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Author
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Topic: Convergent Evolution as Reuse of Design
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William A. Dembski
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Member # 7
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posted 16. September 2003 00:53
From a design-theoretic perspective, most cases of convergent evolution seem properly explained not as similar adaptations responding to similar selection pressures but as reuse of an existing invention. Is there any way to test this claim? Within the field of technological evolution, once a good idea first emerges, it tends to be quickly reused thereafter. Are there any cases where a novel biological structure first emerges (say, in the fossil record) and thereafter is found in rapid succession to reappear in other organisms for which the structure could not reasonably be regarded as being shared through common ancestry?
Claim: To the degree that reappearances of the structure by independent evolutionary pathways (and perhaps across vast biogeographical distances) are temporally coincident, to that degree does convergent evolution provide evidence for reuse of design. Why? Because a blind watchmaker would not be able to reuse designs arising from independent evolutionary pathways but would rather have to reevolve them, and such reevolution, though path dependent, is not temporally constrained. Million dollar question: Are there any biological structures that at the point of innovation suddenly, within a short temporal window, reappear in other organisms that do not share a common ancestor exhibiting that structure?
[Note: I have yet to read Simon Conway Morris's latest book -- Life's Solution. Perhaps he has an answer in its pages. It seems that this is the sort of question Rupert Sheldrake would be interested in answering, and perhaps has already answered.]
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Pim van Meurs
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posted 16. September 2003 01:15
You may be interested in the following publication
"Convergent evolution of gene circuits" by Gavin C Conant and Andreas Wagner published in Nature Genetics 22 June 2003,volume 34 no. 3 pp 264 - 266
quote:
Convergent evolution is a potent indicator of optimal design. We show here that convergent evolution occurs in genetic networks. Specifically, we show that multiple types of transcriptional regulation circuitry in Escherichia coli and the yeast Saccharomyces cerevisiae have evolved independently and not by duplication of one or a few ancestral circuits.
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yersinia
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posted 16. September 2003 03:30
I agree that the apparent transplant of designs -- e.g. like radios or global positioning systems have been transplanted across "lineages" of cars, planes, etc. -- would be good evidence of design (except in cases where other known mechanisms of information transfer are plausible, e.g. gene transfer in microbes).
However, "convergence" in the classical sense is usually not the "same design" found in two places, it is designs that are superficially similar, but based on different fundamental organizations. The hydrodynamic shapes of fish, icthyosaurs, and dolphins are a common example. On the outside they look somewhat similar, but their insides are no closer than any pair of fish-reptile or reptile-mammal would be. Almost certainly the modifications to the developmental genes are totally different as well (although we don't really know the genes involved yet).
In other words, from a design perspective it looks more like two designers, working independently, reached similar solutions via very different routes, rather than one designer making a design and then transplanting it (like, say, if dolphins had gills).
A classic example is the 1771 quote by a French explorer about Madagascar:
quote:
May I announce to you that Madagascar is the naturalist's promised land? Nature seems to have retreated there into a private sanctuary, where she could work on different models from any she has used elsewhere. There you meet bizarre and marvelous forms at every step....
There's an even better old quote somewhere about naturalists wondering about different creators but I can't seem to find it at the moment.
I'm not sure if these kinds of convergences would do much for Dembski even if the temporal progression he suggests were found somewhere (assuming such things could be dated, I imagine that good dating of convergence events would only be attainable for mammalian skeletal features). On evolution, we would expect that the convergence event in question would correlate with the emergence of a particular environment/niche.
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Argon
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posted 16. September 2003 09:53
William Dembski writes:
quote:
From a design-theoretic perspective, most cases of convergent evolution seem properly explained not as similar adaptations responding to similar selection pressures but as reuse of an existing invention.
The design-theoretic perspective is not limited to postulating intelligent intervention or invention as an explanation. Thus, from a design-theoretic perspective, all cases of convergence can be properly explained as either a reuse of an "invention" by an "intelligent agent" or the outcome of basic, "natural" mechanisms.
How can one suggest that "most cases of convergent evolution seem properly explained" as in reuse of an existing invention without first having performed a survey of convergent features in biology? I suppose the question depends on the mechanism by which existing "inventions" are reused: i.e. via "natural" modes or through "intelligent intervention", and whether through the horizontal transfer of features or via a modification or existing parts during linear descent.
Could you be more specific Bill?
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gedanken
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posted 16. September 2003 10:54
While the specifics may contain substantially debatable or even possibly quite incorrect concepts or reasoning, I think that the direction in this thread is very interesting.
In my thread Does intelligence imply “motive”? several of us have been discussing the possible modification of the “Explanatory Filter” methodologies away from being strictly eliminative toward considering various aspects of the designer. In that thread one of the concepts to consider (in part) was “motive”. (The name of the thread may have been somewhat misleading, and probably needed a few words to indicate its association with study of the Explanatory Filter.)
This thread also connects well with that sort of consideration of “motive”. For example the designer may have motive of reuse because that simplifies the job of design. Very specifically a designer of limited means (e.g. one who is not omnipotent and of creative capacity to organize entire universe system-wide configurations) might be very motivated to reuse designs due to the savings of some sort of “thinking” resources (like search time, ect.). So re-use of concepts, especially in sequential time order, points to a designer with such limitations.
But even more important in my view is how the re-use aspect affects prior probabilities or likelihood in a Bayesean consideration. One of the considerations we gave in the thread mentioned above is the issue of leaving out a possible natural non-intelligent cause in the analysis of a particular case of inferred design. For example, is “re-use” a signal that the particular pattern has high value in terms of fitting in with the particular environment at the particular position in the universe?
As a preliminary, consider that there is evidence in “re-use” that a particular form had some sort of “vlaue” in terms of fitting in with a particular environment. By “value” I do not mean a cognitive or personal “value”, I mean a matter of an increased pattern fit by some pattern fitting measure, defined independently of particular views of intelligence or intelligent agents. An agent, wishing lifeforms to survive, could have motive to fit that pattern. A natural process that provides energy for systems that grow in apparent complexity could have “value” in that sense of providing a better survival value for lifeforms. So clearly whether “designed” or not, the “re-use” of a particular pattern in living systems and our ability to examine how that re-used aspect provides for successful reproduction of that organism containing the pattern indicates some “value” concept that is directed toward organism survival.
For if a pattern had high value in terms of fitting in with the particular environment in some respect, then the particular configuration could have some sort of “survival value” as above, and could be a source of information for a search procedure that used natural processes, and was blind in many respects but not blind toward that particular kind of information. In this particular environment, this criterion for example for a Darwinian-like search algorithm existing in natural processes does not indicate that the information came from outside of the environment. Specifically the indication of that “value” as a potential criterion in either natural or intelligent search would not per se indicate a smuggling of the criterion into an algorithm by intelligent means. For example the NFL theorems would not indicate a displacement of that criterion beyond the environmental consideration of the “value”—remembering that the NFL theorems only apply to average over all possible “landscapes”, and restricting to this particular “landscape” in which we have already recognized a “value” in some form for re-use makes them irrelevant to our discussion in this environment.
Then we also have benefit of being able to use this aspect of “re-use” as a consideration in judging the likelihood of a designer acting. Consideration of the designer’s need for “re-use” is but one in a long sequence of designer considerations that could be useful to consider. Taken together, a proposition for some primitive details about the designer could be given.
Very importantly—don’t miss my point here—if the consideration of “re-use” is of any importance whatsoever, it is important in that it is a detail about the designer. It is not a case of considering the observed characteristics in the system in consideration in a completely eliminative manner since we have not eliminated the consideration of the potential “usefulness” of “re-use” to the designer. This is an encouraging trend, and I encourage Dr. Dembski to follow its implications for design pattern recognition procedure development, and for all participants to further develop this and other concepts of non-eliminative consideration of the designer.
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nosivad
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posted 16. September 2003 12:49
I refer Dembski to my paper 'Ontogeny, Phylogeny and the Origin of Biological Information". nosivad
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nosivad
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posted 16. September 2003 14:53
The implications of this thread by Dembski are being discussed at some length (58 posts so far) at Terry Trainor's Forum under the title "Superficial Resemblance?". I am interested in what the responses of Dembski and the other contributors to this thread might be. nosivad
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RBH
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posted 16. September 2003 15:53
Can you supply a URL for that thread, nosivad? Thanks!
RBH
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nosivad
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posted 16. September 2003 23:17
RBH Excuse the delay. Just plug in Terry Trainor and from the home page you will find directions to the forum. nosivad
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Pim van Meurs
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Member # 541
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posted 16. September 2003 23:22
Not many people may know this Terry but I found his link
Seems to have gotten side tracked on the issue of the 2nd law of thermodynamics though
I think the relevant misconception is that quote:
There is no conceivable way that the similarities between marsupial and placental saber-toothed cats could have arisen by Natural Selection, especially when both forms were doomed to extinction.
Natural selection is further "constrained" by physical limitations, common descent, genetic constraints, chemical constraints. Ruse in his latest book describes some relevant factors which further 'guide'/constrain natural selection/varaiation. The suggestion that "there is no conceivable way" suggests more an argument from ignorance than an argument that looks at the evidence.
Perhaps Nosidav could tell us how he reached the conclusion of "no conceivable way"? And is Nosivad familiar with how evolutionary theory explains these similarities?
[ 16. September 2003, 23:51: Message edited by: Pim van Meurs ]
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Cre8ionist
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Member # 140
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posted 16. September 2003 23:38
In the neighborhood, so have to toss in at least a point or two:
Yersinia,
quote:
However, "convergence" in the classical sense is usually not the "same design" found in two places, it is designs that are superficially similar, but based on different fundamental
organizations. The hydrodynamic shapes of fish, icthyosaurs, and dolphins are a common
example. On the outside they look somewhat similar, but their insides are no closer than
any pair of fish-reptile or reptile-mammal would be. Almost certainly the modifications to
the developmental genes are totally different as well (although we don't really know the
genes involved yet).
This makes sense as you say where the genes aren't known, however, what about the cases used by Spetner? A couple of them are genotypic rather than phenotypic. For instance, how about the enzyme lysozyme
found in the stomach of ruminants and langur monkeys.
quote:
In the forward part of the stomach of both the langur and the ruminant there is a special fermentation chamber. Both types of animals use bacteria to break down cellulose. Cellulose is the main component of the leaves and grass in the animal's diet. There is food value in the cellulose, but the animal cannot digest it on its own. It doesn't have the right enzymes. It hands that job over to bacteria, which it hosts in the fermentation chamber. The bacteria do have the right enzymes. The animal lets them eat and digest the cellulose in the leaves and the grass it eats. Then the animal transfers the bacteria to a rear compartment of the stomach and digests them. Lysozyme breaks down the bacterial cell wall, and allows the animal to digest the nutrients in the bacterium.
So in this case, it appears that there is convergence wrt the stomach, but also, it appears that there is convergence of the lysozyme.
Another case he mentions deals with a gene which controls eye development:
quote:
....a striking identity was reported between an insect gene and a vertebrate gene [Quiring et al. 1994]. This gene has been found to control eye development both in insects and in vertebrates, including humans. The genes in these two different phyla are 94% identical. This new finding makes convergence look so improbable that, even without making any probability calculation, the authors suggest that
the traditional view that the vertebrate eye and the compound eye of insects evolved independently has to be reconsidered.
I find the whole convergence topic interesting, especially wrt the marsupial/placental convergence, some examples of which I find startling, so I'll be watching the thread to see if anything comes of it.
No time to post in the other thread tonight.................................Cre8
[ 17. September 2003, 00:16: Message edited by: Cre8ionist ]
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Pim van Meurs
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Member # 541
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posted 16. September 2003 23:56
Creationist raises a good argument that what seems to be convergent evolution in fact is divergent evolution.
quote:
The genes iin these two different phyla are 94% identical. This new finding makes convergence look so improbable that, even without making any probability calculation, the authors suggest that
the traditional view that the vertebrate eye and the compound eye of insects evolved independently has to be reconsidered.
Indeed the evidence of the monophyletic origins of the eye seems to become stronger lately. Somehow this makes more sense to me than a suggestion of 40 or so independent evolution pathways of the eye.
As far as Spetner's comments on lysozymes I found this somewhat unconvincing argument quote:
More than 30 years ago I predicted that contradictions to neo-Darwinian theory would emerge when probability calculations could be made of so-called convergences. Such calculations can now be made. From the assumed convergence of the lysozyme enzymes common to ruminating cows and ruminating langur monkeys, one can set an upper-limit probability of 10^54 to the probability that they evolved independently through random point mutations. It is less than the probability of your winning the New York State Lottery seven weeks in a row. Most people would consider such an event impossible.
Source
Notice the problem?
Some links to lysozymes
Gastric Lysozyme in Foregut Fermenters
quote:
It thus appears that evolution of foregut fermentation was accompanied by recruitment of lysozyme as a lytic digestive enzyme, and that selection of this enzyme to act in stomach fluid has driven its molecular evolution. It also turns out that colubine monkeys such as languars, which are also foregut fermenters, also show high levels of expression of stomach-type lysozyme. Thus, gastric lysozymes are also a good example of convergent evolution of proteins in distantly related species (cows and languars) that happen to share a digestive strategy.
There is a good table in this pdf on page 6 which shows the differences and simularities in the gens.
Also relevant
quote:
Detection of convergent and parallel evolution at the amino acid sequence level.
Zhang J, Kumar S.
Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park 16802, USA. zhang@imeg.bio.psu.edu
Adaptive evolution at the molecular level can be studied by detecting convergent and parallel evolution at the amino acid sequence level. For a set of homologous protein sequences, the ancestral amino acids at all interior nodes of the phylogenetic tree of the proteins can be statistically inferred. The amino acid sites that have experienced convergent or parallel changes on independent evolutionary lineages can then be identified by comparing the amino acids at the beginning and end of each lineage. At present, the efficiency of the methods of ancestral sequence inference in identifying convergent and parallel changes is unknown. More seriously, when we identify convergent or parallel changes, it is unclear whether these changes are attributable to random chance. For these reasons, claims of convergent and parallel evolution at the amino acid sequence level have been disputed. We have conducted computer simulations to assess the efficiencies, of the parsimony and Bayesian methods of ancestral sequence inference in identifying convergent and parallel-change sites. Our results showed that the Bayesian method performs better than the parsimony method in identifying parallel changes, and both methods are inefficient in identifying convergent changes. However, the Bayesian method is recommended for estimating the number of convergent-change sites because it gives a conservative estimate. We have developed statistical tests for examining whether the observed numbers of convergent and parallel changes are due to random chance. As an example, we reanalyzed the stomach lysozyme sequences of foregut fermenters and found that parallel evolution is statistically significant, whereas convergent evolution is not well supported.
and
quote:
Adaptive evolution in the stomach lysozymes of foregut fermenters
Caro-Beth Stewart, James W. Schilling & Allan C. Wilson
The convergent evolution of a fermentative foregut in two groups of mammals offers an opportunity to study adaptive evolution at the protein level. The appearance of this mode of digestion has been accompanied by the recruitment of lysozyme as a bacteriolytic enzyme in the stomach both in the ruminants (for example the cow) and later in the colobine monkeys (for example the langur). The stomach lysozymes of these two groups share some physicochemical and catalytic properties that appear to adapt them for functioning in the stomach fluid1,2. To examine the basis for these shared properties, we sequenced langur stomach lysozyme and compared it to other lysozymes of known sequence. Tree analysis suggests that, after foregut fermentation arose in monkeys, the langur lysozyme gained sequence similarity to cow stomach lysozyme and evolved two times faster than the other primate lysozymes. This rapid evolution, coupled with functional and sequence convergence upon cow stomach lysozyme, could imply that positive darwinian selection has driven about 50% of the evolution of langur stomach lysozyme.
Maybe time to start a different thread on this
[ 17. September 2003, 00:20: Message edited by: Pim van Meurs ]
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Rex Kerr
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posted 17. September 2003 00:47
I can think of one positive answer to Dembski's million dollar question: the appearance of calcified exoskeletons in the pre-Cambrian/early Cambrian.
And I can think of another: development of antibiotic resistance in bacteria placed on plates containing the antibiotic ampicillin.
The latter example shows brute force convergence, where you can pick up many indpendently generated yet identical mutations that cause resistance.
Here, however, we have good reason to believe that this is not design. Among other things, the rate of recovering identical mutations is pretty close to what we expect given mutation rates.
One can do similar experiments with genes on plasmids to demonstrate horizontal gene transfer.
Now, returning to the Cambrian, we have to ask: can calcified structures be generated by brute force convergence? To answer this question, looking at the structure alone simply isn't sufficient.
So I would rephrase Dembski's question on molecular terms: Are there any enzymatic, structural, or signaling complexes that at the point of innovation suddenly, within a short temporal window, reappear in other organisms that do not share a common ancestor exhibiting that complex?
And the $900,000 follow up questions: Is highly improbable that this complex was independently generated from a common ancestor, to the degree of similarity observed, simply by chance/brute force? Is the scope, speed, number, etc. of these complexes inconsistent with known mechanisms of horizontal gene transfer?
There aren't any cases I know of where I can answer all three of these questions positively, but examples of this type would strongly argue for re-use rather than convergent evolution (if the first two are answered positively) or lateral transfer (if all three are answered positively).
Structural re-use vs. convergence is, unfortunately, too ill-defined on its own for me to know what to do with it. Possibly once we understand development vastly better we could start setting meaningful bounds on these things, but we're a long way off from that.
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nosivad
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posted 17. September 2003 08:40
I ask Pim or anyone else to provide a documented example of how the environment in any way, including Natural Selection, has been instrumental in the emergence and further basic modification of any higher (diploid) life form. I have proposed that, to use the language of this forum, the information for phylogeny like that for ontogeny was "front loaded" and present from the beginning. The enormous genetic identity of all living beings renders this intepretation by far the most reasonable. It also renders the whole notion of "convergent evolution" obsolete as well as offering an explanation for atavism. Evolution has been an historical, irreversible and self-limiting process which cannot accomodate any role for chance. To quote Leo Berg (Nomogenesis page 406)- "The struggle for existence and natural selection are not progressive agencies, but being, on the contrary, conservative, maintain the standard". Also from the same source - "Evolution is in a great measure an unfolding of pre-existing rudiments". I, along with Pierre Grasse, completely concur. nosivad
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gedanken
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posted 17. September 2003 09:46
Nosivad sure made it hard to find his "Terry Trainor" forum. I plugged in "Terry Trainor" into search, and got 14,000 pages.
Anyway Pim found it, and here is a link to actual thread "Superficial resemblance?". (URL was very long, best in UBB code.)
[ 17. September 2003, 15:40: Message edited by: gedanken ]
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