Swinging from one tree of life to another!

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Thu, 02/02/2017 - 14:28

Dave Matson

Sorry for the delay.

"You said: 'I need to see the full context whenever a quote from a reputable source seems to run counter to accepted science. Quite often the real meaning only emerges in its full context, especially if quotes have been cherry-picked somewhere along the line. It's a subtle area and limited quotes can easily mislead non-scientists.'
The problem is that you are assuming that my intention behind these quotes is to undermine the tree."

==[There is no problem, valiya! This is a general truth that we can all agree on. Even legitimate scientists, working in a complex field, can be carelessly quoted so that they seem to say something unintended. That is especially true of cherry-picking creationist quotes. It's also true of an honest person who, not knowing the subtleties, seizes on quotes in a way that was never intended. Honest people can also rely on dishonest quotes without realizing it. Sometimes careless or over simplified statements by scientists can add to the confusion. That's why I must see the full context of a quote that seems suspicious.]==

"'You said: 'What you choose to believe is your own business, valiya. I'm just saying that a reputable university is a highly credible source. Do you agree with that?'

You have to appreciate that we are coming from two very different schools, and you are aware of the ongoing debate between the schools. We have our own reasons to distrust each other’s schools. That’s the basic premise you have to first accept. Scientists like Michael behe, Stephen Meyers and William Dembinski might be unacceptable to you…
and I will share similar sentiments towards your authorities."

==[All the reputable international scientific organizations representing fields close to biology hold that descent with modification (evolution) is a fact. The scientific debate has been over for years. The debate today is basically a religious debate and Behe, Dembinski, and others may have their PhDs but their creationist works are directed to the lay reader. Their arguments are not good enough to interest the peer-reviewed, scientific journals where real science is reported. Denton, for example, made that horrible argument against the evolutionary tree generated by cytochrome c. Behe's "Black Box" argument simply doesn't hold water for obvious reasons. On and on it goes with these creationist/ID authors! When they do real science, as they sometimes do, they do get their articles published in serious journals.]==

"I believe there is a very strong tendency to suppress any argument or hypothesis that tries to attack Darwinism in the academic circles. So, it makes no sense in a debate of this nature to simply emphasize on the credibility of your authorities and present their credibility as a proof in of itself to support your claim."

==[Valiya, I'm not using these quotes to cut our discussion short! By all means, let us look at the evidence. I just want you to realize that universities are one of the best sources for scientific information on any subject. They are superior, for example, to popular magazines on science such as "The New Scientist."

Scientists win their greatest awards by overthrowing orthodoxy. Why would they circle their wagons to defend it? Maybe an old, rear guard might lean that way, but a younger generation of scientists (like Einstein, or the authors of "punctuated equilibrium" Stephen Jay Gould and Niles Eldredge) soon kick in the door. But they have to prove their case. Slick, superficial arguments that fool lay readers, by such people as Behe or Denton, are not going to impress real scientists who know their stuff. Your complaint makes no sense at all to me. It's the old conspiracy theory that flying saucer buffs and other pseudoscience buffs ultimately rely on when they run out of ideas. It's not worthy of you.

Creationists have been howling against evolution for about for 150 years, and evolution just gets stronger! Whenever they argue against evolution, creationists make the most elementary errors. Also, science journals report science--not religious theories. That seems pretty basic.]==

"It would be better if you focus on your case rather than eulogizing or discrediting authorities." ==[If a quoted source has some problems they should be pointed out.]==

"You said: “Since you gave quotes, valiya, that strongly suggested (not clear without the full context) that the evolutionary tree was "in tatters" or defunct, I decided to present this site which is about 20 years more recent than your quotes.”
New Scientist gives the full context, it obviously is not trying to misrepresent scientist, is it? This is one more example where anybody that even appears to attack drawinism is clamped down upon."

==[New Scientist is a secondary (popular) source and the quotes it used (in a personal essay rather than a straight report) gave the false impression (especially to anyone without a background in evolution) that the evolutionary tree was totally destroyed. As I pointed out with the Berkeley source (one of the best university sources) that is a huge misrepresentation of the facts! Shouldn't that sort of thing be pointed out? Why do you see it as just one more example of an unfair attack on anyone challenging evolution? I think that this is a lame excuse.]==

"You said: Here is a typical quote: 'The power of that idea {evolutionary tree} can … to cutting edge cancer research.'
Shouldn’t you be giving references also for me to check the context?" ==[That came out of the University of Maine web site that I gave you.]==

"You said: 'The key word is "accident." If you roll dice, I think you will find it rather difficult to get anything resembling an evolutionary tree. If you see one in nature it is not by accident!'

You are talking as if you are dealing with some binary option in front of you. You either have the tree or you don’t… no no. That’s not what it seems to be. It’s way more complicated than that… and that’s why there is so much noise going on (between evolutionists themselves) about the tree. There is an appearance of a tree, but a lot of things just don’t add up… and there are problems all over."

==[Valiya, take a good look at the simple, evolutionary tree featured in the University of Maine website that I gave you, the one from cytochrome c. It was derived in 1978 and was one of the first (of several) molecular evolutionary trees. Do you honestly think that such detailed and accurate information came out of a comparative study of cytochrome c by complete accident, that it just happened to reflect evolutionary understanding? The passage of time, itself, is preserved in these molecules and the message is "evolution" loud and clear!

You see problems all over, valiya, but you have no background to understand what they mean or their seriousness. You have no means to judge quotes. These problems are not fatal to the evolutionary tree as my two university sources demonstrate. University sites don't feature discredited stuff! Major changes have been made due to gene sequencing, but the main effect has been on the base of the evolutionary tree which was always rather uncertain.]==

"Here is what a research paper says: Thus, in two-thirds of the cases, a genealogy results in which humans and chimpanzees are not each other's closest genetic relatives. The corresponding genealogies are incongruent with the species tree. In concordance with the experimental evidences, this implies that there is no such thing as a unique evolutionary history of the human genome. Rather, it resembles a patchwork of individual regions following their own genealogy.
Reference:https://academic.oup.com/mbe/article/24/10/2266/1072057/Mapping-Human-Ge..."

==[Thank you, valiya, for providing another full reference! Do you really understand what you are reading here? Without some scientific background, how could you? I read the same article and find the types of unexpected discoveries that make science so interesting. I see no refutation of the general concept of an evolutionary tree. However, there is evidence (if this paper is correct) that DNA may not, at least for the finest details of the evolutionary tree, give only one branch arrangement. Different parts of the DNA may give slightly different branch arrangements for the last stage of the human, chimp, and gorilla evolution.

Some parts of the DNA support the orthodox view, namely that chimps and humans are directly related. Other parts of the DNA seem to say that humans may have branched from an ancestor group that only a little later split into chimps and gorillas. That would mean that chimps and humans are not directly related, but they would still share a close, common ancestor. The paper is 10 years old and it would be interesting to see what was finally decided. Unfortunately, I don't have the time to pursue it.]==

"Can you explain how the fogginess at the base of the tree has been cleared now? From the research sites I visited, it seemed like there was so much HGT taking place low below it’s a fuzzy confused mass of web! If anything, we now know that it’s futile to pursue the hunt for a common universal ancestor. Root gone!"

==[Valiya, as far as I know it is still foggy, but I haven't followed the details so don't quote me on that! "Root gone" may be fatal to a real tree, but here it is just a case entangled strands, like some kind of swamp tree. It's not like something was missing! Almost all the usual details of the evolutionary tree are higher up and are unaffected by this confusion among bacterial lineages. They still point squarely to evolution! In fact, some diagrams don't even use "roots," something you will learn about when you visit the "Tree Room" on the Berkeley site I gave you. That life uses the same DNA code is prime evidence of a single, universal, common ancestor. I don't think that scientists have given up on searching for the universal common ancestor, but their job is now more difficult.]==

"In the research paper I gave reference above, it spoke of how there are problems even between the closest branches in the tree, where the noise levels are supposed to be least. So, how much more confusing it would get as you go farther and farther deeper." ==[Actually, the end branches are sometimes the toughest to work with because the small differences might be masked by small errors! That's another reason for visiting the "Tree Room" on the Berkeley site.==]

"You said: 'When the evidence for supernaturalism becomes stronger than the well tested evidence for the laws of nature, then is the time to talk about supernaturalism. God might have made the sun by pure magic, but we will never learn anything if we don't try to find a naturalistic explanation.'

You got me wrong. I am not saying insert god wherever there is a gap in understanding. What I am saying is just because we have to pigheadedly find a naturalistic explanation, let’s not come up with reasons that require a bigger leap of faith than god. When Newton couldn’t understand the force between objects, he just called it action at a distance, and left it at that. If he had pursued it with materialistic bias, then he would have never called it force, because then it indicates that there is an agent behind it. Let’s just call a spade a spade. If it is force, it is force. If we see design let’s call it that. Why worry about who the agent is and stuff like that."

==[As I pointed out, science is not being pigheaded when it seeks a naturalistic answer. There is no such thing as a supernatural-based science. When you go there, science turns into a philosophical or theological debating society with no hope of progress. Conceivably, it might turn out that some things in our universe have no scientific explanation. Then is the time to turn to theology, but whose theology? Are we talking about the many gods of India or the spirits worshiped by Native Americans? If science ever fails, the door doesn't open for conservative interpretations of Islam, Christianity, or some other religion. It just means that we have reached the end of what we can objectively know. So far, science is doing a fantastically great job with its natural explanations!

By the way, valiya, Newton's force is defined by F=ma. It says nothing about an agent!]==

"You said: 'Give it a rest, valiya! This is a known trap that creationists have fallen into, including Denton and, now, yourself. What is measured is the number of differing mutations in the respective cytochrome c of various life forms. Starting at the point where all life branched off from bacteria, the "evolutionary tree" path to present day bacteria is just as long as that path is to modern horses, just as long as the path to modern yeast. Since the timelines are equally long, we would expect to see the same mutational differences between bacteria and horses and bacteria and yeast!'

This is an answer I expected from you. The idea of molecular clock. But this is such a baseless claim. I will present the research paper that explains it below."

==[As I said, this is a well known blunder. Valiya, you are in a hole and are furiously digging yourself deeper! Your best strategy is to admit that you made a mistake and move on. You cited another paper, but I didn't notice anything (a fairly quick glance) that said that the results applied to the cytochrome c study. Why shouldn't mutations statistically occur at the same rate in the SAME AREA of the cytochrome c molecule? Based on the tree model, evolutionists expect to see similar distances between bacteria and all other creatures higher up. Aside from the special confirmation that Denton (and yourself) unwittingly gave to the evolutionary tree, the fact is that a rather nice tree emerges from the cytochrome c data that is in magnificent agreement with comparative anatomy. All of that says that we are justified IN THIS INSTANCE in assuming a reasonably constant rate of mutation.]==

Sat, 02/04/2017 - 23:57

(Reply to #62) #63

Valiya

Hi Greensnake

My apologies for the delay too.

Let me first of all lay out the ground for my argument. You seem to be missing the central point of where I am coming from.

What I am basically stating is that there is an orthodoxy in the scientific community that is disallowing any honest discussion on Darwinian theory of evolution. Yes, you may beg to differ, but that’s my stand point. Therefore, you can’t expect me to bring you proofs to the effect that ‘evolution has been disproven’ or ‘evolution is wrong’ and such statements from mainstream journals that is part of that orthodoxy. However, what I can present are lateral proofs from mainstream journals that are actually challenging Darwinism but always interpreted in other ways so the central tenet is never shaken. So, you should walk with me a bit to be able to appreciate my argument. If you are simply going to dismiss my arguments because the full article (from which proofs are presented) don’t undermine the central tenet… then I don’t see this discussion going too far.

Let me cut straight to the core issues of our discussion.

You said (regarding human-chimp ancestry): I see no refutation of the general concept of an evolutionary tree. However, there is evidence (if this paper is correct) that DNA may not, at least for the finest details of the evolutionary tree, give only one branch arrangement. Different parts of the DNA may give slightly different branch arrangements for the last stage of the human, chimp, and gorilla evolution.”

My intention behind this proof was not to show that evolutionists have discarded the tree, but just to point out that different genes tell different stories about the tree. Yes, may be the story differs by just one step in the lineage, nevertheless a difference. And we are seeing noise at the highest tips of the tree where it’s supposed to be least expected. If you agree so much… please let me know, so we can proceed.

You said: [Valiya, take a good look at the simple, evolutionary tree featured in the University of Maine website that I gave you, the one from cytochrome c. It was derived in 1978 and was one of the first (of several) molecular evolutionary trees. Do you honestly think that such detailed and accurate information came out of a comparative study of cytochrome c by complete accident, that it just happened to reflect evolutionary understanding? The passage of time, itself, is preserved in these molecules and the message is "evolution" loud and clear!

Let me lay out the basics again. When you are positing a theory, even if 99 things match up and one doesn’t, then that should be taken as a serious challenge to the theory. If Kepler’s planetary motion works fine with all the planets except say mercury, then that’s not something you can simply wish away. The theory has to be adjusted to fit the evidence.

But what has happened in the case of evolution is that whenever evidence comes in direct contradiction to what it predicts, then you invoke more outrageous explanations to preserve the theory, instead of honestly taking a lesson from the evidence.

The Cambrian explosion contrary to expectation has gotten more unexplainable as fossil finds are showing that there were more innovative body plans than previously thought… all without any precursors. We see there is clearly not a tree but a forest. The fossil evidences are clearly in disarray.

And then came molecular tree mapping techniques. Everything was great in the beginning, but then evidences started pouring in that undermines the notion of LUCA. This is a tree without a root. Evolutionists now say that what we are seeing is not one ancestor but a community of ancestors. No less an expert than Carl Woese says this. Ref: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4008548/

But you seem to take it easy. You said: You are happy with the fact that you can see a tree above the root, and don’t care much for all the humongous problems in the root. However, the root accounts for a majority of the history of the tree of life. In the 3.5 billions years of life’s history, about 85% of it is the root.

And then there is the more recently emerging orphan genes problems. You must be knowing about it. But of course, even that is not going to undermine the tree. How do these novel genes appear suddenly in such a species specific manner… evolutionists say that could be due to gene duplication and such processes, which according to the proof I had provided in our last discussion, is a process whose mechanism we know very little about.

And more specifically on Cytochrome C, I presented Denton’s study that highlighted the equidistance of different clades to an out group. You invoked molecular clock to explain that phenomenon, and that’s why I presented the research that severely attacks the notion of molecular clock. But instead of answering the problems it raises, you are saying that it doesn’t mention anything with respect to Cytochrome C. Why should it make any specific reference to cyctochrome c, when it attacks the very basic concept of molecular clock which includes even cytochrome c?

So basically this is how the circular logic of evolution works. You start out with the assumption that all organisms are connected to a tree that converges on a common universal ancestor. The fossil evidence did not hold up. And so you turn to molecular evidence. Things were hunky-dory as you mentioned initially. But soon problems began to surface there too. There are tons of exceptions turning up to the rule.

You said regarding molecular clock: “Why shouldn't mutations statistically occur at the same rate in the SAME AREA of the cytochrome c molecule? Based on the tree model, evolutionists expect to see similar distances between bacteria and all other creatures higher up.

How do you expect mutations to occur at the same rate in any given molecule between two different species when mutations are driven by selection pressures? Do you then say the mutations had the same selective advantages between the two distinct lineages? Can you explain that to me? If you had not read the article I gave carefully, please do so. Because it raises these very questions that I am asking here.

Sun, 02/05/2017 - 02:35

(Reply to #63) #64

Nyarlathotep

valiya s sajjad - What I am

valiya s sajjad - What I am basically stating is that there is an orthodoxy in the scientific community that is disallowing any honest discussion on Darwinian theory of evolution. ...Therefore, you can’t expect me to bring you proofs to the effect that ‘evolution has been disproven’ or ‘evolution is wrong’ and such statements from mainstream journals that is part of that orthodoxy.

When you can't find what you need, claim a conspiracy!

Sun, 02/05/2017 - 09:19

(Reply to #64) #65

ThePragmatic

LoL... where have I heard

LoL... where have I heard that tactic before? Hmm...
Oh, that's right: From all kinds of people with unjustified beliefs. From the "alien astronauts genetically engineered humans" faith heads, to "the holocaust never happened" faith heads, to the "God exists" faith heads.

Sun, 02/05/2017 - 19:07

(Reply to #65) #66

Dave Matson

Hi valiya:

"What I am basically stating is that there is an orthodoxy in the scientific community that is disallowing any honest discussion on Darwinian theory of evolution. Yes, you may beg to differ, but that’s my stand point. Therefore, you can’t expect me to bring you proofs to the effect that ‘evolution has been disproven’ or ‘evolution is wrong’ and such statements from mainstream journals that is part of that orthodoxy."

==[Valiya, you defend an exceedingly awkward position! On one hand you want us to believe that there are good scientific arguments against evolution; on the other hand you are telling us that the great, scientific academies of the world just don't get it or, else, are involved in a gigantic conspiracy!! Infinitely more likely, I think, is that you just don't get it!

Am I to believe that of the hundreds of peer-reviewed, scientific journals not even a dozen would step up and expose such a conspiracy? Editors pride themselves on the accuracy and integrity of their journals. Who would want to read a scientific journal that knowingly supports falsehoods or whose authors are too stupid to know better? Scientific careers depend on getting good information and journals are judged accordingly. How would such an orthodoxy even be enforced on a younger generation of scientists who would like nothing better than to kick in the doors? That's how Nobel Prizes and scientific reputations are won, remember? There are no prizes for circling the wagons (as creationists and religions do).

The strongest of all scientific orthodoxies was the one Darwin went up against, an orthodoxy rooted in religion. Yet, in ten short years or so he won over a large portion of the scientific community because he had real evidence! Creationists have had over a HUNDRED YEARS and more to make their case against evolution. Have they won over as much as 10% of the leading biologists and geologists? Do even one out of every ten respected universities take a stand against evolution? Hardly! Evidence has accumulated since Darwin's time that he could not even have dreamed of! Today, evolution, at least among scientists, is regarded as a fact of life. Above all, scientists are interested in advancing their knowledge of a field, not in defending something they don't believe in!

I can only conclude that religion has put blinders on you, valiya. But it's not a religious issue! A large percentage of Christians have no problem with evolution, even the Pope, even those who might not accept abiogenesis. I understand that there are also quite a few Muslims who accept evolution.

Note that I am not asking you to quote journals. I am asking for a serious argument that rebuts the number one proof of evolution, the evolutionary tree. (So far you have found none.) That argument must be based on an understanding of the subject. Attacking straw men, due to ignorance of the subject, doesn't count.

The actual explanation for the evolutionary tree is simplicity itself. (It is the refinements that get complicated.) You have a large molecule (such as cytochrome c or DNA) that can collect mutations (in places) without harming or benefiting the organism. As long as a species remains intact, the members of that species will have more or less the same pattern of mutations in those molecular areas since the genes they inherit circulate throughout the population. (You choose molecules with a slow enough mutation rate so that interbreeding in the population has a chance to spread them around more or less evenly.) But, if a species diverges then both species drift in their own random directions with regards to the mutation pattern of those molecules. The more recent the divergence, the more similar their two mutation patterns. When this data is put together in the best statistical fit, we get the evolutionary tree--not a creationist grass pattern, random noise or something else. Call it the evolutionary bush if you want. Same concept.

The same evolutionary tree follows from comparative anatomy. You look at sets of characteristics, especially details unrelated to evolutionary success. Recently diverged species will share many such similarities; distant "cousins" will share only a few, basic traits that cannot easily be evolved away. The fossil record leads to yet another evolutionary tree, which is constructed by noting when each type of fossil first appears, where it appears, and the details of that fossil. That these various trees substantially agree with one another is the number one proof of evolution, the proof that you have yet to overthrow.]==

"However, what I can present are lateral proofs from mainstream journals that are actually challenging Darwinism but always interpreted in other ways so the central tenet is never shaken." ==[It is your interpretation of these articles that is suspect, valiya, given that you lack the background to properly evaluate them. Scientists often challenge some aspect of evolution, but that is completely different than rejecting the fact of evolution.]==

"You said (regarding human-chimp ancestry): 'I see no refutation of the general concept of an evolutionary tree. However, there is evidence (if this paper is correct) that DNA may not, at least for the finest details of the evolutionary tree, give only one branch arrangement. Different parts of the DNA may give slightly different branch arrangements for the last stage of the human, chimp, and gorilla evolution.'

… Yes, may be the story differs by just one step in the lineage, nevertheless a difference. And we are seeing noise at the highest tips of the tree where it’s supposed to be least expected. If you agree so much… please let me know, so we can proceed."

==[Valiya, why do you continue saying that noise is least expected at the tips of the tree? An area of slight difference is exactly where the noise is most bothersome! Minor differences in the evolutionary tree hardly refute the concept of the evolutionary tree, especially since that concept was used in demonstrating those differences!]==

"You said: '[Valiya, take a good look at the simple, evolutionary tree featured in the University of Maine website that I gave you, the one from cytochrome c. …'

==[You are mistaken, valiya. You are thinking of mathematics where that is very true, indeed! It's no accident that your Kepler example is mathematical in essence. In general, science often deals with imperfect data, statistical analysis (where the highly probable is not necessarily the actual), and theories that may be simplified conceptions that are usually made stronger by minor adjustments. It all depends on that "one" observation that doesn't fit in. Usually it's inconsequential. In all cases the interpretation involves scientific judgment. Since you don't appear to have any scientific competence, you are hardly in a position to decide what is important and what is not important with respect to observations that don't match up.]==

"But what has happened in the case of evolution is that whenever evidence comes in direct contradiction to what it predicts, then you invoke more outrageous explanations to preserve the theory, instead of honestly taking a lesson from the evidence." ==[Without a scientific background, valiya, you are hardly in a position to decide what constitutes an "outrageous" explanation. Are you accusing scientists (and myself) of not being honest with the evidence? Given that you are ignorant in this area, just maybe you are grabbing onto things that are really no threat to the concept of an evolutionary tree or bush. Isn't that a better explanation than assuming dishonesty or stupidity on the part of scientists? After all, they are the ones who have put in years of high-level study, not yourself, and they are very much interested in discovering the truth!]==

"The Cambrian explosion contrary to expectation has gotten more unexplainable as fossil finds are showing that there were more innovative body plans than previously thought… all without any precursors. We see there is clearly not a tree but a forest. The fossil evidences are clearly in disarray." ==[Some of the "Cambrian explosion" fossils DO HAVE reasonable precursors! Given the fact that boneless, shell-less creatures rarely get preserved, it's not hugely surprising that many precursors are unknown 500 million years later. If you want to get a fast update on the fossil record, read Dr. Donald Prothero's book "Evolution: What the Fossils Say and Why it Matters." He knows the fossil record firsthand, being an internationally known geologist, and he also explains to the lay reader why the "Cambrian explosion" is only an interesting puzzle--not a refutation of evolution.]==

"And then came molecular tree mapping techniques. Everything was great in the beginning, but then evidences started pouring in that undermines the notion of LUCA. This is a tree without a root. …But you seem to take it easy. You said: You are happy with the fact that you can see a tree above the root, and don’t care much for all the humongous problems in the root. However, the root accounts for a majority of the history of the tree of life. In the 3.5 billions years of life’s history, about 85% of it is the root."

==[Your whole "root" diversion is irrelevant to our discussion! Okay, so the evolutionary "tree" or "bush" or whatever metaphor a scientist might wish to use does not have a simple "trunk" where various lines of prokaryotes cleanly branch off of. So what? That was mostly a guess to begin with, and it turns out that the evolution of life is more complicated. Does that in any way, shape, or form invalidate the clear evolutionary relationships (99% of the detail in the evolutionary tree) above the trunk? Of course not! It's not about a literal tree that must have a nice trunk. It's about unimpeachable evidence for evolution, and that's exactly what the "tree" diagram shows at the multi-cellular level.]==

"And more specifically on Cytochrome C, I presented Denton’s study that highlighted the equidistance of different clades to an out group. You invoked molecular clock to explain that phenomenon, and that’s why I presented the research that severely attacks the notion of molecular clock. But instead of answering the problems it raises, you are saying that it doesn’t mention anything with respect to Cytochrome C. Why should it make any specific reference to cyctochrome c, when it attacks the very basic concept of molecular clock which includes even cytochrome c?"

==[Denton's whole concept was wrong-headed, and you are still digging deeper that hole you fell into! This diversion about molecular clocks does not in any way validate Denton's conceptual blunder. In fact, Denton's argument presupposes a working molecular clock! He was trying to exploit the mutational data for cytochrome c. Finally, where is your expertise in interpreting this article to support your extreme conclusion that molecular clocks are totally worthless? I've long been aware that molecular clocks are not perfect, but neither are they useless.]==

"So basically this is how the circular logic of evolution works. You start out with the assumption that all organisms are connected to a tree that converges on a common universal ancestor." ==[Valiya, how do you get one genetic code if life today traces back to many independent origins? The only thing that was more or less assumed was that the trunk of the evolutionary tree began at one point from which several lines of prokaryotes cleanly diverged. The rest of the "tree" (99% of the details) plainly shows the expected evolutionary relationship.]==

"The fossil evidence did not hold up. ==[Really? It's news to me! Your misunderstanding of the "Cambrian explosion" does not refute the solid fossil support for evolution, evidence that takes several directions.]== And so you turn to molecular evidence. Things were hunky-dory as you mentioned initially. But soon problems began to surface there too. There are tons of exceptions turning up to the rule." ==[DNA evidence is being used to this day to tease out evolutionary relationships, including the historical migrations of humanoids out of Africa. Data from cytochrome c (and certain other molecules) still yield magnificent versions of the evolutionary tree. These evolutionary tree patterns don't happen by chance and the general agreement between the fossil record, molecular data, and anatomical study only has one thing in common--evolution! They all reflect changes over time. There is no other explanation known.]==

"You said regarding molecular clock: 'Why shouldn't mutations statistically occur at the same rate in the SAME AREA of the cytochrome c molecule? Based on the tree model, evolutionists expect to see similar distances between bacteria and all other creatures higher up.'

How do you expect mutations to occur at the same rate in any given molecule between two different species when mutations are driven by selection pressures?"

==[Your lack of a scientific background is displayed here valiya! We're not talking about any given molecule! Cytochrome c happens to have an area where mutations can occur without affecting the function of its active site. A similar situation holds for DNA. Point mutations in those areas are neutral and are invisible to selection pressures.]==

Mon, 02/06/2017 - 03:51

(Reply to #66) #67

Valiya

Hi Greensnake

You said: ==[Your lack of a scientific background is displayed here valiya! We're not talking about any given molecule! Cytochrome c happens to have an area where mutations can occur without affecting the function of its active site. A similar situation holds for DNA. Point mutations in those areas are neutral and are invisible to selection pressures.]==

What you are saying contradicts the fundamental notions of evolution. You are saying that a mutation that is invisible to selection pressures can still enjoy selection. How can a mutation that is not selected take over the population? You are making it sound ridiculous. If things were this easy then why are evolutionists breaking their heads over finding exaptations to answer irreducible complexity? They can simply say that non-functional intermediaries were “neutral” mutations that had just happened quietly without affecting the functional areas of the DNA.

Secondly, these are not arguments that I am bringing to the table on my own. These are arguments in the peer reviewed article that I posted earlier…
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3184610/

Here is the quote that explains it:

Quote: “It has been commonly interpreted to mean a constant mutation rate, which in turn directly provoked the molecular clock hypothesis. However, this hypothesis must negate the idea of selection, the cornerstone of Neo-Darwinism. While the Neo-Darwinian selection theory has spectacularly failed the molecular test, its ad hoc substitute for the domain of molecular evolution, the molecular clock hypothesis, is also imperfect and widely known to have countless contradictions. It is also obviously incoherent or schizophrenic to have two vastly different and non-connected theories of evolution, one for phenotype evolution based on the idea of selection and the other for molecular evolution based on the negation of the idea of selection.”

The quote is there, the context is there (which is clearly debunking the molecular clock hypothesis), do you still want to turn a blind eye saying I am too ignorant to understand these things, or are you going to engage the argument seriously?

You said: “[DNA evidence is being used to this day to tease out evolutionary relationships, including the historical migrations of humanoids out of Africa. Data from cytochrome c (and certain other molecules) still yield magnificent versions of the evolutionary tree. These evolutionary tree patterns don't happen by chance and the general agreement between the fossil record, molecular data, and anatomical study only has one thing in common--evolution! They all reflect changes over time. There is no other explanation known.]==

It is exactly, this proof that I attacked using Denton’s matrix. And you dismissed it giving the molecular clock hypothesis. And I have provided you a detailed article that debunks the hypothesis. Since you are refusing to read the article and engage in an honest discussion, let me give more quotes from the article to show how emphatically the author rejects the hypothesis.

Quote: “The genetic equidistance result has been independently confirmed for numerous proteins and numerous species. This result is the most remarkable result of molecular evolution since it was completely unexpected from classical Neo-Darwinian theory. However, what has become popular known today is not the result itself but the molecular clock interpretation of it (Avise, 1994; Li, 1997; Nei and Kumar, 2000). Even the original discoverer of this result, E. Margoliash, has subsequently avoided highlighting the result. In a 1967 paper, Fitch and Margoliash compared the cytochrome c of 20 species (Fitch and Margoliash, 1967). Table 3 of the paper clearly showed the genetic equidistance result, for example, the yeast Saccharomyces has 57 mutational differences from the yeast Neurospora, 57 from monkey, 56 from human, and 58 from kangaroo. But Fitch and Margoliash did not comment on the obvious equidistance and instead concluded the opposite. “Indeed, from any phyologenetic ancestor, today’s descendants are equidistant with respect to time but not, as computations show, equidistant genetically. Thus the method indicates those lines in which the gene has undergone the more rapid changes. For example, from the point at which the primates separate from the other mammals, there are, on the average, 7.5 mutations in the descent of the former and 5.8 in that of the latter, indicating that the change in the cytochrome c gene has been much more rapid in the descent of the primates than in that of the other mammals.”

Note how the cyctochrome C mutation rate differs between primates and other mammals, when it should have been the same if the molecular clock hypothesis were true.

Next quote: Unlike the genetic equidistance result, most other independent results show that different species have different mutation rates or clock rates (Avise, 1994; Goodman et al., 1974; Jukes and Holmquist, 1972; Laird et al., 1969; Langley and Fitch, 1974; Li, 1997; Nei and Kumar, 2000). A recent study of DNA and protein sequences of ancient fossils (Neanderthals, dinosaurs, and mastodons) challenged a fundamental premise of the molecular clock hypothesis (Huang, 2008a). It shows that genetic distance had not always increased with time in the past history of life on Earth. Neanderthals are more distant than modern humans are to the outgroup chimpanzees in non-neutral DNA sequences, contrary to expectations from the molecular clock interpretation of the equidistance result (Huang, 2008a). This result of Neanderthals has been independently confirmed using protein sequences (Green et al., 2008). So, how can the molecular clock hypothesis be both correct (consistent with the genetic equidistance result) and wrong (inconsistent with results of variable clocks and ancient fossils).

You said: “Finally, where is your expertise in interpreting this article to support your extreme conclusion that molecular clocks are totally worthless? I've long been aware that molecular clocks are not perfect, but neither are they useless.]==

A layman may not understand the intricacies of the article, but anybody would be able to say that the author has debunked the molecular clock hypothesis, rather vehemently. If you say that you don’t get it, then I really doubt your ability to grasp English language.

Here is what the author says in the Conclusion part of the article:

“The equidistance result could trigger many interpretations but the idea of constant mutation rate has become the most popular. However, there is no independent evidence for it other than the equidistance result that originally provoked it. It is merely a tautology. The observation of frequent violations of the constant mutation rate has misled many to automatically assume that there is no equidistance result in many cases. The study here establishes the fact that the equidistance result is extremely robust and universal that is independent of variation in mutation rates. The equidistance result shows the outcome of evolution but does not directly reveal any information about the actual mutation process in the past history of life on Earth. New ideas are needed to explain the equidistance result that must grant different mutation rates to different species and must be independently testable.”

Note, he calls the molecular clock hypothesis a “mere tautology’ which is a serious logical fallacy. To call a hypothesis a tautology is the worst insult you can think of heaping on it.

You said: “"The fossil evidence did not hold up. ==[Really? It's news to me! Your misunderstanding of the "Cambrian explosion" does not refute the solid fossil support for evolution, evidence that takes several directions.]==

That’s news to you because you have to take out your blinkers and prepare to read the research papers for what they are, instead of dismissing anything that even remotely critiques Darwinism as creation biased. Let me request you once again… please present your arguments, instead of making emphatic statements. Do you have proof to show that Cambrian fossils have precursors, then bring it up here please.

You said: ==[Your whole "root" diversion is irrelevant to our discussion! Okay, so the evolutionary "tree" or "bush" or whatever metaphor a scientist might wish to use does not have a simple "trunk" where various lines of prokaryotes cleanly branch off of. So what? That was mostly a guess to begin with, and it turns out that the evolution of life is more complicated. Does that in any way, shape, or form invalidate the clear evolutionary relationships (99% of the detail in the evolutionary tree) above the trunk? Of course not! It's not about a literal tree that must have a nice trunk. It's about unimpeachable evidence for evolution, and that's exactly what the "tree" diagram shows at the multi-cellular level.]==

If the trunk is missing that means a long chunk of evolutionary history is missing. We just have guesses to fill that gap. And coming to your branches which is just a sprout emerging from a mountain of messy web, it is riddled with problems too. The way you are dancing around the problem of cytochrome c and molecular clock is a case in point. Add to it the orphan genes… evidence after evidence is mounting up against the tree of life.

And if you are thinking of taking heart from the fact that HGT’s have just corrupted the signals in the trunk, wait before you read this article. There is growing evidence to show that even among higher animals, gene transfer is the rule rather than the exception. Check this link.

http://www.sciencemag.org/news/2015/03/humans-may-harbor-more-100-genes-...

You said: ==[Some of the "Cambrian explosion" fossils DO HAVE reasonable precursors! Given the fact that boneless, shell-less creatures rarely get preserved, it's not hugely surprising that many precursors are unknown 500 million years later.”

Can you provide some proofs of that… however you have qualified your statement by giving reasons as to why fossils can’t be found. The reasons why something doesn’t exist is not proof of its existence.

You said: “If you want to get a fast update on the fossil record, read Dr. Donald Prothero's book "Evolution: What the Fossils Say and Why it Matters."

Thanks for suggesting the book. But I would also expect you to engage in some serious arguments in a discussion of this nature. We can go on endlessly exchanging names of books… but that would not serve the purpose of this forum very much, would it? Give me an outline of the arguments in that book, and I will give you my counter arguments.

You said: ==[Valiya, why do you continue saying that noise is least expected at the tips of the tree? An area of slight difference is exactly where the noise is most bothersome! Minor differences in the evolutionary tree hardly refute the concept of the evolutionary tree, especially since that concept was used in demonstrating those differences!]==

Two points here. Chimps and humans are extremely closely related… and mapping our ancestry to a common ancestor should be the easiest. That’s what we would expect. But in a case of yet another twist in the tale, lo we find noise there as well.

Secondly, I have already mentioned that the purpose of that example is not to topple the tree wholesale. But to show the nagging problems… cumulatively they all add up to make anyone seriously reconsider the theory. So your appeal to the whole tree being intact is not very logical. Especially, now that you have agreed that the trunk and root are gone. And all you are left with is a small sprouting of branches, which too are running into problems.

I think the important part of my arguments end here. The rest are just responses to some of your other criticisms which I think is not at the center of our discussion.

You said==[Without a scientific background, valiya, you are hardly in a position to decide what constitutes an "outrageous" explanation. Are you accusing scientists (and myself) of not being honest with the evidence? Given that you are ignorant in this area, just maybe you are grabbing onto things that are really no threat to the concept of an evolutionary tree or bush. Isn't that a better explanation than assuming dishonesty or stupidity on the part of scientists? After all, they are the ones who have put in years of high-level study, not yourself, and they are very much interested in discovering the truth!]==

I am not the one who is saying it is outrageous. Experts are saying so. Take for example the article on molecular clock. The author calls it a ‘tautology’… outrageous would have been a more polite word.

You said: ==[You are mistaken, valiya. You are thinking of mathematics where that is very true, indeed! It's no accident that your Kepler example is mathematical in essence. In general, science often deals with imperfect data, statistical analysis (where the highly probable is not necessarily the actual), and theories that may be simplified conceptions that are usually made stronger by minor adjustments.

You think so? Here is what the same article on molecular clock has to say on the subject: ““In mathematics or physics, one exception is sufficient to doom any theory. The science of biology or any scientific discipline for that matter should not be held to a lower standard. When one allows exceptions, one has effectively rendered the theory non-testable and non-scientific. Such a theory would be no different from a false theory that happens to explain a fraction of nature while being contradicted by the rest. The only way to distinguish a true theory from a false or incomplete one is to see if it has not a single factual exception within its domain of application or relevance.”

Wed, 02/08/2017 - 23:12

(Reply to #67) #68

Dave Matson

Hi valiya:

"You said: ==[Your lack of a scientific background is displayed here valiya! We're not talking about any given molecule! Cytochrome c happens to have an area where mutations can occur without affecting the function of its active site. A similar situation holds for DNA. Point mutations in those areas are neutral and are invisible to selection pressures.]=="

"What you are saying contradicts the fundamental notions of evolution. You are saying that a mutation that is invisible to selection pressures can still enjoy selection."

==[The mutations simply accumulate in these areas like craters on the moon. They are neither selected for nor against by evolution, that's why they are called neutral mutations!]==

"If things were this easy then why are evolutionists breaking their heads over finding expatiations to answer irreducible complexity?" ==[Valiya, the scientific community has dismissed "irreducible complexity" a long time ago! It's not part of a SCIENTIFIC debate.]== "They can simply say that non-functional intermediaries were “neutral” mutations that had just happened quietly without affecting the functional areas of the DNA." ==[I have no idea what you are trying to say here!]==

"Secondly, these are not arguments that I am bringing to the table on my own. These are arguments in the peer reviewed article that I posted earlier… ==[I give you credit for quoting a peer-reviewed paper.]==
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3184610/
Here is the quote that explains it:
Quote: 'It has been commonly interpreted to mean a constant mutation rate, which in turn directly provoked the molecular clock hypothesis. However, this hypothesis must negate the idea of selection, …'" ==[How does selection act on neutral mutations?]==

==[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. Yes, when molecular data goes beyond tree branching and attempts to establish times of divergence, becoming a "molecular clock" as it were, various pitfalls do exist. But that doesn't mean that the molecular clock is no good. Here is what Wikipedia has to say under "Molecular Clock."]==

==['Molecular clock users have developed workaround solutions using a number of statistical approaches including maximum likelihood techniques and later Bayesian modeling.'

'The molecular clock technique is an important tool in molecular systematics, the use of molecular genetics information to determine the correct scientific classification of organisms…' I.e., the branching pattern of the evolutionary tree.]==

==[Dr. Simon Ho (a separate source from Australia National University) reached this conclusion at the end of a very instructive article:

'Over its lifetime, the clock has successfully negotiated its way through numerous challenges, undergoing various refinements and improvements, and it thus remains an important tool in evolutionary biology. Moreover, with the rapid accumulation of new genetic data, particularly as a result of the many genomic sequencing projects that are currently underway, it seems that the molecular clock will continue to shed light on the tempo and timescale of evolution for years to come.']==

==[Under the same key phrase "Molecular Clock," indeed the very first topic in the Wikipedia article, the blunder that Denton made with his cytochrome c argument is exposed by the correct interpretation of the genetic distances. You seem determined to defend Denton's blunder to the death! Do read that first topic and note that the data Denton claimed refuted the evolutionary tree are actually PREDICTED by it.]==

"The quote is there, the context is there (which is clearly debunking the molecular clock hypothesis), do you still want to turn a blind eye saying I am too ignorant to understand these things, or are you going to engage the argument seriously?" ==[I think we have yet another example of why lay readers should be careful about interpreting scientific papers! My quotes above, which could be backed up by dozens of other authorities if necessary, show that the molecular clock is still a useful tool. It has not been debunked.]==

"It is exactly, this proof that I attacked using Denton’s matrix. And you dismissed it giving the molecular clock hypothesis. And I have provided you a detailed article that debunks the hypothesis. Since you are refusing to read the article ==[Maybe I just don't agree with your interpretation of it.]== and engage in an honest discussion, let me give more quotes from the article to show how emphatically the author rejects the hypothesis."

==[Valiya, in my last post I pointed out that Denton's matrix ASSUMES the validity of a molecular clock!! His entire argument would make no sense at all if the number of mutations didn't uniformly correspond to time! In its very first topic under "molecular clock," Wikipedia gives the CORRECT interpretation of data found in Denton's matrix. I gave you the reasons earlier, so I won't repeat myself. How much deeper are you going to dig this hole you are in? Before you accuse someone of a dishonest discussion, you really should double-check your own facts and arguments!]==

"You said: 'Finally, where is your expertise in interpreting this article to support your extreme conclusion that molecular clocks are totally worthless? I've long been aware that molecular clocks are not perfect, but neither are they useless.]==
A layman may not understand the intricacies of the article, but anybody would be able to say that the author has debunked the molecular clock hypothesis, rather vehemently. If you say that you don’t get it, then I really doubt your ability to grasp English language."

==[I guess a lot of scientists don't get your conclusion from that paper either, judging by the quotes I gave above. Would you like some more quotes?]==

"Here is what the author says in the Conclusion part of the article:
'…The equidistance result shows the outcome of evolution but does not directly reveal any information about the actual mutation process in the past history of life on Earth. New ideas are needed to explain the equidistance result that must grant different mutation rates to different species and must be independently testable.”
Note, he calls the molecular clock hypothesis a “mere tautology’ which is a serious logical fallacy. To call a hypothesis a tautology is the worst insult you can think of heaping on it." ==[Valiya, please explain carefully the "molecular clock hypothesis" and then tell us why the author considers it a tautology. We can compare notes and maybe learn something about interpreting a scientific paper.]==

"Let me request you once again… please present your arguments, instead of making emphatic statements. Do you have proof to show that Cambrian fossils have precursors, then bring it up here please."

==[Valiya, I can't help but point out that it's such a common fact that you can throw a stone on the Internet and, if it lands on a scientific-based website about the "Cambrian explosion," then you will learn about soft-bodied life before the Cambrian! Give it a try! I did, and I even skipped the usual Wikipedia site, landing on "biologos.org/common-questions/scientific-evidence/cambrian-explosion". Here's what it 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)" ]==

==[Footnotes:
"7. M.A. Fedonkin, “Vendian faunas and the early evolution of metazoa,” In, J.H. Lipps and P.W. Signor (eds.), Origin and Early Evolution of the Metazoa (New York: Plenum Press, 1992), p.87-129. G.M. Narbbonne, M. Laflamme, C. Greentree, and P. Trusler, “Reconstructing a lost world: Ediacaran rangeomorphs from Spaniard’s Bay, Newfoundland,” Journal of Paleontology 83, no. 4 (2009): 503-523.

8. David Campbell and Keith Miller, “The ‘Cambrian Explosion’: A Challenge to Evolutionary theory?”
- See more at: http://biologos.org/common-questions/scientific-evidence/cambrian-explos..."]==

"If the trunk is missing that means a long chunk of evolutionary history is missing." ==[Please explain how a messy (not missing) trunk invalidates all the upper branches?]== ... And coming to your branches which is just a sprout emerging from a mountain of messy web, it is riddled with problems too. ==[More than just a "sprout," valiya! It's everything we knew about plant and animal relationships before we could pry into the secrets of bacteria--and it unequivocally gives the evolutionary tree! That didn't happen by accident!]==

"The way you are dancing around the problem of cytochrome c and molecular clock is a case in point." ==[Who's doing the dancing, valiya? You just keep digging away in that pit, getting deeper and deeper instead of escaping! (See above.)]==

"And if you are thinking of taking heart from the fact that HGT’s have just corrupted the signals in the trunk, wait before you read this article. There is growing evidence to show that even among higher animals, gene transfer is the rule rather than the exception. Check this link..." ==[Is that why DNA and certain molecules like cytochrome c work so well in giving us the evolutionary tree? We do get evolutionary trees, valiya, and they bear a remarkable resemblance to each other! 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.]==

"You said: “If you want to get a fast update on the fossil record, read Dr. Donald Prothero's book "Evolution: What the Fossils Say and Why it Matters."
Thanks for suggesting the book. But I would also expect you to engage in some serious arguments in a discussion of this nature." ==[I'm under the impression that I have refuted all your points, valiya! What more do you require?]==

"We can go on endlessly exchanging names of books… but that would not serve the purpose of this forum very much, would it?" ==[How many books have I mentioned? A couple? I offer them either as reference reading for yourself or to document accepted, scientific opinion. They are not intended as substitutes for arguments and facts.]==

"Chimps and humans are extremely closely related… and mapping our ancestry to a common ancestor should be the easiest. That’s what we would expect. But in a case of yet another twist in the tale, lo we find noise there as well." ==[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.]==

"Secondly, I have already mentioned that the purpose of that example is not to topple the tree wholesale. But to show the nagging problems… cumulatively they all add up to make anyone seriously reconsider the theory. ==[Who, outside of creationists, for example? Can you name one, major university or one leading refereed scientific journal that has reconsidered the fact of evolution?]== So your appeal to the whole tree being intact is not very logical. ==[Logical enough to agree with comparative anatomy and the fossil record, logical enough to prove evolution!]== Especially, now that you have agreed that the trunk and root are gone.

==[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). That common ancestor, the single species that gave rise to all of life, existed some 3.5 to 3.8 billion years ago." (Evolution: The First Four Billion Years - edited by Michael Ruse and Joseph Travis), p.84]==

"You said==[… Given that you are ignorant in this area, just maybe you are grabbing onto things that are really no threat to the concept of an evolutionary tree or bush. Isn't that a better explanation than assuming dishonesty or stupidity on the part of scientists?]==
I am not the one who is saying it is outrageous." ==[Yes you are, valiya! It may not be obvious to you, but you are applying your own interpretation which usually goes far beyond what that scientist is saying. Problems with the molecular clock (essentially worked around these days) turn into reasons for rejecting the clocks altogether! Confusion about the "trunk" of the evolutionary tree turn it into a dead tree!]==

"You said: ==[You are mistaken, valiya. You are thinking of mathematics where that is very true, indeed! It's no accident that your Kepler example is mathematical in essence. In general, science often deals with imperfect data, statistical analysis (where the highly probable is not necessarily the actual), and theories that may be simplified conceptions that are usually made stronger by minor adjustments.]=="

"You think so? Here is what the same article on molecular clock has to say on the subject: ““In mathematics or physics, one exception is sufficient to doom any theory. The science of biology or any scientific discipline for that matter should not be held to a lower standard. When one allows exceptions, one has effectively rendered the theory non-testable and non-scientific."

==[I am sorry to hear this nonsense from a scientist. Maybe Shi Huang had a bad day and was careless. It happens all the time among the tens of thousands of scientists speaking under all conditions, some of whom are not up to speed on the philosophical basis of science! And, of course, that one quote, whether careless or ignorant, will be picked up by creationist quote hunters who invariably use it out of context.

Since you seem dazzled by his "authority" on philosophical matters, let me list several reasons why a promising theory might contradict a "fact." 1) The theory may be incomplete and need minor adjustments; 2) The theory may be incorrectly applied; 3) There may be bad numerical data leading to a false conclusion; 4) There may be an undetected, systematic error in the equipment; 5) The data set may be too small or reflect hidden biases in its collection; 6) The data may be good, and the equipment may be good, but there might be an error in laboratory procedure; 7) Where animals or people are tested, expectations and unconscious clues from the researcher may wrongly suggest a failure of the theory. Most successful theories ARE in contradiction with at least some facts at times. It all depends on the contradiction. Most are inconsequential; a few are fundamental. It comes down to good scientific judgment, the one thing the lay reader seriously lacks.]==

Fri, 02/10/2017 - 11:54

(Reply to #68) #69

Valiya

HI Greensnake

You 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, which is that intermediate mutations enjoyed selective advantage because they served some other function different from what they are doing now. However, according to your molecular clock hypothesis a mutation can get selected even when it is neutral (non-functional) and accumulate at a constant rate over a period of time. It’s really not about whether irreducible complexity is accepted or rejected, but rather that the clock hypothesis contradicts the fundamental idea of evolution.

When I posted, "They can simply say that non-functional intermediaries were “neutral” mutations that had just happened quietly without affecting the functional areas of the DNA” you said==[I have no idea what you are trying to say here!]==

If you say that mutations can simply build up irrespective of whether they enjoy selection or not, then in order to dismiss irreducible complexity, evolutionists need not have taken recourse to ‘exaptation’… they could have simply invoked neutral mutation.

You said: ==[How does selection act on neutral mutations?]==

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.

You 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.

You said: Here is what Wikipedia has to say under "Molecular Clock."]== 'The molecular clock technique is an important tool in molecular systematics, the use of molecular genetics information to determine the correct scientific classification of organisms…' I.e., the branching pattern of the evolutionary tree.]==

It is exactly this attitude that Shi Huang was addressing in his article. He says that ‘molecular clock’ is a derived assumption based on molecular equidistance between organisms. And when they find non-equidistance, they attribute it to the difference in time scales, even while other evidences such as fossils point in the other direction. The author had cited many examples where this dissonance exists. 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!

You said: ==[Under the same key phrase "Molecular Clock," indeed the very first topic in the Wikipedia article, the blunder that Denton made with his cytochrome c argument is exposed by the correct interpretation of the genetic distances. You seem determined to defend Denton's blunder to the death! Do read that first topic and note that the data Denton claimed refuted the evolutionary tree are actually PREDICTED by it.]==

I didn’t find it… please copy paste the URL. Moreover, the main crux of the answer to Denton is based on molecular clock, which I have shown is just a tautology.

You said: ==[I think we have yet another example of why lay readers should be careful about interpreting scientific papers! My quotes above, which could be backed up by dozens of other authorities if necessary, show that the molecular clock is still a useful tool. It has not been debunked.]==

If you think my interpretation of it is wrong, then please give quotes from Shi Huang’s paper and prove to me that my interpretation is wrong. He particularly criticizes evolutionists who support the hypothesis in the paper. I have given you examples and quotes from it. Just because there are many scientists who think one way, it doesn’t mean no other scientist can differ with them. When Jay Gould came up with his PET theory, many were against it. If someone had thought like you back in those days, they would have interpreted PET as adding strength to gradualism because a majority of scientist was still supporting gradualism. That’s why I am appealing to you to engage the argument instead of dabbling in genetic fallacy.

You said: ==[Valiya, in my last post I pointed out that Denton's matrix ASSUMES the validity of a molecular clock!! His entire argument would make no sense at all if the number of mutations didn't uniformly correspond to time!”

You are indulging in circular reasoning big time! Not surprising because that’s what the whole hypothesis is founded on – as Shi Huang rightly called it ‘tautology.’ If Denton had assumed the validity of molecular clock, then he should NOT have been very surprised with his findings. He 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. In order to answer him, evolutionists invoked the ‘molecular clock’. So the clock is not an assumption Denton starts off with, rather it is the answer to his criticism.

And you are going in circles because you assume that equidistance occurs due to the ‘clock’ and since Denton noticed equidistance, it must have meant ‘clock’ to him. But equidistance does not prove the clock. It is only an assumption evolutionists make.

You said: ==[Valiya, please explain carefully the "molecular clock hypothesis" and then tell us why the author considers it a tautology. We can compare notes and maybe learn something about interpreting a scientific paper.]==

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.

Now let me explain why Shi Huang thinks it is a tautology. He says that the only verifiable fact in this whole scheme of things is genetic equidistance. We can factually conclude that organism A and organism B are equally distant from organism C. But there is no way we can verify if this has happened because mutations in them accumulated at a constant rate. Moreover, several organisms that we know from fossil records and other evidences to have shared the same evolutionary time are NOT genetically equidistant. In other words, molecular clock is invoked whenever there is genetic equidistance between organisms, but it has NO explanatory power to further our understanding on the phenomenon.

A tautology basically means to use two words that mean the same thing without adding anything to the meaning. Like for example an ‘evening sunset’ (sunsets have to be in the evening, right). Molecular clock simply means two organisms that are genetically equidistant, that’s all… it does not add any further meaning to the idea of equidistance. There is no way to verify molecular clock hypothesis nor does it have any explanation for the cases that contradict it.

Shi Huang even gives an analogy to explain it further. Here it is: “The tautology fallacy of the constant mutation rate interpretation can be illustrated by a simple example. Two turtles and a rabbit are running a 1-mile race. No one watches the race and one is only informed of the race result by a video camera aimed at the finish line. The result of the race is that the turtles and rabbit arrive at the finish line at approximately the same time in 1 hour. To explain this fact, one can deduce from the fact the same speed hypothesis. One can also deduce from the fact many other hypotheses such as ‘God did it’. To determine which hypothesis is correct, one must perform independent tests of the predictions of each hypothesis. For it to be a true explanation and not a tautology, the same speed hypothesis or any other hypothesis must be backed up by independent evidence. Of course, any independent tests of running speed would reveal that the two turtles have similar speeds while the rabbit is much faster. After performing such independent tests, one can conclude that the same speed hypothesis is likely a true explanation for the two turtles but cannot be true for the rabbit. The hypothesis is a real explanation for the two turtles but is merely a tautology for the rabbit.”

You 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.

http://www.nature.com/nature/journal/v493/n7430/abs/nature11777.html

Also, by this, you are contradicting your earlier claim that the Precambrian fossils are not preserved because they were soft bodied. So, if soft bodied creatures have been preserved then the vast gap in the fossil records will continue to be a headache for evolution. That is the reason that the ‘developmental evolution’ proponents have appropriated the Cambrian explosion in support of their theory. They think only ‘evo devo’ can explain the sudden emergence all the body plans of the major phyla (in other words, the precursors are missing because these forms evolved really quickly through developmental evolution).

You said: ==[Please explain how a messy (not missing) trunk invalidates all the upper branches?]== ...

I am trying to show to you how one by one the different parts of the tree are running into trouble. The root and the trunk doesn’t make any more sense for the evolution theory (so it doesn’t matter whether they are there or gone), and the upper branches have problems that contradict the expectations of the tree… convergence, genetic equidistance, genetic noise even in closely related branches are examples of the problem.

You said: ==[Is that why DNA and certain molecules like cytochrome c work so well in giving us the evolutionary tree? We do get evolutionary trees, valiya, and they bear a remarkable resemblance to each other!”

You keep insisting cytochrome c works so well… but it works only by invoking the ‘tautological’ molecular clock, which begs for a new explanation for genetic equidistance, a phenomenon that was totally unexpected in the Darwinian tree of life. So your insistence that the tree is fine would be right only if you are willing to wink at all the exceptions that are mounting. But then again you have your scientific philosophy that biology can’t be held to the high standard of physics.

You 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. LUCA is no longer an organism but a community… the trunk has become a web…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.’

You 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. I don’t deny the fact that there are many scientists who are trying hard to do everything in order to protect this theory. So, it’s not very surprising you are able to bring the kind of proofs you have shown. 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. So, I am expecting you to bring me answers to the problems they have raised. What’s the point of you bringing me a Wikipedia article about molecular clock that’s discussing an issue about divergence of life? My contention is that molecular clock hypothesis is a tautology because there are many observations that contradict this hypothesis as highlighted by Shi Huang. The examples are there. Have evolutionists tried to explain those contradictions? If there is no explanation, don’t you think that’s a serious problem?

You said: ==[Who, outside of creationists, for example? Can you name one, major university or one leading refereed scientific journal that has reconsidered the fact of evolution?]==

I think I had made it very clear to you where I am coming from. I am arguing that there are many serious internal contradictions in the evolution theory. And I have been furnishing the proofs of those problems raised by evolutionist themselves. 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. But that’s another debate.

You 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. You then believe that this assumption is a fact. Therefore, when you see even a thousand evidences that contradict this assumption, you overlook all that because the assumption has ossified into a fact in your mind. (When I say you, I am talking about evolutionists). 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? No, no, the evolutionist would explain, after all it’s a fact that similarity arises from common ancestry. So he keeps that fact (assumption) intact in all situations, except where it doesn’t fit the evidence, in which case he would fall back on other explanations. Do you see the circularity of reasoning there?

You said: “That common ancestor, the single species that gave rise to all of life, existed some 3.5 to 3.8 billion years ago." (Evolution: The First Four Billion Years - edited by Michael Ruse and Joseph Travis), p.84]==

Single species? Carl Woese might beg to differ with you. He says it was a community, because the genes tell a story of a mixture of different genetic contents that have given rise to all the novelties that we see today.

I have shown to you and explained above that it’s a credible scientist who thinks that some of the theories in evolution are mere fallacies. I really don’t know why you can’t see it in that article. It has been so precisely spelt out. So if you have anyone to blame it is the scientists themselves, not me.

You said: “==[I am sorry to hear this nonsense from a scientist. Maybe Shi Huang had a bad day and was careless. It happens all the time among the tens of thousands of scientists speaking under all conditions, some of whom are not up to speed on the philosophical basis of science! And, of course, that one quote, whether careless or ignorant, will be picked up by creationist quote hunters who invariably use it out of context.”

This typically underlines your ostrich mentality. You are talking about a peer reviewed article and where it differs with your point of view, you so frivolously dismiss it as a ‘bad day’ for the scientist. I think you still have not given the paper a good read. This is not some sort of an afterthought he added at the foot of his paper. He in fact starts out by making this statement on science, because the entire paper is premised on this argument… he undermines the clock hypothesis primarily by underlining the exceptions to it. And he says these exceptions render the hypothesis weak. He goes on to say that if biology as a science should be exempted from the standard of exceptions, then it would make its hypotheses and theories unfalsifiable.

Tue, 02/14/2017 - 18:21

(Reply to #69) #70

Dave Matson

My apologies to those who are

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.

Fri, 02/17/2017 - 04:11

(Reply to #70) #71

Valiya

Hi Greensnake

It’s a little frustrating when you raise a challenge and I provide a detailed answer, you simply move on to the next challenge without engaging the arguments. You had challenged me to prove from Shi Huang’s paper that molecular clock is a tautology. I had done that. I want you to give your feedback on that. Either prove that my interpretation is wrong, or concede that point to me. Once you do that, we will move further. I will surely come back on all the points you raised in your last post. But let’s get the first points out of the way.

Fri, 02/17/2017 - 04:43

(Reply to #71) #72

Nyarlathotep

valiya s sajjad - For it to

valiya s sajjad - For it to be a true explanation and not a tautology, the same speed hypothesis or any other hypothesis must be backed up by independent evidence.

For what it is worth, that is actually wrong. It is very easy to come up with a "true explanation" that is a tautology, that doesn't require any independent evidence: they finished at the same time because they had the same average velocity. You can take that to the bank! :P
---------------------------------
And let me get this straight: they have a gross approximation method, that works OK for some thing and not for others; and your complaint is that they use it on the things it works for?...

Fri, 02/17/2017 - 14:11

(Reply to #72) #73

Dave Matson

Hi valiya:

"It’s a little frustrating when you raise a challenge and I provide a detailed answer, you simply move on to the next challenge without engaging the arguments. You had challenged me to prove from Shi Huang’s paper that molecular clock is a tautology. I had done that. I want you to give your feedback on that."

==[Actually, I asked you to explain Shi Huang's argument since I wasn't taking a technical stand. I can see where he is coming from with his tautological statement which would be logically correct if you restricted yourself to a narrow viewpoint which seemed to be his concern, but in the light of actual workarounds the conclusion is irrelevant to our own discussion. 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. 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.

Therefore, your attempt to discredit molecular trees on the basis of Shi Huang's quote is wrongheaded. Those evolutionary trees are here to stay, and the only thing remaining to discuss is how to interpret them. I pointed out that the straightforward, natural interpretation is that they record time in various ways. 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.

Sun, 02/19/2017 - 02:53

(Reply to #73) #74

Valiya

Hi Greensnake

YOU SAID: ==[Actually, I asked you to explain Shi Huang's argument since I wasn't taking a technical stand. I can see where he is coming from with his tautological statement which would be logically correct if you restricted yourself to a narrow viewpoint which seemed to be his concern, but in the light of actual workarounds the conclusion is irrelevant to our own discussion.”

Therefore let me conclude that you concede that my interpretation of Shi’s paper is correct. Thank you. Regarding your opinion that Shi restricts his attack of molecular clock to some ‘narrow view’, I DO NOT think so. He attacks the hypothesis wholesale.

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.

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. So it is quite baseless for you to reiterate your first argument about how the clock corroborates the tree and so on… these have been called into question by some researchers. You will have to answer the problems raised by Shi.

The fundamental problem with your line of reasoning is that instead of presenting arguments you are simply asking me accept your assumptions because they are coming from reputed institutions or scientists. I want you to first present the full line of argument and then give your sources as proof with due links. I will further show you how you are indulging in this genetic fallacy in the points below.

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. I would like to hear your explanation of those differences. I can cite many evolutionists who have raised these issues and feel that this is quite a SERIOUS problem. Are you saying that these exceptions should be overlooked for the larger picture? Then I beg to differ. If you say that these exceptions have been explained, please present those explanations (I REQUEST YOU TO PRESENT THE ACTUAL ARGUMENTS - NOT SWEEPING GENERALIZATIONS LIKE ‘MOST SCIENTISTS FEEL SO THEREFORE I SHOULD AGREE WITH THEM’)

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. In some cases the fossils agree with the assumption. IN some cases the fossils DON’T agree. Therefore, it really has no explanatory power. This is what Shi has been arguing.

Now coming to your points in your first posts.

Before I take your points, let me give a general outline of what I think is fundamentally wrong with your arguments.

You are digressing into sideline issues, and are looking away from the central arguments I presented. You need not have wasted so much time on ‘irreducible complexity’ as that was just a simple example I gave to attack the molecular clock/neutral mutation hypothesis. My line of argument was something like this: irreducible complexity is refuted by using exaptation – which is based on the mainstream Darwinian theory of selection – 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.’ Exaptation was just an example I gave for the Darwinian mechanism. So your refutation of irreducible complexity doesn’t add much to our discussion. Hope that’s clear.

YOU SAID==[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.]==

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. Here is another paper that refutes neutral mutation. Check this out. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3032973/

And this is what another research paper says: “Although numerous theoretical, comparative, and experimental studies have long treated the mutation rate as a static quantity for a given organism or species, the overwhelming evidence, as presented in this article, is that mutation rates cannot be considered constant, even within a genome.”

For the full article check out this link: https://academic.oup.com/mbe/article/20/12/2091/978568/Neutral-Mutations...

YOU SAID==[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?]==

You keep insisting cytochrome c works well, while I have shown you that not all evolutionists think so. Cytochrome c works only if neutral mutation/clock hypothesis is right. But is it? That’s the question we have to first sort out.

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.

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. I have not seen you refute Shi’s arguments still. I can see that you are shuffling your feet now – first you said my interpretation of Shi is wrong, and now you seem to be hinting that Shi himself could be wrong. This despite the fact that he made his case in a peer-reviewed paper. To put it simply, Shi says there are many cases where the clock hypothesis doesn’t match the evidence (for example fossil records). Do you have any research papers where scientists have explained these exceptions? If you have them, please bring them on. Or are you arguing that biology can’t be held to the high standard of physics and so the exceptions should not be made a big issue out of. Make your position clear.

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. Take for example irreducible complexity, which you had belabored on in your last post. You invoke exaptation by showing a few examples of parts that are primitive precursors. IN that case it’s to do with descent with modification. But when it comes to the camera eyes between humans and octopus, it’s not descent with modification, but it’s convergence. One would be justified in asking why can’t the so called exaptations also be a sort of convergence instead of being descent with modification? What is your basis to assume that one is descent and the other is convergence…. it’s just assumption nothing more than that. This unfalsifiable assumption is at the center of the evolution theory. It’s true that there is no naturalistic explanation for life yet – and evolution theory pretends to fill that gap largely based on assumption, and hence the assumption is treated as if it’s some sacrosanct scientific theory.

YOU SAID: ==[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.]==

Look, even ‘natural selection’ is very useful (or was useful) in explaining a lot things. However, now neutralists are arguing that the selection has very minimal role in evolution. (In fact, they are putting forth the same kind of argument that creationists once made against evolution… that the power of selection to select minor changes that are too insignificant to be in the radar of selective forces is questionable). SO much for your claims of scientific usefulness of a hypothesis!

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. You first claimed that Denton began by assuming the molecular clock. To counter that I explained that he was surprised to find the equidistance between yeast and horse, precisely because he did not accept the clock hypothesis. If he had, there is no need for any surprise. And then you came back explaining why Denton should not have been surprised, because molecular theory predicts it. This is such circular reasoning. Are you saying that Denton accepts the clock (in which case he should not have been surprised) or that he does not accept the clock (in which case his surprise would be justified)?

YOU SAID==[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!]==

This is another example of your going in circles. I explained the molecular clock because you challenged me to explain it and interpret why Shi thinks it is a tautology. You just took the first part of my answer and assumed that I was in agreement with it and even misused it to establish your case against denton– but no, immediately after that explanation I go on to prove why it is actually a tautology. But you ignored that part fully. Now, of course, after I particularly brought your attention to that gap, you have given me your feedback.

YOU SAID==[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.]==

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.

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. Even the weak excuse of showing some multicellular life forms to make a sweeping extrapolation to Cambrian precursors don’t really hold up. Because scientists now feel the Ediacaran forms are not Cambrian fauna ancestors.

YOU SAID: “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.”

I didn’t say you said ‘It’s Impossible”…. here is what I stated: “Also, by this, you are contradicting your earlier claim that the Precambrian fossils are not preserved because they were soft bodied.” Anyways… what I am drawing your attention to is the vast latitude you have at your disposal to invoke chance for any evidence that can possible turn up. 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.

YOU SAIDL “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.”

Then why did you bring it up as an evidence in the first place? I was only responding to what you brought forth.

YOU SAID: “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.]==

That’s the assumption I am referring to. Since something cannot come out of thin air, let’s just assume that Cambrian fossils had primitive ancestors. If we find the missing links, well and good – but if we don’t find them, well let’s just blame it on the unfavorable factors for fossilization – after all we know that primitive ancestors did exist because it is a FACT, right?

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?

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? Exaptation? None of these are observed facts… all these are elliptical assumptions made from other observed facts. You just find that a chimp is like a man… therefore you assume that we are related. You just find that a bacteria is equidistant from yeast and horse, and from that you assume constant mutation rate… I hope you get my point. So, you really need to rethink who is in some fantasy world.

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.

YOU SAID: ==[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.”

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. While we are still grappling with how one cell could have emerged fortuitously, here we are invoking a community. Yes, once you have that community all that you say about interbreeding and all that could have occurred. 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?

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’? You are playing a cat and mouse game…. please engage the arguments.

YOU SAID==[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.]==

Not at all. A design-based worldview will be even more effective because then you can think of drawing up as many different trees you want based on various features – and yet not be guilty of contradiction because you are not driven by any dogmatic assumptions of common ancestries.

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!

Sun, 02/19/2017 - 15:35

(Reply to #74) #75

Alembé

Hi Valiya,

Forget the fancy philosophy, I can demonstrate evolution in my lab.
Take a pure culture of bacteria that is completely killed by, say 50 ug/ml (micrograms per milliliter) of an antibiotic.
Split culture into two and freeze down one half.
Starting with very low concentrations of antibiotic (say 0.001 ug/ml) grow the other culture in slowly increasing amounts of antibiotic, passaging the bacteria into new media every few days and slowly increasing the antibiotic concentration.
After a period of time, possibly weeks or months, the culture grown in the presence of increasing antibiotic will evolve to have greater tolerance for that antibiotic to where it can grow in that killing concentration of 50 ug/ml, i.e. it will become resistant. It will have evolved new biochemical mechanism(s) to resist and/or detoxify the antibiotic.

There, evolution demonstrated in the lab. Q.E.D.

Is this relevant to everyday life? Ask the relatives of people who have died from MRSA - Methicillin-resistant Staphylococcus aureus - something that did not exist 60 years ago but evolved under the pressure of antibiotic use and abuse.

Sun, 02/19/2017 - 15:49

(Reply to #75) #76

Nyarlathotep

You see Alembe, you are

You see Alembe, you are clearly part of the conspiracy. You just exposed yourself! Remember we have it on valiya s sajjad's "authority" that not a single nucleotide can change!

valiya s sajjad - So far, there is no known example in the living world of any mutation that causes an increase in information by even a single nucleotide.

Sun, 02/19/2017 - 16:25

(Reply to #76) #77

Alembé

Hi Nylar,

I'm going to wait a bit and then throw out the complication that different species of bacteria exchange antibiotic resistance genes horizontally by plasmids, etc. thereby totally bypassing all that parent to offspring heredity stuff. Ooops, too late!

Mon, 02/20/2017 - 00:17

(Reply to #77) #78

Valiya

HI Alembe

I think, i had already answered this point. This kind of resistance arises through a degradation of biological information. Therefore, this cannot be extrapolated to explain the rise of complex genetic information through mutation + selection.

Mon, 02/20/2017 - 00:49

(Reply to #78) #79

Nyarlathotep

I love how valiya s sajjad

I love how valiya s sajjad just mixes up the adjectives to try to make a new idea so it will be resistant to past evidence he's been shown. Think about it: what is the difference between "complex genetic information" and "genetic information"? Probably nothing (who knows, he won't define the terms in a way were they can be objectively sorted). This then allows only him to sort any inconvenient facts away from his claims.

Mon, 02/20/2017 - 08:11

(Reply to #79) #80

Alembé

Hi Valiya,

So, you won’t accept developing antibiotic resistance by modifying one’s DNA as evolution, claiming that it involves “degradation of biological information.”

Therefore, let us go and steal some genes, add some genes from another organism, incorporate them into our DNA, thereby “upgrading” our biological information.

I propose stealing some DNA from a syncitial virus to make a better human placenta:

http://blogs.discovermagazine.com/loom/2012/02/14/mammals-made-by-viruse...

Mon, 02/20/2017 - 22:34

(Reply to #80) #81

Valiya

Hi Alembe

Thanks for the link. It was interesting. But how would this be an explanation for evolution? You are just showing how one piece of genetic information is appropriated by another organism for its benefit. It doesn't explain how that piece of information came about in the first place. Selection might explain the survival of the fittest, not the arrival of the fittest. That's the explanation I am looking for.

Tue, 02/21/2017 - 00:01

(Reply to #81) #82

Nyarlathotep

valiya s sajjad - Selection

valiya s sajjad - Selection might explain the survival of the fittest, not the arrival of the fittest. That's the explanation I am looking for.

You are so close yet so far. Think about what you just said:

Take a random population
kill off the less fit in higher numbers than the more fit (survival of the fittest)

What does that leave you? By removing the less fit, you just transformed your population into the more fit (or perhaps the fittest). You see survival of the fittest (which you just endorsed) already answers your question

Tue, 02/21/2017 - 05:01

(Reply to #82) #83

Valiya

Hi Nyarl

If you kill off the less fit in higher numbers, what that leaves you is the more fit. I agree. But the question is where did that more fit arrive from? It's only if you have something called 'more fit' can you eliminate the 'less fit', right?

Tue, 02/21/2017 - 06:02

(Reply to #83) #84

Nyarlathotep

Oh come one, you can't be

Oh come one, you can't be serious. Even the most die hard fundie realizes that there are small differences between the offspring of an organism. So that gives us:

slight variation between different members of the same group
the general elimination of the less fit variations, generally leaving the more fit variations

That is evolution by natural selection in a nutshell (the rest is just nitty-gritty details for the biologists to deal with). That is what is crazy about people who rail against evolution, there is nothing controversial about it: if you have variation and elimination based on that variation, you will get evolution; and variation and the elimination based on variation are things we all observe!

Another point worth mentioning is: it doesn't matter where the variation comes from! If you have variation (and we all know that you do, just from observations in daily life) you will have evolution. In fact, where the variation comes from was not known when the theory was coined!

The real scandal of evolution, is that it took until the 1850's to put that together (IMO). But you can't seem to put it together either. Anyway, you are right on the threshold, don't turn away now...Who am I kidding, I'm sure you will.

Tue, 02/21/2017 - 06:31

(Reply to #84) #85

Valiya

Hi nyarl...

This time it's my turn to say close yet far!
Variations between offspring is not any mystery. All the variations come from the parents. Period. In other words, If i have black eyes and my brother has blue eyes, the genes for the blue eyes has indeed come from my parents. Yes, probably blue eyes are more charming and he might have better chances at wooing girls and spread his genes further and thus outdo me in the survival race... but that's a different story. The question of where did the fitness arrive is not answered by variation.

Tue, 02/21/2017 - 06:52

(Reply to #85) #86

Nyarlathotep

As I already told you, the

As I already told you, the source of the variation (or as you said fitness) doesn't matter. There clearly is variation, there clearly is survival of the fittest, therefore there is evolution.

Get this through your head: if the variation (or fitness) comes from mutation, god, aliens, or magic; you will get evolution. Which is why your railing against it is so silly.

Wed, 02/22/2017 - 00:47

(Reply to #86) #87

Valiya

Hi Nyarl

The source of variation DOES matter. Evolution has two engines, 'Mutation' and 'Selection'... an example that accounts for just one does not explain evolution.

Wed, 02/22/2017 - 03:14

(Reply to #87) #88

Nyarlathotep

You've put the cart before

You've put the cart before the horse. We have variation, we have survival of the fittest. Therefore we have evolution. You have already granted it.

valiya s sajjad - an example that accounts for just one does not explain evolution.

Notice, that explaining evolution is a very different matter than addressing its existence. You have already conceded enough to guarantee its existence.

Wed, 02/22/2017 - 06:51

(Reply to #88) #89

Valiya

Nyarl

As far as I know evolution is trying to explain the emergence of life from the primitive single cell to the complex forms we see today. That’s the main challenge the theory is attempting to address. From what nyarl is saying evolution only seems to explain how organisms disappear. Therefore, it can only account for the many species that are not existing today… but NOT for the millions that are in existence.

Wed, 02/22/2017 - 07:19

(Reply to #89) #90

Nyarlathotep

That isn't what I'm saying at

That isn't what I'm saying at all. I'm saying that variation and natural selection leads to change in the population over time; which is exactly what evolution is: Δx/Δt.

Wed, 02/22/2017 - 22:02

(Reply to #90) #91

Valiya

Nyarl

And what I am saying is that variation + natural selection does not lead to any new change... it just changes the population from one existing trait to another existing trait... no new traits. If that's what you mean by evolution... that's fine with me.

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