Universal Common Descent Dilemma

  1. Despite lack of observational basis, Darwin proposed Universal Common Descent (UCD) saying:Therefore I should infer from analogy that probably all the organic beings which have ever lived on this earth have descended from some one primordial form, into which life was first breathed“. He also said elsewhere (referring to UCD): “…the littlest creature (or four or five of them)…” With his remarks, Darwin left the door open to creation (“life was first breathed”), but since then, Neo-Darwinists have rejected creation and replaced it with belief in undirected abiogenesis while maintaining belief in UCD.
  2. UCD is incompatible with the current view of Earth as just an ordinary planet circling an ordinary star located nowhere special inside an ordinary galaxy. If Earth is “nothing special” and abiogenesis is an ordinary “arising” of life from non-living matter, spontaneous abiogenesis would be a trivial common occurrence here on Earth as well as throughout the Universe, and we would have many “trees of life” instead of one. However, until now, all abiogenesis experiments have failed to produce life, spontaneous generation has been rejected, and the Fermi paradox stands, all these keeping the single “tree of life” and UCD hypothesis still alive and still inexplicable.
  3. Conditions for starting life should be similar to those required for sustaining it. The Big Bang model mandates a beginning of life. Furthermore, once started life must be sustained by the same or very similar environment. And since life is being sustained now on Earth, abiogenesis should be ongoing contrary to all observations to date. Tidal pools, deep sea hydrothermal vents, and the undersurface of ice caps have been hypothesized to originate abiogenesis due to their persistent energy gradients, but no abiogenesis or its intermediate phases have been observed around these sites. Given these, the only methodological naturalistic alternative is ‘limited window of opportunity for abiogenesis which suggests primordial life substantially different than all known forms of life, and perhaps originating on another planet followed by panspermia. However, this alternative defies Occam’s razor and the absence of supporting evidence including the earliest ever known fossils (stromatolites) that are of commonly occurring cyanobacteria rather than of alien origin.
  4. Universal Common Descent requires an inexplicable biologic singularity. All known forms of life are based on the same fundamental biochemical organization, so either abiogenesis happened only once or it happened freely for a while but then it stopped when the ‘window of opportunity’ closed and only one organism survived to become the Last Universal Common Ancestor (LUCA) of all existing life on Earth. However, these two biologic singularities should be unacceptable given the lack of evidence and the assumption of continuity in nature. Furthermore, the second scenario requires two discontinuities: one for the cessation of abiogenesis and the second one for the bottleneck leading to LUCA.
  5. In conclusion, UCD hypothesis leads to a number of bad and very bad scenarios: a) Earth is “nothing special” should lead to a “forest of life” rather than a single “tree of life” and to ubiquitous abiogenesis (unobserved); b) Alien life plus panspermia is refuted by the Fermi paradox and oldest known stromatolites fossils; c) Single event abiogenesis is an unsupported and therefore unacceptable singularity; d) ‘Window of opportunity’ abiogenesis followed by LUCA bottleneck is even less acceptable double-singularity. And this brings us back to Darwin’s “open door” to creation, perhaps the most rational alternative that fits all biologic observations.

Pro-Con Notes

Con: Maybe abiogenesis is happening a lot. I think the already existing life would dispose of it quickly though.

Pro:  if so, 1. We should be able to duplicate abiogenesis in the lab; 2. We should see at least some of the intermediate abiogenesis steps in nature; 3. Existing life can only process what looks like food. Cellulose is a well known organic material that cannot be broken down by a lot of organisms and is known to last as very long time in dry conditions.

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1,101 thoughts on “Universal Common Descent Dilemma

  1. CharlieM,

     But I suppose it depends on the definition of clone.

    Actually, it depends on the definition of ‘gene’. If one insist that regulatory sequence is not a gene , one can say regulation sits outside the gene. Regardless, it is still genetic, and heritable.

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  2. Allan Miller:
    CharlieM,

    Actually, it depends on the definition of ‘gene’. If one insist that regulatory sequence is not a gene , one can say regulation sits outside the gene. Regardless, it is still genetic, and heritable.

    What is the process by which regulation is modified, small mutations and natural selection?

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  3. Entropy:

    CharlieM:
    If I said that plants use carbon dioxide and sunlight to produce energy would you automatically assume that I was saying plants are conscious? They stated it accurately, “the cell uses its genes”. That is what happens.

    Nope. What happens is much harder to explain if explained properly, which is why they use those shortcuts. Plants don’t “use carbon dioxide to produce energy,” their chlorophyl reacts to photons in a way that cascades into several chemical reactions that result in CO2 reacting with water and thus forming some carbohydrate, etc, etc. See how much longer it takes to say that? Thus the teleologically-sounding shortcut.

    It doesn’t matter how many words you use to explain it you are still talking about the aims of the system.

    In what way you’d say “the cell uses its genes” other than consciously? In having those genes and the genes doing what they’re going to do regardless of whether the cell could even want them to do it or not?

    The cell does not want anything because it does not have conscious will. I was just quoting the wording from the link. The point is that researchers cannot escape from using teleological language because of the teleology found throughout life.

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  4. phoodoo: What is the process by which regulation is modified, small mutations and natural selection?

    Small mutations, large mutations, natural selection, and drift. That ought to about cover it. Can you think of any other process that I left out?

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  5. CharlieM:
    It doesn’t matter how many words you use to explain it you are still talking about the aims of the system.

    I’m not talking about any aims. I’m talking about chemicals being chemicals. No intentions involved.

    CharlieM:
    The cell does not want anything because it does not have conscious will.

    Therefore there cannot be any intentions or aims involved. So simple and straightforward.

    CharlieM:
    I was just quoting the wording from the link. The point is that researchers cannot escape from using teleological language because of the teleology found throughout life.

    You’re quoting the wording because you think they really meant it teleologically. Again, they do that because it’s faster, not because there’s any actual teleology there. They talk that way because our language developed around beings who do have intentions (ourselves). That makes it hard to have short ways of describing things doing what they do just because that’s the way it is. No intentions involved.

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  6. Entropy:

    CharlieM:
    You think that a couple of master genes suddenly spring into action and everything follows from there? I would say you are not even scratching the surface.

    Why would you think I’d think of it happening “suddenly”? The fact is: two master genes start the process of differentiation. The trigger is the fertilization. But even that’s not above the genes, but concomitant, since the way these “signals” are detected use gene products as well.

    For the sake of clarity can you give us examples of these two genes in a specific organism?

    Here’s where you should try and clarify, rather than try and obfuscate the issue further. So, you didn’t mean that the cell is conscious, then what do you mean when you say “the cell uses it’s genes”? Then for the second part you should clarify what you mean by: “above the genes.”

    Firstly see my posts above.

    Secondly The actions of the cell are a determining factor in which genes it expresses. Think of a leukocyte involved in capturing an invader and engulfing it by phagocytosis. On detecting the signal the leukocyte springs into action and it accomplishes this by means of coordinated expression of its genes. It acts above the genes. The genes do not control the cell, the cell controls its genes.

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  7. phoodoo: What is the process by which regulation is modified, small mutations and natural selection?

    Not necessarily small. Just as segments of coding sequence can be shifted around, so can genetic segments that include promoters and/or repressors. This can variously bring a gene under, and remove it from, the influence of a particular factor.

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  8. Alan Fox: Descent with modification from a common ancestor assumes the prior existence of the common ancestor. (Well, I say assumes but the almost universal genetic code is a strong indicator of shared ancestry.)

    The consilient evidence of the branching relatedness of all extant and extinct life on Earth is not the least dented by your musings.

    Is this supposed to be an answer to my:
    “What does that even mean: “descent with modification”? Modification of what? …considering that not even monozygotic twins are identical.”

    …because it doesn’t seem to answer the questions.

    As you know, there’s another OP that deals with “consilience” and shows it to be a very flimsy argument.

    Mung, you seem to know something. Would you share? Modification of what?

    Better yet, what would “descent without modification” look like? Anyone?

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  9. Allan Miller
    I saw a connection between information (the Shannon variety) and sequence divergence (part of the argument on common descent) and so constructed a post on that connection. You suggested I take it elsewhere, while admitting at the same time you don’t understand it well enough to know where it belongs.

    I know where it belongs. Just not what you wanted to say on that topic. But never mind – for a second I thought you had a half-decent argument there.

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  10. CharlieM: The actions of the cell are a determining factor in which genes it expresses. Think of a leukocyte involved in capturing an invader and engulfing it by phagocytosis. On detecting the signal the leukocyte springs into action and it accomplishes this by means of coordinated expression of its genes. It acts above the genes. The genes do not control the cell, the cell controls its genes.

    If one insists on thinking in terms of hierarchical metaphors (“above”, “control”) one won’t be able to understand how complex dynamical systems involve a mutual constraints of wholes and parts.

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  11. CharlieM:
    For the sake of clarity can you give us examples of these two genes in a specific organism?

    Look for the link I gave you above.

    CharlieM:
    Firstly see my posts above.

    I saw those. They don’t explain what you mean.

    CharlieM:
    Secondly The actions of the cell are a determining factor in which genes it expresses.

    And the genes it expresses are a determining factor in the actions it takes. Again, it’s concomitant.

    CharlieM:
    Think of a leukocyte involved in capturing an invader and engulfing it by phagocytosis. On detecting the signal the leukocyte springs into action and it accomplishes this by means of coordinated expression of its genes.

    And it detects those signals using proteins that were translated from RNA transcribed from its genes. As I said, it’s concomitant.

    CharlieM:
    It acts above the genes. The genes do not control the cell, the cell controls its genes.

    Nope. It acts by the interactions between the products of its genes and its environmental conditions. Read what Kantian Naturalist wrote.

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  12. Nonlin.org: I know where it belongs. Just not what you wanted to say on that topic. But never mind – for a second I thought you had a half-decent argument there.

    No you didn’t.

    It wasn’t even an argument; just pointing out another way to look at divergence. ID-ists are all over Shannon information. Until, that is, we look at signal degradation in a common descent relationship. Then, they blink uncomprehendingly.

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  13. Nonlin.org: “What does that even mean: “descent with modification”? Modification of what?

    The genotype and thus the phenotype. Monozygotic twins in humans, when one fetilized egg splits, start out as genetically identical but as the embryos develop, mutations can and do occur which result in the genotypes no longer being strictly identical. Although the differences are small enough that identical twins are strikingly similar in appearance as adults. But environmental and developmental factors have an effect where twins environments, exposure to pathogens, education, trauma vary.

    The two essential elements in descent with modification are imperfect reproduction of the genotype and variable success in individuals of a population in getting their particular genotype or part of it into the next generation.

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  14. Kantian Naturalist: If one insists on thinking in terms of hierarchical metaphors (“above”, “control”) one won’t be able to understand how complex dynamical systems involve a mutual constraints of wholes and parts.

    Right, a few comments ago Charlie was invoking the analogy of a termite nest to describe the relationship between genes and a developing organism. So should we conclude that the nest directs his own construction by controlling the termites? I don’t think so. Never mind, Charlie has moved on to another analogy: the macrophage hunting its prey, because then it becomes evident how the genes are subservient to the cell. The termite mound is already forgotten.

    Analogies and metaphors can help one’s understanding, but they can only take us so far. A lot of misunderstandings around here (not just Charlie) seem to be caused by reluctance to let go of analogies when they become an impediment to understanding.

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  15. Entropy: You missed the point. What Rum is advising is for you to understand how that works. Whether there’s more complications is not the issue. The issue is understanding how it works. The model produced from the classic, Nobel-winning, experiments, has a simple-yet-powerful explanatory logic, and would help you get a better grasp as to how gene regulation operates. Then you’d be able to judge what “more complex” actually means in that context. Then you’d realize that focusing on whether somebody said “more complex” doesn’t cut it. You have to actually understand what they’re talking about.

    Here is a video (Robert Tjian (Berkeley/HHMI) Part 1: Gene regulation: An introduction) that is worth watching and gives a good brief introduction to the transcription process. I have included an image below and to go along with it here is some of his commentary:

    It turns out there are a host of other, I’ll call them ancillary factors in addition to the multi-subunit regulated RNA polymerase itself that are necessary for you to build up an ensemble that is necessary to form an active, ready to activate transcriptional pre-initiation complex or a PIC. And this is kind of the picture we are getting to and even this picture with many many colours and many many different polypeptides that adds up to probably greater than eightyfive individual proteins that all have to kind of fit together like a jigsaw puzzle. Its probably not even the whole story. You’ll have noticed I still have one big red question mark there because I think as we begin to study specific cell types and specific processes like embryonic development or germ layer formation, additional components that are not here present here in this prototypic pre-initiation complex will come into play

    Maybe you are an expert and already know all this, but even so it pays to think deeply about it to get some sort of comprehension of the complexities involved. To say that embryonic development is initiated by master genes is to gloss over what is actually involved. The image below is an extremely simplified static snapshot which bares the same comparison to reality as a child’s stick drawing would compare to an actual functioning human. And this is fair enough so long as this point is grasped. It is just a very, very simple aid to understanding and is not meant to be taken as reality.

    The actual, real life, initiation of the transcription is a dynamic, ever changing process which needs to be extremely precise and is complex beyond anyone’s understanding, even the experts.

    So when asked how the genes control development, giving an answer that it is initiated by a couple of “master genes” and pointing me to a wikipedia link is no real answer. Notice the big red question mark in the image, that is just one area of uncertainty.

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  16. Allan Miller:
    CharlieM,

    Oh, good grief! Yes, convergent evolution is a thing. However, it is vanishingly rare at the molecular level, the level I am struggling manfully to get you consider.

    As I said in regard to gene transfer: “Think: how do they know it’s anomalous?”.

    And how do we know that DNA sequences were exchanged between unrelated species by horizontal gene transfer? Because that is the only way in which blind evolutionary processes could achieve this. Horizontal gene transfer is a theory invoked to save blind evolutionary theories.

    But if there is wisdom involved in evolution then the same sequences could be used by separate organisms because these are the sequences that are most suitable for that particular organism. Physical DNA does not need to be transferred.

    And we rarely see such an exact match as in the case of the butterfly and the cone snail because modifications are necessary to suit the individual needs of the host organism which are very rarely exactly the same as any other host.

    That is my opinion on the matter.

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  17. CharlieM: Notice the big red question mark in the image, that is just one area of uncertainty.

    Oooh, I just love areas of uncertainty.

    Nice vid BTW. Here are your options:
    1) Be a total wimp, keep whining “it’s soooo complex. We will NEVER understand”, and give up.
    2) Watch Part 2 that explains some of that stuff.

    Your choice

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  18. DNA_Jock: As I wrote before

    If you really don’t understand why adding an extra thousand targets degrades the significance of the match, I’m not sure I can help you out.

    Maybe 80,000 targets.
    Now I don’t think that the match is pure random coincidence, but to humor you I ignored the effect of selection. You do not appear to understand even the simplest of concepts.

    Why would they be targets? You are assuming that the 63 letter string is aiming for something. Very teleological 🙂

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  19. CharlieM: The actual, real life, initiation of the transcription is a dynamic, ever changing process which needs to be extremely precise and is complex beyond anyone’s understanding, even the experts.

    Prokaryotic transcription is pretty precise, but less complex. Eukaryotic transcription is not so precise at all; it’s more Rube Goldberg-esque. That’s why it’s a good idea to learn the basics before trying to understand the complexities.

    So when asked how the genes control development, giving an answer that it is initiated by a couple of “master genes” and pointing me to a wikipedia link is no real answer.

    Well, it might not be a complete answer, but at least it is a start.
    Which [jazz hands] “Oh Lordy me, it’s so complicated!” is not.

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  20. DNA_Jock: I am puzzled as to why you and Sal are determined to deny the hierarchical nature of the control of gene expression — is it in homage to a poorly-thought-through IC argument, or something else?

    I do not deny hierarchies. Cascades by their very nature are hierarchical.

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  21. CharlieM: Why would they be targets? You are assuming that the 63 letter string is aiming for something. Very teleological

    That’s like saying the mutual attraction of opposite charges in magnets is teleological. If that’s teleological to you, then the concept you have in mind when you use the word teleological is vacuous. It is equivalent to saying “some things are more likely to occur than other things”. Oh gee really?

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  22. Corneel:

    CharlieM: I have not objected that cells with the same genome should have identical phenotypes. I said that if everything came from the genes they would be clones. But I suppose it depends on the definition of clone. Would you say that Dollie the sheep was a clone?

    In that case, this statement of yours makes no sense:

    What is it that is handed down through the generations of cells in the growth of a buttercup? […] If it is the information in the form of the genetic code, why are the offspring not all clones.

    Ehrm, barring somatic mutations*, all the cells in an individual buttercup ARE genetic clones. Are you sure that is what you meant?

    No I didn’t mean that the genes should be the same, I meant the cells should be the same.

    CharlieM: No. If we are to discuss the ultimate causes, we need to talk philosophy.

    Have it your way. Good luck finding the philosophical cause for cell differentiation.

    Cell differentiation is not the ultimate cause.

    CharlieM: And what is wrong with that? In order to compare the differences and similarities between ontogony and phylogeny we need to study both.

    The issue is that you are NOT studying the differences, you are dismissing them as “details” in order to salvage your analogy.

    ETA: * and the gametes

    To call them details is not to dismiss them. What do you think it means to study something in detail?

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  23. CharlieM: Why would they be targets? You are assuming that the 63 letter string is aiming for something. Very teleological

    ROFL
    No, I was performing ID-math(tm) and thus using ID-language: the T in P(T|H) stands for “target”. Read Dembski.

    You still have not explained why increased Dpp copy number results in embryonic cells assuming more dorsal fates, under your archetype theory.

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  24. Allan Miller:
    CharlieM,

    Actually, it depends on the definition of ‘gene’. If one insist that regulatory sequence is not a gene , one can say regulation sits outside the gene. Regardless, it is still genetic, and heritable.

    One of the multitude of regulatory sequences required may be a gene but the regulatory apparatus is not.

    On a related note. where does the initial RNA polymerase come from in the newly fertilized egg?

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  25. Allan Miller: ID-ists are all over Shannon information. Until, that is, we look at signal degradation in a common descent relationship. Then, they blink uncomprehendingly.

    🙂

    I’d never really thought of common descent in terms of signal passed from sender to receiver, so thanks for that.

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  26. John Harshman: Do you know what “drift” means?

    Yes John, I do. I also know that random genetic drift and neutral theory are two different things.

    ETA: A little back-story for those not following along over at the Peaceful Science blog. The theory of neutral evolution killed off Darwinism back in 1968. So when John failed to mention neutral evolution I was shocked. Shocked I say.

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  27. John Harshman: Small mutations, large mutations, natural selection, and drift. That ought to about cover it. Can you think of any other process that I left out?

    What about regulation that is modified during individual development?

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  28. Mung: I also know that random genetic drift and neutral theory are two different things.

    Yes, just as dogs and poodles are too different things. I suppose that if I said that dogs and cats are the common pets, you would tell me that I forgot to mention poodles.

    So when John failed to mention neutral evolution I was shocked.

    You were shocked because you don’t know what drift and neutral evolution are; you only know the names.

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  29. CharlieM: What about regulation that is modified during individual development?

    That isn’t evolution. Of course mutation, selection, and drift can change DNA sequences that change regulation. But that isn’t what you meant, is it?

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  30. Entropy: I’m not talking about any aims. I’m talking about chemicals being chemicals. No intentions involved.

    Therefore there cannot be any intentions or aims involved. So simple and straightforward.

    You’re quoting the wording because you think they really meant it teleologically. Again, they do that because it’s faster, not because there’s any actual teleology there. They talk that way because our language developed around beings who do have intentions (ourselves). That makes it hard to have short ways of describing things doing what they do just because that’s the way it is. No intentions involved.

    You introduced the word, “intention” not me. Some people are so frightened of the suggestion that there might be some sort of direction in the evolution of life, they even feel the need to deny it in individual development.

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  31. Kantian Naturalist: If one insists on thinking in terms of hierarchical metaphors (“above”, “control”) one won’t be able to understand how complex dynamical systems involve a mutual constraints of wholes and parts.

    There is nothing wrong with thinking about different levels. Think about an individual multi-cellular organism and the depth of levels it contains from the level The organs are contained within the organism, the cells within the organs,and the organelles within the cells. These facts do not stop us thinking about the processes within and between each of these levels.

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  32. CharlieM:
    You introduced the word, “intention” not me.

    Then what the heck do you mean by aim Charlie? What do you think that teleological means? In my understanding of those words, both imply intention, so it would be you who introduced the concept, if not the literal term.

    CharlieM:
    Some people are so frightened of the suggestion that there might be some sort of direction in the evolution of life, they even feel the need to deny it in individual development.

    Leaving aside yet-another-misuse-of-language (natural “selection,” for example, gives evolution a “direction,” only not an “intentional” one), what makes you think this is about fear?

    At least in my case, this is about basic philosophical foundations. We cannot claim that there’s “aims” or “teleology” unless we had the proper evidence for such a thing. In the meantime, what we see is things being what they are, and we should avoid concluding from mere metaphorical language, and/or from mere anthropomorphisms.

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  33. John Harshman: You were shocked because you don’t know what drift and neutral evolution are; you only know the names.

    There was no debate or controversy over random genetic drift John. There was one over the neutral theory. Random genetic drift did not kill Darwinism in 1968.

    They are not the same.

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  34. Mung:
    There was no debate or controversy over random genetic drift John. There was one over the neutral theory …

    One implies the other Mung.

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  35. Entropy: What do you think that teleological means?

    End-Directed. Directed towards an end. It makes no claim about whether the directedness or the end are natural or not.

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  36. Mung,

    Truly sorry Mung, but I’m asking Charlie. With your definition there’s still problems, but I won’t go there to avoid confusing the issue further.

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  37. Entropy: Look for the link I gave you above.

    I saw those. They don’t explain what you mean.

    And the genes it expresses are a determining factor in the actions it takes. Again, it’s concomitant.

    And it detects those signals using proteins that were translated from RNA transcribed from its genes. As I said, it’s concomitant.

    Nope. It acts by the interactions between the products of its genes and its environmental conditions. Read what Kantian Naturalist wrote.

    No one is denying the interactions between levels. What I am saying is that in normal circumstances everything within works for the benefit of the whole and when this is not the case we end up with sickness and death. Proteins which are not required are broken up in order to maintain the viability of the cell, and surplus cells are killed off to maintain the viability of the organism. The viability of the organism is the determining factor.

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  38. Corneel: Right, a few comments ago Charlie was invoking the analogy of a termite nest to describe the relationship between genes and a developing organism. So should we conclude that the nest directs his own construction by controlling the termites? I don’t think so.

    The whole is the termite mound, nest and all the termites, not just the nest. You can’t get away from thinking in terms of the separate parts. When I say whole, I mean whole. From a hierachical point of view the upper levels include the lower levels, they are not exclusive.

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  39. Mung: End-Directed. Directed towards an end. It makes no claim about whether the directedness or the end are natural or not.

    That makes the use of the word teleological to describe a process where the outcomes aren’t equiprobable, question-begging. One does not need to invoke “direction”, as that implies intent, to explain that some things are more likely than others.

    Are magnets “directed”? How do you know?

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  40. CharlieM,

    Allan: As I said in regard to gene transfer: “Think: how do they know it’s anomalous?”.

    Charlie: And how do we know that DNA sequences were exchanged between unrelated species by horizontal gene transfer? Because that is the only way in which blind evolutionary processes could achieve this. Horizontal gene transfer is a theory invoked to save blind evolutionary theories.

    It’s also a thing, readily observed.

    Still, I don’t know why you feel the need to keep side-stepping my very straightforward question. Regardless of the mechanistic path by which genes are supposed to end up held in common without passing through ‘vertical’ descent, how are these anomalies discovered? What makes them stand out? What are they anomalous with respect to?

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  41. CharlieM,

    But if there is wisdom involved in evolution then the same sequences could be used by separate organisms because these are the sequences that are most suitable for that particular organism. Physical DNA does not need to be transferred.

    So if, for example, we observe an intracellular parasite/symbiont such as Wolbachia in cells, and also discover Wolbachia genes in the nuclei of the host species, we are not justified in saying that they were physically transferred? Somehow, we should prefer the notion that the host and Wolbachia both need the ‘most suitable’ genes, despite one being an insect and the other a bacterium?

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  42. CharlieM,

    One of the multitude of regulatory sequences required may be a gene but the regulatory apparatus is not.

    The extent of a gene is somewhat labile, depending on what one wishes to convey. It’s best not to get too dogmatic about what is or isn’t. The term was, after all, coined long before anyone knew anything about the underlying molecular biology. A gene for fair hair, say, may simply involve a switch (for all I know; it’s just an example).

    On a related note. where does the initial RNA polymerase come from in the newly fertilized egg?

    It was already there in the egg. The initial copies would have been transcribed from the mother’s DNA. Post fertilisation, in the diploid it is up for grabs depending on dosage, dominance effects etc.

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  43. CharlieM:
    So when asked how the genes control development, giving an answer that it is initiated by a couple of “master genes” and pointing me to a wikipedia link is no real answer.

    I cannot give you a full course on embryonic development here, right? However, as DNA_jock said, it’s a start.

    What seems to be happening is that you focus too much into those details and lose the thread.

    The point of contention was that you argued that somebody else would get into knots defending the argument that cell differentiation was controlled by a master gene. I said that it’s better to try and figure it out, rather than argue, and that the results from embryology say that it’s a couple master genes.

    The complexity of cell regulation doesn’t tell you whether it’s a couple “master” genes controlling that differentiation or not. It just tells you that there’s complexities to how such regulation happens. Still, from the results in the study of cell differentiation, it’s just a couple “master” genes that start the process of differentiation (and, from what I remember, one was more important than the other).

    In your diagram, you have a generic transcriptional “machinery”complex. What makes the difference between starting a cascade of cell differentiation and expressing a gene whose product is involved in metabolism, for example? The answer is: the specific transcription factor(s) involved in either. So, again, no matter how complex you want to make transcription, cell differentiation is still controlled by a couple “master” genes in many-if-not-all animals (in some organisms it’s just one “master” gene, in some others there might be more, but I haven’t seen such examples yet).

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  44. CharlieM:
    And how do we know that DNA sequences were exchanged between unrelated species by horizontal gene transfer?

    By checking several lines of evidence, from the genes displaying codon-usages foreign to the host cell, to it looking suspiciously-too-similar to the gene in the unrelated species, to our everyday experience with mobile elements. Many of them very well characterized.

    CharlieM:
    Because that is the only way in which blind evolutionary processes could achieve this.

    While there’s much better evidence than that, what else do you think is involved, if not “blind” phenomena? How could we test for such a thing? if it’s just your imagination, why should we propose that without the evidence to support it? Do you understand that we have to go by what we can test, not by the way you’d like things to be?

    CharlieM:
    Horizontal gene transfer is a theory invoked to save blind evolutionary theories.

    As I explained, this is false. However, I’m curious: save them from what exactly?

    CharlieM:
    But if there is wisdom involved in evolution then the same sequences could be used by separate organisms because these are the sequences that are most suitable for that particular organism. Physical DNA does not need to be transferred.

    By what mechanisms would those organisms end up with such almost-identical DNA sequences independently, and within a very short time frame? Why would the gene be abundant in one lineage, as if vertically-inherited, while being restricted to one strain in the other lineage as if it came from the lineage where it’s abundant? How can we test for your proposed mechanism? How does your mechanism explain that the gene-we-call-transferred is surrounded by sequences betraying mobile element involvement in the transfer if it wasn’t a transfer? Etc.

    CharlieM:
    That is my opinion on the matter.

    Thank you for that, but it looks as if your opinion is philosophically inept and founded in very shallow knowledge/understanding at best.

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  45. Rumraket: That makes the use of the word teleological to describe a process where the outcomes aren’t equiprobable, question-begging. One does not need to invoke “direction”, as that implies intent, to explain that some things are more likely than others.

    What a load of nonsense.

    Objects not attached to the surface of the earth (water in a sink going down a drain) will create a vortex going the opposite direction. So in the Northern hemisphere, it moves clockwise. In the Southern hemisphere, it moves counter clockwise. On the equator, water goes straight down.

    No implication at all that the water intends to go clockwise, counter-clockwise, or straight down.

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