Got it. I work with SnpEff quite a bit, so I was thinking that PolyPhen was more similar to that method than it actually is.
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I have read your post, I am now happy that you completely refuted @NLENTS claim that Behe misrepresented the table 7 by cutting off, since the table does not provide any positive evidence that mutations are constrictive, If there is no positive evidence in the table for constructive mutations what was the purpose of hiding the rest of the table?, So, that was false accusation which was no relevance to the issue at all, just to shift real discussion into the discussion that Behe has a hidden agenda. But, now I am happy, ENV was able to force all of you to admit the falsehood of the accusation and to return real science discussion. You made good points, and I am sure that your points will be addressed. Even though, it was already addressed by Behe with post reply to Lenski.
Behe and ENV did misrepresent that table. They claimed that those were conclusions. They weren’t. They were observations.
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As I said when I pointed out the altered table 2 months ago:
Are we supposed to believe that Behe did that little switcharoo without thinking that a large fraction of his lay readers would just see a big list of entries saying “damaging” and come away with the impression that these were the majority of variants, or even all of them?
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Well, as long as you’re happy!
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Scientific conculsions should be based on observations, is not it?
The problem of biology is it does not much realy on observations but realy on the theory that was put forward in 1859. That makes conlusions be felxible, if an observation at sightest supports the theory, it is accepted, if observations do not support theory, the concusions are drown not from the observation, but imaginary wishfull thinking that fits the theory
Conclusions should be based on observations, but that doesn’t mean you are allowed to misrepresent observations as conclusions. Behe claimed that he agreed with the conclusions of the paper. That wasn’t true. Behe took the same observations and arrived at the opposite conclusion to that found in the paper. Behe tried to give his claims more credence by claiming he agreed with the authors when in fact he doesn’t agree with them.
Baseless accusations aren’t worth much.
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the conclusion of the paper does not say mutations are constructive, it just makes suggestion that mutations had certain effect, but that effect you can come either by constrictive mutations or by degradative mutations. Behe claims that the effect is due to degradative mutation by replying on the observation made in the paper
Where does the paper say that?
First, the paper does not say mutations are constructive
Second, a scientist can read already published works and can make conclusions, observations that are not explicit in the paper more explicit to a wider audience,
Third, Yes, the author of the paper did not write explicitly that certain effect, is due to degradative mutation, but the author of the paper did not write certain effect, is due to constructive mutation either.
Forth, Behe just made what was implicit in the paper more explicit, which itself neither contradicts observations made in the paper nor the conclusion of the author.
I totally agree. However, it is improper to make your own conclusions and then claim they are the authors’ conclusions.
The conclusion drawn by the authors of the paper is that there was an increase in function in the portion of APOB responsible for clearing cholesterol from the bloodstream. Implicit in their conclusion is that there were constructive mutations in APOB.
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I can state that i have no connection with any of people from DI, They do not know me. I do not know them personally either. but it hurts me that the scientific community was unfair to ID and misrepresented so much in the last 2 decades…Revealing the truth is important, if not me, then who?
what I am making here, is just encouraging to the discussion, in order for ENV to be able to more explicitly respond to the criticism, because sometimes when seeing responses like “Nuh uh!”, it makes hidden, where the disagreement lies, certainly not in table 7, but after your post now disagreement is more explicit where it lies and i summarised like above
Hi @Edgar_Tamarian, the problem with this is that there is positive evidence that some of the mutations described by Liu et al., and listed in the parts of Table S7 that Behe omitted, are constructive. As I stated just a few posts back:
However, ALL of the mutations listed in Table S7 of Liu et al. are in genes that show clear indications of being under positive selection. While benign mutations in these genes may be neutral, they may also be beneficial or constructive. Indeed, to cite an example from the data Behe omits, at least one of the benign changes in the polar bear OR5D14 gene must be constructive or beneficial, since this gene that is under positive selection only carries mutations flagged by PolyPhen2 as benign. To give another example, the sole missense mutation in another gene under positive selection – EHD3 – must be beneficial or constructive (PolyPhen2 flags this change as benign).
Table S7 actually has positive evidence for constructive mutations in at least three of the genes of interest. And this is probably an underestimate.
So, the question remains - why did Behe hide the evidence for constructive mutations in the polar bear?
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Why does this hurt you so much?
How do you know what you heard from this was true? Maybe scientists haven’t been unfair to them.
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The paper (really its just polyphen) cannot say constructive because it can only output two things: “benign” or “damaging” and ultimately these are just predictions for the human protein. There are no direct predictions for the polar bear APOB. You can say that the mutations are damaging, but the paper written by humans says the opposite. All the evidence of polar bears living full and healthy lives indicates that these are positive (constructive) mutations.
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We will not go far from you. in your review, you argue that
He [Behe] includes a lengthy appendix that argues that the blood-clotting cascade is irreducibly complex, but fails to mention Kenneth Miller’s simple, elegant scheme for its stepwise evolution»
K. R. Miller, in Philosophy of Biology: An Anthology, A. Rosenberg, R. Arp, Eds. (Wiley-Blackwell, 2004), pp. 439–449
but you fail to mention that in very the same book just a few pages behind Behe responded to the criticism of blood cascade clotting.
M. J. Behe, in Philosophy of Biology : An Anthology, A. Rosenberg, R. Arp, Eds. (Wiley-Blackwell, 2004), pp. 427–438.
worse than that, more lengthy responses are available
A Response to Critics of Darwin’s Black Box
is this fair enough?, to cite only one side of the debate and then declare dismantled,
For showing, that Behe failed in the regard of blood clotting cascade as irreducible complexity, you had to gather all information on it, consider all responses and counter-responses, and show at which point Behe fails. You did not do that, you referred to old critic whom Behe responded…by the way, to do all of this is outside of the scope of the review Darwin Devolves, which means you should not touch that topic in the review if it requires I guess more than 10-page elaborate work.
Instead, you had to bring your argument about the effective clearance of cholesterol from the
blood.
That point would be in the main topic of the book, but no, by mentioning old circulated, washed criticism you wanted to show that Behe always was wrong in the past, now is wrong and from that follows in future most likely will be wrong. and that review has its audience, Yes, it is written in Science journal, but the way it is written to reach to the public and lay public will never check whether Behe responded to it or not, if @swamidass says so, then it is, why to bother ourself check all references.
and this kind of unfairness Yes, Hurts me why? because I am human
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Isn’t that what Behe did? Are you agreeing with us? I’m confused…
By now it is simply not possible that whoever is writing is not aware of this. The author hasn’t read the 9th commandment it seems. The only possible alternative is that the author didn’t read ANY of the responses, which makes it just as bad since this person is then writing rebuttals to something s/he hasn’t even read.
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