done
>but teh people keep coming and oh'ing and ah'ing ....

I don't ooh and ah at "magic shows" which are more like
the scene in the _Mad_ magazine take-off on "Butch Cassidy
and the Sundance Kid" where the "Somedunce Kid" character
says he's got the quickest draw in the West, and when
someone calls on it, he just stands there motionless
and then says, "Want to see it again?"

"That's a very old and very tired joke, Kid" comes the
answer.

"Really? I thought it was a gas," says the Kid.

=============end of excerpt from Directed panspermy (Was: Phylogenetic classification)

[Clark Dorman]

The following message is a courtesy copy of an article
that has been posted as well.

Peter Nyikos <nyi...@math.SC.EDU> writes:
> mat...@ix.netcom.com (Matt Silberstein) writes:
> >In talk.origins Peter Nyikos <nyi...@math.SC.EDU> wrote:
> >>mat...@ix.netcom.com (Matt Silberstein) writes:

[he said / she said etc. deleted, suspiciously and selective, no doubt]

> as Clark Dorman has done more recently.

^^^^^^^^^^^^

> that Bruce Salem had encountered her before, talking about

^^^^^^^^^^^

> I've mentioned to you often enough, Keith Cochran, even

^^^^^^^^^^^^^

> tactics you and Myers initiated?

^^^^^

> deletia, a la James Keegan, I just might start complaining

^^^^^^^^^^^^

There are an amazing number of demons in Nyikos's world; I'm just
surprised that Peter didn't bring up Paul Gans and the non-saintly
Andrew.

I am, actually, anxiously awaiting your latin-laden bat-evoluton
just-so-story; it just might be interesting and educational. I've
given up on waiting for a real Irredicible Complexity FAQ though.

The sad part about all of this is that there appears to be a
(well-hidden) intellect behind all the rhetoric. You should let it
come out and play every once and a while.

--
Clark Dorman "Evolution is cleverer than you are."
http://cns-web.bu.edu/pub/dorman/D.html -Francis Crick

[Wade Hines]

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

>>Wade Hines wrote:
[JT]

>> >"But plausibility is about the weakest criterion one can apply
>> >to an evolutionary hypothesis."
>
>>> Same question as above. We know that 'truth is stranger than
>>> fiction' as common observation such that plausibility is a poor
>>> substitute for evidence but to complete the picture, is the lack
>>> of plausibility then to be taken as evidence against? That
>>> just doesn't seem to add up.

>Why not? It's very easy to come up with plausible stories about
>something, especially if we're talking about history. Thus,
>plausible stories don't amount to much, as Dorit notes. However,
>it is much harder to show that a story is implausible because one
>is swimming against the current of another's imagination. Thus,
>if implausibility is shown, this means more.

>Look at it this way. If I could show that it was plausible that
>Jones murdered Smith, it wouldn't mean much (he was in town
>when the murder happened). However, if I could show it was implausible
>that Jones murdered Smith (he was not in town when the murder
>happened), that would mean much more. And I'm not talking about a court
>of law, I'm simply talking about one's curiosity concerning Jones' involvement.

Your standards of plausibility mix the term nicely with possibility.
Implausible is not necessarily imposssible, and would be the wrong word
to use in an impossible case. Possible does not imply plausible. Plausible
means worthy of belief. I'm using it in another way, meaning more like
"not unreasonable to believe". If you tell me Jones murdered Smith,
some more banter like "Oh, tell more", "Yes. Jones was in town when
Smith was murdered in town." I don't think you've hit on plausible.
If Smith was strangled, and Jones was out of town, you've got a good
case for impossible regarding Jones being the strangler but if Smith
was poisoned I'ld reserve any judgement either way without more info.
But this is just getting the words straight and not about your analogy.

If I told you a strange but true story you might very well find it
implausible. This might mean that given 100 similar stories, you could
believe that one of them were true, but not all of them. Maybe
tehy involve the odd story of how teh rake wound up on the roof.
I'll leave the wild stories to your imagination but leave you with the
final thought that you seem to be conclusing that the roof was
designed with a rake on top because the non of the other stories
seem very plausible to you.

>>>>I should put the above two sentences in my sig-file as many
>>>>around here seem to think plausible stories are all that needed.

>Well, as y'all can see, I couldn't resist. ;)

>>> This may be the horse after teh cart. There's a fellow around
>>> this newsgroup who tries to make much out of the lack of
>>> stories that he considers plausible. Even if one factors out
>>> the issues surrounding his lack of training by which to adequately
>>> judge plausibility, the main push for plausible stories seems
>>> to be from taunting from the design advocate side. So please
>>> don't confuse this with people confusing stories with proof.

>I see. Since y'all run in a pack, you can't help but view the other
>side this way, eh? ;)

No no please. I don't view you in a pack with Peter. He may be trying
to run with you (be of one blood and other come ons) but I've not seen
you agree with Peter on much of substance and he is quite at odds with
your over your take on just so stories. The point you seem to be
avoiding with your little joke, is that scientists are making up
just so stories as proof. They make them up to shut up some of the
fools who try to make hay with the lack of such stories for some things.

You seem to be trying to have it both ways. Just so stories actually
actively give rise to doubts in your mind, and the lack of them does
as well, according to this post of yours. I don't think I want to go
to your house and play monopoly by your rules.

>>>>This is why as I am consistently portrayed as one who argues
>>>>"evolution can't happen" as those plausible stories are ONLY
>>>>effective in reply to such a position. When folks argue
>>>>with me, it would be prudent for them to do so with the foreknowledge
>>>>that Dorit and I concur.

>>> I'ld like some more foreknowledge about what the lack of plausible
>>> stories means. Just to round out the picture you see.

>The lack of plausible stories can mean either one of two things:

>1. A lack in the story-teller due to lack of imagination and/or lack
>of understanding at the moment. In other words, "we don't know"
>may mean nothing more than "we don't know."

How could it mean anything else? A find tautalogy it is, and tautalogies
are of course, true.

>2. The essence of the story is misguided, i.e., X didn't evolve.
>If X didn't evolve, one might expect it would be hard to come up
>with plausible stories, especially when they are so easy to invent.
>(Note: X didn't evolve does not mean evolution never occurs).

Very well written. Thank you for the completeness.
Let some alien sample the new phage based delivery systems for
DNA-ase and try to figure out how they evolved.

>Choosing between 1 and 2 is a judgment call, but if one's worldview
>handicaps them into thinking #2 cannot be true, then there is no real
>choice for them. As for me, I suspect it is because of #2. Thus,
>I seek to flesh out an alternative approach. I may turn out to be
>wrong. So what?

It's nice of you to be so upfront about how a persons world view can
bias their conclusions. There's been so much heat generated by those
who don't feel asking you about your world views is appropriate but
obviously you find it relevent.

But I'm somewhat at a loss for how you got from 1 or 2 over to 2.
You suggest those who can't accept 2 are left with only 1 and I can
follow your logic there even if I don't think that most of the
folks you are currently debating actually fall into that camp.

Given 1 or 2, and the further point that evolution definately,
observably, historically, does occur: does one pick or lean
between the two choices?

On the face of this most hypothetical and sketchy scenario, I
don't see how one could choose. So let's flesh things out.

Take a very recently developed system. Consider the just don't
know case and think about the kinds of evidence one would expect
to find for an evolutionary scenario. BAck to your murder analogy,
if 10 were known to be in the house with Smith, and only Jones and
Smith were not in the dining room when a pipe wrench entered Jones
cranium, I'ld really have to doubt that Jones simply evolved
that pipe wrench, yes I would. Jones would need one mighty find
just so story.

But where I am quite obviously leading, consider an anceint system
whose origins track back to or beyond the last common cellular
ancestor by evolutionary hypotheses. What are the expectations
herea nd how does one pick between Julie 1 and Julie 2 as indicated
above with the noted addition of evolution being a fact in some
well documented cases.

I think Darwin's case relied heavily of intuition in the form of
just so story fits to sparse data, in his day. I think that intuition
has been found to be wildly correct based on molecular data. I think
this is an old story by now but that it just keeps getting stronger
as more data comes in. Now there are enough ecologists with agendas
to invent and distort and promote gaia nonsense such that just so
stories can displace actual science, but that's letting popular
misunderstandings suggest that real science is inept and, no, I don't
think that biology is nothing more than just so stories, even if
that's the sort fo thing you find more of in mall book stores or
even undergraduate biology texts (they are more for MDs than scientists
anyways).

>> Some just so stories have very specific requirements
>> on sequence homology data. In other words, tehy are testable.
>> The same can be said of pjust so stories predicting transitional
>> fossiles which may at some point be discovered, or alternative
>> transitions might be found to rule a particular just so story
>> out. But this is so basic, you know this quite well, so you must
>> have meant something else. I just can't figure out what it was.

>I never said all just-so stories are equally bad. There are bad
>ones. And really bad ones. ;)

The same might be said of jokes and the following might be added:
some bad jokes are true stories and some really bad jokes are
true stories. I'm not sure what you imply by the bad just so stories.

I tried out the why is the polar bear white on someone after having
seeded tehm with the arctic hare being white to avoid preditors.
They suggested, in a just so story, "to hide from killer whales?"
I'ld call that a very very bad just so story. I'm not sure if
that means that being white to sneak up on seals is a bad
just so story.

>> >This doesn't mean all evolutionary explanation have to involve them.
>> >From the analyses Dorit cites, one can reach a decent interpretation
>> >outlining evolutionary *relationships*. But when Darwinism is then
>> >employed to explain the origin of the relationships, the just-so
>> >mindset re-surfaces. Those just-so stories then mean something to
>> >folks who can't accept intelligent designers because they show
>> >a plausible way something that "looks designed" could come about without
>> >an intelligent designer. But as Dorit says, this is the weakest criterion
>> >we can apply. Yet it is exactly at this point that the debate about
>> >design occurs.

>> What an interesting juxtaposition. We have "looks designed" and what
>> I suppose results from a _plausible_ just so story, which we might
>> call "looks evolved". The looks evolved is being dismissed for the
>> poor evidenciary relationship between its looks and its actual
>> history. What, one wonders, is the analogue to "looks designed"?

>Well, you've side-stepped my point. As for the "looks designed"
>vs. "looks evolved" comparision, I don't dismiss the "looks evolved"
>thingies because of the poor evidence. You seriously need to
>consider that I don't think things like the bacterial flagella
>"looks evolved." Things that look like they've evolved are things
>I tend to think *did* evolve. If you've read some of my articles

I must be missing your point. All along here I thought that you
were equating good just so stories with the likes of looks evolved
and saying that too much is made of looks. I've hopelessly misunderstood
it seems.

>about DNA replication, you don't see me claiming that *E. coli*
>was "designed," *Pseudomonas putida* was "designed,' etc., now do you?
>Instead, I show (and will show) that the pattern of "looks evolved"
>leads to a "looks designed" event.

We are using a different vocabulary it seems.

Now for the record, I didn't say you thought DNA rep or flagella
looked evolved. Quite clearly, you think they don't and are trying
to connect that to look designed. The further points seemed to me
that just so stories might make something look evolved but you
don't thinks such looks amount to much. Meanwhile, by an asserted
IC nature you claim things look designed based on your take on other
IC things. I'm quite simply trying to use what I saw as your own
logic against you to get equal treatment for looks evolved and looks
designed. But alas, I've gotten it all muddled again. What do you
expect for a bear of such little brain.

>> >Darwinists need to realize that just-so stories have long given
>> >rise to skepticism from people from all sorts of different background
>> >beliefs. They are ususally quick to blame those background beliefs
>>
>> How backwards! Just so stories should not "give rise" to skepticism,
>> they just shouldn't go very far to alleviate it as "truth is
>> stranger than fiction", right?

>What "should" happen is a matter of opinion. It's simply a fact
>that just-so stories often *do* arouse skepticism.

>> Your rhetorical manuevering attempts
>> to say that evolutionary theory has been nothing more than
>> just so stories, leveraging your own interpretation of "coming
>> of age" to support this assertion.

>There's a difference between "evolutionary theory" and particular
>explanations that purport to explain a particular biological
>feature.

Oh indeed. ON this I heartily concur. Many particular biological
features are as yet, inadequately understood by me. Far far more
are better understood by others but I'll expect that many are
still poorly understood by anyone even if nice enough just so stories
exist. This tends to go back to case 1 though where sometimes a cigar
is just a cigar and unknown is just unknown. (which by the way doesn't
preclude did not evolve)

>> That's how it reads. Surely
>> you won't stand and defend such a position and will claim I
>> misrepresent you, so take this is my feeble attempt to clarify
>> your point as there may be others with such low reading
>> comprehension skills as mine who would likewise misunderstand.

>If you were truly interested in merely clarifying, you wouldn't
>put words in my mouth. You'd simply ask.

Indeed. And I was trying to give you an out if it was sloppiness
on your part that lead to my misunderstanding though I didn't
feel it was as you are a most deliberate writer who I think is
quite in control of the impressions you create.

>> But then, what is your point if it isn't that evolutionary
>> theory is principly supported by (just so stories) unworthy
>> support?

>That particular evolutionary explanations, told through Darwinian
>filters, have been little more than just-so stories for quite some
>time. IMO, Dorit comes very close to admitting this probably because
>he thinks its safe since now we can replace them in these "coming-of-age"
>times. Dorit doesn't seem to realize that evidence that indicates
>organisms A and B share a common ancestor doesn't automatically
>mean that the events associated with the divergence and lineage-specific
>transformations that led to organisms A and B had anything to do with
>Darwinism.

Fascinating when you consider the position you seem to hold in other
posts where designers were here some 3 1/2 billion years ago and
haven't been back since. I really do need a score card to follow
where you differ with standard simple extrapolations.

>> Are you denying the existence of strong support?

>Of evolution? Not at all.

Yet are so quick to invoke alternatives as suggested above.

>> Do you think that because populist "understanding" of eovolution
>> is a bundle of plausible just so stories that the scientific
>> theory can be conflated with with these same stories?

>Popular understanding? I've learned some in the university and even encounter
>them on this board from folks who would not like it if I said they
>had a "populist understanding" of evolution.

Would that stop you from saying it? If it served you that is?

>> >for the skepticism. But they never seem to realize the just-so
>> >element of their belief naturally arouses skepticism regardless of
>> >background beliefs. Dorit essentially admits this and does so probably
>> >because he thinks we are finally about to abandon those just-so stories.
>>
>> Let's remember that next time you accuse others of trying to read
>> too much into what you write.

>Let's not. Y'see, Dorit doesn't post on this board, otherwise, I'd
>simply ask him. I do post on this board, so you have no excuse for
>not asking me.

>> I again complain about your
>> misrepresentation of just so stories actively promoting
>> skepticism rather than being a weak justification for abandoning
>> skepticism. I'ld almost suggest that you are too smart to make
>> such a mistake on accident.

>You can complain all you want. I simply said they often arouse
>skepticism, regardless of background beliefs. That's a fact.

It's a new fact to me and one I'm somewhat skeptical about.

>> >We should be so lucky.
>>
>> But then Gould would have to take up writing romance novels.

>Panda's In Paradise? Panda's In Heat?

>> >Thirdly, Dorit fails to consider that one might build a case for
>> >intelligent design as the best explanation *because* of the comparative
>> >data, considerations of mechanisms, and what we know from experimentally
>> >manipulating systems. After all, this is exactly what I am doing in
>> >my discussion of oriC and DNA replication. And guess what? It looks
>> >like all these analyses simply mean that the just-so stories have
>> >now simply extended into the molecular realm.
>
>> Whoops there goes another irony-o-meter.
>> The double standard you take to 'looks evolved' and 'looks designed'
>> with respect to biological systems is so hard for me to understand.

>Because there is no double-standard. Not to mention that this paragraph
>says nothing about 'looks evolved' and 'looks designed.'

It's that different vocabulary issue again. I thought you've said that
DNA replication looks designed to you and I think that just so stories
make things "look evolved". I guess I've just missed that so very few
thinks look evolved to Julie. Try to work with what I meant by
"look evovled" and "look designed". You'll see the double standard
I mean. Then you can show how it is in some way apples and oranges
and we can move on, but I don't yet know how you'll try to do that
and an anxious to see.

>> There must be something in your philosphy of science or perhaps
>> just philosophy that I'm missing because from where I sit, the
>> contrasted standard screams out its irrational inconsistency.

>You shouldn't let those knee jerks take your eyes off the words. ;)

When the IRA stops by to cap someones knees, is the kick a reflex
or a recoil as the bullet smashes the bone?

>--
>Any one of us can come up with multiple, plausible stories concerning the
>evolution of a given biological feature. But plausibility is about the
>weakest criterion one can apply to an evolutionary hypothesis.
>- Robert Dorit, Biology Dept., Yale University

Anyone can assert design as an alternative to evolution, and free from
specific notions of what sort of designer and what intent the designer
had, no effective refution of such assertions is possible. Go for it.
Party on. Cowabunga.

[Peter Nyikos]

howard hershey <hers...@indiana.edu> writes:

>howard hershey wrote:
>>
>> Peter Nyikos wrote:
>> >
>> > howard hershey <hers...@indiana.edu> writes:

>[snip]

Couldn't deal with my on-topic comments, eh? Even the one
you picked out here, you can't deal with in any sincere
way, so you go into a manic clown act:

>> > Hard to tell until you start fleshing them out.
>>
>> Just the way you have fleshed out the IC-specific mechanism by which
>> they arose?

Nobody seemed to have any more problems with it on the "directed panspermy"
threads when last I checked. If *you* have problems with it,
please say so.

>[snip]

>I have to admit that the insistence that I flesh out my admitedly
>simplistic and non-detailed (as befits the evidence)

Wrong. Check the thread, "A scenario for bat evolution?"
next week to see how one *can* flesh out scenarios even
in the absence of direct evidence. Sure,
there's no guarantee that my scenario is correct, but
that's utterly beside the point. The point of my "just-so story"
will be that bats *could* have evolved by Darwin-Spencer
principles of "survival of the fittest" and hence the
creationist's claim [which has even made it into textbooks
for high school students, like one published by ABEKA]
that bats violate these principles is incorrect.

I think I've said often enough that I have a completely
different attitude towards just-so stories than Julie;
often enough so that you've probably gotten the message
by now, and are merely indulging in Usenet Treadmill
Salesmanship here.

pathway to cillia
>is somewhat amusing coming from someone whose response to the real
>problems of abiogenesis is "First, we posit an alien..."

Not "problems". "problem": the bacterial flagellum.

Your last comment, if taken at face value, would indicate that you
think there were no technological civilizations anywhere in the universe
more than 3.5 billion years ago. If so, then it would logically
follow that you believe our own existence is a near-miracle in your eyes.

But you believe just the opposite, don't you? You stuck
in that snide remark about aliens because you were stuck in
a "boys will be boys" mode, didn't you?

>Reminds me of the economist trapped in a pit who suggested that he could
>get out by positing a ladder.

You are only digging yourself deeper into the pit with the
sign that says, "I, Howard Hershey, think that Usenet is
one big joke where the teasing we do has no connection
with reality."

[howard hershey]

howard hershey wrote:
>
> Peter Nyikos wrote:
> >

> > howard hershey <hers...@indiana.edu> writes:
> >
> > >Wade Hines wrote:
> > >>
> > >> iz...@cleveland.Freenet.Edu (Julie Thomas) writes:
> > >>

> [snip]

> >
> > So, when do you plan to write *your* scenario for bat
> > evolution? :)
> >
>

> First, I posit an intelligent alien race. The aliens sent the bats in a
> sleeping berth looking for planets with sutible caves. This is
> reasonable because 1) there are a lot of planet with potential aliens
> and 2) if the aliens were intelligent enough they could easily build a
> bat.

I forgot to mention that this will be my argument for purposes of this
thread until April 1, 1998.

[Laurence A. Moran]

In article <5vahh5$h...@alexander.INS.CWRU.Edu> iz...@cleveland.Freenet.Edu
(Julie Thomas) writes:

>Here's the recipe for making a just-so story. First, survey
>the biological world for structures/functions. Find those
>that seem useful for coming up with a precursor to the system
>in question and patch them together without much regard for
>biochemical and/or genetic details. Place the patchwork in
>an imaginary creature from the distant past which has conveniently
>gone extinct. Invoke a vague selective pressure that selects
>for the patchwork and then imagine it is plastic and amenable
>to further selective modification that just happens to arive
>at the system in question.

Julie, this reminds me that you haven't responded to my earlier posts
on DNA replication. I hope that your offensive description of a just-so
story doesn't apply to what I have posted.

BTW, according to my interpretation of your essays, you are postulating
an "imaginary creature" from the ancient past. This "conveniently extinct"
creature had all of the irreducibly complex features of DNA replication
that you have reconstructed from your analysis. It was this imaginary
creature that was created by the intelligent designers. Is this a fair
way to describe your particular just-so story?

I also believe that you have "surveyed the biological world for structures/
functions" in order to find those that meet your criteria for intelligent
design. I believe that you created a "precursor to the system in question"
(DNA replication) "without much regard for biochemical and/or genetic
details". In several cases I have tried to show you where I disagree with
your interpretation of biochemistry.

In other words, you are being incredibly hypocritical in the above paragraph.
Not only are you being hypocritical you are also being offensive. You
know very well that the term "just-so story" is used by evolutionary biologists
in a very different way. It does not refer to senarios that are backed by
evidence and that conform to the modern understanding of evolution.

Larry Moran

[Matt Silberstein]

In talk.origins Peter Nyikos <nyi...@math.SC.EDU> wrote:

>CC: Julie, because I am curious about the mammalian hearts bit,
>and because I don't want her wasting any more time on what
>look to me like trumped-up charges on Silberstein's part.
>
>mat...@ix.netcom.com (Matt Silberstein) writes:
>
>>In talk.origins Peter Nyikos <nyi...@math.SC.EDU> wrote:
>
>>>mat...@ix.netcom.com (Matt Silberstein) writes:
>>>
>>>in back-and-forth with Julie, against whom he made what looks
>>>like a suspiciously selective deletion earlier in this thread.
>>>
>>Again I ask what kind of standard you use. And are you merely saying
>>that I deleted deliberately rather than by accident?
>
>It *looks* that way to me, yes.

Wow, such a standard and such an accusation. I actually snipped out
something because I wanted to snip out that piece. So trashy and
immoral. I guess what I should do is get one of those neat
Snip-O-Random newsreaders.

> And I was amused by Paul Myers's
>off-the-wall tirade which COMPLETELY MISSED my point about
>him being able to give you an extended lecture on the subject
>of dishonest marked deletia.
>

??? What does Paul have to do with this at all?

>Y'see, *he* caught *me* in what may well have looked to him like
>a dishonest *marked* deletion on *my* part, and broke his
>habit of never following up directly to me, probably because
>he thought he had a chance to go for my net.jugular; for sure,
>he played his chance to plausibly hit me to the hilt, just
>as Clark Dorman has done more recently.
>

So what. Here is a rather direct statement. I am not Paul Myers, you
are not Julie Thomas. You have pointed out that I not only intended to
snip something, I actually did the snip and even marked it. I have
pointed out multiple occasions where you have snipped something and
not marked it. At no time did I ever attribute any purpose or
intention to your action. Now there were times when I had "suspicions"
about your actions, but since I had the same evidence as everyone
else, I did not see any purpose in discussing my suspicions. OTOH, you
are making a big deal out some snippage and your "suspicions" which
are either banal or unstated.

>Myers's post, and my reply, are highly instructive already on this
>subject, but I'm sure he could go a lot more deeply into
>the topic with you in e-mail if you are interested.
>

No, I am not. I am not Paul and do not see any reason to get into a
discussion in public or private about his actions. I am willing to
discuss my actions, I am willing to discuss yours, but only in the
same public forum that they took place in.

>But it's really amusing to see Paranoid Paul #1 guess that
>my whole point was how "ghastly awful and nasty" he was,
>whereas I wasn't even going to *hint* at how he capitalized
>on my marked deletion, but only to let y'all know that
>he knows what "dishonest marked deletia" are
>all about. I believe you are hundreds of times more willing
>to learn about the topic from him than from me.
>

If the topic is deletion, then it looks to me like you are not going
to discuss your actions or mine, so we may be left with Paul's. If so,
then if I want to discuss such, I will do so with Paul in a response
to a post by Paul. I have asked you questions about your deletions and
your standards. When you answer those questions we can have a
discussion. If you want to "teach" me about deletion then you should
start by answering those questions.

> If not, what does
>>"selective" mean in this context. Finally, does this sudden appearance
>>of comments on my deletions have anything to do with my recent posts
>>that pointed out your unmarked deletions?
>
>You mean the ones you did almost a month ago? Get real!
>

Instantiation complete. I think I have done it more and less than a
month ago, but I don't really remember the dates.

>>BTW, I have don't remember your responding to any of those comments. I
>>also want to point out that I just mentioned where you did not mark
>>the deletion. No judgements, no "suspicions", no "selective". Just the
>>objective comment.
>
>Good, then there's no need for me to reply. Unmarked deletia,
>in and of themselves, are not a cause for concern.
>

Why are they somehow less worthy of suspicion than marked deletia? It
seems to me that unmarked deletions have a significant potential to
deceive a reader, whether that deception is intended or not. And it
seems to me hard to snip out a single sentence, from the middle of a
paragraph, by accident. To do so and not mark the deletion, especially
when this has happened in the past, suggests a desire to "hide" that
sentence.

>>>>>>This is one of the delightful almost claims. "Darwinism" (or, more
>>>>>>correctly evolutionary biology) may be better off with folks like you,
>>>>>>but Darwinism is not a belief.
>>>>>
>>>>>So you believe it is not a belief.
>>>>>
>>>>If you want to play the game of using private definitions, then I
>>>>suppose you can find such a definition to support your claim. But
>>>>"Darwinism" (or, more correctly, evolutionary biology) does not fit
>>>>the standard definition of belief. I do not believe in evolution or
>>>>Natural Selection. I accept that these are the best explanations for
>>>>the our observations.
>>>
>>>And, since you have shown yourself to lack the competence to
>>>evaluate it, this "acceptance" is a belief in a pretty
>>>strong sense of the word.
>
>>I am aware that you are convinced that you know everything about my
>>scientific competence.
>
>Skip the rhetorical excesses, Matt, and let the people out
>there know what they are the secret code for.
>

Cute Peter, You have found another way to avoid dealing with
substance.

Again I will try to make this clear. I have (twice, IIRC) admitted to
use of "rhetorical excess" in this newsgroup. I have a tendency, in
vocal communication, towards "grandiose" speech. I talk of a movie as
the best movie, a meal as the greatest. I don't really mean they are
either objectively or subjectively the greatest, it is just an attempt
to show enthusiasm. I have tried to curb this habit, but such things
are hard for most of us to deal with. I am able to keep most of this
out of my written posts, but twice I have turned a "most" to an "all".
When challenged and presented with evidence (even if I had to find
such myself) I have admitted the error and corrected the statement.

But in all of this there has been no secret code and certainly no
admission of such a code. Now if you think you see a code (with,
possible, the same talent that lets you see our purposes and lets you
see purpose in other systems) then you need to present you evidence.
You can certainly assert such, but I have denied it. And all we have
is your bare assertion and my denial.

>> As I remember, it was a single phrase in one
>>post that showed you that I know nothing at all about science.
>
>On the contrary, it was your dogged defense of it, in the
>face of repeated explanations on my part, that did the trick.
>You even whined about how I kept going back to earlier
>things you said and deleting all your (off-topic, as I
>kept explaining) new points. Each time I did that, I
>did it because my earlier explanations were inadequate,
>and I kept coming up with new ways of getting my message
>across--which were also inadequate.
>

As I said, you think that you have a complete understanding of my
competence. Big deal. As I have said before, even if such were true,
and even if I had no competence at all in science, it would not
matter. What matters is if the statements are correct.

>>BTW, it is amusing to see how you are complaining about some lack on
>>my part, but you have no comments on Julie's rhetorical games.
>
>WHAT rhetorical games? Are you going to come up with
>some trumped-up charges like the ones you came up with
>about me playing some "plausible deniability" game,
>just so you could strut your stuff for ~1000 lines
>to show me how a real pro like you plays the game?
>

No, I meant here "So you believe it is not a belief" kinds of
statements. Or don't you see that as a rhetorical trick?

>>>> You, OTOH, seem to believe that IC systems are
>>>>the product of intelligence.
>>>
>>>No, only that two of them are, and for reasons you can't
>>>even begin to comprehend, by the looks of it.
>>>
>>And for reasons that neither your nor Julie seem willing to discuss.
>
>I can't discuss her private thoughts with anyone, since
>I am not privy to them.
>

I did not ask you to discuss her private thoughts, I did not even know
her private thoughts were the topic. There is a big gap in your
argument from IC to design and I would like to discuss it. I will
discuss this with anyone who proposes that IC implies design.
Unfortunately none of the people who have proposed such have engaged
in that discussion.

>>And your position in not the same as Julie.
>
>Of course not, and I HAVE been quite willing to discuss
>MY reasons and have BEEN discussing them on the "directed
>panspermy" threads, and yesterday I even brought the
>bacterial flagellum "(really!)" thread back to topic to
>discuss it with none other than one Matt Silberstein.
>

I don't know which thread you mean, but I am glad of this.

>> You need to stop thinking
>>of yourself as a pack, you have significant differences.
>
>And I've pointed them out often enough, so your first
>clause is a Pee Wee Hermanism.
>

Again you do this. Astounding.

I am reminded of a great joke about LBJ when he was running for the
Senate. He told his campaign manager to accuse his opponent of having
carnal knowledge of this farm animals. The manager responded that he
"could not accuse him of being a pig fucker." LBJ said "I just want to
hear him deny it."

>> Julie made
>>the explicit claim that IC systems usually come from intelligence
>
>That's a subjective statement that I don't know how to
>evaluate.
>

??? Look at the quote, tell me what you think of the logic.

>so
>>the presences of IC means the system was probably designed. Not just
>>the two under consideration, but IC systems in general. I do not
>>remember your comment on the circular logic involved.
>
>I took your "evidence" for the circular logic to be "rhetorical
>excess", and was waiting for you to decode it. Which you have,
>below, after a fashion.
>

Really Peter? Did you do this? Even in the thread where I made the
comment immediately following Julie's statement? I guess those two
admissions of error have given you free reign to ignore anything I
write. Then do so, if makes you happy, consider every single word an
example of rhetorical excess and ignore it all. But if you just do so
selectively, then be careful. You will take a chance of ignoring, not
because you consider it excess, but because you don't want to respond
or can't respond. You are setting yourself up for a strong possibility
of self-decseption, at best, and dishonesty at worst.

>>>> Therefore you claim that when we see an
>>>>IC system, it must come from an intelligent entity.
>>>
>>>Don't you ever get tired of "rhetorical excess" as to
>>>what Julie has claimed?
>>>
>>You are so right, it is not "must", it is just "usually". Here is the
>>quote in question:
>
>>JT> When this is coupled with my common experience where IC is tied
>>JT> to intelligent design (intelligence easily generates IC and IC
>>JT> usually stems from intelligence),
>
>Well, that's her personal experience.

First, I wonder how you know that this is just "personal experience"
in a way that other statements may not be. Second, it does not really
matter, the logic is circular. Third, it is just plain wrong. We are
discussing systems where we don't know where they come from. So she
does have experience with IC systems with unknown provenance. Fourth,
I would like to discuss this "personal experience" with Julie since
this seems a key support for her claim. And, finally, fifth, this does
not see all that different from Behe's logic.

>Of all things Julie
>talks about, I am least able to comment on her personal
>experiences.

[digression snipped]

>>Now this seems like she is assuming the conclusion.
>
>To me it seems like she is just elaborating on her personal
>observations.
>

??? At best, you are claiming that she meant something different than
she said. You are implying that she meant "most IC systems I have
observed stem from intelligence". Even if this were true, it is not a
very strong argument. Mere proportion does not tell us much. Do these
systems classify in some meaningful way. For instance, it probably
will turn out that none of the IC system with known provenance are
biological. If that was her statement (rather than the one she made)
then her logic is still flawed, but flawed differently. She would then
be claiming that some human designed systems have a quality, IC. Some
systems of unknown origin have the same quality, so they probably were
designed. I could apply the same logic as follows. Some human designed
systems have a quality, non-IC. Some systems of unknown origin have
the same quality, so they probably were designed. We have just argued
that all systems are probably designed.

Lets make this clear. It seems we have two possible versions of this
logic. First, as stated originally by Julie:

P1) Intelligence can generate design
P2) IC usually comes from intelligence

C1) The presence of IC means that it was probably designed.

But C1 is really a restatement of P2. (Which is usually what happens
in ((simple)) deductive logic.

Your rewording (which I admit seems somewhat likely, but certainly is
not stated) goes:

P1) Intelligence can generate design
P2) Most IC systems I see come from human design

C1) Most other IC systems come from design.

Is that what you are claiming she probably meant? And if so, do you
support this logic or not?

>>>Why don't you save us all a lot of trouble and mark your
>>>"rhetorical excesses"?
>
>>Why don't you mark where you snip, Peter?
>
>Because it's time consuming to do it every time, and because
>it's strictly optional on Usenet.

It may be optional, but is has a strong potential to deceive. And if
marked deletions raise suspicions, then unmarked ones, when
discovered, raise them in spades (or even no trump). As for time
consuming, so is using a spell checker, but it helps communication and
is worth the effort.

[digression deleted]

>
>
>>[...] Why don't you
>>explain why the marked deletions made by others raise your suspicions,
>
>Stop smuggling in words like "the".

I can't really see how the use of an article in this case changes the
meaning. Sometimes it can have a profound change, but I just don't see
it in this case. If you don't like it, consider it removed.

>When I get suspicious,
>I usually restore the suspicious deletion on the spot,
>and let people see the devious comments that were made
>plausible thru the deletion. That's exactly what I did with
>you. Have you owned up to what your deletion was all about
>like a responsible adult, or have you just continued the diversionary
>tactics you and Myers initiated?
>

??? About the best I can do here is point out that this still does not
answer the question. What you have not done is explain what suspicions
were raised or how they were raised. Above you say that you are
suspicious that I did the deletion deliberately. I admit that. If you
are suspicious about some ulterior motive then you will need to
explain your position a little bit better.

First, you should suggest what motives you are thinking about. Second,
as I have said, the general case of the ability to detect intention
and purpose from events is absolutely on target in all this IC/ID
discussion. So any elaboration you can give will be helpful.

>If I complained about every deletion you made, or even about
>one-tenth of them, I'd be a laughingstock, and rightly so.
>

No comment.

[digression deleted]
>
[other stuff deleted, deliberately]

[PZ Myers]

In article <34190B...@indiana.edu>, howard hershey
<hers...@indiana.edu> wrote:

>howard hershey wrote:
>>
>> Peter Nyikos wrote:
>> >

>> > howard hershey <hers...@indiana.edu> writes:
>> >
>> > >Wade Hines wrote:
>> > >>
>> > >> iz...@cleveland.Freenet.Edu (Julie Thomas) writes:
>> > >>

>> [snip]

>> >
>> > So, when do you plan to write *your* scenario for bat
>> > evolution? :)
>> >
>>

>> First, I posit an intelligent alien race. The aliens sent the bats in a
>> sleeping berth looking for planets with sutible caves. This is
>> reasonable because 1) there are a lot of planet with potential aliens
>> and 2) if the aliens were intelligent enough they could easily build a
>> bat.
>
>I forgot to mention that this will be my argument for purposes of this
>thread until April 1, 1998.

You also forgot to mention 3) all your opponents are liars and hypocrites,
and *that* will really be the focus of your argument now and forever.

--
PZ Myers
http://fishnet.bio.temple.edu/

[howard hershey]

Peter Nyikos wrote:
>
> howard hershey <hers...@indiana.edu> writes:
>

> >Peter Nyikos wrote:
> >>
> >> howard hershey <hers...@indiana.edu> writes:
> >>
> >> >Wade Hines wrote:
> >> >>
> >> >> iz...@cleveland.Freenet.Edu (Julie Thomas) writes:
> >> >>

> >[snip]

> >>
> >> So, when do you plan to write *your* scenario for bat
> >> evolution? :)
> >>
>

> >First, I posit an intelligent alien race. The aliens sent the bats in a
> >sleeping berth looking for planets with sutible caves. This is
> >reasonable because 1) there are a lot of planet with potential aliens
> >and 2) if the aliens were intelligent enough they could easily build a
> >bat.
>

> You are indulging in a One Shade of Gray Meltdown. Bats are
> a problem, sure, but it is possible to come up with a plausible
> *detailed* scenario just on the basis of orthodox Darwin-Spencer
> mechanisms. You'll see that next week.
>
> And I expect it
> to inspire you to come up with a similarly plausible scenario
> on the evolution of the bacterial flagellum. :-)

Not until you show me what is wrong with my 'aliens created bats'
argument.

Just because you can make up a just so story about bats based on little
evidence doesn't mean my 'aliens did it' arguement is wrong. Bats
clearly are IC. There is no transitional fossil of any relevance
(AFAIK) to intermediate states of bat wing. The final form of the wing
has the 'function' of flight. Only a crumudgeon would mention the
homology between the bones of the bat's wing and similar but different
bones in the fingers of penquins. Unless you can show me every
selective pressure that led to the two *in detail*, I will continue to
call your argument 'starman Behe'. There just has to be an intelligent
designer of bats.

[howard hershey]

Peter Nyikos wrote:
>
> iz...@cleveland.Freenet.Edu (Julie Thomas) writes:
>
> >In a previous article, nyi...@math.SC.EDU (Peter Nyikos) says:
>
> >>howard hershey <hers...@indiana.edu> writes:
>
> >>[deletia of long preamble, most of which was dealt with in my
> >>first followup]
>
> >>Chapter 3. Cilia and Flagella
>
> [...]
>
> >Of course, this leads to all sorts of other questions. Why
> >would an organism use microtubules instead of actin? Where did
> >the microtubules themselves come from considering that bacteria
> >have none?
>
> Interesting. So cilia are confined to eukaryotes? No wonder
> they call those protozoans "ciliates".
>
> [Trivia: some ciliates actually have a slightly different
> genetic code than we do. It took
> me a while to make even Keith Robison appreciate the fact that the
> problem of explaining how this could have happened
> is fundamentally far more difficult than accounting for
> the different genetic code in mitochondrie, but Keith finally
> acknowledged the seriousness of the problem, and relayed
> some good ideas on how it could have happened. ]
>

Just in case somewone might confuse the above with what really
happened. First, Peter was clueless that there was a slightly different
genetic code in some of the ciliates (I don't remember whether it was
Wade, Keith, or myself who first informed Peter that the genetic code
even in nuclear genes was not completely universal and I don't remember
whether it was Keith or myself that gave him the just-so story of
evolution of the different code system via conversion of a stop codon to
an amino acid codon). Peter's sole contribution was his being clueless
and asking how such a thing could happen. Not to knock the role of
honest questioner.

[snip]

[John Mazor]

Peter Nyikos <nyi...@math.SC.EDU> wrote in article
<1997091214...@milo.math.sc.edu>...
>
> iz...@cleveland.Freenet.Edu (Julie Thomas) writes:

(snip)

>
> Are you kidding? Howard has burned his bridges behind him
> with his snide remarks about aliens. :-)
>
> He wouldn't dare risk postulating organisms for which there
> is no direct evidence. :-)
>
> [Note the smileys. AFAIK no one has ever accused Howard
> of such anal-retentive qualities :-) as consistency.]

Here Peter demonstrates either his ignorance of psychology, or his
unwillingness to let facts get in the way of a good ad hominem. Since when
is "consistency" per se a hallmark of an anal personality? OTOH, you,
Peter, have one of the most anal personalities ever seen, and you rarely
let concerns over consistency get in the way of inflicting your ego on the
Web.

(Julie Thomas here)

> >Any one of us can come up with multiple, plausible stories concerning
the
> >evolution of a given biological feature. But plausibility is about the
> >weakest criterion one can apply to an evolutionary hypothesis.
> >- Robert Dorit, Biology Dept., Yale University
>
> That's within science. In the big outside world these plausibility
> arguments are very important politically.
>
> Peter Nyikos -- standard disclaimer --
> Professor, Dept. of Mathematics
> University of South Carolina
> Columbia, SC 29208
>

Are you willing to open a thread on the politics of neo-conservastism,
creationism, and the implications thereof (including, but not limited to,
the hypocrisy of current neo-Illuminati)?

[John Mazor]

Matt Silberstein <mat...@ix.netcom.com> wrote in article
<341a69ee...@nntp.ix.netcom.com>...

> In talk.origins Peter Nyikos <nyi...@math.SC.EDU> wrote:

(snip)

> >And I've pointed them out often enough, so your first
> >clause is a Pee Wee Hermanism.
> >
> Again you do this. Astounding.
>
> I am reminded of a great joke about LBJ when he was running for the
> Senate. He told his campaign manager to accuse his opponent of having
> carnal knowledge of this farm animals. The manager responded that he
> "could not accuse him of being a pig fucker." LBJ said "I just want to
> hear him deny it."
>

Peter has a tin ear when it comes to politics. He probably still is
desperately leafing through an almanac, looking for the place name "Foggy
Bottom" in any of the 50 states so he can refute my private e-mail to him
(unacknowledged to this date, even though he publicly blabbed another
e-mail of mine to him when it suited his purpose) pointing out his error in
referring to the Senator from Foggy Bottom, when Foggy Bottom is in the
District of Columbia and therefor has no Senator, either in the U.S. Senate
or in a state legislature.

But then again, Peter has a tin ear on *any* communication that criticizes
him or calls any of his pronouncements into question.

(snip)

[John Mazor]

Laurence A. Moran <lam...@bioinfo.med.utoronto.ca> wrote in article
<5vbqqk$j...@bioinfo.med.utoronto.ca>...

>
> In article <5vahh5$h...@alexander.INS.CWRU.Edu>
iz...@cleveland.Freenet.Edu
> (Julie Thomas) writes:
>

> >Here's the recipe for making a just-so story. First, survey
> >the biological world for structures/functions. Find those
> >that seem useful for coming up with a precursor to the system
> >in question and patch them together without much regard for
> >biochemical and/or genetic details. Place the patchwork in
> >an imaginary creature from the distant past which has conveniently
> >gone extinct. Invoke a vague selective pressure that selects
> >for the patchwork and then imagine it is plastic and amenable
> >to further selective modification that just happens to arive
> >at the system in question.
>

> Julie, this reminds me that you haven't responded to my earlier posts
> on DNA replication. I hope that your offensive description of a just-so
> story doesn't apply to what I have posted.
>
> BTW, according to my interpretation of your essays, you are postulating
> an "imaginary creature" from the ancient past. This "conveniently
extinct"
> creature had all of the irreducibly complex features of DNA replication
> that you have reconstructed from your analysis. It was this imaginary
> creature that was created by the intelligent designers. Is this a fair
> way to describe your particular just-so story?
>
> I also believe that you have "surveyed the biological world for
structures/
> functions" in order to find those that meet your criteria for intelligent

> design. I believe that you created a "precursor to the system in
question"

> (DNA replication) "without much regard for biochemical and/or genetic
> details". In several cases I have tried to show you where I disagree with
> your interpretation of biochemistry.
>
> In other words, you are being incredibly hypocritical in the above
paragraph.
> Not only are you being hypocritical you are also being offensive. You
> know very well that the term "just-so story" is used by evolutionary
biologists
> in a very different way. It does not refer to senarios that are backed by
> evidence and that conform to the modern understanding of evolution.
>
>
> Larry Moran
>
>

Your on-target reply is exactly why I have tried to keep posters from
jumping on Julie with irrelevant arguments about her supposed religious
preferences, political agendas, or aliens in flying saucers (as opposed to
directed panspermy, which IMHO almost certainly occurred, but not
necessarily here). There's enough here, in her own words, to refute her
exposition on scientific and logical grounds.

Now if we could only entice Peter into a thread on the political aspects of
neoconservatism and creationism. ;-)

[Dave Haas]

howard hershey wrote:
>
> Peter Nyikos wrote:
> >
> > howard hershey <hers...@indiana.edu> writes:
> >
> > >Peter Nyikos wrote:
> > >>
> > >> howard hershey <hers...@indiana.edu> writes:
> > >>

> > >> >Wade Hines wrote:
> > >> >>
> > >> >> iz...@cleveland.Freenet.Edu (Julie Thomas) writes:
> > >> >>

Imagine 30 - 40 million years of random and non random physical
changes coupled with gradual and some sudden (relatively) changes in
the biological environment. Then imagine these complex factors
acting on millions of gene pools over the entire planet with its
different macro and micro environments.
Why is it surprising that after enough selection something as complex as
a bat could evolve from a small mammal? You don't need to make any new
structures. All you need to do is change a few regulator genes which
changes the morphology a bit.

The fact that we find it difficult to understand what happened in the
distant past simply reflects a lack of information and imagination. The
human brain is a mammal brain and as such needs help in seeing beyond
simple concepts and ideas.
Humans did not evolve a brain equipped to easily handle concepts beyond
their
experience.

Why does it surprise you that we have found no fossils? What are the
chances that
one of the millions of vertebrate lines will leave us nicely preserved
fossils?
Fossil forming conditions are rare and erosion wipes out the majority of
sedimentary rock. For example, we have no fossil flowers to give us any
idea of what the ancestors of flowering plants looked like.

Can you imagine a million? Here is an analogy. If your desk gets
covered with .1 mm of dust each year. (about one tenth the diameter of
this period.) how much dust would accumulate on your desk in 1,000,000
years? .1 mm X 1,000,000 = 100,000 mm or 10 meters of dust! Now
imagine a billion or three.

D. Haas

[howard hershey]

You haven't been following this thread very closely, have you? :-)
Do I get Loki points for this? I think I should.

[howard hershey]

Julie Thomas wrote:
>
> In a previous article, hers...@indiana.edu (howard hershey) says:
>
> >Wade Hines wrote:
> >
> >> iz...@cleveland.Freenet.Edu (Julie Thomas) writes:
> >
> > >I haven't seen Howard's reply. Perhaps someone can e-mail it to
> > >me. I recently read Dorit's review, however. I doubt I'll
> > >have time to critique it, but he did make a good point:
> >
> > >"Any one of us can come up with multiple, plausible stories
> > >concerning the evolution of any given biological feature."
> >
> > >Note that he admits that *ANY* biological system can be accounted
> > >for by such story-telling. As I've always said, they tell us
> > >more about a person's ability to imagine than the natural world.
>
> >Not if the stories have to be congruent with what we know about how
> >biological systems work.
>
> If only this were true. Are cells with RNA genomes congruent
> with what we know about how biological systems work? Nope.

The one-eyed man is king on the island of the blind. RNA genomes
certainly can work for certain organisms.

> Are cells that replicate their DNA genomes for thousands, maybe
> millions years, with a semi-functional R-loop mechanism congruent
> with what we know about how biological systems work? Who knows?

The one-eyed man is king on the island of the blind. Can you imagine
that airlines ever flew prop planes? Sure props are still useful (and
used) in small planes, but no current major airliner uses one to fly
passengers. Unless you can show me an airline that currently uses prop
planes, I will refuse to believe that any ever did or could. All you can
point to is faked pictures and histories.

> These just-so storied almost invariably postulate hypothetical
> creatures with imaginary systems which show only how the author
> is creative at pasting together different features of modern systems.
> It's the modern version of inventing unicorns and mermaids.
> But we usually haven't the foggiest notion if these imaginary
> entities could indeed exist in a way that is congruent with what
> we know about how biological systems work. Everytime a just-so
> story is told at the molecular level, we end up talking about a sloppy,
> unregulated, simple system when what we known about how those biological
> systems work doesn't seem to support such a sloppy, unregulated, simple state.

Current enzymes have secondary activities.

> You yourself have invoked DNA polymerases that could only replicate
> 10-20 nucleotides in a tiny, little genome. But is this *life*?

More so than what came before and less so than what came after.

>
> >As I pointed out in my review, I think that
> >Behe is asking a different question than he thinks he is asking. Behe
> >is really asking "Why did this system evolve?" or more accurately "What
> >specific selective forces were involved in the evolution of this
> >system?"
>
> Which is the milk of Darwinism! You seem to forget that Behe's
> problem is with *Darwinian* evolution and not simply evolution itself.

No. Behe's problem is with *any* natural law explanation for evolution,
not just natural selection. So when there is no direct evidence for a
particular natural law mechanism, even though what evidence exists is
compatible with known natural law mechanisms in terms of rate and amount
of change needed (although there is often no evidence whatsoever - but
science doesn't develop ideas from "I don't know how this happened." It
develops it from "This mechanism works here. It could be responsible
for this similar situation."), he asserts that the 'system' he describes
cannot be done by natural selection. But he provides absolutely zero
evidence that *any* system 'appeared' in an IC-specific mechanism rather
than in an 'evolution by known natural law' mechanism. Specifically, no
system is presented that convincingly argues for instantaneous
construction or construction via useless intermediates (IC-specific
mechanisms appear to be a null set, whereas evolution by natural law
mechanism or indirect mechanism does not seem to be a null set). I have
specifically described possible ways to support either IC-specific
mechanism in the thread "Testing for IC-specific mechanisms".

>
> >This last is potentially answerable by science, but in most
> >cases we do not have sufficient evidence to do more than provide some
> >reasonable inferences (a just-so story).
>
> And as I said, it then looks like Darwinism and just-so stories are
> joined at the hip. And whether or not they are "reasonable" is in the
> eye of the beholder. Or shall we say it's "story-dependent?" ;)

Science works from examples with the most evidence toward those with
less. Are you saying that the usual description of the evolution of the
hemoglobins is simply a just-so story unsupported by evidence?

>
> >Unfortunately, Behe also
> >confounds this with the more teleological (and ultimately unanswerable)
> >question which also reads "Why did this system evolve?" and answers that
> >in the same way that old Bill Paley does. The question Behe *claims* to
> >be asking, "*How* could this system evolve by natural law mechanisms?"
> >can often actually *be* answered.
>
> Sure. As Dorit notes, "Anyone of us can come up with multiple,
> plausible stories concerning the evolution of a given biological feature."
> Big deal.

And one can always say that the 'little green men' or gods did it. Only
the evolutionary just-so stories are potentially falsifiable. Perhaps
you have an alternative mechanism to natural law mechanism for
generating the IC systems?

>
> >The observed changes in genes and
> >proteins that are required to produce the current differences from
> >reasonable ancestral forms (typically by duplication and divergence,
> >sometimes by scrambling of protein motifs, often with considerable
> >neutral drift) are *congruent with* the idea that these differences
> >arose by natural selection (acting primarily in a conservative fashion)
> >acting on random mutations (the only kind of mutation that we have ever
> >observed) of various kinds, from duplication to point mutation and
> >neutral drift by fixation of random mutations.
>
> As a criterion, congruency seems no better than plausibility. In fact,
> what is the difference between the two?
>
> Furthermore, I could likewise adopt such a standard. The notion that
> certain IC systems are designed is congruent with the capabilities
> of intelligence.

Its also congruent with evolution by natural law mechanism.

>
> >The way that you
> >disprove the "How did this evolve?" question is by either presenting a
> >different observable and/or testable mechanism by which it could occur
>
> Intelligent intervention qualifies.

So do 'little green men'. If you cannot see the problem with positing
an intelligent designer every time you can't explain something, you do
not have as firm a grasp on what science does as I think you do.
Positing intelligent designers in the absence of positive evidence *for*
same is cheap and worthless. Of course, I am now positing an alien in
some of my arguments with Peter (until April 1, 1998) so I can fully
understand the pleasures of this particular scientifically worthless and
simplistic argument.

>
> >or by presenting evidence that the observed differences are too great to
> >be accomplished in the time available by these *known* natural law
> >mechanisms.
>
> Sure. This would be very powerful evidence. But it is not needed.

Then what evidence do you think you need to determine that something
cannot possibly be produced by known natural law mechanisms? The fact
that no one has yet produced such? The absence of evidence?

>
> >Answering this question does not require any attempt to
> >describe which specific selective forces were at work. All it asks is
> >whether the observed extent of changes can be due to known natural law
> >mechanisms or not.
>
> I see. So the design theorist must show that something CANNOT be due
> to "natural law mechanisms." We're back to proving the impossible.
> It doesn't matter (to me) if one can imagine just-so stories congruent with
> "natural law mechanisms" that generate a system. It doesn't matter (to me)
> if the system doesn't seem to violate any "natural law mechanisms." What
> matters is whether the "natural law mechanism" is the *best* explanation.
> Howard's whole argument appears to be a needlessly complicated way of saying,
> "If an explanation doesn't violate natural law mechanisms, it *is* the best
> explanation" and, BTW, I'm using the term "natural law mechanisms" to mean
> nonintelligent intervention. But that's not an argument - it's an assertion.

In science, natural law mechanisms are necessary. For an ID argument to
be a scientific argument, you need to show that there is an absolute
*necessity* for an ID if you cannot show evidence for the ID itself
directly. Otherwise you are simply positing an IPU. I do not think it
impossible to show that some system appeared in a way that is absolutely
incompatible with known natural law mechanisms of evolution (and
certainly it is not impossible to describe a set of criteria that make
the need for a new kind of mechanism necessary - see the thread "Testing
for IC-specific mechanisms" for specific initial ideas based on the
IC-ness property that all parts are necessary for function.

>
> >So far, the clear answer is yes, all of the observed
> >differences are within the range of changes over time that can be
> >explained by known natural law mechanisms. There is no reason to
> >propose unseen mechanisms.
>
> Sure there is. Just because it *can* be vaguely explained in such ways
> doesn't mean it *best* accounts for the system.

Positing an alien (or god or IPU) is *always* an easy idea. Aliens can
explain it all (whatever 'it' is). Unless you have evidence that 1)
aliens actually exist and 2) actually go about designing systems and 3)
actually did so in this case, your ideas are scientifically worthless.
You cannot even do the simpler step of showing that the system appeared
in an IC-specific fashion.

>
> Look. As I see it, the molecular world of life is loaded with things that
> are quite unlike anything we see in the rest of nature. The closest
> analog to these things are our machines. If one doesn't have an
> aversion to proposing intelligent causation, one seeks to explore
> these strange similarities without a need to force them into
> a nonintelligent origin. Of course, I'm not saying that folks like
> Howard are rationally obligated to agree. Howard is satisfied with
> any explanation as long as it is congruent with "natural law mechanisms."

Actually, for many of them, I am not satisfied, but forced to say that
"We don't know because we have no clear evidence." Knowing that there
are things you are ignorant of is the first step to knowledge. Positing
an alien doesn't get you very far.

> But I'm not. Because of my perceptions, because I "see" little machines,
> I require something more than an explanation congruent with "natural
> law mechanisms" to show that the analogy between molecular machines
> and intelligently-derived machines is faulty at its very core.
> As I have said again and again, we simply see the same data
> differently.

You have presented no evidence to support *any* alternative model of
'development' of any system, IC or otherwise. You are just willing to
say, "I posit an alien" where I would say "We don't really know, but it
is not an insurmountable problem for natural law mechanism."

> Thus, I'm more interested in determining if a truly
> scientific approach under a design paradigm can be created that
> interprets, and even illuminates, the workings and origin of these
> machines. I'm not interested in convincing Howard or Larry or Matt, etc.,
> to join me in my approach.

One can easily study the present functioning of systems without
reference to their origin. That, of course, says nothing about their
origin. Aside from the ideas of testing whether there really is such a
thing as a IC-specific mechanism of 'appearance' rather having it
represent merely the null set steeped in the absence of evidence (the
gaps in knowledge). AFAIK, no one has presented a 'system' which they
can argue, from direct historical evidence, occured in an IC-specific
fashion.
>
> {snip}

>
> >
> >> I'ld like some more foreknowledge about what the lack of plausible
> >> stories means. Just to round out the picture you see.
>
> The lack of plausible stories can mean either one of two things:
>
> 1. A lack in the story-teller due to lack of imagination and/or lack
> of understanding at the moment. In other words, "we don't know"
> may mean nothing more than "we don't know."
>
> 2. The essence of the story is misguided, i.e., X didn't evolve.
> If X didn't evolve, one might expect it would be hard to come up
> with plausible stories, especially when they are so easy to invent.
> (Note: X didn't evolve does not mean evolution never occurs).
>
> Choosing between 1 and 2 is a judgment call,

If you have evidence that X actually occurred in a fashion that is
incompatible with evolutionary principles (an IC-specific fashion), it
wouldn't be a 'judgement call'. Absent that, it isn't a judgement call
either. We have and can observe natural selection. It exists and can
be tested. No one has observed the ID and it is untestable.

> but if one's worldview
> handicaps them into thinking #2 cannot be true, then there is no real
> choice for them. As for me, I suspect it is because of #2. Thus,
> I seek to flesh out an alternative approach. I may turn out to be
> wrong. So what?

So go ahead. Present the system with the best evidence that it appeared
in an IC-specific fashion. Don't present systems where all you can do
is assert that it is unlikely (in your opinion) that it occured by
natural law so positing an alien is O.K.
>
[snip]

> > Whoops there goes another irony-o-meter.
> > The double standard you take to 'looks evolved' and 'looks designed'
> > with respect to biological systems is so hard for me to understand.
>
> Because there is no double-standard. Not to mention that this paragraph
> says nothing about 'looks evolved' and 'looks designed.'

Sure there is. Unlike the ID, natural selection and the other natural
law mechanisms for evolution have all been observed and tested in the
present. Where is the observable ID mechanism? You weigh the two
mechanisms as being equally likely explanations of natural events. That
is a double standard.

[Bruce Salem]

In article <1997091115...@milo.math.sc.edu>,
Peter Nyikos <nyi...@math.SC.EDU> wrote:
>
>sa...@pangea.Stanford.EDU (Bruce Salem) writes:
>
>>Because they are God's Creations, when biology clearly shows that
>>many features are imperfect and kludgy. I hope that Peter doesn't have
>>hemmaroids, to wit!
>
>I do.
>{people on talk.abortion] went into paroxysms
>over how "tasteless" it was for me to mention the fact that
>I have hemorrhoids in public.

Well, lots of people do, and the reason is that the vascular
supply for that part of the body did not evolve to withstand the large
hydraulic head that it gets as a result of people going around most of
the time as bipeds. It is an imperfect structure for which there was
no selection. Being a pain im the ass is not always lethal.

Bruce Salem

--
!! Just my opinions, maybe not those of my sponsor. !!

[Julie Thomas]

In a previous article, hers...@indiana.edu (howard hershey) says:

Quoting Dorit, I said:

"Any one of us can come up with multiple, plausible stories
concerning the evolution of any given biological feature."

>>>Note that he admits that *ANY* biological system can be accounted
>>>for by such story-telling. As I've always said, they tell us
>>>more about a person's ability to imagine than the natural world.

Howard replied:

>>Not if the stories have to be congruent with what we know about how
>>biological systems work.

I said:

>> If only this were true. Are cells with RNA genomes congruent
>> with what we know about how biological systems work? Nope.

Howard replies:

>The one-eyed man is king on the island of the blind. RNA genomes
>certainly can work for certain organisms.

Really? Perhaps Howard would provide the evidence behind his sense
of certainty. It better be *really* good since he is so certain and it
better not refer to viruses as I asked if "cells with RNA genomes" can
exist. So I'll sit back and wait for Howard to demonstrate that RNA
genomes "certainly can work" in cellular organisms.

>> Are cells that replicate their DNA genomes for thousands, maybe
>> millions years, with a semi-functional R-loop mechanism congruent
>> with what we know about how biological systems work? Who
>>knows?

>The one-eyed man is king on the island of the blind. Can you imagine
>that airlines ever flew prop planes? Sure props are still useful (and
>used) in small planes, but no current major airliner uses one to fly
>passengers. Unless you can show me an airline that currently uses prop
>planes, I will refuse to believe that any ever did or could. All you can
>point to is faked pictures and histories.

Wow. Howard likens the history of evolution to the history of intelligent
interventions. Of course, we have hard evidence that planes once used
prop engines (we don't know that the R-loop mechanism was once the
sole mechanism of replication). We also know that prop engines are
older than jet engines (we don't know this about the R-loop mechanism
and the oriC). We also know that jet engines were designed and
intelligence was employed not only in the design, but in the
implementation of jet engines as replacement of prop engines. Maybe
Howard's right. Maybe intelligent intervention was employed time and
time again in evolutionary history.

But the point remains that there is no evidence that cells can replicate
their DNA genomes for thousands, maybe millions or years, with a semi-
functional R-loop mechanism. Instead of employing airline analogies,
Howard should find modern bacteria that do solely employ such a
mechanism and this mechanism should be found in these bacteria's
lineage extending prior to the appearance of the oriC. Until then, my
point remains and the claim about original R-loop replication is nothing
more than an imaginary story (BTW, I will soon be posting on all this
DNA stuff in some detail).

So y'see, when Howard claims just-so stories have to be congruent with
what we know about biology, note how quickly the claim changes when
it comes to the actual just-so stories. What is congruent with what we
know about biology is that cells have DNA genomes and bacteria have
employed the oriC system since their last common ancestor. Howard's
point is that this doesn't mean this has always been true. Who could
argue with that? The point is not a "past must have been the same as
the present" claim. The point is that there is no evidence that cells ever
existed, or even could exist, in the way Howard and others imagine.
They may as well argue that cells didn't need a membrane in the past
and the current genetic code was simply one among hundreds that
existed once upon a time.

>> These just-so storied almost invariably postulate hypothetical
>> creatures with imaginary systems which show only how the author
>> is creative at pasting together different features of modern systems.
>> It's the modern version of inventing unicorns and mermaids.
>> But we usually haven't the foggiest notion if these imaginary
>> entities could indeed exist in a way that is congruent with what
>> we know about how biological systems work. Everytime a just-so
>> story is told at the molecular level, we end up talking about a sloppy,
>> unregulated, simple system when what we known about how those
>>biological systems work doesn't seem to support such a sloppy,
>>unregulated, simple state.

>Current enzymes have secondary activities.

Note how the current becomes the key to the past when it happens to
fit Howard's point. I could opt to take Howard's position and note that
just because the the current social security number has dozens of
applications must mean that it originally had all those other
applications, right?

Instead, I'll simply stick to the evidence. I have already outlined in
some detail (in my original article on DNA replication and IC) why citing
secondary activities is an insufficient response. For such a response to
have any meaningful impact, it must be specific and relevant.

>> You yourself have invoked DNA polymerases that could only replicate
>> 10-20 nucleotides in a tiny, little genome. But is this *life*?

>More so than what came before and less so than what came after.

This may be true in Howard's imagination. If only he could point to a
cellular organism that existed in reality. Then we might have some
reason to think something more than Howard's imagination was
involved.

Howard said:

>>As I pointed out in my review, I think that Behe is asking a different
>>question than he thinks he is asking. Behe is really asking "Why did
>>this system evolve?" or more accurately "What specific selective forces
>>were involved in the evolution of this
>>system?"

So I replied:

>> Which is the milk of Darwinism! You seem to forget that Behe's
>> problem is with *Darwinian* evolution and not simply evolution itself.

>No. Behe's problem is with *any* natural law explanation for evolution,
>not just natural selection.

Not true. I thought you read his book? Behe clearly notes that design
merely indicates intelligence. Do you think the application of
intelligence violates natural law? BTW, what *is* this thing you call
"natural law?"

>So when there is no direct evidence for a particular natural law
>mechanism, even though what evidence exists is compatible with
>known natural law mechanisms in terms of rate and amount of change
>needed (although there is often no evidence whatsoever - but science
>doesn't develop ideas from "I don't know how this happened." It
>develops it from "This mechanism works here. It could be responsible
>for this similar situation."), he asserts that the 'system' he describes
>cannot be done by natural selection. But he provides absolutely zero
>evidence that *any* system 'appeared' in an IC-specific mechanism
>rather than in an 'evolution by known natural law' mechanism.
>Specifically, no system is presented that convincingly argues for
>instantaneous construction or construction via useless intermediates
>(IC-specific mechanisms appear to be a null set, whereas evolution by
>natural law mechanism or indirect mechanism does not seem to be a
>null set).

These are nothing more than Howard's opinions. Maybe he convinced
himself with his vague explanation about the origin of cilia, but I found
it totally unconvincing.

>I have specifically described possible ways to support either IC-specific
>mechanism in the thread "Testing for IC-specific mechanisms".

Sure. Perhaps in the future I'll give it some serious attention. But as of
now, I do not think your ways are the only way.

>>>This last is potentially answerable by science, but in most
>>>cases we do not have sufficient evidence to do more than provide
>>>some reasonable inferences (a just-so story).

>> And as I said, it then looks like Darwinism and just-so stories are
>> joined at the hip. And whether or not they are "reasonable" is in the
>> eye of the beholder. Or shall we say it's "story-dependent?" ;)

>Science works from examples with the most evidence toward those
>with less. Are you saying that the usual description of the evolution of
>the hemoglobins is simply a just-so story unsupported by evidence?

No, so far I have been focusing on only a small subset of IC candidates.
And hemoglobin was not one of them.

>>Unfortunately, Behe also confounds this with the more teleological
>>(and ultimately unanswerable) question which also reads "Why did
>>this system evolve?" and answers that in the same way that old Bill
>>Paley does. The question Behe *claims* to be asking, "*How* could this
>>system evolve by natural law mechanisms?" can often actually *be*
>>answered.

>> Sure. As Dorit notes, "Anyone of us can come up with multiple,
>> plausible stories concerning the evolution of a given biological
>>feature." Big deal.

>And one can always say that the 'little green men' or gods did it. Only
>the evolutionary just-so stories are potentially falsifiable.

Really? Then fess up. How does one falsify the notion that cells once
had RNA genomes? How does one falsify the notion that cells once
existed with only the R-loop mechanism for initiating DNA replication?

>Perhaps you have an alternative mechanism to natural law mechanism
>for generating the IC systems?

Intelligent intervention. This mechanism is known to be quite capable
of generating IC systems. And with the current advances in molecular
genetics and biochemistry, we now know that intelligence can generate
biological IC systems.

>>The observed changes in genes and
>>proteins that are required to produce the current differences from
>>reasonable ancestral forms (typically by duplication and divergence,
>>sometimes by scrambling of protein motifs, often with considerable
>>neutral drift) are *congruent with* the idea that these differences
>>arose by natural selection (acting primarily in a conservative fashion)
>>acting on random mutations (the only kind of mutation that we have
>>ever observed) of various kinds, from duplication to point mutation
>>and neutral drift by fixation of random mutations.
>
>> As a criterion, congruency seems no better than plausibility. In fact,
>> what is the difference between the two?
>
>> Furthermore, I could likewise adopt such a standard. The notion that
>> certain IC systems are designed is congruent with the capabilities
>> of intelligence.

>Its also congruent with evolution by natural law mechanism.

Fine. As I've said, we simply see the same things differently. I have no
problem with this. Do you?

>>The way that you disprove the "How did this evolve?" question is by
>>either presenting a different observable and/or testable mechanism
>>by which it could occur

>> Intelligent intervention qualifies.

>So do 'little green men'.

Any intelligent entity would qualify. But there is no need to get ahead
of the data and start speculating on the identities of the designers.

>If you cannot see the problem with positing an intelligent designer
>every time you can't explain something, you do not have as firm a
>grasp on what science does as I think you do.

If you think I posit an intelligent designer every time I can't explain
something, you do not have even a loose grasp on what I think.

>Positing intelligent designers in the absence of positive evidence *for*
>same is cheap and worthless.

I don't agree. If SETI picked up a pattern that allowed others to infer
an intelligent cause, would you call this cheap and worthless because no
one has found other positive evidence of ETI?

>Of course, I am now positing an alien in some of my arguments with
>Peter (until April 1, 1998) so I can fully understand the pleasures of
>this particular scientifically worthless and simplistic argument.

Whatever.

>>>or by presenting evidence that the observed differences are too great
>>>to be accomplished in the time available by these *known* natural
>>>law mechanisms.

>>Sure. This would be very powerful evidence. But it is not needed.

>Then what evidence do you think you need to determine that
>something cannot possibly be produced by known natural law
>mechanisms? The fact that no one has yet produced such? The
>absence of evidence?

It seems that Howard, like so many others, needs to argue from a
position where their opponents must defend a claim that something
possibly could not happen.

>>>Answering this question does not require any attempt to
>>>describe which specific selective forces were at work. All it asks is
>>>whether the observed extent of changes can be due to known natural
>>>law mechanisms or not.

>>I see. So the design theorist must show that something CANNOT be
>>due to "natural law mechanisms." We're back to proving the
>>impossible. It doesn't matter (to me) if one can imagine just-so stories
>>congruent with "natural law mechanisms" that generate a system. It
>>doesn't matter (to me) if the system doesn't seem to violate any
>>"natural law mechanisms." What matters is whether the "natural law
>>mechanism" is the *best* explanation. Howard's whole argument
>>appears to be a needlessly complicated way of saying, "If an
>>explanation doesn't violate natural law mechanisms, it *is* the best
>>explanation" and, BTW, I'm using the term "natural law mechanisms"
>>to mean nonintelligent intervention. But that's not an argument - it's
>>an assertion.

>In science, natural law mechanisms are necessary.

But must they also be sufficient? Y'see, I do indeed employ natural law
mechanisms and from where I sit, they converge on design events.

[Keep in mind that I interpret Howard's term "natural law mechanisms"
to simply mean mechanisms without reference to any intelligent
intervention.]

>For an ID argument to be a scientific argument, you need to show that
>there is an absolute *necessity* for an ID if you cannot show evidence
>for the ID itself directly. Otherwise you are simply positing an IPU.

This is simply a mere assertion. I don't see any relationship between
IPU's and design. I do see a relationship between design and
intelligence.

>I do not think it impossible to show that some system appeared in a
>way that is absolutely incompatible with known natural law
>mechanisms of evolution (and certainly it is not impossible to describe
>a set of criteria that make the need for a new kind of mechanism
>necessary - see the thread "Testing for IC-specific mechanisms" for
>specific initial ideas based on the IC-ness property that all parts are
>necessary for function.

Good for Howard. I'm simply not interest in arguments about absolute
incompatibilities. IMHO, it's just Howard's back-door way of trying to get his
opponents to argue in a way where the "could-have-happened" world
becomes important again.

>>>So far, the clear answer is yes, all of the observed
>>>differences are within the range of changes over time that can be
>>>explained by known natural law mechanisms. There is no reason to
>>>propose unseen mechanisms.

>> Sure there is. Just because it *can* be vaguely explained in such
>>ways doesn't mean it *best* accounts for the system.

>Positing an alien (or god or IPU) is *always* an easy idea.

Why does Howard have this aversion to the word "intelligence?" And
while positing an intelligent cause is as easy as posting Howard's
"natural law mechanisms," a good deal of work is required to determine
which is the best explanation (especially when Howard et al. have the
luxury of simply reading someone else's opinions while us design folks
have to clear the table and essentially start from scratch).

>Aliens can explain it all (whatever 'it' is).

Then why don't I invoke intelligence to explain it all? Also, note that
Howard is acting like a good member of the pack. In his argument with
me, he's picked up Moran's "alien design" label.

>Unless you have evidence that 1) aliens actually exist and 2) actually
>go about designing systems and 3) actually did so in this case, your
>ideas are scientifically worthless.

Whatever It would be interesting to see if Howard sang the same song
if SETI pulled in a message.

>You cannot even do the simpler step of showing that the system
>appeared in an IC-specific fashion.

This is Howard's opinion. I think I have done this already with the oriC
system. Furthermore, there is no evidence to think the bacterial flagella
appeared in a non-IC way. It's IC everywhere we look and was most
likely IC in the last common ancestor.

>>> Look. As I see it, the molecular world of life is loaded with things
>>>that are quite unlike anything we see in the rest of nature. The
>>>closest analog to these things are our machines. If one doesn't have
>>>an aversion to proposing intelligent causation, one seeks to explore
>>> these strange similarities without a need to force them into
>>> a nonintelligent origin. Of course, I'm not saying that folks like
>>> Howard are rationally obligated to agree. Howard is satisfied with
>>> any explanation as long as it is congruent with "natural law
>>>mechanisms."

>Actually, for many of them, I am not satisfied, but forced to say that
>"We don't know because we have no clear evidence."

This would not be surprising if one has only two choices - I don't know
or "natural law mechanisms."

>Knowing that there are things you are ignorant of is the first step to
>knowledge.

But by golly, we gotta know ETI actually exists before we can proceed
wth design explanations, right?

>Positing an alien doesn't get you very far.

Especially if the alien is not intelligent. But I have begun to find that ID
does get me farther than I ever expected. Thus, don't make the mistake
of confusing your perceptions and opinions with statements of fact.

>> But I'm not. Because of my perceptions, because I "see" little

>>machines,I require something more than an explanation congruent

>>with "natural law mechanisms" to show that the analogy between

>>molecular machine and intelligently-derived machines is faulty at its

>>very core. As I have said again and again, we simply see the same
>>data differently.

>You have presented no evidence to support *any* alternative model of
>'development' of any system, IC or otherwise.

Again, this is Howard's opinion. I'm sure the Pack agrees, but I know
that others don't.

>You are just willing to say, I posit an alien" where I would say "We
>don't really know, but it is not an insurmountable problem for natural
>law mechanism."

Where did I say, "I posit an alien?" Besides, that you don't know about
the origin of a system not very relevant. No one "knows." You should
take your natural law mechanisms and come up with the best
explanation from within the confines of you assumptions. Is it *better*
than intelligent intervention?

For example, you pooh-poohed Behe's notion that the origin of cilia involved
intelligent intervention to account for its IC features. In it's
place, you offered digestive tract cells from multicellular organisms that
have rigid projections supported by tight bundles of actin filaments to
explain the origin of motile cilia employing loosely tied microtubules in
unicellular creatures. Why was this a *better* explanation than design?
Why is no explanation ("I don't know") a *better* explanation than
design? Simply because they don't invoke intelligent intervention??
Would intelligence be unable to generate cilia?

>> Thus, I'm more interested in determining if a truly
>> scientific approach under a design paradigm can be created that
>> interprets, and even illuminates, the workings and origin of these
>> machines. I'm not interested in convincing Howard or Larry or Matt,
>>etc., to join me in my approach.

>One can easily study the present functioning of systems without
>reference to their origin. That, of course, says nothing about their
>origin.

No, but you can infer Ur-IC from looking at various species. You can
then weigh explanations that invoke similar activities. If they are weak
and/or easily open to reinterpretation, then there is no longer a reason
to think such a system arose without intelligent intervention. But the IC
nature of the system has a cause. And given that intelligent
intervention is quite capable of generating IC systems, it appears to
some of us folks that design becomes the best explanation. Epecially
when they look so darned designed. ;)

>Aside from the ideas of testing whether there really is such a
>thing as a IC-specific mechanism of 'appearance' rather having it
>represent merely the null set steeped in the absence of evidence (the
>gaps in knowledge). AFAIK, no one has presented a 'system' which
>they can argue, from direct historical evidence, occured in an IC-
>specific fashion.

Yeah, like Howard has direct historical evidence that cells existed with
RNA genomes or once replicated their DNA solely with R-loop
mechanisms or cilia began as some type of microvillus or cells once used
DNA polymerases to replicate their genomes 10-20 nucleotides at a
time.

{snip}

>>> I'ld like some more foreknowledge about what the lack of plausible
>>> stories means. Just to round out the picture you see.
>
>> The lack of plausible stories can mean either one of two things:
>
>> 1. A lack in the story-teller due to lack of imagination and/or lack
>> of understanding at the moment. In other words, "we don't know"
>> may mean nothing more than "we don't know."
>
>> 2. The essence of the story is misguided, i.e., X didn't evolve.
>> If X didn't evolve, one might expect it would be hard to come up
>> with plausible stories, especially when they are so easy to invent.
>>(Note: X didn't evolve does not mean evolution never occurs).
>
>> Choosing between 1 and 2 is a judgment call,

I should have said this choice is a judgment call for folks like me. I
realize others cannot seriously consider option #2.

>If you have evidence that X actually occurred in a fashion that is
>incompatible with evolutionary principles (an IC-specific fashion), it
>wouldn't be a 'judgement call'.

No need to demonstrate impossibilities, absolute incompatibilities, etc.

>Absent that, it isn't a judgement call either. We have and can observe
>natural selection. It exists and can be tested. No one has observed the
>ID and it is untestable.

I think Howard has it backwards. Yes, we can observe natural selection.
But who has *observed* it to create an IC system like the bacterial
flagellum or DNA replication? But we have observed intelligent design
to create IC systems, including biological systems.

>> but if one's worldview
>> handicaps them into thinking #2 cannot be true, then there is no real
>> choice for them. As for me, I suspect it is because of #2. Thus,
>>I seek to flesh out an alternative approach. I may turn out to be
>> wrong. So what?

>So go ahead. Present the system with the best evidence that it
>appeared in an IC-specific fashion.

I've done this with the bacterial flagellum. I'm doing this with DNA
replication in bacteria. And I will soon begin with another system.

>Don't present systems where all you can do is assert that it is unlikely
>(in your opinion) that it occured by natural law so positing an alien is
>O.K.

Why is Howard so obsessed with controlling what I write? He can't
even get it straight about what I actually posit! ;)

[snip]

>>> Whoops there goes another irony-o-meter.
>>> The double standard you take to 'looks evolved' and 'looks designed'
>>> with respect to biological systems is so hard for me to understand.

>> Because there is no double-standard. Not to mention that this
>>paragraph says nothing about 'looks evolved' and 'looks designed.'

>Sure there is.

This is simply the shared perception of Howard and Wade.

>Unlike the ID, natural selection and the other natural law mechanisms
>for evolution have all been observed and tested in the
>present.

Cite the observations and tests which show how something like DNA
replication or the bacterial flagellum evolved via the "natural law
mechanisms."

>Where is the observable ID mechanism?

Visit a molecular biology lab.

>You weigh the two mechanisms as being equally likely explanations of
>natural events. That is a double standard.

Actually, I find it far more likely that intelligence generated the
systems of DNA replication and the bacterial flagella than whatever
unspecified nonintelligent events that lurk behind your "I don't know."
;)

Well, I have to get back to writing about more systems that appeared as
IC systems. Oh yeah, did it look like I was I kinda hard on Howard? If
so, don't worry. Howard has already asserted that I am unable to think
and can merely copy things from books.
--

Any one of us can come up with multiple, plausible stories concerning the

[Julie Thomas]

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

>In article <5vahh5$h...@alexander.INS.CWRU.Edu> iz...@cleveland.Freenet.Edu
>(Julie Thomas) writes:
>

>>Here's the recipe for making a just-so story. First, survey
>>the biological world for structures/functions. Find those
>>that seem useful for coming up with a precursor to the system
>>in question and patch them together without much regard for
>>biochemical and/or genetic details. Place the patchwork in
>>an imaginary creature from the distant past which has conveniently
>>gone extinct. Invoke a vague selective pressure that selects
>>for the patchwork and then imagine it is plastic and amenable
>>to further selective modification that just happens to arive
>>at the system in question.
>

>Julie, this reminds me that you haven't responded to my earlier posts
>on DNA replication.

Don't worry. But while we're at it, this reminds me that you haven't
responded to about 50% of the material in my earlier replies. And
it's been more than two months and I'm still waiting for you to
show me how the type III secretory system shows us how the bacterial
flagella evolved.

>I hope that your offensive description of a just-so story doesn't apply
>to what I have posted.

Oh boy. The man who accuses me of being dishonest because he thinks
he knows me better than I know myself is complaining about something
he finds "offensive?" And then he'll go on to accuse *me* of being
hypocritical? Not to mention that he claimed I argued evolution
could not happen and aliens must have designed things while also
claiming *I* lacked reading comprehension. Go figure.

[Laurence A. Moran]

In article <5vi5lv$j...@alexander.INS.CWRU.Edu> iz...@cleveland.Freenet.Edu
(Julie Thomas) writes:

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

>>Julie, this reminds me that you haven't responded to my earlier posts
>>on DNA replication.
>
>Don't worry. But while we're at it, this reminds me that you haven't
>responded to about 50% of the material in my earlier replies. And
>it's been more than two months and I'm still waiting for you to
>show me how the type III secretory system shows us how the bacterial
>flagella evolved.

If you are referring to the second half of your original essay on DNA
replication then you are correct. I'm not sure I'll ever get to it.

As for bacterial flagella I don't intend to engage you on that topic. It
would require more work than I have time for.

>>I hope that your offensive description of a just-so story doesn't apply
>>to what I have posted.
>
>Oh boy. The man who accuses me of being dishonest because he thinks
>he knows me better than I know myself is complaining about something
>he finds "offensive?"

Earlier you stated that my reference to "alien design" was offensive so
I stopped using it. I still believe that your philosophical (religious)
position is relevant to the discussion. But in any case what is your point?
Do you think it's okay to use the offensive term "just so story" because
others offend you? Would you please answer the implied question. Does
your description of a "just so story" apply to the things I have posted
on DNA replication.

> And then he'll go on to accuse *me* of being
>hypocritical? Not to mention that he claimed I argued evolution
>could not happen and aliens must have designed things while also
>claiming *I* lacked reading comprehension. Go figure.

Why are you avoiding the question? Do you think that a counter-attack
will cover up for your inability to address the issue?

Do you have a problem with reading comprehension? (-:

(For the record, I maintain that Julie's main agrument for intelligent
design is that the evolution of a DNA replication system could not have
happened. I supported my claim with quotations from Julie's essay.
Anyone who takes the time to read the essay will see that she talks
mostly about the improbability of an evolutionary explanation. She
refers to such explanations disparagingly as "just so stories". So
Julie is correct on this point. I can't imagine why she denies that
she is arguing against evolution.)

Larry Moran

[jeff wiel]

howard hershey (hers...@indiana.edu) wrote:
[supersize snip]
: Not until you show me what is wrong with my 'aliens created bats'
: argument.

: Just because you can make up a just so story about bats based on little
: evidence doesn't mean my 'aliens did it' arguement is wrong. Bats
: clearly are IC. There is no transitional fossil of any relevance
: (AFAIK) to intermediate states of bat wing. The final form of the wing
: has the 'function' of flight. Only a crumudgeon would mention the
: homology between the bones of the bat's wing and similar but different

: bones in the fingers of penquins. Unless you can show me every

: selective pressure that led to the two *in detail*, I will continue to
: call your argument 'starman Behe'. There just has to be an intelligent
: designer of bats.

This seems to be a reflux of the "what good is half a wing" argument. To
generalize, I ask what good is half of any organ? For instance, what good
is half an ass? Now, partial donkeys might, in fact, be useless, proving
the donkey to be IC, however, the preponderance of willfully stupid,
ignorant and risibly specious arguments from some parties on t.o leads me
to believe that half an ass is in fact used in their generation.

[PZ Myers]

In article <5vi5lv$j...@alexander.INS.CWRU.Edu>, iz...@cleveland.Freenet.Edu
(Julie Thomas) wrote:

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

> >In article <5vahh5$h...@alexander.INS.CWRU.Edu> iz...@cleveland.Freenet.Edu
> >(Julie Thomas) writes:
> >

> >>Here's the recipe for making a just-so story. First, survey
> >>the biological world for structures/functions. Find those
> >>that seem useful for coming up with a precursor to the system
> >>in question and patch them together without much regard for
> >>biochemical and/or genetic details. Place the patchwork in
> >>an imaginary creature from the distant past which has conveniently
> >>gone extinct. Invoke a vague selective pressure that selects
> >>for the patchwork and then imagine it is plastic and amenable
> >>to further selective modification that just happens to arive
> >>at the system in question.
> >

> >Julie, this reminds me that you haven't responded to my earlier posts
> >on DNA replication.
>
> Don't worry. But while we're at it, this reminds me that you haven't
> responded to about 50% of the material in my earlier replies. And
> it's been more than two months and I'm still waiting for you to
> show me how the type III secretory system shows us how the bacterial
> flagella evolved.
>

> >I hope that your offensive description of a just-so story doesn't apply
> >to what I have posted.
>
> Oh boy. The man who accuses me of being dishonest because he thinks
> he knows me better than I know myself is complaining about something

> he finds "offensive?" And then he'll go on to accuse *me* of being

> hypocritical? Not to mention that he claimed I argued evolution
> could not happen and aliens must have designed things while also
> claiming *I* lacked reading comprehension. Go figure.

No, he claimed, as I have claimed, that the basis of your argument
is that certain, specific features of eukaryotes did not evolve, but
were "designed", a vague and unspecified process that may or may not
have been carried out by aliens.

If you disagree with that assessment, how about giving us an equally
succinct but accurate summary of your position, rather than just
saying "Did not!"

[howard hershey]

Julie Thomas wrote:
>
> In a previous article, hers...@indiana.edu (howard hershey) says:

[snip]

>
> >The one-eyed man is king on the island of the blind. Can you imagine
> >that airlines ever flew prop planes? Sure props are still useful (and
> >used) in small planes, but no current major airliner uses one to fly
> >passengers. Unless you can show me an airline that currently uses prop
> >planes, I will refuse to believe that any ever did or could. All you can
> >point to is faked pictures and histories.
>
> Wow. Howard likens the history of evolution to the history of intelligent
> interventions. Of course, we have hard evidence that planes once used
> prop engines (we don't know that the R-loop mechanism was once the
> sole mechanism of replication). We also know that prop engines are
> older than jet engines (we don't know this about the R-loop mechanism
> and the oriC). We also know that jet engines were designed and
> intelligence was employed not only in the design, but in the
> implementation of jet engines as replacement of prop engines. Maybe
> Howard's right. Maybe intelligent intervention was employed time and
> time again in evolutionary history.

Either you are very dense about the uses and misuses of analogy (which I
doubt) or you know that point of the analogy is that without evidence of
history, one cannot use a description of current systems to imply much
of anything about the past. All modern jetliners use jet engines (a
fact close enough to all cells use DNA for our purposes). Some much
smaller current planes use props (also a fact close enough to some
viruses using RNA for purposes of our analogy). Both propulsion systems
can be used for flight (just as both DNA and RNA can be used as genetic
material). When I ask the question of how the design of airplanes
evolved over time from the first airplane, I cannot limit myself to the
possiblity that only jets were used in large planes because all present
planes have jets. There are multiple possible explanations at this
point, absent any historical information: Independent (polyphyletic)
design with props for some small planes and jets for large ones and some
small ones. Design of initial planes with jets with the small prop
planes being a secondary modification or specialization. Design of the
initial planes as prop driven with jets being a more modern innovation
and props being a vestigial design used in particular vestigial
environments. If there is no direct evidence, one is, of course, left
with speculation or 'just-so' stories. One can argue for or against one
of these possibilities, but, absent evidence, you cannot build a
convincing case. That said, the *least likely* explanation is that
large passenger jets arose instantaneously without previous
experimentation with smaller planes of either the jet or prop variety on
the basis that most human designs initially involve experimentation with
smaller scale machines first (a human design principle that can be
observed in new designs humans make in the observable present) to work
out the design bugs before moving on to experiment with larger more
expensive ones. So saying that passenger jets had to always use jets
because you cannot find a single large prop passenger jet being made at
the present time does not impress me as being a useful way to decide
what the history of passenger planes was like. Now, if you had some
evidence that jet plane construction were to be impossible at the time
that the first plane was constructed (perhaps evidence that it was
composed of materials that would fall apart under jet propulsion), you
might infer that the first plane used props and that jets came later.
But it would just be a 'just-so' story.

>
> But the point remains that there is no evidence that cells can replicate
> their DNA genomes for thousands, maybe millions or years, with a semi-
> functional R-loop mechanism. Instead of employing airline analogies,
> Howard should find modern bacteria that do solely employ such a
> mechanism and this mechanism should be found in these bacteria's
> lineage extending prior to the appearance of the oriC. Until then, my
> point remains and the claim about original R-loop replication is nothing
> more than an imaginary story (BTW, I will soon be posting on all this
> DNA stuff in some detail).
>
> So y'see, when Howard claims just-so stories have to be congruent with
> what we know about biology, note how quickly the claim changes when
> it comes to the actual just-so stories. What is congruent with what we
> know about biology is that cells have DNA genomes and bacteria have
> employed the oriC system since their last common ancestor. Howard's
> point is that this doesn't mean this has always been true. Who could
> argue with that? The point is not a "past must have been the same as
> the present" claim. The point is that there is no evidence that cells ever
> existed, or even could exist, in the way Howard and others imagine.

And I fully agree. Of course, you have no evidence that they were
always the same either (and looking at living organisms, change doesn't
seem to be impossible for living organisms).

> They may as well argue that cells didn't need a membrane in the past
> and the current genetic code was simply one among hundreds that
> existed once upon a time.

[snip]

>
> >Current enzymes have secondary activities.
>
> Note how the current becomes the key to the past when it happens to
> fit Howard's point. I could opt to take Howard's position and note that
> just because the the current social security number has dozens of
> applications must mean that it originally had all those other
> applications, right?

Are you saying that enzymes in the past didn't have secondary
activities? That is a general property of enzymes. I see no reason to
think enzymes in the past were different. DnaA, for example is active
in transcription as well as replication.

>
> Instead, I'll simply stick to the evidence. I have already outlined in
> some detail (in my original article on DNA replication and IC) why citing
> secondary activities is an insufficient response. For such a response to
> have any meaningful impact, it must be specific and relevant.
>

[snip]

>
> So I replied:
>
> >> Which is the milk of Darwinism! You seem to forget that Behe's
> >> problem is with *Darwinian* evolution and not simply evolution itself.
>
> >No. Behe's problem is with *any* natural law explanation for evolution,
> >not just natural selection.
>
> Not true. I thought you read his book? Behe clearly notes that design
> merely indicates intelligence. Do you think the application of
> intelligence violates natural law? BTW, what *is* this thing you call
> "natural law?"

So Behe is positing a 'natural law' alien which is indistinguishable in
its visibility to a 'supernatural' intelligence. Big deal. Call me
when he has some evidence that the evolution of IC systems occur in an
IC-specific way that requires an alien.

> >So when there is no direct evidence for a particular natural law
> >mechanism, even though what evidence exists is compatible with
> >known natural law mechanisms in terms of rate and amount of change
> >needed (although there is often no evidence whatsoever - but science
> >doesn't develop ideas from "I don't know how this happened." It
> >develops it from "This mechanism works here. It could be responsible
> >for this similar situation."), he asserts that the 'system' he describes
> >cannot be done by natural selection. But he provides absolutely zero
> >evidence that *any* system 'appeared' in an IC-specific mechanism
> >rather than in an 'evolution by known natural law' mechanism.
> >Specifically, no system is presented that convincingly argues for
> >instantaneous construction or construction via useless intermediates
> >(IC-specific mechanisms appear to be a null set, whereas evolution by
> >natural law mechanism or indirect mechanism does not seem to be a
> >null set).
>
> These are nothing more than Howard's opinions. Maybe he convinced
> himself with his vague explanation about the origin of cilia, but I found
> it totally unconvincing.

As do I. I found it vague, sketchy, and not fleshed out. But that is
all the evidence allows. And the fully fleshed out IC description
is...posit an alien or ID and let him/her/it/them do it in
his/her/its/their mysterious ways.

So, exactly what does it mean for a system to 'appear' in an IC-specific
fashion if not either all at once or via useless intermediate stages?
Is that my opinion alone? I remember reading exactly those ideas in the
extremely limited discussion Behe presents on how IC-ness could occur in
ways contrary to standard evolution. What evidence does Behe provide
that any system arose in an IC-specific way? What about you?

>
> >I have specifically described possible ways to support either IC-specific
> >mechanism in the thread "Testing for IC-specific mechanisms".
>
> Sure. Perhaps in the future I'll give it some serious attention. But as of
> now, I do not think your ways are the only way.

Then is yours simply more recitation of the details of some current
system in a non-comparative or comparative only within limits way
followed by the assertion that you can't imagine how this could evolve
and the dare to anyone to present a 'just-so' story for you to knock
down (without presenting *any* explanation of your own)? How does that
develop the evidence *for* IC-ness as a mechanism that differs from
evolution? But if you have a better way of testing the reality of
IC-ness as something having a real impact in evolution, please do tell.
I am perfectly willing to listen to that type of evidence.

>
> >>>This last is potentially answerable by science, but in most
> >>>cases we do not have sufficient evidence to do more than provide
> >>>some reasonable inferences (a just-so story).
>
> >> And as I said, it then looks like Darwinism and just-so stories are
> >> joined at the hip. And whether or not they are "reasonable" is in the
> >> eye of the beholder. Or shall we say it's "story-dependent?" ;)
>
> >Science works from examples with the most evidence toward those
> >with less. Are you saying that the usual description of the evolution of
> >the hemoglobins is simply a just-so story unsupported by evidence?
>
> No, so far I have been focusing on only a small subset of IC candidates.
> And hemoglobin was not one of them.

I wonder why? Too much evidence? Again science works from examples
with the most evidence toward those with little, not the other way
around. There are always examples where the answer is "We really don't
know."
>
[snip]

>
> Really? Then fess up. How does one falsify the notion that cells once
> had RNA genomes? How does one falsify the notion that cells once
> existed with only the R-loop mechanism for initiating DNA replication?

One reason why these should be taken with a large grain of salt. I only
present them because I was asked to come up with one compatible with
evolution. I would be perfectly willing

>
> >Perhaps you have an alternative mechanism to natural law mechanism
> >for generating the IC systems?
>
> Intelligent intervention. This mechanism is known to be quite capable
> of generating IC systems. And with the current advances in molecular
> genetics and biochemistry, we now know that intelligence can generate
> biological IC systems.

So you posit an alien (ID). Do you have any evidence for same? How did
this intelligent intervenor work? If he/she/it/they worked by a
mechanism indistinguishable from evolutionary mechanisms, fine, no
problem. I can certainly live with even a supernatural God that evolves
life and its mechanisms by natural law means. After all, even Behe
admits that IC systems *can* evolve, if only indirectly. OTOH, if
he/she/it/they worked by some other mechanism (like one of the two
IC-specific mechanisms I specified), then we would have a problem. I
would have to see some evidence that some system somewhere actually did
appear by one of these mechanisms.

>
> >>The observed changes in genes and
> >>proteins that are required to produce the current differences from
> >>reasonable ancestral forms (typically by duplication and divergence,
> >>sometimes by scrambling of protein motifs, often with considerable
> >>neutral drift) are *congruent with* the idea that these differences
> >>arose by natural selection (acting primarily in a conservative fashion)
> >>acting on random mutations (the only kind of mutation that we have
> >>ever observed) of various kinds, from duplication to point mutation
> >>and neutral drift by fixation of random mutations.
> >
> >> As a criterion, congruency seems no better than plausibility. In fact,
> >> what is the difference between the two?
> >
> >> Furthermore, I could likewise adopt such a standard. The notion that
> >> certain IC systems are designed is congruent with the capabilities
> >> of intelligence.
>
> >Its also congruent with evolution by natural law mechanism.
>
> Fine. As I've said, we simply see the same things differently. I have no
> problem with this. Do you?

Sure. For all the systems where I would say, "We have no evidence, but I
think we should apply known natural law mechanisms that explain systems
where more evidence exists." you would say, "We have no evidence, so I
will posit that it was done by alien intelligences for which I also have
no evidence." I can live with that.

> >>The way that you disprove the "How did this evolve?" question is by
> >>either presenting a different observable and/or testable mechanism
> >>by which it could occur
>
> >> Intelligent intervention qualifies.
>
> >So do 'little green men'.
>
> Any intelligent entity would qualify.

No. You need an intelligent entity that existed at the proper time and
place and with the skills to do the job.

> But there is no need to get ahead
> of the data and start speculating on the identities of the designers.

About evidence that they existed? Positing an invisible ID to explain
events is cheap.

>
> >If you cannot see the problem with positing an intelligent designer
> >every time you can't explain something, you do not have as firm a
> >grasp on what science does as I think you do.
>
> If you think I posit an intelligent designer every time I can't explain
> something, you do not have even a loose grasp on what I think.
>
> >Positing intelligent designers in the absence of positive evidence *for*
> >same is cheap and worthless.
>
> I don't agree. If SETI picked up a pattern that allowed others to infer
> an intelligent cause, would you call this cheap and worthless because no
> one has found other positive evidence of ETI?

And you don't even have that much evidence.
[snip stuff better reponded to when Julie discusses ideas on how to test
for IC-specific mechanisms]

>
> >Unless you have evidence that 1) aliens actually exist and 2) actually
> >go about designing systems and 3) actually did so in this case, your
> >ideas are scientifically worthless.
>
> Whatever It would be interesting to see if Howard sang the same song
> if SETI pulled in a message.

Then you would have some evidence that aliens actually exist.

>
> >You cannot even do the simpler step of showing that the system
> >appeared in an IC-specific fashion.

[snip]

>
> >Actually, for many of them, I am not satisfied, but forced to say that
> >"We don't know because we have no clear evidence."
>
> This would not be surprising if one has only two choices - I don't know
> or "natural law mechanisms."

Again, "I don't know" is better than "First, we posit an ID" when there
is no independent evidence for even the existence of IDs at the right
time and place.

>
> >Knowing that there are things you are ignorant of is the first step to
> >knowledge.
>
> But by golly, we gotta know ETI actually exists before we can proceed
> wth design explanations, right?

It sure would help ground design explanations in reality. But if you
can show that IC-systems appear by IC-specific mechanisms, you would
also be in a better position to infer that, at the very least, there are
natural law mechanisms that we don't know about.

>
> >Positing an alien doesn't get you very far.
>
> Especially if the alien is not intelligent. But I have begun to find that ID
> does get me farther than I ever expected. Thus, don't make the mistake
> of confusing your perceptions and opinions with statements of fact.

I am assuming an (increasingly hypothetical) alien intelligent enough to
do what you want him/her/it/them to do at the time and place you need it
done.

>
> >> But I'm not. Because of my perceptions, because I "see" little
> >>machines,I require something more than an explanation congruent
> >>with "natural law mechanisms" to show that the analogy between
> >>molecular machine and intelligently-derived machines is faulty at its
> >>very core. As I have said again and again, we simply see the same
> >>data differently.
>
> >You have presented no evidence to support *any* alternative model of
> >'development' of any system, IC or otherwise.
>
> Again, this is Howard's opinion. I'm sure the Pack agrees, but I know
> that others don't.

All you have done is describe a current system, assert that it is
unlikely to have evolved and posit an ID to solve the problem that
arises from your assertion.

>
> >You are just willing to say, I posit an alien" where I would say "We
> >don't really know, but it is not an insurmountable problem for natural
> >law mechanism."
>
> Where did I say, "I posit an alien?" Besides, that you don't know about
> the origin of a system not very relevant. No one "knows." You should
> take your natural law mechanisms and come up with the best
> explanation from within the confines of you assumptions. Is it *better*
> than intelligent intervention?

Almost any natural law explanation is better than positing an invisible
ID to come down and perform magic by instantaneous creation or stepwise
via useless intermediates. Even supernaturally guided evolution (the
invisible hand) is better.

[snip]

>
> No, but you can infer Ur-IC from looking at various species. You can
> then weigh explanations that invoke similar activities. If they are weak
> and/or easily open to reinterpretation, then there is no longer a reason
> to think such a system arose without intelligent intervention. But the IC
> nature of the system has a cause. And given that intelligent
> intervention is quite capable of generating IC systems, it appears to
> some of us folks that design becomes the best explanation. Epecially
> when they look so darned designed. ;)

IOW, unless one can come up with a *really* good 'just-so' story for
producing something via natural law mechanisms, it is always better to
invoke an invisible designer for which we have zero evidence.
Appearance of design is, after all, sufficient evidence that it was
designed by an intelligence.

>
> {snip}
>
> >>> I'ld like some more foreknowledge about what the lack of plausible
> >>> stories means. Just to round out the picture you see.
> >
> >> The lack of plausible stories can mean either one of two things:
> >
> >> 1. A lack in the story-teller due to lack of imagination and/or lack
> >> of understanding at the moment. In other words, "we don't know"
> >> may mean nothing more than "we don't know."
> >
> >> 2. The essence of the story is misguided, i.e., X didn't evolve.
> >> If X didn't evolve, one might expect it would be hard to come up
> >> with plausible stories, especially when they are so easy to invent.
> >>(Note: X didn't evolve does not mean evolution never occurs).
> >
> >> Choosing between 1 and 2 is a judgment call,
>
> I should have said this choice is a judgment call for folks like me. I
> realize others cannot seriously consider option #2.

I certainly can consider possibility #2. But unless there is some
positive evidence for that particular 'just-not-so' explanation, #1 is
the only option (no judgement call). We don't know means 'we don't
know', not 'we have evidence that it wasn't evolution'. The latter is
one of the possible options included in 'we don't know'.

> >If you have evidence that X actually occurred in a fashion that is
> >incompatible with evolutionary principles (an IC-specific fashion), it
> >wouldn't be a 'judgement call'.
>
> No need to demonstrate impossibilities, absolute incompatibilities, etc.

I don't ask for that. I ask for more than a simple assertion that it is
unlikely to have occurred by evolution because it is an IC system.
Specifically, I ask for evidence that some system appeared via an
IC-specific mechanism.

>
> >Absent that, it isn't a judgement call either. We have and can observe
> >natural selection. It exists and can be tested. No one has observed the
> >ID and it is untestable.
>
> I think Howard has it backwards. Yes, we can observe natural selection.
> But who has *observed* it to create an IC system like the bacterial
> flagellum or DNA replication?

Systems with no evidence to support any mechanism, including IC-specific
ones.

> But we have observed intelligent design
> to create IC systems, including biological systems.

Sure. Now when you have humans around. But when the highest life form
was a bacteria (if that)?

>
> >> but if one's worldview
> >> handicaps them into thinking #2 cannot be true, then there is no real
> >> choice for them. As for me, I suspect it is because of #2. Thus,
> >> I seek to flesh out an alternative approach. I may turn out to be
> >> wrong. So what?

One does not leap from "I cannot come up with an evolutionary
explanation." immediately to "The ID did it." unless one *really* wants
to avoid saying "I don't know." or one has actual evidence that there
was an ID at the time and place capable of doing it. You cannot simply
posit one and think anyone will agree with you.

I think Peter would call this a "Shades of Gray Meltdown" or some such.

>
> [snip]
>
> >>> Whoops there goes another irony-o-meter.
> >>> The double standard you take to 'looks evolved' and 'looks designed'
> >>> with respect to biological systems is so hard for me to understand.
>
> >> Because there is no double-standard. Not to mention that this
> >>paragraph says nothing about 'looks evolved' and 'looks designed.'
>
> >Sure there is.
>
> This is simply the shared perception of Howard and Wade.
>
> >Unlike the ID, natural selection and the other natural law mechanisms
> >for evolution have all been observed and tested in the
> >present.
>
> Cite the observations and tests which show how something like DNA
> replication or the bacterial flagellum evolved via the "natural law
> mechanisms."

Irrelevant. The *mechanisms* of natural selection and drift et.al. have
been observed. *Any* explanation of DNA replication or bacterial
flagellum has to take these mechanisms into account. That no detailed
explanation for some particular system currently exists does not mean
that one can chuck all natural law explanations and posit an alien ID.

>
> >Where is the observable ID mechanism?
>
> Visit a molecular biology lab.

It would be more convincing if the molecular biology lab were imbedded
in the early Precambrian, unless you think time and place are
irrelevant.

>
> >You weigh the two mechanisms as being equally likely explanations of
> >natural events. That is a double standard.
>
> Actually, I find it far more likely that intelligence generated the
> systems of DNA replication and the bacterial flagella than whatever
> unspecified nonintelligent events that lurk behind your "I don't know."
> ;)

And the reason for this is what? Your gut feeling? Your evidence for
the existence of relatively highly intelligent organisms in the
Precambrian? Your distaste for natural selection? Your religious
belief in a Designer that does *not* work via natural law mechanisms
whenever you feel uncomfortable with that idea? [If someone were to ask
me, like they asked Haldane, what I thought about God, I would have to
say that He (She/It/They) has a decided preference for acting via
natural law mechanisms.]