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Self-organization

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  • #16
    Originally posted by rwatts View Post
    Unlike conventional evolution, this kind begins with a qualitative jump in phenotype, namely the sudden appearance of a self-organized molecule which natural selection then builds a controlling mechanism around.
    You could have said a "different" or even "new" phenotype. It seems unlikely, but possibly you meant more than just "different" or "new."
    The greater number of laws . . . , the more thieves . . . there will be. ---- Lao-Tzu

    [T]he truth I’m after and the truth never harmed anyone. What harms us is to persist in self-deceit and ignorance -— Marcus Aurelius, Meditations

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    • #17
      Originally posted by Truthseeker View Post
      You could have said a "different" or even "new" phenotype. It seems unlikely, but possibly you meant more than just "different" or "new."
      Truthseeker, what on earth are you trying to say?

      Comment


      • #18
        Originally posted by rwatts View Post
        Truthseeker, what on earth are you trying to say?
        Frankly, "qualitative jump" does not seem to be a big improvement on "new."
        The greater number of laws . . . , the more thieves . . . there will be. ---- Lao-Tzu

        [T]he truth I’m after and the truth never harmed anyone. What harms us is to persist in self-deceit and ignorance -— Marcus Aurelius, Meditations

        Comment


        • #19
          Originally posted by Truthseeker View Post
          Frankly, "qualitative jump" does not seem to be a big improvement on "new."
          What they are getting at is, that, at the molecular level, sometimes it happens that a new system of molecules "pops" into existence thanks to self-assembly happening. This is qualitatively (and quantitatively) different to a new molecule or system of molecules evolving by a small jump, followed by selection, then another small jump, followed by selection.

          Comment


          • #20
            You apparently think that differences between two systems of molecules can be measured. I am skeptical that can be accomplished except in rare cases.

            I'm willing to drop my objection here if you wish.
            The greater number of laws . . . , the more thieves . . . there will be. ---- Lao-Tzu

            [T]he truth I’m after and the truth never harmed anyone. What harms us is to persist in self-deceit and ignorance -— Marcus Aurelius, Meditations

            Comment


            • #21
              Self-organization? Isn't that the skill that any self-respecting teenager living at home with their parents lack?

              Comment


              • #22
                Originally posted by Chrawnus View Post
                Self-organization? Isn't that the skill that any self-respecting teenager living at home with their parents lack?
                I plead the fifth.
                "Kahahaha! Let's get lunatic!"-Add LP
                "And the Devil did grin, for his darling sin is pride that apes humility"-Samuel Taylor Coleridge
                Oh ye of little fiber. Do you not know what I've done for you? You will obey. ~Cerealman for Prez.

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                • #23
                  Originally posted by Truthseeker View Post
                  You apparently think that differences between two systems of molecules can be measured. I am skeptical that can be accomplished except in rare cases.

                  I'm willing to drop my objection here if you wish.
                  ???

                  Again, I don't know what you are objecting to Truthseeker. For example, there is nothing odd about measuring the molecular weight of a water molecule as opposed to a carbon dioxide molecule. There is nothing odd about determining the atoms that constitute each molecule. And researchers do understand the chemical reactions by which both arise in nature.

                  Comment


                  • #24
                    Originally posted by Chrawnus View Post
                    Self-organization? Isn't that the skill that any self-respecting teenager living at home with their parents lack?
                    Yeah. It generally brings about a war between parents and offspring that lasts a few years. Peace is finally reached when each side goes its own way (that is the teenager grows up and steps into the wide world). Then each side gets back to friendship, but on a new level.

                    Comment


                    • #25
                      Evolutionary constraints and self-organization …

                      … is considered next by the researchers.

                      In effect self_organization constrains evolutionary possibilities and a lot of research has been done concerning this. To show an example, the authors consider the dynamics of seeding (and diffusion processes). Often self-organization relies on a particular density of components before the self-organization can begin. And often a means of achieving this density is first to seed the environment with molecules around which the components can form. Sometimes this seeding can be via a chemical diffusion process. In small, compact volumes, seeding or diffusion is relatively efficient and easy to achieve, but if the volume gets too large, then the process breaks down. A high enough density of seeding molecules cannot be achieved quickly enough and so component formation cannot begin and thence self-organisation proceed. Or should it eventually proceed, then it does so at the wrong time. Hence self-organization by seeding or diffusion reactions constrains the size to which cells can grow.

                      One way around this is for the cell to compartmentalize, breaking itself up into units of small volumes and the seeding or diffusion processes occurring only within these smaller volumes.

                      The authors then discuss the development of the field of study called “Evo-Devo”, which is concerned with the consequences of development for evolutionary theory. One theory within evo-devo concerns itself with the development of tooth cusps in mammals. And one particular model concerns itself with conserved genes interacting with each other via diffusion reactions. That is, in the area of the developing embryo’s teeth, genes make proteins (activators or inhibitors) which diffuse across the environment to control other genes, either by activating or inhibiting them. The upshot of these reactions are the variations in morphology and numbers of teeth cusps. Although perhaps not directly related to self-organization, but more to diffusion models, they refer to this paper:-

                      A gene network model accounting for development and evolution of mammalian teeth


                      Returning to the theme of their paper, the authors note that self-organization models have been proposed for understanding cell morphology, and that these models are broadly significant to evolution. They offer this paper:-

                      Before programs:
The physical origination of multicellular forms

                      - as an example. Its authors propose and argue for a period of relatively free evolution unconstrained by genetic programs in which chemical and physical processes played a significant role in cell morphology and behaviour. Genes only really took over at a later stage.

                      Concluding the section, the authors note that “… an understanding of self-organization is necessary for an appreciation of the relationship between genotype and phenotype that is central to evolutionary developmental biology.”


                      To be continued ….

                      Comment


                      • #26
                        Originally posted by rwatts View Post
                        Evolutionary constraints and self-organization …

                        … is considered next by the researchers.

                        In effect self_organization constrains evolutionary possibilities and a lot of research has been done concerning this. To show an example, the authors consider the dynamics of seeding (and diffusion processes). Often self-organization relies on a particular density of components before the self-organization can begin. And often a means of achieving this density is first to seed the environment with molecules around which the components can form. Sometimes this seeding can be via a chemical diffusion process. In small, compact volumes, seeding or diffusion is relatively efficient and easy to achieve, but if the volume gets too large, then the process breaks down. A high enough density of seeding molecules cannot be achieved quickly enough and so component formation cannot begin and thence self-organisation proceed. Or should it eventually proceed, then it does so at the wrong time. Hence self-organization by seeding or diffusion reactions constrains the size to which cells can grow.

                        One way around this is for the cell to compartmentalize, breaking itself up into units of small volumes and the seeding or diffusion processes occurring only within these smaller volumes.

                        The authors then discuss the development of the field of study called “Evo-Devo”, which is concerned with the consequences of development for evolutionary theory. One theory within evo-devo concerns itself with the development of tooth cusps in mammals. And one particular model concerns itself with conserved genes interacting with each other via diffusion reactions. That is, in the area of the developing embryo’s teeth, genes make proteins (activators or inhibitors) which diffuse across the environment to control other genes, either by activating or inhibiting them. The upshot of these reactions are the variations in morphology and numbers of teeth cusps. Although perhaps not directly related to self-organization, but more to diffusion models, they refer to this paper:-

                        A gene network model accounting for development and evolution of mammalian teeth


                        Returning to the theme of their paper, the authors note that self-organization models have been proposed for understanding cell morphology, and that these models are broadly significant to evolution. They offer this paper:-

                        Before programs:
The physical origination of multicellular forms

                        - as an example. Its authors propose and argue for a period of relatively free evolution unconstrained by genetic programs in which chemical and physical processes played a significant role in cell morphology and behaviour. Genes only really took over at a later stage.

                        Concluding the section, the authors note that “… an understanding of self-organization is necessary for an appreciation of the relationship between genotype and phenotype that is central to evolutionary developmental biology.”


                        To be continued ….
                        interesting!?!?!
                        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


                        • #27
                          Some very recent and related research.

                          Layperson’s writeup:-

                          Research demonstrates shared rules of development can predict patterns of evolution in different species

                          Paper:-

                          

Shared rules of development predict patterns of evolution in vertebrate segmentation




                          Thanks to poster Atheistoclast from TR for bringing this to our attention.

                          Comment


                          • #28
                            Some really, really recent research on the importance of self-organisation in the RNA world:-

                            http://www.colorado.edu/news/release...primordial-dna

                            Comment


                            • #29
                              Cellular Hardware and Genetic Software


                              In this section, the authors pull their idea together, by considering it in terms of computers - software and hardware. And it’s not quite what one might expect.

                              It’s good that they do this because there were several places in the paper at which I found it hard to make sense of a point they were making, and there were one or two occasions where their examples did not quite seem to fit the point they were making. Perhaps the problem is with me and my lack of knowledge, but then over the years I’ve come to understand that scientists can write good papers, they can write bad papers and perhaps most often, they write reasonable papers. Possibly other papers they cited to also needed to be read, in order to flesh out their self-organisation argument to understand it some detail and with better clarity. I did this on a couple of occasions and certainly this seemed to happen.

                              This section, however, seemed to sum up their argument providing reasonable clarity in the process.

                              The cell is the basic unit of biological organisation and it, and many of its components (e.g. DNA, membranes, organelles) constitute the hardware. The cell’s software constitutes the programs implemented on this hardware which allows for adaptive responses to the environment as well as information storage and transmission.

                              And this is just like with computers - the hardware aspect and the software aspect, and while we place so much emphasis on a computer’s software, it is in fact the hardware that gives the computer its “grunt” and constrains the computer’s ability to do things.

                              However, in the context of the cell, while the same applies, it’s actually a lot more complex, because the hardware itself can also act like software. The self organising properties of cellular components also allow for adaptive responses and they are also transmitted from generation to generation, often not via the code stored in DNA. Thus when a cell membrane divides, the adaptive information encoded within it does not necessarily get transferred via the software code in the DNA. It’s transmitted across generations by the very act of cellular division. However, again, this is not the whole story, because the DNA does contain software which modulates the properties of the membrane. And this software itself does evolve via the conventional Darwinian mechanisms and is fundamentally different to the evolving software/hardware of self organising systems.

                              In other words, there is a complexity within life that’s well beyond a simple application of the computer software/hardware analogy. And within this new paradigm, evolution is a lot more than just changes, over time, to the cell’s software.

                              The authors write:-

                              Originally posted by link at OP
                              n a nutshell, the current view of genes and the evolutionary process is a Platonic ideal in which genes are seen as permanent forms that propagate through time within a relatively unimportant cellular background. One can summarize the evolutionary process this way (it is particularly convenient mathematically), but this is not an explanation of how evolution constructs the mechanisms of life. In other words, we currently focus on the evolution of changes to the software, and neglect the evolution of both the hardware and the ways that the hardware and software interact.
                              They continue:-

                              Originally posted by link at OP
                              To describe the problem in traditional terms, with the evolution of an eye, for example, we can trace a trajectory from simple to complex. At each step we can explain how selection made a change to the system that improved function. We are not merely concerned with changes in gene frequency, but changes in function and how they are caused by selection's alteration of structures. To do this sort of evolutionary biology at the molecular level, we need to recognize how genes exert their effects on cellular processes with elaborate self-organizing rules.


                              To be continued ….

                              Comment


                              • #30
                                Conclusions

                                The authors write:-

                                Originally posted by link at OP
                                The nature of pattern-forming processes within the cell challenges the traditional view of genetic circuit boards.
                                Exemplifying this challenge, they refer to these papers:-

                                Self-organization versus Watchmaker: stochastic dynamics of cellular organization.

                                Self-organization versus Watchmaker: ambiguity of molecular recognition and design charts of cellular circuitry.

                                The traditional view has genes, structural or enzymatic doing the work within the cell. But this new paradigm suggests that there is more going on. Gene products might do more than just act independently or in concert with each other to facilitate cellular processes and structures, and thus evolve in this context. Quite possibly, the new paradigm argues, there is another aspect of cells not really considered before. Systems within cells can form via self-organising principles and genes have nothing to do with evolution in this context. Rather, they evolve to control these novel systems.

                                In essence then, these self-organizing systems constrain what kind of evolution is possible at the genetic level. And interestingly, the authors propose that “saltatory changes are more important than traditionally thought, as self-organizing mechanisms do not seem to be the products of slow, incremental change”. That is, evolution might well proceed by jumps in many instances. Perhaps a bit of a whiff of the long rejected “hopeful monster” theory.

                                Putting this into some kind of context, they refer back a few hundred years and the synthesis of urea by Wohler. It caused a rewriting of the textbooks by showing that organic molecules, the molecules of living things were essentially no different to the molecules of non living substances. Continuing into the modern era with the ideas of Turing, and others such as Nicolis and Prigogine (order out of chaos, and an associated Nobel Prize), they feel that a change in perspective is currently underway.

                                They advocate a change in the biology curriculum. Evolutionary biologists often study physical sciences and this is necessary because physical processes do govern what can happen evolutionary. For example, cell sizes are determined largely due physical considerations such as the surface area to volume ratio which provides a limit to gas exchange processes. Electrostatics are important for an understanding of enzyme behaviours. And so on. Hence they hope:-

                                Originally posted by link at OP
                                … that an appreciation of the fundamental roles played by physical pattern-formation mechanisms will soon be treated in the same manner.

                                The end.

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