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Author
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Topic: Response to Jason Rosenhouse
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Cornelius G. Hunter
Member
Member # 81
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posted 28. August 2004 15:05
In this thread I respond to Jason Rosenhouse's critique of my essay, "Why Evolution Fails the Test of Science." [Hunter, 2004] Rosenhouse is Assistant Professor at James Madison University and he maintains an evolution blog. His critique is here:
http://evolutionblog.blogspot.com/2004/08/hunter-part-one.html
http://evolutionblog.blogspot.com/2004/08/hunter-part-2.html
http://evolutionblog.blogspot.com/2004/08/hunter-part-3.html
In this post I address his criticisms in the order he presents them.
The Fossil Record
Rosenhouse first addresses my section entitled "The Fossil Record." The section begins by explaining that the fossil record contains substantial evidence for evolution. I followed this with evidential problems in the fossil record. My point was that while there is positive evidence in the fossil record, that evidence is compromised by a number of important problems.
For instance, in the synapsid reptile to mammal transition there is a plethora of similar fossil species. Included are species with finely graded changes in the jaw anatomy. While this is evidence for evolution, we must also consider problems with this evidence. Ever since Stephen Jay Gould extolled these fossils as providing a "lovely sequence of intermediates," they have too often been assumed to be without issue. But across the reptile-mammal transition ancestral-descendant relationships are not obvious. Also, there are large gaps between and within the reptiles and mammals. Organisms must have evolved so rapidly that they appear fully formed and diverse in the fossil record. And amidst this spread of fossil species convergent evolution must have occurred many times, as many similar designs, in similar species, could not have derived from a common ancestor.
Examples of these can readily be found in paleontology textbooks [e.g., Benton, Carroll, Kemp, and Romer]. Rosenhouse, however, is apparently unaware of these basics of the fossil record, and expresses disbelief of any such outstanding issues. Regarding the cases of supposed convergent evolution [e.g., Benton, 291; Carroll, 377; Romer, 184], Rosenhouse can only confess that "I can't imagine what he's talking about."
Regarding the well-documented cases of gaps and apparent rapid evolution, Rosenhouse is still unable to see the issue. Kemp writes that quote:
The apparent rate of morphological change in the main lineages of the mammal-like reptiles varies. The sudden appearance of new higher taxa, families and even orders, immediately after a mass extinction, with all the features more or less developed, implies a very rapid evolution. [Kemp, 327]
Likewise, Carroll writes that quote:
The transition between pelycosaurs and therapsids has not been documented. It may have involved an environmental shift, as well as changes in morphology and physiology. The therapsids are already quite diverse when they first appear in the Upper Permian of Russia. [Carroll, 397]
With evolution, we must believe that the process speeds up so as to conveniently leave no trace in the fossil record. This results in new organisms, fully formed and diverse (rather than in a lineage). But Rosenhouse misses the point and wonders out loud what the alternative is. "Partially formed fossils?"
Rosenhouse continues to misread my essay. For instance, I explained how the horse sequence has been touted for years as strong evidence, but that in fact the horse-like fossil species do not align as was once thought. In fact, they persist unchanged and co-exist in the fossil record. Nonetheless, in textbooks and museums a sanitized version of the horse sequence too often continued to be used as an outstanding example of evolution. I used a Niles Eldredge quote to illustrate the situation.
Rosenhouse criticizes my use of the Eldredge quote. Rosenhouse says I have misrepresented Eldredge because Eldredge does not question evolution; rather, Eldredge is merely bemoaning the over simplified, speculative presentation of the horse fossils. I agree, and in that passage I did not attribute anything more than this to Eldredge.
The problem is not that I misrepresented Eldredge's point, but that Rosenhouse misrepresented my point. Rosenhouse next quotes Eldredge decrying the erroneous claim that the order of the horse fossils had been manipulated in order to mislead the public. But, of course, I said no such thing. The problem is not that the order was misrepresented, but that the nature of the fossil record was misrepresented. The actual fossil record presents a dizzying array of species with little evidence of gradual change. Instead, what we see are species appearing and persisting in virtually unchanged condition.
What Huxley failed to understand, and what Darwin knew very well, was that evolution had to be presented as gradual. Allowing for jumps would have opened the door to a non natural explanation. Darwin's arguments for evolution would have had much less traction if, in the end, he was to admit that his new found process just happened to act in quick spurts so that new species appeared abruptly. Saltations would have to wait until a later time, after evolution was firmly in place as the accepted explanation.
A century later, Eldredge and co-worker Stephen Jay Gould could safely propose the notion of punctuated equilibrium. Then, and only then could the nature of the fossils be simultaneously confessed and assimilated. With evolution firmly in place as a fact, any such evidential problems could be relegated to the question of how, not whether, evolution occurred. Hence, Rosenhouse admits that while inferring specific lines of descent among fossil species is a thorny problem, nonetheless he reassures us that this "has nothing to do with whether fossils provide strong evidence for common descent."
Finally, Rosenhouse argues that quote:
There is no rival theory that makes the same predictions about the fossil record that evolution does. That is why the fossil record provides such good evidence for evolution.
It is true that no other theory makes the same predictions as evolution. In fact, evolution can accommodate everything from species persisting unchanged for eons to the abrupt appearance of new species in the fossil record.
The advanced trilobites, for instance, can appear before the less advanced ones, and placental mammals can predate marsupials in Australia. Major new designs can appear out of nowhere, as though planted there. Furthermore, if on a distant planet we found that nothing but bacteria had lived there for billions of years, that too would become a prediction of evolution. Yes, Rosenhouse is correct that only evolution makes all these predictions. But there is a difference between fulfilled predictions and good evidence.
The DNA code
In Part two of Rosenhouse's critique he examines my discussion of the DNA code. I used the DNA code as an example of the non scientific aspects of evolution. Unfortunately Rosenhouse continues to misread my essay and use erroneous arguments. For instance, Rosenhouse says that the universality of the DNA code and associated cellular machinery is a prediction of common descent, for without them "it would be essentially impossible to argue that any two modern species share a common ancestor somewhere in the past."
Taken at face value, Rosenhouse's claim means that common descent is false since the DNA code is not universal. Variations of the code exist in nature. Therefore, will Rosenhouse reject common descent? No, Rosenhouse surely is thinking of more significant variations. How much more significant? We don't know, for Rosenhouse has not defined any criteria. If Rosenhouse wants to claim the universality of the DNA code as a prediction of common descent, he will need to explain why the known variations do not violate this prediction. Specifically, he will need to explain what are the limits of DNA code evolution.
This would be a daunting task given the limited state of our knowledge. Beyond this, it would also be daunting because evolution routinely considers ad hoc and speculative explanations for what we observe in nature. It would be different if we were testing a more straightforward, more easily modeled hypothesis, such as Kirchhoff's Voltage Law. In that case predictions could be computed mathematically using well-defined equations. But evolution and common descent are broad processes, driven by a wide range of causes and influences. Hence, these processes are capable of explaining a wide range of phenomena, especially given the level of speculation that is often permitted. It is not easy to show why an observable, such as variations in the DNA code, would falsify common descent.
This is, however, not the main problem presented by the DNA code. I pointed out in the essay that the DNA code and associated machinery are highly complex. Evolution lacks a detailed explanation of how it evolved. Rosenhouse complains that this is a topic for the origin of life, not evolution: "Evolutionary theory has nothing to say one way or the other about the origin of the code. The code is simply taken as a given."
Actually, evolutionary theory has plenty to say about the origin of the code, it just isn't very specific. The problem is not that the origin of the code has nothing to do with evolution, the problem is that evolution is unable to explain, beyond handwaving, how protein synthesis arose. Nonetheless, my point does not hinge on categorical definitions. Rosenhouse can draw the line between evolution and the origin of life problem however he likes. Evolutionists such as Mark Ridley still rely on the argument that homologies such as the DNA code would not exist "if the species had independent origins." [Ridley, 49]
Homology
In Part three of Rosenhouse's critique he examines my discussion of the homology evidence for evolution. Homologies are an important evidence for evolution. They reveal the persistence of designs that don't seem necessary. Are not the contingencies of the evolutionary process a better explanation for these designs than any necessity of biology? As Darwin rhetorically asked: quote:
What can be more curious than that the hand of a man, formed for grasping, that of a mole for digging, the leg of the horse, the paddle of the porpoise, and the wing of the bat, should all be constructed on the same pattern, and should include similar bones, in the same relative positions? [Darwin, 434]
Evolution, so the argument goes, is constrained to use what is available. The pentadactyl pattern is a repeated design because it was available. The problem with this argument, however, is that there also exist repeated designs that could not have been inherited from a common ancestor. As I wrote in the essay:
quote:
The marsupial-placental convergence is a popular example. Over millions of years and in different corners of the earth the marsupial and placental lineages, supposedly evolving from a mouse-like species, produced a host of similar designs. Everything from sabre-toothed carnivores and wolves to flying squirrels and anteaters were produced independently. Nature is full of lesser-known examples. From salamanders to cacti we find striking similarities that must have arisen independently. If biology is ruled by contingency rather than necessity then why do we find duplicated designs? When similarities are found among allied species they are cited as powerful evidence for evolution. When similarities are found among distant species, they are noted as cases of convergent evolution. Evolution can explain either case but the explanations presuppose evolution. This is not powerful evidence for the theory. [Hunter, 2004, 199-200]
Rosenhouse misses the point. He responds: quote:
Biologists usually make a distinction between homologous characters and analogous characters; the former are the ones that are most plausibly explained via common descent. Hunter is suggesting that biologists are being arbitrary in their determinations about which characters are homologous and which are analogous.
My point was that these homologies are not powerful evidence for the theory, not that the assignments are arbitrary. Rosenhouse then begs the question as he explains how evolutionists judge which characters are homologous and analogous, for this process relies on evolution for their identification. [Hunter, 2001, 27-29]
Another problem with the homology evidence arises from embryology. The problem is that designs that appear to be homologous sometimes arise from different embryonic development patterns or from different genes. This is a well known problem. [Alberch, 51, 56; de Beer, 16] As Brian Hall wrote: quote:
Because there are so many examples of homologous structures arising from nonhomologous development processes, I believe homology can no longer retain its historical links to shared embryonic development. [Hall, 1]
In my essay I gave an example of two closely related frog species with similar eye lenses that develop differently. Rather than acknowledge that this is a legitimate issue, Rosenhouse complains that I did not provide sufficient details of the case: "Hunter's argument here is far too vague to be replied to." In science, it is important to consider all the evidence and test a theory rather than protect it from evidential problems.
Problems with the homology evidence also appear at the molecular level. Rosenhouse quotes my first paragraph on this topic and again complains that my explanation is "too vague to be responded to." He wants to know what functional reasons there might be for molecular differences between different species. He agrees such reasons are conceivable, but writes that "it is safe to say that no one has a plausible suggestion for what that functional reason might be." Actually, I gave six such suggestions in the next paragraph. [Hunter, 2004, 201]
Rosenhouse also ignores the subsequent paragraphs where I discuss non-coding regions of DNA. For instance, non coding regions in the mouse and human genomes have been found to be practically identical. This was a great surprise to evolutionists as they expected the regions to contain more differences.
Rosenhouse misses this, and writes: quote:
Hunter doesn't even consider what to my mind is the most compelling sort of molecular evidence for common descent: patterns of similarities in the noncoding portions of the genome. Since these genes (sic) do not code for proteins their similarities cannot be explained functionally (unless, of course, the noncoding DNA also serves some deeply concealed function that demands very specific sequences of nucleotides). And the sheer quanitity of these similarities makes it implausible to attribute them to chance alone.
It is true that some of the genomic data support evolution, but some of it does not. Like the rest of biology, what we find is a sometimes subtle, sometimes confusing set of evidences. Some of the evidence points to evolution, but on the whole it does not. What is more obvious are the many examples of high complexity in biology that leave evolution without an explanation. The thesis of my essay is that there is a striking disparity between the quality of the biological evidence for evolution and the high claims and confidence of evolutionists. And that there is something to be learned from this disparity.
While the biological evidence raises questions and doubts about evolution, evolutionists claim their theory is a fact. For them, evolution is not an idea that just might be wrong, though they don't think so. No, it must be true. And anyone who doesn't agree must be up to no good. Rosenhouse spells this out in his mission statement:
quote:
For more than a century Darwin's theory of evolution has been the cornerstone of biological research. This status was hard-won through countless successes in the field and the laboratory. Today it remains one of the most vibrant and productive areas of scientific research.
Some people, motivated almost entirely by religious conviction, are unimpressed by this track record. They believe that evolution poses a threat to morality and decency and sundry other forms of goodness. As a result, they avail themselves of every opportunity to denigrate the accomplishments of Darwin and the scientists who succeeded him. This denigration takes the form of fallacious scientific arguments, ad hominem attacks against scientists, and an endless stream of propaganda designed to fire the passions of scientificaly ignorant people.
These folks, who call themselves things like "creationists" or "intelligent design theorists", have the ear of numerous politicians at all levels of government. Their main goal is not to produce new science or learn new things about nature. Rather, they want to inject their bad arguments in to science classrooms, with the intention of changing what they perceive as the atheistic inclinations of modern society.
Presenting creationist ideas in science classes as if they have any scientific merit would be a terrible disservice to our students. It is tantamount to telling them lies. For this reason, creationism in all its forms must be opposed.
It is little wonder that Rosenhouse is not particularly interested in exploring the nuances and difficulties of the evidence. After all, these are merely propaganda brought about by people who want to denigrate the work of scientists. Unfortunately, these ad hominem attacks are not unusual. Rosenhouse's sentiment is, in fact, quite typical and it sets up an atmosphere in which rational debate is impossible.
Hence, while Rosenhouse may not have addressed the evidential problems I wrote about, he did, nonetheless, find that my essay is "very bad," that my arguments are "embarrassingly bad" with "elementary misunderstanding," that I am guilty of "intellectual perversity," that I am "completely confused," and that I am "lazy." Other than that I assume the essay was perfect.
Notes
Alberch, P., "Problems with the interpretation of developmental sequences," Systematic Zoology, 34:46-58, 1985.
Benton, M. J., Vertebrate Paleontology, 2d ed., Chapman and Hall, 1997.
Carroll, R. L., Vertebrate Paleontology and Evolution, W.H. Freeman, 1988.
Darwin, C., The Origin of Species, 6th ed., Collier Macmillan, 1872, 1962 repr.
de Beer, G., Homology: An Unsolved Problem, p. 16, 1971.
Hall, B. K., "Homology and Embryonic Development," Evol Biology, 28:1-37, 1995.
Hunter, C.G., Darwin’s God: Evolution and the Problem of Evil, Brazos Press, 2001.
Hunter, C.G., “Why Evolution Fails the Test of Science,” in Uncommon Dissent: Intellectuals Who Find Darwinism Unconvincing, (Ed. W. Dembski) Intercollegiate Studies Institute / University of Chicago Press, 2004.
Kemp, T. S., Fossils and Evolution, Oxford University Press, 1999.
Ridley, M., Evolution, Blackwell Scientific, 1993.
Romer, A. S., Vertebrate Paleontology, 3d ed., Univerisity of Chicago Press, 1966.
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Salvador T. Cordova
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Member # 959
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posted 29. August 2004 22:49
Thank you Dr. Hunter for Posting. I would hope Dr. Rosenhouse will visit ISCID so that the two of you can dialogue directly.
If he is not representing your position correctly he should withdraw his statement. In terms of scientific dialogue, I recommend he come here and post. That would be a fruitful course of action in the interest of science.
Perhaps you could at least get on his blog and invite him to ISCID. I don't know, it's just a thought. If he shows up, he could clear the air maybe. I'm glad some annonymous poster linked to this thread. ![[Big Grin]](biggrin.gif)
quote:
Rosenhouse writes:
Hunter holds a PhD in biophysics from the University of Illinois, making him the only contributor among those I have read so far to actually have some scientific credentials.
Rosenhouse is a math professor not a biologist. Further he wrote:
quote:
Rosenhouse writes:
Moving right along, the next essay in Uncommon Dissent that I read was “Why Evolution Fails the Test of Science” by Cornelius Hunter. Hunter holds a PhD in biophysics from the University of Illinois, making him the only contributor among those I have read so far to actually have some scientific credentials.
Rosenhouse obviously did not yet "read so far" in that he fails to mention the credentials of:
Marcel Shutzenberger
Michael Denton
Michael Behe
Frank Tipler
David Berlinski
Roland Hirsh
I would hope he visits here to defend his claims against your work. That is what is troubling, the substance of his criticism is not scientific.
quote:
Rosenhouse writes:
And the sheer quanitity of these similarities makes it implausible to attribute them to chance alone.
That's right, therefore common design is a possibility. This is strengthened by the chapter in Michael Denton's book, Evolution a Theory in Crisis, regarding the "Biochemical Echo of Typology". I invited Rosenhouse to comment on the precision of the sequence divergences in cytochrome-c. It was a topic actually amenable to his background in discrete mathematics. He has not responded. In fact, I'd be willing to debate him publicly at James Madison University if he so chooses and is willing to have the debate recorded.
The similarity to sequences argue more for design rather than Darwinian evolution, even under the presumption of common descent. Even on the assumption common descent happened, there is strong evidence of ID.
Dr. Hunter, thank you for posting. It reassures many of us, who read your books that you are not ducking the hard questions.
regards,
Salvador
[ 20. September 2004, 22:04: Message edited by: Salvador T. Cordova ]
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Cornelius G. Hunter
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Member # 81
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posted 31. August 2004 17:56
In my essay I briefly summarized why the DNA code is not strong evidence for evolution. [1] One reason is that the code, and protein synthesis in general, is phenomenally complicated. There is no detailed scientific description of what could have produced cellular protein synthesis. Nonetheless, evolutionists say that the problem is solved. [2]
This alone is a remarkable statement. As an introduction, I noted some obvious reasons why the DNA code and protein synthesis are complicated:
quote:
The DNA code is routinely used as strong evidence for evolution, but why? Everyone knows that one cannot use a code without having a method for encoding and deciphering the information that is being transmitted. And of course the sender and receiver must be using the same code for the system to work. Volumes are written on the cellular machinery that is involved in nature’s scheme for using the DNA code and we still don’t understand all the details. It is phenomenally complex and is not easily explained as a product of Darwin’s evolutionary process [1]
Unfortunately Rosenhouse had difficulty seeing the implications. "I have no idea," he writes, "what the point of [the second] sentence is." Well, the mere existence of a code implies complexity because the use of the code requires both sender and receiver to have knowledge of the code and to be appropriately equipped. This is one of the reasons why evolutionists struggle to explain the code's existence.
In fact, the DNA code had to have arisen from an elaborate evolutionary pathway (of which a great many are proposed). Some evolutionists believe that the genetic code arose as a result of interactions with clay minerals. Others try to explain it as a result of non enzymatic chemical reactions, and yet others have tried stereochemical approaches. An entirely different set of hypotheses holds that the genetic code arrived on earth from outer space, either on meteors, comets, spores driven by radiation pressure or even deliberately planted by extraterrestrial beings.
In addition to the origin of the code, there are also a variety of hypotheses about how the modern code could have evolved from a simpler code. Perhaps fewer amino acids were originally coded for, or perhaps the code distinguished between classes of amino acids, rather than specific amino acids. Perhaps the alphabet was originally binary, or perhaps the words were only two letters long. Perhaps the original machinery was imprecise so that a given gene did not always code for the same protein.
One thing that evolutionists do agree on is that there is a great deal of uncertainty about how the genetic code came about. [3] All the various hypotheses are grappling with the problem of finding a non Darwinian mechanism for the genetic code. Because the code is chemically arbitrary, it holds no apparent competitive advantage over any other code. Swap in another code and things would work just as well, and therefore Darwin’s law of natural selection is powerless to help explain the origin of the code. But, on the other hand, protein synthesis is a highly complex process. The DNA code did not just pop into existence via a "frozen accident."
Also, given that the DNA code is to have evolved in an elaborate process, then in separate lineages different codes could have evolved, resulting in different codes in today's species. Also, as I mentioned earlier, the code is acknowledged to have evolved its variants, and it is difficult to place a bound on how far it could conceivably evolve. Evolution does not require for there to be universal genetic code.
Next, Rosenhouse is confused about how the code is used. He envisions the sender and receiver as "the parents and offspring of a given species," rather than (i) the DNA / RNA polymerase complex, and (ii) the ribosome and tRNA, respectively. If proteins are required in the protein synthesis process, then where did those proteins come from in the first place? It is a classic "chicken-or-the-egg" problem.
Rosenhouse tries to avoid all this by saying that, properly understood, the evolution of the code is not a part of evolution, but rather the origin of life (OOL) problem. So why does Rosenhouse draw the evolution / OOL line where he does? Does he see a genuine distinction, such that in the former designs arose via evolution, but in OOL the designs are likely not to have evolved? If this is the case then why not simply say so?
On the other hand, if this is not the case, then the distinction reduces to a convenient word-play so as to draw attention away from the hard problem of DNA code evolution. But there are plenty more such complexities in biology that cannot be hidden away under the OOL umbrella. We could ask Rosenhouse how echolocation evolved. He wouldn't have a clue, but I dare him to tell us it is an OOL problem.
Notes
1. Hunter, C.G., “Why Evolution Fails the Test of Science,” in Uncommon Dissent: Intellectuals Who Find Darwinism Unconvincing, (Ed. W. Dembski) Intercollegiate Studies Institute / University of Chicago Press, 2004, p. 208.
2. Hunter, p. 196.
3. See for example, Leslie E. Orgel, "The Origin of Life--How Long Did it Take?," Origins of Life and Evolution of the Biosphere, pp. 91-96, Vol. 28, 1998; Mitchell K. Hobish, "Studies on Order in Prebiological Systems at the Laboratory of Chemical Evolution," Origins of Life and Evolution of the Biosphere, pp. 124, Vol. 28, 1998; Jacques Ninio, Molecular Approaches to Evolution, p. 89, Princeton University Press, 1983.
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Cornelius G. Hunter
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Member # 81
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posted 02. September 2004 01:34
Here I reply to Jason Rosenhouse's August 31, 2004 blog entry at:
http://evolutionblog.blogspot.com/
Rosenhouse makes several good points. Unfortunately, these are easily lost among the many ad hominums and strawman renditions of my points (more than ten by my count). He also makes several mistakes.
Rosenhouse says that I am "full of it," a "major league crank" and a "fool," that I include references to look good, hoping that readers will not check them out, and that I parrot ID talking points. Also, he consistently overstates my points, making me look unreasonable and making for an easy target.
As an overview, Rosenhouse says the fossil record is compelling evidence for evolution whereas my position is that while there is plenty of evidence, there are important problems as well. I explain here why Rosenhouse fails to support his claim.
Rosenhouse begins by arguing that the fossil record is strong evidence for evolution. His first point is that just because we cannot infer specific lines of descent from fossils doesn't mean the fossils are not strong evidence of common descent. Rosenhouse argues against a strawman version of my point:
quote:
But pile of bones A does not come with a little tag to tell us how it is related to piles of bones B and C. That's just a fact about fossils, not an indictment of evolutionary theory.
Of course, I never said any such thing. Rosenhouse makes a good argument though, that features in a fossil sequence that appear to be transitional are evidence for common descent. Rosenhouse wants this to be compelling evidence, but how can it be compelling when there are significant problems with the evidence? Rosenhouse's answer is that the problems are not relevant:
quote:
Hunter … conflates two different questions. Namely, “Does the fossil record provide strong evidence of common descent?” with “Can we infer specific lines of descent from fossils alone?”
Actually, there are several issues with the fossil evidence, and we cannot simply ignore them in evaluating the evidence. Rosenhouse wants the fossil evidence to be compelling, so he urges we ignore the issues, as though they belong in a different compartment that has no bearing on the quality of the evidence. What are the problems with the fossil evidence? First, there is the issue that specific lines of descent are difficult to infer, such as in the reptile-mammal transition.
It is true that a fundamental limit of the fossils is that they cannot indicate lines of descent. As Rosenhouse says, the fossils do not come with little tags on them. But this misses the point.
Evolution texts and popular treatments have consistently portrayed the fossils as aligning in nice, clean sequences of species, compelling one to believe they were all part of one evolutionary lineage. See [1] for a recent example.
These reconstructions are anything but a realistic portrayal of the fossil evidence. The real fossils present us with a dizzying array of species. Included are gaps, dead ends, and convergences, but nothing so obvious as what the textbooks portray. This is true of the horse-like fossils, the whale sequence, and yes the reptile-mammal transition. And this is why the metaphor finally changed from a tree to a bush.
What if the real fossils looked like the textbook illustrations? What if they came out of the ground in nice clean sequences with no ambiguities. This would make for stronger evidence for evolution than the fossil evidence that we do have. The fact that there are myriad fossil species, with unclear ancestral relationships, detracts from the compelling storyline that evolutionists have traditionally presented. Anyone who has seen raw fossil data knows they are not nearly so suggestive of evolution as the artist's rendition. A clean sequence of fossils arranged nicly in a diagram is tremendously suggestive. Evolutionists do not typically use the unadulterated real data in textbooks. That would not be pedagogical. But sometimes pedagogy is at odds with accuracy.
No, this does not completely nullify the fossil evidence. No one ever said that. And, of course, evolution can explain such fossils. But there is no unique explanation. The line might be here, or it might be there. This demonstrates the arbitrariness in assigning evolutionary lineages. The question here is not whether evolution can explain the data, but how well the data serves as evidence if one is not presupposing evolution to begin with. It is understandable that evolutionists are not particularly concerned about these ambiguities. But this does not mean the evidence is compelling.
Another issue is the many gaps between fossils. Of course, evolutionists have traditionally explained this as a consequence of the fossil record being incomplete. This explanation was stretched beyond its limit, and the punctuated equilibrium hypothesis was a correction. As Eldredge wrote:
quote:
Attempts to salvage evolutionary theory have been made by claiming that the pattern of stepwise change usually seen in the fossils reflects a poor, spotty fossil record. Were the record sufficiently complete, goes the claim, we would see the expected pattern of gradational change. But there are too many examples of this pattern of stepwise change to ignore it any longer. [2]
Instead, what we need is a rapid spurt of change which, conveniently, leaves no trace of itself in the fossil record. Impossible? Of course not. Again, to forestall the coming strawman, the point is not that this makes evolution impossible. But it is an evidential issue to be considered. When evolution cannot explain how these phenomenal complexities are to have arisen, and when it crafts itself to explain the absence of fossil evidence, then it begins to look like Antony Flew's gardener.
Another issue is the ever-called upon mechanism of convergence. Rosenhouse refers to this as a "bizarre assertion" :
quote:
In my original post I commented that I couldn't imagine what Hunter was getting at here. I still can't. Why could many similar designs not have derived from a common ancestor? Multiple lineages starting from the same ancestor begin with an identical design. Over time, the different lineages evolve differing variants of this design. Where's the mystery here?
Of course, similar designs could have derived from a common ancestor. Once you've accepted the idea that phenomenally complex things arise from random forces, then there is nothing wrong with this process repeating itself a few times. Again, at issue is not whether evolution can explain convergences, but how they affect the fossil evidence. Similarities, we are told, are evidence of shared common ancestor. But in the case of convergences, we must say similaries arose independently. Therefore similarities are not such strong evidence of a common ancestor. Hence, on the one hand Rosenhouse claims there is no problem here because evolution can explain convergences, on the other hand he still wants to downplay the extent to which they occur.
First, he questions my references, and tries to discredit them with the ad hominum that I have given them "in the hope that people sympathetic to his cause will not check them out."
Then he misreads my references. He says I should have read Carroll (Vertebrate Paleontology and Evolution) more carefully, but Carroll states that the therocephalians and cynodonts "may have evolved separately." The point here is not that they necessarily did evolve separately, but that such a thing is easily accommodated by evolution.
Regarding my Benton reference, here is the quote:
quote:
Kemp, Row and Martinez et al. have denied the validity of the 'gomphodonts' as a natural group. They argue that their broad occluding cheek teeth are convergences that evolved independently at least three times. If this view is correct, then the third stage in the evolution of cynodonts to mammals was also achieved in the Early Triassic with the herbivorous diademodontids. [3]
Finally, Rosenhouse notes that the convergence noted in Romer is minor. That was a good point. But then Rosenhouse finally, and inadvertently, discovers one of the evidential issues with convergences. He correctly writes:
quote:
Rampant convergent evolution would be a problem if we found several lineages evolving major, complex morphological innovations in parallel.
But that is precisely what we do find. The marsupial-placental convergence is a popular example. Over millions of years and in different corners of the earth the marsupial and placental lineages, supposedly evolving from a mouse-like species, produced a host of similar designs. Everything from sabre-toothed carnivores and wolves to flying squirrels and anteaters were produced independently. Nature is full of lesser-known examples. From salamanders to cacti we find striking similarities that must have arisen independently.
Rosenhouse next notes that he could not locate my Kemp quote. Oops, I'm sorry about that, I got my Kemp references mixed up. I had the right page number (327) but the wrong title. The quote is
quote:
The apparent rate of morphological change in the main lineages of the mammal-like reptiles varies. The sudden appearance of new higher taxa, families and even orders, immediately after a mass extinction, with all the features more or less developed, implies a very rapid evolution. [4]
In any case, Rosenhouse says "I suspect that Kemp was not presenting this statement as some sort of problem for evolution." This has been a constant theme. Rosenhouse criticizes me for using quotes from evolutionists. The quotes show evidential issues, but the evolutionists do not question the theory. So I'm misrepresenting the evolutionist right?
Here Rosenhouse puts me in an impossible position. Imagine if I had used quotes from evolution skeptics. Then I would be blamed for not fairly representing the theory. The fact that these evolutionists do not doubt evolution indicates the validity of these concerns. These are not contrived concerns being raised by skeptics of evolution.
Amazingly, Rosenhouse is unable to conceive of any issue raised in the Kemp quote above: "Why does Hunter think this is helpful to his cause?" Rosenhouse describes how we should expect evolutionary rates to be rapid after a mass extinction. Is Rosenhouse saying that slow rates after an extinction would falsify evolution? Of course not, so we really don't expect fast rates. We "expect" whatever we see. This illustrates the flexibility of evolution. It can sustain the sudden appearance of new species, as though they were planted there, without a second thought.
Finally, Rosenhouse wants me to spell out the details for him.
quote:
If Hunter's concern is that certain specific structures appear without a clear fossil history, then he should spell out precisely which structures he has in mind and what sorts of fossilizable intermediates he expects to find.
You've got to be kidding me. What does Rosenhouse want me to do, tick off the design details of the myriad examples of sudden appearance? This is an unfortunate debating tactic. When in trouble, go on the offensive. What is lacking in Kemp's quote? New species, families and even orders appeared abruptly. This is not suggestive of evolution.
Rosenhouse next moves on to the horse-like fossils:
quote:
The horse fossils we have are compelling evidence for common descent because they document that animals having features transitional between small, primitive, vaguely horse-like animals on the one hand, and modern horses on the other, actually existed.
But transitional features are not "compelling evidence" for common descent. Certainly, they are evidence, but there are problems too. First, each of the various horse-like species persists unchanged for millions of years only to have a new specie appear along side it, coexisting before the first finally becomes extinct. What we see is the persistence of species once they appear. And persistence in a virtually unchanged condition. This is hardly "compelling evidence." Oops, I forgot, this is just my ignorance coming to the fore. Rosenhouse has already told us we must not consider these facts:
quote:
"That the fossil record documents a large number of stable horse-like species has no relevance to the question of whether the horse fossils we have provide strong evidence of common descent." --Rosenhouse
No wonder evolutionists think evolution is a fact. All evidence supports the theory, unless it doesn't, in which case it doesn't matter.
A second problem is that transitional features do not require common descent as an explanation. What appear to be transitional features may indicate a relationship via common descent, or they may not.
I had previously pointed out that the horse-like fossils had been misrepresented too many times in museum exhibits and textbooks. I used an Eldredge quote to illustrate this. Again, Rosenhouse objected, saying "But there was no misrepresentation of the nature of the fossil record."
Of course there was misrepresentation. Why did the Chicago Field Museum of Natural History admit in an exhibit that "Once We Told the Horse Story Wrong"? The point is that the horse-like fossils are all over the map while evolutionists were drawing up illustrations with nice clean sequences.
Finally, I made the point that punctuated equilibrium did what Darwin could not do a century before:
quote:
What Huxley failed to understand, and what Darwin knew very well, was that evolution had to be presented as gradual. Allowing for jumps would have opened the door to a non natural explanation. Darwin's arguments for evolution would have had much less traction if, in the end, he was to admit that his new found process just happened to act in quick spurts so that new species appeared abruptly. Saltations would have to wait until a later time, after evolution was firmly in place as the accepted explanation.
A century later, Eldredge and co-worker Stephen Jay Gould could safely propose the notion of punctuated equilibrium. Then, and only then could the nature of the fossils be simultaneously confessed and assimilated. With evolution firmly in place as a fact, any such evidential problems could be relegated to the question of how, not whether, evolution occurred. Hence, Rosenhouse admits that while inferring specific lines of descent among fossil species is a thorny problem, nonetheless he reassures us that this “has nothing to do with whether fossils provide strong evidence for common descent.”
Rosenhouse ignores my point and criticizes me for associating punctuated equilibrium with saltations. He makes the bizarre and erroneous statement that "Punctuated Equilibrium has nothing to do with saltations." Saltations are seen in fossil record [5], and the purpose of punctuated equilibrium was to explain them. Rosenhouse follows this with another strawman: "In fact, it [punctuated equilibrium] has nothing to do with mechanisms at all." Of course, I never said that it did.
What Rosenhouse did manage to do was avoid digesting my point and instead end his reply with more strawmen and ad hominums, and making the absurd statement that I am "only interested in parroting ID talking points."
Notes
1. Zimmerman, C., Evolution: The Triumph of an Idea, HarperCollins, 2001, p. 138.
2. Niles Eldridge, “An Extravagance of Species,” Natural History, p. 50, Vol. 89, No. 7, The American Museum of Natural History, 1980.
3. Benton, M. J., Vertebrate Paleontology, 2d ed., Chapman and Hall, 1997, p. 291.
4. Kemp, Mammal-like Reptiles and the Origin of Mammals, Academic Press, 1982, p. 327.
5. Mayr, E., Toward a New Philosophy of Biology: Observations of an Evolutionist, The Belknap Press of Harvard University Press, 1988, Ch. 26: "Speciational evolution through punctuated equilibrium."
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Salvador T. Cordova
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posted 02. September 2004 09:02
quote:
Dr. Hunter wrote:
Again, at issue is not whether evolution can explain convergences, but how they affect the fossil evidence.
For what it's worth, Evolutionary Paleobiologist Simon Conway Morris in Life's Solution Cambridge Press 2003.
quote:
page 126-128:
biological convergence can mean many things and operate at many levels. As I shall argue, however, there are some common implications, despite apparantly bewildering range of examples....
I believe the topic of convergence is important for two main reasons. One is widely acknowledged, if as often subject to procrustean procedures of accommodation. It concerns phylogeny, with the obvious circularity of two questions : do we trust our phylogeny and thereby define convergence (which everyone does), or do we trust our characters to be convergent (for whatever reason) and define our phylogeny? As phylogeny depends on characters, the two questions are inseperable...
Even so, no phylogeny is free of its convergences, and it is often the case that a biologist believes a phylogeny because in his or her view certain convergences would be too incredible to be true.
During my time in the libraries I have been particularly struck by the adjectives that accompany descriptions of evolutionary convergence. Words like, 'remarkable', 'striking', 'extraordinary', or even 'astonishing' and 'uncanny' are common place. It is well appreciated that seldom are the similarities precise, and this in itself is as concrete a piece of evidence for the reality of evolution as can be provided. Even so, the frequency of adjectival surprise associated with descriptions of convergence suggests there is almost a feeling of unease in these similarities. Indeed, I strongly suspect that some of these biologists sense the ghost of teleology looking over their shoulders.
Morris summarizes the situation well...
The presumption of a single common ancestor does not automatically imply Darwinian Evolution. Denton's work, published in Peer-Reviewed Journal of Theoretical biology explores protein convergence. And he argues that natural selection does not drive the evolution of proteins.
quote:
The folds are evidently determined by natural law, not natural selection, and are ‘lawful forms’ in the Platonic and pre-Darwinian sense of the word
Michael J. Denton, Craig J. Marshall and Michael Legge. The Protein Folds as Platonic Forms: New Support for the Pre-Darwinian Conception of Evolution by Natural Law. J. Theor. Biol. (2002) 219, 325–342
Even on the assumption of common descent, there is an aspect of the molecular evidence that argues too strongly for common design. Few people appreciate that there is a severe enigma that would require multiple molecular clocks synchronized over a wide range of species and then mutations restricted to loci for no reason except to create molecular hierarchies in some proteins.
Rosenhouse cited Theobold's article to deal with cytochrome-c. Theobold in a response article appeals to "a posteriori predictions" of Macro Evoltuion. That's one of the few places on the net such a phrase is used. "a posteriori predictions" is an apt term for Darwinian theory.
quote:
Morris writes 134:
Convergence is pervasive. And moving from animals, let us take a particularly strinking example in the plants.
page 138:
Birds themselves provide further compelling examples of evolutionary convergence
page 139:
Within the mammals also there are compelling examples of convergence
etc. etc.
Simon Morris tries to explain the convergences away as no problem for evolution. But it is a problem. Arriving at common solutions independently imply that unlikely combinations were arrived at. One might presume that the same selection pressure yielded the same results, but that presumes such a selection pressure can even exist in principle and deliver the required specificity. Even on the presumption of common descent, Darwinian selection mechanisms are not necessarily the driving force.
Genetic algorithms cannot solve passwords (analogous to Irreducible Complexity). Genetic algorithms need feed back to be able to converge on a solution. The Darwinists assume that such feedback paths always exists to create the features we see, when we know from first principles this is not warranted, and more likely wrong.
Thornhill and Ussery did a good job of strengthening Behe's argument of IC. Their rather less than enthusiastic paper begrugingly recognized the problems Behe perceived. They offered "co-option" and "reduction of function" as solutions, but those are suspiciously weak tautologies.
As you say, what is problematic also is the fact converged solutions are arrived at through different developmental pathways.
Rosenhouse keeps arguing for all these proofs of common descent. We can grant that for the sake of argument. But common descent does not imply evolution proceeded by Darwinian mechanisms.
Rosenhouse refers to my offerings as "brain dead" and that the readers of your work are scientficially illiterate.
Rosenhouse seems to like you, since in he skipped over several credentialed scientists in the book to read your essay first.
regards,
Salvador
[ 20. September 2004, 22:06: Message edited by: Salvador T. Cordova ]
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Cornelius G. Hunter
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posted 02. September 2004 16:54
Salvador:
Thanks for your post, however, did you really quote Morris correctly? Did he really write that
quote:
It is well appreciated that seldom are the similarities precise, and this in itself is as concrete a piece of evidence for the reality of evolution as can be provided.
??
If so, now I've heard everything. Not only are similarities evidence for evolution, differences are too. Does he elaborate on how he comes to this strange conclusion?
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Salvador T. Cordova
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posted 03. September 2004 01:53
Dr. Hunter,
I really appreciate what you have written. When Jason Rosenhouse has offered a valid criticism you have acknowledge it and even accepted correction. I know for a fact that people in my personal life who read and discuss these threads are appreciative of such a truth seeking attitude.
quote:
Rosenhouse wrote:
Rampant convergent evolution would be a problem if we found several lineages evolving major, complex morphological innovations in parallel.
And Simon Morris could not have offered a better appraisal of the the enigma of convergence and " the ghost of teleology" which it suggests. ![[Cool]](cool.gif) Yes indeed, we have problem for evolution because we do have "complex morphological innovations in parallel".
Which leads to your comment and question.
quote:
Salvador:
Thanks for your post, however, did you really quote Morris correctly? Did he really write that
quote:
It is well appreciated that seldom are the similarities precise, and this in itself is as concrete a piece of evidence for the reality of evolution as can be provided.
??
If so, now I've heard everything. Not only are similarities evidence for evolution, differences are too. Does he elaborate on how he comes to this strange conclusion?
Indeed, I was so struck with how out of place that comment was I almost put an ellipsis "..." in my quotation.
Yes, I did quote it correctly, as strange a comment as it was. What is apparant however is the sense of astonishment, and also your point that phylogeny is weakened. There is actually scattered throughout the literature a comparable problem with protein convergence!!!
quote:
page 290 Life's Solution:
FREEZING CONVERGENCE, PHOTOSYNTHETIC CONVERGENCE
A variety of proteins are able to confer protection against ice growth, but there is at least one striking example of convergence. It involves two groups of fish, the Artic cod and (in freezing waters around Antartica) a group knon as notothenioids. These groups are not closely related, but both produce effectively identical protein antifreezes that are based on ta sequence of tri-peptide repeats. Several lines of evidence show, however, that the genes responsible for the production of this protein are completely different.
Morris gives the endnotes and citations for these claims. However he devotes an entire section to Genes and Networks which touches on a growing problem in biology:
quote:
page 237:
Another problem, and equally serious, is the news emerging from the genome projects in which DNA is mapped and the total number of genes tallied.
The sense is that if there is convergence of the same product via different pathways, the argument from homology is weakened more, even at the biochemical level.
Further even in the same organism we have homologies that have independent pathways:
quote:
page 335, Nature's Destiny by Denton:
A curious aspect of the development of the namatode and one that would never have been predicted is that although the organism is bilaterally symmetrical--that is, its left and right halves are mirror images of each other--the equivalent organs and cells on the right- and lefthand sides of the body of the larva are not derived from equivalent cells in the embryo In other words, identical components on the right and left sides of the body are generated in different ways from different and nonsymemetrically placed progenitor cells in the early embryo and have therefore lineage patterns which are in some cases completely dissimilar. This is like making the right and left headlight on an automobile in completely different ways and utilizing completely different process.
Even individual cells of the same cell type in any one organ, such as, say, the muscle cells, gland cells, or nerve cells of the pharynx, are also derived from different lineages. For example, one particular cell progenitor of the pharynx gives rise to muscle cells, interneurons, gland cells, and epithelial cells. Another progenitor gives rise to to muscle and gland cells.
What would be a really nasty problem would be convergence of any supposed errors or junk, which I don't think we are too far away from discovering such examples. I'm cautiously optimistic.
Now, in answer to your question, does Morris (Simon not Henry ![[Wink]](wink.gif) ) justify his strange conclusion? I don't think so. He did however do the following, for the phrase "It is well appreciated that seldom are the similarities precise" he attached the following endnote.
quote:
endnote 111:
Despite the similarities that define any evolutionary convergence, there are also subtle and interesting differences, a point of very considerable importance for those interesed in explaining the realities of evolution: destinations are similar, seldom identical. Even so, on occasion the degree of similarity is astonishing. K. C. Emberton (see Evolution vol. 49, pp. 469-475, 1995), for example, notes a convergence between two land snails so precise that only a dissection allows them to be distinguished.
So to my mind Morris does not give a really good justification. He does explore some experimental attemts to create convergent evolution using E. Coli and some other examples. However, I disagree with him and Denton in that even if organism converge at the same solution, that such a convergence is inevitable. Even if platonic, pre-Darwinian forms exist based on physics, the actualization of those forms is not an inevitablity.
Denton echoes again something you wrote in your essay, concerning developmental pathways of organisms as noted in "The Failure of Homology", Evolution a Theory in Crisis.
quote:
page 143-145 from Evolution a Theory in Crisis:
Homology provided Darwin with apparently positive evidence that organisms had undergone descent from a common ancestor....
The validity of evolutionary interpretation of homology would have been greatly strengthened inf embryological and genetic research could have shown that homologous structures were specified by homologous genes and followed homologous patterns of embryological development. Such homology would indeed be strongly suggestive of "true relationship; of inheritance from a common ancestor". But it has become clear that the principle cannot be exteded in this way.
Also, One of the best examples of convergence is the Basic Pentadactyl Design. You mentioned it on page 199 of your essay. Denton also concurs that the Pentadactyl Design is a problem for the argument of homology:
quote:
page 151:
The evolutionary interpretation of homology is clouded even further by the uncomfortable fact that there are many cases of 'homologous like' resemblance which cannot by any stretch of the imagination be explained by descent from a common ancestor. The similar pentadactyl design of vertebrate fore- and hindlimbs provides a classic example. We have seen that the forelimbs of all the terrestrial vertebrates are constructed according to the same pentadactyl design, and this is attributed by evolutionary biologists as showing that all have been derived from a common ancestral source. But hindlimbs olf all vertebrates also conform to the pentadactyl patter and are strikingly similar to the forelimbs in bone structure and in their detailed embryological development. Yet no evolutionist claims that the hindlimb evolved from the forelimb, or that hindlimbs and forelimbs evolved from a common source....
The hand and foot are also based on the same design, with five digits in both hand and foot....
Here is a case of profound resemblance which cannot be explained in terms of a theory of common descent....
We seem forced to propose that during the course of evolution the gradual accumulaton of tiny independent and random changes in two independent structures -- the pectoral and pelvic fins of a fish -- hit on an identical yet apparently arbitrary ground plan for the design of the fore-and hindlimbs of a tetrapod. The problem is even more perplexing considering that neither the initial structures -- the pelvic and pectoral fins of a fish -- nor the end products of the process -- the fore- and hindlimbs of a tetrapod -- are in any strict sense identical.
With the Pentadactyl design, we have a case where dissimilarities in a convergence argue against evolution by common descent.
regards,
Salvador
[ 20. September 2004, 22:06: Message edited by: Salvador T. Cordova ]
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charlie d.
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posted 04. September 2004 10:19
First, a quick scientific comment regarding Denton and pentadactyly in fore- and hindlimbs. It is at the very least misleading, if not completely erroneous, to say that "no evolutionist claims that the hindlimb evolved from the forelimb, or that hindlimbs and forelimbs evolved from a common source....". The fact is, the basic developmental pathways, signals, and digit specification mechanisms are shared between forelimbs and hindlimbs. We are segmental animals, and finding the same structural plan repeated along the body axis (think vertebrae, miotomes) is actually not surprising at all. Just like one doesn't need to hypothesize that the right and left eye independently evolved inverted retinas, because we are bilaterians, one doesn't need to look further than Hox genes to understand how both tetrapod fore- and hindlimbs develop though similar plans. Here and here are two recent papers describing limb and digit formation in terms of variations on the same Hox gene-regulated developmental scheme (less technical reviews of the data are here and here). Although the details of these mechanisms were not known at the time Denton wrote that quote, the general pattern certainly was, so I am a little surprised of that statement (I don't have Denton's book, so I can't check what was said in the ellipses in the quote).
Second, a board-related comment: if irrelevant cheerleading/toadying/boasting accompanies every comment, and people engage in open self-congratulation every time they think they have scored a point in the discussion, the tone will quickly degenerate, which I thought the moderators were trying to avoid. I understand traffic is slow these days, but I can see another nosivad-like debacle brewing. Let's cut the razz, and stick to the facts. My $0.02.
[ 04. September 2004, 10:37: Message edited by: charlie d. ]
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Cornelius G. Hunter
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posted 04. September 2004 14:32
I respond to Richard at:
http://evolutionblog.blogspot.com/2004/09/does-this-guy-have-job.html
Richard, you said:
quote:
I'm still waiting for Cornelius to reveal some of his "preponderance of evidence" against evolution. All I can see in his posts to the ISCID forum is a list of things that science hasn't fully explained. (I should add that I haven't seen his original essay in "Uncommon Dissent".) Gaps in scientific knowledge--which exist in all areas of science--are not a reason for throwing out theories which are based on what we do know.
Well, that is the issue. What is it that we do know? We do know that organisms are complex, with many examples of designs that are not likely to have evolved. Darwin did not solve this problem scientifically. Instead, he said that the skeptic needs to show that the evolution of such designs is impossible. That is not a solution. In fact, it is essentially impossible. The problem of complexity is a serious problem, and there is a preponderance of such evidence.
For instance, we also know that small scale change appears to be limited. Not only do we not have reason to think it is unbounded, but small scale change entails, again, complexity. [1]
Complexity is also obvious in the fossils. What do we know? We know that fossil species remain essentially unchanged for long, geological, periods of time. And we do know that complexity appears early and often. For example, the trilobite eye of 400 Myr was said to be "an all-time feat of function optimization." [2]
One of the most important evidences for evolution is similarities in design. But what we do know is that similarities are ubiquitous that could not have been inherited from a common ancestor. You ask:
quote:
I'm also still waiting for Cornelius to explain why he thinks features like sabre teeth could not evolve independently in two lineages. These features are adaptations to a particular way of making a living (e.g. hunting large prey in the case of sabre teeth). Why couldn't two different lineages, which make their living in similar ways, evolve similar adaptations?
Again, this is asking for the impossible. I cannot prove the independent evolution of features is impossible. But what we do know is that these same designs would have had to have evolved on different continents, over geological time periods. This happens over and over, but evolution is a contingent process. There many ways to solve design problems in biology. The design space is large and multi dimensional in biology, with many different potential solutions. This is why evolutionists maintain that if we were to replay natural history, we would get a different world with different species and designs. There are no pre determined solutions. But these convergences contradict this and call into question Darwin's argument that similarities are strong evidence for evolution. You ask:
quote:
And I'd like to know how Cornelius explains away the evidence for evolution, of which he agrees some exists.
Well, as I've explained, there are many problems with the evidence. Typically, otherwise faulty theories to have supporting evidence. You asked:
quote:
Why, for example, do all organisms share the same basic DNA code, but also have minor variations which happen to follow a pattern consistent with the taxonomic hierarchy revealed by other evidence? Does he invoke a common designer, who decided to design his species this way for reasons unknown? Or does he refuse to give any explanation at all?
What if the minor variations did not follow the phylogenetic pattern? Would you say evolution is false? I suspect that you would not. After all, above you demonstrate that you have no problem with massive morphological convergence. So why can't the DNA code evolution repeat itself in different lineages? The problem, then, is that you are claiming something as evidence, but evolution predicts the opposite as well.
Also, in this case you are claiming evidence that isn't even real. The DNA code variations do not line up phlogenetically. They are scattered across various types of organisms. For example, the UAR codon is observed to switch from "stop" to "Gln" in green algae, various ciliates, and some diplomonads. Likewise, the UGA codon is observed to switch from "stop" to "Trp" in other various ciliates and two firmicutes. [3]
Finally, briefly, thank you Salvador for the additional information. You wrote that "What would be a really nasty problem would be convergence of any supposed errors or junk." Actually, such things have been found. And thanks to Charlie for the critique of Denton and board-related comment.
Notes
1. Hunter, C., Darwin's Proof: The Triumph of Religion over Science, Brazos Press, 2003, pp. 24-5.
2. Shawver, L., "Trilobite eyes: An impressive feat of early evolution," Science News, 105:72, 1974; Levi-Setti, R., Trilobites, 2d ed., University of Chicago Press, 1993, p. 29.
3. Knight, D., "Rewiring the keyboard: evolvability of the genetic code," Nature Reviews-Genetics, 2:49-59, 2001.
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charlie d.
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posted 04. September 2004 15:24
Since Cornelius brought up the genetic code thing again, I may add the comment that genetic code changes of the type commonly found in different organisms are not that surprising either. Indeed, some of the very first mutants characterized in bacteria bear "suppressor of amber" mutations, which lead to variant genetic codes because of mutations in tRNA genes (usually, changing "stop" codons into coding ones). While these mutations are selectively disfavored in wild-type bacteria, they are strongly selected in bacteria which bear other mutations that introduce stop codons into essential genes ("amber" mutations, hence the "suppressor of amber" name).
Thus, although we cannot reconstruct the phylogenetic history of each organism with a variant genetic code to understand how and why their variant codes arose, we have a pretty clear molecular understanding of how the universal genetic code can and does evolve into the variants observed.
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Scott
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posted 05. September 2004 02:46
quote:
Cornelius G. Hunter wrote:
Salvador:
Thanks for your post, however, did you really quote Morris correctly? Did he really write that?
quote:
It is therefore my strong belief that the topic of convergence is very far from being just another example of the frustrating imprecisions of biology where apparent rules and laws melt into exceptions and counter-examples. To echo the idea that convergence might give some surprising insights into a deeper structure of biology, there is some evidence that might at first seem to be simply anecdotal. During my time in the libraries I have been particularly struck by the adjectives that accompany descriptions of evolutionary convergence. Words like, 'remarkable', 'striking', 'extraordinary', or even 'astonishing' and 'uncanny' are commonplace. It is well appreciated that seldom are the similarities precise [111], and this in itself is as concrete a piece of evidence for the reality of evolution as can be provided. Even so, the frequency of adjectival surprise associated with descriptions of convergence suggests to me that there is almost a feeling of unease in these similarities. Indeed, I strongly suspect that some of these biologists sense the ghost of teleology looking over their shoulders. Nor is this an unworthy sentiment. The eeriness of convergence is central to how evolution navigates across the combinatorial immensities of biological 'hyperspace'. And when we look at some of these examples of of convergence, it is not difficult to see why.
- Simon Conway Morris, Life's Solution: Inevitable Humans in a Lonely Universe, pp.127-128
quote:
111. Despite the similarities that define any evolutionary convergence, there are also subtle and interesting differences, a point of very considerable importance for those interested in explaining the realities of evolution: destinations are similar, seldom identical. Even so, on occassion the degree of similarity is quite astonishing.
The quote was reasonably precise. I have provided a bit more of the context.
To the extent that evolution is "common descent," similarities are taken as evidence for evolution. To the extent that evolution is "descent with modification," differences are taken as evidence for evolution. I guess that was the genius of Darwin's idea.
quote:
In Darwin's day, Sir Richard Owen (1804-92), a comparative anatomist and the first curator of the British Museum (Natural History), championed a neoplatonic version of structuralism. Owen believed that homologies shared among all vertbrates represented a theoretical design plan in the mind of God, a common pattern that God used to create animals. Darwin transformed this ideal plan into a real ancestor. With this concept of the common ancestor, Darwin could also explain the typological data uncovered by comparative anatomists, in addition to the functionalistic evidence of adaptation that he explained by natural selection. The dualistic approach that Darwin took ensured his success. Rather than resolving the structuralist/functionalist debate, he embraced the apparent contradiction in a single, simple theory.
- Todd Charles Wood and Megan J. Murray, Understanding the Pattern of Life, p. 15
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Cornelius G. Hunter
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posted 05. September 2004 03:33
Thanks Charlie. What do you think about the evolvability of the code beyond the minor variations we observe? Lewin, from the evolutionary perspective, writes:
quote:
Evolution of the code could have become "frozen" at a point at which the system had become so complex that any changes in codon meaning would disrupt existing proteins by substituting unacceptable amino acids. [1]
It seems that evolutionists take this position in spite of, rather than because of molecular biology. They need to take this position because the code is universal, not because changing it is inconceivable. Since proteins can easily tolerate substantial sequence substitutions, it seems there would often not be strong selective pressure against codon reassignments.
This point is compounded when one considers that most amino acids have multiple codons, so a single codon reassignment would have limited impact. In other words, switching a codon from alanine to valine does not mean no more alanines.
And this point is yet further compounded when one considers how many codon reassignments could be between similar amino acids, reducing the impact even more. Switching CUC from leucine to isoleucine not only would result in only a few substitutions in a protein, but those substitutions would have limited sequence impact since leu and ile are fairly similar.
Furthermore, the evolutionary perspective seems additionally strained when one considers that evolution, simultaneously, views protein sequence fitness landscapes as mostly neutral. For instance, the evolutionary view of the similarities between molecular and morphological phylogenies is not so much that there is any functional necessity but that ~neutral mutations accumulate in the different lineages independently (if there is a functional necessity then the molecular phylogenies would not provide independent evidence of evolution as is claimed). Why then is it so inconceivable that a few amino acids per protein could not be reassigned due to a single codon reassignment?
Placing such a strict limitation on DNA code changes also seems to contradict the ease with which evolution contemplates massive change. Evolution envisions substantial protein change over time. Regardless of the selective pressures, why could not DNA code changes be part of that process? Proteins could evolve accordingly if a particular codon reassignment introduced some selective pressure. What do you think?
Notes
1. Lewin, B., Genes VII, Oxford, 2000, p. 169.
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charlie d.
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posted 05. September 2004 09:38
The problem of course is that codon reassignments bring global proteome changes. So, while it is a good rule of thumb to say that a single or few conservative substitutions will not disrupt the structure or function of a given protein, one may expect that at least some protein will be affected if all the residues encoded by a certain codon are replaced.
This is not just a off-the-cuff prediction, by the way - people have been playing around with genetic codes for many years. To my knowledge (but you may want to verify this, since this is not my field), even in organisms with limited proteomes, such as E. coli, artificial changes to the code by tRNA manipulation result in decreased viability (just like suppressor of amber mutations). Thus, a code variant would be expected to evolve, like suppressor of amber, only in conditions in which it can effectively counterbalance some other selection pressure. Those conditions should be quite rare.
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Salvador T. Cordova
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Member # 959
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posted 05. September 2004 14:36
quote:
Second, a board-related comment: if irrelevant cheerleading/toadying/boasting accompanies every comment, and people engage in open self-congratulation every time they think they have scored a point in the discussion, the tone will quickly degenerate, which I thought the moderators were trying to avoid. I understand traffic is slow these days, but I can see another nosivad-like debacle brewing. Let's cut the razz, and stick to the facts. My $0.02.
No problem Charlie D. Sorry, I had a hard time containing my glee. I edited my post to withdraw my some of my gloating.
quote:
Dr. Hunter wrote:
Finally, briefly, thank you Salvador for the additional information. You wrote that "What would be a really nasty problem would be convergence of any supposed errors or junk." Actually, such things have been found.
As I suggested, I have cautious expectation that this is indeed the case. But some data and examples would be nice (hint, hint).
quote:
Simon Conway Morris wrote:
It is therefore my strong belief that the topic of convergence is very far from being just another example of the frustrating imprecisions of biology where apparent rules and laws melt into exceptions and counter-examples.
This echoes the theme of the book. Morris acknowledges that convergence is a potential example of "frustrating imprecisions". But his thesis that convergence is a proof of evolution is not scientifically founded. Contrary to Morris's suggestion, he does not solve the problem in his book, only makes it more evident.
So I will suggest some empirical and theoretical considerations to highlight why convergence is not resolvable by Darwinian evolution.
Formally speaking CSI is a purely statistical phenomenon. The falsifiable postulate is that CSI comes only from intelligence. Having worked in both Automatic Target Recognition sytems and on Finger Print Identification systems the idea of correlations of digital information is crucial, and CSI is a digital correlation.
Though I have not embraced the grand claim that only intelligence can make CSI, I argue for the less ambitious claim there exists CSI that can only be designed.
If we have protein sequences evolving independently in different lineages and if the expressing mechanism is via different pathways and genes this leads to a problem particularly in the "non-functional" regions of the expressed protein. Formally speaking, from a pure statistical standpoint, such convergent proteins are provisionally CSI. The correlations are seen somewhat in Dayhoff Diagram. I agrue that those correlations, even if presumed to occur most efficiently via common descent, they fatally weaken the selectionist and neutralist views of protein evolution.
Since this is brainstorms I offer something for research and it relates to Dr. Hunter's essay and comments particularly on convergence.
If we have examples of "non-functional" regions of protein, particularly if they arrive via different developmental pathways, and evolved independently in various lineages, we have evidence against the netreutralist evolutionary viewpoint. As Rosenhouse hinted at, in the cases of non-selectable parts of biology, the coincidence is too strong for raw chance.
Since have situations were raw chance won't work we could appeal to Darwinian seection as the cure all, but if one appeals to selectionist explanations one is left with an unfalsifiable hypothesis based on pure speculation. As Molecular Genetecist Denton points out in Evolution a Theory in Crisis, "The Biochemical Echo of Typology"
quote:
The difficulties associated with attempting to explain how a family of homologous proteins could have evolved at constant rates has created chaos in evolutionary thought. The evolutionary community has divided into two camps -- those still adhering to the selectionist position, and those rejecting it in favor of the neutralist. The devastating aspect of this controversy is that neither side can adequately account for the constancy of the rate of molecular evolution, yet each side fatally weakens the other.
We have prelimary support from the makers of Avida (Ofria) that the precise hierarchical relationships are vulnerable to "configurational entropy" (my term) caused by the presumption of neutral drift or un-coordinated selection pressures. The explanations are rather complicated, and it deals with discrete mathematics. The internet is not the easiest way to convey the reasons why but I posted my attempt at very fragmented sketch in :
Biotic Message of Nested Hierarchies which sketch the problem from the aspect of discrete mathematics and then a discussion from the makers of Avida (Ofria) in
Darwinian-Avidian Demonstrations of Non-Formation of Nested Hierarchies. A solution is evolution progressing under some pre-programmed "natural law" or Intelligent Design.
Now let me offer the kind of example which might be worth exploring expermintally and can lead to empirically falsifiable experiments.
Again I visit Nematode Convergence. The Nematode has two independent pathways for Vulva development. If we set up an experiment where by we knockout one of the developmental pathways and demonstrate that the population grows as fast or faster than Nematodes with both developmental pathways in place we have illustrated a system that is a credible example of complexity evolving outside of selection forces.
If the nematode example fails, we can try others. But the important thing, according to selectionist population genetics, there might be a good chance for the experiment to succeed on the assumption that the knocked out developmental pathway for the vulva doesn't compromise any other viability in the organism. We can at least try and find out.
I'm glad the issue of convergence has been brought to the table, not only because it weakens phylogenic arguments, but it poses theoretical problems for the neutralist and selectionist views of evolution. And perhaps most importantly, it may lead to empirically falsifiable predictions or at the very least, novel areas of pure observational inquiry.
Salvador
for completeness
Here is background on this example of convergence by Molecular Genetecist Denton in Nature's Destiny writes page 337-338:
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Another very intriguing aspect of development in higher organisms which has become increasingly apparent over the last ten years, and which is bound to impose additional constraints against any sort of bit-by-bit undirected change, is the use of partially or totally redundant components to buffer organisms against random mutational error and ensure reliability, particularly during development. As one authority points out: "The idea that redundancy may be quite common in cell and develoopmental biology has its origin in Spemann's (1938) idea of double assurance, a term taken from engineering."
The strategy of using several different means to achieve a particular goal where each of the individual means is sufficient by itself to achieve the goal is used in all manner of situations to guarantee that the goal will always be achieved, even if one or more of the means fail. Missiles, for example, are often guided to their targets using a number of different automatic guidance systems, including ground-based radar, map matching, inertial guidance systems, following a graded signal (heat-seeking). Even if one fails, the missile will still home in unerringly on its target. Reliability of information storage on computer discs is increased by encoding the information in two or more different ways. The functional reliability of complex machines such as aircraft and particularly space vehicles invariably involves the use of redundant components. The space shuttle's on-board inertial guidance system, which it uses during boosting into orbit and during reentry, consists, according to the McGraw-Hill Encyclopedia of Science and Technology of "five redundant computers and three inertial measurement units. Dual star trackers are used for periodic realignment in space....A radar backup system is provided for safety during launch and landing." (My emphasis.) Another instance where redundancy is exploited to increase reliability is in human and animal navigation, where most often a number of different and individually redundant clues are followed to minimize the risk of navigational error, which might accrue from following only one type or set of clues.
It now appears that a considerable number of genes, perhaps even the majority in higher organisms, are completely or at least partially redundant. One of the major pieces of evidence that this it the case has come from so-called gene knockout experiments, where a gene is effectively disabled in some way using genetic-engineering techniques so that it cannot play its normal role in the organisms's biology. A classic example of this came when a gene coding for a large complex protein known as Tenascin-C, which occurs in the extracellular matrix of all vertebrates, was knocked out in mice, without any obvious effect. As the author of a paper commenting on this surprising result cautions: "It would be premature to conclude that [the protein] has no importan function ...[as] it is conserved in every vertebrate species, which argues strongly for a fundamental role." The protein product of the Zeste gene in the fruit fly drosophila, which is a component of certain multiprotein complexes involved in transcribing regions of the DNA, can also be knocked out without any obvious effect on the very processes in which it is known to function.
The phenomenon of redundant genes is so widespread that it is already acknowledge to pose something of an evolutionary conundrum. Although in the words of the author of one recent article, "true genetic redundancy ought to be, in an evolutionary sense, impossible or at least unlikely," partially redundant genes are common. As another authority comments in recent review article: "Arguments over whether there can be true redundancy are moot for the experimentalist. The question is how he functions for partially redundant genes can be discovered given that partial redundancy is the rule." (My emphasis.)
And it seems uncreasingly that it is not only individual genes that are redundant, but rather that the phenomenon may be all-pervasive in the development of higher organisms, existing at every level from individual genes to the most complex developmental processes. For example, individual nerve axons, like guided missiles or migrating birds, are guided to their targets by a number of different and individually redundant mechanisms and clues. The development of the female sexual organ, the vulva, in the namatode provides perhaps the most dramatic example to date of redundancy exploited as a fail-safe device at the very highest level. A detailed description of the mechanism of formation of the nematode vulva is beyond the scope of this chapter, suffice it to say that the organ is generated by means of two quite different developmental mechanism, either of which is sufficient by itself to generate a perfect vulva.
It seems increasingly likely that redundancy will prove to be universally exploited in many key aspects of the development of higher organisms, for precisely the same reason it is utilized in many other areas--as a fail safe mechanism to ensure that developmental goals are achieved with what amounts to a virtually zero error rate. A very high degree of redundancy in the specification of the development of higher organism is almost certainly not in the least bit gratuitous, but rather of necessity. Probably no system remotely as complex as a higher organism could possibly function without a large measure of redundancy in many or even every aspect of its design.
Now, this phenomenon poses an additional challenge to the idea that organisms can be radically transformed as a result of a succession of small independent changes, as Darwinian theory supposes. For it means that if an advantageous change is to occur, in an organ system such as the namatode vulva, which is specified in two completely different ways, then this will of necessity require simultaneous changes in both blueprints. In other words, the greater the degree of redundancy, the greater the need for simultaneous mutation to effect evoutionary change and the more difficult it is to believe that evoutionary change could have been engineered without intelligent direction. Redundancy also increases the difficulty of genetic engineering, as it means that the compensatory changes that must inevitably accompany any desired change must be necessarily increased.
[ 05. September 2004, 14:41: Message edited by: Salvador T. Cordova ]
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Salvador T. Cordova
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posted 05. September 2004 15:18
quote:
charlie d wrote:
First, a quick scientific comment regarding Denton and pentadactyly in fore- and hindlimbs. It is at the very least misleading, if not completely erroneous, to say that "no evolutionist claims that the hindlimb evolved from the forelimb, or that hindlimbs and forelimbs evolved from a common source....". The fact is, the basic developmental pathways, signals, and digit specification mechanisms are shared between forelimbs and hindlimbs. We are segmental animals, and finding the same structural plan repeated along the body axis (think vertebrae, miotomes) is actually not surprising at all. Just like one doesn't need to hypothesize that the right and left eye independently evolved inverted retinas, because we are bilaterians, one doesn't need to look further than Hox genes to understand how both tetrapod fore- and hindlimbs develop though similar plans. Here and here are two recent papers describing limb and digit formation in terms of variations on the same Hox gene-regulated developmental scheme (less technical reviews of the data are here and here). Although the details of these mechanisms were not known at the time Denton wrote that quote, the general pattern certainly was, so I am a little surprised of that statement (I don't have Denton's book, so I can't check what was said in the ellipses in the quote).
First of all, my reading of the article didn't seem to indicate how many species were examined. As I showed with the bilateral symmetry of the nematode expressed through to different develomental pathways, we can't make the rote generazation that symmetries are automatically generated the same way in every organism even though such homology are reasonbly inferred to exits.
The discovery of more counter examples, such as in the nematode, in terms of pentadactyl development would strengthen Denton's argument. Here we have a case of areas ripe for novel investigation. But even if we find that the homology is universally controlled by the same sets of genes, it raises a potenially worse problem for natural selection as now evolution of features require selection pressure to act on several features simultaneously.
In Proceedings of National Academy of Science article on developmental biology, we have the following rather curious fact regrading expression of the pentadactyl form:
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A similar dose-response is observed in the morphogenesis of the penian bone, the baculum, which further suggests that digits and external genitalia share this genetic control mechanism.
The article goes on to relate the fact that the number of toes (ok, Digits) is tied to penis characteristics. How in the world from a scientific standpoint do we formulate selectionist pressures to account for this curious fact? This brings to bear the rather difficult issues of morphological convergence when genes have such deeply integrated diverse, non-modular roles. Denton in Evolution a Theory in Crisis explores the problems posed by pleiotropy to Darwinian Evolution in "The Failure of Homology". He further elaborates the problem in Nature's Destiny. I believe exploration of these topics will lead to further fruitul areas of pure observational data gathering.
Charlie pointed to the fact that convergence of the pentadactyl is attributable to the same genes, but this is complicated by the fact that the same genes affect other parts of the organism. Simply arguing for effeciency of re-use is problematic, because then how can one account for the evolution of genes that are so deeply integrated into the biology of the organism.
PS
to pre-empt any complaints about Denton, it is a myth that he has recanted materially on anything in his book Evolution a Theory in Crisis, he has seemed to have always accepted common descent since he rejected creationism in his teens, therefore any complaints of his recanting are ill founded.
[ 05. September 2004, 15:25: Message edited by: Salvador T. Cordova ]
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