Hi valiya:

"Therefore let me conclude that you concede that my interpretation of Shi’s paper is correct."

==[Not quite! Shi does not seem to be claiming that molecular clocks are worthless as does your interpretation of his paper. He seems to be saying that the lengths of evolutionary tree branches are based on the assumption that molecular clocks are running at the same rate, meaning that it would be a tautology to argue that equal branches are evidence of the molecular clock running at the same rate. However, in many cases a clock can be calibrated by radiometric ages taken from the fossil record.]==

"Secondly, until you explain what the workarounds are, I have no reasons to lump your conclusion that ‘actual workarounds make Shi’s conclusion irrelevant to our discussion’… It is very relevant, and until the embarrassing exceptions are not explained, the clock’s credibility is in question."

==[That there ARE workarounds is affirmed in one or two of the sources I gave you, valiya. I don't have any reason to question those sources. The fact that molecular clocks are highly useful, within appropriate theoretical and statistical limitations, is demonstrated by scientists around the world who put them to use. That's the reality, valiya. Are you going to continue denying that reality?]==

"YOU SAID: 'It is an obvious fact of the scientific world that molecular clocks are extremely useful, and the evolutionary trees they produce (when calibrated with respect to the fossil record and constructed with the various workarounds and limitations in mind) are valid within appropriate limits.'
I presented Shi’s paper to prove to you that evolutionists have problems with the molecular clock. It IS by comparing with fossil record and other factors you mentioned that Shi arrived at his conclusions. …"

==[Fact: Molecular clocks are highly useful tools employed by scientists around the world. Quoting Shi's paper to "refute" an observable fact is an act of extreme folly!! It's like digging up some quote to prove that the sky is not really blue on a nice day! Either Shi is a complete idiot or else you have misunderstood his paper. I would bet on the latter since you have no scientific background. Anyone who even reads popular science magazines should be aware of the usefulness of molecular clocks.]==

"YOU SAID: 'The general validity of these evolutionary trees derived from molecules are reflected in their remarkable agreement with each other and with cladistics and the fossil record.'
There you go again with your tall statements. There are serious exceptions to your claims, where the molecular tree disagrees with the fossil record."

==[Valiya, remember my little point about noise level? If the "noise level" doesn't drown out the picture, then you DO HAVE a picture! Fact: The general validity of these evolutionary trees derived from molecules is in remarkable (not perfect) agreement with the trees derived from cladistics and the fossil record. (Consider cytochrome c for example.) That there is ANY match at all among such independent sources is astounding if one rejects the only known explanation--evolution.]==

"YOU SAID: 'Specifically, they record the divergence time between any two species (within the parameters of the molecule) and their common ancestor. No other rational explanation is known. Thus, we have a very strong reason for accepting evolution.'
This is circular argument. When you find molecular equidistance, you assume common divergence time."

==[Valiya, the longer the divergence time between two species the greater their molecular differences are with respect to neutral mutations! How can you have a problem with that? At the very least it clarifies the branching pattern of the evolutionary tree. With good calibration, it can even give reasonable times for divergence. Nothing circular about that!]==

"In some cases the fossils agree with the assumption {for molecular clocks}. IN some cases the fossils DON’T agree. Therefore, it {molecular clocks} really has no explanatory power."

==[By that reasoning the theory of gravity has no explanatory power! Some things agree with it and some things don't. A simplistic view of gravity is that everything must fall down if not powered by muscles or machines. Hot air balloons float upward, so gravity must be wrong! When insignificant noise becomes more important than the general picture in your mind, then you are like a train that has left the tracks. It is never enough (outside of mathematics) to point out conflicting data. You must also show that it is statistically or theoretically significant. In your simplistic view of molecular clocks, there can be no conflicting data.]==

"… – however, if neutral mutation can drive evolution, then why do you need exaptation? Therefore, irrespective of whether irreducible complexity is true or false, the evolutionists have to make up their mind between ‘neutral theory’ and conventional Darwinian mechanism of ‘mutation + natural selection.’"

==[As I have said several times now, and please listen this time, neutral mutations would have nothing to do with natural selection. They would be invisible to natural selection. I also pointed out that a statistical analysis for constructing evolutionary trees does not require that a given neutral mutation to become fixed in a population, so there doesn't seem to be any contradiction with natural selection. It is enough to get a statistical measurement of the differences in neutral mutation sites between two species. (Are you now conceding that Behe's "irreducible complexity" is not all that it is cracked up to be?)]==

" '…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.]=='
It is NOT my concern. It is the concern of evolutionists who disagree with the neutral mutation hypothesis. How many papers would I have to present before you recognize that there are serious differences of opinion on this matter. …"

==[Scientific papers often support all sides of a complex issue valiya. Note that even if mutation rates are not constant it is still reasonable to expect that the longer two species have diverged the greater will be their differences at neutral mutation sites. This is actually borne out by cytochrome c, DNA, and certain other molecules. Thus, we have a reasonable hypothesis for using molecules to recover evolutionary trees, at least up to the point of saturation. Would you please address the argument and not throw scientific papers (that you don't understand) at me!

We are getting lost among the trees, valiya, and not seeing the forest. The bottom line is that the usefulness of molecular clocks to scientists around the world is a FACT of life, a fact not changed one bit by the controversy over neutral mutations. A second FACT of life is that remarkably similar evolutionary trees are derived from cytochrome c, DNA, and certain other molecules.]==

"Here is another paper that refutes neutral mutation. …"

==[Refutes? Apparently you are not aware that the controversy is still going on. Quoting one side of it hardly refutes the other side!! It does demonstrate that your interpretation of these papers is suspect. You should have used the word "criticizes" or "attacks" instead of "refutes." You are hardly in a position to decide the issue!]==

"YOU SAID==[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.]=="

"I don’t understand your logic. How can cytochrome c give rise to an evolutionary tree REGARDLESS OF MUTATION RATES. Without mutation rates (constant rate) you cannot explain the cytochrome tree where for example yeast and horse are equidistant to bacteria. SO you may call it FACT or whatever you like… but bear in mind there are also other names for it: TAUTOLOGY."

==[That a decent evolutionary tree can be derived from cytochrome c is a LABORATORY FACT valiya! It exists whether or not it makes any sense to you! Facts are primary, right? That the evolutionary tree derived from cytochrome c is in remarkable agreement with that of DNA, cladistics, and the fossil record shows that it is truly an evolutionary tree and not some artifact. Evolution is the only rational explanation.]==

"YOU SAID: '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.]=='"

'This is the genetic fallacy I have been saying. You simply want me to accept or reject arguments based on who is saying them. Sorry. I am not game for that. There are scientists with equal qualifications on both camps. …"

==[Valiya, you must be way deep into denial to actually deny the FACT that molecular clocks are useful tools employed by scientists around the world! Nothing that you can possibly say, quote, or show will refute a demonstrable fact!! The reason molecular clocks are used is because they work, not perfectly but good enough. If you insist on denying demonstrable facts then how can we have a serious discussion?]==

"YOU SAID==[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?]=='"

"As I stated earlier, the evolution theory is based on some huge assumptions which are unfalsifiable."

==[Please cite one noted university or a couple of famous biologists or paleontologists who do not accept the basic fact of evolution. Scientists around the world, being among the world's most brilliant minds, could hardly miss something that you find so obvious! There would have to be a coordinated, enforced, worldwide conspiracy of silence for scientists to overlook such a fatal flaw and unanimously assert that basic evolution is a fact!

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 on several different levels. Once again I'll put the question to you: Valiya, are you still in denial here?]==

"However, now neutralists are arguing that the selection has very minimal role in evolution."

==[No, they are not! They are talking about genetic drift of neutral mutations at the molecular level. The general validity of natural selection is not being challenged at all! Once again we have evidence that these scientific papers you quote are way above your head.]==

"I HAD SAID: "… {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."
AND YOU SAID==[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.]==
This is a classic example of your circular reasoning."

==[This is a classic example of your refusal to accept a demonstrable fact! Denton's argument is dead wrong. It's been pointed out on numerous occasions by others. If you wish to continue in this fantasy that's your business, but don't ask me to join you in this diversion. A serious discussion begins with the facts and centers on their interpretation. You still haven't accepted the facts!]==

"And here is another U turn. Why does Denton think distance between bacteria and yeast should be different from that of bacteria and horse. Precisely because he doesn’t start with the assumption of the molecular clock! So your earlier claim that he begins from that assumption has been defeated."

==[Let me guess. Denton is trying to argue that the cytochrome c mutation data collected in his matrix contradict the expectations of evolution, therefore he makes that data worthless by not accepting its validity! That's rich! You have really outdone yourself, valiya! Of course he accepted the validity of the cytochrome c matrix data which is essential to his argument, meaning that he also accepted the molecular clock as a useful measurement. Why does Denton think distance between bacteria and yeast should be different from that of bacteria and horse? He mistakenly measured from the earliest ANCESTOR of yeast and horses. Yeast is primitive so, gee!, the distance between it and bacteria must be fairly small; horses are complex so, gee!, the distance between bacteria and horses should be huge. He observed that the distances given by cytochrome c are all about the same and concluded that evolution was busted. Not! As I pointed out, we are actually measuring between the PRESENT representatives of horses and yeast and modern bacteria.]==

"YOU SAID==[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?'
The point that is being debated is if Cambrian life had precursors or not."

==[Let me guess. We know that multi-cellular life forms existed before the Cambrian, that some of them look suspiciously like precursors to Cambrian life, and that any soft, precursor forms would not likely be preserved in typical strata just before or within the Cambrian. We do know that soft-bodied forms also existed within the Cambrian due to the extremely rare Burgess shale site in western Canada. So, gee!, that absence of clear evidence of soft-bodied precursors to the Cambrian "explosion" must mean they didn't exist! Valiya, absence of evidence is not proof of absence, especially in this situation.

A scientist would argue that since soft-bodied, multi-cellular life existed well before the Cambrian, and within the Cambrian itself, that there is no justification for believing that the Cambrian "explosion" came out of thin air. True, there is some debate as to whether the Cambrian "explosion" came out of the Ediacaran life. But with soft-bodied, complex life already on deck, and the fact that it is rarely preserved, it would be silly to conclude that nothing preceded the Cambrian.]==

"If you don’t find any fossils – you say ‘look they were too soft bodied to be preserved’ – if you happen to find a few fossils, you would then say “well, most were not preserved but a few could have been due to some chancy factors.’ I mean, there is really no way we can deal with an argument of that nature."

==[The soft-bodied, Cambrian fossils in the Burgess shale of western Canada seem to have originated in a local, underwater landslide half a billion years ago. The fossil-bearing strata doesn't stretch very far! Yet, until some recent finds in China, that was the only decent window into the soft-bodied life forms of the Cambrian, forms that were not preserved in the usual Cambrian deposits. So, yes! valiya, there are good reasons to think that soft-bodied, precursor life forms leading to the Cambrian fauna were not preserved.]==

==[Perhaps a lesson on fossil preservation is in order. At one time Passenger Pigeons were so numerous in North America that the main flock blackened the sky and took, I am told, days to pass by! So, how many fossils of passenger pigeons do you think we should find in the fossil record after millions of years of existence? Thousands? Tens of thousands? Try 130 or so! In the Grand Canyon we have footprints of animals of which we have not found a single fossil! That the soft-bodied precursors of the "Cambrian explosion" were not preserved is a reasonable assumption, especially since the many soft-bodied creatures of the Cambrian, itself, are only preserved in a few, rare places.]==

"YOU SAID==[Fact: Soft-bodied animals were also integral to the Cambrian Period as shown by the very rare Burgess Shale find in British Columbia, Canada."]==
Bingo. Now add to it a ton of imagination and you have a beautiful tree of life emerging. After all we know that the tree is a FACT, don’t we?"

==[What ARE you talking about? Yes, the "tree" is a LABORATORY FACT. It's your job to argue that it isn't a fact for evolution.]==

"YOU SAID: “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!]==
What is the observed fact? The molecular clock? Common ancestry? …"

==[To refresh your memory, valiya, about 4 long discussions ago I pointed out that your many criticisms of the evolutionary tree (derived from cytochrome c) were hardly fatal in light of the University of Maine website I gave you. You countered with the absurd claim that any contradiction with a fact was fatal to a theory. I explained to you that this was only true for mathematics. You dogmatically continued to cling to your absurd claim and even brought in an odd quote by Shi Huang which, in your mind, settled the matter. I responded to that silly quote by laying out 7 solid, factual reasons why a contradiction with a fact need not be fatal to a theory and noted that most real contradictions were inconsequential. You dogmatically continued with your strange claim and I finally pointed out (in the above quote) that my statement was a demonstrable fact of life (obviously following from the 7 points I had given you) and that continuing to deny it constituted a flight into fantasy. Does that bring you up to date?

You have this dogmatic tendency, valiya, to cling to an idea no matter how wrong it is, a dogmatic tendency that is oblivious to reality! I stand by my simple statement of fact and I will not be diverted into lengthy side discussions that ignore a demonstrable fact.]==

"YOU SAID: '==[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!'
Genetic fallacy again. You are saying “Just listen to my scientists because they are right, and just ignore all other papers and scientists who contradict them, because those who contradict what is right are obviously wrong.” Good logic."

==[Another straw man! My reply was in response to your wild blanket claim that the whole idea of the evolutionary tree was in tatters! Once again you had buried yourself in sources that were over your head, to which you added your own biased interpretation. Once again you could no longer see the real world. And now you slip, once again, into your fantasy of an evolutionary tree in tatters. Yes, the concept of the evolutionary tree has its limitations as does any complex methodology, but it is clearly a valid concept for organizing life--which is why it is found in any university textbook on biology, geology, paleontology, taxonomy, or even molecular biology.]==

==[That similar evolutionary trees can be derived from cladistics, DNA, and cytochrome c is a LABORATORY FACT. Your flight into hand-picked scientific papers, from which you produce dubious interpretations that often go far beyond what the author is actually saying, can hardly overturn reality! This "we got our scientists and you got your scientists" nonsense doesn't walk. A basic tally of who stands where in the scientific world would make that very clear. Again, check out any university textbook on biology or geology. Check out any serious encyclopedia or any other universally accepted source of scientific knowledge. Check out Wikipedia. The evolutionary tree, imperfect as it may be, is a fact of science valiya! And that's what I'm going to call it from now on.

If you wish to continue denying reality, valiya, that's your business. Just don't ask me to take part in your flights of fantasy in which demonstrable facts are "refuted." Your must give an alternate explanation for the evolutionary tree that makes more sense than evolution.]==

"Carl Woese says LUCA is a community because from his analysis he could make out that everything did not start from a single cell! So we are now essentially looking a group of cells – all of which originated independently of each other. … But do you have any clue about how any one individual cell could have risen from non-life, leave alone an entire community of cells?"

==[Your question deals with the subject of abiogenesis and is irrelevant to both our discussion of the evolutionary tree and to evolution itself. Are you suggesting that because we don't have the answer right now that there is no answer?]==

"YOU SAID==[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.'
Would you consider peer reviewed voices also as ‘crackpots’ and ‘wild speculations’?"

==[I don't see that in my brief glance of the material you quoted. I have criticized some of your interpretations that seemed to go far beyond what was actually being said. That this material is over your head was humorously demonstrated on a couple of occasions when you quoted material that actually supported my position!]==

"YOU SAID==[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?]==
Have you calculated the odds of ‘random mutation’ + natural selection giving rise to new information? There are evolutionists who are saying that’s impossible, which is why you have new hypothesis and explanations coming every day. Any naturalistic explanation of life will run into this probability problem. But if you want to persist in your dogma-driven worldview that everything should have a materialistic explanation, then you would have to make leaps of faith to cross huge chasms of odds!"

==[Please answer my question, valiya! I was explaining why the root of the evolutionary tree can't begin with a community of cells that had arisen independently. One cell in such a community no doubt crossed the crucial boundary that marks the root of today's evolutionary tree. It survived and its descendents gave rise to all life today.

Valiya, we have clear evidence that new species have arisen, not only in a human lifetime but more dramatically so over the last few thousand years. Since a new species clearly implies new information, I'd say that the odds are certain! Who are these "evolutionists" who think that evolution can happen without generating new information? Do you even know what you are talking about? The story sounds kind of hokey. Anyway, it's irrelevant to our discussion.

Valiya, I hope that you will stop butting your head against demonstrable facts and finally offer us your interpretation of evolutionary trees, an interpretation more believable than evolution. I say that evolutionary trees are the number one proof of evolution.]==