Vanderzyden

Hello everyone.

It's time for me to ante-up. For clarity, I am starting a new topic to address the "Sci-girl" challenge. First, I will re-post her text. I will follow it with my answer.


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Scigirl,

Indeed, this is a challenge. However, I am using that term in the sense of education, not an impenetrable segment of Darwinist armor. I appreciate the opportunity to think this through and engage in dialogue. And yes, I have several questions. You will find them throughout my reply.

To begin, I want to say that you cannot expect to be persuasive because you observe similarity and, from that alone, claim that humans and apes share a common ancestor. We must go beyond what is claimed as the end product—that is, similarity—to a discussion of the means. This raises the first question:

HOW did it happen?

Well, you know that this is the BIG, BIG question. No doubt Darwin was troubled in his last days concerning this very thing. But wait, don’t answer just yet. Below you will find a number of problems which erode the assumptions you have made in advancing your “challenge.”


The phylogenetic conundrum

Yes, I am familiar with phylogenetic trees. The only illustration in the The Origin of Species contains a rudimentary tree of life. Many more, of course, have been constructed since then. In my reading, I find substantial difficulties that contradict your claim that “By and large, the trees still held true” following re-analysis by molecular biologists. Here are some of the problems:

a. Genetic sequence comparisons are very difficult—often inconclusive.
b. Biologists assume DNA sequence differences arise from beneficial mutations and these mutations accumulate--in widely DIFFERENT organisms, at the SAME RATE--over long periods of time. Of course, these are very, very broad assumptions having no supportive evidence (so far). Furthermore, there are NO BENEFICIAL mutations, only those that produce abnormality.
c. It is amazing, then, that some Darwinist biologists confidently employ calculations based upon the sequence differences as a "molecular clock" in determining the length of time back to the common ancestor. As might be expected, there is wide disagreement among those who perform independent analysis. The long and short estimates for the initial divergence of animal phyla differ by 530 million years, which is approximately the same as the estimate for age of the Cambrian explosion. It is therefore difficult to place any weight on such methods as a positive demonstration of Darwinism. [references available upon request]
d. The only real data on these “trees” comes from living organisms, which are at the very tips of the twigs at the ends of the branches. Everything else is hypothetical, based on methodological assumption and sequence comparison.
e. None of the trees or sub-trees (e.g. those based on DNA, rRNA, or protein production) seem to corroborate, even in the slightest.

Lest you think me facetious or glib, I provide you with a few quotations from scientists:

-- “...scientists started analyzing a variety of genes from different organisms and found that their relationships to each other contradicted the evolutionary tree of life derived from rRNA analysis alone." [James Lake, Ravi Jain, Maria Rivera, "Mix and Match in the Tree of Life", Science 283 (1999), pp. 2027.]

-- "With more and more sequences available, it turned out that most protein phylogenies contradict each other as well as the rRNA tree." [Herve Phillipe and Patrick Fortrerre, "The Root of the Universal Tree of Life is not Reliable", Journal of Molecular Evolution 49 (1999) p. 510]

-- "No consistent organismal phylogeny has emerged from the many individual protein phylogenies so far produced. Phylogenetic incongruities can be seen everywhere in the universal tree, from its roots to the major branchings within and among the various [groups] to the makeup of the primary groupings themselves. " [Carl Woese, "The universal ancestor", Proceedings of the National Academy of Sciences 95 (1998), p. 6854]

It would seem that these “trees of life”, in which you place such confidence, are really nothing but a collective “briar patch of Darwinism”. Do you agree?


Homologous Hogwash

Before I address the essence of your challenge, let me bring something else to your attention: homology. Obviously Darwin considered homology essential to his work. But he said nothing to about HOW homologous structures “at once explain themselves” on his theory. His followers recognized the difficulties in justifying the theory, and therefore re-defined homology to be the inheritance of features from a common ancestor. But again, this redefinition does nothing to EXPLAIN THE MECHANISM.

You’ll also notice that the re-definition amounts to a circularity: if homology is now defined as similarity by means of common descent, it is circular reasoning to declare that it is also the evidence for common descent. Common ancestry demonstrates homology, which itself demonstrates common ancestry. On this new view, common ancestry is both the definition and the explanation of homology. This silliness has not gone unnoticed:

"By making our explanation into the definition of the condition to be explained, we express not scientific hypothesis but belief. We are so convinced that our explanation is true that we no longer see any need to distinguish it from the situation we were trying to explain. Dogmatic endeavors of this kind must eventually leave the realm of science."

-- philosopher of biology Ronald Brady, "On The Independence Of Systematics", Cladistics 1 (1985)

There are three ways to avoid this circularity:

1. Maintain the neo-Darwinian definition, but cease to infer common descent from it:

"Common ancestry is all there is to homology, homology is the anticipated and expected consequence of evolution. Homology is not evidence of evolution." ["Homoplasy, homology and the problem of 'sameness' in biology", Homology (Novartis Symposium 222; Chichester, UK: John Wiley & Sons, 1999) pp. 27, 45.]

2. Retain the pre-Darwinian definition of homology (simply as structural similarity), while acknowledging that descent with modification may not be the best explanation for it. (Of course this is extremely unpopular with modern Darwinists!)

3. Maintain the new definition, but seek evidence which is independent of homology.

You probably know that #3 is the approach of many scientists today. In addition to genetic live-specimen and fossil comparisons and embryology, we have developmental genetics.


Developmental Genetics

The modern explanation for homologous features is that they are the result of being programmed by similar genes in a common ancestor. It remains to be seen whether homologous structures in two different organisms are produced by similar genes. Also it must be shown that homologous structures are not produced by different genes. However, scientific investigation has not shown this to be the case:

"Because homology implies community of descent from ... a common ancestor it might be thought that genetics would provide the key to the problem of homology. This is where the worst shock of all is encountered ... [because] characters controlled by identical genes are not necessarily homologous ... [and] Homologous structures need not be controlled by identical genes."

Conclusion: "... the inheritance of homologous structures from a common ancestor ... cannot be ascribed to identity of genes."

--Gavin de Beer, "Homology: An Unsolved Problem (London: Oxford University Press, 1971), p. 15-16"

Consider this: A common--and striking--observation is that non-homologous structures arise from the same gene. Geneticists find that genes required for proper development in fruit flies may also be found in mice and sea urchins. Also, gene transplants demonstrate functional replacement of genes from mice to flies.

Lack of correspondence between genes and structures is seen clearly from observations of the Distal-less developmental gene, which is found in fruit flies. Genes with very similar sequences have been found in the DNA of mice, sea urchins, spiny worms, and velvet worms, none of which are homologous. Some conclusions:

-- "This association between of regulatory gene and several non-homologous structures seems to be the rule rather than the exception." [Gregory Wray, "Evolutionary dissociations between homologous genes and homologous structures" pp. 189-203 in homology (Novartis Symposium 222; Chichester, UK: John Wiley & Sons, 1999), pp. 195-196]

-- "What mechanism can it be that results in the production of homologous organs, the same 'patterns', in spite of their not being controlled by the same genes? I asked this question in 1938, and it has not been answered." [Gavin de Beer, "Homology: An Unsolved Problem (London: Oxford University Press, 1971), p. 16"]

I provide all of this here to show only a few of the difficulties that arise when we read you uncritically repeating what you have heard your mentors say: that man has come from—and is nothing more than—the ape. In general, there are immense (seemingly insurmountable) mountains to climb in demonstrating macroevolution to be even a loose representation of reality. From the evolutionists, we hear plenty of public assertions, and yet we are become increasingly aware of the long-standing tension that exists in halls of the life sciences. There is plenty of dogma, but still we have no convincing explanation. It is as though a big white elephant were walking around, and yet no one notices.

Permit me one more comment about your assumptions. You mention the fossil record, as though it supports your case. It is now well documented by repeated study of the global fossil record that many classes and phyla appear to have come to life suddenly and simultaneously, with no antecedent transitional forms. Molecular evolutionary biologists don’t like to talk about it much, but the Cambrian explosion stands firmly against Darwinian hypotheses. Darwin knew it, and so do we. But, I digress—this is yet another topic for a future post.

So, scigirl, with these difficulties, I would think that you need to bring forward another set of assumptions. Now let’s look at the specific problems with the proposal.


Problems with the Robert Williams article

<a href="http://www.gate.net/~rwms/EvoEvidence.html" target="_blank">http://www.gate.net/~rwms/EvoEvidence.html</a>

Here is a key excerpt:

“There are two potential naturalistic explanations for the difference in chromosome numbers - either a fusion of two separate chromosomes occurred in the human line, or a fission of a chromosome occurred among the apes. The evidence favors a fusion event in the human line. One could imagine that the fusion is only an apparent artifact of the work of a designer or the work of nature (due to common ancestry)…”

First, notice that we are not told why the evidence favors a fusion event in the human line (as though it favors fission in other lines). Given what I’ve learned about molecular biology, I would not expect combinations, but genetic divisions. Please explain.

Second, we must ask what evidence is available to support the occurrence of natural chromosome fusion. No evidence is given in the Williams. In fact, it’s never stated clearly, but presented only as an implicit assumption. Please tell me where I can find definitive information on this supposed phenomena.

This is the second part of the key paragraph:

“…The common ancestry scenario presents two predictions. Since the chromosomes were apparently joined end to end, and the ends of chromosomes (called the telomere) have a distinctive structure from the rest of the chromosome, there may be evidence of this structure in the middle of human chromosome 2 where the fusion apparently occurred. Also, since both of the chromosomes that hypothetically were fused had a centromere (the distinctive central part of the chromosome), we should see some evidence of two centromeres.”

We notice in this passage a confusing non-sequitur. We are told that a common ancestry scenario (which one?) makes two predictions. But Williams doesn’t list these predictions. (I realize you attempt to do this on his behalf—see below). Furthermore, he doesn’t relate the “predictions” with the supposed evidence he briefly explains in the next two sentences.

You state three predictions:

1. Humans and chimps should have similar numbers of chromosomes.
2. The chromosome patterns should be similar.
3. If there was indeed a chromosome fusion event, there would be evidence of that fusion.

I have addressed prediction #3 above, where I ask for evidence of natural fusion.

Let’s look at the other two predictions. In my other post, “Please define evolution”, I asked for a concise definition of prevailing evolutionary theory. You may agree with me that no precise definition has been put forward. In your reply, perhaps you can begin with your explanation of evolution—classical or otherwise—from which we may infer the predictions you are claiming. Maybe in such an explanation we will find the answer another question that I have for you:

What specific neo-Darwinist prediction calls for the same, or similar, number of chromosomes among chimps and humans?

(An interesting corollary: What predictions are made concerning future, super- or subhuman species?)

In your challenge, the chromosome comparison is made between human chromosome #2 and two chromosomes from each of several ape species. But this is not enough information. What is the chromosome number in each of the non-human species? What is the function of the chromosome in each of the apes? Are they the sex chromosomes? What is the degree of dissimilarity among all the chromosomes? These questions must be answered before we can make any correlations with respect to predictions #1 and #2.

Let’s examine the basis for comparison. Williams also writes: “...why are the remnants of a telomere and centromere (that should never have existed) found at exactly the positions predicted by a naturalistic fusion of the chimp ancestor chromosomes 2p and 2q?”

But this is to make something out of perhaps nothing at all. There are only four base-pair combinations. So, sequence comparisons begin at a level of 25% similarity. Surely, when we examine the chromosomes of other species, we will find centromere and telomere patterns that are similar to humans and chimps in the vicinity of the centromere and the telomere. Think about it in simple terms: of all the species, how many will we find that end with three guanines, one adenine, and two thymines, plus the phosphate (5'TTAGGG)? Methinks many.

I am disappointed by the lack of explanation for the speculative fusing of the two chimp chromosomes This is all we are given:

“The second prediction - remnants of the 2p and 2q centromeres is documented in reference [4]. The normal centromere found on human chromosome 2 lines up with the 2p chimp chromosome, and the remnants of the 2q chromosome is found at the expected location based upon the banding pattern.”

Where, exactly is the location of the supposed “remnants” of the 2q chimp chromosome?
Another important consideration for prediction #1: Surely you must realize that humans have nearly the same number of chromosomes as other non-homologous species:

Class -- Order, total # of chromsomes

Protozoa -- Euglena, 45
Arachnida -- Agalena, 44
Reptila -- Hemidactylus, 46
Aves -- Rhea, 42-68; Passer, 40-48; Anas, 43-49
Mammalia -- Erinaceus, 48; Lepus, 36-46; Peromyscus, 48; Microtus, 42, 46; Apodemus, 46, 48, 50; Ratus, 46; Rhesus, 42, 48

Why don’t we consider many of these others as sharing a common ancestry with humans? Like individual DNA homology, chromosome comparison is not a basis for determining common ancestry with any of the apes. As explained above, structural or genetic homology is insufficient to demonstrate common descent among distinct species.

Do we find substantial genetic similarity between apes and humans? Perhaps. Genetic identity? Most certainly not. We are largely dissimilar from the apes, especially when compare everything but the DNA. You may find this to be an interesting article, written by anthropologist Jonathan Marks.

<a href="http://ist-socrates.berkeley.edu/~jonmarks/aaa/marksaaa99.htm" target="_blank">http://ist-socrates.berkeley.edu/~jonmarks/aaa/marksaaa99.htm</a>

Here is an excerpt:

“We’ve been studying chimpanzees for 300 years, but DNA sequences for barely 20 years. We are far more familiar with apes than we are with DNA. Consequently, the appropriate way to compare these data is not to contrast the genetic and anatomical comparisons through modern eyes, but to compare the genetics today with the anatomical comparisons when those were as new and as exciting as DNA comparisons are today…the point I wish to make is that the paradox of the anatomical difference and the genetical similarity is illusory – it’s an artifact of the intellectual history of comparing. How familiar we are at the turn of the millennium with the physical differences and how unfamiliar we are with the whole notion of genetic difference.”

I think that is enough for now. I realize the length of this post, but I needed to get it off my chest

Oh, incidentally, you may want to think twice about advancing the “robot assembly” analogy. With it, you unwittingly employ an example which is equally suitable for a creationist.

Scigirl, I have reviewed the other “challenges” you have posted—those having the title “Questions for X”. Please do not reply with the demand for an alternate theory or insist that I argue from science alone. It isn’t necessary. You are the Darwinist, and apparently insist that the search for definitive proof for macroevolution is important work that will benefit mankind. However, any attempt to force the burden of proof for your proposal onto your opponents must necessarily be seen as an evasive maneuver in facing tough questions.

The burden rests on the shoulders of the Darwinists. If you would be persuasive, you must go beyond simple comparisons to ELUCIDATE, with strong EXPLANATORY FORCE, a MECHANISM that would produce the similarity in question. In short, let me state that your presentation is by no means evidence for macroevolution. What you provide is not a demonstration that it occurs, now or in the past. It is nothing more than an emphatic declaration of supposed results. This type of hypothesis has nothing to distinguish it from other neo-Darwinian proposals. I therefore find it suitable to conclude with another comment from the science historian John Durant. Twenty years ago, he made a dire plea for sensibility to take hold in the scientific community:

“As things stand at the present time, we are in urgent need of the de-mythologisation of science.”

--the Oxford historian of science John Durant, at a meeting of the British Association for the Advancement of Science, 1983

The world awaits.

Vanderzyden

[ August 26, 2002: Message edited by: Vanderzyden ]</p>

Doubting Didymus

Welcome back, vanderzyden.

I am ready to reply to your answer immediately

You might want to check back in exactly two full weeks.

lpetrich

I'll show that I can respond more promptly than Vanderzyden:


It's not simply similarity, it's evidence of vestigial telomeres in the middle of fused chromosomes.

On the contrary, gene-sequence family-tree construction has often been very successful, with several genes often agreeing, not only with each other, but with macroscopic-feature family trees.

It's been recognized, however, that molecular family trees are not a magic bullet, because several effects can confound them:

Unequal rates of evolution, leading to long-branch attraction
Mutation saturation
Rapid divergence

But the present-day state of the art is such it is possible to sequence enough genes to make possible ignoring the long-branch ones, and also to successfully ignore rapidly-evolving regions of genes.

A gross misunderstanding of molecular evolution, but then again, I wonder if VZ has ever read any of the primary literature on evolution, as I have.

Much molecular evolution is caused by a steady stream of neutral mutation. Yes, neutral mutations, mutation with zero alteration of gene-product performance. Mutations that turn a codon into another that codes for the same amino acid are an obvious example; they are called "synonymous" as opposed to "nonsynonymous" mutations. Mutations that turn an amino acid into a chemically similar one are another example, especially when that amino acid is not absolutely critical to the protein's function.

And variations in rate of molecular evolution have been recognized to exist, though it is not clear what causes them.

Demonstrably false. Bacteria have been known to evolve new metabolic capabilities -- they have clearly had beneficial mutations.

And that ignores neutral mutations.

I wonder if VZ will reveal those references as promptly as I have made my response. The problem here is that VZ may simply be quoting some earlier research, which may have been affected by poor statistics (not enough sequences, inadequate compensation for rate variations, ...).

I predict that, as more genes get sequenced, such problems will get resolved.

Not to mention fossils. I wonder what VZ would consider convincing evidence -- traveling back in time in a time machine?

There are lots of counterexamples.

(VZ's out-of-context quotes snipped)

They refer to efforts to find the older parts of the Family Tree of Life -- parts which have been confused by lateral gene transfer. Which can easily happen among bacteria.

This is like saying that natural selection is "those that survive survive".

Homology can be recognized from cases of structural similarity coexisting with functional dissimilarity. Thus, flower petals are homologous to leaves, since their structures are similar, though their functions are different. Petals and leaves are a good example of "serial homology", homology between different body parts. Arthropod antennae, mouthparts, and legs are another good example of serial homology; the mutation Antennapedia makes a fruit fly grow legs where its antennae ought to be.

(Gavin de Beer on how homology need not imply shared genetic mechanisms, and vice versa...)

VZ is simply quoting someone's WARNING; this had been published in 1971, which was prehistory by the standards of present-day evolutionary developmental biology ("evo-devo").

I'm not sure what VZ considers non-homologous; is he claiming that arthropod, echinoderm, and vertebrate development mechanisms are independently evolved, as if they had originated separately from single-celled organisms?

In fact, just the opposite has been found, with the famous Hox genes having a strongly-conserved ordering wherever they have been found. Also, dorsoventral inversion has been confirmed by development-gene comparisons; a fly's belly is homologous to a frog's back (the central nervous system is there), and a fly's back is homologous to a frog's belly (the heart and main blood vessels are there).

However, the Distal-less gene being involved with limb formation suggests that they are all homology -- and that many limbs had emerged as ectopic (out-of-place) features.

In what way are we supposed to be "nothing but" apes?

More like what VZ would consider convincing evidence.

VZ, what do you think had happened? Did some extraterrestrial visitors do some genetic engineering to produce all that wonderful Cambrian fauna? Imagine a floating lab in which some whimsical genetic engineers construct new organisms.

After you explain why you expect divisions to happen, but not combinations, O VZ.

And fusion is inferred because that requires the fewest number of chromosome changes. Splitting would require several splitting events in the ancestors of each the great apes -- splitting at the same spot each time. This is either a bizarre coincidence or a bizarre contrivance.

What predictions did you expect to see, O VZ?

Why is additional info supposed to be necessary?

However, if one compares large numbers of them, the statistics become MUCH better -- comparing n of them has a probability of coincidence of 1/4^n. And this rapidly becomes VERY tiny.

That is 1/4^6 or ~0.00025 And several such sequences have an even lower probability of all being coincidence. VZ thus shows his statistical illiteracy.

It was most likely some kind of accident, some sort of chromosome-handling screwup in some germline cell.

SO WHAT? Chromosomes' contents can and do get rearranged; there's a map that's been recently constructed comparing human and mouse chromosomes -- a map that shows a large number of rearrangements between the two species.

VZ seems to think that all he needs to consider is overall features, considering them in broadbrush fashion while ignoring critical details. I wonder if he'd enjoy it if someone used that as a method of Bible interpretation.

LOL. What species are we the most like, then? Comparing everything but the DNA does show that the great apes are the species most like our species. In anatomy, that was recognized in the mid-19th-cy., and Charles Darwin used the anatomical closeness of chimpanzees and gorillas to predict that our species had emerged in Africa -- a very successful prediction, it must be said. And in behavior, chimps are the most human-like of nonhuman species.

Pseudo-evolutionary creationism, perhaps, in which the evolution takes place in the minds of the designers.

Grow up, VZ. Are you conceding that you have no alternative theory to offer?

No, scigirl is placing the burden of proof where it belongs -- on whoever is proposing a new theory. Charles Darwin had accepted that burden, and so should you, O VZ.

monkenstick

Would I be right in assuming that these articles refer to prokaryotes and unicellular eukaryotes? (certainly not vertebrates, certainly not primates) I am pretty confident that these articles are in fact referring to horizontal gene transfer, a phenomenon in bacteria and primitive eukaryotes which has been known about for quite some time. It really has no impact at all on the question of chimp/human common ancestry. I'm off to see if these articles are what I think they are, and that you are (as creationists do ALL THE TIME) quoting out of context something which has no bearing on the argument.

monkenstick

surprise surprise, the articles are in fact about horizontal gene transfer, specifically in prokaryotes. HGT has no bearing on chimp/human common ancestry. Unless you can show an instance of horizontal gene transfer in primates, then these quotes can be dismissed as irrelevant to the question scigirl posed to you.

Jack the Bodiless

This thread is titled "An Answer to the Chromosome Challenge".

And the answer is... ?

Stripped of the usual obfuscation and out-of-context (and in this case irrelevant) quotes, we have NO explanation of how a human chromosome is so clearly composed of the fusion of two chimpanzee chromosomes!
PREDICTION ONE: "Since the chromosomes were apparently joined end to end, and the ends of chromosomes (called the telomere) have a distinctive structure from the rest of the chromosome, there may be evidence of this structure in the middle of human chromosome 2 where the fusion apparently occurred".

PREDICTION TWO: "Also, since both of the chromosomes that hypothetically were fused had a centromere (the distinctive central part of the chromosome), we should see some evidence of two centromeres"

It is quite clear that you are actively struggling to preserve your state of ignorance. You will not answer the challenge (even on a thread allegedly dedicated to that purpose), nor will you allow yourself to read and comprehend even the articles posted by yourself on this topic!

This is a textbook example of cognitive dissonance.

Daggah

Well, damn...I came in this thread hoping that maybe once a creationist HAD actually responded to this challenge...and I see that even when they try, they usually end up evading the actual issue at hand.

Can't say I'm surprised.

Oolon Colluphid

Cobblers. It’s mutations in general.

(And the rarity of mutations depends on how you look at the term ‘rare’. According to <a href="http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/M/Mutations.html#Frequency_of_Mutations" target="_blank">here</a>, for instance, every cell in your body contains about 120 new mutations. There’s an awful lot of potential sites in DNA that could mutate, which chews up the odds rather. )

And whether a mutation is beneficial, harmful or neutral depends on the environment it turns up in.

Gross misunderstanding. Mutations are taken to accumulate at a steady rate, but they are best used in closer lineages. Within primates, for example, not necessarily for comparing mouse to moss.

Define ‘supporting evidence’ then. Back in the 70s when Ramapithecus was considered, on the fragmentary remains, to be in the human lineage, the human / ape divergence was put at about 12my. The molecular clock put it at 4my. Since then, the fossils have vindicated the clock. Why might that be?

According to Answers in Genesis’s <a href="http://www.answersingenesis.org/Home/Area/faq/dont_use.asp" target="_blank">Arguments we think creationists should NOT use</a>:

Care to argue with AiG as well as all real scientists?

Yes please. You should note that the molecular clock is not an assumption, it is a well-vindicated mechanism, carefully calibrated from well-dated fossils, which, lo and behold, new fossils agree with. So your references should be fascinating. But please, if they’re from AiG, don’t bother. Peer-reviewed scientific journals only please.

TTFN, Oolon

Automaton

I hope scigirl doesn't mind, but I'd like to take issue with some of the particular distortions, misunderstandings and obfuscations of this "response," if I may. Similarity does in fact prove a lot. Large-scale similarity in an language-like code leads us directly to the inference of a common ancestor. Take for example two test papers handed in that were almost precisely the same, except for a few words. Would you not assume a common ancester for the work?
But this is the very question we are posing you! if not derivation of multiple types from a single common ancestor, how could you probabilistically justify similarity?
Why would Darwin be troubled by this? This explanation of homology was one of the central aspects of his theory.

Your following objections are to all other aspects of phylogeny except the problem at hand. What does the "molecular clock" have to do with a simple comparison that does not involve mutation-rate dating? Are you being deliberately evasive?
Yes, well... This appears to be your central claim here. Of course, it is unsupported.
And neutral mutations. In fact, most difference arises from this genetic drift caused by neutral mutations, them being more common.
Yes, we all share the same molecular genetic machinery, regardless of being different organisms, thus assuming that the second law of thermodynamics remains constant over time, we all should mutate at the same rate. Considering mutations are random, even though genetics and environmental situations are different, averaged-out over the long run, neutral and beneficial mutation accumulation should even out to one common rate. This rate can be calculated.
Are you serious? The fact of beneficial mutations is incredibly well-established in biology (and in fact are a mathematical consequence of genomes just as mutations in general are, as evidenced by computational models)! Just flick briefly through any of the available literature, at all. In plants, there's the common cases of hybridization (which is made possible through a mutation) and mass polyploidy (multiplication of chromosomes), the latter of which often increases in robusticity. There's insects becoming resistant to pesticides, bacteria becoming resistent to antibiotics and forming new metabolic pathways (this is even being employed to combat pollution), there are literally thousands of examples. Or maybe look at a specific one, of an increase of functional complexity, <a href="http://www.molbiolevol.org/cgi/reprint/12/3/514.pdf" target="_blank">here</a> (this one is mentioned in Kenneth Miller's Finding Darwin's God, which I highly recommend you read.)
References requested!
What about the fossil record? And isn't it just amazing how homology, the fossil record and molecular phylogeny all miraculously converge?
Where are you getting this from? It's polite to include references when one makes assertions of this nature. This is borderline on ridiculous. You know proteins are merely the genome expressed? It would be surprising, even if common descent was false, if they didn't corraborate. And the problem of rRNA comparisons not corroborating other genetic comparisons was solved, ironically, and this is mentioned in one of the articles below you quote as "proof" this process is flawed, as seen below...
The full quote is as follows:

• The clonal theory began to crumble a decade ago when scientists started analyzing a variety of genes from different organisms and found that their relationship to each other contradicted the evolutionary tree of life derived from rRNA analysis alone. To explain the differences between the evolutionary trees reconstructed from eukaryotic rRNAs and from proteins, Sogin (2) proposed a chimeric origin for eukaryotic genomes, with rRNA genes coming from one organism and genes encoding proteins coming from another. Analyses of DNA-dependent, RNA polymerases (3) and heat shock protein (hsp70) gene sequences from different organisms (4) supported theories of chimeric evolution(5-10).

Taken from
<a href="http://cas.bellarmine.edu/tietjen/Diversity/mix_and_match_in_the_tree_of_lif.htm" target="_blank">here</a>. This problem was addressed in the article and solved in the very next sentence, when it is shown that the "discrepancy" is produced from scientists ignoring horizontal gene transfer!
The full article can be viewed <a href="http://nsmserver2.fullerton.edu/departments/chemistry/evolution_creation/web/PhilipeForterre1999.pdf" target="_blank">here</a>. It addresses the same problem, in dealing with the molecular phylogenies of the "root of the tree", and ignores the solution posed above, but also addresses alternate ones (accelerated rates of evolution due to loss of translation apparatus). Note: Unreliable phylogenies for the root of the tree does not equate to phylogeny as a whole to be unreliable. This has nothing to do with the chimpanzee/human phylogenetic clue as given to you above, for example.
The full quote is:

• Phylogenetic incongruities can be seen everywhere in the universal tree, from its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves. Yet there is no consistent alternative to the rRNA phylogeny, and that phylogeny is supported by a number of fundamental genes.

So Woese's broad statement isn't so strong as you would like us to think, and it certainly isn't a majority position among scientists in the field. From <a href="http://www.pnas.org/cgi/content/full/95/12/6854" target="_blank">here</a>.
No. I disagree. And this still has nothing to do with the issue at hand, the chimp/human chromosomal fusion.
What on earth are you talking about? The mechanism is Darwinian evolution!

And by the way, you seem to misunderstand the actual definition of homology. The term was coined in 1848 by Richard Owen that refers simply to the structural/morphological similarities between organisms (even he recognized that these pointed to common descent). This definition has never been revised, changed, or otherwise altered, from this fundamental core, and certainly has not been defined in any sense as "traits inhereted from a common ancestor" -- which would be technically all traits observed in organisms today. At dictionary.com (<a href="http://www.dictionary.com/search?q=homology" target="_blank">here</a>) it is defined in the following manner: "2. (Biol.) Correspondence or relation in type of structure in contradistinction to similarity of function; as, the relation in structure between the leg and arm of a man; or that between the arm of a man, the fore leg of a horse, the wing of a bird, and the fin of a fish, all these organs being modifications of one type of structure."
No, this would not be a circularity. If "homology" is indeed defined as "similarity by means of common descent", finding instances of this "homology" would, by definition, be evidence of common descent. Maybe you are thinking of the fallacy of equivocation - using the definition of homology in terms of pure similarity, stating an uncontroversial instance of this, then swapping it for your definition, then stating this would be evidence for common descent. I know of no research papers that commit this (and would be surprised if they even made it past peer review.)
Common ancestry demonstrates what? How can common ancestry demonstrate something? I think you are trying desperately to find a circularity where there is none.
This quote conveniently fails to mention anything about homology, and for all we know, could be talking about something completely unrelated! Care to provide a full context (say, a paragraph before and after?) for this quote? I seriously doubt it says what you want it to say.
There is no "neo-Darwinian definition" that is seperate from the standard biological use of the word. By the way, what does any of this have to do with the challenge at hand?
I suggest you read this carefully: [H]omology is the anticipated and expected consequence of evolution. We observe an "anticipated and expected consequence" of some theory, and yet, this is somehow not evidence for that theory?
Now you have simply created a false trilemma to suit your needs. You have in no way supported your assertion that "descent with modification may not be the best explanation" for homology, so you have absolutely no reason to exclude the forth, and correct, option: That observed homology, under its accepted biological definition, is evidence for common descent.
And... This is a direct extrapolation of the explanation of homology from common descent, and the modern genetic idea that genes code for function. You seem to be now taking issue with the latter. (!?!) What on earth else codes for function then? Invisible scrolls with equally invisible Function Pixies? I don't understand... But anyway.
This quote is hopelessly out of date. There have been tremendous breakthroughs in genetics since 1971! I'd also like to request some more context for this quote.
So what? Individual (you're more than probably talking about homeobox) genes must be taken in context of the other genes around it. In the case of homeobox, some of these may be the same, but the enzymes that transcript developmental body-plan proteins into useful structures would be wildly different. Otherwise, genotype wouldn't relate to phenotype at all, and this is clearly not the case.
Again, your twisting of this around is miraculously flawed.
Oh no, you have found out our dreadful, and closely-guarded secret! That we are nothing more than poor, uncritical, deluded fools, that repeat that which is sacred to our fragile dogmas. Get a life.
And you are continuing to uncritically ignore and evade a key piece of evidence for this fact, put right to your face, in the very post you are "responding to".
Please stop with the meaningless rhetoricizing and get to the facts...
And yet another topic you likely just gleamed from Well's disasterpiece (as most of your "quoted" and pre-wrapped anti-evolutionary material seems to come from there.) I don't even have the patience to be bothered with this lie about the Cambrian explosion right now...
About time! Yes, we are told why the evidence points to a fusion, in the very next paragraph!

• The first prediction (evidence of a telomere at the fusion point) is shown to be true in reference 3 . Telomeres in humans have been shown to consist of head to tail repeats of the bases 5'TTAGGG running toward the end of the chromosome. Furthermore, there is a characteristic pattern of the base pairs in what is called the pre-telomeric region, the region just before the telomere. When the vicinity of chromosome 2 where the fusion is expected to occur (based on comparison to chimp chromosomes 2p and 2q) is examined, we see first sequences that are characteristic of the pre-telomeric region, then a section of telomeric sequences, and then another section of pre-telomeric sequences. Furthermore, in the telomeric section, it is observed that there is a point where instead of being arranged head to tail, the telomeric repeats suddenly reverse direction - becoming (CCCTAA)3' instead of 5'(TTAGGG), and the second pre-telomeric section is also the reverse of the first telomeric section. This pattern is precisely as predicted by a telomere to telomere fusion of the chimpanzee (ancestor) 2p and 2q chromosomes, and in precisely the expected location. Note that the CCCTAA sequence is the reversed complement of TTAGGG (C pairs with G, and T pairs with A).
  
  The second prediction - remnants of the 2p and 2q centromeres is documented in reference 4. The normal centromere found on human chromosome 2 lines up with the 2p chimp chromosome, and the remnants of the 2q chromosome is found at the expected location based upon the banding pattern.

Why are you being deliberately ignorant?
On that page there is a link on the word fusion... This leads to <a href="http://www.cs.colorado.edu/~lindsay/creation/translocation.html" target="_blank">a page</a> which describes (more or less) what you ask for. Chromosomal fusion is at least as well documented in the literature as chromosomal fission.
No non-sequitur is commited. You are simply ignoring the predictions. They are provided right below the image of the chromosomes, and are also quoted above inmy post.
Based on morphological similarity, humans and chimps are relatively closely related species, and share a recent common ancestor. From this, it is infered that they should have a relatively similar number of chromosomes, scigirl explains this, relatively meaning that humans should have a closer amount of chromosomes to chimps then say to mice.
None.

Oh well, that's enough for me now. I can't be bothered with any more of this. I'm sure others will have much more thorough refutations than I could manage. Bye.

[ August 27, 2002: Message edited by: Automaton ]</p>

Coragyps

Yowza! That might be redundant now! <img src="graemlins/notworthy.gif" border="0" alt="[Not Worthy]" />