Does evolution even have a mechanism?
Steven Carr
Dembski claims that in 'No Free Lunch' he attempts to quantify the
chance that a sequence of Darwinian steps can create a flagellum.
Does he do that? Or does he calculate the chance that a random
group of proteins can come together in one big step to create
a flagellum?
How can Demsbki claim that there is no proposed gradual Darwinian
mechanism which can lead to a flagellum and also claim that he can
quantify the probability of this proposed sequence of events? If he
has never seen it, how can he do maths on it?
Dembski still cries 'foul' that science rules out magic, simply because
there is no evidence that magic has occurred.
Jon Fleming
I haven't read NFL, but Richard Wein has, and he indicates that it's
just a slightly more sophisticated version of the tornado in a
junkyard; calculating the probability of an irrelevant scenario. From
<http://talkorigins.org/design/faqs/nfl/>:
"The only biological object to which Dembski applies his method is the
flagellum of the bacterium E. coli. First, he attempts to show that
the flagellum could not have arisen by Darwinian evolution, appealing
to a modified version of Michael Behe's argument from irreducible
complexity. However Dembski's argument suffers from the same
fundamental flaw as Behe's: he fails to allow for changes in the
function of a biological system as it evolves.
Since Dembski's method is supposed to be based on probability and he
has promised readers of his earlier work a probability calculation, he
proceeds to calculate a probability for the origin of the flagellum.
But this calculation is based on the assumption that the flagellum
arose suddenly, as an utterly random combination of proteins. The
calculation is elaborate but totally irrelevant, since no evolutionary
biologist proposes that complex biological systems appeared in this
way. In fact, this is the same straw man assumption frequently made by
Creationists in the past, and which has been likened to a Boeing 747
being assembled by a tornado blowing through a junkyard."
He justifies these claims later in the document, but it's somewhat
long for quoting here and is much easier to follow with the HTML
typography.
...
(change nospam to group to email)
zosdad
Larry Moran:
========
ID research problem: bacterial flagellum and type III secretory system
When I recently spoke at the University of Toronto, Larry Moran, a
molecular biologist on faculty there, claimed that the type III
secretory system (a type of pump) was an evolutionary precursor to the
bacterial flagellum. Larry, as many evolutionists, thinks that
co-optation is the way you get irreducibly complex systems like the
bacterial flagellum. Basically, systems targeted for other uses get
co-opted into systems with novel uses. In this way a pump supposedly
gets co-opted for use in a flagellum.
Now, it seems that there is an experiment that one can do to test the
co-optation hypothesis. There are about 40 or so genes needed to form
a bacterial flagellum. Of these 10 are homologous to the 10 genes
needed for the type III secretory system (the exact numbers are not
important, but that's what memory serves me).
It would therefore be interesting to take the 10 homologous genes for
the type III secretory system and substitute them for the
corresponding genes for the bacterial flagellum to see whether a
working flagellum results. Alternatively, one could take the
homologous genes for the bacterial flagellum and substitute them for
the corresponding genes for the type III secretory system to see
whether a working secretory system results.
CONJECTURE ON THE BASIS OF ID: In neither case will there be a
functioning system. These systems are too tightly specified and won't
tolerate the discrepancies between the homologues.
CONJECTURE ON THE BASIS OF DARWINIAN THEORY: It's likely that
functioning systems will result since homologous proteins should be
robust under substitution.
Such an experiment would not decisively confirm one theory over the
other. Still, it would provide epistemic support. Also, the fact that
such an experiment arises out of taking seriously the possibility of
design suggests that intelligent design itself needs to be taken
seriously as a research project. Mike Gene has argued as much also.
Finally, as a postscript, it's worth noting that the evolutionary
biology community is not clear which came from which, the flagellum
from the secretory system or vice versa. According to Nguyen L,
Paulsen IT, Tchieu J, Hueck CJ, Saier MH Jr. (Phylogenetic analyses of
the constituents of Type III protein secretion systems, J Mol
Microbiol Biotechnol 2000 Apr;2(2):125-44), the flagellum came first
based on phylogeny comparisons of sequences.
========
Now, I think his predictions/conjectures do not logically follow,
since homologous *does not* mean "similar enough to be substitutable",
that is a ridiculous straw man. There are cases where genes are
substitutable (e.g. the eyeless gene in Drosophila and in mouse), and
AFAIK numerous other cases where they are not, particularly if the
genes *have changed function*, which almost by definition means that
they wouldn't be substitutable.
That said...even with the above caveat about Dembski demanding
something that doesn't necessarily follow from common descent &
homology...I do seem to recall a rather close relationship between
flagellation and virulence factor secretion in certain bacteria...
nic
PS: Did Moran actually argue that flagella descended from *currently
known* type III secretion systems, which AFAIK are all (a) eukaryotic
virulence systems and therefore (b) must postdate the origin of
eukaryotes which plus (c) they are apparently phylogenetically
restricted compared to flagella therefore (d) *currently known* type
III virulence systems are descended from, rather than ancestral to,
flagella. It seems to me that given the strong bias science has
towards research on disease organisms, this isn't shocking, and we can
hypothesize a more basal type III transport system with a function
useful in a prokaryote-only world...
zosdad
> Check out this latest bit from Dembski, it may intrigue such folks as
> Larry Moran:
>
> ========
> ID research problem: bacterial flagellum and type III secretory system
The reference is the ISCID discussion board, here's the link which I
forgot:
http://www.iscid.org/ubb/ultimatebb.php?ubb=get_topic;f=6;t=000079
> type III secretion systems, which AFAIK are all (a) eukaryotic
> virulence systems
To clarify regarding Type III secretion systems, I meant to say that
all published examples of which I am aware are *in* eubacteria and are
used *for* attacking eukaryotic cells (e.g., humans are attacked by
the eubacterial disease plague, aka Yersinia pestis, which uses a Type
III secretion system to attack eukaryotic cells, etc.), which is what
I was trying to say with "eukaryotic virulence systems".
nic
Drearash
>From: niiic...@yahoo.com (zosdad)
>Date: 5/7/02 9:46 PM Eastern Daylight Time
>Message-id: <74227462.02050...@posting.google.com>
>
>niiic...@yahoo.com (zosdad) wrote in message
>news:<74227462.02050...@posting.google.com>...
>> Check out this latest bit from Dembski, it may intrigue such folks as
>> Larry Moran:
>>
>> ========
>> ID research problem: bacterial flagellum and type III secretory system
>
>The reference is the ISCID discussion board, here's the link which I
>forgot:
>
>http://www.iscid.org/ubb/ultimatebb.php?ubb=get_topic;f=6;t=000079
>
Add Dembski to the list of those who do not understand the concept of homology,
as indicated by his proposed experimental test. Homologous does not mean
identical or even homofunctional (I made up that last word).
Von Smith
Fortuna nimis dat multis, satis nulli.
<snip>
Laurence A. Moran
In article <74227462.02050...@posting.google.com> nic writes:
>Check out this latest bit from Dembski, it may intrigue such folks as
>Larry Moran:
You certainly got MY attention!
>========
>ID research problem: bacterial flagellum and type III secretory system
This was posted on the "International Society for Complexity, Information
and Design Forum" ....
http://www.iscid.org/ubb/ultimatebb.php?ubb=get_topic;f=6;t=000079
This is a moderated forum. Criticism of design isn't welcome. Criticism
of evolution is a requirement.
>When I recently spoke at the University of Toronto, Larry Moran, a
>molecular biologist on faculty there, claimed that the type III
>secretory system (a type of pump) was an evolutionary precursor to the
>bacterial flagellum. Larry, as many evolutionists, thinks that
>co-optation is the way you get irreducibly complex systems like the
>bacterial flagellum. Basically, systems targeted for other uses get
>co-opted into systems with novel uses. In this way a pump supposedly
>gets co-opted for use in a flagellum.
Dembski presented his standard talk to a group of Christian academics who
invited him to Toronto. His main point was that there were major flaws in
our understanding of evolution. He spent most of his time attacking the
concept of biological information. He proposed an explanation of how life
came to be based on engineering/design principles with lots of hand-waving
about information theory. His talk was notably deficient in real biology.
In fact, the only significant example he mentioned was the bacterial
flagellum. Dembski claimed that flagella are irreducibly complex and
couldn't have arisen by naturalistic means (i.e. evolution). He clearly
implied that this was a major problem for "Darwinists" but could easily
be explained if flagella were created de novo by God.
During the question period I pointed out that there wasn't much biology
in Dembski's talk. I said that this was a surprise since he was attacking
biology. On the other hand, it was understandable since Dembski is not
an expert in biology. Dembski relies on others, especially Michael Behe,
to find potential problems with standard evolutionary explanations. I'm
pretty sure that Dembski was upset with me for suggesting that he didn't
know much about biology. He doesn't think it's fair to publicly expose
his lack of training in the science that he criticizes.
I also pointed out that there are reasonable explanations of the evolution
of bacterial flagella. I asked Dembski why he didn't reveal these
explanations to his audience since real scientists would always present
the other side of the story.
A member of the audience shouted out that perhaps *I* should explain how
flagella evolved. I replied that I didn't have time to do this in detail
but the best evidence suggested that flagella arose from a primitive type
III secretory apparatus.
Before I discuss Dembski's comments let's make certain that we don't lose
sight of the main point. Dembski and Behe claim that bacterial flagella
are irreducubly complex and there is no possible evolutionary mechanism
that can produce irreducibly complex systems. In other words, there is a
major flaw in "Darwinism" that can only be explained by postulating an
intelligent designer who makes irreducibly complex things.
Dembski now seems to be admiting that there IS a naturalistic explanation
of bacterial flagella. This is what I wanted him to do in his talk. He
now says that flagella could have evolved from primitive type III secretory
pores that were later co-opted to produce part of a propulsion mechanism.
It doesn't really matter whether we have a correct and detailed explanation
of the evolutionary history of flagella. The important point is that there
is a perfectly reasonable pathway to irreducibly complex systems such as
flagella. This pathway does not require intelligent designers. I expect
Dembski to mention this in all of his presentations from now on. He should
tell his audiences that "Darwinists" can explain the evolution of
irreducibly complex systems in many different ways. One of these ways is to
invoke a pathway that co-opts something that already had a function in a
primitive organism. Dembski should also admit that there are dozens and
dozens of well-known examples of such co-opting. (For example, wings
evolved from arms, sepals and petals evolved from leaves, lens crystallins
evolved from enzymes etc. etc.) It is no longer correct to claim that the
evolution of flagella is impossible. The best he can do is to criticize the
specific explanation(s) that scientists offer and explain why intelligent
design is a better explanation. (Of course, in order to explain why
intelligent design is a better explanation he'll actually have to describe
how the intelligent designer might have made bacterial flagella, and
when. I'm not holding my breath.)
>Now, it seems that there is an experiment that one can do to test the
>co-optation hypothesis. There are about 40 or so genes needed to form
>a bacterial flagellum. Of these 10 are homologous to the 10 genes
>needed for the type III secretory system (the exact numbers are not
>important, but that's what memory serves me).
The bacterial flagellum IS an example of a type III secretory mechanism.
During the formation of flagella the main membrane components form a pore
compex that eventually secretes the protein flagellin. The flagellin
proteins polymerize outside the cell to form the flagellum. The hypothesis
is that flagella arose by modification of a primitive type III secretion
system that was used to secrete a number of different proteins. The
data suggests that flagella evolved several billion years ago. Over time
one particular class of secretory pore came to specialize in secreting
flagellin and this flagellin polymerized on the outer surface of the
pore to form the flagellum.
The way in which flagella form in modern bacteria is a reflection of the
way they evolved in the first place. The first part of the structure to
form is the export mechanism. This is followed by export of flagellin and
formation of the flagellum. The original pore becomes the support and motor
once it's finished its job of secreting flagellin. The key proteins of the
export apparatus (type III secretory pore) in flagella are homologous to
proteins in modern examples of export complexes. This is further evidence
that secretion pores and parts of the flagellum share a common ancestor.
>It would therefore be interesting to take the 10 homologous genes for
>the type III secretory system and substitute them for the
>corresponding genes for the bacterial flagellum to see whether a
>working flagellum results. Alternatively, one could take the
>homologous genes for the bacterial flagellum and substitute them for
>the corresponding genes for the type III secretory system to see
>whether a working secretory system results.
This would be a fun experiment.
>CONJECTURE ON THE BASIS OF ID: In neither case will there be a
>functioning system. These systems are too tightly specified and won't
>tolerate the discrepancies between the homologues.
Interesting. If we can substitute proteins from other type III secretory
systems then intelligent design is disproven. Anyone want to bet that this
test will be ignored once the experiment is done?
>CONJECTURE ON THE BASIS OF DARWINIAN THEORY: It's likely that
>functioning systems will result since homologous proteins should be
>robust under substitution.
I can't evaluate this one since I don't know of any Darwinian Theory that
says any such thing.
Dembski forgot a third possibility ....
CONJECTURE ON THE BASIS OF UNDERSTANDING BIOLOGY: It may be possible to
substitute homologous proteins from different type III secretory complexes.
On the other hand, they may not be able to substitute.
>Such an experiment would not decisively confirm one theory over the
>other. Still, it would provide epistemic support. Also, the fact that
>such an experiment arises out of taking seriously the possibility of
>design suggests that intelligent design itself needs to be taken
>seriously as a research project. Mike Gene has argued as much also.
This is crazy. Nobody is taking seriously the possibility of design.
Dembski is simply saying that if the experiment doesn't work then the
negative result supports design. If he really wants to be taken seriously
as a biologist then he'd better be thinking of experiments to find the
intelligent designer. At the very least, he could give us some idea of
how and when this designer created bacterial flagella. How many genes were
created in the initial design? Which ones? When did it happen? Were
different flagella made in different species or did the designer just make
one type in one species and the rest arose by evolution? Why did the
designer decide to make flagella but not other molecular machines that
have an obvious evolutionary history?
>Finally, as a postscript, it's worth noting that the evolutionary
>biology community is not clear which came from which, the flagellum
>from the secretory system or vice versa. According to Nguyen L,
>Paulsen IT, Tchieu J, Hueck CJ, Saier MH Jr. (Phylogenetic analyses of
>the constituents of Type III protein secretion systems, J Mol
>Microbiol Biotechnol 2000 Apr;2(2):125-44), the flagellum came first
>based on phylogeny comparisons of sequences.
The idea that flagella might have evolved from a primitive secretory
apparatus does not mean that modern type III secretion of virulance factors
has to represent the direct descendant of this primitive apparatus. I don't
really care whether all other modern type III secretion systems are derived
secondarily from flagella or whether they are direct descendants of the
primitive secretion system. In either case, the similarity between the
export system in flagella biogeneisis and other secretion systems seems
compelling. What we're trying to do is offer a reasonable mechanism for the
evolution of irreducible complexity. Such reasonable explanations exist and
they rely on well-known principles of biology such as evolving a new
function from something that had another function. The evolutionary
explanations are at least as reasonable as postulating an intelligent
designer who created a few complicated structures from time to time.
>======== END OF DEMBSKSI QUOTE
>Now, I think his predictions/conjectures do not logically follow,
>since homologous *does not* mean "similar enough to be substitutable",
>that is a ridiculous straw man. There are cases where genes are
>substitutable (e.g. the eyeless gene in Drosophila and in mouse), and
>AFAIK numerous other cases where they are not, particularly if the
>genes *have changed function*, which almost by definition means that
>they wouldn't be substitutable.
I agree. But note that Dembski seems to be putting intelligent design on
the line by suggesting that if the genes could substitute then intelligent
design might be falsified!
>That said...even with the above caveat about Dembski demanding
>something that doesn't necessarily follow from common descent &
>homology...I do seem to recall a rather close relationship between
>flagellation and virulence factor secretion in certain bacteria...
>
>nic
>PS: Did Moran actually argue that flagella descended from *currently
>known* type III secretion systems,
Of course not.
>which AFAIK are all (a) eukaryotic virulence systems and therefore
>(b) must postdate the origin of eukaryotes which plus (c) they are
>apparently phylogenetically restricted compared to flagella therefore
>(d) *currently known* type III virulence systems are descended from,
>rather than ancestral to, flagella.
The export system involved in flagellum biogenesis IS a type III secretory
mechanism. As you point out, the other well-known type III secretory
complexes are associated with the export of virulence proteins in pathogenic
bacteria. These specialized protein export complexes could have evolved
from the type III secretion system of flagella.
>It seems to me that given the strong bias science has
>towards research on disease organisms, this isn't shocking, and we can
>hypothesize a more basal type III transport system with a function
>useful in a prokaryote-only world...
It wouldn't surprise me either to find other type III systems that have
nothing to do with flagella or virulance factors. Let's not forget that
this discussion about which came first has nothing to do with the
postulated evolution of irreducibly complex flagella from a primitive
protein secretion complex.
Larry Moran
David Jensen
lam...@bioinfo.med.utoronto.ca (Laurence A. Moran) wrote in
<abbv9q$24f8$1...@bioinfo.med.utoronto.ca>:
You'll turn Dembski into a scientist yet, Larry.
pz
David Jensen <da...@dajensen-family.com> wrote:
> On Wed, 8 May 2002 19:49:20 +0000 (UTC), in talk.origins
> lam...@bioinfo.med.utoronto.ca (Laurence A. Moran) wrote in
> <abbv9q$24f8$1...@bioinfo.med.utoronto.ca>:
>
>
> >
> >In article <74227462.02050...@posting.google.com> nic writes:
> >
> >>Check out this latest bit from Dembski, it may intrigue such folks as
> >>Larry Moran:
> >
> >You certainly got MY attention!
> >
> >>========
> >>ID research problem: bacterial flagellum and type III secretory system
> >
> >This was posted on the "International Society for Complexity, Information
> >and Design Forum" ....
> >
> >http://www.iscid.org/ubb/ultimatebb.php?ubb=get_topic;f=6;t=000079
> >
I think Larry ought to post his reply to ISCID. Maybe he could win the
$100 prize!
[snip]
--
pz
John Wilkins
worth capturing for posterity, not least because Larry has really hit
hard at Dembski's foundations.
--
John Wilkins
Occasionally making sense
Dunk
Wilkins) wrote:
>I know I've already nominated a POTM, but this little exchange seems
>worth capturing for posterity, not least because Larry has really hit
>hard at Dembski's foundations.
Dembski has foundations?
I thought of nominating this one a little earlier, but I knew someone
would soon do it. It has been said that Larry should be excluded from
POTM to leave room for others, but in this case I second the
nomination.
Dunk
John Wilkins
Perhaps we should stipulate that any Larry post that exceed, say, 50
lines should automatically become a FAQ...
--
John Wilkins
Occasionally entertaining others
Marty Fouts
pdu...@paleblue.net (Dunk) writes:
I suggest a POTM hall of fame. I nominate Larry as the first
inductee.
cats...@yahoo.com
Wilkins) wrote:
>I know I've already nominated a POTM, but this little exchange seems
>worth capturing for posterity, not least because Larry has really hit
>hard at Dembski's foundations.
[snip Larry's excellent adventure]
>--
>John Wilkins
>Occasionally making sense
>
FWIW, I agree and . . . uh . . . third the nomination, I think.
---------------
J. Pieret
---------------
EGOTIST, n.
A person of low taste, more interested in himself than in me.
- Ambrose Bierce -
Laurence A. Moran
It would never be posted. You aren't allowed to criticize anyone in
the intelligent design community. However, it's okay to say that
evolutionists are incompetent.
Larry Moran
pz
They also get quite touchy if you dare to criticize their ideas.
> However, it's okay to say that evolutionists are incompetent.
Not to mention dishonest and conspiratorial.
--
pz
June
I think you should at least try to post. After all, he specifically
mentions you and your remarks as the basis of his post. If they won't
let *you* respond to his post, they would be even more exposed than they
are already wrt open and scientific debate.
Give it a shot.
--
My 2¢ ß-}
June
Andy Groves
<snip>
>
> >It would therefore be interesting to take the 10 homologous genes for
> >the type III secretory system and substitute them for the
> >corresponding genes for the bacterial flagellum to see whether a
> >working flagellum results. Alternatively, one could take the
> >homologous genes for the bacterial flagellum and substitute them for
> >the corresponding genes for the type III secretory system to see
> >whether a working secretory system results.
>
> This would be a fun experiment.
>
> >CONJECTURE ON THE BASIS OF ID: In neither case will there be a
> >functioning system. These systems are too tightly specified and won't
> >tolerate the discrepancies between the homologues.
>
> Interesting. If we can substitute proteins from other type III secretory
> systems then intelligent design is disproven. Anyone want to bet that this
> test will be ignored once the experiment is done?
I wonder what Dembski makes of experiments where mouse genes rescue
fly phenotypes. Oh wait, those molecular cascades aren't irreducibly
complex, are they?
> >CONJECTURE ON THE BASIS OF DARWINIAN THEORY: It's likely that
> >functioning systems will result since homologous proteins should be
> >robust under substitution.
>
> I can't evaluate this one since I don't know of any Darwinian Theory that
> says any such thing.
No, but it makes a lovely strawman argument.
Andy
zosdad
When is Dembski going to get it through his head that cooption is rife
in evolution?
http://www.iscid.org/papers/Dembski_ObsessivelyCriticized_050902.pdf
==========
4. Tornado in a Junkyard
Richard Wein charges that the techniques I develop for calculating
probabilities for irreducibly complex biochemical systems is all akin
to calculating probabilities for the random formation of an airplane
by a tornado whirling through a junkyard (the metaphor is Fred
Hoyle's, if memory serves me correctly). Actually, no one has yet to
perform this calculation, so if that's all I've accomplished, it's
still a contribution to the applied probability literature. I would
say, however, that I've actually accomplished quite a bit more than
Wein attributes to me.
Briefly, I propose that the probability of a discrete combinatorial
object (e.g., an irreducibly complex biochemical system) decomposes
into three probabilities: the probability of the origination of the
components of the object, the probability of all the components being
localized in one place, and the probability of the components being
properly configured once they are localized. These probabilities
multiply since each of the three events (origination, localization,
and configuration) is conditioned on the preceding event (there is no
assumption of probabilistic independence being slipped in here). Also,
there is nothing here that requires these probabilities to be uniform
probabilities (one of Wein's concerns) or that precludes Darwinian
processes from constructing a discrete combinatorial object in accord
with these probabilities. A Darwinian process might with reasonably
probability gradually localize the components for a discrete
combinatorial object and then configure them.
So what's at issue is not the technique of decomposing the probability
of a discrete combinatorial object into a set of more manageable
probabilities (this technique may properly be regarded as a positive
contribution on how to form some reasonable probability estimates for
difficult practical problems), but its application to biology and
specifically for the numbers we plug in. Now, I did stress in NFL that
to settle the design question for such objects when they are
irreducibly complex biochemical systems will require that scientists
agree on the probabilities and be convinced that no one is cheating.
The issue, then, is whether I was cheating with the numbers. I don't
believe I was, and here's why.
First off, let's be clear that Wein is blowing smoke when he claims a
system like the bacterial flagellum evolved by co-optation so that
natural selection gradually enfolded parts as functions co-evolve. As
I pointed out in the last section, this sounds all fine and well, but
Wein offers no detailed testable model for how this might actually
happen in specific cases like the flagellum. We've already discussed
the type III secretory system and its inadequacy as an evolutionary
precursor to the flagellum. But even that supposed precursor is now
thought to have arrived after the flagellum (see Nguyen L, Paulsen IT,
Tchieu J, Hueck CJ, Saier MH Jr., Phylogenetic analyses of the
constituents of Type III protein secretion systems, J Mol Microbiol
Biotechnol 2000 Apr 2(2):125-44). Franklin Harold in The Way of the
Cell (Oxford, 2001) refers to all nontelic scenarios currently
proposed to explain such systems as "wishful speculations." The
biological community doesn't have a clue how such systems emerge.
Next, all the biological community has to mitigate the otherwise vast
improbabilities for the formation of such systems is co-optation via
natural selection gradually enfolding parts as functions co-evolve.
Anything other than this is going to involve saltation and therefore
calculating a probability of the emergence of a multipart system by
random combination. But, as Wein rightly notes, "the probability of
appearance by random combination is so minuscule that this is
unsatisfying as a scientific explanation." Wein therefore does not
dispute my calculation of appearance by random combination, but the
relevance of that calculation to systems like the flagellum And why
does he think it irrelevant? Because co-optation is supposed to be
able to do it.
What we have, then, is a known material mechanism (co-optation powered
by natural selection) that by unknown steps is supposed to produce a
bacterial flagellum. That's the only live mechanistic option. Now, why
should we believe it? What I offer in chapter 5 of NFL are reasons not
to believe it. I tighten Michael Behe's notion of irreducible
complexity to include a minimality condition so that no system with
the same function of lower complexity can perform the same function.
That was a problem with Behe's original definition because it allowed
for John H. McDonald-type mousetrap examples. In such examples,
however, the function in question stays put. What Wein wants to argue,
however, is that irreducible complexity can never preclude complex
systems arising from precursor systems whose function do not stay put
but co-evolve with the systems.
I submit that there is no live possibility here but only the illusion
of possibility. Wein tacitly agrees that I've correctly calculated the
probability of the emergence of the flagellum apart from co-optation.
Does Wein have a probability calculation that breaks the emergence of
the flagellum into manageable steps each of which is reasonably
probable and for each of which he actually calculates the probability?
No. Yet Wein is confident that my probability calculation is in error
and that the actual probability is much higher even though he cannot
offer even the semblance of such a calculation. On what basis then
does Wein maintain this confidence. Is he prepared to offer a
Saganesque type argument of the sort "the flagellum is here so it
can't have been all that improbable"?
For Wein to account for systems like the flagellum, functions of
precursor systems must co-evolve. But that means the space of possible
functions from which these co-evolving functions are drawn is
completely unconstrained. This provides yet another recipe for
insulating Darwinian theory from critique, for the space of all
possible biological functions is vast and there is no way to establish
the universal negative that no sequence of co-evolving functions could
under co-optation have led to a given system. Are we then at an
impasse, with both Wein and me saying essentially "prove me wrong" (in
my case, prove to me that my calculation doesn't hold by doing a
probability calculation of your own; in Wein's case, prove to me that
co-optation with co-evolving functions didn't happen)? Let me suggest
that there are further reasons to be deeply skeptical of Wein's
co-optation scenario. First, specified complexity is used to nail down
design in cases of circumstantial evidence, so if there should happen
to be design in nature, specified complexity is how we would detect
it. Thus, my probability calculation for the flagellum, in the absence
of a counter-calculation by Wein, is prima facie evidence of
biological design. This may not provide sufficient reason for
convinced Darwinists to abandon their paradigm, but it gives evolution
skeptics reason to consider other options, including design.
Second, there is a whole field of study developed by Russian
scientists and engineers known under the acronym TRIZ (Theory of
Inventive Problem Solving) that details patterns of technological
evolution (see, for instance, http://www.ideationtriz.com). As it
turns out, human problem solving breaks into two types, routine
problems and inventive problems. Routine problems are known to submit
to Darwinian type trial-and-error solutions. Inventive problems, by
contrast, are known to require an intuitive leap. This distinction has
turned out to be very robust, with inventive problems not submitting
to the solution strategies that work for routine problems. Since
co-optation is itself an engineering metaphor, TRIZ research provides
strong reason to think that systems like the flagellum, that are
elegant and highly integrated, do not admit a gradual routinized
decomposition of the sort required by the Darwinian mechanism. Wein
disagrees and sees technological evolution in a different category
entirely, and even mentions that human engineers will often engineer
from the ground up whereas biological evolution won't. But in fact,
engineers are stuck with existing resources as much as biology. Wein
gives no evidence of knowing the TRIZ literature. If he did know it,
and if he were not so biased a critic, he would perhaps more readily
grant the connection between technological and biological evolution.
Third, and perhaps most telling, Wein needs fitness to vary
continuously with the topology of configuration space. Small changes
in configuration space need to correlate with small changes in
biological function, at least some of the time. If functions are
extremely isolated in the sense that small departures from a
functional island in configuration space lead to complete
nonfunctionality, then there is no way to evolve into or out of those
islands of functionality by Darwinian means. To clear away this
obstacle to the Darwinian mechanism, Wein argues that the laws of
nature guarantee the continuity that permits the Darwinian mechanism
to flourish. According to Wein, smooth fitness landscapes are the norm
because we live in a world with regular laws of nature and these are
supposed to ensure smoothness. Here is how Wein puts it:
Fitness functions are determined by rules, not generated randomly. In
the real world, these rules are the physical laws of the Universe. In
a computer model, they can be whatever rules the programmer chooses,
but, if the model is a simulation of reality, they will be based to
some degree on real physical laws. Rules inevitably give rise to
patterns, so that patterned fitness functions will be favoured over
totally chaotic ones. If the rules are reasonably regular, we would
expect the fitness landscape to be reasonably smooth. In fact,
physical laws generally are regular, in the sense that they correspond
to continuous mathematical functions, like "F = ma", "E = mc 2 ", etc.
With these functions, a small change of input leads to a small change
of output. So, when fitness is determined by a combination of such
laws, it's reasonable to expect that a small movement in the phase
space will generally lead to a reasonably small change in the fitness
value, i.e. that the fitness landscape will be smooth. On the other
hand, we expect there to be exceptions, because chaos theory and
catastrophe theory tell us that even smooth laws can give rise to
discontinuities. But real phase spaces have many dimensions. If
movement in some dimensions is blocked by discontinuities, there may
still be smooth contours in other dimensions. While many potential
mutations are catastrophic, many others are not.
This argument is rubbish. It invokes continuity of physical laws to
underwrite continuity of fitness landscapes when the two notions of
continuity are entirely different. In physical laws like F = ma, if
you vary the quantity m slightly, the quantity F varies slightly as
well. In general with physical laws, continuity is a matter of
coordinating different quantities associated with physical entities.
But that's not at all what's going on with fitness landscapes. Fitness
landscapes coordinate a physical quantity, position in configuration
space, with a teleological property, a function belonging not to a
physical space but to a space of functions characterized by a
functional logic. Fitness assigns a quantity to that function, but
that quantity is entirely derivative from the function.
This is not to say we can't speak of continuity or smoothness of
fitness landscapes. But it is to say that we can't use continuity of
physical laws to underwrite it. Indeed, we have plenty of examples
where there is no such continuity. Consider the case of written
language and meaning. Written language is represented in character
strings and there is a natural way to think of written texts as being
close to each other in terms divergence of corresponding characters
(the more divergence, the farther apart). How much can you randomly
perturb written texts and still maintain their meaning (i.e.,
function)? Is it possible by small changes to the text always to
maintain some meaning and thereby transform a poem by Keats into one
by Ginsburg? What about computer source codes? Can gradual random
changes to the code change a computer game into an accounting program
all the while maintaining some function of the source code? Perhaps
there is, but we have no evidence of anything like this, nor do human
designers attempt anything like this. To think that continuity of
physical laws underwrites continuity of fitness landscapes is without
justification and another case of Darwinians taking seriously what is
merely an illusion of possibility.
Finally, for all the length of Wein's critique, he ignored what I
expect will be my most important contribution to assessing the
probabilities of biological systems, namely, my definition of
perturbation probabilities in terms of perturbation tolerance and
identify factors and their use in assessing the probability of
evolving individual polypeptides and polynucleotides. Wein writes:
"Since he can't calculate this directly, he uses an approximation that
he calls a perturbation probability. We need not concern ourselves
with the details." Perhaps the details are not important, but the
application is. Wein contends that the only biological system to which
I apply my probabilistic techniques is the bacterial flagellum. In
fact, I have my eye on much different
fish.
In section 5.10 of NFL, I indicated how perturbation probabilities
apply to individual enzymes and how experimental evidence promises
shortly to nail down the improbabilities of these systems. The beauty
of work being done by ID theorists on these systems is that they are
much more tractable than multiprotein molecular machines. What's more,
preliminary findings of this research indicate that islands of
functionality are not only extremely isolated but completely
surrounded by a sea of nonfunctionality (not merely polypeptides
having different functions but polypeptides incapable of function on
thermodynamic grounds -- in particular, they can't fold). For such
extremely isolated islands of functionality, there is no way for
Wein's method of co-evolving functions to work.
Prediction: Within the next two years work on certain enzymes will
demonstrate overwhelmingly that they are extremely isolated
functionally, making it effectively impossible for Darwinian and other
gradualistic pathways to evolve into or out of them. This will provide
convincing evidence for specified complexity as a principled way to
detect design and not merely as a cloak for ignorance.
==========
Ian Musgrave & Peta O'Donohue
Address altered to avoid spam, delete RemoveInsert
Yes, I strongly agree with this. An almost exactly worded argument was
used by Dembski in reply to Richard Weins critique, so it is important
that this argument be countered. Of course, the probability that ISCID
will post it is small, but the attempt should be made regardless.
Cheers! Ian
=====================================================
Ian Musgrave Peta O'Donohue,Jack Francis and Michael James Musgrave
reyn...@werple.mira.net.au http://werple.mira.net.au/~reynella/
Southern Sky Watch http://www.abc.net.au/science/space/default.htm
Andy Groves
> G'Day All
> Address altered to avoid spam, delete RemoveInsert
>
> On Wed, 8 May 2002 23:01:39 +0000 (UTC), pz <my...@mac.com> wrote:
>
> >In article <puajdu0v3ojgjo9ea...@4ax.com>,
> > David Jensen <da...@dajensen-family.com> wrote:
> >
> >> On Wed, 8 May 2002 19:49:20 +0000 (UTC), in talk.origins
> >> lam...@bioinfo.med.utoronto.ca (Laurence A. Moran) wrote in
> >> <abbv9q$24f8$1...@bioinfo.med.utoronto.ca>:
> >>
> >>
> >> >
> >> >In article <74227462.02050...@posting.google.com> nic writes:
> >> >
> >> >>Check out this latest bit from Dembski, it may intrigue such folks as
> >> >>Larry Moran:
> >> >
> >> >You certainly got MY attention!
> >> >
> >> >>========
> >> >>ID research problem: bacterial flagellum and type III secretory system
> >> >
> >> >This was posted on the "International Society for Complexity, Information
> >> >and Design Forum" ....
> >> >
> >> >http://www.iscid.org/ubb/ultimatebb.php?ubb=get_topic;f=6;t=000079
> >> >
> >
> >I think Larry ought to post his reply to ISCID. Maybe he could win the
> >$100 prize!
>
> Yes, I strongly agree with this. An almost exactly worded argument was
> used by Dembski in reply to Richard Weins critique, so it is important
> that this argument be countered. Of course, the probability that ISCID
> will post it is small, but the attempt should be made regardless.
I would also suggest e-mailing a copy to Dembski (and perhaps other
wedgies) directly.
Andy
TomS
<991ea4ae.02051...@posting.google.com>, gro...@cco.caltech.edu
stated..."
Don't you think that there are wedgies who scan talk.origins?
(Maybe sort of apprentise quote-miners?)
Tom S.
Andy Groves
Certainly. But they can claim that they don't. If Larry e-mails them
his comments, it makes it that much harder for them to stand up at
their next talk and ignore what he said.
Andy
pz
wrote:
See: <http://www.iscid.org/ubb/ultimatebb.php?ubb=get_topic;f=6;t=000076>
--------------
"In order to clarify the way that I operate, and to answer some
frequently asked questions, I've written what amounts to the
following:
To begin, let me state that I've always disliked the prospects of
giving rules for moderation. Why? Because I trust my instinct (my
subjective sense) more than I trust my ability to define lists. So,
with that in mind, this is an attempt to give Brainstorms
participators a sense of my ethos: how I operate.
Brainstorms is not intended to be a discussion board to promote
intelligent design. Despite this fact, many are under the impression
that it is. This is easy to understand, given the fact that the
society is ID friendly. In any case, to set the record straight,
William Dembski, the executive director of ISCID, came to me and
said, "Do whatever you want with this discussion board. It's all
yours, even if that means keeping me in check." So, I started to
think about what I wanted to see. The easiest solution would have
been to just recreate the standard talk.orgins format of harsh and
bitter debate between people, who quite frankly, dislike each other.
But I have become quite tired of seeing civilized people ramming
things down each other's throats. How could Brainstorms be
different? Well, for starters, it could be a creative outlet rather
than a debating forum. The positive would be emphasized rather than
the negative. That was the vision I started with. I wanted to see
positive hypotheses developed in a friendly but critical
environment. Criticism was to be welcomed, but only when focusing on
the relevant ideas. Attempts to reconstruct strawmen would not be
tolerated. The typical worn-out and rehashed talk.orgins type
debates would not be welcomed here. In addition, I wanted this to be
a forum where serious Darwinists, teleologists, and
self-organizationalists could come together cooperatively. To some
degree (though not to the extent of my vision) this has come to
pass.
Maintaining this board has been quite a challenge. Desiring to be
fair yet knowing that you have to crack down sometimes can be
unnerving (everyone is going to think you are biased at some point).
Early on, at Brainstorms, we received a rush of posters who were
ingrained with the talk.origins battle warrior mentality. To some
degree we all are, I would expect. But some simply can not break out
of it, and thus I had to take serious action and ban participants
after they were given several chances to comply with my requests. To
this day, I still see fragments of this mentality even pop up in
posts from established members. However, I discovered an important
insight early on: don't micromanage the board by moderating every
slip of the tongue, but focus on the newbies. So, that is what I
have been doing ever since. When new or unactive participants start
a new thread, it receives my fullest attention and I moderate,
hoping to initiate the new member as soon as possible. This way,
nobody gets comfortable in the talk.origins battle mentality.
Still, I do occasionally find reason to warn established members.
The infraction that draws my wrath most strongly is an unfair or
irrelevant reading of another's post. Regardless, I will be the
first to acknowledge that I am a subjective human being who makes
mistakes. I am more than happy to discuss my decisions off board at
mode...@iscid.org. If I become convinced that I was wrong, I will
make a public apology.
Ok. Having said the above, I'd like to emphasize that my main
intention in moderating is to avoid escalation. Sometimes I email
the participant behind the scenes. Sometimes I publicly moderate.
Normally, I like to deal with newer users by making a public
moderation. In addition, if I feel like a thread needs redirection,
I'll make the moderation public. Minor infractions are dealt with
privately, and are most abundant. They will often involve a
suggestion for wording change.
Here are some general questions for critics of any model (design,
general teleology, darwinian evolution, self-organization, etc).
Again, criticism is welcomed (and even solicited at times) at
Brainstorms. But it has to be a certain type of criticism.
1. Is the criticism constructive or destructive?
2. Does the criticism give a fair reading to the idea that is being
criticized?
3. Are the criticisms designed to show once and for all that a
certain model has been "exploded"?
4. Is there an either/or mentality (warrior in a battle mindset)?
5. Does the critic give his dialogue partner the benefit of the doubt?
Here are some general questions I ask myself as I moderate
Brainstorms:
1. Length of post: quick pithy comments will be deleted or merged
with other posts.
2. Is the poster at Brainstorms to make a point, to win a battle, etc?
3. Is the post antagonistic?
4. Does the post have promise: will it lead to productive dialogue.
5. Does the post cover new territory?
6. Does the post look like a cookie cutter argument found elsewhere
on the internet?
7. Was the post written casually or with care?
8. Does the post add insight to the discussion?
9. Is the post on topic (or within a manageable range)?
10. How much of the post is "quotes" and how much is original
content. I will slim down or delete posts that are quote for quote
refutations.
--------------
Not only do some of them read it, they're quite bitter and whiny about
it. It's kind of pathetic to see someone try to rationalize his overt
censorship of contrary points of view by complaining about a more open
forum -- but then, complaining about everyone else rather than providing
one's own solution is the Dembski strategy, anyway.
--
pz
Laurence A. Moran
>More from Dembski on the flagellum...
>
>When is Dembski going to get it through his head that cooption is rife
>in evolution?
>
>http://www.iscid.org/papers/Dembski_ObsessivelyCriticized_050902.pdf
[snip]
Dembski says ...
>First off, let's be clear that Wein is blowing smoke when he claims
>a system like the bacterial flagellum evolved by co-optation so that
>natural selection gradually enfolded parts as functions co-evolve. As
>I pointed out in the last section, this sounds all fine and well, but
>Wein offers no detailed testable model for how this might actually
>happen in specific cases like the flagellum.
Let's be clear on what Dembski is saying here. To the best of our
knowledge flagella arose over two billion years ago. We would like
to know something about the history of this molecular machine. Dembski
and his intelligent design friends claim that flagella could not have
arisen by evolution because they are irreducibly complex. They say
that flagella were designed by some intelligent designer. Scientists
think that flagella evolved from simple precursors. One possibility is
that flagella evolved from a primitive secretory system that was later
co-opted to specialize in flagella biogenesis.
Note that neither Dembski nor any other anti-evolutionist has ever
offered a detailed model of how their supposed design event happened.
They have never told us which components were part of the original
design. They don't tell us whether a single design event occurred
followed by subsequent evolution in other species or whether
a slighlty different flagellum was designed for each of several
thousand species. They don't tell us when the designer did the deed -
was it several billion years ago or only 6000 years ago? They don't
even tell us who the designer was! Yet. in spite of this amazing lack
of information on their part, they feel free to criticize scientists
for not having a "detailed testable model" of something that took
place over two billion years ago. This is the worst form of hypocrisy
and unethical behavior and Dembski shouldn't be allowed to get away
with it. Somebody's "blowing smoke" and it ain't the scientists.
It's about time that the intelligent design community put their money
where their mouth is. They need to show us a model of how life evolved
by intelligent design. I suggest they start with their favorite
molecular machine, the bacterial flagellum. How and when was it
designed?
>We've already discussed the type III secretory system and its
>inadequacy as an evolutionary precursor to the flagellum.
Dembski doesn't know enough biology to even understand the evolutionary
pathway that scientists are proposing. The idea is that the flagellum
arose from a primitive secretory system of the type III form. Dembski
seems to think that this requires flagella to evolve from modern
virulence secretion systems that are also type III systems. His
mindset won't allow him to think of simple primitive systems that
could have been the precursor of flagella.
Dembski says ...
>But even that supposed precursor is now thought to have arrived
>after the flagellum (see Nguyen L, Paulsen IT, Tchieu J, Hueck CJ,
>Saier MH Jr., Phylogenetic analyses of the constituents of Type III
>protein secretion systems, J Mol Microbiol Biotechnol 2000 Apr
>2(2):125-44).
The modern virulence secretory systems may have evolved from flagellar
systems in the relatively recent past (<500 million years). They
may also have evolved independently of flagella and simply share
a common ancestor with the flagella type III secretory components. The
actual historical pathway of virulence secretory systems doesn't have
much to do with the senario for the evolution of flagella and the
co-opting of a primitve secretory system that existed over two billin
years ago. However, I note with interest that Dembski seems to
concede the point that flagella and virulance factor secretion are
related in some way and he seems to have no objection to the evolution
of one from the other over billions of years. This leads me to wonder
what he has in mind when he attacks evolutionists. It sounds to me like
he's very confused about his own position on these issues.
Dembski says....
>Franklin Harold in The Way of the Cell (Oxford, 2001) refers to
>all nontelic scenarios currently proposed to explain such systems
>as "wishful speculations." The biological community doesn't have a
>clue how such systems emerge.
Isn't it interesting how the intelligent design community can always
find at least one scientist who disputes current speculative models?
Isn't it interesting that there is very little of this kind of debate
and dissent within the intelligent design community? Why is that?
It's because the intelligent design community doesn't have any models
to dissent from.
Dembski knows very well that as soon as he puts a specific model on
the table he'll come under heavy attack from the scientific community.
He also knows that some of his intelligent design buddies might object
to the Dembski version of intelligent design. That's probably why
Dembski and his friends press their attack on everything scientists
say and avoid coming up with anything of their own. As I pointed out
earlier, this is hypocritical and unethical. It's also cowardly.
If Franklin Howard thinks that the scientific senarios of the ancient
history of life are "wishful speculations" then I wonder what he
thinks of the intelligen design idea? Does anyone here think that
Dembski would dare to quote real scientific opinions about the idea
that some intelligent designer created bacterial flagella?
>Next, all the biological community has to mitigate the otherwise
>vast improbabilities for the formation of such systems is co-optation
>via natural selection gradually enfolding parts as functions co-evolve.
Nonsense. There are lots and lots of ideas about how irreducibly
complex systems arose by evolution. Co-opting other systems is only
one of the possibilities. Dembski needs to learn a lot more biology
before he can discuss these things intelligently.
Furthermore, biologists aren't interested in silly calculations about
the probability of an event that has already occurred. It's only the
anti-evolutionists who have a fixation about this.
Dembski continues ...
>Anything other than this is going to involve saltation and
>therefore calculating a probability of the emergence of a multipart
>system by random combination.
Nonsense. Dembski doesn't understand the biology so he tries to
set up a strawman argument about saltation being the only other
possibility. Shame.
Dembski says ....
>But, as Wein rightly notes, "the probability of appearance by random
>combination is so minuscule that this is unsatisfying as a scientific
>explanation." Wein therefore does not dispute my calculation of
>appearance by random combination, but the relevance of that calculation
>to systems like the flagellum And why does he think it irrelevant?
>Because co-optation is supposed to be able to do it.
>What we have, then, is a known material mechanism (co-optation powered
>by natural selection) that by unknown steps is supposed to produce a
>bacterial flagellum.
What we have is a unknown intelligent designer that by unknown steps
is supposed to produce a bacterial flagellum. See? Two can play at that
silly game.
>That's the only live mechanistic option. Now, why should we believe
>it?
That's all there is to intelligent design. Why should we believe it?
>What I offer in chapter 5 of NFL are reasons not to believe it.
Dembski's anti-evolution position is well-known. Now its time for him
to come out of the closet with intelligent design. We're tired of silly
anti-evolution arguments that have no substance.
Larry Moran