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.

1,101 Replies to “Universal Common Descent Dilemma”

  1. Allan Miller
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    says:

    CharlieM: You obviously do not understand the buttercup analogy. We can place smooth muscle, skeletal muscle and heart muscle in an order of relationship because of their similarity, this does not mean that one has arisen from the other. The alternative explanation is that they all are material expressions of the archetypal dynamic pattern.

    Analogies in the way you are using them are unhelpful. We have a known process that is expected to produce a branching pattern. When we analyse the data, we recover a branching pattern. That’s not proof that the data were produced by the process, but it’s a very solid strike in its favour. No other explanation for this pattern is offered, just a faint ‘ain’t necessarily so’.

    More significantly still, that pattern comes from some pretty low level data – digital sequence. Equating that to an ‘analogue’ hierarchy is a common tactic, because for some reason you people simply will not look at the digital. Erik was all about cups and vases, fmm’s obsessed by fur colour, you’re on about muscle … there was a time when ‘analogue’ characters of organisms were all we could group (though even then we had a curious amount of non-independence of character states). That time is past.

  2. Rumraket Rumraket
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    CharlieM: Children fall and scrape their knees without the presence of bitumen

    Irrelevant. The point still remains that any past event cant can be interpreted to be the intended step towards any particular future circumstance. But that is all it is, an interpretation.

    but multicellular organisms cannot exist without the presence of prokaryotes.

    You don’t know that, but even if that was true it would again miss the point, which is that you are just offering an untestable interpretation of history.

  3. Mung Mung
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    CharlieM: Darwinian evolution seems to have no limits to its ability.

    It boggles the mind. Godlike in it’s powers. Yeah verily, amen.

  4. Corneel Corneel
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    CharlieM: Chloroplasts are not what is essential. You are confusing what has become essential in most individual living plants with what is essential to plant nature in general. What is essential for all forms of life is that they take in energy to live and grow. We take in chloroplast containing substance as an energy source every time we eat green plants.

    The essential nature of plants is growth, the essential nature of animals is growth and sentience. We contain the essence of plants in that we grow and we contain the essence of animals in that we are sentient.

    If the essential nature of plants is growth, then why do buttercups produce flowers? What is the essential nature of cyanobacteria? What is the essential nature of sponges (they don’t look particularly sentient to me)?

    Are you making up this stuff as you go?

  5. Mung Mung
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    colewd: Darwins original concept of all life originated from a single ancestor required explaining transitions.

    Descent with modification.

  6. CharlieM CharlieM
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    John Harshman:

    CharlieM: If you understand the example of the buttercup leaves I referred to in my last post you will see that I don’t believe that one caused the other.

    What you believe or don’t believe is irrelevant. If you have a claim to make, you need to support it with evidence. Of course you always deny making claims, which means you don’t have to support anything.

    I do have good evidence that the lower leaves are not the cause of the upper leaves. Do you believe that they are?

    The leaves along the stem of the plant can be grouped in a hierarchical series, schoolkids that were given the task could do it. yet the earlier was not the cause of the later.

  7. CharlieM CharlieM
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    John Harshman: Yes, typical creationist trope: if we don’t know everything, therefore we know nothing. (Yes, yes, you aren’t a standard creationist; but you share much with them, including this particular habit.) It just isn’t true. Preservation is rare in some environments and common in others. There are no eukaryotes in ancient stromatolites, and the preservation environment is such that they ought to be there if they were present. And there are environments in which eukaryotic cells are preserved, environments which were present at various times throughout the several billion years in which there are no eukaryote fossils. Your appeal to ignorance is invalid.

    We have been reminded on more than one occasion here that absence of evidence is not evidence of absence. But as it happens there is some evidence. See below.

    CharlieM: Added to this is the fact that it cannot be stated with certainty that the ancient stromatolites were caused by cyanobacteria alone.

    In fact, if I recall, there are several sorts of bacteria in the Gunflint Chert. But how is that relevant? As long as there are cyanobacteria, which there are, and no eukaryotes, which there aren’t, that makes the point that there were cyanobacteria before there were eukaryotes. Your recent statement that it doesn’t matter which came first suggests you may realize that.

    You might want to look at this wikipedia entry on the subject of a eukaryote called Kakabekia from the Gunflint Chert. See also this webpage from National Resources, Canada where they also name eoastrion as being present.

  8. CharlieM CharlieM
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    John Harshman: What options are you considering? Do you have any evidence favoring any of those options? Or will you just retreat from any claims at all?

    The option that mitochondria and proteobacteria have a common origin but are not derived one from the other (as in the example of the buttercup leaves).

  9. CharlieM CharlieM
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    dazz: Is there any observation that would convince you that your “theory” is wrong? IOW is there any possible object, entity, shape, organism, etc.. whose existence would be incompatible with your “theory”?

    I don’t have a theory. I just look at the evidence and explore the possibilities.

  10. CharlieM CharlieM
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    says:

    Allan Miller: Analogies in the way you are using them are unhelpful. We have a known process that is expected to produce a branching pattern. When we analyse the data, we recover a branching pattern. That’s not proof that the data were produced by the process, but it’s a very solid strike in its favour. No other explanation for this pattern is offered, just a faint ‘ain’t necessarily so’.

    More significantly still, that pattern comes from some pretty low level data – digital sequence. Equating that to an ‘analogue’ hierarchy is a common tactic, because for some reason you people simply will not look at the digital. Erik was all about cups and vases, fmm’s obsessed by fur colour, you’re on about muscle … there was a time when ‘analogue’ characters of organisms were all we could group (though even then we had a curious amount of non-independence of character states). That time is past.

    There is a branching pattern in my cellular development as an adult human from a single fertilized egg. This does not mean that my present specialized cells have descended from my other cells which are morphologically closest to them.
    The argument for mitochondria being descended from prokaryotes is because of their morphological similarity.

    And don’t forget that my form was in some respects determined from the beginning.

  11. CharlieM CharlieM
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    Rumraket: Irrelevant. The point still remains that any past event cant can be interpreted to be the intended step towards any particular future circumstance. But that is all it is, an interpretation.

    You don’t know that, but even if that was true it would again miss the point, which is that you are just offering an untestable interpretation of history.

    And without the aid of a time machine how do we test the proposal that mitochondria descended from bacteria billions of years ago?

  12. CharlieM CharlieM
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    Mung: It boggles the mind. Godlike in it’s powers. Yeah verily, amen.

    There are quite a few here who would say that my mind is already boggled 🙂

  13. Entropy Entropy
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    CharlieM:
    The argument for mitochondria being descended from prokaryotes is because of their morphological similarity.

    Not only that. Also because of “mitoproteins” are similar in sequence to proteins in prokaryotes. Because the mitochondrial chromosome is circular (as in most prokaryotes). Because mitochondrial ribosomes have proteins more similar in sequence to those of prokaryotic ribosomes than to non-mitochondrial eukaryotic ribosomes. Because there’s a variety in how much mitochondria resemble prokaryotic cells across organisms and, in some protists, we find internal symbionts that can also live outside (as if we were watching stages in the evolution of mitochondria and mitochondria-like organelles), etc.

  14. John Harshman John Harshman
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    CharlieM: I do have good evidence that the lower leaves are not the cause of the upper leaves. Do you believe that they are?

    Is this actually the claim you want to make? You might as well make the bold statement that kittens are cute.

  15. John Harshman John Harshman
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    CharlieM: We have been reminded on more than one occasion here that absence of evidence is not evidence of absence. But as it happens there is some evidence. See below.

    Never liked that facile rule. Absence of evidence is evidence of absence if we would expect to see that evidence given presence.

    You might want to look at this wikipedia entry on the subject of a eukaryote called Kakabekia from the Gunflint Chert.See also this webpage from National Resources, Canada where they also name eoastrion as being present.

    What makes you think that either of these is a eukaryote?

  16. Allan Miller
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    says:

    CharlieM: There is a branching pattern in my cellular development as an adult human from a single fertilized egg. This does not mean that my present specialized cells have descended from my other cells which are morphologically closest to them.
    The argument for mitochondria being descended from prokaryotes is because of their morphological similarity.

    Another unhelpful analogy. Your form is, at least in part, determined by differential gene expression and cell adhesion. There is no sensible equivalent in the diffused corpus of a set of descendant individuals, however tempting it might be to analogise them.

    Eta – just looked harder at your last paragraph; that is exactly what I was talking about upthread, about the flat refusal to comprehend the digital. Morphology is NOT the reason mitochondria cluster with alpha proteobacteria.

  17. Allan Miller
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    says:

    You seem to be skating towards ‘why are there still monkeys’ territory, Charlie. Nobody is suggesting that mitochondria are derived from modern alpha proteobacteria, but that they are their closest relatives – common ancestry, not the derivation of one from the other. As with the common ancestry of your cells with the original zygote, the only sense in which your analogy holds up.

  18. CharlieM CharlieM
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    John Harshman: What makes you think that either of these is a eukaryote?

    Did you look at the Wikipedia link I provided:

    Kakabekia
    Scientific classification
    Domain: Eukaryota

    I’ll continue with this discussion tomorrow if I get the time.

  19. John Harshman John Harshman
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    says:

    CharlieM: Did you look at the Wikipedia link I provided

    Ah, thanks. So a single word in a Wikipedia stub is what makes you think that. And you didn’t bother to look at the sole reference in that stub, which contradicts the assertion.

  20. Nonlin.org
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    Alan Fox: Present some evidence that falsifies UCD. I promise I’ll look at it.

    Falsify is too much to ask for, considering that the burden is on he that comes up with the story.

    Showing that the UCD story is logically inconsistent is more than enough and this OP does that… as does this other one: http://theskepticalzone.com/wp/nested-hierarchies-tree-of-life. And then of course this one: http://theskepticalzone.com/wp/natural-selection-evolution-magic/

    But some people see straw armies everywhere.

  21. Nonlin.org
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    Allan Miller: What has a common genetic code to do with the question of UCD of extant life? Are you sure you have fully grasped the basic material?

    This OP does not address “the question of UCD”. It is much more limited in scope. Read again.

  22. Nonlin.org
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    Allan Miller: There was a time when endosymbiotic theory was controversial. There are aspects of Margulis’s extreme version of ‘pan-endosymbiosis’ that are now firmly rejected. In each case: why? What methodology was applied by the scientific community to separate the ‘just-so’ from the ‘just-ain’t-so’?

    Yada, yada, yada. But no experimental evidence. So what’s new in neo-neo-neo Darwinism?

    Sure, breeding dogs into cats (if we had the technology) would be evidence for “evolution” because everything is.

  23. Nonlin.org
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    J-Mac: Does anyone here ever get deja vu?
    I mean, how can you repeat the same arguments so many times, especially the ones that contradict your own beliefs?

    A lot of words and very few ideas indeed. Sad.

  24. Nonlin.org
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    Joe Felsenstein: Using the original Szostak / Hagen definition, it will include cases where natural selection can increase Functional Information. gpuccio says that when one observes a certain level of FI, one can reliably infer the presence of Design. That is not true for Szostak and Hagen’s original definition of FI.

    The whole idea of “Functional Information” is bogus if it helps: http://theskepticalzone.com/wp/biological-information-2
    However, is that supposed to be related in any way to this OP?

  25. Nonlin.org
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    says:

    Allan Miller: Thermodynamic entropy gives a statistical tendency toward dissipation. Opposition to this tendency is not ‘miraculous’, but statistically quite likely in small doses. But with increasing time, the statistical tendency gives a definite arrow. And so with sequence divergence: small amounts of homoplasy are statistically quite likely, but the arrow leads more generally towards loss of the original info in both lineages. Creationists love to point to the anomaly as casting suspicion on the whole endeavour – it’s nothing but anomaly! But what makes them anomalous?

    What do you mean? Maybe you have something to say, maybe you don’t. But let’s move this to http://theskepticalzone.com/wp/biological-information-2/ where it belongs.

  26. Joe Felsenstein Joe Felsenstein
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    Nonlin.org: The whole idea of “Functional Information” is bogus if it helps: http://theskepticalzone.com/wp/biological-information-2

    I disagree. For that matter, most “ID advocates” and creationists who comment here disagree with nonlin.org about that. Does that ever worry nonlin.org?

    However, is that supposed to be related in any way to this OP?

    It came up long after the OP, in the comments. Does nonlin.org need me to help them find where?

    I am certainly not trying to turn this thread into a discussion of FI, for which we had a 1,971-comment thread of its own (about the logic or lack of logic of gpuccio’s statements that FI cannot be created by natural selection).

  27. Allan Miller
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    Nonlin.org: Yada, yada, yada. But no experimental evidence. So what’s new in neo-neo-neo Darwinism?

    Haha. Another cardboard cutout iconoclast, same old bull with a side order of cocksure certitude.

    The only valid evidence is experimental evidence. I’ll be sure to tell the geologists and the astrophysicists.

    Sure, breeding dogs into cats (if we had the technology) would be evidence for “evolution” because everything is.

    No, it would be evidence of (not for) evolution because you would be doing descent with modification, not commencing a lineage with no antecedents. You gave me 2 choices, I had to pick one.

  28. Allan Miller
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    Nonlin.org: This OP does not address “the question of UCD”. It is much more limited in scope. Read again.

    What? Are we talking about the same OP? If it’s not about the question of UCD, what’s all the discussion of UCD about?

  29. Alan Fox Alan Fox
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    Nonlin.org: Showing that the UCD story is logically inconsistent is more than enough and this OP does that…

    Nonsense! It merely highlights your misunderstanding. OOL is a separate issue from UCD.

  30. Allan Miller
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    Nonlin.org: What do you mean? Maybe you have something to say, maybe you don’t. But let’s move this to http://theskepticalzone.com/wp/biological-information-2/ where it belongs.

    It belongs squarely here, even if over your head. I was connecting the informatic issue back to the OP. The evidence for UCD is gradually eroded by entropy, in the Shannon sense. But this erosion is itself informative, because it is possible to arrange these differences in a data set into a ‘tree’ topology. This gives a probabilistic direction to change, which is relevant when people try to argue that the direction of travel between prokaryotes and eukaryotes is simply reversible, or that ‘it could be convergence’. It isn’t, for reasons closely analogous to the irreversibility of statistical thermodynamics. Local departures from expectation are permissible, but these cannot be summed up into one big anomaly, because the overarching pattern is divergent.

  31. CharlieM CharlieM
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    Corneel: If the essential nature of plants is growth, then why do buttercups produce flowers?
    Are you making up this stuff as you go?

    I don’t know if you have ever had to look after a garden with buttercups growing in it. But if you did you would know how prodigious they are at producing runners. The plant does not stop growing just because it produces flowers. You are picking on part of the flower in isolation. I am considering the nature of the plant as a whole.

    What is the essential nature of cyanobacteria? What is the essential nature of sponges (they don’t look particularly sentient to me)?

    When comparing organisms I do not think it is helpful to treat bacteria as equivalent to the likes of mammals or birds. I would say that in the case of bacteria we should regard whole species or type as a single diffuse organism. in which case the way they spread in colonies shows that they have a plant like or more aptly vegetative nature. You pick sponges as an example because they are not very animal like. Well looking at the whole of life everything is related and in a state of flux. Sponges are at one extreme lower end of animal life demonstrating their plant like qualities and little in the way of sentience. Primates are at the higher extreme of animal life showing advanced sentience and tending towards self consciousness.
    Again you have isolated an extreme example and not considered animal life taken as a whole.

  32. CharlieM CharlieM
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    Entropy: Not only that. Also because of “mitoproteins” are similar in sequence to proteins in prokaryotes. Because the mitochondrial chromosome is circular (as in most prokaryotes). Because mitochondrial ribosomes have proteins more similar in sequence to those of prokaryotic ribosomes than to non-mitochondrial eukaryotic ribosomes. Because there’s a variety in how much mitochondria resemble prokaryotic cells across organisms and, in some protists, we find internal symbionts that can also live outside (as if we were watching stages in the evolution of mitochondria and mitochondria-like organelles), etc.

    Here you are demonstrating that mitochondria and bacteria are closely related and we agree on that. What you are not telling us is the nature of the relationship. Is it parent and offspring and if so which is the parent? Are they siblings, cousins or what? Those questions you have not answered.

    I have just discovered that there are actually researchers who are looking at other options rather than the prokaryote to eukaryote scenario although they don’t seem to be well represented in the literature.

    We have “Prokaryotes First hypotheses”, “”Eukaryotes First hypotheses”, and the “Nuclear Compartment Commonality hypothesis”
    From royalsocietypublishing.org

    In 2015, the Royal Society of London held a meeting to discuss the various hypotheses regarding the origin of the Eukarya. Although not all participants supported a hypothesis, the proposals that did fit into two broad categories: one group favoured ‘Prokaryotes First’ hypotheses and another addressed ‘Eukaryotes First’ hypotheses. Those who proposed Prokaryotes First hypotheses advocated either a fusion event between a bacterium and an archaeon that produced the first eukaryote or the direct evolution of the Eukarya from the Archaea. The Eukaryotes First proponents posit that the eukaryotes evolved initially and then, by reductive evolution, produced the Bacteria and Archaea. No mention was made of another previously published hypothesis termed the Nuclear Compartment Commonality (NuCom) hypothesis, which proposed the evolution of the Eukarya and Bacteria from nucleated ancestors.

    So when I read that it is a fact that eukaryotes have evolved from prokaryotes, I wonder how those who say this can be so certain. Should they not be a bit more hesitant in making such pronouncements? I would say that their thinking is biased by their beliefs.

  33. CharlieM CharlieM
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    John Harshman:

    CharlieM: I do have good evidence that the lower leaves are not the cause of the upper leaves. Do you believe that they are?

    Is this actually the claim you want to make? You might as well make the bold statement that kittens are cute.

    So we have here a hierarchical series in which the individuals in the series are not related by a line of descent.

    Do you agree?

  34. Allan Miller
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    says:

    CharlieM:

    So when I read that it is a fact that eukaryotes have evolved from prokaryotes, I wonder how those who say this can be so certain. Should they not be a bit more hesitant in making such pronouncements? I would say that their thinking is biased by their beliefs.

    You would be wrong. I can give, and have given, actual reasons why I support prokaryotes first. My ‘beliefs’ in that regard are biased by my knowledge of biology, the logic of phylogenetic analysis, the fundamental implausibility of gathering together a viable single-chromosome circular genome from a distributed linear one, and generating from it a bizarre kind of ‘upside down diversity’ among modern descendants such that it looks like the opposite of what happened.

    All you do is scuttle off to the internet and try and whip up a controversy, so you can do the Creationist palms-upward thing: ‘what’s a poor boy to believe?’.

  35. CharlieM CharlieM
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    Allan Miller: Another unhelpful analogy. Your form is, at least in part, determined by differential gene expression and cell adhesion. There is no sensible equivalent in the diffused corpus of a set of descendant individuals, however tempting it might be to analogise them.

    Differing genetic makeup in the family tree of individuals is equivalent to differential gene expression in individual development and ecological niches are somewhat equivalent to cellular interaction such as adhesion.

    Eta – just looked harder at your last paragraph; that is exactly what I was talking about upthread, about the flat refusal to comprehend the digital. Morphology is NOT the reason mitochondria cluster with alpha proteobacteria.

    Morphology is a big part of the reason. For instance their similar sizes, plasmid like DNA, lack of histones and lack of a nucleus. I’m not ignoring the fact that there might be similarities in DNA sequence. Do you know how closely the DNA sequences of mitochondria and bacteria match?

  36. CharlieM CharlieM
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    Allan Miller:
    You seem to be skating towards ‘why are there still monkeys’ territory, Charlie. Nobody is suggesting that mitochondria are derived from modern alpha proteobacteria, but that they are their closest relatives – common ancestry, not the derivation of one from the other. As with the common ancestry of your cells with the original zygote, the only sense in which your analogy holds up.

    Yes and that is the point I am making with my analogy. Your gluteus maximus and trapezius are very closely related in that they are both skeletal muscles, but no one would suggest that one developed from the other. But when it comes to mitochondria and bacteria that is exactly what is suggested.

  37. Corneel Corneel
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    CharlieM: I don’t know if you have ever had to look after a garden with buttercups growing in it. But if you did you would know how prodigious they are at producing runners. The plant does not stop growing just because it produces flowers. You are picking on part of the flower in isolation. I am considering the nature of the plant as a whole.

    No, you are not. You are merely picking the part of the flower that confirms your broad-brush characterisation while closing your eyes for any aspect that runs counter to it. It is trivially easy to find examples of plants that do stop growing when they flower; agaves are famed for it, but I guess you’ll just dismiss it as another “extreme example”.

    CharlieM: When comparing organisms I do not think it is helpful to treat bacteria as equivalent to the likes of mammals or birds.

    Why not? What happened to looking at life as a whole, I wonder?

    CharlieM: I would say that in the case of bacteria we should regard whole species or type as a single diffuse organism. in which case the way they spread in colonies shows that they have a plant like or more aptly vegetative nature.

    Problem: what’s a “species” and what’s a “type” and which ones “spread in colonies”? Many bacteria are motile: Perhaps you have read somewhere on this site about the “bacterial flagellum”. Care to guess what those bacteria use that for?

    The thing you seem to be unable to grasp is that bacteria are spectacularly diverse, far more diverse than animals. Your glaring disinterest in anything-that-is-not-an-animal is not a valid excuse to sweep them all on one heap.

    CharlieM: You pick sponges as an example because they are not very animal like. […] Again you have isolated an extreme example and not considered animal life taken as a whole.

    I picked sponges in an attempt to show you that your idea of an animal is like that of a three-year old who just learned “zebra” and “elephant” from a book with a lot of pictures. Sponges are not “plant like”; they are animals just like zebras, ostriches, jellyfish and earth worms. The only person continuously cherry picking an extreme example is you, whenever you take humans as the only and ultimate yardstick to measure all other organisms against.

  38. CharlieM CharlieM
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    John Harshman: Ah, thanks. So a single word in a Wikipedia stub is what makes you think that. And you didn’t bother to look at the sole reference in that stub, which contradicts the assertion.

    In what way does it contradict it?

    Retired microbiologist Moselio (Elio) Schaechter writes that:

    Kakabekia barg­hoor­ni­ana. It is known to exist both as an ancient fossil and as a present-day cultivable creature. Just as curious is that it has been shuttled across the great biological di­vide, now to apparently having landed firmly in the eukar­yotic camp

    I’m not saying that he is correct only that he seems to think they have been found to be more like eukaryotes.

  39. Allan Miller
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    CharlieM,

    Differing genetic makeup in the family tree of individuals is equivalent to differential gene expression in individual development

    No it isn’t.

    and ecological niches are somewhat equivalent to cellular interaction such as adhesion.

    “Somewhat equivalent”? Nothing like, I think is the phrase you are grasping for.

    Morphology is a big part of the reason. For instance their similar sizes, plasmid like DNA, lack of histones and lack of a nucleus. I’m not ignoring the fact that there might be similarities in DNA sequence. Do you know how closely the DNA sequences of mitochondria and bacteria match?

    Well enough to give strong support to the nesting of mitochondria in or very near alpha proteobacteria (and not the generality of bacteria, or some other clade within them).

  40. Allan Miller
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    CharlieM: Yes and that is the point I am making with my analogy. Your gluteus maximus and trapezius are very closely related in that they are both skeletal muscles, but no one would suggest that one developed from the other. But when it comes to mitochondria and bacteria that is exactly what is suggested.

    Is not. It is ‘suggested’ that they share common ancestry.

  41. Entropy Entropy
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    says:

    CharlieM:
    Here you are demonstrating that mitochondria and bacteria are closely related and we agree on that. What you are not telling us is the nature of the relationship. Is it parent and offspring and if so which is the parent? Are they siblings, cousins or what? Those questions you have not answered.

    The point was that the evidence that mitochondria evolved from ancient bacteria is not merely “structural” similarity. I leave it to you to decide which of those relationships you’re asking about make sense given that information.

    CharlieM:
    I have just discovered that there are actually researchers who are looking at other options rather than the prokaryote to eukaryote scenario although they don’t seem to be well represented in the literature.

    I’m not surprised that they’re not well represented in the literature, they’d have to describe their scenario in a sensical way, and that would be quite a challenge. I’d have to read something by those authors to see how the propose to solve all the issues that came to my mind as soon as I read that paragraph, but I don’t see the relevance to endosymbiosis.

    CharlieM:
    So when I read that it is a fact that eukaryotes have evolved from prokaryotes, I wonder how those who say this can be so certain. Should they not be a bit more hesitant in making such pronouncements? I would say that their thinking is biased by their beliefs.

    As far as I’m concerned, I’ve never used the “it’s a fact” phrasing. What I always say is that the evidence indicates that’s the way it happened. For eukaryotes first to be viable, they would have to have evolved from a kind of prokaryote other than bacteria and archaea, with that lineage leaving no “sister” lineage to today’s eukaryotes (as far as we know). So, in structural terms, that would have been a prokaryote, with primitive non-membraned nucleus, etc.

    I’d still expect the endosymbiosis events to have happened after the evolution of bacteria, because of the similarities between specific lineages of bacteria and their endosymbiotic counterparts.

    I think you’re reading too much into those alternatives. I suspect that you’re imagining that the eukaryote-first guys are proposing full-fledged multicellular, mitochondria+chloroplasts+plastid bearing, plant+animal eukaryotes being first. If so, I’d suggest reading a bit father than some small summary, because I think you’ll find that’s not the case. Oh, and make sure that your source is legitimate.

  42. Mung Mung
    Ignored
    says:

    Allan Miller: You gave me 2 choices, I had to pick one.

    Next time you get only one choice.

  43. Rumraket Rumraket
    Ignored
    says:

    CharlieM: And without the aid of a time machine how do we test the proposal that mitochondria descended from bacteria billions of years ago?

    We compare the predictions of hypotheses to data.

    That can’t be done with your pointless conjectures. That thing that happened could only happen because that thing in the past had to happen first to make it possible – is true for anything. It can’t not be the case in so far as there is any causality to history at all.

  44. DNA_Jock
    Ignored
    says:

    Entropy [to CharlieM]: I think you’re reading too much into those alternatives. I suspect that you’re imagining that the eukaryote-first guys are proposing full-fledged multicellular, mitochondria+chloroplasts+plastid bearing, plant+animal eukaryotes being first. If so, I’d suggest reading a bit father than some small summary, because I think you’ll find that’s not the case. Oh, and make sure that your source is legitimate.

    That does seem to be Charlie’s take.
    However, as Ford Doolittle notes,

    EF [eukaryotes first] is not a claim that members of the clade designated Eukarya or Eukaryota—which comprises the last eukaryotic common ancestor (LECA) and all its descendants—gave rise to either of the prokaryotic clades, Bacteria and Archaea. Nor does EF, in any version of which we are aware, imagine that alpha-protoeobacterial or cyanobacterial cells are escaped mitochondria or plastids.

  45. Allan Miller
    Ignored
    says:

    DNA_Jock,

    I just read that too! My fingers wiggled briefly over the keyboard …

  46. Allan Miller
    Ignored
    says:

    The question hinges (if we are to take the distinction between eu- and pro- as being the presence or absence of of a nucleus, which is kind of definitional) on whether the engulfing partner had a nucleus or not at the time of fusion. It’s a reasonably safe bet the bacterial component didn’t.

  47. Allan Miller
    Ignored
    says:

    Worth also considering Wolbachia. A definitive bacterium (alpha, as it happens), it is an intracellular parasite so successful that it has colonised 60% of insect species. Some actually suffer if the Wolbachia component is removed, though this isn’t universal. Like mitochondria, it has transferred many genes to the host and, again like mitochondria, has evolved strategies that favour females, in whose cytoplasm it mainly travels, selecting for countermeasures in the host DNA. This is only circumstantial, but there are strong hints there of a mechanism by which a bacterium can become integrated into a cell, and its self-interest suppressed.

    Another system of interest: the exosymbiosis of Nanoarchaeon and Ignicoccus, two Archaea. In this, the two cells are in physical contact, and interestingly there is export of ATP from one to the other (the larger to the smaller, in this case). And, again, significant gene transfer between the partners.

  48. CharlieM CharlieM
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    says:

    Corneel:

    CharlieM: I don’t know if you have ever had to look after a garden with buttercups growing in it. But if you did you would know how prodigious they are at producing runners. The plant does not stop growing just because it produces flowers. You are picking on part of the flower in isolation. I am considering the nature of the plant as a whole.

    No, you are not. You are merely picking the part of the flower that confirms your broad-brush characterisation while closing your eyes for any aspect that runs counter to it. It is trivially easy to find examples of plants that do stop growing when they flower; agaves are famed for it, but I guess you’ll just dismiss it as another “extreme example”.

    And that is my point. This plant grows until it flowers. The cessation of growth on flowering signals the end. All its energy is spent on growing or preparing for the next generation to carry on the cycle of growth and decay. In contrast to this humans grow until maturity, then growth ceases, reproductive capability begins at puberty and then steadily declines with age. All the while conscious learning (which I would say is a spiritual activity) continues throughout life until the point where the body deteriorates enough so that even this is not possible. Having a nervous system allows sentience, having a well developed brain allows conscious learning. Just look at how much energy is required for us to maintain a functional brain and you will realise how important an organ it is. We would not need such a brain if mere survival was the reason for its existence. Some types of lower animal have survived virtually unchanged for millions of years with a rudimentary brain.

    All of the plants energy is used up in growth and reproduction, it never reaches the stage of being able to learn. We have growth in common with plants but then we develop further in the way I have described. That, in essence, is the difference.

  49. CharlieM CharlieM
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    Corneel:

    CharlieM: When comparing organisms I do not think it is helpful to treat bacteria as equivalent to the likes of mammals or birds.

    Why not?

    I am being constantly told that bacteria are not even the equivalent of a single human cell but are remarkably similar to the organelles within a cell. And now you are asking why should they not be treated as the equivalent of multicellular eukaryotes?!

    What happened to looking at life as a whole, I wonder?

    Looking at life as a whole does not mean ignoring the detail. In fact the opposite is the case. In order to make the necessary connections the life processes should be studied in intimate details.

  50. CharlieM CharlieM
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    says:

    Corneel:

    CharlieM: I would say that in the case of bacteria we should regard whole species or type as a single diffuse organism. in which case the way they spread in colonies shows that they have a plant like or more aptly vegetative nature.

    Problem: what’s a “species” and what’s a “type” and which ones “spread in colonies”?

    It is not a problem. I leave it to the experts to determine the various groupings.

    I would say that species of eukaryotes would be the equivalent of genii, orders, families or even higher classifications of prkaryotes depending on which ones are considered.

    Many bacteria are motile: Perhaps you have read somewhere on this site about the “bacterial flagellum”. Care to guess what those bacteria use that for?

    What is your point? Individual human cells can be sessile, motile, single, clustered, elongated, spherical, long lived or short lived.

    The thing you seem to be unable to grasp is that bacteria are spectacularly diverse, far more diverse than animals. Your glaring disinterest in anything-that-is-not-an-animal is not a valid excuse to sweep them all on one heap.

    Again what is your point? I am very interested in all forms of life. To class bacteria as equivalent to higher eukaryotes is to sweep all into one heap. Can you explain in what way they are more diverse than eukaryotes?

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