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Author
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Topic: Ontogenetic Depth and the Origin of Animals
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Art
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Member # 179
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posted 10. February 2003 00:15
Two comments that pertain to this thread.
Paul asked recently: quote:
If H. erythrogramma and H. tuberculata were not related by common descent, how would you know it? Give the question some thought.
I think the litany of lines of evidence that has been given in this thread is pretty solid, and can sort out negative as well as positive instances of common ancestry. For example, gross (e.g., genome structure, gene expression strategies) and intricate (sequence variation and the like) measures are the primary ways we would conclude that tobacco mosaic virus and poliovirus do not share any sort of common ancestry.
On an unrelated note, Paul has commented on heritable radical variation of early development. I wonder if he has thought on the phenomenon of apomixis in plants. It seems to me that this fits the bill to a tee - it involves a fundamental change of the very first step in development, and can be varied in a decidedly (and surprisingly simple) heritable manner.
(The somewhat larger context - the facts that plants possess at least three different ways by which a single cell can yield a fully developed individual, and that these different ways each can be affected by heritable variation - is also of some possible interest for this thread.)
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Paul A. Nelson
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posted 10. February 2003 11:12
Thanks for the follow-ups, gentlemen.
Yersinia wrote, in response to my question, "If H. erythrogramma and H. tuberculata were not related by common descent, how would we know it?"
quote:
Well, if the sequences of the two species failed to group together against other randomly chosen species (e.g., one species groups with humans, another with liverworts), that would be a pretty good indication.
If echinoderm junk DNA encoded "made by Rael, 5 million B.C.", that too would be a good indication.
Many further hypotheticals along these lines could be suggested.
Art wrote:
quote:
I think the litany of lines of evidence that has been given in this thread is pretty solid, and can sort out negative as well as positive instances of common ancestry. For example, gross (e.g., genome structure, gene expression strategies) and intricate (sequence variation and the like) measures are the primary ways we would conclude that tobacco mosaic virus and poliovirus do not share any sort of common ancestry.
Francis -- I couldn't find a direct answer to my question from your posts; sorry.
OK, next question to Yersinia, and Art, if he's interested. Why would the patterns you suggested indicate lack of shared ancestry? There's a point to this question, so please bear with me.
While awaiting your answers, here's the story about Raff, Heliocidaris, and my dissertation work that I promised. When I arrived at the University of Chicago in the fall of 1985, Bill Wimsatt (who later became my Ph.D. supervisor) was deep in the throes of his work on the concept of "generative entrenchment" (GE). Generative entrenchment is a general or generic feature of complex systems with multiple interacting parts, including the developmental architectures of animals. The CPU of your computer is far more deeply entrenched, in the computer's normal functions, than the color of the computer's plastic case: that is, more of the computer's functions depend on the proper operation of the CPU than they do on the case color. In a parallel sense, early cleavage stages in animals are more deeply entrenched than later developmental stages, because of the asymmetric causal structure of ontogeny. If cleavage fails, game's over. If your limbs fail to develop, a later event, you'll be badly hindered, but still alive.
Anyway: Bill was writing up his ideas on GE, and Raff, whom Bill knew well as a friend and colleague from evo-devo circles, had just begun to publish on Heliocidaris. Raff had long been very unhappy with the bona fides of classical neo-Darwinism, and was looking for model systems in which to study macroevolution, which he felt neo-Darwinism more or less ignored. Because of the radical divergences of indirect- and direct-development in Heliocidaris, as well as in other groups (e.g., frogs), Raff -- once, an outspoken advocate of theories like GE -- had come to doubt that early development was functionally constrained. (Raff's other and even more significant reason for doubting GE is that the architectures of early development in the Metazoa are clearly different; if the Metazoa share a common ancestor, then early development must evolve, somehow.) Bill had a strong case for GE on both broad theoretical grounds and experimental data, but here were Raff's sea urchins as a glaring counterexample.
So Bill and I began discussing Raff's arguments. At the time, I was struggling with how one tested the theory of common descent, a puzzle that later became the opening question of my dissertation. As I read Raff's papers, it struck me that the only possibility off-limits -- indeed, never seriously at issue -- was that H. erythrogramma and H. tuberculata did not share a common ancestor.
Now, that's OK, in one respect. Science would never make any progress if everything was up for grabs. On the other hand, it is possible that common descent is false, and we should want to be able to discover that. So when was common descent observationally at risk?
As I put this question to Bill, and to the other members of my dissertation committee, they were at first annoyed. (Or embarrassed -- the same kind of polite embarrassment one has for people who say that the plays of Shakespeare were actually written by Francis Bacon or someone else. ![[Smile]](smile.gif) ) But I persisted. And the merits of the question began to emerge.
For instance, for a long time evolutionary biologists argued that we know common descent is true because animals develop in similar ways. There's a two-fold reason, biologists said: (1) development is functionally constrained (GE and related theories), and (2) animals inherit their functional constraints (including developmental) from their immediate ancestors. Thus, if common descent is true, and development is functionally constrained, one should expect to observe the conservation of embryonic form and process. We do observe such conservation; ergo, common descent is corroborated.
Except we don't observe embryonic conservation (or it's not the case as often as it is). All right: so who's going to pay for the failed prediction? Raff decided that GE would pay, not common descent, despite the fact that GE is strongly supported by experimental evidence.
I pointed this out to my dissertation committee, and the pattern of reasoning became a chapter in my dissertation. Common descent plus some other theory predict an outcome; the outcome is not observed; the other theories pay the cost, not common descent.
I mention all this because Heliocidaris and other indirect- and direct-developers (frogs and ascidians, for instance) were not seen to provide strong enough counterexamples to the strength of GE-type arguments. Heliocidaris etc. merit a section in my dissertation, but not much more than that.
In other words, there was a real problem with testing common descent.
My question again to Yersinia, Art, or anyone else who wants to chime in: Why would some biological patterns be inconsistent with common descent? If there is a deeper reason, explain what it is.
P.S. to Yersinia: Smith et al. were not testing common descent, they were assessing single-copy DNA distance. Their study would have tested common descent only if they had specified an outcome inconsistent with common ancestry, but of course they didn't.
P.P.S. In the years since I completed my Ph.D. (August 1998), there has been an explosion of publication on the question of common descent -- the main reason I'm still revising for publication myself! (And Leigh Van Valen is a scrupulous editor, bless him.) In 1994, Richard Lewontin argued to me in a letter that common descent was functionally an axiom of historical biology. The theory, he said, was simply not at issue for evolutionists. Since then, other authors, e.g., Kenneth Weiss at Penn State, have argued that common descent is, in fact, a genuine axiom (he writes that "we insist on a point source [single ancestor] for the whole of life." See his paper, "We Hold These Truths to Be Self-Evident," Evolutionary Anthropology 10 (2001):199-203.
So the subject has grown immensely richer, and polite embarrassment on the topic, while still frequent, isn't quite so pronounced, much to my relief.
[ 10. February 2003, 11:37: Message edited by: Paul A. Nelson ]
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Frances
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posted 10. February 2003 12:25
Dear Paul,
Perhaps it may be helpful to the focus of this discussion to look at the posting by Yersinia which captured the essentials.
quote:
A continuum of modifications of the pluteus has evolved, ranging from obligately feeding pluteus to loss of all larval features. These modifications include facultative planktotrophy (Emlet 1986), nonfeeding plutei (Okazaki 1975; Olsen et al., accepted), armless nonfeeding larvae, and brooded embryos that lack a larval stage. The changes resulting in direct development are expressed as a pattern of heterochronies, in which many features of indirect larval development are deleted
or abbreviated, and features of adult development are initiated early and are accelerated in rate. The evolution of direct development is accompanied by changes in oogenesis.
It seems that there may be evidence for a transitional sequence after all? Paul seems to object though because these intermediates are not for Heliocidaris. This is surprising because it seems that Paul would accept an evolutionary pathway for other species which show similar retarded development but would hold heliocidaris to be a special case? Why? After all the evidence shows that such intermediates are possible for other species. Is Heliocidaris special in some form? Certainly the evidence shows that contrary to Paul's suggestion in his talk, developmental networks can be changed to lead to significant morphological variations. Which is the argument in the paper by Smith
quote:
The changes resulting in direct development are expressed as a pattern of heterochronies, in which many features of indirect larval development are deleted or abbreviated, and features of adult development are initiated early and are accelerated in rate.
It may indeed be that the ideas of GE are not supported by the evidence which suggests les and less support for your thesis. Thus while certain 'essential' developmental genes seem to be strongly conserved (although they stil show some evidence of evolutionary patterns), the timing and expression of these genes seems to be controlled by less conserved gene networks.
To address Paul's common descent side question: When is common descent at risk? Yersinia and others provided for examples but given the vaste amount of evidence in favor of common descent, the likelyhood of common descent becoming at risk has decreased significantly, just like the probabilities of Einstein's theories being rejected becoming smalller and smaller over time.
Paul you suggest a scenario in which the two heliocidaris do not share a common ancestor. What is your likely mechanisms and explanations absent common descent?
Perhaps we should determine if such an alternative explanation has any merrits.
p.s. Smith et al and others did test 'common descent' despite the fact that they did not 'specify' outcomes inconsistent with common descent. For the same reason testing the constancy of the speed of light can disprove Einstein when one were to find a persistent inconsistency that showed higher than speed of light.
p.p.s While common descent may have become more of an interest lately because of the early roots being confused by a stage of horizontal transfer, common descent still is a very viable, may I say the only viable(?) intepretation of the evidence. Note that common descent does NOT require a single common ancestor btw, even Darwin realized this. "The grandeur of Darwin’s view was
“of life having been breathed by the
Creator into a few forms or into one.”" from Kenneth Weiss's paper. Paul's interpretation of a 'common point source' needs to be interpreted in its context it seems. I doubt that Weiss was arguing a literary interpretation given his introduction to the topic.
p.p.p.s Lets refocus though on the Heliocidaris and their relevance to Paul's comments in his talk. Does Paul btw propose an alternative explanation of the evidence? It would be interesting indeed to compare.
[ 10. February 2003, 12:46: Message edited by: Frances ]
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Paul A. Nelson
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posted 10. February 2003 12:33
Frances,
The "intermediates" mentioned by Yersinia are in other sea urchin genera, not Heliocidaris. It's a bad habit in evolutionary reasoning (stemming from Darwin) to go fishing outside the group in question for apparent intermediates. Raff himself, in later publications, doesn't do this, but has tried to understand Heliocidaris evolution by comparing H. erythrogramma and H. tuberculata.
You write:
quote:
To address Paul's common descent side question: When is common descent at risk?
What's your answer to this question, Frances? I'm curious.
[ 10. February 2003, 12:36: Message edited by: Paul A. Nelson ]
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yersinia
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Member # 324
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posted 10. February 2003 14:51
Hi Paul,
Well, I figured you'd been through all this before.
quote:
The "intermediates" mentioned by Yersinia are in other sea urchin genera, not Heliocidaris. It's a bad habit in evolutionary reasoning (stemming from Darwin) to go fishing outside the group in question for apparent intermediates. Raff himself, in later publications, doesn't do this, but has tried to understand Heliocidaris evolution by comparing H. erythrogramma and H. tuberculata.
But you, my dear Paul, are just as much reasoning from other organisms when you point to a pattern of developmental conservation. The notion of generative entrenchment is based on looking at many other organisms. Seems that you share our bad habits, Paul. :-)
What your whole account here misses, just as it is missed in the essay that Francis linked, is that common descent and "generative entrenchment" are both subject to evaluation by other, independent evidence. You like to look at things in a very isolated, cut-up-into-little-pieces way. But what you have to do is look for additional evidence that strengthens or weakens each hypothesis.
For example, the hypothesis of strict generative entrenchment would predict no viable intermediates between types of development. But such intermediates exist, there appear to be all manner of development pathways between direct and indirect development. Art mentioned another similar case in plants which I think brings up a fundamental point about development: we have to remember that we are talking about cells, and we have innumerable cases of "out-of-place" structures developing where they shouldn't be, basically because a developmental program was turned on in these cells.
And furthermore, we have had much progress in the past 25 years learning the molecular biology of development and developing and testing theories on how developmental processes may change. There are several articles on just this mechanistic topic for Heliocidaris. Despite 25 years of highly committed work in antievolutionism we don't even have a similar scrap of a hypothesis for an alternative to common descent.
Speaking of common descent, there are all kinds of evidence unrelated to development which can be used to test the hypothesis of common descent for Heliocidaris. Sure, like the evaluation of most hypothesis, supplemental hypotheses are required -- for example, you have to know something about the mechanisms of mutation and substitution to say something about sequence divergence. But all of these supplementary hypotheses are similarly testable on their own ground -- e.g., we can observed sequence divergence in separated laboratory populations and then see if the trees reconstructed with the sequences match actual patterns of descent.
E.g., an awful lot of this testing of supplementary hypotheses is discussed here.
quote:
Phylogenetic Reconstructions: Reliability
In order to establish their validity in reliably determining phylogenies, cladistic methods have been empirically tested in cases where the true phylogeny is known with certainty, since the true phylogeny was directly observed.
Bacteriophage T7 was propagated and split sequentially in the presence of a mutagen, where each lineage was tracked. Out of 135,135 possible phylogenetic trees, the true tree was correctly determined by cladistic methods in a blind analysis. Five different statistical cladistic methods were used independently, and each one chose the correct tree (Hillis et al.1992 ).
In another study, 24 strains of mice were used in which the genealogical relationships were known. Cladistic analysis reproduced almost perfectly the known phylogeny of the 24 strains (Atchely and Fitch 1991).
Bush et. al. used phylogenetic analysis to retrospectively predict the correct evolutionary tree of human Influenza A virus 83% of the time for the flu seasons spanning 1983 to 1994.
In 1998, researchers used 111 modern HIV-1 (AIDS virus) sequences in a phylogenetic analysis to predict the nucleotide sequence of the viral ancestor of which they were all descendants. The predicted ancestor sequence closely matched, with high statistical probability, the actual HIV sequence found in an HIV-1 seropositive African plasma sample collected and archived in the Belgian Congo in 1959 (Zhu et al.1998 ).
In the past decade, phylogenetic analyses have played a significant role in successful convictions in several criminal court cases (Albert et al. 1994; Arnold et al. 1995; Birch et al. 2000; Blanchard et al. 1998; Goujon et al. 2000; Holmes et al. 1993; Machuca et al. 2001; Ou et al. 1992; Veenstra et al. 1995; Vogel 1997; Yirrell et al. 1997), and phylogenetic reconstructions have now been admitted as expert legal testimony in the United States (97-KK- 2220 State of Louisiana v. Richard J. Schmidt [PDF]) . The legal test in the U. S. for admissibility of expert testimony is the Daubert guidelines (U. S. Supreme Court Case Daubert v. Merrell Dow Pharmaceuticals, Inc., 509 U.S. 579, 587-89, 113 S. Ct. 2786, 2794, 125 L. Ed. 2d 469, 1993). The Daubert guidelines state that a trial court should consider five factors in determining "whether the testimony's underlying reasoning or methodology is scientifically valid": (1) whether the theory or technique in question can be and has been tested; (2) whether it has been subjected to peer review and publication; (3) its known or potential error rate; (4) the existence and maintenance of standards controlling its operation; and (5) whether it has attracted widespread acceptance within the relevant scientific community (quoted nearly verbatim). Phylogenetic analysis has officially met these legal requirements.
Innumerable additional cases could be cited, e.g. studying disperal abilites of species can be done independently of concerns about common descent but is important for making biogeographic predictions based on common descent.
So, in short, Paul, you need to defend your assumption that supplementary hypotheses are not subject to evaluation independent from common descent.
[edit to fix random internet cutoff]
[ 10. February 2003, 15:11: Message edited by: yersinia ]
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Argon
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posted 10. February 2003 19:32
Regarding how common descent may be "at risk":
Walter ReMine proposed several patterns of life that would, to paraphrase Walter, "resist evolutionary explanations" (i.e. common descent with modification). His book received glowing reviews from numerous leaders in the ID movement, including Behe and Johnson. While the general consensus is that Walter's proposed patterns are not observed, that does not mean that common descent cannot, in principle, be rejected.
Other events such as horizontal transfer also place common descent at risk. In fact, we know that horizontal transfer has occured at various stages in the development of life. That is why I was careful to say "In most cases, common descent is no longer a question".
So no, common descent is not a concept that gets a "free pass". It is clearly false in some cases (e.g. known examples of horizontal transfer) and remains an open question at some deep divisions of life (e.g. the eubacterial/archaebacterial split).
Further, it must be obvious to ID theorists that with respect to the evolutionary modification of early-stage developmental pathways via functional intermediates, "design can do that." Again, the issue is not "common descent" but the mechanisms behind evolution.
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yersinia
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posted 10. February 2003 20:49
Hi Argon,
Regarding Lateral Gene Transfer, I agree that this is a good case of what we might call "traditional lineal common descent" having been tested and rejected, based in part on statistically major disagreements between various gene trees for various single-celled critters. Of course, we had supporting evidence that descent was not always vertical for single-celled microorganisms because we can observe them trading genes in the lab, so we have a pretty clear mechanism for how heredity can be partially horizontal for single-celled organisms.
The question then is what to we call this. How much lateral transfer does it take before we just give up on the notion of a "lineage" and start treating the gene-trading groups as one intercommunicating gene pool. This starts to sound like a species, which after all is what we were tracing the descent of originally...
I have not yet seen a satisfactory terminology to describe all of these potential complexities, particularly where the transfer of hereditary material is a combination of vertical and horizontal. In any case it does appear to be essentially (not quite completely, there are viral transfers) irrelevant for metazoans with protected germ-line cells.
[/terminological ramble]
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Argon
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posted 10. February 2003 22:31
Yersinia wrote:
"I have not yet seen a satisfactory terminology to describe all of these potential complexities, particularly where the transfer of hereditary material is a combination of vertical and horizontal."
As illustrated in the excellent movie, "The Thing" (both versions). Taken to an extreme you begin to encounter notions like that of Periannan Senapathy (Independent birth of organisms link here).
continued:
"In any case it [horizontal transfer] does appear to be essentially (not quite completely, there are viral transfers) irrelevant for metazoans with protected germ-line cells."
Agreed. And of course the reason for this conclusion is that tests for the lineal descent of many metazoan genes as well as metazoan species have mostly confirmed the relationships.
But to get back to Paul Nelson's difficulties... If common descent truly was an "axiom" that could not be tested independently, how is it that some genes, or plastids & mitochondria for that matter are now generally thought to have arisen via horizontal transfer? To me, this makes the "problem" seem less of a fundamental flaw in logical reasoning and more like a philosophical molehill. The problem is not that common descent is given a free pass, it's that data isn't terribly supportive for anyone advocating the frequent de novo creation of unrelated species over an extremely short period time. There is no doubt that the data could have been different and more supportive of separate creation events, but the designer[s] didn't oblige in that direction. That is why, for example, Mike Behe considers himself an "evolutionist" (me too, FWIW).
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yersinia
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posted 11. February 2003 01:15
This article discusses in more detail than I could understand the ecological and mutational mechanisms behind the switch between direct and indirect development in frogs.
quote:
Bioessays 2001 Mar;23(3):233-41
Frogs without polliwogs: evolution of anuran direct development.
Callery EM, Fang H, Elinson RP.
Department of Biochemistry and Cell Biology, SUNY, Stony Brook, NY 11794, USA.
Direct development is the assumption of the adult morphology without progression through an intervening, morphologically distinct, free-living larval phase. We discuss the ecological factors contributing to the evolution of this derived life-history strategy in frogs, and the developmental modifications that facilitate such an unusual mode of embryogenesis. Studies on the Puerto Rican tree frog, Eleutherodactylus coqui, have identified several such modifications, including developmental adaptations for dealing with increased egg size, and loss of tadpole structures. Surprisingly, this direct developer still undergoes a thyroid hormone-dependent metamorphosis, which occurs before hatching. We suggest how the ancestral biphasic developmental pattern may have been rearranged during the evolution of direct development.
Also mentioned in the article is the fact that direct development appears (in subgroups of) several phyla, e.g. echinoderms but also urochordates and molluscs ("and several other phyla").
Rather like the echinoderm situation, in frogs there appear to be all manner of intermediates between indirect and direct development, e.g. tadpoles that swim freely but don't feed and instead live off the yolk of their bigger eggs.
Lots of articles related to this one here.
[ 11. February 2003, 01:16: Message edited by: yersinia ]
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yersinia
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posted 11. February 2003 01:32
Argon,
I think I agree on the problems with calling common descent an "axiom". It is no more "axiomatic" than the ancient age of the earth is axiomatic. Rather, both are conclusions reached from data. FWIW I think the evidence is pretty darn strong for the common descent of all known life from an ancestral population of bacteria. Before that, things get truly murky and the number of possibilities for currently-unnamed combinations of horizontal and vertical heredity increases markedly.
I can, however, see the advantage of construing common descent as an "axiom": axioms can be freely denied by people who happen to have different axioms. Proposing a testable explanation that explains the data better is then no longer necessary.
[edit to fix typo]
[ 11. February 2003, 02:39: Message edited by: yersinia ]
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Josh
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posted 11. February 2003 09:52
I'm not posting this to be argumentative or to profess what I believe. I just want to know how you guys would answer the following.
1) Close similarity in DNA and amino acid sequences, which will group next to each other, to the exclusion of everything outside the genus, to a high degree of statistical confidence.
Why does this prediction fail if a designer created two closely related species?
2) Close similarity in chromosome number, structure, and gene arrangement on the chromosomes.
Same question?
3) Essentially all genes will be shared by both species.
And again, I don't see how you can rule out the idea that a designer created very similar animals.
4) The two species will have shared mistakes in non-functional pseudogenes
How do you prove something non-functional, isn't it impossible to prove a universal negative? Even if you can delete the gene and the organism survives, it doesn't mean that it has no function whatsoever and doesn't contribute to the organisms' fitness. Perhaps there is an environmental situation/selection not reproducible in the lab, making these things a requirement.
Also, how do we know for sure that these sequences, even if we could somehow completely prove that all pseudogenes (and similar genetic elements that seem uselesss) are completely worthless didn't occur after the creation of these beings over time?
Please don't literature bomb me, cause I don't hardly have time to read all of it, also, if I missed your defense of these points earlier, I apologize. I am just interested in how ardent evolutionists view this line of thinking, and how they distinguish it as an inviable option.
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Paul A. Nelson
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posted 11. February 2003 10:08
Guys,
First, on the axiomatic character of the theory of common descent. I was reporting what others have argued, not my own opinion. Here's Kenneth Weiss of Penn State (2001) discussing common descent -- what he calls one of the "basic principles of darwinian biology" (p. 199):
quote:
The assumption of a point source is important to the entire theory, so we insist upon spontaneous generation in the beginning, but must forbid it at any other time. (pp. 199-200)
At the end of his article, Weiss argues that "shared ancestry is inviolate" (p. 203). This is exactly the same claim Lewontin made in his June 1994 letter to me (given the assumption of common descent, he wrote, "all the rest is commentary" [i.e., all the rest about evolution]). The systematist Kevin de Queiroz argues that "if we truly live in a Darwinian era, the axiom of common ancestry should be readily accepted" (1988, 245). And so on.
Please bear in mind that when I post here, I'm reporting the views of others in addition to discussing my own position. I toyed with the idea that common descent was an axiom some years ago (in 1993):
http://www.arn.org/docs/nelson/pn_darwinianparadigm061593.htm
I came to reject this view, however, because the evolutionary biologists with whom I work most closely talked me out of it. From Chapter One of my monograph, "On Common Descent":
quote:
When I reported my conclusions [that common descent was an axiom] to Bill Wimsatt, however, supporting them by citing one of his own mentors (Richard Lewontin), Bill surprised me by disagreeing vigorously. He had never thought of Common Descent as anything even remotely resembling an axiom or necessary truth of biology, he said, and if the theory were so regarded, that would be a mistake. Common Descent might turn out to be false. Nor did Leigh Van Valen, another evolutionary theorist to whom I proposed the "necessary truth" interpretation of the theory, find it persuasive. Hypotheses of common ancestry flow from biological evidence, Van Valen and Wimsatt argued, and they could be overturned by evidence. There is nothing axiomatic about them.
Second -- Yersinia, you suggested above some patterns of biological evidence that you said would be inconsistent with common descent. I asked you why they would be inconsistent, but couldn't find an answer to that question in your next series of posts.
So I'll ask it again. Why would the patterns you mentioned refute common descent? There must be some grounds, and it's important to know what those grounds are. You've made clear under what circumstances you think common descent is well-supported. Under what evidence, and why, would you say that common descent was not supported? (You've provided hypothetical evidence above -- please give the "why." Let me stress that this question is directly relevant to our debate re the significance of Heliocidaris and other such cases. I'm not trying to yank your chain or whatever; if you were here in Chicago, and we were sipping tea at a philosophy of science/ev bio colloquium, I'd ask exactly the same question, and would even pass you the sherry if you wanted it, as long as I could help myself to the bottle as it passed. <grin>).
Third -- on to new points.
Yersinia wrote:
quote:
But you, my dear Paul, are just as much reasoning from other organisms when you point to a pattern of developmental conservation. The notion of generative entrenchment is based on looking at many other organisms. Seems that you share our bad habits, Paul. :-)
Maybe! Hang around ev bio departments long enough, and you'll inevitably be corrupted, I guess... ![[Big Grin]](biggrin.gif)
Seriously: Generative entrenchment is not a phylogenetic hypothesis. But your use of other echinoderm taxa to provide "intermediates" between H. erythogramma and H. tuberculata -- which is exactly how Frances understood your post, BTW -- is such a hypothesis, and an illegitimate one. You'd never get it published in a systematics journal, because it doesn't make any biological sense. And that's the reason Raff doesn't appeal to these other groups to explain the evolution of Heliocidaris.
Yersinia writes:
quote:
For example, the hypothesis of strict generative entrenchment would predict no viable intermediates between types of development. But such intermediates exist, there appear to be all manner of development pathways between direct and indirect development.
Actually, no, if by "developmental pathway," one means something that can be observed to change viably. Neither Raff nor anyone else has ever succeeded in heritably perturbing the specific developmental pathways of Heliocidaris, whether indirect or direct. The "viable intermediates" you mention take on that status only when one strings together unrelated groups, which is biologically nonsensical.
Here's a PubMed treasure hunt for you. Find an example of the observed heritable modification of early cleavage patterns in any metazoan, that is, where the novel pattern is stably transmitted beyond the first generation. Gastropod shell coiling (levo-to-dextro or vice versa) doesn't count.
There's a long tradition in 20th century evolutionary theory of explaining why viable macromutations are rarely, if ever, observed. Ever wonder why?
Generative entrenchment (GE) predicts that the developmental pathways of any species are subject to discoverable constraints. GE can be bled of its predictive strength, however, by the theory of common descent, if the latter is privileged when predictions (made by conjoining the two theories) fail. I'd say we know far more about GE than we do about common descent; so why should common descent get the pass?
Argon wrote, re the problem of testing common descent:
quote:
To me, this makes the "problem" seem less of a fundamental flaw in logical reasoning and more like a philosophical molehill.
Then you (Argon) should have no trouble saying how you would test common descent, i.e., the theory that all organisms on Earth share a common ancestor. If you think that theory isn't true, however, explain why. Give the test that the theory has failed, or provide the evidence that it cannot explain.
Refs
de Queiroz, Kevin. 1988. Systematics and the Darwinian Revolution. Philosophy of Science 55:238-259.
Weiss, Kenneth. 2001. We Hold These Truths to Be Self-Evident. Evolutionary Anthropology 10:199-203.
[ 11. February 2003, 11:06: Message edited by: Paul A. Nelson ]
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yersinia
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posted 11. February 2003 10:57
Josh,
Ack, I just wrote a post and the server crashed, or something. Unfortunately I don't have time to re-write. Briefly, look here:
Pseudogenes:
Plagiarized Errors and Molecular Genetics
http://www.talkorigins.org/faqs/molgen/
Chromosome differences, e.g. the one large difference between human, chimp, gorilla, and orang chromosomes.
Discussed in detail here
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Paul A. Nelson
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posted 11. February 2003 11:01
I'll be able to contribute to this thread for another day or so, and then I'll have to leave for lectures at the University of Connecticut, Dartmouth, and Northeastern.
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yersinia
Member
Member # 324
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posted 11. February 2003 11:34
Paul writes, again,
quote:
Why would the patterns you mentioned refute common descent?
The postulated process of common descent involves:
1) Reproduction. The genes of organisms are copies of those of their parents. If you deny this premise, Paul, let me know.
2) Small, stochastic changes in the above copying process. Basically I'm talking about neutral point mutations in degenerate positions in codons (and their substitution in the population by drift) although we could go into endless complexity discussing other mutations and population genetics. If you deny this premise, Paul, let me know.
Simulate the process:
(A) Start with a sequence. Copy it, producing a child, and destroy the parent. Repeat this many times, allowing for a small chance of a mutation each generation. The sequence will slowly change.
(B) Now, duplicate the sequence so you now have two identical sequences. Repeat process (A) with both sequences.
After a while you will end up with two sequences that are moderately different from each other.
After a while, repeat B, so you now have 4 sequences. Perform A on these sequences.
Result: you will have four sequences, and a similarity tree will place them in two groups, reflecting the recency of their common ancestry. This is a simply nested hierarchy produced by a process of common descent. This nested hierarchy pattern will be produced *every time* by this process as long as the sequence length is reasonably long, the chance of change in any particular generation is small, and the location of the sequence changes is at least somewhat random. Eventually the sequences will diverge so far that similarity will be randomized, but if the probability of change is small this will take a long time.
You can reproduce this on a computer if you like.
We get nested hierarchies from the above types of simulation. We get them in experimentally separated lab populations. We get them in "natural experiments" where isolated populations have been founded e.g. on islands (or in HIV infection of individuals). In all these cases the sequence similarity trees match the actual, independently known pattern of descent. I just think that when we see the same pattern in sea urchins, we should reach the same conclusion.
Agree or disagree, Paul?
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