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Thread: Are there no beneficial mutations?

  1. #51
    tWebber shunyadragon's Avatar
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    Quote Originally Posted by lee_merrill View Post
    But I need specific references!

    Blessings,
    Lee
    You are making the claim therefore your the one that needs specific references beside the religious agenda of Behe, which you have provided none! Your also consistently ignoring references provided by The Lurch in previous threads that trashed Behe's argument.
    Last edited by shunyadragon; 03-13-2020 at 04:05 AM.
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  2. #52
    tWebber Roy's Avatar
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    Quote Originally Posted by TheLurch View Post
    Roy said that he didn't do any computer analysis, …
    Yup. Behe didn't do any computer analysis. He took the results of some-one else's computer analysis, deleted the sections that didn't align with his claims, and quote-mined the rest as if it was all that was available.

    There's a summary here. I've checked the original paper by Liu et al, and can confirm both that Behe left out most of the data, and that "damaging" doesn't mean what Behe claims it does.
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  3. #53
    Evolution is God's ID rogue06's Avatar
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    Quote Originally Posted by TheLurch View Post
    No, its main function is to carry oxygen. It's only a small component of the circulatory system, and has related proteins that don't circulate at all, but hold oxygen.


    Roy said that he didn't do any computer analysis, and Roy's statements have been accurate so far. So how did Bene define function for these proteins?


    If Behe is right, and evolution operates largely by eliminating function, then the genomes of organisms should be positively littered with damaged and inactivated genes. If you take two related species and compare their genomes, you should see distinct sets of damaged genes in each; as you go further, you should see those sets increase. That is a necessary and testable consequence of Behe's contention.

    Except it's not really testable, in that we already have a ton of genome sequences, and we know that it's not true.

    Behe is either ignorant of developments in biology, in which case we shouldn't trust what he says about biology, or he's intentionally misleading his readers.

    We can also see it in individual examples we discussed in the last thread (or earlier in this one; i'm easily confused). Place bacteria under extreme selection, and they disable the proofreading feature of their DNA polymerase in order to increase their mutation rate. Per Behe, this is adaptive and typical of evolution. But if you look at bacterial genomes, the proofreading feature is omnipresent. It's clearly adaptive, and evolution clearly disfavors its inactivation during evolution.

    Which shows that Behe's being misleading by making that argument. So why would you recommend i dive into a book that's misleading?
    Please pardon the pedantism, but it is testable. And the results clearly demonstrate that Behe's contention is incorrect.

    I'm always still in trouble again

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  4. #54
    tWebber TheLurch's Avatar
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    Quote Originally Posted by rogue06 View Post
    Please pardon the pedantism, but it is testable. And the results clearly demonstrate that Behe's contention is incorrect.
    Yeah, was mostly just a turn of phrase - it is not testable in the sense of "possible to test", in that the test has already been done.
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  5. Amen shunyadragon amen'd this post.
  6. #55
    tWebber lee_merrill's Avatar
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    Quote Originally Posted by Roy View Post
    Yup. Behe didn't do any computer analysis. He took the results of some-one else's computer analysis, deleted the sections that didn't align with his claims, and quote-mined the rest as if it was all that was available.

    There's a summary here. I've checked the original paper by Liu et al, and can confirm both that Behe left out most of the data, and that "damaging" doesn't mean what Behe claims it does.
    Source: Evolution News

    Answering Objection 3: Did Behe omit contrary information from the chart? Behe’s blog post responding to Objection 2 only showed a portion of the damaging mutation chart from Liu et al., but Behe did this for good reason: The table is large (49 lines x 8 columns), and for clarity he wanted to present only the data that was required to refute the critics. In this case, critics had challenged Behe’s estimates of the number of polar bear genes that experienced damaging mutations. The chart data Behe presented was sufficient to show he was correct. One critic even admitted Behe “isn’t lying exactly” since he was just showing the “relevant information.” In a reply to the critics’ complaints, we reprinted the full table and showed why none of the data Behe left out contradicts his thesis. Some of it represented results that predicted mutations were damaging — data that clearly supports Behe! The remainder entailed mutations that were predicted to be “benign” — but this does not contradict Behe either: Behe’s “devolution” model is only challenged by “constructive” mutations, but he fully allows that benign or neutral mutations are common and even form the “the bulk of changes at the molecular level,” as he writes in Darwin Devolves.

    Source

    © Copyright Original Source



    Blessings,
    Lee
    Last edited by lee_merrill; 03-14-2020 at 10:45 AM.
    "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)

  7. #56
    tWebber lee_merrill's Avatar
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    So how did Bene define function for these proteins?
    The function is usually pretty obvious, as in APOB in polar bears, where "Indeed, as Behe pointed out, cholesterol may be removed by decreasing the activity of APOB." (Source)

    If Behe is right, and evolution operates largely by eliminating function, then the genomes of organisms should be positively littered with damaged and inactivated genes.
    Only if the mutations become fixed in the population, correct?

    Place bacteria under extreme selection, and they disable the proofreading feature of their DNA polymerase in order to increase their mutation rate. Per Behe, this is adaptive and typical of evolution. But if you look at bacterial genomes, the proofreading feature is omnipresent. It's clearly adaptive, and evolution clearly disfavors its inactivation during evolution.
    Well, again, this adaptation would have to become fixed.

    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)

  8. #57
    tWebber lee_merrill's Avatar
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    Quote Originally Posted by shunyadragon View Post
    You are making the claim therefore your the one that needs specific references beside the religious agenda of Behe, which you have provided none! Your also consistently ignoring references provided by The Lurch in previous threads that trashed Behe's argument.
    Where have I ignored a reference posted by The Lurch? And Darwin Devolves is full of such references, we are discussing one, by Lui et. al.

    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)

  9. #58
    tWebber shunyadragon's Avatar
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    Quote Originally Posted by lee_merrill View Post
    Source: Evolution News

    Answering Objection 3: Did Behe omit contrary information from the chart? Behe’s blog post responding to Objection 2 only showed a portion of the damaging mutation chart from Liu et al., but Behe did this for good reason: The table is large (49 lines x 8 columns), and for clarity he wanted to present only the data that was required to refute the critics. In this case, critics had challenged Behe’s estimates of the number of polar bear genes that experienced damaging mutations. The chart data Behe presented was sufficient to show he was correct. One critic even admitted Behe “isn’t lying exactly” since he was just showing the “relevant information.” In a reply to the critics’ complaints, we reprinted the full table and showed why none of the data Behe left out contradicts his thesis. Some of it represented results that predicted mutations were damaging — data that clearly supports Behe! The remainder entailed mutations that were predicted to be “benign” — but this does not contradict Behe either: Behe’s “devolution” model is only challenged by “constructive” mutations, but he fully allows that benign or neutral mutations are common and even form the “the bulk of changes at the molecular level,” as he writes in Darwin Devolves.

    Source

    © Copyright Original Source



    Blessings,
    Lee
    You're citing Behe in a Creationist pseudo-science rag. This does not show any research just a claim. I want to see independent peer reviewed science research that demonstrates Behe's conclusions.
    Glendower: I can call spirits from the vasty deep.
    Hotspur: Why, so can I, or so can any man;
    But will they come when you do call for them? Shakespeare’s Henry IV, Part 1, Act III:

    go with the flow the river knows . . .

    Frank

    I do not know, therefore everything is in pencil.

  10. Amen Seeker amen'd this post.
  11. #59
    tWebber TheLurch's Avatar
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    Quote Originally Posted by lee_merrill View Post
    The function is usually pretty obvious.
    In other words, he has no objective criteria laid out for how to determine the function or whether it's impaired. And, in the case of proteins with multiple phenotypes, like hemoglobin, it will come down to "the function is what Behe says it is, because Behe will tell us what's obvious." And if other scientists disagree with his decision, then Behe will be correct, because that's what we need to see happen.

    Welcome to creationist science!

    Quote Originally Posted by lee_merrill View Post
    Only if the mutations become fixed in the population, correct?
    Do you even pay attention to your own arguments? (No need to answer; we've already seen that you don't.) That's a completely nonsensical caveat that you're trying to introduce, presumably because you have no answer for the actual problems with Behe's argument.

    I will, however, explain why. There are two options for mutations that don't become fixed. One is that they float around at low levels in the background, either because they're barely beneficial, neutral, or not so harmful that there's a strong selection against them. The second is that they are strongly selected against, and therefore lost entirely.

    But Behe's entire argument (and thus yours) is that evolution strongly selects for mutations that damage things. His argument is not "evolution makes things that are mostly neutral and float around harmlessly in the background" - it is that evolution breaks stuff because it selects for things that damage their gene's function. The examples he uses are cases where it has been fixed - hypermutators in the long term evolution experiment, altered lipid metabolism in polar bears, etc.

    And because it's Behe's argument, it's the argument you have been making.

    Until, apparently, the argument becomes inconvenient so you try to distance yourself from it.

    So again, i'll ask you: if Behe is right, and evolution acts by breaking things, why don't we actually see evidence of that in genomes?
    And i'll add a follow up question: if we don't see evidence of this in genomes, and you persist in thinking Behe's argument has merit, what could possibly convince you that his argument has issues?

    Just to make the issue completely clear, let's imagine that Behe proposed "evolution breaks stuff" prior to the genome era. The necessary conclusion would still be that, if this were the case, speciation would be a matter of accumulating broken stuff. Because, if it weren't, then Behe's model would have to be "evolution sometimes breaks stuff, but it's not important in speciation" - which it most certainly is not. But, in the pre-genome era, we can't test that. Years past, we sequence genomes, and find that there are relatively few broken genes, and no pattern to their presence.

    That would obviously be a problem for Behe's contention. Why are you pretending its not just because we had the genomes sequenced already?
    Last edited by TheLurch; 03-16-2020 at 05:51 AM.
    "Any sufficiently advanced stupidity is indistinguishable from trolling."

  12. Amen rogue06, Seeker amen'd this post.
  13. #60
    tWebber lee_merrill's Avatar
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    Quote Originally Posted by TheLurch View Post
    In other words, he has no objective criteria laid out for how to determine the function or whether it's impaired.
    The computer models give a pretty clear idea as to function, and to whether it has been impaired.

    ... if Behe is right, and evolution acts by breaking things, why don't we actually see evidence of that in genomes?
    Well, that's what Behe does, he examines evidence in genomes. What he finds is that most often, evolution selects degradative mutations. This stands to reason, because that is mostly what evolution has as its raw material to work with, most mutations that are not neutral will damage genes.

    Now we don't see this in speciation (is my view) since speciation events such as the massive radiations require supernatural invention. Nature cannot do this, so we have to look elsewhere.

    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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