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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 11. September 2003 16:38
Here's the most recent article I can find on the topic of cladogram & stratigraphy correlation:
"The tree of life and the rock of ages: Are we getting better at estimating phylogeny?"
BioEssays 24 (2002):203-207.
Matthew A. Wills
Department of Biology and Biochemistry, The University of Bath, Claverton Down, Bath, BA2 7AY
email: Matthew A. Wills (m.a.wills@bath.ac.uk)
Abstract
In a recent paper,([1]) palaeontologist Mike Benton claimed that our ability to reconstruct accurately the tree of Life may not have improved significantly over the last 100 years. This implies that the cladistic and molecular revolutions may have promulgated as much bad black box science as rigorous investigation. Benton's assessment was based on the extent to which cladograms (typically constructed with reference only to distributions of character states) convey the same narrative as the geochronological ages of fossil taxa (an independent data set). Fossil record quality varies greatly between major clades, and the palaeontological dating yardstick may be more appropriate for some groups than others.
[ 11. September 2003, 16:44: Message edited by: Paul A. Nelson ]
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Grape Ape
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Member # 399
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posted 11. September 2003 16:51
Here's a more recent one Paul:
Science. 2003 Jun 13;300(5626):1698-700.
Dating the tree of life.
Benton MJ, Ayala FJ.
quote:
The relative merits of molecular and paleontological dates of major branching points in the tree of life are currently debated. In some cases, molecular date estimates are up to twice as old as paleontological dates. However, although it is true that paleontological dates are often too young (missing fossils), molecular dates are often too old (statistical bias). Intense study of the dating of major splits in the tree of mammals has shown rapprochement as fossil dates become older and molecular dates become younger.
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yersinia
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Member # 324
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posted 11. September 2003 17:13
Are you trying to say something by posting these paper refs, Paul? Directly answering my question would be simpler...
The various recent papers by Benton, Wills, etc., address various detailed topics, e.g. whether or not the fossil record is "good" according to this or that criterion, whether or not the early origin of some taxa implied by some molecular studies is real or an artefact, etc.
But the only important question in this thread is the broad one of whether or not there is a statistically significant positive correlation between stratigraphy and phylogenetic trees. I'm pretty sure I know what Benton thinks, but first, what say you, Paul?
[ 11. September 2003, 17:15: Message edited by: yersinia ]
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Nel
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Member # 614
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posted 11. September 2003 17:24
Nic writes:
quote:
But the only important question in this thread is the broad one of whether or not there is a statistically significant positive correlation between stratigraphy and phylogenetic trees.
If you were to ask me this question, I would not say that the statistical agreement is
high, but for only a small number of groups for which there is little ambiguity. There are some morphological traits, like placenta, that unite large groups and were invented once. The difficulty in all this comes in when characters can be the product of independant evolution, resolution of deep branches, recent clusters of species etc.
[ 11. September 2003, 17:31: Message edited by: Nelson-Alonso ]
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Rex Kerr
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Member # 632
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posted 11. September 2003 23:49
Paul Nelson gave a link to an interesting question about ORFans, i.e., genes with relatives in only one sequenced organism.
This isn't the same as finding many "homologous" ORFs where there is no recent common ancestry and no shared ORFs with near neighbors--this was my "common descent is dead" case.
So my view of ORFans is that we haven't sequenced nearly enough closely related organisms to tell if there are too many ORFans to fit a model of common descent. Sequencing projects so far have intentionally been sequencing widely divergent organisms; common descent would predict that you'd find quite a few ORFs in that case. (Many other models would predict this too, so it's not a point in favor of common descent; neither, however, is it contradictory.)
Let's look at human and chimp, C. elegans and C. briggsae, D. melanogaster and D. pseudoobscura. If they each have piles of ORFans, then we have to ask if ORFans are really expressed and if they do anything. If the answer is yes, then common descent may still be okay, but standard evolutionary explanations of gene origin are probably dead. (Note: "piles" means "a quanity so far above the upper bound of what any known mechanism could possibly generate as to be immensely improbable".)
Edited for a typo.
[ 13. September 2003, 00:32: Message edited by: Rex Kerr ]
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Pim van Meurs
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Member # 541
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posted 12. September 2003 00:40
An interesting hypothesis may be that ORFans may be different in genotype but similar in phenotype. It would be interesting to see if neutral evolution could explain the existance of these ORFans.
Another interesting statistic is that while the total number of ORFans is increasing, their percentage is decreasing. Also addition of a closely related organism causes a large drop in the percentage of ORFans of the relative. This suggests to me that common descent may not be dead after all :-)
Since most ORFans tend to be biased to short length, the suggestion of neutral evolution may be of interest.
Then again, I am no biologist so buyer beware...
Actually Niles Donegan seems to have presented a reason why ORFans may be present namely the small amount of complete genome sequences.
According to his report in NCSE reports 2003 vol 23(2), Paul suggested that ORFans should be considered unique and that evolution cannot explain them. It may be too soon for this conclusion especially given the above statistics.
[ 12. September 2003, 02:42: Message edited by: Pim van Meurs ]
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charlie d.
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Member # 159
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posted 12. September 2003 09:13
An article with a very good and clear discussion of ORFans, and issues with their identification, is here.
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Cre8ionist
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Member # 140
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posted 12. September 2003 09:38
Hey Pim, let me start here as this will be a springboard for the rest....
quote:
Btw what are kool aid drinking evolutionists?
1>2>3
1
"914 followers of Jim Jones perished in a
remote Guyana jungle after obeying
orders from Jones to drink cyanide-laced
Kool-Aid."
2
Sean Hannity says "
Clinton Kool-Aid drinkers will defend the Clinton-Gore administration
regardless of such serious evidence and seek to paint as obsessive those of
us who try to assign it blame."
You know, the sex with an intern and lying under oath aren't really that bad, no matter what you say, Clinton was the greatest President of all time crowd. He basically thinks they'll commit moral and/or intellectual suicide to protect Clinton, in essence, drinking the Kool-Aid for him.
3
I think there are certainly evolutionists who could be called Darwinian Kool-Aid drinkers.
That is, regardless of the evidence, Darwin must be defended. Reread Pim's post and make up your own mind. But in short he states:
quote:
What is so special about the origin of trilobites btw?
Almost as though Pim you expect that we are to believe that you're not familiar with the trilobite problems presented by IDers. Who here believes that Pim hasn't heard the arguments associated with the Trilobite, raise your hands? Yup, that's what I thought, I don't see any hands raised. But seriously now, since G-Ape seems to have echoed the same rhetoric I'll give a refresher for those who genuinely aren't familiar with the problems, then I'll have to move on, unless someone would really like to provide the missing data. This isn't my thread and this isn't really the topic, though it's come up several times:
Basically stated, the trilobite is especially difficult for Darwin, because: it's got eyes which are more complex than later arthropods, bass ackwards for Darwinism, and it was a hard shelled creature which is found abundantly in the fossil record, but alas, its evolutionary ancestors are missing....surprise!
Couple of quotes, then follow the link at the end for more info on the second quote....
quote:
The schizochroal compound eye of the trilobite (a horseshoe crab-like organism of the past), for example, contains the only known lens in the biological world which corrects for focusing problems that result from using non-flexible lenses. The designs of the schizochroal lenses, in fact, are the very same designs that man himself has developed to correct for the same problems. Furthermore, the design of the schizochroal eye combines this optimum focusing capability with the optimum sensitivity to motion
provided by the compound eye as well as the stereoscopic (3-D) vision provided by closely spaced eyes.
The design of the schizochroal eye makes it unique among eyes; perhaps even to the point of being the best optical system known in the biological world. This design, in fact, seems to far exceed the needs of the trilobite. The origin of the design of the
schizochroal eye is not understood by means of any known natural cause. Rather, it is best understood as being due to an intelligent (design-creating) cause, through a process involving remarkably high manipulative ability.(Kurt Wise, My favourite
evidence for creation!, Creation Ex Nihilo, Sept.-Nov. 1989, Vol. 11 No. 4, p. 29)
quote:
We have seen that the first abundant, well represented metazoan fossils, the trilobites, were complex beyond imagination in every detail, with compound eyes, with swimmerets and gills, with legs and antennae, and with complex, even intricately sculpted forms. They had fully functional muscular and nervous systems. Their eyes were developed by processes not only similar to those of other arthropods, but like those of vertebrates, including man. The complex system of development of cephalized forms was already present and functioning. A thousand other complexities of molecular biology shared by modern forms were operative. Where did these complexities come from? There is no evidence of any earlier form from which they could have been derived. Furthermore, there is no evidence for the existence of a mechanism in biological systems for adding information to complex systems (Spetner, 1998). To argue that they came from Precambrian forms that were not preserved because they had no hard parts is to argue again from the ABSENCE OF EVIDENCE. The absence of evidence, in science has to be construed as the evidence of absence. There is no Precambrian evolutionary sequence because there was no Precambrian evolution. Evolution as an explanation for the existence of complex living systems is a religious view held by those who wish the world to have no Originator (meaning). Trilobites and all other forms appear on the scene as fully formed, fully competent organisms, period.
The Trilobite: Enigma of Complexity
..................................Cre8
[ 12. September 2003, 09:51: Message edited by: Cre8ionist ]
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Grape Ape
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Member # 399
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posted 12. September 2003 10:48
Cre8, thanks for the link to the trilobite article (though it contains some errors).
Unfortunately, the issue that Walter raised with the trilobites was that they're analagous to a "rabbit in the Cambrian", which implies that they're somehow way out of place in the fossil record. Simply saying, "hey, trilobites were complex" isn't the same as showing that they're appearance defies the standard phylogeny. In order to do so, they would have to have derived characters that were specific to later arthropods, like insects, arachnids, or centipedes. Or for that matter they could have characters that were specific to non-arthropods, like birds or mammals. Having primitive characters (like muscles and nerves) or unique characters (like a certain kind of eye) doesn't tell us anything about their pylogenetic relationship to other animals. What are important are shared, derived characters.
For fun and profit:
Fossil Evidence For Trilobite Predecessors
Trilobite Systematics
Evolutionary Trends in Trilobites
Are Naraoids Trilobites?
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charlie d.
Member
Member # 159
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posted 12. September 2003 11:43
Actually, there is now reasonable evidence that Arthropods existed well before the Cambrian. This critter is Parvancorina:
See also here and here.
More about fossil organisms with relationships to trilobites, including further discussion on Naraoia, is found here (The page seems to be under development, but there are some interesting comments, links and references).
As for quote:
The absence of evidence, in science has to be construed as the evidence of absence.
I guess that says it all. Yikes! ![[Eek!]](eek.gif) (I wonder why the argument applies only to science and not to, say, theology. ![[Wink]](wink.gif) ).
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yersinia
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Member # 324
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posted 12. September 2003 12:06
Or ID.
Speaking of Kool-Aid drinkers, Cre8tionist, what are we to think of someone who quotes the flagrantly false arguments of a rube like Spetner?
quote:
Furthermore, there is no evidence for the existence of a mechanism in biological systems for adding information to complex systems (Spetner, 1998).
Apolipoprotein AI Mutations and Information
http://www.talkorigins.org/faqs/information/apolipoprotein.html
Evolutionary increases in information
http://www.antievolution.org/people/wre/evc/argresp/information.html
The Origin of "Information" via natural causes
http://www.antievolution.org/cgi-bin/ikonboard/ikonboard.cgi?s=3f61ecde2855ffff;act=ST;f=9;t=6
Follow some of those trilobite links, I learned that the "classic" trilobites are actually just a subgroup of a wider variety of trilobite-like critters, which would have to be discussed in detail for Kurt Wise, or you, to even have a chance of making a successful argument.
I will be the first to say that I don't know squat about the schizochroal compound eye of the trilobite. Since we know how complex eyes might be produced gradually but in a geologically short period (remember that Nilsson and Pelger paper), however, why should some other complex eyes impress us?
PS: Oh yeah, and everyone is right about Remine/Cre8tionist being totally confused about what the argument was in the first place. Precambrian rabbits would be a problem because they would appear long before their phylogenetic common ancestors, far outside the usual sloppy error bounds allowed by the fossil record.
[ 12. September 2003, 12:10: Message edited by: yersinia ]
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Walter ReMine
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Member # 906
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posted 12. September 2003 12:45
Grape Ape writes:
quote:
"Good grief, what do you want us to do, wait millions of years to see if these things happen? Go back in time and set up a video recorder?"
No. But natural selection theory indicates our experimental demonstrations cannot be extrapolated. The contour and warping of the fitness terrain is complex, so experimental demonstrations over a small portion of the fitness terrain are unlikely to apply over other larger portions of the fitness terrain. Such extrapolations have no scientific validity, according to natural selection theory itself.
Fortunately this may be remedied by finding suitable fossils that fill-in the morphological gaps between species, thereby reducing the required magnitude of our experimental demonstrations. However, after nearly 150 years since Darwin's Origin, there still exists a wide-spread, systematic lack of correspondence between our experimental demonstrations of evolution and the morphological gaps in the record. Our experimental demonstrations do not span the numerous, systematically-placed, large morphological gaps. That causes the failure of this demonstration-based evidence for evolution.
There is, however, the alternate approach of using pattern-based evidence, and this includes virtually all the major evidence for macro-evolution. That is, it is based on pattern, rather than on sufficient experimental demonstrations of macro-evolution. This approach is inherently weaker scientifically, but in principle it can be sufficient, if the patterns are consistent and unique to evolution (which I claim they are not).
==================================
quote:
"Once again, what you're doing is claiming that there's no pattern (or that a pattern is not predicted) simply because anomalies exist, and we have an explanation for them."
No, he mis-stated my argument. The "existence of anomalies" has nothing to with it, except perhaps that they serve to probe evolutionary theory to help display its structure, or lack of it. My argument is that macro-evolutionary theory -- as practiced by modern evolutionists -- is a vast structureless smorgasbord, it makes no serious predictions.
quote:
"It is possible both to predict an observed pattern and also explain the rare deviations from that pattern. There is simply no reason why the explanation for the anomaly negates the expectation of the pattern."
He's focusing on the 'anomaly' and missing the forest. Let me put it this way. Suppose there were no hierarchical patterns in life -- just lots of transposition patterns. By the approach used by modern evolutionists, they would immediately abandon descent-with-modification and immediately embrace transposition (e.g. HGT) -- all based on pattern and their ability to "explain" it. Also, this would give evolutionists a way out from their greatest problems with life's patterns, namely:
- The systematic absence of gradualism over large-scales (as measured by our experimental demonstrations).
- The systematic absence of clear-cut lineages and ancestors.
- The abundance of so-called "convergence."
Indeed, evolutionists themselves have stated the above three items as reasons to seek HGT explanations. This is a no-risk, no-lose strategy for evolutionists. If life's hierarchy pattern holds, then evolution wins (descent with modification). But if the hierarchy pattern doesn't hold, then evolution wins (HGT). Evolution wins either way.
(Note: But of the two, the observed pattern of life is far harder for evolutionists to scientifically/testably explain -- and that, I suggest, is a key reason for it's existence.)
==================================
quote:
"I'm afraid you've done nothing to explain why we shouldn't expect trilobites in the Cambrian."
That isn't what I said. I said trilobites in the Cambrian are every bit as awkward for evolutionists to explain as rabbits in the Cambrian. The issue is both complexity and lineage. Trilobites are every bit as complex as rabbits. And trilobites (like rabbits) have no clear-cut lineage leading to them. They just show up in the Cambrian.
quote:
"[Trilobites]They're primitive arthropods, and we find them exactly where we should find them according to the phylogenetic tree."
There is no clear-cut lineage leading to trilobites, so he cannot be speaking of a genuine "phylogenetic tree" as I would use that term. He must mean a hierarchical tree -- a cladogram or phenogram -- which do not indicate any real ancestors, nor the fossil sequence of any real organisms. For example, if trilobites didn't show up until the Pleistocene, that would be fully compatible with the cladogram or phenogram -- his so-called "phylogenetic tree." In other words, his above claim is mistaken.
quote:
"Rabbits, on the other hand, contain many derived characters that we shouldn't expect to see until well after the appearance of primitive mammals."
I am aware of the standard evolutionary story, (but gee he tells it so well!). His reference to "derived characters" means he is referring to cladograms. But there is nothing within a cladogram that predicts the sequence of any real organisms. Rather, cladograms speak of various hypothetical organisms showing up first, such as the 'first mammals' -- a hypothetical creature having mammal characters. The moment you speak of those 'first mammals' as being real, and leaving real fossils, you are no longer speaking of a cladogram. Rather, you have shifted, mostly likely to a paraphyletic group (which are emphatically dis-recognized within cladistics). This shifting to-and-fro between systematic methods is a common source of illusion -- through confusion.
So let me make it simple for you. If you never identify a clear-cut ancestor or descendant for organism X (which evolutionists generally do not), then organism X can comfortably appear any place in the fossil sequence -- and the only serious problem remaining for evolutionists is whether the organism is 'too complex' to have appeared so suddenly from the available forbearers.
Without clear-cut ancestors and lineage, evolutionists are basically saying, "We never find rabbits earlier than a certain time in the fossil sequence, therefore we'd be really shocked to find rabbits at an earlier time." But we don't need evolutionary theory for that prediction.
quote:
"Simply saying, "hey, trilobites were complex" isn't the same as showing that they're appearance defies the standard phylogeny. In order to do so, they would have to have derived characters that were specific to later arthropods, like insects, arachnids, or centipedes. Or for that matter they could have characters that were specific to non-arthropods, like birds or mammals. Having primitive characters (like muscles and nerves) or unique characters (like a certain kind of eye) doesn't tell us anything about their phylogenetic relationship to other animals. What are important are shared, derived characters."
His reference to "derived characters" is misleading. Because "derived characters" do not place organisms into any ancestor-descendant pairings (with a real ancestor, and a real descendant). Therefore organisms identified merely by "derived characters" are compatible with any fossil sequence. The point is simple. Ancestors should occur before descendants -- but if evolutionists don't identify clear-cut ancestors (which they generally don't), then evolution is compatible with any fossil-sequence. Once you get past his misleading verbiage, he is demanding that I (an ANTI-evolutionist) must first identify a clear-cut lineage before I can show the trilobites are out-of-sequence! In other words, his so-called 'test' requires the ANTI-evolutionist to provide compelling evidence for macro-evolution! That is the no-lose, no-risk, illusion of "testing" that I described previously. Evolutionists posture like there is a serious test of their theory, when there isn't.
==================================
He lists the following as "predictions" of evolution:
- "the existence of transitional forms, etc." -- That's a classic illusion-filled phrase. The public quite reasonably interprets "transitional form" to mean that a clear-cut lineage has been identified. But under that definition they are systematically absent. So instead, evolutionists define transitional form differently, in several various ways that lead to all kinds of mischief. For example, my opponent at the University of Minnesota debate, Massimo Pigliucci, uses seals as "transitional forms" because they're transitional between land and sea! He thereby argues that transitional forms are abundant! At any rate, we're gonna have a great big fight over the phrase "transitional form".
- "Fossil record shows that recent animals are more similar to extant ones than ancient animals;" -- That may be micro-evolution, or it may be the standard evolutionist hyperbole exaggerations about "similarity". It's hard to tell from his statement. One would have to take his examples case by case.
- "Nested hierarchy." and "Independent convergence of phylogenetic trees from different methods (genetic, morphological, paleontological, etc.)" -- No, macro-evolutionary theory does NOT predict a nested hierarchy. Non-hierarchical patterns are produced by Transposition (HGT), and by Atavism, and by other blends of mechanisms in the evolutionists' theoretical smorgasbord.
==================================
quote:
"You can't say that it doesn't make these predictions merely because there are a handful of exceptions, and that these exceptions can be explained."
I didn't say that. He implicitly misrepresented what I said. This isn't about a "handful of exceptions". It's about the fact that key evidence against common descent -- non-hierarchical patterns -- are taken as evidence for an even more powerful evolutionary explanation: Transposition. This is a no-lose, no-risk strategy for evolutionists.
quote:
"Common descent can certainly be disproven, but to do so you will have to demonstrate that these patterns do not exist, or that contrary patterns exist instead."
He has correctly exposed the evolutionist thinking on this! Yet he fails to realize that the observed pattern of life resists explanation by common descent (see items A, B, C above), and SIMULTANEOUSLY resists Transposition explanations (within fossil-bearing organisms -- the multicellular organisms).
==================================
quote:
"However, it is simply not logical to insist that evolutionary theory doesn't make predictions based on biogeography, ..."
He's talking about biogeography (e.g. Darwin's finches) which are micro-evolution, and are un-impressive as evidence for macro-evolution. I believe everyone in this forum is discussing macro-evolution, and I additionally made that explicit in my posts. Let me say it again: Macro-evolutionary theory makes no serious predictions. Not even in biogeography.
==================================
quote:
"You and Paul have claimed that common descent is protected from empirical disconfimation."
No, I claimed common descent (as practiced by modern evolutionists) is well protected, not perfectly protected -- in its modern incarnation (punk ek, etc.) common descent is far less risky or testable than people realize. I think Paul Nelson is trying to wake you up to that.
On the other hand, macro-evolutionary theory is far more protected -- as practiced by modern evolutionists, macro-evolutionary theory seems perfectly protected from any conceivable data. That theory includes the whole grab-bag of stuff: transposition (HGT), atavism, loss, replacement, incompleteness, cladogenesis, anagenesis, "It came from Space!", and many others.
I'm pretty careful about distinguishing between "common descent" versus "evolutionary theory". As I said in my first post, I don't equate the two. Perhaps he missed that.
-- Walter ReMine
The Biotic Message
All indented quotations above were posted by Grape Ape.
[ 14. September 2003, 02:44: Message edited by: Walter ReMine ]
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Pim van Meurs
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Member # 541
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posted 12. September 2003 12:46
I find it particularly ironic how Creationist uses the 'kool aid' term to describe some evolutionists, I wonder if there are any similar 'creationists' as well :-)
Such as those who portray the trilobite as an example against common descent without a full understanding of the fossil records of such trilobites which surely shows a beautiful evolutionary pattern.
A guide to the order of the trilobite
especially the Evolutionary trends[
Trilobite eye
quote:
How did schizochroal eyes evolve?
All early trilobites (Cambrian), had holochroal eyes and it would seem hard to evolve the distinctive phacopid schizochroal eye from this form. The answer is thought to lie in ontogenetic (developmental) processes on an evolutionary time scale. Paedomorphosis is the retention of ancestral juvenile characteristics into adulthood in the descendent. Paedomorphosis can occur three ways: Progenesis (early sexual maturation in an otherwise juvenile body), Neoteny (reduced rate of morphological development), and Post-displacement (delayed growth of certain structures relative to others). The development of schizochroal eyes in phacopid trilobites is a good example of post-displacement paedomorphosis. The eyes of immature holochroal Cambrian trilobites were basically miniature schizochroal eyes. In Phacopida, these were retained, via delayed growth of these immature structures (post-displacement), into the adult form.
Just like the 'eye' itself, the trilobite seems hardly to be that hard to understand.
More on the trilobite eye
Trilobite phylogeny
Cheers.
[ 12. September 2003, 13:10: Message edited by: Pim van Meurs ]
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Pim van Meurs
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posted 12. September 2003 12:57
Walter still seems to argue a strawman namely that a handful exceptions are taken as evidence to extend the theory of evolution. But this is how science works, one does not throw away a perfectly working theory just because of some minor discrepancies, rather one extends the theory to incorporate the newly acquired knowledge. Unless of course a better explanation that describes all the data is presented.
the pattern shows that while common descent is a very strong pattern, there is evidence that other mechanisms such as horizontal transfer may complicate the matters at the root of the tree. Does this require us to reject common descent? Of course not.
Walter suggests that "in its modern incarnation (punk ek, etc.) common descent is far less risky or testable than people realize."
I agree with the less risky part since common descent has withstood quite a bit of testing and attempts to falsify. Evolutionary theory's strength seems to be considered a weakness by Walter.
I am not really sure where Walter is going with his minor objections to the strengths of evolutionary theory.
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