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The lungfish genome, tetrapods, and junk DNA

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  • TheLurch
    replied
    Originally posted by lee_merrill View Post
    No, for example, hemoglobin Behe said was probably not designed, evolution probably could get there.
    Yes, because it didn't fit his original definition of specified complexity. Not because of selectability.

    Originally posted by lee_merrill View Post
    It could evolve if the path was essentially selectable, now I question whether you have demonstrated a selectable path after gene duplication.
    Well, please point out the steps i mentioned that don't appear to be selectable then. Saying "i question it" without telling us what you question isn't useful.

    Leave a comment:


  • lee_merrill
    replied
    Originally posted by rogue06 View Post
    Umm... you do realize that you just confirmed what I said, right? He's saying that IC systems cannot have evolved. That it had to have "arise[n] as an integrated unit, in one fell swoop."
    Only "then if a biological system cannot be produced gradually it would have to arise as an integrated unit...", if there is a selectable path to an IC structure, then Behe agrees it can evolve.

    You seem to have forgotten this post concerning the nonsense about the flagellum. While you cavilingly tried to nitpick it, I answered everyone of your objections and all you succeeded at was yet again exposing your unfamiliarity with even the fundamentals of basic biology.
    "One thing is lacking though, which is the function of this assembly while it is evolving." That would not be a nitpick, nor a lack of knowledge of biology. And you are the one who did not answer my questions, what is the function after the rod is added? when the hook is added? on the way to a flagellum.

    But rather than going over the same ground, John H. McDonald from the University of Delaware provided a very simple but elegant rebuttal to Behe's mousetrap example.
    Behe responded to McDonald:

    Source: Behe

    (1) McDonald’s reduced-component traps are not single-step intermediates in the building of the mousetrap I showed; (2) intelligence was intimately involved in constructing the series of traps; 3 if intelligence is necessary to make something as simple as a mousetrap, we have strong reason to think it is necessary to make the much more complicated machinery of the cell.

    Source

    © Copyright Original Source



    And now you changed your reply to say that his reliance was on merely a small fraction of those 139 pages.
    But again, that was a sample. And this 90% is the critical part for judge Jones to demonstrate his understanding, "intelligent design as science".

    Even worse, after summarily dismissing "fifty-eight peer-reviewed publications, nine books, and several immunology textbook chapters about the evolution of the immune system" as simply addressing a different subject, Behe admitted that he wasn't even familiar with most of them! For instance

    Q: I'm going to read some titles here. We have Evolution of Immune Reactions by Sima and Vetvicka, are you familiar with that?

    A: No, I'm not.


    How can anyone proclaim that something was "addressed to a different subject" when they don't even know what it even says?
    Well, the point was that what Behe said, and what judge Jones reported, were two different things. And Behe's point in regard to the books and articles is that he had read some recent articles, and found them lacking. Surely if one of these books or articles presented to him were conclusive, they would have been at least referenced in later papers.

    Blessings,
    Lee

    Leave a comment:


  • lee_merrill
    replied
    Originally posted by TheLurch View Post
    Right, his point was that it was impossible to select for something that only worked when it was completed. Again it could not be selected for at all, ever, under any circumstances. That was his argument then, and therefore something like the proteasome, which only works if most of its parts are present, could never occur through selection. Now, he's willing to accept that it could, as long as the unselected steps don't cross a threshold.
    No, for example, hemoglobin Behe said was probably not designed, evolution probably could get there.

    This is a fundamental misconception on your part. Duplications, in this case, are just like any other mutation. Point mutations, duplications, deletions - all of them just occur. Selection only kicks in after they occur. The two issues are orthogonal.
    I was gearing off what you said: "Gene duplications happen every single generation in humans, all completely unselected."

    I described aspects of selection when i first introduced the proteasome, and you accepted those at the time, to the extent that you agreed the proteasome could evolve. Go back and read the thread.
    It could evolve if the path was essentially selectable, now I question whether you have demonstrated a selectable path after gene duplication.

    Blessings,
    Lee

    Leave a comment:


  • rogue06
    replied
    Originally posted by lee_merrill View Post
    That's not quite accurate, here is Behe's description:
    Source: Darwin's Black Box, pp. 49-50

    An irreducibly complex biological system, if there is such a thing, would be a powerful challenge to Darwinian evolution. Since natural selection can only choose systems that are already working, then if a biological system cannot be produced gradually it would have to arise as an integrated unit, in one fell swoop, for natural selection to have anything to act on.

    © Copyright Original Source

    Umm... you do realize that you just confirmed what I said, right? He's saying that IC systems cannot have evolved. That it had to have "arise[n] as an integrated unit, in one fell swoop."

    Originally posted by lee_merrill View Post
    Not really, the argument of Darwin's Black Box is quite sound, as shown by his critics being answered in A Mousetrap for Darwin.
    *snort*

    You seem to have forgotten this post concerning the nonsense about the flagellum. While you cavilingly tried to nitpick it, I answered everyone of your objections and all you succeeded at was yet again exposing your unfamiliarity with even the fundamentals of basic biology.

    But rather than going over the same ground, John H. McDonald from the University of Delaware provided a very simple but elegant rebuttal to Behe's mousetrap example. Beginning with just a wire loop held open under tension and proceeding with a step-by-step evolution of it (with each step representing a single mutational even), which produced a modest but still functional change to the previous mousetrap until we end up with the supposedly irreducibly complex mousetrap:





    Originally posted by lee_merrill View Post
    No, this is "90.9% (or 5,458 words) of Judge Jones’ 6,004- word section on intelligent design as science", not of the whole document. I must ask again if you have evidence of Judge Jones understanding the issues under debate.
    That is pretty much an acknowledgment that it was only a tiny portion of the entire 139 page document.

    And it is apparent that you didn't understand the argument since previously you said

    Originally posted by rogue06 View Post
    So you haven't actually read the decision, but uncritically trusted what a source that has been shown again and again, over and over to be anything but trustworthy told you. Unbelievable

    Would you say that these samples, all combined constitutes 90% of a 139 page decision? You can say that with confidence?
    Originally posted by lee_merrill View Post
    Yes, I would say they probably did their homework.


    And now you changed your reply to say that his reliance was on merely a small fraction of those 139 pages.

    Originally posted by lee_merrill View Post
    And it appears he mischaracterized Behe's answer in his opinion:

    Source: Discovery

    Judge Jones claimed that biochemist Michael Behe, when confronted with articles supposedly explaining the evolution of the immune system, replied that these articles were “not ‘good enough.’” In reality, Behe said the exact opposite at trial: “it’s not that they aren’t good enough. It’s simply that they are addressed to a different subject.” (emphasis added) The answer cited by Judge Jones came not from Behe, but from the ACLU’s proposed “Findings of Fact,” which misquoted Behe, twisting the substance of his answer.

    Source

    © Copyright Original Source

    Indeed he is saying in effect that they aren't good enough because Behe erroneously declared none of the "fifty-eight peer-reviewed publications, nine books, and several immunology textbook chapters about the evolution of the immune system" didn't address the subject. They weren't good enough -- even though he admitted that many of them were "not just [about] the immune system generally, but actually the evolution of the immune system."

    Even worse, after summarily dismissing "fifty-eight peer-reviewed publications, nine books, and several immunology textbook chapters about the evolution of the immune system" as simply addressing a different subject, Behe admitted that he wasn't even familiar with most of them! For instance

    Q: I'm going to read some titles here. We have Evolution of Immune Reactions by Sima and Vetvicka, are you familiar with that?

    A: No, I'm not.


    How can anyone proclaim that something was "addressed to a different subject" when they don't even know what it even says?

    Think of it this way. If someone declared that the Bible never said anything about the birth of Christ but then admitted they weren't familiar with the Gospels of Matthew or Luke, what would say about that person? Well?

    But let's go on. Immediately after admitting that he wasn't familiar with Evolution of Immune Reactions even though he had rejected it out of hand as addressing a different subject, he was provided with a list of more books that specifically dealt with the subject at hand

    Q: Origin and Evolution of the Vertebrate Immune System, by Pasquier.Evolution and Vertebrate Immunity, by Kelso. The Primordial Vrm System and the Evolution of Vertebrate Immunity, by Stewart. The Phylogenesis of Immune Functions, by Warr. The Evolutionary Mechanisms of Defense Reactions, by Vetvicka. Immunity and Evolution, Marchalonias. Immunology of Animals, by Vetvicka. You need some room here. Can you confirm these are books about the evolution of the immune system?

    A: Most of them have evolution or related words in the title, so I can confirm that, but what I strongly doubt is that any of these address the question in a rigorous detailed fashion of how the immune system or irreducibly complex components of it could have arisen by random mutation and natural selection.


    What!? He "strongly doubts"? He doesn't know? If he was familiar with them it wouldn't be "I strongly doubt." Any yet he declared, without any doubt that "simply that they are addressed to a different subject."

    What a charlatan.

    The questioning continued, pointing out how many specifically dealt with transposition and natural selection, the issue at hand, and just kept feeding Behe enough rope to hang himself. Finally it reached this point

    .Q: You haven't read those chapters?

    A: No, I haven't.

    Q: You haven't read the books that I gave you?

    A: No, I haven't. I have read those papers that I presented though yesterday on the immune system.

    Q: And the fifty-eight articles, some yes, some no?

    A: Well, the nice thing about science is that often times when you read the latest articles, or a sampling of the latest articles, they certainly include earlier results. So you get up to speed pretty quickly. You don't have to go back and read every article on a particular topic for the last fifty years or so.


    So out of the "fifty-eight peer-reviewed publications, nine books, and several immunology textbook chapters about the evolution of the immune system" that Behe had dismissed out of hand as not having addressed the subject he had not read any of the books, none of the chapters, and only some of the articles.

    Is it finally starting to sink in yet Lee?
    Last edited by rogue06; 02-21-2021, 09:50 AM.

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  • TheLurch
    replied
    Originally posted by lee_merrill View Post
    Not really, the argument of Darwin's Black Box is quite sound, as shown by his critics being answered in A Mousetrap for Darwin.
    It's only sound if you accept that Behe has answered his critics. Which i don't.

    Leave a comment:


  • TheLurch
    replied
    Originally posted by lee_merrill View Post
    Source: Darwin's Black Box, p. 104

    I emphasize that natural selection, the engine of Darwinian evolution, only works if there is something to select—something that is useful right now, not in the future.

    © Copyright Original Source

    Right, his point was that it was impossible to select for something that only worked when it was completed. Again it could not be selected for at all, ever, under any circumstances. That was his argument then, and therefore something like the proteasome, which only works if most of its parts are present, could never occur through selection. Now, he's willing to accept that it could, as long as the unselected steps don't cross a threshold.

    Originally posted by lee_merrill View Post
    So duplications are unselected,
    This is a fundamental misconception on your part. Duplications, in this case, are just like any other mutation. Point mutations, duplications, deletions - all of them just occur. Selection only kicks in after they occur. The two issues are orthogonal.

    Originally posted by lee_merrill View Post
    how about the sequence of mutations to modify the gene and add it to a proteasome? There needs to be a selectable path.
    I described aspects of selection when i first introduced the proteasome, and you accepted those at the time, to the extent that you agreed the proteasome could evolve. Go back and read the thread.

    Leave a comment:


  • lee_merrill
    replied
    Originally posted by rogue06 View Post
    The whole point of Darwin's Black Box, the central premise of irreducible complexity, is that some things consist of a series of parts in which the removal of any single part would cause the entire thing to cease functioning. That it could not have possibly evolved.
    That's not quite accurate, here is Behe's description:
    Source: Darwin's Black Box, pp. 49-50

    An irreducibly complex biological system, if there is such a thing, would be a powerful challenge to Darwinian evolution. Since natural selection can only choose systems that are already working, then if a biological system cannot be produced gradually it would have to arise as an integrated unit, in one fell swoop, for natural selection to have anything to act on.

    © Copyright Original Source



    That was the argument that got reduced to rubble and the rubble subsequently smashed to dust in the Kitzmiller case
    Not really, the argument of Darwin's Black Box is quite sound, as shown by his critics being answered in A Mousetrap for Darwin.

    And looking at your source what they provided would fill up a few pages. Hardly 90% of 139 pages. Do you honestly think that is 125 pages worth?
    No, this is "90.9% (or 5,458 words) of Judge Jones’ 6,004- word section on intelligent design as science", not of the whole document. I must ask again if you have evidence of Judge Jones understanding the issues under debate. And it appears he mischaracterized Behe's answer in his opinion:

    Source: Discovery

    Judge Jones claimed that biochemist Michael Behe, when confronted with articles supposedly explaining the evolution of the immune system, replied that these articles were “not ‘good enough.’” In reality, Behe said the exact opposite at trial: “it’s not that they aren’t good enough. It’s simply that they are addressed to a different subject.” (emphasis added) The answer cited by Judge Jones came not from Behe, but from the ACLU’s proposed “Findings of Fact,” which misquoted Behe, twisting the substance of his answer.

    Source

    © Copyright Original Source



    Blessings,
    Lee
    Last edited by lee_merrill; 02-20-2021, 02:13 PM.

    Leave a comment:


  • lee_merrill
    replied
    Originally posted by TheLurch View Post
    Not in Darwin's Black Box he didn't, to the best of my ability to remember. Again, his whole point in that book was that it was not possible for these things to be selected for, since they supposedly needed all their parts in order to function.
    Source: Darwin's Black Box, p. 104

    I emphasize that natural selection, the engine of Darwinian evolution, only works if there is something to select—something that is useful right now, not in the future.

    © Copyright Original Source



    Gene duplications happen every single generation in humans, all completely unselected. That's a non-issue. And, unless it's only a partial duplication, it will have function, obviously.
    So duplications are unselected, how about the sequence of mutations to modify the gene and add it to a proteasome? There needs to be a selectable path.

    Blessings,
    Lee

    Leave a comment:


  • rogue06
    replied
    Originally posted by TheLurch View Post
    No, he hasn't. His whole point of irreducible complexity was that there was no possible way to build a complex, interacting system, where every part was essential. This was because it needed all parts present in order to function. That is the ENTIRE thesis of Darwin's Black Box - that selection was irrelevant, because you needed every part in place before you had any function that could be selected for.

    It behooves you to pay attention to your own arguments.

    I already know you don't pay attention to mine, which is why i'm not surprised that you don't remember that i already went over the selectable steps for building a proteasome.
    The whole point of Darwin's Black Box, the central premise of irreducible complexity, is that some things consist of a series of parts in which the removal of any single part would cause the entire thing to cease functioning. That it could not have possibly evolved.

    That was the argument that got reduced to rubble and the rubble subsequently smashed to dust in the Kitzmiller case

    Leave a comment:


  • rogue06
    replied
    Originally posted by lee_merrill View Post
    Yes, I would say they probably did their homework.
    In spite of all the times they've been shown to not only not doing their homework and being duplicitous to boot? Look again at how they even lied about his commencement address.

    And looking at your source what they provided would fill up a few pages. Hardly 90% of 139 pages. Do you honestly think that is 125 pages worth?

    If not then you are in no position to act like you know how much of the plantiff's work he cited.

    Originally posted by lee_merrill View Post
    From all your objections, I gather that you claim Judge Jones understood the arguments. If you do not claim this, we have no disagreement.
    They are not, at least for anyone with even a modicum of understanding about basic biology or even science in general, difficult to comprehend. Unfortunately you have repeatedly demonstrated that doesn't include you or else you wouldn't keep making all of the inane comments and claims that you have in your posts.

    Originally posted by lee_merrill View Post
    That is simply not true, and I advance their arguments here, and they hold up pretty well.
    The truly scary thing here is I'm sure you believe that's true. Sort of like the Black Knight in Monty Python's in Search of the Holy Grail, who insisted he was still winning even has he kept getting his limbs lopped off


    In case you aren't familiar with the reference.

    I should note that the word for an illegitimate child is used twice



    For someone who has repeatedly revealed that you don't possess the barest minimal understanding of even the most fundamental principles of basic biology the only thing left to say is that what you do have is a pretty bad case of Dunning–Kruger syndrome.

    And again, keep in mind what I said here

    Remember the old adage of "Fool me once shame on you. Fool me twice shame on me." IOW, your continued reliance on them reflects poorly on you and your trustworthiness for conveying accurate, reliable information. It doesn't just color your reputation when discussing matters of science but everything else you say as well. That unfortunately means your dependability in being a witness for Christ. Think about that.


    Lee, that isn't meant as an insult but as a caution.


    Leave a comment:


  • TheLurch
    replied
    Originally posted by lee_merrill View Post
    Assuming there is no selectable path! Behe has indeed acknowledged that a selectable path is transversable.
    Not in Darwin's Black Box he didn't, to the best of my ability to remember. Again, his whole point in that book was that it was not possible for these things to be selected for, since they supposedly needed all their parts in order to function.

    Maybe you could find something in that book to show i'm wrong. But given that it was central to his argument, i'd be very surprised.

    Originally posted by lee_merrill View Post
    But each step is not selectable in your analysis, gene duplications for starters, and then is there function after each change in the duplicated gene?
    Gene duplications happen every single generation in humans, all completely unselected. That's a non-issue. And, unless it's only a partial duplication, it will have function, obviously.

    Leave a comment:


  • shunyadragon
    replied
    Originally posted by lee_merrill View Post
    Assuming there is no selectable path! Behe has indeed acknowledged that a selectable path is transversable.
    But each step is not selectable in your analysis, gene duplications for starters, and then is there function after each change in the duplicated gene?

    Blessings,
    Lee
    [/QUOTE]


    You cannot assume 'no selectable path' nor that each step is not selectable.


    Leave a comment:


  • lee_merrill
    replied
    Originally posted by TheLurch View Post
    No, he hasn't. His whole point of irreducible complexity was that there was no possible way to build a complex, interacting system, where every part was essential. This was because it needed all parts present in order to function. That is the ENTIRE thesis of Darwin's Black Box - that selection was irrelevant, because you needed every part in place before you had any function that could be selected for.
    Assuming there is no selectable path! Behe has indeed acknowledged that a selectable path is transversable.

    I already know you don't pay attention to mine, which is why i'm not surprised that you don't remember that i already went over the selectable steps for building a proteasome.
    But each step is not selectable in your analysis, gene duplications for starters, and then is there function after each change in the duplicated gene?

    Blessings,
    Lee

    Leave a comment:


  • TheLurch
    replied
    Originally posted by lee_merrill View Post
    No, Behe has maintained throughout that evolution can proceed down selectable pathways. It behooves you then to show there is an essentially selectable pathway to the proteasome.
    No, he hasn't. His whole point of irreducible complexity was that there was no possible way to build a complex, interacting system, where every part was essential. This was because it needed all parts present in order to function. That is the ENTIRE thesis of Darwin's Black Box - that selection was irrelevant, because you needed every part in place before you had any function that could be selected for.

    It behooves you to pay attention to your own arguments.

    I already know you don't pay attention to mine, which is why i'm not surprised that you don't remember that i already went over the selectable steps for building a proteasome.

    Leave a comment:


  • lee_merrill
    replied
    Originally posted by TheLurch View Post
    Actually, thinking about this, there's a very obvious way to show that Behe had to redefine things.

    Under his original definition, Behe would have claimed that it was impossible for the proteasome to evolve.
    Under his present one, he can accept that it might have.
    No, Behe has maintained throughout that evolution can proceed down selectable pathways. It behooves you then to show there is an essentially selectable pathway to the proteasome.

    Blessings,
    Lee

    Leave a comment:

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