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Imitating biology

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  • Originally posted by lee_merrill View Post
    And here is Brenner's Encyclopedia of Genetics:

    Source: Brenner

    In the first phase, genetic drift causes each subdivision to undergo a random walk in allele frequencies to explore new combinations of genes.

    Source

    © Copyright Original Source



    Blessings,
    Lee
    Congratulations - that's closer! Still not drift, but it's at least something to do with genetic drift and gene frequencies.

    But let's step back and look at the larger situation, shall we? You've been arguing for pages that a random walk is a good model for genetic drift. The ONLY reason you have given for that to be the case is that you think so. When asked for supporting evidence, all you've been able to do is share the results of google searches for "random walk + drift". You don't even bother - or are completely incapable - of trying to understand whether they're relevant to the issue you're trying to argue.

    What does that leave us with? You either know what these citations say, and are incredibly dishonest - just hoping that nobody will notice the fact that you're throwing irrelevancies out in the hope it'll look like you have an argument. Or you have insufficient knowledge of biology to know that what you're putting out is irrelevant.

    Which is it?

    I'm not going to participate in this conversation further until you answer that question.
    "Any sufficiently advanced stupidity is indistinguishable from trolling."

    Comment


    • Originally posted by lee_merrill View Post
      No, the average of the distribution is indeed, the center.
      Yes, for a coin flip where you've assigned an ordered value you can select a well defined center. If DNA consisted of coins with value [-1, 1], then the average value would be 0 for each "base-pair". For one consisting of unordered values [GTCA], you'd have to represent the average as a vector [G:0.25,T:0.25,C:0.25,A:0.25], for each base-pair.

      That would be the center, not "whatever starting point you made." That's been your point but its wrong. Our DNA is not located at the "average-position" which isn't a well-defined notion for DNA at any rate. It's has a value somewhere deep in the phase-space (a fancy way of talking about a huge number of configurations - in this case all of them) of the DNA chain.

      Each mutation, because it is random, increases (by neccessity) the phase-volume that any DNA can be in. Increasing the number of possible configurations. Random mutations by themselves offer no garranty that the DNA is conserved. Quite the opposite.

      What conserves DNA has nothing to do with random mutations. It is selection pressures alone that cause that tendency, but even so about 100 random mutations slips into the gene pool per person per generation.


      Yes, you have a lot of variation, when there are a lot of sites to mutate, but I stand by Wikipedia's statement that the average position is still zero.
      Wikipedia specifies nothing like this for DNA.

      Yes, the variation increases, but variation, and average, and the position after N trials, are different concepts.
      Exactly, that's the point. Over time the variation of DNA increases, however DNA has no well defined average position in terms of a particular strand of DNA. The DNA we have now, isn't an "average position", it is merely an arbitrary position.

      Comment


      • Originally posted by TheLurch View Post
        Congratulations - that's closer! Still not drift, but it's at least something to do with genetic drift and gene frequencies.
        I'm not sure how "something to do with genetic drift" is "not drift," though.

        The ONLY reason you have given for that to be the case is that you think so. When asked for supporting evidence, all you've been able to do is share the results of google searches for "random walk + drift". You don't even bother - or are completely incapable - of trying to understand whether they're relevant to the issue you're trying to argue.
        Well, I think they are indeed relevant! "A random walk with adsorbing boundaries" MIT characterized genetic drift. And Wikipedia agrees: "In population genetics, random walk describes the statistical properties of genetic drift."

        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 Leonhard View Post
          That would be the center, not "whatever starting point you made." That's been your point but its wrong. Our DNA is not located at the "average-position" which isn't a well-defined notion for DNA at any rate. It's has a value somewhere deep in the phase-space (a fancy way of talking about a huge number of configurations - in this case all of them) of the DNA chain.
          Well, the starting point for a random walk of DNA is the molecule of DNA with which you start.

          Each mutation, because it is random, increases (by neccessity) the phase-volume that any DNA can be in. Increasing the number of possible configurations. Random mutations by themselves offer no garranty that the DNA is conserved. Quite the opposite.
          And the variation does increase, but the average position does not move.

          Wikipedia specifies nothing like this for DNA.
          But their results are generalizable to DNA.

          The DNA we have now, isn't an "average position", it is merely an arbitrary position.
          The starting point can be arbitrary, but on average, a random walk won't take you anywhere. Can you show me mathematically how a random walk can have an average position that moves from the starting point?

          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
            I'm not sure how "something to do with genetic drift" is "not drift," though.
            And that's because you don't really understand biology, but have convinced yourself that your ignorance isn't a problem.

            Originally posted by lee_merrill View Post
            Well, I think they are indeed relevant! "A random walk with adsorbing boundaries" MIT characterized genetic drift. And Wikipedia agrees: "In population genetics, random walk describes the statistical properties of genetic drift."
            Without looking it up, could you tell me what "adsorbing boundaries" means in this context?
            "Any sufficiently advanced stupidity is indistinguishable from trolling."

            Comment


            • Originally posted by TheLurch View Post
              Without looking it up, could you tell me what "adsorbing boundaries" means in this context?
              As I recall, it refers to a trait being fixed in the population, where all individuals have one trait. To be more specific, the random walk can take an individual to a place where it stays fixed, and the trait cannot be changed. As I recall...

              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
                As I recall, it refers to a trait being fixed in the population, where all individuals have one trait. To be more specific, the random walk can take an individual to a place where it stays fixed, and the trait cannot be changed. As I recall...

                Blessings,
                Lee
                I recall? This does not take into consideration the natural genetic diversity in the population, which is the 'raw materials' for evolution. I do not know of any population of life where all individuals are genetically the same.
                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.

                Comment


                • Originally posted by lee_merrill View Post
                  As I recall, it refers to a trait being fixed in the population, where all individuals have one trait. To be more specific, the random walk can take an individual to a place where it stays fixed, and the trait cannot be changed. As I recall...
                  You're wrong. It's a specific technical term describing the mechanisms used in the model. You're describing the result of the model.

                  Again, you haven't the slightest clue what you're talking about. You'd think this being demonstrated nearly every time you post would trigger a bit of humility and self reflection. But i guess that's asking a bit much.
                  "Any sufficiently advanced stupidity is indistinguishable from trolling."

                  Comment


                  • Originally posted by TheLurch View Post
                    You're wrong. It's a specific technical term describing the mechanisms used in the model. You're describing the result of the model.
                    I described how the model worked:

                    Source: MIT

                    We need to describe it using a random walk with adsorbing boundaries. This sounds scary, but it’s very simple. Imagine instead of our random walkers from the previous page having an infinite line to step on, they have a line of a fixed number of spaces with a ice cream shop at either end of the line. When a walker reaches either ice cream shop instead of continuing to flip the coin and move, the walker will spend the coin on a cone and stay at the ice cream space to enjoy an afternoon snack.

                    Source

                    © Copyright Original Source



                    And genetic drift is reasonably described by a random walk, as shown by this source.

                    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 shunyadragon View Post
                      This does not take into consideration the natural genetic diversity in the population, which is the 'raw materials' for evolution. I do not know of any population of life where all individuals are genetically the same.
                      No, it's a trait that can get fixed, not that all individuals are the same genetically.

                      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
                        Yet a sparse landscape will make it likely that evolution will get stuck on a local optimum, regardless of the temporal stability, the ease of motion, etc.

                        Blessings,
                        Lee
                        Yes, and it has been documented many times that the animals become extinct.
                        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.

                        Comment


                        • Originally posted by lee_merrill View Post
                          No, it's a trait that can get fixed, not that all individuals are the same genetically.

                          Blessings,
                          Lee
                          What is the problem with some traits that are fixed and others change and diversify?
                          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.

                          Comment


                          • Originally posted by lee_merrill View Post
                            I described how the model worked:
                            Yet, when asked about it, you got the description wrong. Which shows that all you're capable of doing is copying and pasting - you can't even understand the quotes you're using.

                            Originally posted by lee_merrill View Post
                            And genetic drift is reasonably described by a random walk, as shown by this source.
                            By that standard, going to an ice cream shop reasonably describes genetic drift, since they used that as part of the model too.

                            As i said earlier, this is for teaching. You cannot find any cases in the peer reviewed literature where a random walk is used to model it.

                            Why do we have to go around in circles on these things? Is it because you can't remember discussions for more than 2 days?
                            "Any sufficiently advanced stupidity is indistinguishable from trolling."

                            Comment


                            • Originally posted by shunyadragon View Post

                              What is the problem with some traits that are fixed and others change and diversify?
                              I'm not sure what you are asking here, I see no problem with this.

                              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
                                Yet, when asked about it, you got the description wrong. Which shows that all you're capable of doing is copying and pasting - you can't even understand the quotes you're using.
                                I think I got the description right, though.

                                By that standard, going to an ice cream shop reasonably describes genetic drift, since they used that as part of the model too.
                                No, that was just a way of giving an analogy to their model.

                                As i said earlier, this is for teaching. You cannot find any cases in the peer reviewed literature where a random walk is used to model it.
                                I found something pretty close. And are you saying MIT is wrong?

                                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

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