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Author
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Topic: Ontogenetic Depth and the Origin of Animals
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Paul A. Nelson
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Member # 26
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posted 09. September 2003 14:00
Two propositions:
1. Horizontal gene transfer (HGT) is compatible with naturalistic evolution.
2. "Massive genetic mix-and-matching" is not.
What distinguishes (2) from (1)?
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Argon
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Member # 276
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posted 09. September 2003 16:18
I'm becoming interested in how Paul answers his question: If two organisms are not related by common descent, how does one determine this?
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Rex Kerr
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Member # 632
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posted 09. September 2003 21:32
Rates distinguish (1) from (2). Also, (2) isn't strictly incompatible with naturalistic evolution, assuming that we can find a naturalistic mechanism for it. However, (2) robs naturalistic evolution of much of its support, since it is the lack of (2) which is one of the strongest predictions of a naturalistic evolutionary model (given our observation about the scarcity of HGT relative to inheriting genes).
Hundreds of sequences shared between, say, Caenorhabditis briggsae and mice and not humans or Caenorhabditis elegans would certainly look a lot more like (2) than (1), given that the inferred rate of transfer would have to be very high relative to the known mechanisms for such transfer (i.e. none, though a viral mechanism could be imagined).
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Walter ReMine
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Member # 906
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posted 10. September 2003 08:02
On testing common descent via the fossil-sequence
I was pointing out the modern evolutionists' no-risk, no-lose strategy, where virtually any conceivable data (that's bold-italics) is viewed as "evidence for evolution" or at least compatible with it. If it were any other theory, evolutionists themselves would immediately call it a non-science.
Macro-evolutionary theory makes no serious predictions. Instead it adapts to data like fog adapts to landscape. The theory is so scarce of real testable predictions that evolutionists must resort to something grotesquely extreme like the following:
quote:
"Rabbits in the cambrian would be quite a shock." (Pim van Meurs, Sept. 9, 2003)
Yes, rabbits can't fly, so we don't expect them in the sky. And they can't breathe under water, so we don't expect them in the Cambrian environment. Duh. We don't need evolutionary theory in order to make those predictions. But what about marine organisms that are every bit as complex as rabbits? Say, trilobites, for one? We find them abundantly in the Cambrian, and, like rabbits, they have no clear-cut macro-evolutionary lineage or ancestors. Is that a shock to evolutionists? It ought to be! But evolutionists accommodate it nonetheless -- (as well as all animal phyla in the Cambrian Explosion).
Evolutionists would likewise accommodate "rabbits in the Cambrian" through some version of:
- Reworking/redeposition of fossils -- which misleadingly placed some rabbit fossils where they shouldn't be.
- Overthrusts -- which misleadingly placed older fossils on top of younger.
- Errors in radiometric dating -- which happened to occur in this case, thereby misleadingly making the rabbits appear to be in the wrong fossil-sequence.
- Incompleteness -- "The ancestors existed in the Precambrian, but were not preserved within the incomplete fossil record." (NOTE: That is precisely an evolutionary explanation attempted for the hard-exoskeleton trilobites, where their ancestors were claimed to be "soft-bodied" and didn't leave fossils. That explanation would work at least as well for those "soft-bodied" rabbits.)
- Branching, or cladogenesis -- the organisms in questions do not have an ancestor-descendant relationship, therefore they can occur in any fossil-sequence without refuting evolution. (NOTE: Since this is the predominant mode of evolutionary thought today, it strongly protects evolution from testing via the fossil sequence.)
- "It came from Space!" -- For example, where the existence of rabbits in the Cambrian would be taken as evidence that ancient astronauts once visited Earth, or that the necessary genes for rabbits rained down like viruses from Space -- some version of directed panspermia.
Those are all part of the smorgasbord known as evolutionary theory, and are actively invoked by evolutionists. Yes, rabbits in the Cambrian would be "quite a shock" -- but evolutionists would accommodate it -- Evolutionists have already demonstrated their willingness to accommodate other equally-implausible cases.
If evolutionary theory predicts anything, it predicts the ancestors should occur before the descendants. But to cash that out, we must identify real ancestors (and their descendants), and do this without using fossil-sequence data (as that would be circular). Since real ancestors (as opposed to hypothetical, imaginary ancestors) exist only as fossils, we must identify them by first identifying clear-cut lineages through morphology-space. Indeed, the classical Darwinists expected to find those in abundance, and their research program (which centered around Darwinian Systematics) attempted to find them. But after more than a hundred years their research program had failed dismally to identify clear-cut ancestors, and by the mid-1970s classical Darwinism (its theory, its systematics, and its expectations) were being replaced by other theories (punk ek) and other systematics (cladistics and phenetics) which never identify real ancestors! Therefore, modern evolutionary theory is protected from falsification by the fossil-sequence. Evolutionists accomplished that by retreating from the expectations of classical Darwinism.
You frequently hear evolutionists bluster (falsely) that "even a single fossil out-of-sequence would refute evolution." But evolution is thoroughly protected from any such test. (See the above list, for example.) Indeed, this so-called "test" turns the tables on an anti-evolutionist. To show that two fossils are out-of-sequence, the ANTI-evolutionist must first identify a clear-cut lineage!!! In other words, the ANTI-evolutionist must first supply compelling evidence for evolution!!! This again is a no-risk, no-lose proposition for evolutionists. Heads they win; tails you lose.
Since clear-cut lineages are systematically absent, how do evolutionists create the illusion of a test? Answer: By going to grotesque extremes (e.g. about "rabbits in the Cambrian"). I say that practice demonstrates the extreme weakness of evolutionary theory. Imagine someone proposing that Newtonian mechanics be tested by seeing whether planets move in square orbits! The real power of Newtonian mechanics is demonstrated instead by its accurate, fine-scale predictions of subtle planetary motions. By contrast, evolutionary theory is a structureless smorgasbord and lacks fine-scale predictions (instead it is flexibly accommodated to the data after the fact), and evolutionists are left to pursue grotesque extremes in an attempt to impress us and create the illusion their theory is risky and testable.
In my view, evolutionists are saying, "We've never seen organism X in the Cambrian, therefore we'd be shocked to find organism X in the Cambrian, and we'd have to change our evolutionary story quite a bit." I find that most unimpressive, especially when that same observed set of facts can be explained by ecological requirements, or by theories of intelligent design.
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Pim van Meurs writes:
quote:
"Walter objects to evolutionary theory's ability to incorporate new knowledge, new mechanisms which make it hard to refute." (Pim van Meurs, Sept. 9, 2003)
Once again he misrepresents me. I object to the evolutionists' chronic misrepresentations of me, and the empty posturing they pursue with it. (For comparison, see my previous posts, and the top of this post.)
-- Walter ReMine
The Biotic Message
[ 10. September 2003, 08:14: Message edited by: Walter ReMine ]
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Cre8ionist
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Member # 140
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posted 10. September 2003 09:18
You've nailed it Walter:
quote:
Macro-evolutionary theory makes no serious predictions. Instead it adapts to data like fog adapts to landscape.
Consider convergent evolution as another landscape adaptation (used to explain away the huge placental/marsupial problem amongst others). Or what of parallel evolution? The list goes on and on.... Evolutionists have a seemingly endless supply of rabbits in their hat. But is today's evolution theory, with its HGT and it's symbiosis ala Margulis really all that similar to the one Darwin wrote of? Or has it shape -shifted into one that would have been reviled were it proposed only 30 or 40 short years ago? One last question, would this shape shifting really have occurred (especially in such a short time) without design theorists lurking the halls of science? Anyway, got some work to do....................................Cre8
[ 10. September 2003, 09:28: Message edited by: Cre8ionist ]
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charlie d.
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Member # 159
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posted 10. September 2003 09:36
quote:
Reworking/redeposition of fossils Overthrusts
Errors in radiometric dating
Incompleteness
Branching, or cladogenesis
"It came from Space!"
Honestly, Walter!
Reworking, overthrust and radiometric errors need to be confirmed by independent evidence. They are not some sort of default, hand-waving explanation for any weird finding.
Incompleteness is a fact all historical sciences have to cope with, but it would not make rabbits in the Cambrian any more acceptable than a Cadillac buried inside an Egyptian pyramid.
Your description of cladogenesis is simply wrong (where do you get that out-of-sequence fossils can be accomodated by cladistic models?); you may want to refresh that part.
As far as "It came from space", the only person here to claim anything like that about otherwise unexplainable features is Mike Gene, an ID advocate.
Talk about misrepresentations!
As for Paul's original questions, I think Rex answered them already. Again, we could not tell HGT if evidence for vertical descent lines were not predominant. Note also that common descent is not such a dogma. For instance, if Woese's hypothesis for early cellular evolution is correct, it will mean that we won't be able to establish vertical descent lineages before a certain point in time with the same level of certainty we can for the later points. Quite simply, we'll live with it.
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Paul A. Nelson
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Member # 26
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posted 10. September 2003 10:40
Charlie wrote:
quote:
Again, we could not tell HGT if evidence for vertical descent lines were not predominant.
But that wasn't my question, nor does Rex's reply provide an answer.
You say that some conceivable pattern of distribution of genes -- "mix-n-match" -- would be inconsistent with naturalistic common descent; but that currently-observed distributions are consistent.
Fine, but unless you can describe the distributions that would falsify common descent, there's little reason to take the prediction seriously. It's evanescent. HGT is always available as a post hoc mechanism to explain away any incongruent distribution. "The reason for believing in the occurrence of ancient HGT is relatively simple," wrote James R. Brown recently. "Genes are not found where they are expected to be" ("Ancient Horizontal Gene Transfer" Nature Reviews Genetics 4 [2003]:121-132; p. 121).
You wrote, re Walter's summary of cladistic methodology:
quote:
Your description of cladogenesis is simply wrong (where do you get that out-of-sequence fossils can be accomodated by cladistic models?); you may want to refresh that part.
You may want to read some systematics (cladistics) textbooks before giving Walter advice:
quote:
Perhaps a central problem with the traditional paleontological method has been the tendency to equate a chronocline -- the sequential distribution of character-states through time -- with an ancestral-descendant sequence of taxa possessing those character-states....there can be no prior reason against expecting primitive character-states later in the record and derived states earlier....whenever sister-species have unequal survivorship in the fossil record, it is an expectation of the phylogenetic process that some taxa occurring earlier in the fossil record will possess derived character-states relative to those occurring later in the record. Because unequal survivorship of sister-species is a common phenomenon, the early occurrence of derived character-states should also be common.
Niles Eldredge and Joel Cracraft, Phylogenetic Patterns and the Evolutionary Process (New York: Columbia University Press, 1980), pp. 56-58; emphasis in original.
Walt "got" the treatment of stratigraphic distribution in cladistic methodology from the systematics literature, where it has been much debated over the past two decades.
[ 10. September 2003, 10:54: Message edited by: Paul A. Nelson ]
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Pim van Meurs
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Member # 541
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posted 10. September 2003 11:49
Creat; One last question, would this shape shifting really have occurred (especially in such a short time) without design theorists lurking the halls of science?
Interesting question to pursue, Cre8t. But it seems to me that these mechanisms have little to do with design and more to do with scientific research. IF design theorists were somehow responsible for this they would deserve some credit but I have seen no evidence to support this. Are you intending to take this beyond speculation since it would make for some interesting evidence.
As far as Walter's use of overtrusts, or radiometric dating, these explanations are not invoked in an 'ad hoc' manner but follow from investigations of contradictory datasets. Walter seems to have built an over simplification of what science is all about.
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Grape Ape
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Member # 399
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posted 10. September 2003 12:41
Paul Nelson writes:
quote:
Fine, but unless you can describe the distributions that would falsify common descent, there's little reason to take the prediction seriously.
Paul, a random distribution would falsify common descent. You could argue that one could still accept common descent and just believe it was swamped out by "noise", but it would lose its appeal as a device for explaining why our genomes are the way they are.
This is the crux of the matter that seems to be ignored by yourself and that bizzare post by Remine. There are patterns in comparative genomics, comparative morphology, and the fossil record. These patterns are what are predicted by evolutionary theory. Yes, anomalies do exist, though we typically have perfectly good explanations for them like HGT. But you guys are trying to pretend as if evolutionary theory doesn't make predictions simply because there also exist explanations for the anomalies. That's just weird. The way in which we explain anomalies must not only be independently verifiable (as HGT is), they also must not be so common as to swamp out the pattern that they deviate from. Otherwise, we would scrap the theory which explains the pattern and accept the ones which explain the anomalies (which wouldn't be "anomalous" in that case). You guys seem to be arguing that we would hold on to evolutionary even if the patterns that it predicts didn't hold true, simply because we have good explanations for the anomalies.
Crap, say I. First of all, you don't know how the evidence would be treated if things were different than they are now. To pretend that you know how "evolutionists" would react if the evidence were the complete opposite is nothing more than soft-headed arm-chair psychology. I can state without reservation that there would be decidedly less support for evolution if it were all anomaly and no pattern. Secondly, common descent is only as good as it's able to explain the similarities and differences between organisms. Take away its ability to explain these things (by having sequences be randomly distributed, or by getting rid of the heirarchy) and there's no need to invoke it. We would instead invoke HGT, or whatever other process, and toss common descent by the wayside.
But of course this is all irrelevant because that's not the way things are. There exist patterns -- very strong ones -- and the goal is to provide an explanation for them. Cre/ID is inherently incapable of doing so because it can't tell us why one pattern should be expected over another, or why we should expect any pattern at all. Heck, you guys don't even have the hard work of having to explain anomalies, because you can't even have anomalies until you have some expectation of pattern. The only such expectations I've seen attempted are entirely ad hoc in that the whimsy of the designer could have easily chosen the opposite. And you guys accuse us of being ad hoc when explaining anomalies?
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charlie d.
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Member # 159
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posted 10. September 2003 12:45
Paul:
If you cannot find a statistically robust correlation between the phylogenetic trees of many indipendent sequences within a group of organisms, iow if the analysis of multiple sequences does not result in a consensus phylogenetic tree for those organisms, then you have no way to establish a nested hyerarchy of common descent. If this were the rule in phylogenetic analysis, certainly CD would be in serious trouble. On the other hand, if you do commonly find statistically significant consensus trees, HGT can be one of the possible explanations for the exceptions.
As for cladistics and out-of-sequence fossils, thanks for the lesson of course, but everybody here, including Walter, was talking about the "rabbit in the Cambrian" type of out-of-sequence. Do you think cladistics would allow to simply ignore rabbits in the Cambrian?
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Grape Ape
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Member # 399
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posted 10. September 2003 12:54
[Deleted because I cross-posted with charlied and said the same thing.]
[ 10. September 2003, 12:55: Message edited by: Grape Ape ]
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Nel
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Member # 614
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posted 10. September 2003 13:00
Charlie writes:
quote:
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
I am not sure I understand this. It seems to me that HGT should be detectable in some way or other, for example, by different gene trees showing different heritage, even if vertical lineages were not predominant. But maybe you meant something else?
[ 10. September 2003, 13:11: Message edited by: Nelson-Alonso ]
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Paul A. Nelson
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Member # 26
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posted 10. September 2003 14:42
Grape Ape wrote:
quote:
There are patterns in comparative genomics, comparative morphology, and the fossil record. These patterns are what are predicted by evolutionary theory.
I'd take claims like this a lot more seriously if the evolutionary predictions I knew best (e.g., about the conservation of developmental pathways leading to homologous anatomical structures) weren't regularly reupholstered, and put out for sale on the sidewalk as "new research problems." For instance, when I was an undergraduate (1980-84) studying evolutionary biology, my anatomy, genetics, and ev bio instructors told me that -- on the basis of common descent -- one should expect to find the development of non-homologous organs, such as the eyes of flies and vertebrates, regulated by non-homologous genes.
Pax-6.
Oh -- deep homology! Guess we didn't really understand development in relation to homology and non-homology. New research problem; common descent continues as before.
Flexibility in the face of anomalous findings isn't a bad thing, necessarily. One doesn't want one's central theories to tumble the first time they hit a bump in the road.
But common descent is remarkably well-protected from empirical challenge. That's OK (see above, bump in the road metaphor); but that also means that claims about "predictions" and all that need to be viewed with a bemused eye.
[ 10. September 2003, 14:43: Message edited by: Paul A. Nelson ]
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charlie d.
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Member # 159
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posted 10. September 2003 14:50
If every tree looked different from every other tree, all you could conclude is that there is no evidence of vertical transmission, without which speaking of "horizontal" is meaningless. Basically, you'd say that all species are genetic mosaics, and all mechanistic hypotheses (massive transfer of genes between lineages, whimsical designer, completely independent evolution of every lineage, etc etc) would be equivalent in the absence of other data.
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Argon
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Member # 276
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posted 10. September 2003 15:15
Paul Nelson writes:
quote:
But common descent is remarkably well-protected from empirical challenge.
The linear descent of plastids in eukaryotic lines weren't protected from empirical challenges.
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