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Nice defense of Evolution

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  • Nice defense of Evolution

    This was a message sent to me by someone on Facebook a while back, and I thought you guys could like it. It talks about epistemology of science and the difference between evolution and creationism. Wothout further ado, here it is:

    Hello Gabriel,

    I am 47 years old, I have a doctorate in structural biochemistry and I am a teacher. I do research mainly on artificial intelligence and bioinformatics. But I am not an "evolutionist." The term "evolutionist" is a term used by creationists to give the idea that creationism is on par with a scientific theory like evolution, but it has nothing to do with each other.

    Evolution, to me, is like electromagnetism, gravity or organic chemistry. I do not believe in these phenomena and theories by personal conviction, but rather because they are clearly the best source of explanations for such things. Note that the theory of evolution gives you rigorous mathematical models of population genetics, explains how species characteristics have become fixed, underlies all modern genetics and proteomics, and so on.

    Creationism says only that it was God who did all this but that explains nothing. You can't use creationism for anything in practice. It is a mere religious choice. And that results in another important difference. The creationist is creationist first, by his faith and personal conviction. Then he may be interested in looking for more information, but this will be secondary. The so-called “evolutionist” is simply someone interested in understanding things and who has no problem believing in something today and tomorrow if a better explanation is found that justifies changing their beliefs.

    As for wanting to "know which is the most correct [theory] based on the evidence," it is not just a matter of being correct or not. Consider the theory of relativity and all the mathematical models derived from it, which allow us to have a GPS system, send probes to other planets, calculate the position of the planets, the mass of the sun and a ton of other stuff. If one proposes to replace this with “God makes things move,” the problem is not just which one is right or correct. One must also consider that the latter is completely useless. You can't do anything with it.

    The same goes for the theory of evolution and creationism. The theory of evolution is not just speculation and talk. These are rigorous mathematical models that allow you to do things like analyze genomes, optimize the use of antibiotics and vaccines, estimate the risk of a species becoming extinct due to loss of genetic diversity, and so on.

    Another important aspect related to this is the specificity of the theory. Imagine the world was very different. There were trilobite fossils mixed with rabbit fossils, there were species with DNA and carbon-based molecules, other with silicon, others with completely different molecules. There were vulture-headed monkeys and goat-legged lizards, and dragons and so on. Whatever you imagine is compatible with creationism. In any case, it could have all been the creation of an omnipotent god.

    But the theory of evolution only applies to very narrow cases. For example, if a set of species evolved from a common ancestor, those species are distributed in a family tree and must have similarities to each other, the differences must be grouped into their respective branches, and so on. Only a very small subset of what could be is compatible with the theory of evolution. And it is precisely what we observe. For example, chickens still have the teeth genes inherited from their reptilian ancestors: https://www.scientificamerican.com/…...icken-grows-…/

    Of course, an omnipotent god could also have created the chicken with crocodile genes and inactivated the genes so that they would not express themselves. But it's hard to see why the in the world he would do such a thing.

    In short, creationism is a personal belief of some people who want to believe that this was all done by their god. They are in their rights. But it explains nothing, is of no use in practice, and if we want to understand reality, evolution is a much better and more grounded alternative. As for "evolutionism," this is like calling "gravitationalism" to someone who believes that there is gravity just to appear that the contrary belief has any merit. :)

    As for the [creationist] statement you asked me to counter:

    '' [...] we don't see random changes doing that to enzymes (increasing their specificity) on a scale which could possibly account for all of life's specified complexity ''.

    I cannot rebut this statement because, if I interpret it correctly, it seems to me to be true.

    Suppose ‘’we don't see’’ means we can't observe in the lab. If that is what he means, then of course we cannot see changes in the scale needed to explain the full complexity of life because this is a process that has been going on for four billion years.

    But that is like claiming that you have never seen anyone grow to age 80. You're only 25 years old, so it's impossible to have seen someone born, grow up and grow old until 80. But it would be nonsense because we can see some people getting older from 79 to 80, others from 78 to 79 and so on. Putting the puzzle pieces together it is obvious that people can grow old from birth to 80.

    This is what happens with evolution. If you look at only one enzyme you have no idea what has happened in the last 4 billion years. But if you put the pieces together, looking at this change here, that one there, the fossil remains, the similarities and differences in today's species, and so forth, all of this together is immense evidence for evolution, and none of that creationism can explain because, unlike evolution, creationism explains nothing. In fact, if you have read many creationist books, you may have noticed that the only thing they talk about is the theory of evolution. They can't explain why our retina is upside down but that of the octopus is right, why the recurrent laryngeal nerve passes under the subclavian artery, why the dolphin is genetically more like us than the shark, and a million other things.

  • #2
    Please feel free to share any insights and/or comments.

    Comment


    • #3
      Excellent review of the evidence for evolution and the billions of years of history, which would be very much in agreement with 99% of all scientists in the relevant fields from biology, organic chemistry, evolution, geology to cosmology.
      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


      • #4
        Errata: ''[...]believing something today AND ANOTHER tomorrow if a[...]

        Comment


        • #5
          Originally posted by Seeker View Post
          If you look at only one enzyme you have no idea what has happened in the last 4 billion years. But if you put the pieces together, looking at this change here, that one there, the fossil remains, the similarities and differences in today's species, and so forth, all of this together is immense evidence for evolution...
          Let's take this quote, which seems to me to be handwaving. How does this demonstrate evolution of enzymes?

          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


          • #6
            Originally posted by lee_merrill View Post
            Let's take this quote, which seems to me to be handwaving. How does this demonstrate evolution of enzymes?

            Blessings,
            Lee
            The scientific research references cited concerning the role of enzymes in abiogenesis and evolution have been demonstrated many many times in previous threads, but you choose to self-imposed ignorant based on a religious agenda.
            Last edited by shunyadragon; 10-25-2019, 09:07 PM.
            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


            • #7
              Originally posted by lee_merrill View Post
              Let's take this quote, which seems to me to be handwaving. How does this demonstrate evolution of enzymes?

              Blessings,
              Lee
              You mean the evolution of increased enzyme specificity? If so, that can be explained too, although it can get a bit technical.

              Comment


              • #8
                Originally posted by lee_merrill View Post
                Let's take this quote, which seems to me to be handwaving. How does this demonstrate evolution of enzymes?

                Blessings,
                Lee
                One point you never have been able to comprehend in terms of the role of enzymes in abiogenesis and evolution, despite numerous scientific references provided in previous threads, is that enzymes themselves do not evolve. The scientific literature previously cited demonstrated the increased specificity of enzymes in the process of abiogenesis and evolution. If an enzyme or a particular combination of enzymes works the process selected for that enzyme or combination. When the enzyme or combination did not work it was selected against that enzyme or combination. It has been demonstrated that new enzymes are produced in the process of the selectivity of natural evolution.

                Source: https://pdfs.semanticscholar.org/0fff/2c3f5e604bd8928611182d531507d74b752d.pdf


                The nature of chemical innovation: new enzymes by evolution*

                Frances H. Arnold

                Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, Pasadena, CA 91125, USA
                Quarterly Reviews of Biophysics (2015), 48(4), pages 404–410 doi:10.1017/S003358351500013X

                Abstract. I describe how we direct the evolution of non-natural enzyme activities, using chemical intuition and information on structure and
                mechanism to guide us to the most promising reaction/enzyme systems. With synthetic reagents to generate new reactive intermediates and
                just a few amino acid substitutions to tune the active site, a cytochrome P450 can catalyze a variety of carbene and nitrene transfer reactions.
                The cyclopropanation, N–H insertion, C–H amination, sulfimidation, and aziridination reactions now demonstrated are all well known in
                chemical catalysis but have no counterparts in nature. The new enzymes are fully genetically encoded, assemble and function inside of
                cells, and can be optimized for different substrates, activities, and selectivities. We are learning how to use nature’s innovation mechanisms
                to marry some of the synthetic chemists’ favorite transformations with the exquisite selectivity and tunability of enzymes.

                © Copyright Original Source



                One comment often dishonestly misrepresented and misused by Creationists is the use of 'directed' in scientific literature. 'Directed' here refers to natural chemical and structural nature that cause the result, and not outside 'directed' cause of the natural chemical processes.
                Last edited by shunyadragon; 10-26-2019, 09:47 AM.
                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


                • #9
                  Originally posted by Seeker View Post
                  You mean the evolution of increased enzyme specificity? If so, that can be explained too, although it can get a bit technical.
                  One problem with the creationist arguments is rooted in the following:

                  As for the [creationist] statement you asked me to counter:

                  '' [...] we don't see random changes doing that to enzymes (increasing their specificity) on a scale which could possibly account for all of life's specified complexity ''.
                  The problem is that the only thing that is 'random' is the outcome of the individual cause and effect events within a limited range limited by the Laws of Nature. The variation in the range of possible outcomes of individual cause and effect results is described as fractal in what we know as Chaos Theory. The outcome of the chain of cause and effect outcomes is not random, but determined within the limits of the Laws of NAture, environment and the circumstances surrounding the chain of cause and effect outcomes.

                  This relates to the use of the terminology 'directed' in scientific literature. The outcome of the series of cause and effect outcomes in nature is 'directed' by the Laws of NAture, environments, chemical and structural properties of chemical in nature.
                  Last edited by shunyadragon; 10-26-2019, 10:19 AM.
                  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


                  • #10
                    Originally posted by lee_merrill View Post
                    Let's take this quote, which seems to me to be handwaving. How does this demonstrate evolution of enzymes?
                    Easiest way is just sequence comparisons. So, take a current antibiotic resistance enzyme or nylonase or something like that, figure out what proteins it is most closely related to, then compare their genes. See which mutations occurred, make the intermediate proteins, and test those. You'll eventually figure out the pathway that took it from the past to the present.

                    Now, you could object that we don't actually see each individual step take place, but we don't see each individual step involved with a seed growing into mature tree, but nobody seems to object to growth being the explanation - there's no "tree creationism."
                    "Any sufficiently advanced stupidity is indistinguishable from trolling."

                    Comment


                    • #11
                      As TL has mentioned we have actually seen enzymes evolve.

                      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 that’s not the argument." --Tassman

                      Comment


                      • #12
                        Originally posted by Seeker View Post
                        This was a message sent to me by someone on Facebook a while back, and I thought you guys could like it. It talks about epistemology of science and the difference between evolution and creationism. Wothout further ado, here it is:

                        Hello Gabriel,

                        I am 47 years old, I have a doctorate in structural biochemistry and I am a teacher. I do research mainly on artificial intelligence and bioinformatics. But I am not an "evolutionist." The term "evolutionist" is a term used by creationists to give the idea that creationism is on par with a scientific theory like evolution, but it has nothing to do with each other.

                        Evolution, to me, is like electromagnetism, gravity or organic chemistry. I do not believe in these phenomena and theories by personal conviction, but rather because they are clearly the best source of explanations for such things. Note that the theory of evolution gives you rigorous mathematical models of population genetics, explains how species characteristics have become fixed, underlies all modern genetics and proteomics, and so on.

                        Creationism says only that it was God who did all this but that explains nothing. You can't use creationism for anything in practice. It is a mere religious choice. And that results in another important difference. The creationist is creationist first, by his faith and personal conviction. Then he may be interested in looking for more information, but this will be secondary. The so-called “evolutionist” is simply someone interested in understanding things and who has no problem believing in something today and tomorrow if a better explanation is found that justifies changing their beliefs.

                        As for wanting to "know which is the most correct [theory] based on the evidence," it is not just a matter of being correct or not. Consider the theory of relativity and all the mathematical models derived from it, which allow us to have a GPS system, send probes to other planets, calculate the position of the planets, the mass of the sun and a ton of other stuff. If one proposes to replace this with “God makes things move,” the problem is not just which one is right or correct. One must also consider that the latter is completely useless. You can't do anything with it.

                        The same goes for the theory of evolution and creationism. The theory of evolution is not just speculation and talk. These are rigorous mathematical models that allow you to do things like analyze genomes, optimize the use of antibiotics and vaccines, estimate the risk of a species becoming extinct due to loss of genetic diversity, and so on.

                        Another important aspect related to this is the specificity of the theory. Imagine the world was very different. There were trilobite fossils mixed with rabbit fossils, there were species with DNA and carbon-based molecules, other with silicon, others with completely different molecules. There were vulture-headed monkeys and goat-legged lizards, and dragons and so on. Whatever you imagine is compatible with creationism. In any case, it could have all been the creation of an omnipotent god.

                        But the theory of evolution only applies to very narrow cases. For example, if a set of species evolved from a common ancestor, those species are distributed in a family tree and must have similarities to each other, the differences must be grouped into their respective branches, and so on. Only a very small subset of what could be is compatible with the theory of evolution. And it is precisely what we observe. For example, chickens still have the teeth genes inherited from their reptilian ancestors: https://www.scientificamerican.com/…...icken-grows-…/

                        Of course, an omnipotent god could also have created the chicken with crocodile genes and inactivated the genes so that they would not express themselves. But it's hard to see why the in the world he would do such a thing.

                        In short, creationism is a personal belief of some people who want to believe that this was all done by their god. They are in their rights. But it explains nothing, is of no use in practice, and if we want to understand reality, evolution is a much better and more grounded alternative. As for "evolutionism," this is like calling "gravitationalism" to someone who believes that there is gravity just to appear that the contrary belief has any merit. :)

                        As for the [creationist] statement you asked me to counter:

                        '' [...] we don't see random changes doing that to enzymes (increasing their specificity) on a scale which could possibly account for all of life's specified complexity ''.

                        I cannot rebut this statement because, if I interpret it correctly, it seems to me to be true.

                        Suppose ‘’we don't see’’ means we can't observe in the lab. If that is what he means, then of course we cannot see changes in the scale needed to explain the full complexity of life because this is a process that has been going on for four billion years.

                        But that is like claiming that you have never seen anyone grow to age 80. You're only 25 years old, so it's impossible to have seen someone born, grow up and grow old until 80. But it would be nonsense because we can see some people getting older from 79 to 80, others from 78 to 79 and so on. Putting the puzzle pieces together it is obvious that people can grow old from birth to 80.

                        This is what happens with evolution. If you look at only one enzyme you have no idea what has happened in the last 4 billion years. But if you put the pieces together, looking at this change here, that one there, the fossil remains, the similarities and differences in today's species, and so forth, all of this together is immense evidence for evolution, and none of that creationism can explain because, unlike evolution, creationism explains nothing. In fact, if you have read many creationist books, you may have noticed that the only thing they talk about is the theory of evolution. They can't explain why our retina is upside down but that of the octopus is right, why the recurrent laryngeal nerve passes under the subclavian artery, why the dolphin is genetically more like us than the shark, and a million other things.
                        While "creationists" will use the term "evolutionist" their favorite by far is "Darwinist" or "Darwinism." It's like calling gravitational theory "Newtonism" or atomic theory "Daltonism."

                        Just plain silly.

                        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 that’s not the argument." --Tassman

                        Comment


                        • #13
                          Originally posted by TheLurch View Post
                          Easiest way is just sequence comparisons. So, take a current antibiotic resistance enzyme or nylonase or something like that, figure out what proteins it is most closely related to, then compare their genes. See which mutations occurred, make the intermediate proteins, and test those. You'll eventually figure out the pathway that took it from the past to the present.
                          Well, with nylonase it appears to be essentially two selectable mutations, which no one disputes can happen. But to have a path of many mutations requires a search of protein space, which Dougas Axe has shown to be prohibitive.

                          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


                          • #14
                            Originally posted by lee_merrill View Post
                            Well, with nylonase it appears to be essentially two selectable mutations, which no one disputes can happen. But to have a path of many mutations requires a search of protein space, which Dougas Axe has shown to be prohibitive.

                            Blessings,
                            Lee
                            Douglas Axe may believe this, but virtually all the other scientist in Biology do not, and his bias is apparent as a devoted follower of the Discovery Institute. He has done any actual research nor not published or submitting anything related to evolution in a peer reviewed biology journal outside the Discovery Institute.

                            Much of this work like the rest of the discovery institute base their work on the dishonest misuse of statistics and probability to justify a religious agenda, with a heavy dose of 'arguing from ignorance' and not the sound scientific research in the biological science related to the field of organic chemistry and evolution.

                            It is an unsubstantiated claim, and has not been shown to be prohibitive in the peer reviewed literature in the biological sciences..
                            Last edited by shunyadragon; 10-27-2019, 10:20 AM.
                            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


                            • #15
                              Originally posted by lee_merrill View Post
                              Well, with nylonase it appears to be essentially two selectable mutations, which no one disputes can happen. But to have a path of many mutations requires a search of protein space, which Dougas Axe has shown to be prohibitive.
                              No, what he showed was that if you have no selection on intermediate steps, then proteins frequently get disabled after several mutations. But nobody's proposing that proteins stop being under selection when evolving - with a few exceptions, the exact opposite occurs.

                              I'm not even sure what Axe's experiment is relevant to; it resembles nothing like anybody is suggesting happens in biology.

                              On a more general note: don't argue based on material from the Discovery Institute - they are invariably wrong.
                              "Any sufficiently advanced stupidity is indistinguishable from trolling."

                              Comment

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