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The lungfish genome, tetrapods, and junk DNA

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  • Originally posted by TheLurch View Post
    Yes, because it didn't fit his original definition of specified complexity. Not because of selectability.
    Source: Darwin's Black Box, p. 221

    The starting point, myoglobin, already can bind oxygen. The behavior of hemoglobin can be achieved by a rather simple modification of the behavior of myoglobin, and the individual proteins of hemoglobin strongly resemble myoglobin. So although hemoglobin can be thought of as a system with interacting parts, the interaction does nothing much that is clearly beyond the individual components of the system.

    © Copyright Original Source


    I.e. the path is selectable, myoglobin => hemoglobin.

    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.
    It's the same thing with the blue structure. It's a ring, and all members of the ring are descendants of a single ancestral protein. It only took one protein-protein interaction to make the ring, then another to get it to link to the red structure, and then a series of duplication/diversification events to create lots of individual, specialized genes instead of a single, generalist version.
    I question the "series of duplication/diversification events" as selectable.

    What about all that stuff on top? That's all built out of individual protein-protein interactions. Once the scaffolding was in place, interactions among them could be selected for, and have in a couple of places.
    Just two? I need a basically selectable paths throughout.

    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)

    Comment


    • Originally posted by lee_merrill View Post
      Source: Darwin's Black Box, p. 221

      The starting point, myoglobin, already can bind oxygen. The behavior of hemoglobin can be achieved by a rather simple modification of the behavior of myoglobin, and the individual proteins of hemoglobin strongly resemble myoglobin. So although hemoglobin can be thought of as a system with interacting parts, the interaction does nothing much that is clearly beyond the individual components of the system.

      © Copyright Original Source


      I.e. the path is selectable, myoglobin => hemoglobin.
      There's absolutely nothing in what you cite about selection. So why are you pretending there is? Have you decided the rest of us can't read now?

      Originally posted by lee_merrill View Post
      I question the "series of duplication/diversification events" as selectable.
      I explained how they provide biological advantages, and therefore could be selected for. What part of that do you have issues with?
      "Any sufficiently advanced stupidity is indistinguishable from trolling."

      Comment


      • Originally posted by TheLurch View Post
        There's absolutely nothing in what you cite about selection. So why are you pretending there is? Have you decided the rest of us can't read now?
        "The behavior of hemoglobin can be achieved by a rather simple modification of the behavior of myoglobin...", therefore, both are selectable, therefore, the path is selected.

        I explained how they provide biological advantages, and therefore could be selected for. What part of that do you have issues with?
        I don't see this in the thread, could you quote where you explain how each step has a biological advantage?

        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)

        Comment


        • Originally posted by lee_merrill View Post
          "The behavior of hemoglobin can be achieved by a rather simple modification of the behavior of myoglobin...", therefore, both are selectable, therefore, the path is selected.
          No, that's not true. If it were, any pathway with selectable end points would have a selectable path between them, and Behe wouldn't have an argument at all.

          Originally posted by lee_merrill View Post
          I don't see this in the thread, could you quote where you explain how each step has a biological advantage?
          I can give you the equivalent by memory: the diversification creates a greater range of protein substrates that can be digested, and is therefore advantageous.
          "Any sufficiently advanced stupidity is indistinguishable from trolling."

          Comment


          • Originally posted by lee_merrill View Post
            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.
            He's declaring that they couldn't have evolved until after they had "arise[n] as an integrated unit, in one fell swoop." IOW, they didn't evolve they just magically appeared after which point they could start evolving.

            Originally posted by lee_merrill View Post
            "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.
            All were answered in detail in that thread in spite of your notorious bad memory resulting in you now claiming otherwise.

            Originally posted by lee_merrill View Post
            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

            Interesting that you keep going to the Discovery Institute's representation of the trial rather than the actual transcript. But I guess in that way you can be spoon fed the bits they want you to see and not the context and uncomfortable things like how Behe was forced to admit that he hadn't read but a few of the "fifty-eight peer-reviewed publications, nine books, and several immunology textbook chapters about the evolution of the immune system" that he had disdainfully dismissed out of hand as addressing a different subject.

            If you were looking at the transcripts you could show whether or not Behe had done more than simply made an assertion without basis like he did with the literally dozens of examples that refuted his claims with an arrogant hand wave.

            Moreover, none of those steps required intelligence but as McDonald accurately stated would represent a single mutational event.

            Originally posted by lee_merrill View Post
            But again, that was a sample. And this 90% is the critical part for judge Jones to demonstrate his understanding, "intelligent design as science".
            If you had more than just the sample that the Discovery Institute provided you should supply it. And again you are deliberately (to the point of dishonestly) ignoring that it is standard practice to quote heavily from the findings of fact offered by the side you think was correct only adding a few elaborations or clarifications here and there.

            Not to mention how you have breezed right over without rebuttal how your source cannot be trusted in that they got caught making false statements about Jones plagiarizing his commencement speech resorting to disreputable quote mines to give a deliberately false impression.

            Tell me Lee, if they did so there as I demonstrated, why do you believe that they wouldn't do so elsewhere? Or is this just something you'll close your eyes to and ignore?


            Now getting back to your statement here... You are aware that Behe was forced to concede that in order for Intelligent Design to qualify as a valid scientific theory that you would have to distort the definition of scientific theory to the point that it would include things like astrology, right? I'm not talking about astronomy but astrology -- the pseudoscientific belief that you can divine information about human affairs and terrestrial events by studying the movements and relative positions of celestial objects.

            Now I know that the Discovery Institute tells their lemmings that isn't true so let's look at the transcript again.

            Q: And using your definition, intelligent design is a scientific theory, correct?

            A: Yes.

            Q: Under that same definition astrology is a scientific theory under your definition, correct?

            A: Under my definition, a scientific theory is a proposed explanation which focuses or points to physical, observable data and logical inferences. There are many things throughout the history of science which we now think to be incorrect which nonetheless would fit that -- which would fit that definition. Yes, astrology is in fact one, and so is the ether theory of the propagation of light, and many other -- many other theories as well.

            Q: The ether theory of light has been discarded, correct?

            A:That is correct.

            Q: But you are clear, under your definition, the definition that sweeps in intelligent design, astrology is also a scientific theory, correct?

            A: Yes, that's correct.


            Ouch.

            Behe then continues by giving his own personal definition for "theory," which only confirms that you have to change it to the point that it includes crap like astrology. In science "theory" has a very specific meaning: What "theory" means in science

            IOW, Jones did demonstrate his understanding of "intelligent design as science." That it isn't. That it is pseudoscientific claptrap on par with astrology.

            Originally posted by lee_merrill View Post
            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.
            Yeah, let's just gloss over how Behe got nailed for making a sweeping claim that he couldn't even begin to back up. In a court of law.

            After getting caught with his pants down for telling that whopper, Behe's "explanation" for why it wasn't just that it wasn't good enough fell apart like a house of cards in a hurricane. His assertion that "It's simply that they are addressed to a different subject" got flushed leaving him with nothing more than "it's not good enough."




            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)
            "Of course, human life begins at fertilization thatís not the argument." --Tassman

            Comment


            • Originally posted by TheLurch View Post
              There's absolutely nothing in what you cite about selection. So why are you pretending there is? Have you decided the rest of us can't read now?
              More like yet another example that Lee does not possess even the slightest clue about the most basic aspects of biology and yet feels confident to lecture on it.

              Dunning–Kruger syndrome

              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)
              "Of course, human life begins at fertilization thatís not the argument." --Tassman

              Comment


              • Originally posted by rogue06 View Post
                Yeah, let's just gloss over how Behe got nailed for making a sweeping claim that he couldn't even begin to back up. In a court of law.
                I think the fundamental need to redefine science so that Behe's version of intelligent design is something that's under-emphasized. Beyond the astrology issue, Behe wants to change how science approaches the unknown. For the origin of a biological system, we have a successful theory - evolution - that should be the default explanation in the absence of any other evidence. In other words, if we describe a new feature of biology, we default to assuming "it came about through evolution", since evolution successfully explains the vast majority of things we've looked at in detail. Should, for whatever reason, evolution prove insufficient to explain a system, the default shifts to "we don't know yet."

                Behe makes two changes to how science functions in this regard. One, without convincing any scientists, he believes that he has found a set of circumstances where evolution is always insufficient. But he's done that without considering all the known mechanisms by which evolution occurs, which is why his argument hasn't convinced the scientific community. And, despite his lack of success, he wants that to dethrone the default explanation.

                But it gets worse. Rather than simply shifting to "we don't know yet", which is how science has functioned for centuries, he wants design to be the default explanation. He does this without any evidence in favor of design whatsoever (this is the whole false dichotomy issue that was discussed extensively at Dover).

                It's a radical change to science, and one that seems to be under appreciated. Behe really does want to throw science as we know it out
                "Any sufficiently advanced stupidity is indistinguishable from trolling."

                Comment


                • This might be worthy of a thread of its own

                  Originally posted by TheLurch View Post
                  I think the fundamental need to redefine science so that Behe's version of intelligent design is something that's under-emphasized. Beyond the astrology issue, Behe wants to change how science approaches the unknown. For the origin of a biological system, we have a successful theory - evolution - that should be the default explanation in the absence of any other evidence. In other words, if we describe a new feature of biology, we default to assuming "it came about through evolution", since evolution successfully explains the vast majority of things we've looked at in detail. Should, for whatever reason, evolution prove insufficient to explain a system, the default shifts to "we don't know yet."

                  Behe makes two changes to how science functions in this regard. One, without convincing any scientists, he believes that he has found a set of circumstances where evolution is always insufficient. But he's done that without considering all the known mechanisms by which evolution occurs, which is why his argument hasn't convinced the scientific community. And, despite his lack of success, he wants that to dethrone the default explanation.

                  But it gets worse. Rather than simply shifting to "we don't know yet", which is how science has functioned for centuries, he wants design to be the default explanation. He does this without any evidence in favor of design whatsoever (this is the whole false dichotomy issue that was discussed extensively at Dover).

                  It's a radical change to science, and one that seems to be under appreciated. Behe really does want to throw science as we know it out
                  Kenneth Miller (who, coincidentally, was the plaintiff's lead expert witness at Kitzmiller) devotes an entire chapter of his Only a Theory: Evolution and the Battle for America's Soul to just that issue, discussing, in chapter seven (Closing the American Scientific Mind), the goal of ID:

                  Its goals went far beyond merely carving out a little scientific respectability for antievolutionism, and extended all the way to a complete redefinition of the way science -- all of science -- is done. The proponents of ID seek nothing less than a true scientific revolution, an uprising of the first order that would do a great deal more than just displace Darwin from our textbooks and curricula. They seek the undoing of four centuries of Western science, and that surely should be enough to make anyone sit up and pay attention.


                  As we can see with Behe and other ID proponents (or is that cdesign proponentsists ​) they seek to bastardize science to the point where crap like astrology is a legitimate scientific theory.

                  Miller also spells out how the "cdesign proponentsists" are seeking to insert the equivalent of cultural relativism into the natural sciences and wanting nothing less than the dismantling of the scientific method (the cornerstone of all scientific thought) noting

                  Quite the consciously Johnson then set about developing a strategy that would subject science to the same relativistic critique that had already affected the rest of academia. That strategy would become known as the Wedge...


                  "Johnson" here is a reference to Phillip E. Johnson, the lawyer who the I.D. community fondly refers to as the godfather and "Mahatma" of their movement, author of the "Wedge strategy" (an attempt to split Americans away from "naturalistic science" by portraying science as we know it as innately antireligious and forcing them to choose between science and religion) which he outlined in The Wedge Document.

                  Again quoting Miller

                  The real target of the movement, as the document makes clear, is the whole of science, and materialistic foundations of the scientific process


                  Effectively, they want to hurl science back into the early Middle Ages.
                  Last edited by rogue06; 02-22-2021, 05:35 PM. Reason: accidentally added a "the" into the quote

                  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)
                  "Of course, human life begins at fertilization thatís not the argument." --Tassman

                  Comment


                  • Originally posted by TheLurch View Post
                    No, that's not true. If it were, any pathway with selectable end points would have a selectable path between them, and Behe wouldn't have an argument at all.
                    Well, I would say that myoglobin converts to hemoglobin in a few selectable steps, adding globulin groups.

                    I can give you the equivalent by memory: the diversification creates a greater range of protein substrates that can be digested, and is therefore advantageous.
                    Then that would be a selectable pathway, and the proteasome can develop through evolution, according to Behe.

                    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)

                    Comment


                    • Originally posted by TheLurch View Post
                      But [Behe]'s done that without considering all the known mechanisms by which evolution occurs...
                      No, Behe looks in the Edge of Evolution at what evolution has actually done, with all its mechanisms available, and concludes from there.

                      Rather than simply shifting to "we don't know yet", which is how science has functioned for centuries, he wants design to be the default explanation.
                      Well, Dembski proposed a "probability bound" as part of concluding design, so design is not the default explanation. An event has to be inordinately improbable by natural causes before design is considered.

                      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)

                      Comment


                      • Originally posted by lee_merrill View Post
                        Well, I would say that myoglobin converts to hemoglobin in a few selectable steps, adding globulin groups.
                        Based on what?

                        Originally posted by lee_merrill View Post
                        Then that would be a selectable pathway, and the proteasome can develop through evolution, according to Behe.
                        Again, according to Behe's more recent definition. Not according to his original one.
                        "Any sufficiently advanced stupidity is indistinguishable from trolling."

                        Comment


                        • Originally posted by TheLurch View Post
                          Based on what?
                          How about here?

                          Source: Pharmaceutical Intelligence

                          Primitive Globin – Very primitive animals had only a myoglobin-like, single-chain ancestral globin for oxygen storage and were so small that they did not require a transport protein. Roughly 500 million years ago the ancestral myoglobin gene was duplicated. One copy became the ancestor of the myoglobin genes of all higher organisms. The other copy evolved into the gene for an oxygen transport protein and gave rise to the hemoglobins.

                          Source

                          © Copyright Original Source



                          Again, according to Behe's more recent definition. Not according to his original one.
                          Source: Darwin's Black Box

                          Some features of the cell appear to be the result of simple natural processes, others probably so.

                          © Copyright Original Source


                          So "simple natural processes" here would include mutation and selection.

                          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)

                          Comment


                          • Originally posted by lee_merrill View Post
                            How about here?
                            You said it was a few selectable steps. This doesn't mention any of the steps, or whether they were selectable.

                            Now, you may think i'm being unreasonable asking for that - if so, let me know and i'll explain why.

                            (In any case, i find it interesting that you're now enthused about a case of duplication and diversification.)


                            Originally posted by lee_merrill View Post
                            Source: Darwin's Black Box

                            Some features of the cell appear to be the result of simple natural processes, others probably so.

                            © Copyright Original Source


                            So "simple natural processes" here would include mutation and selection.
                            Look, Lee, i know Darwin's Black Box. His entire argument was that protein systems that have >4 components and fail to work if any one of them is deleted could not evolve. Period. He placed them beyond the ability of mutation and selection to produce. That was the entire thesis of the book - the whole thing was focused on that concept.

                            Are you trying to rewrite history just because you can't accept that Behe was ever wrong, or is there something else going on here?
                            "Any sufficiently advanced stupidity is indistinguishable from trolling."

                            Comment


                            • Originally posted by TheLurch View Post
                              You said it was a few selectable steps. This doesn't mention any of the steps, or whether they were selectable.
                              Well, how about here?

                              Source: University of Nebraska

                              Yet after narrowing down suspects and modeling the behavior of the subunits with various mutations, the team concluded that just two — both along the surface of the beta chain — encouraged the beta to bind with the alpha and, in turn, the alpha-beta duo to bind with another.

                              Source

                              © Copyright Original Source



                              [Behe's] entire argument was that protein systems that have >4 components and fail to work if any one of them is deleted could not evolve. Period. He placed them beyond the ability of mutation and selection to produce.
                              I think you are conflating The Edge of Evolution (a double "CCC", requiring 4 mutations) with Darwin's Black Box. But his argument is that irreducibly complex systems probably cannot evolve, their evolution is unlikely.

                              "Some features of the cell appear to be the result of simple natural processes, others probably so." (Behe) Surely this implies that selectable paths can be followed by evolution.

                              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)

                              Comment


                              • Originally posted by lee_merrill View Post
                                Well, how about here?

                                Source: University of Nebraska

                                Yet after narrowing down suspects and modeling the behavior of the subunits with various mutations, the team concluded that just two — both along the surface of the beta chain — encouraged the beta to bind with the alpha and, in turn, the alpha-beta duo to bind with another.

                                Source

                                © Copyright Original Source

                                I appreciate you finding supportive evidence for your contentions. Next time, you might consider doing so before making the contentions.


                                Originally posted by lee_merrill View Post
                                I think you are conflating The Edge of Evolution (a double "CCC", requiring 4 mutations) with Darwin's Black Box. But his argument is that irreducibly complex systems probably cannot evolve, their evolution is unlikely.
                                Pretty sure i'm not. You can look at the Wikipedia page on it to confirm this.
                                "Any sufficiently advanced stupidity is indistinguishable from trolling."

                                Comment

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