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Author
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Topic: Response to Jason Rosenhouse
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Cornelius G. Hunter
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Member # 81
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posted 16. September 2004 02:57
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The reason I brought up Behe was to point out that the same problems with OOL that cause many evolutionists to consider it a separate subject are present in explaining many steps up the microbe-to-human ladder as well, so evolutionists who cede OOL as a mystery while saying that microbe-to-human is not, are making a mistake.
Good point Darel, I agree. There are plenty of awkward complexities to go around, many of which cannot be swept under the OOL rug no matter how liberal the boundary is set.
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I think that it is fair for evolutionists to draw a distinction between OOL and the microbe-to-human transformation, because their alleged evolutionary mechanism (generation-to-generation variations filtered by natural selection) requires there to be reproducing organisms, and before OOL there were no reproducing organisms.
Well evolutionists such as Rosenhouse are placing the OOL-evolution boundary far later than the creation of reproducing organisms. He wants to say that evolution doesn't begin until you have today's extant DNA code in place which is long after reproducing organisms are supposed to be on the scene.
I agree with you that in order to get evolution going there has to be a preliminary phase to get the first replicators into action, and that this is a different sort of problem than evolution. But why should this initial phase be expanded to include protein synthesis and the DNA code?
The setting of the OOL-evolution boundary at this point attempts to turn what is a problem into a supporting evidence. Obviously, a tremendous amount of change had too occur along the path leading up to the creation of today's extant code. This included a whole bunch of variation and replicating. What a surprise it would be if, in all this, no branching events occurred. But on the other hand, what a surprise it would be if there were branching events and yet the subsequent code evolution was duplicated in the different branches. Yet evolution is forced to choose between one of these unlikely scenarios.
Or in other words, there exists amongst all the species a common design that is highly complex. This means the last common ancestor had to include this design. But this places high complexity way far back at the beginning of evolution. Evolutionists are left not only with the problem of explaining how such a design arose, but how things got that well along without any branching. Things like DNA (encoded for proteins), RNA polymerase, tRNAs, ribosomes and aminoacyl-tRNA synthetases do not just accidentally appear out of nowhere. Yet this incredible ensemble is supposed to have arisen gradually without, in all this lengthy process, any branching into multiple lineages.
By sweeping this under the OOL rug we not only dispense with having to deal with this thorny problem but we're left with what sounds like powerful evidence for common descent. Actually, as I explained above, even given all this the evidence is problematic. But those are details that usually go unnoticed. So you can see that the setting of the OOL-evolution boundary at this point is a consequence of presupposing evolution and structuring the argument accordingly.
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Darel R. Finley
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posted 16. September 2004 09:23
Dr. Hunter,
The primitive replicators of which you speak are part of hypothetical attempts to solve the mystery of OOL. But many evolutionists, if I am correct, are willing to cede OOL as an unsolved and possibly unsolvable mystery (e.g. Crick's "directed panspermia") and attribute to mutation-selection evolution only the changes that followed the appearance of bacteria.
Of course, that scenario would still leave them with many problems, which we have just identified in this thread.
Attempts to push OOL further back than bacteria -- to hypothetical simpler replicators -- don't necessarily present a problem with current evidence, because it can always be proposed that the modern DNA/protein system was simply superior and wiped out its competitors. Of course, that's not evidence; it's an excuse, but to me a plausible excuse.
For the record, I suspect that the simplest bacteria we see on Earth today are probably not much different than the first reproducing organisms, which were not led up to by simpler replicators, but rather appeared as abruptly as did the major phyla later.
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Scott
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posted 16. September 2004 14:00
Dr. Hunter brings up an excellent point, and one which should be applicable to more than just the genetic code.
Why is it that cladogenesis can occur after the fixation of this code, but not before? There must have been viable precursors and intermediates, and yet no branching of these lineages ever occurred?
Any appeal to phyletic evolution (anagenesis) is ad hoc. It is often argued that a nested hierarchy is a prediction of common descent. But for a nested hierarchy, one must have branching. Yet here we have an example of just the opposite.
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Cornelius G. Hunter
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Member # 81
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posted 17. September 2004 01:54
quote:
Attempts to push OOL further back than bacteria -- to hypothetical simpler replicators -- don't necessarily present a problem with current evidence, because it can always be proposed that the modern DNA/protein system was simply superior and wiped out its competitors. Of course, that's not evidence; it's an excuse, but to me a plausible excuse.
Darel:
I'm afraid it is not quite that easy. The argument must be that every intermediate, leading up to the code, was superior to the alternatives at each step in the development of the code. Do you see how far-fetched this explanation becomes? The process must cover a vast amount of evolutionary territory, going from lifeless chemicals to a bacteria with full-blown protein synthesis. And yet through all of that there was only a single viable pathway? I don't think so.
The process that later would create everything from the eagles to jellyfish is now mysteriously constrained. And a mystery it would be, because we have no evidence of any such constraint. In fact, the code is thought to be chemically arbitrary. Many other codes would work just as well. Obviously evolutionists would have no problem if other codes existed. And it is not easy for them to explain why such other codes do not, in fact, exist. Of course they can contrive a just-so story, but this doesn't make the code powerful evidence for common descent.
Also, Scott makes a good point. The nested hierarchy is supposed to be powerful evidence for common descent, but it requires branching. But here branching must not be occurring.
[ 17. September 2004, 04:06: Message edited by: Cornelius G. Hunter ]
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Darel R. Finley
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posted 17. September 2004 09:58
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The process that later would create everything from the eagles to jellyfish is now mysteriously constrained.
Dr. Hunter,
I think I now see your point. The same phenomenon of local-environment specialization, that prevents eagles from wiping out jellyfish, should have allowed some of the evolutionary intermediates leading up to the DNA/protein system to survive in local areas where they are superior or just as good as the modern code.
Perhaps that is why Crick -- co-discoverer of the code itself -- would seriously propose something as non-Darwinistic as directed panspermia.
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Cornelius G. Hunter
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Member # 81
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posted 17. September 2004 16:28
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I think I now see your point. The same phenomenon of local-environment specialization, that prevents eagles from wiping out jellyfish, should have allowed some of the evolutionary intermediates leading up to the DNA/protein system to survive in local areas where they are superior or just as good as the modern code.
Perhaps that is why Crick -- co-discoverer of the code itself -- would seriously propose something as non-Darwinistic as directed panspermia.
Darel:
My point about the eagle and jellyfish is simply that natural processes are supposed to be capable of highly diverse creation, searching out the far corners of the design space. This points out how ad hoc the argument is that there was only a single viable pathway going down the long road from lifeless chemicals to the first bacteria, complete with protein synthesis. There is no good (non ad hoc) reason why during that long process of change there could not have been branching events with subsequent change leading to different codes. How surprising that we have only a single DNA code.
And of course, how surprising that it could arise at all. Hence Crick's suggestion of directed panspermia.
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Cornelius G. Hunter
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Member # 81
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posted 20. September 2004 04:32
This post is in response to Richard Wein who contributes to talkreason.org (e.g., http://www.talkreason.org/articles/Designer.cfm). On Jason Rosenhouse's blog Richard claims that:
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The main argument from IC, which claimed to show that IC systems could not possibly evolve naturally, has been refuted.
The argument, as presented by Ussery and Musgrave in *Why Intelligent Design Fails,* is that there are plausible mechanisms that can explain the evolutionary origin of the bacterial flagellum. Musgrave gives the details of this argument which agrees that the flagellum is IC, but claims that it could evolve indirectly. Motility systems are related to secretory systems, and these secretory systems provide some of the needed functional intermediates leading to the flagellum. In fact, more than 80% of the flagellar proteins have known homologs from a variety of sources.
If a secretory system arose first, then later became associated with an ion pump which would improve secretion, and then a protoflagellar filament arose next as part of the secretion structure, then gliding motility could have resulted, to be refined later into swimming motility. [see Ch. 6 and p. 82 for summary] Maybe this is not the actual pathway, but this pathway, or something like it, could have occurred.
But actually, it is not clear that this pathway, or something like it, really is plausible. First, while the existence of homologs is a first good step, and there is some known interchangeability between different systems, this is still a long way from demonstrating plausibility. Demonstrating such plausibility, without relying on the presupposition of evolution, will require more data.
In fact, the pathway as envisioned requires tremendous evolutionary leaps that are unexplained. The secretory system arose first, but how did that happen? The second step (association with an ion pump) is not as heroic as the first, but still is not trivial. Then the protoflagellar filament arose. Again, how did that happen? How many simultaneous mutations were required? And how was the gliding motility refined into swimming motility? These are not trivial steps.
Am I asking for too much detail? Should we just accept broad explanations such as these when crucial premises and assumptions seem unsupported? No, these types of questions are routinely asked in science.
Regarding the DNA code, Richard wrote:
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Perhaps it would help if I outline why I think the DNA code provides such strong evidence for common ancestry. The reason is that the pattern is far too hierarchical to have occurred by chance; it can only be explained by some sort of process of copying with variations. …
The triplet code has 64 mappings onto 20 amino acids (plus "stop"). So the number of possible codes is 21^64, which is over 10^84. So the probability of even _two_ species having exactly the same code, if they are completely random, is 1 in 10^84. …
Richard improperly uses the null hypothesis. In science, when a null hypothesis is found to be false or improbable it tells us that the theory in question has not yet been falsified. Beyond this, we need to be careful in drawing any further conclusions from the rejected null hypothesis.
Of course, a finding that a null hypothesis is false does not make the theory true. Nor does it necessarily make the evidence any stronger for the theory in question. Consider an example. An astronmer hypothesizes that the celestial bodies rotate about the earth each day. His null hypothesis is that the motion of the celestial bodies is random. He does some experiments, using angle observations of celestial bodies relative to his observatory, showing that his null hypothesis is highly unlikely. Should he now conclude that the observations are strong evidence for his theory? No, his theory has not been falsified, but the evidence is not strong evidence for his theory. We should not think that the fact that the DNA code is obviously not random between species is "strong evidence for common ancestry."
Regarding the trilobite eye, Richard says that the lack of an explanation with any detail for how it evolved is no problem. Why? Because "this is just making the old argument from ignorance." So, summarizing, we have a highly complex structure appearing out of nowhere in the fossil record, that flawlessly eliminates spherical aberration as "dictated by a fundamental law of physics." [1] Evolution cannot explain how it arose, yet this is no problem for evolution. The problem, rather, is with the skeptic who thinks that ignorance is an issue. This is not how science works.
1. Clarkson EN, Levi-Setti R, "Trilobite eyes and the optics of Des Cartes and Huygens," Nature, 254:663-7, 1975.
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Darel R. Finley
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Member # 100
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posted 20. September 2004 08:49
Dr. Hunter,
Once again I will play devil's advocate, or at least critic. I agree with 99% or 100% of what you say, but feel compelled to make tiny comments.
quote:
The secretory system arose first, but how did that happen?
I cringe every time I see this response from an ID proponent. It's not that how the secretory system arose isn't a good question -- it's a great question -- but it's not the question being addressed, which is the plausibility of the secretory system evolving into the flagellum.
When an evolutionist says "I think A could have plausibly evolved into B," it is not a good time to demand to know where A came from, especially when A is known to currently exist. It's just asking to be raked over the coals for changing the subject. I saw this happen to Michael Behe (I think) in a video debate. He was challenged that A could have evolved into B, and responded by demanding to know where A came from. His opponent immediately pounced and came off looking like the clear winner.
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An astronomer hypothesizes that the celestial bodies rotate about the earth each day. His null hypothesis is that the motion of the celestial bodies is random.
If I understand you correctly, you are saying that the astronomer chose the wrong null hypothesis, and should have chosen "the celestial bodies do not rotate about the earth each day." The astronomer's mistake is believing in a false dichotomy where the planets either move randomly or move according to his specific theory. Likewise, Wein is subscribing to the false dichotomy that either Darwinism is true, or each species was designed completely independently of all others. Wein should instead be choosing a focused null hypothesis, such as:
X: The changes involved in the heirarchical branching may show the addition of mutationally unreasonable IC devices.
Y: The changes involved in the heirarchical branching may show unreasonably fast transitions.
Z: Some species may exhibit DNA commonality with pre-existing organisms that is too strong to be coincidence, but violates a tree-pattern of evolutionary branching.
Notice that each null hypothesis contains the word "may." This is unfortunate but necessary since intelligent designers do not have to design strongly IC structures, nor do they have to design at a Darwin-unreasonable rate, nor do they have to mix DNA across coexisting branches. But X, Y, and Z are still useful for refuting the evolutionary hypothesis, if the evidence shows what X, Y, and Z describe -- which, we probably agree, it does. (If the evidence did not exhibit what X, Y, and Z describe, then ID could grasp for the "may" ambiguity, but would still lose to evolution by Occam's razor.)
Side note regarding null hypothesis Z: I think a splendid ID research project would be a genetic study of the platypus. Externally, it appears to be a bizarre mixture of features from mammal, marsupial, bird, and reptile. Would a DNA study back this up, and to a degree of coincidence similar to that expounded by Wein? If any such study has been done, or is underway, I would love to hear about it.
[ 20. September 2004, 09:25: Message edited by: Darel R. Finley ]
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Cornelius G. Hunter
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posted 20. September 2004 12:13
Darel:
One of the points I make in my chapter in Uncommon Dissent is that evolution relies on non scientific reasoning. The idea that IC criticisms that entail tremendous evolutionary leaps should be, themselves, protected from criticism is an example of this. Such leaps are not explained and are crucial to evolution. And once such leaps are protected, then it is hard to imagine what is not possible. The creation of the bacteria flagellum would be plausible, no question. The sub components could have arisen, and then assembled. There is no step that could be questioned. What about the DNA code? If the evolution of the RNA polymerase, tRNAs, ribosomes and aminoacyl-tRNA synthetases are a given, then creation of the code is no problem. Likewise for the trilobite eye, echolocation, etc. Understandably, evolutionists routinely assume that such leaps are feasible, somehow. But such assumptions need to be justified when evolution is not being presupposed. You write:
quote:
When an evolutionist says "I think A could have plausibly evolved into B," it is not a good time to demand to know where A came from, especially when A is known to currently exist. It's just asking to be raked over the coals for changing the subject.
But B already exists as well, so by this logic we ought not question how it arose either. If one is guilty of "changing the subject" when one asks for the details of a vague explanation, then we are not dealing with science. A1, A2, and A3 are supposed to have arisen in just such a way such that they later could comfortably combine to form B. That is quite a claim. If we cannot question it, then it must be correct, and IC must be false. An unjustified claim becomes immune from criticism. But this is not science.
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If I understand you correctly, you are saying that the astronomer chose the wrong null hypothesis, and should have chosen "the celestial bodies do not rotate about the earth each day."
That null hypothesis is not a single hypothesis, but includes an infinity of hypotheses. I'm not saying the astronomer's null hypothesis was necessarily wrong, but he needs to be careful in what he concludes from its rejection.
[ 20. September 2004, 12:35: Message edited by: Cornelius G. Hunter ]
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Darel R. Finley
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posted 20. September 2004 14:15
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But B already exists as well, so by this logic we ought not question how it arose either. If one is guilty of "changing the subject" when one asks for the details of a vague explanation, then we are not dealing with science.
I think you are misunderstanding my point. I didn't mean to imply that existing systems don't need to be explained -- rather, that an evolutionist claim that known system A evolved naturalistically into known system B should be met head-on with the argument that A-to-B is not plausible (or an admission that it is plausible, if that appears to be the case). If instead we immediately challenge Q-to-A, it looks painfully like a dodge. Q-to-A should be reserved for later discussion. It is reasonable for evolutionists to ask for a counterargument to A-to-B in isolation; without any immediate discussion of where A came from.
I note that you did challenge A-to-B head-on, and very nicely I think, but only after leading with a Q-to-A swipe. Perhaps Q-to-A simply should have been mentioned at the end of your A-to-B counterarguments, as an aside.
I make these comments not to nitpick, but because I think it really hurts the perception of the movement. When it happened in that video debate I mentioned ("Firing Line," perhaps?) I could mentally picture viewers all over the world shutting off their openness to ID at that point and deciding that ID is just a scientifically pointless demand that all transitions be explained right now.
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That null hypothesis is not a single hypothesis, but includes an infinity of hypotheses.
I thought a null hypothesis was supposed to be the exlusive logical inverse of the hypothesis -- i.e. if the hypothesis is A then its null hypothesis is notA, but perhaps I am mistaken. If so, then it would appear that most or all null hypotheses -- like my X, Y, and Z -- are useful only for refuting a theory, and not for confirming it.
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Cornelius G. Hunter
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posted 20. September 2004 15:11
Darel:
But he is not asking about A-to-B in isolation. You are mischaracterizing the evolutionist's argument. He is not merely claiming that A-to-B has been shown to be plausible (which it has not as you point out). He is claiming that (i) A-to-B is plausible and (ii) therefore IC is refuted. He has shifted the hard part of the problem to the evolution of A, and then claimed that the evolution of A is off limits.
If components A1, A2 and A3 evolved such that they comfortably combine, then we need to ask how that could happen. We cannot arbitrarily shift the DNA code evolution problem to OOL and be done with it. Likewise, we cannot shift the flagellum problem to earlier evolution and be done with it.
[ 21. September 2004, 02:02: Message edited by: Cornelius G. Hunter ]
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Darel R. Finley
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posted 20. September 2004 15:54
quote:
He is claiming that (i) A-to-B is plausible and (ii) therefore IC is refuted. He has shifted the hard part of the problem to the evolution of A, and then claimed that the evolution of A is off limits.
If A-to-B is plausible, and represents the addition of a new, irreducible core of components that does not exist in A, then I would say that Musgrave has refuted IC. As Behe himself admits, if any one of his major examples of IC were to be explained in a Darwinian fashion, then his case would collapse -- even in the absence of immediate solutions to his other examples. That is why IC is not an argument from ignorance, but rather an inference to the best explanation. (And as Dembski has detailed, an argument from invariance.)
However, if A-to-B does not represent the addition of a new, irreducible core of components, then Musgrave has not even attacked IC with A-to-B, much less successfully refuted it, and you are completely correct that he is evading the "hard part of the problem" -- the appearance of A's irreducible core.
So again I emphasize that Musgrave's A-to-B scenario should be tackled head-on, either by showing that it is not plausible, or showing that it does not add any IC that wasn't already in A. Asking where A came from is a separate (though important) question, and it looks bad to use it in response to Musgrave's A-to-B scenario.
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Salvador T. Cordova
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posted 20. September 2004 18:13
I would like to point out more developments in the problems that convergence poses for common descent.
I found Evolutionary Convergence in Nervous Systems
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Over the past 20 years, cladistic analyses have revolutionized our understanding of brain evolution by demonstrating that many structures, some of which had previously been assumed to be homologous, have evolved many times independently. These and other studies demonstrate that evolutionary convergence in brain anatomy and function is widespread. Although there are relatively few neuroethological studies in which brain and behavior have be studied within an evolutionary framework, three relatively well studied cases are reviewed here: electric communication among gymnotiform and mormyriform fishes, prey capture among frogs, and sound localization among owls. These three examples reveal similar patterns of brain evolution. First, it is clear that novel abilities have evolved many times independently in taxa whose common ancestors lack these abilities....
Collection of neuroanatomical, neurophysiological,
and neuroethological data can be extremely time-consuming even for a single species. Thus, it is not surprising that neuroethology has relatively few comparative case studies in which the anatomical and physiological bases for interesting behavior patterns can be studied within an evolutionary framework [Nishikawa, 1997; Phelps, 2002].
.....
First, it is clear that novel behaviors have evolved many times independently in taxa whose common ancestors lack the behavior, from jamming avoidance, to ballistic tongue projection, to nocturnal prey capture. The list of behaviors and brain structures that have evolved convergently is growing rapidly (see Introduction). It is now clear that convergence is as pervasive in nervous systems as it is in the rest of the biological world [Wray, 2002]....
ISCID Fellow Rick Sternberg Holds 2 PhDs in molecular (DNA) evolution and the other in systems theory and theoretical biology.
He writes concerning convergence:
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Structuralists' lack of commitment to an historical theory of biology allows them to explore the historical evidence more objectively. Moreover, because they focus on formal analysis, struturalists are far more open than neo-Darwinians to the powerful evidence for continuity within species (forms) and discontinuity between and among species . They also allow themselves to wonder about the cause of the amazing repetition of forms across the biological world rather than being forced by prior commitments to accept a major neo-Darwinian epicycle known as "convergent evolution."
Sternberg realizes the fossil record and biology suggest persistence of species and not transmutation.
Also, with respect to the problem of Molecular Convergence, in this article from Discovery Institute:
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Commentary on Papers
optimistic views of sequence data have now been challenged by recent studies that suggest that molecular data, like morphological traits, can exhibit concerted adaptive evolution
...the mitochondrial cytochrome b gene implied... an absurd phylogeny of mammals, regardless of the method of tree construction. Cats and whales fell within primates, grouping with simians (monkeys and apes) and strepsirhines (lemurs, bush-babies and lorises) to the exclusion of tarsiers. Cytochrome b is probably the most commonly sequenced gene in vertebrates, making this surprising result even more disconcerting. (p. 177)
When we presume common descent it results in the a major neo-Darwinian epicycle known as "convergent evolution".
Although the bacterial flagellum is a glamorous example for complexity, I think CSI in the realm of convergence is ripe for exploration.
I should add, it is absolutely pure speculation that natural selection can create large scale complex convergent structure or that time increases functional complexity rather erodes it.
When Rosenhouse said the Tribolite Eye had 200 million years to form, that is pure speculation that Natural Selection will increase complexity over that time.
From all I'm aware, gentetic deterioration and extinction have more direct empirical verification than the speculated large scale increases of functional complexity not to mention theoretical considerations against such possibilities.
[ 20. September 2004, 18:16: Message edited by: Salvador T. Cordova ]
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Cornelius G. Hunter
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posted 21. September 2004 02:01
Darel:
Let me try again. Musgrave is claiming that IC is refuted because the evolution of the Ai's (A1, A2, etc.) is plausible and the evolution from Ai's to B is plausible. His hypothetical explanation includes all these evolutionary pathways. And all these pathways are required to produce the bacterial flagellum and its IC property. Therefore it is appropriate to examine all the pathways. What Musgrave has going for his idea is that the Ai's are known to be functional. But the evolutionary pathways leading up to the Ai's, and the subsequent evolution leading up to B remain in question.
quote:
I thought a null hypothesis was supposed to be the exlusive logical inverse of the hypothesis -- i.e. if the hypothesis is A then its null hypothesis is notA …
Well not exactly. The idea behind null hypothesis testing is to see whether or not the trend being analyzed is statistically significant. There is always the danger of picking out a trend even in random data, so one needs to check for this. Null hypothesis testing answers the question: "how likely is it that my trend could arise as a consequence of random chance in the data?" If the answer is "highly unlikely," then we reject the null hypothesis. But this does not necessarily mean the observations are powerful evidence for the hypothesis in question.
[ 21. September 2004, 02:53: Message edited by: Cornelius G. Hunter ]
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Darel R. Finley
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posted 21. September 2004 16:17
Dr. Hunter,
I'm getting a little lost with these letters, so let me reformulate my position using the secretory system and the flagellum.
Musgrave: I think Darwinian evolution could change the existing secretory system into the existing flagellum, and here's how: [detailed scenario]
How should we respond to this? I suggest in one of these three ways:
Response 1: Musgrave's secretory-to-flagellum scenario is not plausible because [specific refutation of one or more steps in Musgrave's scenario].
Response 2: Musgrave's secretory-to-flagellum scenario is not a refutation of IC because the flagellum contains no irreducible core of components that is not also found in the secretory system. [details]
Response 3: [Response 1 plus Response 2.]
I can think of no other scientifically appropriate response than the three above, and I feel that the following Response 4 is bad form, and works against the credibility of the ID movement:
Response 4: But where did the secretory system come from? Has Musgrave explained that?
The question of the secretory system's origin is not off-limits, or a biological given, or any such thing. But it is simply not a response to Musgrave's scenario, and so should be used at another time and another place. It is changing the subject, and it threatens to turn IC into an argument from ignorance.
Behe's assertion -- that IC falls if even one substantial IC example is explained by mutation-selection -- means that evolutionists are not obligated to explain all steps in the appearance of a system. To refute IC, they need only explain the appearance of one irreducible core of components. If the flagellum contains at least one such core that is not in the secretory system, and the steps of Musgrave's scenario are plausible, then he has refuted IC as an anti-evolution argument, irrespective of whether he has the slightest idea where the secretory system came from.
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