My apologies to those who are hesitant about reading this long post! Hopefully, you will find it absolutely thrilling...well, okay, maybe some useful ideas here and there.

Hi valiya:

Sorry for the delay.

"{Greensnake} said: ==[Valiya, the scientific community has dismissed "irreducible complexity" a long time ago! It's not part of a SCIENTIFIC debate.]==
The irreducible complexity argument was dismissed by appeal to exaptation, …"

==[I'll say it again. Behe's "irreducible complexity" is not part of real science! Why are you using this stuff? Behe's "irreducible complexity" argument suffers from two fatal flaws. First (which you seem to acknowledge), is that structures (including complex molecules) can evolve to serve one need and later be tapped for another need. The idea that a set of complex parts had to evolve simultaneously from scratch to account for a particular structure is, therefore, false.

The second fatal problem is that a structure does not have to be fully complete in order to be useful. One might erroneously think that a lens had to evolve at the same time as a complex eye. In truth, eyes without a lens work well enough for some creatures, so the rest of the eye could be evolving the basics even before a rudimentary lens appeared! A rudimentary lens is better than no lens at all for some creatures, so a complex lens need not have evolved all at once. Evolution doesn't have to leap to some masterpiece all at once. The evolutionary path can be a chain of less perfect structures that are increasingly useful for some creatures in some environments during some periods of time, and that path might eventually arrive at something quite complex (like an eagle's eye). Darwin understood this way back in 1859.]==

==[Fact: Behe's "irreducible complexity" argument is not taken seriously in the scientific community. I'm not going to debate that FACT much further, especially since I've now given you the main reasons for its rejection. If you continue to deny this FACT, preferring his speculation to the general consensus of the scientific community, then I can only conclude that you are out of touch with the real world.]==

"Selection will NOT act on neutral mutation. Which is why a neutral mutation will not enjoy fixation in the population. However, the clock hypothesis suggests that neutral mutations accrue over time, which contradicts the idea of ‘selection’ as the engine of evolution."

==[Why is it necessary for a particular neutral mutation to be fixed in a population? In newly diverging species each would begin to collect its own set of random, neutral mutations that would make up a small percentage of that species' gene pool. As two formerly joined species evolved further and further apart, their gene pools would become more and more different with respect to their neutral mutations. A statistical sampling would measure this difference and allow an estimate of the time since divergence. Various workarounds would compensate for varying mutational rates, but the main point is that there is no need to imagine that a neutral mutation would have to become a standard fixture in the population due to selection. So, your concern here is misplaced.]==

"{Greensnake} said: ==[Wake up and smell the coffee, valiya! Does the evolutionary tree given by that early study of cytochrome c result in a random hash or does it closely parallel the accepted evolutionary relationships? Obviously, cytochrome c works rather well.'
Cytochrome c works rather well, except in cases where they don’t work. Oh but then those are the exceptions right? And exceptions don’t mean anything in biology. In short you have rendered the hypothesis unfalsifiable."

==[It's all about noise level, valiya! When the noise level does not drown out the signal, then you DO HAVE a signal! We do get a lovely evolutionary tree from cytochrome c, a clear signal, so cytochrome c does work rather well. Pointing to some noise is hardly an argument against having a clear signal! Right?]==

==[Fact: Cytochrome c does give rise to a very nice evolutionary tree which is remarkably similar to that produced by comparative anatomy (cladistics). You cannot deny this fact unless you have lost your grip on reality. The FACT is right before us regardless of mutation rates. I've filled in enough of the details. From now on I'm simply going to call the cytochrome c tree what it is--a FACT. Evolution is the only known, rational interpretation of that fact.]==

"{Greensnake} said: ==[Here is what Wikipedia has to say under "Molecular Clock." 'The molecular clock technique is an important tool in molecular systematics, …']==
"It is exactly this attitude that Shi Huang was addressing in his article. He says that ‘molecular clock’ is a derived assumption … . If you are simply going to dismiss them as exceptions (waiting for some future explanation)… then as I said, there is no way I can bring an argument against it. You made it literally unfalsifiable!"

==[Valiya, if you would pull your head out of the doctrinal sand and take a look at the real world you will find that molecular clocks are used extensively in the sciences despite your interpretation of Shi Huang's paper! Obviously, as stated in one or more of the sources I have given, there have been workarounds. Do you actually believe that scientists everywhere would be blindly using broken molecular clocks? The Wikipedia, the University of Berkeley, and the University of Maine websites I gave you are just a few places you can go to see what real scientists are doing. I could add dozens of university websites and other sources. Either Shi Huang was wrong or, more likely, you misinterpreted his paper.]==

==[Fact: The molecular clock is a useful tool employed by scientists around the world. Workarounds have made it useful by reducing or eliminating many problems. You cannot deny this fact unless you have lost your grip on reality. Henceforth, I am just going to call it what it is--a FACT. If you want to remain in denial mode, that's your business.]==

==[Fact: Scientists are not involved in a worldwide conspiracy that continues, decade after decade, to ignore or minimize evidence against evolution. That idea is patently absurd at several levels. Valiya, are you still in denial here?]==

==[Scientists win prizes for kicking in orthodox doors! What kind of scientist, who set out to explore nature's mysteries, would be satisfied to spend his life protecting an orthodoxy he doesn't believe in? That would be absurd. Note that Darwin faced the most stubborn scientific orthodoxy any scientist has ever had to face, yet he won over the majority of the scientific community in a few, short years. If you still want to deny this FACT, then I can only conclude that you are out of touch with reality.]==

"I didn’t find {the Wikipedia material correctly interpreting Denton's matrix}… please copy paste the URL. ==[No need to since your main point follows.]== Moreover, the main crux of the answer to Denton is based on molecular clock, which I have shown is just a tautology."

==[That molecular clocks are scientifically very useful is a fact of life. That cytochrome c produces a clear, evolutionary tree is a fact of life.]==

==[As I stated earlier, Denton USES the molecular clock in arguing that the evolutionary tree presented by cytochrome c is all wrong. How can you use Denton's argument and, at the same time, deny its central assumption? If Denton's matrix doesn't mean anything, because the molecular clock is broken, then his matrix is hardly an argument against evolution! You can't straddle both sides of a contradiction!]==

"… {Denton} found that bacteria is equidistant from a yeast and a horse, which he finds very strange, because these two lineages had diverged long time ago in history and must have undergone different mutation/selection effects."

==[Evolution predicts that bacteria should be equidistant from yeast and a horse! After all, modern bacteria and modern horses share a common ancestor. From that point to the present is the same genetic distance no matter what species you arrive at.]==

"{Greensnake} said: ==[Valiya, please explain carefully the "molecular clock hypothesis" and then tell us why the author considers it a tautology. …]==
Molecular clock hypothesis posits that mutations at the molecular level have a constant rate. Therefore, if organism A and organism B branched out from a common ancestor, they will have equal amount of mutations accumulating in them. If you compare A and B with an outgroup, say C, they both will be genetically equidistant from C – meaning the amount of difference between A and C will be equal to the amount of difference between B and C. Hope that is clear."

==[Nicely stated! Do you know what that means? In Denton's matrix the bacteria are the "outgroup C" whereas the yeast (A) and the horse (B) share a common ancestor. Therefore, the molecular clock hypothesis predicts that yeast and horses will be genetically equidistant from bacteria. Isn't that exactly what Denton's matrix (based on the cytochrome c tree) shows? Obviously, the molecular clock in cytochrome c is working extremely well! Thank you for the help!]==

==[Fact: Denton blundered in arguing that evolution required that the genetic distance (as measured by mutations in the cytochrome c tree) had to be distinctly different between bacteria & yeast, and bacteria & horses.]==

==[Denton's blunder can be visualized by simply drawing an evolutionary tree diagram and tracing the length of the pathways. Start where the bacteria branch off from the base of the tree and trace a line to the leaf that represents modern horses; draw a second line from the same starting point but go to the leaf on the other side of the tree representing modern yeast. The distance is the same, right? It's like going from the base of a Japanese bamboo hand fan to one of the outer points--same distance. The correct answer, given a reasonable drawing of the evolutionary tree, is that the two genetic distances should be equal. Denton was wrong.

If you continue denying this FACT of science, then I'll have to assume that your reasoning facilities have been impaired in some way. Sorry, but I'm just going to call it a FACT from now on.

"There is no way to verify molecular clock hypothesis nor does it have any explanation for the cases that contradict it."

==[Molecular clocks are often calibrated with respect to the fossil record, and you have not begun to acknowledge the various other workarounds that make the molecular clock so useful to scientists around the world. As noted earlier, pointing to "noise" is rather lame if the signal is clear.]==

"{Greensnake} said: ==["Recent discoveries are filling in the fossil record for the Precambrian fauna with soft-bodied organisms like those in the Ediacaran Assemblages found around the world.(7) Late Precambrian fossil discoveries also now include representatives of sponges, cnidarians (the group that includes modern jellyfish, corals and anemones), mollusks and various wormlike groups. Some of the new fossil discoveries, in fact, appear to be more primitive precursors of the later Cambrian body plans. The discovery of such precursors shows that the Cambrian organisms did not appear from thin air.(8)" ]=="

"On Ediacaran fossils, here is a link of an article in Nature magazine that has cast aspersions on the argument that these fossils are ancestors of the Cambrian fauna. …"

==[The point that is being debated here, valiya, is the existence of multi-cellular life BEFORE the Cambrian! Are you now ready to accept that fact? By the way, you falsely accused me of saying that preservation of soft creatures was impossible. I never said any such thing! I am saying that one rarely finds them in the fossil record, so the absence of their fossils in typical Cambrian strata cannot be taken as evidence of soft creature absence. Some researchers do feel that some of the Ediacaran life forms are ancestral to the Cambrian fauna. The matter is still being debated, so quoting one side proves nothing. What is clear is that life had a long history BEFORE the Cambrian. We have no reason to believe that the "Cambrian explosion" came out of thin air.]==

==[Fact: Multi-cellular, soft-bodied life forms existed well before the Cambrian. Valiya, are you still in denial here?]==

==[Fact: Soft-bodied animals were also integral to the Cambrian Period as shown by the very rare Burgess Shale find in British Columbia, Canada."]==

==[Therefore, the fact that Cambrian strata invariably begins with complex, shelled creatures is taken to be a statement about a lack of preservation of soft-bodied animals (suspiciously missing) rather than a lack of soft-bodied precursors.]==

"But then again you have your scientific philosophy that biology can’t be held to the high standard of physics."

==[I gave 7 solid reasons (elementary facts really) as to why one should avoid prematurely throwing out a scientific hypothesis that is contradicted by a fact. That applies to physics as well as biology. That's not how real science is done, valiya.

Fact: Most contradictions between a scientific hypothesis and a fact are inconsequential.
If you still think that a silly quote can overrule an observed fact, then I can only conclude that you have slipped into some fantasy world. I see no point in debating this FACT any further!]==

"{Greensnake} said: “Obviously, these gene transfers from viruses and other sources haven't messed up the multi-cellular portion of the evolutionary tree to any significant extent.]==
Look at the pathetic state of the evolutionary tree… going from one excuse to another."

==[In your imagination, perhaps. Not so pathetic judging by the University of Berkeley and University of Maine websites, to which we could add countless others! Maybe you should go to that University of Berkeley website and actually learn something about evolutionary trees!

Odd, isn't it, that a remarkably similar evolutionary tree can be generated solely from cladistics? Odder still, isn't it, that the fossil record comes up with another matching tree? What could the fossil record, anatomy, DNA, and cytochrome c (not to mention other molecules) possibly have in common to allow remarkably similar tree diagrams? They all record in their own ways the divergence of life over time, valiya. If you know of a better explanation, please inform the scientific world and collect a Nobel Prize.]==

"LUCA is no longer an organism but a community…"

==[Where did that community first get its common genetic code and its unique brand of genetic machinery that makes any kind of interbreeding in that community possible? No doubt some species first crossed the line that led to and established the genetic code and machinery used by all life today. Other forms of life may have existed back then, with different types of genetic machinery, but they would not be the root of today's evolutionary tree. Nor could they breed with organisms having a different genetic code. I'll stand with Professor Michael Benton's statement (Evolution: The First Four Billion Years, p.84) that the genetic evidence clearly points to a root.)]==

"the trunk has become a web…"

==[And in that "web" we see 3 mighty branches that connect at a much deeper level! Just the other day I was looking at the November 2016 issue of Discover magazine, a popular but respectable science magazine. It has a nice, modern, evolutionary tree of life that is focused almost entirely on prokaryotes. There seems to be a lot of order and structure in that web! A fair amount of "webbing" is real due to unorthodox gene transfers among prokaryotes, but let's not overstate the case.]==

"and now at the branches, the confident claims have been reduced to apologetic murmurs like ‘oh there may be noises but it’s not as bad as the trunk.’"

==[In your imagination, perhaps. Please explain the remarkable similarity of the evolutionary tree derived from cladistics and that derived from DNA? How about explaining the similarity of the tree derived from cytochrome c and DNA? And then, there is the fossil record. No, valiya, you can't sweep it all under the rug! This data (the upper branches of the evolutionary tree) reflects a deep reality, and that reality is evolution!]==

"{Greensnake} said: ==[You're the expert, right? If you will go to Wikipedia "molecular clock" and do some reading, you will come across a statement that one of the two most challenging situations for a molecular clock is where life has recently diverged.]==
I think you need to appreciate the basic premise of our discussion. …"

==[Are you admitting that you were wrong in your claim that the most recent twigs on the evolutionary tree present the least "noise"? Or, will you continue to deny this fact as well?]==

"But what I am saying is that there are voices of dissent rising from evolutionists themselves against some of the notions that are quite fundamental to the theory."

==[There will always be dissenting voices, valiya! Views range from "crackpot" to "wild speculation," to "interesting but unlikely," to "worth investigating but uncertain," to "strong but not established," and all the way up to "overwhelming scientific consensus." This is where scientific judgment based on years of actual research experience comes into play. Lay readers, such as yourself, are incompetent to render such judgment. Indeed, on more than one occasion you have actually come up with material favoring my position!! Therefore, when a lay reader points out a "dissenting voice" that doesn't mean much unless care has been taken to show that the view is typical of mainstream science.]==

"My contention is that molecular clock hypothesis is a tautology because there are many observations that contradict this hypothesis as highlighted by Shi Huang."

==[Is that why scientists around the world find molecular clocks to be useful tools? Obviously, you have read more into Shi Huang's paper than is actually there, which is not surprising since you have an ax to grind and lack the scientific background to reign in your imagination. Huang was only noting a problem with molecular clocks, not claiming that they are worthless.]==

"So many observations and evidences have been flying in the face of the theory, and every time a new explanation is given, it runs into more troubles. Yes, the main scientific establishment has not abandoned the theory, and I think it’s a matter of philosophy rather than any hard core scientific reasoning."

==[In your imagination, perhaps. Modern biology would collapse into a heap of disjointed pieces without the framework of evolution. You are not in a position to judge the scientific community, valiya, so it is foolish to offer personal, sweeping opinions.]==

"{Greensnake} said==[Actually, the evidence points clearly to a root "However, it is evident that all living organisms and all organisms known as fossils derive from a single common ancestor (on the basis of the evidence of shared complex characters, such as the DNA-RNA system of inheritance, homeobox genes, and the like).]=="

"This is how you are falling into circular logic. There is this huge assumption that you start out with: similarity means common ancestry."

==[Let me guess! Emerging, independent life forms just happened to all wind up with the same genetic code and the same odd genetic equipment that defines life today! Do you have any idea how long the odds are?]==

"Take for example the concept of convergence. You analyze the similarity/dissimilarity between the various phyla and accordingly attribute common ancestry to them. For example, between crustaceans and primates, the common ancestor is deep down, because the two are very dissimilar. But then you find a trait (eyes) that is quite alike, which tests the theory really hard. You explain it away invoking convergence. An outsider would be tempted to ask that if convergence can explain commonality, then why invoke ancestry for the same phenomenon as a first principle?"

==[Valiya, you don't understand the details of identifying convergent evolution, and you consequently have created a straw man. As always, truth is in the subtle details. I don't want to expand an already lengthy post by giving a lecture on evolutionary convergence. You can get that from the University of Berkeley website that I gave you.]==

So, we come back to the number one proof of evolution--the evolutionary tree. Have you yet figured out a credible alternative interpretation? How is it possible that such diverse sources as the fossil record, cytochrome c, DNA, and anatomy yield remarkably similar evolutionary trees? I can't think of any alternative explanation myself, but then maybe you have some ideas.