Originally posted by lee_merrill
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Nice defense of Evolution
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Originally posted by rogue06 View PostMiller's FDG was written largely as a refutation to Behe, specifically his Darwin's Black Box
I may be wrong though - and I can't find my copy to checkLast edited by Roy; 11-17-2019, 09:18 AM.Jorge: Functional Complex Information is INFORMATION that is complex and functional.
MM: First of all, the Bible is a fixed document.
MM on covid-19: We're talking about an illness with a better than 99.9% rate of survival.
seer: I believe that so called 'compassion' [for starving Palestinian kids] maybe a cover for anti Semitism, ...
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Originally posted by Roy View PostI've read Miller's book - that's not what I remember. My impression was that Miller wrote about how to reconcile evolution with the assumption of a deity.
I may be wrong though - and I can't find my copy to check
Personally I think his Only A Theory was better.
I'm always still in trouble again
"You're by far the worst poster on TWeb" and "TWeb's biggest liar" --starlight (the guy who says Stalin was a right-winger)
"Overall I would rate the withdrawal from Afghanistan as by far the best thing Biden's done" --Starlight
"Of course, human life begins at fertilization that’s not the argument." --Tassman
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Originally posted by lee_merrill View Post"He who throws mud is losing ground."
When you're ready to answer my points, I'm ready to reply some more.
Saying "you don't seem to know much about biology" shouldn't be an insult. BIology's an incredibly complicated topic, and has been the subject of intensive research for well over a century. I have a PhD in a field within biology, and i'll readily admit there's lots of other fields that i don't know well, and need to read up on before i understand at all. I'm in no way saying that you have some general knowledge deficiency."Any sufficiently advanced stupidity is indistinguishable from trolling."
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Originally posted by lee_merrill View PostWell, interesting. Yet in the case of the protein Axe worked with, function and folds do seem related.
Though as far as I can see, Axe was attempting to measure one function to get an idea how other functions would respond to mutations.
The answer comes back to the two points i mentioned above - you need to show both of my statements are wrong. You haven't.
Originally posted by lee_merrill View PostThough I think these results may be consistent, given that a number of mutations are generally required to disable function, as you yourself say: "So, you have to have massive mutational damage before it starts becoming sensitive to additional mutations..."
Yet the conclusion still stands, that "the deleterious effects of mutations, and especially their tendency to undermine the thermodynamic and kinetic stability of protein, is a major constraint on protein evolvability..."
Let's look at this case in Axe's other paper in particular: a situation where any hydrophobic amino acid will do, and you have to mutate 10 of them to kill this one function. So, that means for 9 of the 10, any of the 20 amino acids will do. For the 10th, it's got to be hydrophobic, which means 9 of the 20 amino acids will work. That means there are 4.6 * 10^12 possible amino acid configurations that can be tolerated just at these 10 amino acids alone. For most of the rest of the proteins, any amino acid will do, which gives you an absolutely vast expansion of the configurations that are compatible with the protein's original function.
So, thermodynamics creates a constraint on this one particular function, but it's an extremely loose one. Nobody has ever tested whether these mutations create additional or entirely new functions, either, so we can't generalize and determine if it creates any sort of barrier to new functions.
Incidentally, did you notice that Axe had to assume evolutionary relatedness among versions of this protein in different species in order to even do this work?
An alignment of homologous domain sequences is used to deduce the pattern of hydropathic constraints along chains that form the domain fold."Any sufficiently advanced stupidity is indistinguishable from trolling."
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Originally posted by shunyadragon View PostOK you read the book. Now what??
Blessings,
Lee"What I pray of you is, to keep your eye upon Him, for that is everything. Do you say, 'How am I to keep my eye on Him?' I reply, keep your eye off everything else, and you will soon see Him. All depends on the eye of faith being kept on Him. How simple it is!" (J.B. Stoney)
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Originally posted by TheLurch View PostI'm honestly interested in an answer to the question: given how often you get things wrong or are unaware of key information when it comes to biology, why do you think this is not a Dunning-Kruger situation?
Blessings,
Lee"What I pray of you is, to keep your eye upon Him, for that is everything. Do you say, 'How am I to keep my eye on Him?' I reply, keep your eye off everything else, and you will soon see Him. All depends on the eye of faith being kept on Him. How simple it is!" (J.B. Stoney)
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Originally posted by lee_merrill View PostWell, Miller convinced me that Behe had been refuted, notably with a diagram of blood clotting that was a simple "Y". Then I read Behe's book, and realized that I had been had, blood clotting is complex! A simple "Y" does not describe it.
Blessings,
Lee
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Originally posted by lee_merrill View PostI don't think I'm so smart! But for arguments presented to the general public, I believe I can understand and present them here, and they seem to hold up pretty well.
Blessings,
Lee
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Originally posted by TheLurch View PostAnd how, precisely, would that work? If he's not testing for any functions beyond the one enzymatic activity, or testing for folding, how could he possibly tell anything else? How are these results any more informative than the other protein he looked at where a similar approach left a functional protein?
The answer comes back to the two points i mentioned above - you need to show both of my statements are wrong. You haven't.
1) You cannot know whether mutagenesis has disrupted a protein's folding without measuring whether it's folded, because many mutations inactivate enzymes without disrupting their structure. Axe has never measured this.
2) You cannot know how distant other folds are without determining whether your mutated protein has adopted a different fold. Axe has never measured that either.
The issue is one of whether thermodynamics plays such a large role that proteins end up locked in place, unable to vary enough to reach new functions. The fact that it takes massive mutational change in order to disable them indicates the answer is no.
Let's look at this case in Axe's other paper in particular: a situation where any hydrophobic amino acid will do, and you have to mutate 10 of them to kill this one function. So, that means for 9 of the 10, any of the 20 amino acids will do. For the 10th, it's got to be hydrophobic, which means 9 of the 20 amino acids will work. That means there are 4.6 * 10^12 possible amino acid configurations that can be tolerated just at these 10 amino acids alone. For most of the rest of the proteins, any amino acid will do, which gives you an absolutely vast expansion of the configurations that are compatible with the protein's original function.
Incidentally, did you notice that Axe had to assume evolutionary relatedness among versions of this protein in different species in order to even do this work?
Blessings,
Lee"What I pray of you is, to keep your eye upon Him, for that is everything. Do you say, 'How am I to keep my eye on Him?' I reply, keep your eye off everything else, and you will soon see Him. All depends on the eye of faith being kept on Him. How simple it is!" (J.B. Stoney)
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Originally posted by lee_merrill View PostI don't see how this follows, though, it might take a dozen mutations or more to disable a protein, but that doesn't mean it isn't a long way off to new function.
Which he didn't do."Any sufficiently advanced stupidity is indistinguishable from trolling."
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Originally posted by TheLurch View PostI can respond to the rest later, but you're -this- close to getting it here. What would Axe have to do to actually determine if it's a long way off to a new function? TEST FOR NEW FUNCTIONS.
Which he didn't do.
Blessings,
Lee"What I pray of you is, to keep your eye upon Him, for that is everything. Do you say, 'How am I to keep my eye on Him?' I reply, keep your eye off everything else, and you will soon see Him. All depends on the eye of faith being kept on Him. How simple it is!" (J.B. Stoney)
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Originally posted by lee_merrill View PostWell, I thought we agreed that testing for new function would be prohibitive. So we would need some other way to estimate the distance between functions, which I believe Axe attempted, and succeeded well enough that the editors of the journal thought his work worth publishing.
I have a copy of the full text of the paper, but it seems unnecessarily verbose. At some point when i have the time, I intend to look at how precisely he derived a number for a distance. From what you quote from Evolution News, the estimate starts with a heavily mutated protein, and uses that as the starting point for its calculation of the frequency (note the 1/3), and then compares that figure to the total of every possible amino acid configuration of that length.
One, it's laughably bogus to start the calculation without compensating for the other mutations needed. Two, this assumes that absolutely no other functions are present in any proteins of the same length, which is simply wrong. Finally, it assumes that mutated versions of the protein can't possibly have a different function. Every single aspect of that is comically wrong.
So, i'm assuming this is just a product of the fact that, as usual, the people at Evolution News have no understanding of biology and so misunderstood the paper. I'll know once i look.
Didn't he look at homologous domains, though?"Any sufficiently advanced stupidity is indistinguishable from trolling."
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Originally posted by TheLurch View PostFrom what you quote from Evolution News, the estimate starts with a heavily mutated protein, and uses that as the starting point for its calculation of the frequency (note the 1/3), and then compares that figure to the total of every possible amino acid configuration of that length.
One, it's laughably bogus to start the calculation without compensating for the other mutations needed. Two, this assumes that absolutely no other functions are present in any proteins of the same length, which is simply wrong. Finally, it assumes that mutated versions of the protein can't possibly have a different function. Every single aspect of that is comically wrong.
And how do you think that homology is defined?
Blessings,
Lee"What I pray of you is, to keep your eye upon Him, for that is everything. Do you say, 'How am I to keep my eye on Him?' I reply, keep your eye off everything else, and you will soon see Him. All depends on the eye of faith being kept on Him. How simple it is!" (J.B. Stoney)
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