Swinging from one tree of life to another!

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chimp3's picture
Being that retronasal

Being that retronasal olfaction is the basis for taste can we agree that spitting is a senseless practice?

valiya s sajjad's picture
Hi Alembe

Hi Alembe

Such an honor to engage a scientist in a discussion. With all due respect to your credentials, let me raise a fundamental problem with the evolution theory. I think science has to allow evidences to lead your understanding of the universe, no matter where they lead. However, evolution starts out with a fundamental assumption that acts as a strong filter to the evidences coming in, and sort of preordains the direction that evidences have to take you. The assumption is that any phenomenon has to have a material/naturalistic explanation. It therefore places on randomness and blind forces too great a load than it can bear to explain away the obvious signs of design (planned construction) in nature. This is so because an appeal of design goes against the fundamental assumption that any explanation has to be naturalistic. I am just laying out the basic premise of my argument, Looking forward to your learned response to my argument.

Greensnake's picture
Hi valiya:

Hi valiya:

"The assumption is that any phenomenon has to have a material/naturalistic explanation." [What kind of explanation do you propose, valiya? Supernatural explanations can't be tested. Science logically seeks answers that can be tested, and that has led to its huge success in explaining the universe. (Religion, which uses supernatural "explanations," is stagnant. They have never contributed anything to a modern understanding of our world.) Science doesn't say that other answers are impossible, only that we should first seek the material/naturalistic explanation. Otherwise, science becomes a perpetual debating society and solves nothing.]

"It therefore places on randomness and blind forces too great a load than it can bear to explain away the obvious signs of design (planned construction) in nature." [Given the massive pile of evidence, I would say that the blind forces of nature are in no danger of overload! Valiya, evolution is the leading explanation for the apparent design in nature. Doesn't "planned construction" beg the question?]

Alembé's picture
Hi Valiya,

Hi Valiya,

“The assumption is that any phenomenon has to have a material/naturalistic explanation. It therefore places on randomness and blind forces too great a load than it can bear to explain away the obvious signs of design (planned construction) in nature.”

But it isn’t “randomness and blind force.” Evolution is the result of normal mutation and natural selection by the total environment in which a population of organism exists. Evolution thereby selects those characteristics/organisms which are best able to survive and reproduce in a given environment.

Also note that evolution proceeds from a given starting point and organisms adapt from there. There is a wonderful book called “Your Inner Fish: A Journey into the 3.5-Billion-Year History of the Human Body” by Neil Shubin, which describes how amphibians, reptiles, birds and mammals are all derived from ancestral fish by mutation and adaptation.

When viewed within the framework that I have just described, the “design” is built incrementally from what went before.

valiya s sajjad's picture
hi Alembe

hi Alembe

You said: "But it isn’t “randomness and blind force.” Evolution is the result of normal mutation and natural selection by the total environment in which a population of organism exists. Evolution thereby selects those characteristics/organisms which are best able to survive and reproduce in a given environment."

Mutation is random isn't it? They are accidents in the DNA copying process. And selection is a blind process. Dysfunctional intermediaries are not selected with an eye on some future advantage. That's what i mean by random and blind.

chimp3's picture
Valiya: By 'dysfuntional

Valiya: By 'dysfuntional intermediaries" do you mean that these are steps to goal? Intermediary implies a plan.

valiya s sajjad's picture
Chimp

Chimp

by dysfunctional intermediaries I mean the rudimentary parts in a organ that had no function before the full development of the organ

chimp3's picture
Example please?

Example please?

valiya s sajjad's picture
Chimp

Chimp

the rotary motor in a bacterium flagellum is dysfunctional until it has the flagellum

chimp3's picture
It served a successful

It served a successful purpose of some kind in order to have been selected and continue evolving. Or, are you buying into the irreducible complexity nonsense?

valiya s sajjad's picture
Chimp

Chimp

Are you appealing to exaptation. The different organs they show in different organisms that look something like a flagellum but used for different purposes is just imagination.None of those organs can be shown to be an incomplete flagellum unless you apply a good measure of imagination.

chimp3's picture
Incomplete? You demonstrate a

Incomplete? You demonstrate a lack of basic understanding of evolution . You are arguing I.D.iot nonsense. I suggest you indulge in some modern thinking and leave the iron age behind. Evolution is a fact .

The Pragmatic's picture
Valiya is very much an

@ chimp3
Yes, Valiya is very much an advocate of "irreduceble complexity". And my own findings is that it a waste of time trying to reason with someone who is determined to stay in the comfortable bubble of religion.

@ Valiya
Here is a video showing how the bacterial flagellum is not irreducibly complex:
https://www.youtube.com/watch?v=a_5FToP_mMY
But I'm quite sure you have already seen it, but just choose to ignore it. As well as a lot of scientific articels about it.

valiya s sajjad's picture
Hi Pragmatic

Hi Pragmatic

Hope you are doing fine. I was not responding to some of your posts in other threads - though I was tempted to - thinking you may not be interested in an engagement with me again. Anyways nice to have an exchange with you again.

The idea of exaptation is such an untestable claim, because there is no way we can find critters exhibiting every stage of the complex organ’s evolution. For example, in the bacterial flagellum, okay there was an injection system that looked like a less developed flagellum (but it was not just a simplistic flagellum minus some parts, it had its own modifications), but what about the reducible exaptation of the injection system and the series of primitive exaptations that preceded it? So a lot of it is simply left to our imagination.

Nyarlathotep's picture
valiya s sajjad - but what

valiya s sajjad - but what about the reducible exaptation of the injection system and the series of primitive exaptations that preceded it

And there you have it. We've all seen this argument before. You want science/evolution/whatever to explain every single step in a complicated process that happened in the past. Then you want to subdivide those steps by inserting additional smaller steps between then. Rinse repeat until someone can't give you a solid answer for a tiny piece of the story, you throw your hands up and cry that the whole thing is a conspiracy and that goddidit!.

chimp3's picture
I wonder what valiya thinks

I wonder what valiya thinks of the fossil record and all the species tnat went extinct? Why extinction if there is intelligent design?

The Pragmatic's picture
@ Valiya

@ Valiya

- "So a lot of it is simply left to our imagination."

My intention is not to be rude, but that's a really arrogant comment from someone who proposes magical creation from an undetectable creator or the Universe.

valiya s sajjad's picture
Hi Pragmatic

Hi Pragmatic

I think that's a discussion we are done with... I have never tried to establish god belief through science. Science has its own paradigms and belief is outside that paradigm. Remember the the 'epistemology debate' we had. So, this is a genetic fallacy you are indulging in... 'because a believer is saying it, it has to be wrong' kind of thinking.

The Pragmatic's picture
@ valia

@ valia

Same old valiya.

- "Remember the the 'epistemology debate' "

Oh yes, I remember.

- "this is a genetic fallacy you are indulging in"

When I kept mentioning the logical fallacies that you were using, I seem to remember you getting aggitated and asked me to stop. But you don't mind throwing accusations of logical fallacies around yourself...

- "Science has its own paradigms..."

Yes, but you intentionally try to misuse that. You continously demand an impossible level of evidence from science. It's called moving the goalpost (the strategy that Nyarlathotep described above).

If I show you an intermediate version of the syringe variant, you would give the exact same reply as to the flagellum and demand to se a middle stage. If I then were to show you that middle stage, you would give the exact same reply as to the flagellum again and demand to se another middle stage.

Note that I'm not saying it's wrong to search for the middle stages, but you keep denying the increasing plausibility for each middle stage found. Not because it's implausible, but simply because you don't want it to be true.
No matter how you twist it, it's still more plausible than a undetectable creator of the Universe that magically creates everything.

- "...and belief is outside that paradigm."

When I tried to get you to explain how you knew you had the correct religion, you vehemently denied that you used "a leap of faith", claiming that you could give logical and rational explanations for each step in the process.

But now it seems... you want to separate your belief from "logic and rationality". Do you really believe yourself or do you just think others can't see how you're swapping stance back and forth to suite your needs?

valiya s sajjad's picture
Hi Pragmatic

Hi Pragmatic

You said: “When I kept mentioning the logical fallacies that you were using, I seem to remember you getting aggitated and asked me to stop. But you don't mind throwing accusations of logical fallacies around yourself...”

I only detest when discussions stoop to the level of name calling and expletives. But calling out a logical fallacy is important to make one’s position clear, and I have no issues with that.

You said: “Yes, but you intentionally try to misuse that. You continously demand an impossible level of evidence from science. It's called moving the goalpost (the strategy that Nyarlathotep described above). If I show you an intermediate version of the syringe variant, you would give the exact same reply as to the flagellum and demand to se a middle stage. If I then were to show you that middle stage, you would give the exact same reply as to the flagellum again and demand to se another middle stage.”

In any hypothesis, one way to falsify it is to show there are exceptions to it. Even if you have a thousand evidences that support the hypothesis, and there is one that doesn’t fit it, then the hypothesis should still be considered weak. In the case of exaptation, let’s say you can beautifully explain the entire course of an irreducibly complex organ’s journey from the most primitive to the current complexity, but let’s say there is one stage that you can’t, then that would still render the whole example ineffective. However, like in all areas of evolution, the hypothesis takes refuge behind the vast amounts of evidences that are NOT there, and simply makes sweeping extrapolations to arrive at the conclusion you want based on one or two apparently intermediate stages. Even if you had NOT shown the ‘injection system’ of the bacteria, the hypothesis would still be acceptable to evolutionists, because after all not every intermediary has been preserved in nature – so if you find an intermediary great, but if that too is lacking, then blame it on the selection processes that did not preserve it. Easy cop out. How can anybody falsify this hypothesis?

Secondly, evolutionists themselves say that the flagellum is not an evolved ‘injection system’ rather it’s the other way round. The ‘injection system’ is a devolved flagellum. Here is the link

https://www.ncbi.nlm.nih.gov/pubmed/23028376

Therefore, the irreducibly complex flagellum came first, from which evolved the little more primitive injection system. It does NOT give exaptation any explanatory power in this case.

Finally, when you show examples of a stage-by-stage reduction in complexity through exaptation, it is not just a case of an organ minus a few parts and you have a new organ with a different function. It’s always a case of an organ minus a few parts PLUS A MODIFICATION that give rise to a precursor with a different function.

You said: “No matter how you twist it, it's still more plausible than a undetectable creator of the Universe that magically creates everything.”

That’s a strawman (just calling out a fallacy, no evil designs behind it)… as in our previous conversations, you are attributing claims to me that I never made. I didn’t make any appeal to god. However, even if I were, that still wouldn’t lend credence to the evolution theory. One wrong theory doesn’t make another one right. Each one has to stand on its own merit.

You said: “When I tried to get you to explain how you knew you had the correct religion, you vehemently denied that you used "a leap of faith", claiming that you could give logical and rational explanations for each step in the process.”

I can appeal to logic and rationality even outside the purview of science. In all our discussions, I had made it very clear that belief in God is wholly outside the epistemology of science. I never pretended to prove God through science… but logic and reason, yes! If you think logic and science are one and the same, then that’s a flaw in your understanding.

You said: “But now it seems... you want to separate your belief from "logic and rationality".

NO. I am only separating belief from science… not logic and rationality.

Nyarlathotep's picture
valiya s sajjad - In the case

valiya s sajjad - In the case of exaptation, let’s say you can beautifully explain the entire course of an irreducibly complex organ’s journey from the most primitive to the current complexity, but let’s say there is one stage that you can’t, then that would still render the whole example ineffective

No it doesn't. That isn't how science is done. The real world is a messy place and it is not uncommon for there to be outlier events where there isn't enough data to reconstruct the past. As usual; you have raised the bar so high that it would be impossible to do any science if we were to accept your requirements.

What you are saying is no different than the situation with the fossil record. Every "gap" that is filled by a newly discovered fossil produces two new gaps in the fossil record. Creationists like yourself will never be satisfied until the fossil of every single organism that ever lived has been produced. And even if that could magically be done, you'll still have your fall back claim that scientists are engaged in a conspiracy (which you have basically already used in this thread). That is what I mean by intentionally raising the bar high enough that you will never have to worry about your challenge being met.

The Pragmatic's picture
*pure waste of pixels and

*pure waste of pixels and time*

Greensnake's picture
Hi valiya:

Hi valiya:

"by dysfunctional intermediaries I mean the rudimentary parts in a organ that had no function before the full development of the organ" ==[Are all parts dysfunctional intermediates before an organ has fully evolved? What about the retina of a mammalian eye? Aren't there creatures that have that part even though they don't have the complete mammalian eye?]==

Alembé's picture
“Mutation is random isn't it?

Hi Valiya,

“Mutation is random isn't it? They are accidents in the DNA copying process. And selection is a blind process.”

Mutation is not strictly random. Within the surface molecules of the influenza virus, neuraminidase and hemagglutinin, there are hypervariable regions where extensive mutation occurs. Other domains in these molecules are more conserved.

And selection is not a “blind” process. Staying with the influenza example, virus variants are selected that have lower binding affinities to neutralizing antibodies that the host has produced, thereby allowing a resistant virus population to grow up.

valiya s sajjad's picture
Hi Alembe

Hi Alembe

You said: “Mutation is not strictly random. Within the surface molecules of the influenza virus, neuraminidase and hemagglutinin, there are hypervariable regions where extensive mutation occurs. Other domains in these molecules are more conserved.”

So are you suggesting that there is some pre-determined mechanism behind mutations? Why are mutations taking place only in those regions? If you say it’s predetermined, then that would go against the theory of evolution, because then you would have to explain how that mechanism evolved.

You said: “And selection is not a “blind” process. Staying with the influenza example, virus variants are selected that have lower binding affinities to neutralizing antibodies that the host has produced, thereby allowing a resistant virus population to grow up.”

It is blind to the extent that it does not foresee a future functionality and select accordingly. That’s why even in this example you have given, what is actually happening is a compromise in the design, not an enhancement. The selection is for virus with “LOWER” binding abilities. That’s a compromise. It doesn’t make the virus more sophisticated, but just gives it an edge in survival. Hope the point is clear.

Endri's picture
Your words define my entire

Your words define my entire existence.....literally.

Greensnake's picture
Hi valiya:

Hi valiya:

In this thread (except for the first three paragraphs) my comments will be in brackets… I. e., [my material]

Valiya, I'm glad that you took my suggestion to start this new thread.

If you would explain how evolutionary "trees" are derived from something like DNA or cytochrome c, it would demonstrate that you know something about the subject-- and it would serve as a useful platform for further discussion. Want to give it a try?

----------------------------------------------------

[valiya]…

The tree based on homology is incongruent to the tree based on DNA analysis. [In what way is it incongruent? Is there no resemblance at all or is it just a few outer branches that differ?] Now, there is a serious debate going on between evolutionists regarding which of the two trees is the real tree. [Are we talking about small branches or completely different trees? Can you give us a few details?]

More than anything else, this reveals the subjective nature of the tree construction, which is nothing but an elliptical interpretation of facts. [Doesn't that depend on whether you are talking about differences between a few small branches or the whole tree? Didn't Linnaeus work out the first version of the basic evolutionary tree long before Darwin? Valiya, that proves that it is independent of evolutionary theory!] Often times, people cling to the tree as if it’s an observed fact [But it is! Linnaeus proves it. Don't we get the same "tree" from cytochrome c data? Doesn't the fossil record give us yet another copy? It's not just anatomy looking at homologous structures. All this agreement sounds pretty factual to me.], but the way the stories are being retold proves just that… it’s a story. [What stories, valiya? I think you are misreading relatively minor disagreements. Methods based on statistics and complex models (assumptions that are rarely 100% right for a given set of data) will lead to minor differences. It's the huge similarities that you need to explain.]

The DNA based tree further complicates the story, because what kind of a tree you map out depends on which genes you choose. [It's similar to creating your family tree, valiya. How many ways can you recreate your family tree based on genetic similarity? Can you give us one example of scientists getting a completely different evolutionary tree? We are concerned with the main tree, not minor differences.] In some cases, 50% of the genes point in one way while the other half points the other way. [Can you give us more details here? It's not clear what you are talking about. Any sources?]

If you want to find a brush version of life, you will find that too. [I think you meant "bush." I have no idea what a "brush" version would be.] Just choose your genes wisely. [It's not a choice of a few genes, valiya. It's a statistical study of comparative differences in DNA. And, why does cytochrome c give us the same tree?] In this backdrop, what credibility does the leading proof of evolution, the phylogenetic tree, carry any more? [It carries a lot of credibility, valiya! Your above objections are mistaken.]

valiya s sajjad's picture
Hi Green Snake

Hi Green Snake

Good to engage you once again. I have answered all your posts here.

You said: Valiya, are you sure you understand what these people are talking about? Cherry-picked quotes (probably from creationist sources you relied upon) in such a subtle subject can easily be misunderstood by lay readers!”

Let me at the outset lay out my plan for this discussion. I will be bringing proofs from both evolutionists and creationists. You may have your own prejudices for or against these sites, but let’s not dismiss an argument based on our prejudices. Let’s be more factual, break down the arguments and critique them for what they are.

You said: “Not long ago I was looking at a modern construction of the evolutionary tree on the Internet, this from a university site. Therefore, your quotes need to be examined in their full context in order to understand what they are really saying.”

Can you present that tree? Once again you seem to be basing your plea on the credibility of your source. The fact that it’s from a university does not oblige me to accept it, unless I you show me the tree and how it answers the problems I have raised.

You said: “The odds of getting anything remotely resembling the evolutionary tree by accident is astronomical.”

I will show in a bit how the tree has undergone a paradigm shift, throwing up wholly unexpected phylogenies compared to conventional evo ideas.

You said: “What kind of explanation do you propose, valiya? Supernatural explanations can't be tested. Science logically seeks answers that can be tested, and that has led to its huge success in explaining the universe.”

The very notion that you have to begin by defining a premise for the explanation is in itself a problem. Why start out with such restrictive notions. Just study the evidence and let it lead you to the explanation. If evidences point to a cause that’s beyond naturalistic explanation, should we force a naturalistic explanation on it, just because our contrived principles demand so.

You said: “(Religion, which uses supernatural "explanations," is stagnant. They have never contributed anything to a modern understanding of our world.)”

This is a wrong idea. Almost all of our greatest scientists were theists in one way or another. The idea that science is wedded to atheism is a relatively new one. In fact most of the scientific advancements were made because theistic scientists set out to study the natural world based on the idea that everything in the universe has a purpose (not random) because God’s creation has a plan. Looking at the universe as a well-planned machine is an excellent premise to further our understanding of it. Yes, I agree that would also be a presumptive platform to start off with, but it’s equally weighted against the presumption that everything has to have only a naturalistic explanation.

You said: “Science doesn't say that other answers are impossible, only that we should first seek the material/naturalistic explanation. Otherwise, science becomes a perpetual debating society and solves nothing.”

I agree with you 100 %. But we must make sure that we are not forcing ‘material/naturalistic’ explanations because of some limitations we have artificially imposed upon ourselves. You don’t have to take recourse to the supernatural. But at least let’s discard the so called naturalistic explanation that doesn’t fit the evidence, and look for a better explanation. If there is none we can think of, then let’s wait for more evidence to pile up.

You said: “Valiya, evolution is the leading explanation for the apparent design in nature. Doesn't "planned construction" beg the question?”

Leading explanation, yes. But that doesn’t make it the right explanation. Newton’s universe was the leading explanation at one point of time, until Einstein came along. If that’s the condition of hard science like physics, let’s not get too pigheaded with soft sciences like natural history.

You said: “If you would explain how evolutionary "trees" are derived from something like DNA or cytochrome c, it would demonstrate that you know something about the subject-- and it would serve as a useful platform for further discussion. Want to give it a try?

Here is how I understand it. Cytochrome C is a protein that is fundamental to life, and hence found in all forms of life. A protein is built out of amino acids arranged in highly specified order. By comparing the amino acid buildup in the cytochrome c protein between different lifeforms, we can make an analysis of the relationship between them. More they are alike, more they are closely related in ancestry. The tree emerges through this connection between the various taxa.

You said: “In what way is it incongruent? Is there no resemblance at all or is it just a few outer branches that differ?”

In fact, it’s more than just incongruent. The entire tree has undergone a paradigm shift. It’s not a tree anymore. Perhaps a web. And what’s interesting is that the evolutionary story the web tells is totally different starting from the first common ancestor all the way through to what was believed so far. Here is the link that says it all. It’s an article published in The New Scientist (pro evo, not creationist) titled ‘Why Darwin was wrong about the tree of life’.

http://postbiota.org/pipermail/tt/2009-February/004416.html

NOTE: Obviously, the article does not say that since the idea of the tree has changed, evolution has been falsified. It says that the evo theory has gained credence now and goes on to give its own justification. Hope you wouldn’t bring that up against me saying that the article in fact counters my fundamental argument. This article only suffices to prove my argument to the extent that concept of the tree has been turned on its head, looking nothing like the conventional tree.

Here are some notable quotations from that article. This is not some cherry picked statements, rather you can see it for yourself in the context of the full article. The quotes are:

“Most biologists now accept that the tree is not a fact of nature--it is something we impose on nature in an attempt to make the task of understanding it more tractable. (Science, vol 284, p 2124)

“Thus began the final battle over the tree. Many researchers stuck
resolutely to their guns, creating ever more sophisticated computer
programs to cut through the noise and recover the One True Tree.
Others argued just as forcefully that the quest was quixotic and
should be abandoned.”

You said: “Didn't Linnaeus work out the first version of the basic evolutionary tree long before Darwin?”

That’s the tree that has been hacked down now.

You said: “But it is! Linnaeus proves it. Don't we get the same "tree" from cytochrome c data?”

The cytochrome data, depending on which organisms you choose to compare, will yield different trees. You would have to say that bacteria is more closely related to horses than yeast according to cytochrome c studies. I am sure you are well aware of denton’s matrix and so I am not giving you links to it. But if you want I will give the proof. Denton has factually shown that different taxa that branched off at various periods in the history of evolution are all at the level of cytochrome c equidistant to bacteria. According to Denton this undermines the whole notion of the tree of life. I know you will bring counter arguments to this claim. But I will not preempt you now. When you try to answer that I will give my rebuttal.

You said: “What stories, valiya? I think you are misreading relatively minor disagreements. Methods based on statistics and complex models (assumptions that are rarely 100% right for a given set of data) will lead to minor differences.”

I think the points above will suffice to show that it’s not minor disagreements we are dealing with.

You said: “Can you give us one example of scientists getting a completely different evolutionary tree? We are concerned with the main tree, not minor differences.”

The article (Why Darwin was wrong about his tree) whose link I have given above, sheds light on the battle going on between two teams of scientists – one supporting the tree version and the other web version. Read it and tell me what you think of it.

You said: In some cases, 50% of the genes point in one way while the other half points the other way. [Can you give us more details here? It's not clear what you are talking about. Any sources?]”

In the same article (linked above) you will read this: Some genes did indeed cluster within the chordates, but others indicated that tunicates should be placed with sea urchins, which aren't chordates. Roughly 50 per cent of its genes have one evolutionary history and 50 per cent another," Syvanen says.

Greensnake's picture
Hi valiya,

Hi valiya,

"I will be bringing proofs from both evolutionists and creationists. You may have your own prejudices for or against these sites, but let’s not dismiss an argument based on our prejudices. Let’s be more factual, break down the arguments and critique them for what they are."

==[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. Can you give me the sites from which these quotes were selected? Thank you for giving me the "New Scientist" site. ]==

"You said: 'Not long ago I was looking at a modern construction of the evolutionary tree on the Internet, this from a university site.'

Can you present that tree? Once again you seem to be basing your plea on the credibility of your source. The fact that it’s from a university does not oblige me to accept it, unless I you show me the tree and how it answers the problems I have raised."

==[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? There are probably a number of university sites on evolution, but the best may be from Berkeley which is one of the best universities in the world. "evolution.berkeley.edu/evolibrary/home.php" This site also has a well designed course on evolution for people like yourself who are unfamiliar with the subject, and it even has a "Tree Room" where you can learn all about evolutionary trees! I strongly recommend that you spend some time in "The Tree Room."

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. Here is a typical quote:
[The power of that idea {evolutionary tree} can be seen today in the ubiquity of evolutionary trees (also called phylogenetic trees) in all biological disciplines, from studies of newly discovered species to cutting edge cancer research. … To understand modern biology, we all need to understand how evolutionary trees can be read and used.]
There is not the slightest hint here that the evolutionary tree is defunct! All the more reason to examine your several quotes in a fuller context. Thank you for that one site you did give.

A modern, circular style, version of the evolutionary tree may be found at:
"evolution.berkeley.edu/evolibrary/article/0_0_0/evo_04" ]==

"'You said: “The odds of getting anything remotely resembling the evolutionary tree by accident is astronomical.'
I will show in a bit how the tree has undergone a paradigm shift, throwing up wholly unexpected phylogenies compared to conventional evo ideas." ==[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! One of the things you will learn in "The Tree Room" is that the evolutionary tree is a working hypothesis. The tree shows up everywhere, but like all working hypotheses it is updated in the light of new knowledge. Genetic sequencing (a new and powerful proof of evolution by the way) has caused evolutionists to make major changes near the base of the tree. (The base and the start of the first, great branches were previously very foggy.) Thus, we have a strengthened tree, not a dead tree! ]==

"You said: 'What kind of explanation do you propose, valiya? Supernatural explanations can't be tested. Science logically seeks answers that can be tested, and that has led to its huge success in explaining the universe.'
The very notion that you have to begin by defining a premise for the explanation is in itself a problem. Why start out with such restrictive notions. Just study the evidence and let it lead you to the explanation." ==[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. Thus, we finally explained the sun in terms of nuclear fusion. We must use the laws of nature if there is any possibility of their being right or forfeit any real search for truth.]==

"You said: “(Religion, which uses supernatural "explanations," is stagnant. They have never contributed anything to a modern understanding of our world.)”
This is a wrong idea. Almost all of our greatest scientists were theists in one way or another. The idea that science is wedded to atheism is a relatively new one." ==[Those religious scientists (who became famous) didn't dabble in supernatural or religious explanations. They stuck to natural law even as scientists do today. Before then, a 1000 years of religious dogma revealed very little about our universe.]==

"Looking at the universe as a well-planned machine is an excellent premise to further our understanding of it. Yes, I agree that would also be a presumptive platform to start off with, but it’s equally weighted against the presumption that everything has to have only a naturalistic explanation." ==[No, it's not equally weighted. The supernatural world is still rank speculation; the laws of nature are testable. The smart researcher reaches for the explanations with good track records first and only turns to speculation when he runs out of the former. ]==

"'You said: “Science doesn't say that other answers are impossible, only that we should first seek the material/naturalistic explanation. Otherwise, science becomes a perpetual debating society and solves nothing.'

But at least let’s discard the so called naturalistic explanation that doesn’t fit the evidence, and look for a better explanation. If there is none we can think of, then let’s wait for more evidence to pile up." ==[Isn't that what science does?]==

"You said: 'Valiya, evolution is the leading explanation for the apparent design in nature. Doesn't "planned construction" beg the question?'

Leading explanation, yes. But that doesn’t make it the right explanation. Newton’s universe was the leading explanation at one point of time, until Einstein came along. If that’s the condition of hard science like physics, let’s not get too pigheaded with soft sciences like natural history. ==[Biology is not a soft science, and evolution is the core of modern biology. Is geology also a soft science in your opinion? Does "soft" mean unreliable or just less subject to math? Do you agree that the phrase "planned construction" begs the question?]==

"You said: 'In what way is it incongruent? Is there no resemblance at all or is it just a few outer branches that differ?'

Here is the link that says it all. It’s an article published in The New Scientist (pro evo, not creationist) titled ‘Why Darwin was wrong about the tree of life’.
http://postbiota.org/pipermail/tt/2009-February/004416.html "

==[Thank you, valiya, for the link. With a full context we can see much better! Some biologists have accused "New Scientist" of using a sensationalist cover on that issue and were angry enough to boycott the magazine. "New Scientist" appears to be a popular science news magazine that also uses speculative essays. It doesn't seem as rigorous as I thought. The Berkeley site is considerably more solid.

However, there is a grain of truth behind that article. It has been known for some years that the trunk of the evolutionary tree is not a simple, straight line. Bacteria often share their genes in unorthodox ways, messing up the lineages. But, once we get above the multi-cellular level (where we find the traditional evolutionary tree) the problems are minimal, which is why we get similar evolutionary trees from different sources. "Tree" was never meant to be taken too literally, and now even less so, but it is still a useful label.]==

"You said: 'Didn't Linnaeus work out the first version of the basic evolutionary tree long before Darwin?'
That’s the tree that has been hacked down now." ==[The essay in "The New Scientist" struck me as being over-stated and rather sensationalist. The "tree" is certainly alive and well at the Berkeley site and probably at any university site that deals with evolution. No doubt the first evolutionary tree was less than perfect, but it demonstrates that the whole concept was not in the mind of some evolutionist. Linnaeus was not an evolutionist and did his work before Darwin]==

"The cytochrome data, depending on which organisms you choose to compare, will yield different trees. ==[No, it doesn't.]== You would have to say that bacteria is more closely related to horses than yeast according to cytochrome c studies. ==[We are not talking about the first horse or the first yeast.]== I am sure you are well aware of denton’s matrix and so I am not giving you links to it. But if you want I will give the proof. Denton has factually shown that different taxa that branched off at various periods in the history of evolution are all at the level of cytochrome c equidistant to bacteria. ==[Not surprising since the last, common ancestor of all of them was at the point were bacteria branched off!]== According to Denton this undermines the whole notion of the tree of life. I know you will bring counter arguments to this claim. But I will not preempt you now. When you try to answer that I will give my rebuttal."

==[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! Look at it this way: Today's bacteria and today's yeast have the same common ancestor as do today's bacteria and today's horses. Draw yourself an evolutionary tree with a nice, rounded canopy and trace the paths. (The last, common ancestor would be at the top of the trunk where the branching begins.)

This is an excellent example of why it is necessary to know the subject before criticizing it! I recommend that you enter the "Tree Room" on the Berkeley site and put in half the time you spend on debating evolution. The subject can be tricky, and even Denton (with his PhD) blundered into this trap! ]==

"You said: In some cases, 50% of the genes point in one way while the other half points the other way. [Can you give us more details here? It's not clear what you are talking about. Any sources?]”
In the same article (linked above) you will read this: Some genes did indeed cluster within the chordates, but others indicated that tunicates should be placed with sea urchins, which aren't chordates. Roughly 50 per cent of its genes have one evolutionary history and 50 per cent another," Syvanen says."

==[At that low level of the evolutionary tree, wouldn't chordates and sea urchins share a lot of features? The essay in "New Scientist" (rather than a straight scientific report) tended to be overly dramatic.

The general congruency of anatomical data with molecular data is mentioned in another university site, this time The University of Maine: ["Such trees tend to agree closely with those constructed by evolutionary biologists using morphological data, and provide independent evidence of common descent."] The site is: "chemistry.umeche.maine.edu/CHY431/Evolve2.hmtl" . A rather nice discussion of the evolutionary tree derived from cytochrome c in 1978 is available along with a nice view of that tree.

valiya s sajjad's picture
Hi valiya,

Hi valiya,
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. No. My intention is only to highlight that the credible scientists (evolutionists) have strong differences of opinion regarding the tree. Moreover, I did give you the entire link (as you have rightly acknowledged) from the New Scientist where you will find all the quotes.

"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. 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. It would be better if you focus on your case rather than eulogizing or discrediting authorities.

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.

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?

You said: “A modern, circular style, version of the evolutionary tree may be found at:
"evolution.berkeley.edu/evolibrary/article/0_0_0/evo_04" ]==

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.

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...

You said: “Genetic sequencing (a new and powerful proof of evolution by the way) has caused evolutionists to make major changes near the base of the tree. (The base and the start of the first, great branches were previously very foggy.) Thus, we have a strengthened tree, not a dead tree! ]

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!

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.

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.

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. But before that, let me just bring some perspective on the hollowness of that claim. You say that a bacteria is equidistant from a yeast and horse, because they branched off from a common ancestor and have all continued to evolve at the same rate to this. Therefore you are assuming that that the mutations for all of them have been progressing at a steady rate. How can the mutation rates be equal when mutations are driven by natural selection pressures? Yeast and horse would have branched off long time ago, and evolved to whatever they have become because mutations were deleted and selected in different ways between them. Then how can you appeal to a molecular clock to explain their equidistance from the bacteria.

Check this out: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3184610/

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