|
Author
|
Topic: Ontogenetic Depth and the Origin of Animals
|
Pim van Meurs
Member
Member # 541
|
posted 07. September 2003 01:14
Paul,
Now that you and Ross have presented your paper could we get some update as to the details of the arguments? I am still curious as to the nature of the claims.
Society for Developmental Biology 62nd Annual Meeting Jointly with the International Society of Developmental Biologists July 30 - August 3, 2003
Marriot Copley Place, Boston, MA
65 B58 Understanding the Cambrian Explosion by Estimating Ontogenetic Depth. P.A. Nelson and M.R. Ross. Discovery Inst. and the Univ. of Rhode Island.
Source
I would be interested to see the actual ontogenetic depth measurements and the explanations provided. Would this be possible?
IP: Logged
|
|
Paul A. Nelson
Member
Member # 26
|
posted 07. September 2003 15:31
I'll have a pdf made of the SDB 2003 poster text file, and will post it here with commentary in a few days.
IP: Logged
|
|
Pim van Meurs
Member
Member # 541
|
posted 07. September 2003 22:10
Cool Paul, thank you.
IP: Logged
|
|
Walter ReMine
Member
Member # 906
|
posted 08. September 2003 12:31
quote:
"Walter ReMine proposed several patterns of life that would, to paraphrase Walter, "resist evolutionary explanations" (i.e. common descent with modification)." (Argon, February 10, 2003)
Contrary to Argon's assertion, I do not equate "evolutionary explanations" and "common descent with modification." Evolutionary explanations obviously also include many that would not traditionally be called descent with modification, such as:
- transposition (a.k.a. lateral DNA transfer),
- atavism (a.k.a. genetic throwbacks),
- data "incompleteness" (such as an "incomplete fossil record"), and
- various versions of "It came from Space."
Designing life to resist all evolutionary explanations (not just your personal favorite) and simultaneously make life signal that it came from one designer, and simultaneously be good design for survival, makes for a design challenge that is not easy. I encourage you to look at it.
quote:
"Walter ReMine proposed several patterns of life that would, to paraphrase Walter, "resist evolutionary explanations" .... While the general consensus is that Walter's proposed patterns are not observed, ..." (Argon, February 10, 2003)
Evolutionists have no "general consensus" on my proposal -- nothing whatever in ink, and rampant misrepresentation of my views on the Internet (usually by evolutionists posting under pseudonyms). Argon has done that here. The several "patterns of life" that I identify are widely recognized, and I document them in evolutionists own words. In other words, I thoroughly dispute Argon's claim.
=====================================
Argon attempts to show that evolution is a 'risky' theory -- a testable, scientific theory. He does that first by (falsely) equating "evolution" with "common descent," and then by arguing that there are other evolutionary mechanisms that, if true, would falsify common descent -- One evolutionary theory is 'falsified' only by finding a better evolutionary theory. Here it is in action:
quote:
"Regarding how common descent may be "at risk": .... Other events such as horizontal transfer also place common descent at risk. In fact, we know that horizontal transfer has occurred at various stages in the development of life. .... 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)." (Argon, February 10, 2003)
My book documents various cases where evolutionists use that tactic:
- Evolutionists claim natural selection is testable, because it would be shown false if Lamarckian inheritance (another evolutionary mechanism) were shown as true.
- Evolutionists claim punctuated equilibrium is testable, because it would be shown false if gradual evolution over large-scales were shown by the fossil record.
- Evolutionists claim evolutionary theory is testable, because common descent would be shown false if transposition (i.e. lateral DNA transfer) where shown as true.
Those tactics never put evolutionary theory seriously at risk. Instead, they create the illusion that evolutionary theory is risky, testable, science.
-- Walter ReMine
The Biotic Message
IP: Logged
|
|
Argon
Member
Member # 276
|
posted 08. September 2003 19:03
Walter ReMine writes:
quote:
Designing life to resist all evolutionary explanations (not just your personal favorite) and simultaneously make life signal that it came from one designer, and simultaneously be good design for survival, makes for a design challenge that is not easy. I encourage you to look at it.
Thank you for the correction, Walter.
My original post was to address Paul Nelson's question: "If H. erythrogramma and H. tuberculata were not related by common descent, how would you know it?" Subsequent discussion expanded to what evidence might cause one to suspect common descent. In determining the lineage of particular genes, or even whole organelles, horizontal transfer can give results that are discordant with the patterns expected by common descent. If one attempts to construct a phylogeny based on horizontally transferred genes, it's not likely to provide a pattern that is congruent with organismal trees. I did not intend to address the question of whether the general concept of evolution was at risk, but whether arguments against common descent can be sustained in particular instances. I also suggested that Walter ReMine had proposed other sets of patterns that would potentially go against the notion of common descent. I don't recall Paul either acknowledging or disputing Walter's contribution to ID. But clearly, if Walter's thesis is right, common descent (as a subset of evolutionary explanations) cannot be correct. So there must be patterns that are not compatible with common descent.
[ 08. September 2003, 21:20: Message edited by: Argon ]
IP: Logged
|
|
Walter ReMine
Member
Member # 906
|
posted 09. September 2003 00:39
I had stopped by earlier today firstly to clear up untrue assertions being made about my views. Now back to the topic of the thread.
I believe Paul Nelson is asking: 'If two organisms were not related by common descent, how would you-evolutionists know it?'
Argon writes:
quote:
"But clearly, if Walter's thesis is right, common descent (as a subset of evolutionary explanations) cannot be correct. So there must be patterns that are not compatible with common descent." (Argon, September 8, 2003)
Argon has not answered the question -- he has not told us what evolutionists think -- instead he refers us to an ANTI-evolutionist (Walter ReMine) for the answer.
Here is my answer: Evolutionists would know two organisms were not related by common descent when they can find a better naturalistic explanation. Such as:
- transposition (a.k.a. lateral DNA transfer),
- data "incompleteness" (such as an "incomplete fossil record"),
- multiple origins of life, and
- various versions of "It came from Space."
This is a no-lose, no-risk strategy for evolutionists. To evolutionists, one evolutionary explanation is 'refuted' only by finding a better evolutionary explanation! Argon's discussion is a precise example of this.
-- Walter ReMine
The Biotic Message
[ 09. September 2003, 00:48: Message edited by: Walter ReMine ]
IP: Logged
|
|
Pim van Meurs
Member
Member # 541
|
posted 09. September 2003 01:19
Walter I do not understand your argument
quote:
Evolutionists would know two organisms were not related by common descent when they can find a better naturalistic explanation. Such as:
transposition (a.k.a. lateral DNA transfer),
data "incompleteness" (such as an "incomplete fossil record"), multiple origins of life, and
various versions of "It came from Space."
This is a no-lose, no-risk strategy for evolutionists. To evolutionists, one evolutionary explanation is 'refuted' only by finding a better evolutionary explanation! Argon's discussion is a precise example of this.
Transposition need not point to absence of common descent but it does make tracing the tree more problematic. Nor do multiple origins make common descent problematic, one or multiple roots has no relevance to the validity of evolutionary theory. Data incompleteness can make inferences inconclusive.
Walter seems to object that science would not abandon evolutionary theory as is until something better is found. But that seems quite understandable, evolutionary theory seems to be doing quite well and although it is constantly being updated and modified by new exciting findings, there is really little data that would suggest that it needs to be abandoned. Certainly there does not seem to be any better theory available that explains the data better.
Perhaps Walter may help us understand why he italicized naturalistic in "better naturalistic explanation".
What other explanations are and which ones are relevant to scientific inquiry?
I may be under the faulty belief that Walter rejects common descent so there must be patterns that are not compatible with common descent.
But transposition, incompleteness and multiple origins seem to be minor objections. Are there any scientific grounds on which Walter rejects common descent?
As far as natural selection being testable, there are some good studies of such. Or as talkorigins explains
quote:
The theory of Punctuated Equilibria provides paleontologists with an explanation for the patterns which they find in the fossil record. This pattern includes the characteristically abrupt appearance of new species, the relative stability of morphology in widespread species, the distribution of transitional fossils when those are found, the apparent differences in morphology between ancestral and daughter species, and the pattern of extinction of species. "
Source
Punkeek is a mechanism in addition to other Darwinian mechanisms to explain the fossil record. Punk Eek and gradualism can co-exist quite fine.
Walter continues: Evolutionists claim evolutionary theory is testable, because common descent would be shown false if transposition (i.e. lateral DNA transfer) where shown as true.
Disproving common descent would be a strong disproof of darwinian evolution. But I am not sure if transpositions would disprove common descent.
But Argon was talking about common descent in particular.
But in the end the data supporting common descent, even if it were common descent from multiple roots or if the root were a branch or cannot be identified due to incomplete data and/or horizontal transfer, is quite extensive I would argue.
[ 09. September 2003, 01:20: Message edited by: Pim van Meurs ]
IP: Logged
|
|
charlie d.
Member
Member # 159
|
posted 09. September 2003 07:57
If I understand him correctly, I think Walter means that when data are somewhat hard to fit in a "classic" evolutionary framework, explanations are found that preserve the theory while allowing for exceptions, or modifying the theory peripherally while maintaining its basic principles inact. That is the case for HGT to explain some molecular phylogenetic inconsistencies, punk-eek to explain the alternation of stasis and change in the fossil record, etc. However, these corrective hypotheses are never "ad hoc", but rest on independent evidence and theoretical considerations. For instance, we knew HGT occurred in nature (eg, for bacterial antibiotic resistance) long before it was postulated to have played a role in evolution. [So, actually, the situation is opposite to what Walter states. Common descent would not be "shown false if transposition (i.e. lateral DNA transfer) where shown as true", but rather common descent would be in a bind if it we had no evidence whatsoever that HGT could occur, because then we'd have no explanations compatible with common descent for the occasional phylogenetic tree discrepancies.]
Furthermore, corrections and exceptions are common to any scientific theory, not just evolution; I'd be hard pressed to find a single mature theory that has not been modified this way. This is quite simply how science works. As Pim states, one would have to be crazy to discard a perfectly good, very successful theory at the first difficulty, especially if there is no better alternative available.
IP: Logged
|
|
Walter ReMine
Member
Member # 906
|
posted 09. September 2003 07:58
Pim van Meurs writes:
quote:
"Walter seems to object that science would not abandon evolutionary theory as is until something better is found." (Pim van Meurs, September 9, 2003)
I said no such thing. I object to the evolutionists' chronic misrepresentations of me, and the empty posturing they pursue with it. It's what turns forums like this into a thorough waste of time, and why I will not be staying long.
I was pointing out that evolutionary theory (in all its modern potentialities) is scarcely risky or testable: What would conceivably make evolutionists abandon evolution? Pim van Meurs did not answer that, indeed he confirmed my point by citing many things that would not make him abandon evolution! Evolutionary theory is now so amorphous that it can accommodate virtually any concievable data.
===============
quote:
Perhaps Walter may help us understand why he italicized naturalistic in "better naturalistic explanation". (Pim van Meurs, September 9, 2003)
In my previous post I used the word "naturalistic" to be more precise (perhaps needlessly over-precise), because some explanations within evolutionary theory -- namely data incompleteness (e.g. the incomplete fossil record), and "It came from Space!" -- are not always thought of as evolutionary. But they are naturalistic. Replace it with the word "evolutionary," if that pleases you. In other words: Evolutionists would know two organisms were not related by common descent when they can find a better evolutionary explanation.
The italics are self-explanatory.
-- Walter ReMine
The Biotic Message
IP: Logged
|
|
Paul A. Nelson
Member
Member # 26
|
posted 09. September 2003 09:56
Walter wrote:
quote:
I believe Paul Nelson is asking: 'If two organisms were not related by common descent, how would you-evolutionists know it?'
That's correct.
Walter also wrote:
quote:
Evolutionists would know two organisms were not related by common descent when they can find a better naturalistic explanation.
Again, I think this is correct. As Charlie D has pointed out, on this discussion board and elsewhere, the deeper assumption of evolutionary reasoning -- that is, deeper than universal common descent itself -- is naturalism.
Let me recommend a couple of recent (fascinating) papers on this topic:
Elliott Sober and Michael Steel, "Testing the hypothesis of common ancestry," Journal of Theoretical Biology 218 (2002):395-408.
David Penny, Michael D. Hendy, and Anthony M. Poole, "Testing fundamental evolutionary hypotheses," Journal of Theoretical Biology 223 (2003):377-385.
[ 09. September 2003, 10:00: Message edited by: Paul A. Nelson ]
IP: Logged
|
|
Argon
Member
Member # 276
|
posted 09. September 2003 11:00
Walter writes:
quote:
Here is my answer: Evolutionists would know two organisms were not related by common descent when they can find a better naturalistic explanation.
I think that is a perfectly rational and reasonable scientific approach, so I agree. That's how I answered Paul Nelson's question. I will also add: Or a better, verifiable, and coherent explanation by intelligent intervention (By "intelligent intervention" I don't distinguish between naturalistic or non-naturalistic sources which could include Gods, humans, or hyperintelligent shades of blue). Note that this approach not limited to "metaphysical naturalism". I think that is how ID evolutionists like Michael Behe, Mike Gene and Michael Denton have come to interpret the data too (i.e. for the most part accepting common descent while trying to determine at what points intervention or "direction-guiding" influences happened).
[ 09. September 2003, 11:01: Message edited by: Argon ]
IP: Logged
|
|
charlie d.
Member
Member # 159
|
posted 09. September 2003 11:42
Uhm, Paul, did I really say that? I don't think that a successful alternative explanation to evolution has to be necessarily "naturalistic", altough it has to be "investigatable" and supported by independent evidence.
I could easily imagine that if scientists could make evolution happen in a reliably reproducible way by prayer, and that happened in front of their eyes in some miracolous way, the explanation for the phenomenon would certainly be supernatural, and naturalistic evolution would be rejected as a very cumbersome explanation for what would seem to be a very simple supernatural process. In a more realistic scenario, if we found solid independent evidence of mechanisms of evolution that are clearly not those we know of today, and are compatible with supernatural explanations (eg, mix-and-match of genetic sequences, absence of nested phylogenetic trees, species appearance in the fossil record in a non-ordered temporal fashion, etc etc), creationism would become a very valid alternative, in many ways preferable to naturalistic evolution.
It seems to me that the inability of various forms of creationism to dislodge evolution (as currently understood) as the dominant scientific theory for biological diversity has little to do with naturalism, and much to do with the absence of corroborating evidence for creationism and the abundant evidence for evolution itself.
The only way the evidence can fit creationist scenarios is to make layer upon layer of arbitrary assumptions that make creationism literally indistinguishable from naturalistic evolution (sure, God could have created life with an intrinsic nested hierarchy of anatomical and molecular features, and an artificial fossil record to go with it, but why?). In this case, evolution "wins" as a theory because of parsimony, and again because it's investigatable, while creationism isn't. Until we learn to use prayer to make new species appear, that is. ![[Wink]](wink.gif)
IP: Logged
|
|
Pim van Meurs
Member
Member # 541
|
posted 09. September 2003 11:50
Walter objects to my characterization "Walter seems to object that science would not abandon evolutionary theory as is until something better is found."
Walter: I said no such thing
I was refering to Walter's statement that 'This is a no-lose, no-risk strategy for evolutionists. To evolutionists, one evolutionary explanation is 'refuted' only by finding a better evolutionary explanation! Argon's discussion is a precise example of this. "
Walter wonders what data would be necessary to convince me that evolution did not happen. A good question that becomes harder and harder over time since the supported evidence is so extensive that the bar for rejecting evolution is raised continuously. It's like asking me what would convince me to reject gravity :-)
Rabbits in the cambrian would be quite a shock.
I agree with Walter that incompleteness in data is not necessarily thought of as evolutionary or anti-evolutionary, it seems to be somewhat neutral in this aspect. But I start to understand Walter's 'argument'.
Let me give it a try: Walter objects to evolutionary theory's ability to incorporate new knowledge, new mechanisms which make it hard to refute.
Before I comment let me make sure that I have correctly represented Walter since he seems to be somewhat have somewhat of a 'hair trigger'.
Paul comments: the deeper assumption of evolutionary reasoning -- that is, deeper than universal common descent itself -- is naturalism.
Methodological naturalism to be more precise. My question to Paul is two fold, does he believe that there is something wrong with such methodological foundation and if Paul believes that there is something wrong or incomplete, what scientific foundation for inquiry does Paul propose?
As far as Sober's paper is concerned Here
quote:
The hypothesis that all life on earth traces back to a single common ancestor is a fundamental postulate in modern evolutionary theory. Yet, despite its widespread acceptance in biology, there has been comparatively little attention to formally testing this ‘‘hypothesis of common ancestry’’. We review and critically examine some arguments that have been proposed in support of this hypothesis. We then describe some theoretical results that suggest the hypothesis may be intrinsically difficult to test. We conclude by suggesting an approach to the problem based on the Aikaike information criterion.
it is interesting to see how Sober defines common descent
quote:
The Hypothesis of Common Ancestry says that there exists a single ancestral origin to which all present-day living things trace back. This hypothesis competes with alternative hypotheses that say that the number of ancestors is 2, 3, ..., or n.
Personally I would still consider the alternative hypotheses to be examples of common descent.
quote:
Conclusions:
The hypothesis of common ancestry is central to contemporary evolutionary theory. However, a valid methodology fortesting that hypothesis that allows one to look at suites of characters has
not, until now, been available. We hope that biologists will use the protocol we have described
for different sets of species. It may turn out that all is well with the conventional wisdom on this subject. What Crick defended by considering a
single characteristic the genetic code may be vindicated when one considers sets of characteristics whose functional significance is less well understood. But perhaps it will emerge that for some groups of species, the data do not provide unambiguous support for the idea that there is a single common ancestor. If there is a temps perdu if genealogical connections are unretrievable forevents that are sufficiently far in the past this is something that biology needs to ascertain. And if one of the CA-i hypotheses fares better than CA-1, this too would be a result of considerable interest.
and
Testing fundamental evolutionary hypotheses.
J Theor Biol. 2003 Aug 7;223(3):377-85.
Penny D, Hendy MD, Poole AM.
quote:
Abstract
Sober and Steel (J. Theor. Biol. 218, 395-408) give important limits on the use of current models with sequence data for studying ancient aspects of evolution; but they go too far in suggesting that several fundamental aspects of evolutionary theory cannot be tested in a normal scientific manner. To the contrary, we show examples of how some alternatives to the theory of descent can be formulated in such a way that they lead to predictions that can be evaluated (and rejected). The critical factor is a logical formulation of the alternatives, even though not all possible alternatives can be tested simultaneously. Similarly, some of the limits using DNA sequence data can be overcome by other types of sequence derived characters. The uniqueness (or not) of the origin of life, though still difficult, is similarly amenable to the testing of alternative hypotheses.
Poole has also an interesting paper on LUCA, the last universal common ancestor.
Of interest may also be "Common Ancestry and Natural Selection" by Sober and Orzack
Sober et al consider three hypotheses about natural selection.
quote:
(U) Natural selection has been an influence on the evolution of most traits in most populations.
(I) Natural selection has been an important influence on the evolution of most traits in most populations.
(O) Natural selection has been the only important influence on the evolution of most traits in most populations.
and conclude among others that:
quote:
The fact of adaptation hinders one’s ability to test hypotheses of common ancestry, but the fact of common ancestry helps one test adaptive hypotheses.
[ 09. September 2003, 12:00: Message edited by: Pim van Meurs ]
IP: Logged
|
|
Paul A. Nelson
Member
Member # 26
|
posted 09. September 2003 12:40
Mix and match genes would challenge naturalistic evolution?
Hm.
Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ.
Genome Biology 2003;4(9):R55. Epub 2003 Aug 29.
Omelchenko MV, Makarova KS, Wolf YI, Rogozin IB, Koonin EV.
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. koonin@ncbi.nlm.nih.gov
BACKGROUND: Shuffling and disruption of operons and horizontal gene transfer are major contributions to the new, dynamic view of prokaryotic evolution. Under the 'selfish operon' hypothesis, operons are viewed as mobile genetic entities that are constantly disseminated via horizontal gene transfer, although their retention could be favored by the advantage of coregulation of functionally linked genes. Here we apply comparative genomics and phylogenetic analysis to examine horizontal transfer of entire operons versus displacement of individual genes within operons by horizontally acquired orthologs and independent assembly of the same or similar operons from genes with different phylogenetic affinities.
RESULTS: Since a substantial number of operons have been identified experimentally in only a few model bacteria, evolutionarily conserved gene strings were analyzed as surrogates of operons. The phylogenetic affinities within these predicted operons were assessed first by sequence similarity analysis and then by phylogenetic analysis, including statistical tests of tree topology. Numerous cases of apparent horizontal transfer of entire operons were detected. However, it was shown that apparent horizontal transfer of individual genes or arrays of genes within operons is not uncommon either and results in xenologous gene displacement in situ, that is, displacement of an ancestral gene by a horizontally transferred ortholog from a taxonomically distant organism without change of the local gene organization. On rarer occasions, operons might have evolved via independent assembly, in part from horizontally acquired genes.
CONCLUSIONS: The discovery of in situ gene displacement shows that combination of rampant horizontal gene transfer with selection for preservation of operon structure provides for events in prokaryotic evolution that, a priori, seem improbable. These findings also emphasize that not all aspects of operon evolution are selfish, with operon integrity maintained by purifying selection at the organism level.
(emphasis added)
Okay...well, how about phylogenetic incongruities, such as humans sharing more intron positions with Arabidopsis than with nematodes or flies?
Current Biology3 Sep 2003;13(17):1512-7.
Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution
Rogozin IB, Wolf YI, Sorokin AV, Mirkin BG, Koonin EV.
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 20894, Bethesda, MD, USA
Sequencing of eukaryotic genomes allows one to address major evolutionary problems, such as the evolution of gene structure. We compared the intron positions in 684 orthologous gene sets from 8 complete genomes of animals, plants, fungi, and protists and constructed parsimonious scenarios of evolution of the exon-intron structure for the respective genes. Approximately one-third of the introns in the malaria parasite Plasmodium falciparum are shared with at least one crown group eukaryote; this number indicates that these introns have been conserved through >1.5 billion years of evolution that separate Plasmodium from the crown group. Paradoxically, humans share many more introns with the plant Arabidopsis thaliana than with the fly or nematode. The inferred evolutionary scenario holds that the common ancestor of Plasmodium and the crown group and, especially, the common ancestor of animals, plants, and fungi had numerous introns. Most of these ancestral introns, which are retained in the genomes of vertebrates and plants, have been lost in fungi, nematodes, arthropods, and probably Plasmodium. In addition, numerous introns have been inserted into vertebrate and plant genes, whereas, in other lineages, intron gain was much less prominent.
(emphasis added)
[ 09. September 2003, 12:50: Message edited by: Paul A. Nelson ]
IP: Logged
|
|
charlie d.
Member
Member # 159
|
posted 09. September 2003 12:57
LOL, Paul:
We wouldn't even be able to detect HGT at all if vertical lineages were not predominant, even among prokaryotes where HGT is more common (and for a more skeptical view of the often too easy claims of HGT occurrance, see here). What I was talking about was massive genetic mix-and-matching, which nothing in creationism precludes but would not be predicted by evolution.
As for your second paper, it also depends on what part of the picture you look at: as a creationist, you see the difference between human and nematode vs human and arabidopsis and go "aha!", but of course you are ignoring the pervasive background of "interkingdom conservation" that allows to detect those discrepancies in the first place, and establish which trait is derived and which is ancestral. So, why should intron position be conserved at all, according to creationist scenarios?
IP: Logged
|
|
|
Topic Closed
Printer-friendly view of this topic
