Originally posted by lee_merrill
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Nice defense of Evolution
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Originally posted by lee_merrill View PostSo he hoodwinked the editors of the Journal of Molecular Biology? What you just stated would not seem worthy of publication.
Originally posted by lee_merrill View PostTargeting multiple random changes (10 of them in the paper you cited!) at the sites within a protein that are most likely to be structurally significant doesn't actually tell you anything about how frequent other structures are.
Do you not know that because you didn't read the paper, or because you are incapable of understanding it?
The second issue here is that Axe had tried this earlier with a different protein, and it didn't work. He completely randomized the internal hydrophobic residues, and found that as long as he used a hydrophobic replacement, he could swap them all out and the enzyme would still work. So his results on this protein aren't even generally true, and therefore can't be used to draw general conclusions.
(Sidenote: another indication that Axe is simply shopping for results that let me say what he wants to.)
Originally posted by lee_merrill View Post.
Originally posted by lee_merrill View PostYes, but his work provides a way to estimate the prevalence of protein sequences adopting functional enzyme folds. Just quoting from the title. This gives us an idea of the distance to new function.
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 function. 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.
If you think this work tells us what you're claiming it does, you have to show that both of those statements are wrong."Any sufficiently advanced stupidity is indistinguishable from trolling."
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Two errors in that post that i noticed too late to edit:
"another indication that Axe is simply shopping for results that let him say what he wants to"
"many mutations inactivate enzymes without disrupting theirstructure"
As always, my apologies for typing carelessly."Any sufficiently advanced stupidity is indistinguishable from trolling."
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Originally posted by TheLurch View PostAxe never tested whether the mutant proteins adopted some other structure - he has absolutely no idea whether there's a structure there or not. He simply tested for a single enzymatic activity.
The protein could have adopted a different structure and a different enzymatic activity, and Axe would never be able to tell, because he didn't bother to look.
The second issue here is that Axe had tried this earlier with a different protein, and it didn't work. He completely randomized the internal hydrophobic residues, and found that as long as he used a hydrophobic replacement, he could swap them all out and the enzyme would still work. So his results on this protein aren't even generally true, and therefore can't be used to draw general conclusions.
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.
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.
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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Lee,
Can evolutionary processes make enzymes evolve, or increase their specificity?
Yes, clearly. An example is the blood clotting enzymatic cascade. To put it simply, there are several enzymes, all serine proteases, which are enzymes that cut the peptide bond in the proteins using a serine in its catalytic center.
Picture that in an ancestral species a protease like this existed and was responsible for the activation of the clotting proteins, like thrombin and fibrinogen, which usually are in an inactive state and are activated cutting a piece of the protein. After activated, these proteins interact to form clots, and eventually, also have to be degraded by the protease.
If you have only one protease which does all that, it isn't going to work well. It may do, but the same enzyme that is activating the clotting proteins is also degrading them as well and the process isn't going to be very efficient.
Now suppose that there is a mutation which duplicates the protease gene. This is relatively common, because it is an error in the DNA copy where a strand of DNA is copied twice. Now we have two copies of the same protease, which doesn't help any. But it allows each copy to accumulate mutations independently of the other. So mutations which make one of the copies more efficient at activating the prothrombin than to degrade the clot will allow a faster activation of the blood clotting. On the other hand, mutations which make the other copy more efficient at degrading the clot than to activate the phrotrombin will also be advantageous and give advantage to other mutations which regulate when and where each enzyme is copied. And so on.
Eventually, we have a system like our blood clotting, which has several proteases which are almost equal but slightly different, and which differences correspond to mutations which makes them more efficient in a specific step of the cascade reaction and less efficient in the rest of the steps. That is, MORE SPECIFIC. And all that cannot only be explained by the conjunction of mutations with natural selection, but it is evident when we consider the sequences of proteases and their localization in the genome, which is what we would expect of a process like this of duplication and differentiation of genes.
Does that answer your question of whether enzymes evolve?Last edited by Seeker; 11-12-2019, 02:47 PM.
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Originally posted by Seeker View PostEventually, we have a system like our blood clotting, which has several proteases which are almost equal but slightly different...
So blood clotting is a particularly difficult problem for evolution to solve. I agree that enzymes can evolve, as in the arrival of nylonase by a few selectable mutations, but traversing protein space to a new function by a random walk seems to be prohibitive, and most mutations will degrade an enzyme or be neutral.
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 Post
So blood clotting is a particularly difficult problem for evolution to solve. I agree that enzymes can evolve, as in the arrival of nylonase by a few selectable mutations, but traversing protein space to a new function by a random walk seems to be prohibitive, and most mutations will degrade an enzyme or be neutral.
Blessings,
Lee
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Originally posted by lee_merrill View Post
So blood clotting is a particularly difficult problem for evolution to solve. I agree that enzymes can evolve, as in the arrival of nylonase by a few selectable mutations, but traversing protein space to a new function by a random walk seems to be prohibitive, and most mutations will degrade an enzyme or be neutral.
Blessings,
Lee
This is legitimate peer reviewed science where Behe has not published his ID religious agenda concerning blood clotting.Last edited by shunyadragon; 11-12-2019, 06:47 PM.
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Originally posted by Seeker View PostOn the other hand, mutations which make the other copy more efficient at degrading the clot than to activate the phrotrombin will also be advantageous and give advantage to other mutations which regulate when and where each enzyme is copied. And so on.
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Originally posted by lee_merrill View PostYet function implies a fold, does it not?
Second, it doesn't address the problems I described: the protein could have adopted some other fold, and Axe wouldn't be able to tell. As a result, his experiment is about adopting this one particular fold, and not folds in general. And, as his earlier paper showed, what he's finding with this fold doesn't even apply to others.
Originally posted by lee_merrill View PostAre you saying he should have tested for all possible activities?! That would be prohibitive.
Originally posted by lee_merrill View PostWell, see above...
Originally posted by lee_merrill View PostWell, I can't get to the article to see how he drew his conclusions, but apparently he was onto something:
.
.We describe ways of predicting and analyzing stability effects of mutations, and mechanisms that buffer or compensate for these destabilizing effects and thereby promote protein evolvabilty, in nature and in the laboratory..
So, you have to have massive mutational damage before it starts becoming sensitive to additional mutations, and even then there are known biological mechanism that "buffer or compensate" for the damage.
Sounds like proteins can explore a huge range of sequence space with little difficulty.Last edited by TheLurch; 11-13-2019, 10:53 AM."Any sufficiently advanced stupidity is indistinguishable from trolling."
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Originally posted by shunyadragon View Post
So not a complete scenario, by any means.
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 PostSo it's a simple scenario for a complex system, with acknowledged problems. In addition, his figure 6 ("Time-line phylogeny for appearance (and disappearance) of various clotting factors during the course of vertebrate evolution.") has only 6 of the factors, and one step labeled "Period of invention."
So not a complete scenario, by any means.
Blessings,
Lee
What are your qualification to judge a peer reviewed article? Please enlighten us on specifics of the problems you see.
Behe has not peer reviewed published his claims. He had to print his own book.
Last edited by shunyadragon; 11-13-2019, 05:55 PM.
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Originally posted by TheLurch View PostOne, the answer is no. Look into intrinsically disordered proteins.
... the protein could have adopted some other fold, and Axe wouldn't be able to tell.
Surely the editors would have caught it if his work only applied to one fold.
And, as his earlier paper showed, what he's finding with this fold doesn't even apply to others.
Or not, if you'd bothered to quote through to the end of the abstract.
Sounds like proteins can explore a huge range of sequence space with little difficulty.
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 shunyadragon View PostWhat are your qualification to judge a peer reviewed article?
Please enlighten us on specifics of the problems you see.
Behe has not peer reviewed published his claims. He had to print his own book.
So why exactly are you citing this paper? It seems to be much less comprehensive than the first one you cited, which I did read. It's a lot of work to read these papers, so if you're not going to tell me what you got from them, I'm going to think you're just spraying papers at me without consideration.
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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