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. Kantian Naturalist: What more could you possibly want?

    I’ll tell you what I would want. I would like to be able to value the fact that people can have all sorts of opposing outlooks and that we can discuss and argue about our varying points of view without feeling that it is a personal attack. Of course the internet is probably the most challenging venue in which to achieve this aim. But I like a challenge 🙂

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  2. Allan Miller,

    That doesn’t address the point. I’m asking what is incompatible about having two different replication systems or chromosomal architectures.

    If you put human DNA inside bacteria would you expect it to function or visa versa? This is what compatibility means.

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  3. colewd:
    Allan Miller,

    If you put human DNA inside bacteria would you expect it to function or visa versa?This is what compatibility means.

    Depends how you do it. Like I say, you have 2 systems in your own cells, one ‘bacteria-like’ in the mitochondria and one more ‘archaeon-like’ in the nucleus. They rub along OK for the most part.

    But even without compartments you are pretty much saying that gene transfer is impossible. Most would disagree.

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  4. Allan Miller,

    But even without compartments you are pretty much saying that gene transfer is impossible. Most would disagree.

    So you are reverting to creating a strawman. Why? Gene transfer has nothing to do with this argument.

    You originally said that life’s formation was expected more then once. Given the difficulty of explaining the prokaryotic to eukaryotic transition. Why would Occum’s razor not point us to two origin events?

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  5. colewd:
    Allan Miller,

    So you are reverting to creating a strawman.Why?Gene transfer has nothing to do with this argument.

    It has everything to do with it. Eukaryotic endosymbiosis is all about the merger of genes from one kingdom with another. If you rely on ‘incompatibility’, you are saying that cannot happen. The position ‘gene transfer can happen but endosymbiosis cannot’ is a peculiar one, from where I sit, if your barrier is genetic. Especially given the many examples of more recent endosymbiosis, albeit lacking the deep intimacy of the eukaryotic system.

    You originally said that life’s formation was expected more then once.Given the difficulty of explaining the prokaryotic to eukaryotic transition.Why would Occum’s razor not point us to two origin events?

    Because (among a mountain of other evidence), there is a common genetic code to deal with. There, I’ve said that three times now. Your invocation of Occam’s Razor here is rather one-eyed – it’s as if there is nothing to be explained except the surmounting of an imaginary barrier. If your barrier remains intact, the common genetic code, the deep commonalities of ribosomal and ‘core’ protein repertoire – all these are shoved under your lumpy carpet. Your imagining of all this arising separately, with no possibility of a common origin, is a peculiar, not-very-parsimonious kind of parsimony.

    The barrier to transition you imagine is not seen by anyone else – anyone who understands the compartmentalisation of eukaryotic cells is well aware that two architectures can be supported in the one cell. So I don’t see where the ‘parsimony’ comes in.

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  6. Allan Miller,

    The position ‘gene transfer can happen but endosymbiosis cannot’ is a peculiar one, from where I sit, if your barrier is genetic.

    I am not claiming endosymbiosis cannot happen. What I am claiming is for it to happen the organelle must exist in prokaryotic cells and many do not.

    Because (among a mountain of other evidence), there is a common genetic code to deal with. There, I’ve said that three times now.

    A common code does not entail a common origin especially when that codes organization changes so dramatically.

    Your imagining of all this arising separately, with no possibility of a common origin, is a peculiar, not-very-parsimonious kind of parsimony.

    Your claim of no possibility of separate origin seems in conflict that separate origins is something we should expect.

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  7. colewd:
    Allan Miller,

    I am not claiming endosymbiosis cannot happen.What I am claiming is for it to happen the organelle must exist in prokaryotic cells and many do not.

    ??

    It does not have to exist in all cells, just one …

    A common code does not entail a common origin

    Kinda does though …

    especially when that codes organization changes so dramatically.

    It doesn’t though (admittedly, I am unclear whether you mean the codon assignments or the physical chromosomal architecture. Either way, I still don’t see your barrier).

    Your claim of no possibility of separate origin seems in conflict that separate origins is something we should expect.

    I don’t have a major expectation either way, although I would be inclined towards assuming a relationship – two completely alien systems would be less likely to work together, I feel. But we don’t have to go on feelings, we have data, and that data points very strongly to common origin.

    It could point the other way. But it doesn’t.

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  8. colewd: A common code does not entail a common origin especially when that codes organization changes so dramatically.

    That’s right. As we all know, the Morse code had more than one origin. 😉

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  9. Allan Miller,

    It does not have to exist in all cells, just one …

    Not if you’re trying to claim common origin.

    But we don’t have to go on feelings, we have data, and that data points very strongly to common origin.

    Revert to assertion. Smooth 🙂

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  10. Mung,

    As we all know, the Morse code had more than one origin

    And transmitters of Morse code all had the same origin 🙂

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  11. colewd: And transmitters or Morse code all had the same origin

    And if you find that the transmitters use the same transistors, well, just further proof of common descent!

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  12. Mung,

    And if you find that the transmitters use the same transistors, well, just further proof of common descent!

    Not common descent and not common design just a common depository of transistors shared by separate designers.

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  13. colewd: I am not claiming endosymbiosis cannot happen.What I am claiming is for it to happen the organelle must exist in prokaryotic cells and many do not.

    Me: It does not have to exist in all cells, just one …

    colewd: Not if you’re trying to claim common origin.

    That’s a very confused exchange, and I don’t think it’s me. You referred to endosymbiosis, and ‘an organelle’, which is not an issue of the common origin of the endosymbionts, but one of the endosymbiosis event itself, ie, the common origin of all modern eukaryotes.

    Likewise, your repeatedly stated contention that the genetic systems, in some hand-wavy way, are ‘incompatible’, is about the implausibility of the endosymbiosis event itself, not the implausibility of the endosymbiotic partners being themselves genetically related. You flip flop between those two notions, and it seems you are not clear in your own mind what you mean.

    Allan: But we don’t have to go on feelings, we have data, and that data points very strongly to common origin.

    colewd: Revert to assertion. Smooth

    Dodge the discussion. Neat.

    Well, doesn’t it? If not, why not? You’ve got the actin/tubulin systems, the bimodal coalescence of core eukaryotic genes upon archaea and alpha-proteobacteria, the RNAs, the universality of the two-Class aaRS groupings, the 95-100% commonality of genetic code between any two randomly chosen organisms from across the ToL, structural protein conservation … I mean, yes, I ‘assert’ that these point to common origin, but I don’t know what else to make of these data. Do you?

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  14. Allan Miller,

    , which is not an issue of the common origin

    It is the issue of common origin. Major biologic mechanisms existing in a species that do not exist in the prior species. You cant hand wave this away.

    but I don’t know what else to make of these data. Do you?

    Yes a separate origin because of new features that don’t fit in the old footprint and require a massive amount of novel FI.
    -spliceosome
    -nuclear pore complex
    -chromosome structure
    -golgi apparatus
    -all genes w introns and exons
    -nucleus
    -ubiquitin system in multi cellular
    etc.

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  15. Mung: Nietzsche, Machiavelli, Stalin.

    If you insist.

    Nietzsche:

    There is more wisdom in your body than in your deepest philosophy.

    Machiavelli:

    It must be considered that there is nothing more difficult to carry out nor more doubtful of success nor more dangerous to handle than to initiate a new order of things; for the reformer has enemies in all those who profit by the old order, and only lukewarm defenders in all those who would profit by the new order; this lukewarmness arising partly from the incredulity of mankind, who do not truly believe in anything new until they have had actual experience of it.

    Stalin:

    We can exist peacefully together if we don’t indulge in too much mutual fault-finding in all kinds of trifles.

    Of course Stalin was a peace-loving easy going soul 🙂

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  16. CharlieM: I’ll tell you what I would want. I would like to be able to value the fact that people can have all sorts of opposing outlooks and that we can discuss and argue about our varying points of view without feeling that it is a personal attack. Of course the internet is probably the most challenging venue in which to achieve this aim. But I like a challenge

    Fair enough, I guess.

    Here’s the real problem, though: the fact that one can give a Neoplatonist interpretation of evolution, with quotes by and about Blake, Goethe, and Barfield, is not a reason why anyone should accept that interpretation.

    The others here are asking for reasons as to why a Neoplatonic interpretation is more reasonable than other interpretations, on the assumption that you would not prefer it over other interpretations if you did not have reasons for finding it preferable.

    That is, if your own beliefs are guided by reason. And perhaps they aren’t. Which is fine, up to a point — after all, we all have beliefs that are not entirely rational. (As Wittgenstein put it, “at the bottom of all grounded belief is belief that is ungrounded”.) But then the question would be, what is it you hope to accomplish by publicly sharing your beliefs when you cannot give reasons for them?

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  17. colewd:
    I am not claiming endosymbiosis cannot happen.What I am claiming is for it to happen the organelle must exist in prokaryotic cells and many do not.

    Seems like you don’t understand something. So, here it goes. Please pay attention (or not if you don’t care, but let me know so that I won’t waste more time trying). Endosymbiosis is the way a couple organelles arose (as far as the evidence is concerned). So what you wrote doesn’t make sense. the organelle was, originally, a bacterial cell (a prokaryote), after “endosymbiosed” it lost some genes, which made it dependent on the host cell, thus becoming an organelle. So, saying that for endosymbiosis to happen the organelle had to exist in prokaryotes doesn’t sound right.

    Clear?

    colewd:
    A common code does not entail a common origin especially when that codes organization changes so dramatically.

    The code organization? I think you’re confused here too. The genetic code is the correspondence between codons and amino-acids. It’s the very same for most organisms, and too similar to be coincidence when not identical. Given that, saying that its organization is different doesn’t make sense. Maybe you’re mistaking the genetic code with the chromosome, or something else?

    colewd:
    Your claim of no possibility of separate origin seems in conflict that separate origins is something we should expect.

    It’s ore like the likelihood of separate origins doesn’t make much sense given what’s shared between organisms. The genetic code is one of several things.

    I don’t see any conflict between common origin and finding novel things. Actually, it’s the opposite. You’re asking for a “re-origination” of the genetic code, of lots of metabolic enzymes, etc, that are common, and to put on top of that the origin of those novel features. That’s much more for independent origin than for common origin, since with common origin at least the shared parts are already there.

    I think you’ve got lots of misunderstanding to work on.

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  18. CharlieM:
    Let’s see if we can begin a conversation from a point of agreement. Do you believe that consciousness has evolved?

    This wording looks a bit strange. Consciousness is an activity. An ability if you must. So, if you’re asking if the ability we call consciousness evolved, I’d say yes, this ability evolved. If you mean consciousness as if it was some animal of sorts, then I’d answer that you’re asking a nonsensical question.

    CharlieM:
    And that it is possible, indeed probable, that it will evolve further into the future?

    Here I suspect that you have a “progress” concept of evolution, which is not the way most of us view evolution.

    So, I suspect, that you and John would not find a point of agreement with this question of yours. It looks like you’d be very far apart, starting with what looks like a very different view of consciousness, and ending with a very different view of evolution.

    ETA: I cannot speak for John, which is why I wrote “I suspect.”

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  19. Entropy,

    The code organization? I think you’re confused here too. The genetic code is the correspondence between codons and amino-acids. It’s the very same for most organisms, and too similar to be coincidence when not identical.

    That’s much more for independent origin than for common origin, since with common origin at least the shared parts are already there.

    This is a gross over simplification. DNA in prokaryotic and eukaryotic cells are organized very differently. You know this and we have discussed this previously. There is very little connection between the two cells.

    These cells architectures are completely different. Are you are trying to convince me that an apple came from an orange?

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  20. colewd:
    Allan Miller,

    It is the issue of common origin.Major biologic mechanisms existing in a species that do not exist in the prior species.You cant hand wave this away.

    The question you asked me was this: given my acceptance of the probability of multiple OoL events, why do I think that eukarya, archaea and bacteria are genetically related. I gave my answer – there is a deep commonality between these groups. And you say ‘but there are differences!’. Well, yeah. There are differences. Of course there are differences. Do we expect every organism on earth to be identical, if there were but one coalescent species?

    You cannot hand-wave away the similarities. The most fundamental is the translation system, both mechanism and codon assignment. On parsimony, you most likely get 95-100% codon assignment identity through common ancestry. Likewise the precise division of the codon table throughout between the same 10 Class l and 10 Class ll proteins (unrelated to each other, interestingly). Convergence is unlikely, as is LGT. One might invoke ‘common design’, but I don’t know what would favour that, when your evidence for separate origin is actually the things NOT held in common.

    Yes a separate origin because of new features that don’t fit in the old footprint and require a massive amount of novel FI.

    The question is are bacteria, eukarya and archaea genetically related? None of your list argues against that, and indeed many of them are not, contrary to what you may have picked up on a Creationist website, taxonomically restricted to one domain.

    [-spliceosome] – archaea and eukarya share an intron excision system.

    [nuclear pore complex] neither bacteria nor archaea have nuclei, so this does not argue against their genetic relationship with each other.

    [-chromosome structure] – chromosome structure in archaea and bacteria is generally quite similar. Unburdened by religious goggles, one would not dispassionately look at these two domains and insist that they are unrelated on those grounds. But further, some archaea have histones, capped linear chromosomes … ‘etc’ … which links them to eukarya as well.

    [-golgi apparatus] – ‘things that one finds in Eukaryotic cells, Alex’.

    [-all genes w introns and exons] – archaea have introns

    [-nucleus] both archaea and bacteria lack a nucleus, as mentioned – which is more a similarity than a difference. Admittedly eukarya are different in that regard, but this difference does not trump all shared features.

    [-ubiquitin system in multi cellular] genetic homologues of the ubiquitin system exist in archaea.

    To say nothing of the things you could have mentioned, such as actin and tubulin, or the many other eukaryotic proteins with homologues in archaea or bacteria … etc. A favourite is spo11, which initiates Double Strand Breaks in meiosis, a distinctively eukaryotic activity. It’s identifiably related to an archaeal Type ll topoisomerase. It is hardly a stretch to argue that this is supportive of a genetic relationship.

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  21. Kantian Naturalist: Fair enough, I guess.

    Here’s the real problem, though: the fact that one can give a Neoplatonist interpretation of evolution, with quotes by and about Blake, Goethe, and Barfield, is not a reason why anyone should accept that interpretation.

    I do not like to label people and I am not trying to align myself with any particular philosophy but my own. But I agree that in most respects my beliefs align more with Neoplatonism than say materialism.

    And the problem as I see it is that you have not as yet engaged with any arguments I am making through the quotes that I have given. Take for instance these words from Kathleen Raine:

    Blake never identifies the physical body with the true man. We descend as the Platonists say into the world of generations with the assumption of a physical body.

    What reason could I possibly have for aligning myself with these words? Well, let’s see. I study my physical body and I see that it is constantly changing. Within it the material substances are being moved around and replaced constantly. The form which my body has taken is somewhat more stable that the physical substances. It has altered greatly between conception and adulthood but I can see a certain consistency of form during my adult life. My sense of egohood is even more persistent. It has remained with me since I first woke up to self consciousness when I was a young child. My feelings and passions may have changed and my knowledge has increased but the very fact that I am using the word “my” denotes that my egohood is a stable aspect of my biography. I lose consciousness of my ego every time I go to sleep but it always makes its appearance again when I wake up. It persists. That is my reason for thinking that the ego lies above the physical body and cannot be equated with it.

    I am not alone in believing in a higher reality and I do not believe it is irrational to do so. Can you give a rational reason why you believe reality is limited by the conscious everyday experience of current Western thinking humans?

    The others here are asking for reasons as to why a Neoplatonic interpretation is more reasonable than other interpretations, on the assumption that you would not prefer it over other interpretations if you did not have reasons for finding it preferable.

    That is, if your own beliefs are guided by reason. And perhaps they aren’t. Which is fine, up to a point — after all, we all have beliefs that are not entirely rational. (As Wittgenstein put it, “at the bottom of all grounded belief is belief that is ungrounded”.) But then the question would be, what is it you hope to accomplish by publicly sharing your beliefs when you cannot give reasons for them?

    Yes it something I aim for, to have my beliefs founded in reason To not only believe something but to understand why I believe something is what I strive for.

    Where our beliefs might differ? Let’s take a specific example that is relevant to this thread. The transition from single celled life to multicellularity. Firstly I would say that on the whole in a Darwinian sense prokayotes are much more successful than eukaryotes. Would you agree and if not why not? If some time in the past a prokayote suddenly assimilated another organism in such a fortuitous way that the pair became effectively one, what advantage would that have given it? It was already successful at surviving up to that point and very many of its relatives would remain extremely successful up to the present time. Then through yet another fortuitous event it joined together with like minded mates and multicellularity was born. Can you think of any problems that would come with multicellularity and how they could be overcome? What changes would have to be made to go from a colony of individual organisms to a single multicellular organism? How many more fortuitous events would have to occur for this to happen? And why would it be worth the effort considering how very successful prokaryotes are?

    Instead of having to evoke all these chance events can we see any examples of progress from being single cellular to being a vastly more complex multicellular organism that involves teleology? Yes we can. Every human life goes through this teleological process. Teleology is a much neater answer than a vast string of chance events. It explains the facts better than chance in the same way that modern astronomy can explain the movement of the planets in a much more satisfactory way than the epicycles of old.

    And what in my opinion is the aim of this teleological process? The awakening of consciousness. Consciousness is the one feature of earthly life that goes beyond self preservation. It goes beyond just trying to survive.

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  22. Kantian Naturalist: I’m not sure what to make of that remark.

    Could be the source of more quotes he (John Harshman) might “possibly want”. I provided some just in case. I’m sure he’ll thank me in due course.

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  23. colewd:

    You quoted me:

    Entropy:
    The code organization? I think you’re confused here too. The genetic code is the correspondence between codons and amino-acids. It’s the very same for most organisms, and too similar to be coincidence when not identical.

    That’s much more for independent origin than for common origin, since with common origin at least the shared parts are already there.

    Then you wrote:

    colewd:
    This is a gross over simplification.

    What of it all is an oversimplification? The correspondence between codons and amino-acids, aka the genetic code, is exactly the same between, say, humans and Escherichia coli. Where’s the oversimplification there? We share also several enzymes in our metabolisms. Where’s the oversimplification here?

    colewd:
    DNA in prokaryotic and eukaryotic cells are organized very differently.

    So you were talking about the organization of the DNA molecule, the genome, the chromosomes. Which is why I said you might be confused. The genetic code and the organization of the DNA are not the same thing. Clear now?

    colewd:
    You know this and we have discussed this previously. There is very little connection between the two cells.

    The facts that both cells use DNA as their genetic material, RNA as catalyst and as transcript going into translation (both using translation, as implied here), both translate the same codons for the same amino-acids (same genetic code), both having corresponding rRNAs in their ribosomes, both containing lots of homologous proteins, even sharing steps in their metabolisms, tells me that there’s deep connections between the two.

    colewd:
    These cells architectures are completely different.

    This is a question of focus. Besides the list above, the cells also have a basic lipid-based membrane, foe example. So, sure, there’s differences, but I would not go as far as saying that they’re completely different.

    colewd:
    Are you are trying to convince me that an apple came from an orange?

    I’m not trying to convince you of anything. I’m just trying to correct some mistakes in your thinking that seem to get in the way of your understanding, but I doubt that anything can convince you. At best I expect you to understand that poor understanding doesn’t make evolution false. A huge advance would be to get you to understand that we’re convinced about evolution, and other things in science, for very good reasons.

    Apples didn’t come from oranges, even though their cell structures, DNA organization, etc, etc, etc, etc,, are very very very very very similar. They share common ancestry though.

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  24. Allan Miller,

    Of course there are differences. Do we expect every organism on earth to be identical, if there were but one coalescent species?

    The evidence we have where we know ancestral relationships exist is that the organisms are very similar genetically. The eukaryotic cell is a much larger structure then the prokaryotic cell and as I mentioned has many new organs as you have agreed.

    Do you have any direct evidence that complex new features can come from cell division alone. If not I think you should highly consider a separate origin event for the eukaryotic cell.

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  25. Entropy,

    Apples didn’t come from oranges, even though their cell structures, DNA organization, etc, etc, etc, etc,, are very very very very very similar. They share common ancestry though.

    Can you support this claim?

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  26. colewd: Do you have any direct evidence that complex new features can come from cell division alone.

    Yes. The cit+ mutant in the long term evolution experiment is a good example of a complex feature requiring specific interactions of multiple previous unrelated genetic components.

    Now where is your “direct evidence that complex new features” were created in the historical past by an unknown intelligent designer?

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  27. colewd,

    The evidence we have where we know ancestral relationships exist is that the organisms are very similar genetically.

    The presence of 2 billion years’ accumulated divergence would seem to preclude these organisms from being ‘very similar’. Time alone would thus be sufficient to fool you into thinking divergence was separate creation. You seem unwilling to recognise the impact of time upon residual genetic relatedness. With divergence there must logically come a point, even in truly related sequences, where that relationship is not recoverable statistically. In this instance though, we haven’t actually reached that point. The signal is scrambled, but not yet all noise.

    The eukaryotic cell is a much larger structure then the prokaryotic cell and as I mentioned has many new organs as you have agreed.

    Sure …

    Do you have any direct evidence that complex new features can come from cell division alone.

    Endosymbiosis is not ‘cell division alone’. It introduces a massive amount of genetic material, providing evolutionary raw material and a degree of redundancy that permits a substantial amount of organismal evolution, and it radically changes the energy budget of cells against those that must live by diffusion alone. It allows for phagocytosis, the elimination of cell walls, enlargement, new modes of movement, and introduces selective pressures that favour distant active transport (eg Golgi), which in turn permit further enlargement and complexification. Because of the energetic and genetic change, and the interplay of those genomes, it’s a real step change in evolution. It doesn’t happen every day, but it doesn’t need to in order to be real. See also chloroplasts, and Wolbachia, for ‘interim’ systems less completely integrated than mitochondria.

    If not I think you should highly consider a separate origin event for the eukaryotic cell.

    Unlike you, I cannot simply pretend that the vast evidence of common origin, coalescing inexplicably (on your paradigm) upon archaea and alpha-proteobacteria, and uniting them too further back, does not exist.

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  28. Allan Miller,

    Unlike you, I cannot simply pretend that the vast evidence of common origin, coalescing inexplicably (on your paradigm) upon archaea and alpha-proteobacteria, and uniting them too further back, does not exist.

    What you are pretending is that all the differences don’t exist because you know your claim that life arising is an easy problem is bogus.

    There is no rational reason given what we know to hold on to a single origin of life as a working assumption. There are two may differences to explain for this to be a rational conclusion.

    Endosymbiosis is not ‘cell division alone’.

    Endosymbiosis does not solve the problem of many of the new features of eukaryotic cells. This theory is almost useless if you face the reality of all the new features that don’t exist in prokaryotic cells.

    The presence of 2 billion years’ accumulated divergence would seem to preclude these organisms from being ‘very similar’.

    Your speculation is duly noted.

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  29. colewd: Your speculation is duly noted.

    It’s not speculation, it follows necessarily. In so far as change accumulates over time (and this one isn’t in question, it does), eventually the entire thing will change to the point that there’s nothing left of the original. It is unavoidable.

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  30. colewd,

    What you are pretending is that all the differences don’t exist because you know your claim that life arising is an easy problem is bogus.

    Where have I made that claim? My ‘claim’ is that I don’t see any reason why life should not arise more than once, if it can arise once, by whatever cause. And I know that deep divergence must erode the signal of relatedness, inevitably by increasing the amount of ‘difference’, so difference by itself is not sufficient reason to doubt the common origin of deeply divided clades possessed of fundamentally similar core genes. This seems a pretty unexceptionable claim.

    The available evidence points against survival of more than one of these putative ‘singularities’. If it happened more than once, it has left no modern descendants. You do me a disservice if you think my assessment of this evidence dishonest. It is what I think.

    There is no rational reason given what we know to hold on to a single origin of life as a working assumption. There are two may differences to explain for this to be a rational conclusion.

    We still have to explain the commonalities, and the pattern of differences. There are too many to simply dismiss, merely because it makes you feel less special to be cobbled together from prokaryotes.

    Allan: Endosymbiosis is not ‘cell division alone’.

    colewd: Endosymbiosis does not solve the problem of many of the new features of eukaryotic cells. This theory is almost useless if you face the reality of all the new features that don’t exist in prokaryotic cells.

    Endosymbiosis is not intended to explain every last feature of eukaryotes. It does explain the rooting of gene sets in, respectively, alpha-proteobacteria and archaea, as well as for example the use of n-formyl-methionine as an initiator codon in mitochondria (and bacteria) but not nuclear genes (and archaea).

    Data unknown at the time of proposal of the hypothesis keeps coming in in favour of the engulfing organism being an archaeon. That’s a powerful corroboration of a theory: that data unknown in advance of its discovery comes down in favour of it. How can that be? What, if not an origin in archaea, accounts for the extensive homology with archaea, among genes not targeted to the mitochondrion? How come recently discovered archaea turn out to have – for example – homologues of ubiquitin processing, or Golgi transport (see: Lokiarchaea)? A curious phenomenon, if these homologues have nothing to do with the matter.

    I confidently predict that more supposedly ‘eukaryote’ genes will find homologues in archaea as taxonomic sampling increases. How can I be so sure? Wild guess?

    Allan: The presence of 2 billion years’ accumulated divergence would seem to preclude these organisms from being ‘very similar’.

    colewd: Your speculation is duly noted.

    Your reliance on glib, empty phrases when you can’t think of a sensible refutation is duly noted.

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  31. Rumraket: In so far as change accumulates over time (and this one isn’t in question, it does), eventually the entire thing will change to the point that there’s nothing left of the original. It is unavoidable.

    Is that why people believe in universal common ancestry, because all the signs have been lost due to the vast ages of time involved?

    Using your line of argument, even if there were no reason to believe in universal common ancestry, one could still reasonably believe in it, because, you know, we would EXPECT the data to be missing.

    Talk about protecting your theory from any form of falsification.

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  32. Why not ask Bill how much difference is allowable within the constraints of common ancestry that he is willing to accept?

    Young Earth Creationists are hyper-evolutionists WITHIN the bounds of what is acceptable common ancestry, even for them. But look at all those differences!

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  33. Mung: Talk about protecting your theory from any form of falsification.

    You might as well just call Rumraket a liar.

    But let’s unpack this. Do you expect any signal from the OOL to present day to survive an unlimited time in an evolving biological system like the one we find ourselves in? If so, on what basis? If not, from when to when and how long?

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  34. Mung: Talk about protecting your theory from any form of falsification.

    I’d say that the best way to prevent your theory from even potentially being falsified, the best way ever would be to actually never tell anybody what it is.

    Just like you’ve never told anybody, Mung.

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  35. Mung: Is that why people believe in universal common ancestry, because all the signs have been lost due to the vast ages of time involved?

    No. That would be absurd.

    I’m explaining why we should not expect all loci to show evidence of common descent. I’m not saying those loci which do not exhibit any similarity are evidence for common descent. Why would you even think that?

    Now that I have explained this, which honestly shouldn’t even be necessary, the rest of your post looks pretty silly.

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  36. colewd: There is no rational reason given what we know to hold on to a single origin of life as a working assumption.

    I actually agree with that. We should not commit ourselves to believe there was just one origin of life. Until we know how life originates, we cannot rule out that many origins happened independently.

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  37. Rumraket: It’s not speculation, it follows necessarily. In so far as change accumulates over time (and this one isn’t in question, it does), eventually the entire thing will change to the point that there’s nothing left of the original. It is unavoidable.

    Is there a known estimate of how long it will take for the first organisms now known to share some DNA with the rest, to reach the point of no sequence similarity?

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  38. dazz: Is there a known estimate of how long it will take for the first organisms now known to share some DNA with the rest, to reach the point of no sequence similarity?

    It should not be that hard to do a calculation of that with some basic realistic assumptions about the avg rate of mutation, genome size, generation time and the size of the locus in question? How long will it take for a 1000 basepair locus to be completely changed assuming:

    A pr nucleotide mutation rate of 1 in 10^8 with an equiprobable distribution across genome length.
    The 1000 basepair locus is evolving neutrally.
    A generation time of half a day (12 hrs).
    A genome size of 2.5 million basepairs.

    The only obstacle I see to this calculation is to factor in the probability of multiple hits to the same location (if we assumed multiple hits couldn’t happen I could do the calculation myself). I will leave this one to someone more competent in statistics.

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  39. colewd:
    Can you support this claim?

    Which one? That apples didn’t come from oranges? That oranges and apples share common ancestry? Either way, many scientists did that already.

    Interesting that you focused on the easiest common ancestry to establish. It’s interesting because this means that you’re convinced that common ancestry for prokaryotes and eukaryotes makes better sense than independent origins, yet you doubt about the common ancestry of two plants.

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  40. OK, I’ve tried the following
    Each generation the probability for each loci to remain unchanged is 1-(10^-8) or 0.99999999

    After n generations, the probability for each loci to remain unchanged is 0.99999999^n. So the probability that it’s mutated one or more times is
    1-(0.99999999^n). I’ll call that P(c)

    So for a genome size of 2.5 billion loci, the probability that all of them have mutated would be P(c)^2.5 billion.

    For a 99% probability of all mutated loci: P(c) = 0.99^(1/(25*10^8)) = 0.99999999999597986565860750426664

    That gives me a number of generations of 2623970566

    P(c) = 1-(0.99999999^n)
    0.99999999^n = 1-P(c)
    0.99999999^n = 1-0.99999999999597986565860750426664
    0.99999999^n = 4.020134*10^-12
    n = log(4.020134*10^-12) / log(0.99999999)
    n= -11.395759433793489880272748234627 / -4.3429448407472425164387089585427*10^-9
    n = 2623970566

    At 2 generations per day, that’s 3594478 years.

    So 3 and a half million years, which of course can’t be right. heh

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  41. dazz: So 3 and a half million years, which of course can’t be right. heh

    Hmm. Or is it? We are assuming the locus is evolving at the rate of mutation because all mutations are neutral. Which is of course completely unrealistic.

    The fraction of mutations allowed in functional protein coding genes is much much lower than the neutral rate.

    Assuming something like 99.9% of mutations in the average protein coding gene is deleterious enough to go extinct, that means for every 1 mutation that slips through, 999 mutations must be lost. So for every 1 year, another 999 years must be added. 3.5 million * 999 = ~3.5 billion years.

    That does sound more realistic.

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  42. Rumraket: Hmm. Or is it? We are assuming the locus is evolving at the rate of mutation because all mutations are neutral. Which is of course completely unrealistic.

    The fraction of mutations allowed in functional protein coding genes is much much lower than the neutral rate.

    Assuming something like 99.9% of mutations in the average protein coding gene is deleterious enough to go extinct, that means for every 1 mutation that slips through, 999 mutations must be lost. So for every 1 year, another 999 years must be added. 3.5 million * 999 =~3.5 billion years.

    That does sound more realistic.

    I see, thanks Rum. Of course I forgot about selection and mistook fixation rate for mutation rate… just like… OMFG… I’m becoming a creotard!

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  43. What say you Mung? Agree or disagree with the calculations just performed? Reasonable? Unreasonable? Why?

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  44. Mung: Is that why people believe in universal common ancestry, because all the signs have been lost due to the vast ages of time involved?

    Using your line of argument, even if there were no reason to believe in universal common ancestry, one could still reasonably believe in it, because, you know, we would EXPECT the data to be missing.

    Talk about protecting your theory from any form of falsification.

    Oh, come off it!

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  45. dazz: I see, thanks Rum. Of course I forgot about selection and mistook fixation rate for mutation rate… just like… OMFG… I’m becoming a creotard!

    Yep, it’s fortunate that conservation is sufficient to allow probing of such vast depths of time, where the signal of common descent remains (contra Mung, who thinks we just ‘assume’ it anyway). Neutral evolution would erode signal in a few million years. Which is also useful – a bit like radioactive half lives, different rates allow probing of different depths.

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