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 thoughts on “Universal Common Descent Dilemma

  1. 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!

    To be fair in my initial post I also completely left out the factors of population size and fixation rate. We’ve effectively been treating the population as a size of 1 that reproduces by binary fission with the ancestor dying every time. Which is also completely unrealistic. Doing a more realistic calculation with population size and some avg rate of fixation is above my paygrade. 🙂

  2. Um, folks:

    1. Neutral mutations change DNA beyond recognition in 50-100 million years (with the rates of mutation we have in mammals), but
    2. (as was noted above) if there is natural selection conserving function, a moderate to large fraction of mutations will be rejected, and DNA can be alignable for much longer. This is particularly true for genes which code for RNAs like ribosomal RNA.
    3. Protein sequence can be conserved for much longer, even when the underlying DNA sequence has been saturated with change.

    For deep branchings in phylogenies, functional RNAs and slow-changing protein sequences provide the usable information. For shallow branchings (say, between us and chimps) many protein sequences are too similar to provide much information, but junk DNA is quite useful. It is even possible to do use both kinds of information in the same analysis, using codon models.

  3. Entropy,

    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.

    Common ancestry only explains the similarity. It is at best an incomplete explanation and at worst completely wrong. I think there is no reason to think that prokaryotic cells and eukaryotic cells share a common ancestor given the present data available.

  4. Allan Miller,

    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.

    Fair enough.

    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.

    The evidence points at least two independent survivors. The prokaryotic and eukaryotic cells. I would also add as a minimum multicellular eukaryotes.

    Endosymbiosis is not intended to explain every last feature of eukaryotes.

    Graciously understated as it explains very few features.

    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

    Your assumption that evidence of a homolog supports evolution. This assumption needs support or a transitional mechanism.

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

    What was there to refute? You brushing the origin of 8 major innovations under the carpet and calling them simply differences.

  5. colewd: The evidence points at least two independent survivors. The prokaryotic and eukaryotic cells. I would also add as a minimum multicellular eukaryotes

    Digging the hole a little deeper are you? Are you arguing that all groups of multicellular eukaryotes (yes, there are several) require origins independent of unicellular eukaryotes? What about multicellular bacteria (Yes, they exist as well)?

  6. Joe Felsenstein: 1. Neutral mutations change DNA beyond recognition in 50-100 million years (with the rates of mutation we have in mammals)

    What would be the generation time for that calculation, please? Just curious to know if my math was right. I would get 50 million years for a generation time of 7 years and 100 my for a generation time of 14 years

  7. Corneel,

    Digging the hole a little deeper are you? Are you arguing that all groups of multicellular eukaryotes (yes, there are several) require origins independent of unicellular eukaryotes?

    I am arguing that multicellularity in eukaryotes is a major innovation beyond unicellular eukaryotes and signal a unique origin event.

    As far as multicellular prokaryotes, I have no opinion.

  8. colewd: I am arguing that multicellularity in eukaryotes is a major innovation beyond unicellular eukaryotes and signal a unique origin event.

    So trees, mushrooms, algae, slime molds and humans all derive from a “unique origin event” that was independent from the origin of unicellular eukaryotes? Are you sure?

    colewd: As far as multicellular prokaryotes, I have no opinion.

    Why am I not surprised?

    Why not? Is the transition to multicellularity in “prokaryotes” not as problematic as you hypothesize it to be in eukaryotes?

  9. colewd:
    Common ancestry only explains the similarity.

    Of course. What else did you expect that to explain? Common ancestry just means that some organisms, or some features/characters, diverged from a common ancestor. Nothing else. So, by definition, it would only explain the similarities.

    colewd:
    It is at best an incomplete explanation and at worst completely wrong.

    It doesn’t matter that it’s an incomplete explanation, it’s an excellent one, since those similarities are excessively unlikely to be the result of independent origins. With those similarities taken care of, we can now try and learn how the differences arose. Some are easy: differences between homologous things arises from the simple fact that time goes on, mutations accumulate. Now we’re left with fewer things to explain. That’s called progress.

    colewd:
    I think there is no reason to think that prokaryotic cells and eukaryotic cells share a common ancestor given the present data available.

    Given the amount of things common ancestry explains, I think that common ancestry is a very safe bet. It might be a complicated common ancestry, because of the endosymbiosis, but it still helps quite a bit.

  10. Corneel,

    Why not? Is the transition to multicellularity in “prokaryotes” not as problematic as you hypothesize it to be in eukaryotes?

    I have not looked at it enough to have an opinion. Regarding your prior comment I think there are maybe lots of independent origin events but this is just speculation.

  11. colewd: I have not looked at it enough to have an opinion.

    Very understandable. Yet for eukaryotes you are absolutely positive that multicellularity is a “major innovation” that merits its own origin event, right? Even better: You now speculate that every group of multicellular eukaryotes has its own origin event.
    To be brutally honest, I suspect that the only group you are really interested in is metazoans, and that you are unwilling to defend a separate origin of any of the other multicellular groups. Even for metazoans you will run into trouble, as there is compelling evidence that they (heh, we) derive from within eukaryotes and that (unicellular, sometimes colonial) choanoflagellates are our sister group.

  12. CharlieM: . Can you give a rational reason why you believe reality is limited by the conscious everyday experience of current Western thinking humans?

    I don’t believe that at all & I’m utterly baffled as to why you think I would.

    If anything, I think that the 2nd century Buddhist philosopher Nagarjuna was correct when he argued that, for the same reasons that the Buddha gave for why the self or ego does not have ultimate and substantial independence, nothing else does either.

  13. Corneel,

    You now speculate that every group of multicellular eukaryotes has its own origin event.

    I said their maybe a lot more. A lot more does not mean every group. A unicellular eukaryote to a multicellular eukaryote is a major transition or origin event.

  14. dazz: What would be the generation time for that calculation, please? Just curious to know if my math was right. I would get 50 million years for a generation time of 7 years and 100 my for a generation time of 14 years

    There is always a lot of controversy over whether mutation rates should be measured as per-year or per-generation. Because generation times will vary a lot between, say, elephants and deermice, it is usually more useful to measure mutation rates per year. Using a figure of 10^{-8} changes per site per year, we will get one change per site per 100 million years.

    (If you want to use per-generation in mammals, keep in mind that much of the history of mammals involves little shrewlike things that have generation times of maybe 1-2 years.)

    Basically the number of changes in a site in a completely neutral piece of DNA would then be a Poisson random variable with mean \mu t, where t is the elapsed time in years and \mu is the mutation rate. Keep in mind also that if two species have their common ancestor t years ago, the total branch length separating them is not that number, but 2t.

  15. colewd,

    The evidence points at least two independent survivors.

    But they are not independent. ‘Independent’ would mean that no genes could be traced between the lineages. But in fact they can.

    Allan: Endosymbiosis is not intended to explain every last feature of eukaryotes.

    colewd: Graciously understated as it explains very few features.

    Yeah, only mitochondria and chloroplasts. Hardly worth mentioning really.

    Allan: 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

    colewd: Your assumption that evidence of a homolog supports evolution. This assumption needs support or a transitional mechanism.

    Nonetheless, what else accounts for it? The mechanism for common descent is serial template-based DNA replication. That’s how a sequence gets into B and C, by common descent from an original molecule in ancestor A.

    Meanwhile your mechanism is: ______

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

    colewd: What was there to refute? You brushing the origin of 8 major innovations under the carpet and calling them simply differences.

    Are they not differences, then?

  16. Allan Miller,

    Meanwhile your mechanism is: ______

    Conscious intelligence. Capable of generating large amounts of functional information required to account for macro machines like the spliceosome.

  17. Allan Miller,

    But they are not independent. ‘Independent’ would mean that no genes could be traced between the lineages. But in fact they can.

    So according to Miller there is not such thing as independent organisms 🙂

  18. colewd,

    So according to Miller there is not such thing as independent organisms

    Is that what you meant? There are at least two ‘independent survivors’ because there are at least two of us? Yeesh.

  19. colewd,

    Conscious intelligence. Capable of generating large amounts of functional information required to account for macro machines like the spliceosome.

    Haha. Always a laugh when people deride an explanatory framework and then offer such as their own. How do cars work? Conscious intelligence. How do you make pasta? Conscious intelligence. How did the blackguard escape the locked room, Holmes? Conscious intelligence. Ah, I see.

    In this particular instance, you are offering this banal phrase up in explanation of the genetic commonality between eukaryotes and archaea, because that was the question I was actually posing. Not “where do the differences come from”, but “Why are these sequences rooted in this group?”. Conscious intelligence. Ah, I see.

  20. Allan Miller,

    In this particular instance, you are offering this banal phrase up in explanation of the genetic commonality between eukaryotes and archaea, because that was the question I was actually posing. Not “where do the differences come from”, but “Why are these sequences rooted in this group?”. Conscious intelligence. Ah, I see.

    It’s a mechanism that creates functional information and can explain biological differences. The mechanism you propose is——-?

  21. colewd: It’s a mechanism that creates functional information and can explain biological differences.

    What’s a mechanism? Supernatural twerking tweaking?

  22. colewd: It’s a mechanism that creates functional information and can explain biological differences.

    What observations or experiments do you suggest that might lead to your “it’s” being more than a figment of imagination. Something with entailments would be good.

    colewd: The mechanism you propose is——-?

    En bref, variation followed by selection. There are more details should you be interested. And entailments.

  23. Entropy: So, by definition, it would only explain the similarities.

    Common descent doesn’t explain the similarities either because, you know, things change.

    Entropy: It doesn’t matter that it’s an incomplete explanation, it’s an excellent one, since those similarities are excessively unlikely to be the result of independent origins.

    You’ve done the math have you?

  24. Mung: Common descent doesn’t explain the similarities either because, you know, things change.

    Do you not look a bit like your parents? My wife says I’m turning into my father. (This is not a compliment from my wife BTW)

  25. Alan Fox,

    What observations or experiments do you suggest that might lead to your “it’s” being more than a figment of imagination. Something with entailments would be good.

    This response and your ability to read it is validation that conscious intelligence can create functional information and also decode it.

    What evidence do you have that variation followed by selection can create functional information. How much can it create?

  26. Allan Miller: 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.

    Would it be fair to say then that you recognize that common descent alone is insufficient to explain the similarities? The theory of common descent does not say that similarities will be preserved, or what will be preserved, or what will not be preserved.

  27. colewd:
    Alan Fox,

    This response and your ability to read it is validation that conscious intelligence can create functional information and also decode it.

    All you are saying is that humans have adaptations that facilitate communication by language. A confirmation of common descent and evolutionary processes.

    What evidence do you have that variation followed by selection can create functional information.How much can it create?

    Functional information cannot be quantified. It’s not measurable.

    ETA Failed attempt here

  28. Alan Fox: All you are saying is that humans have adaptations that facilitate communication by language. A confirmation of common descent and evolutionary processes.

    interesting

    So the fact that humans are adapted for language is a confirmation of common decent.

    Is the fact that all other known organisms are not adapted for language also a confirmation?

    peace

  29. Alan Fox: Functional information cannot be quantified. It’s not measurable.

    Pretty sure Joe disagrees. But of course, the creotard version of FI is useless crap

  30. Mung: The theory of common descent does not say that similarities will be preserved, or what will be preserved, or what will not be preserved.

    So what?

  31. colewd: This response and your ability to read it is validation that conscious intelligence can create functional information and also decode it.

    The link between someone being capable of using language and intelligence creating novel biological features is only in your dysfunctional mind

  32. dazz,

    and intelligence creating novel biological features is only in your dysfunctional mind

    Ouch. Coming from our local biology guru 🙂

  33. colewd:
    dazz,

    Ouch.Coming from our local biology guru

    It has zero to do with biology (which you’re so obviously clueless about anyway), your problem is much more fundamental

  34. We’ve had long threads on functional information.

    1. It was defined by Jack Szostak and a little later slightly redefined by Szostak, Hazen and some others. It can be calculated, if one has amounts of function for all possible sequences.

    2. gpuccio and his co-thinkers say that they are using Szostak’s definition, but they actually place additional requirements on the scenario, such that only a particular set of sequences “has function”.

    3. As to whether, when there is natural selection, functional information can be “created”: if one uses Szostak’s definition, it can increase the amount of functional information. If one uses colewd’s / gpuccio’s definition, it can’t because they only declare functional information present when it in effect can’t come about by natural selection.

    4. We had this discussion. It won’t help to have it again.

  35. Joe Felsenstein: It can be calculated, if one has amounts of function for all possible sequences.

    That’s one thing that got me baffled. How would that be done? I’m guessing perhaps there are ways to make useful approximations?

  36. dazz:

    Do you mean, how would you get the levels of function for all possible sequences?

    You may now have a way to find those out, but you can imagine knowing them, and than ask whether natural selection could increase the resulting number. For Szostak’s and Hazen’s definition, it can.

  37. Joe Felsenstein: Do you mean, how would you get the levels of function for all possible sequences?

    Yes

    Joe Felsenstein: You may now have a way to find those out

    Something like protein structure prediction?

    That seems pretty awesome BTW

    Joe Felsenstein: but you can imagine knowing them, and than ask whether natural selection could increase the resulting number. For Szostak’s and Hazen’s definition, it can.

    I understand that, but I don’t see how the increase in FI can be reasonably quantified without a “good enough” picture of the whole fitness landscape

  38. Mung:
    Common descent doesn’t explain the similarities either because, you know, things change.

    It does explain the similarities Mung, because, as you quoted: those similarities are excessively unlikely to be the result of independent origins.

    Mung:
    You’ve done the math have you?

    Yes, I have. But only for the proteins shared by a few prokaryotes and eukaryotes.

  39. dazz: The link between someone being capable of using language and intelligence creating novel biological features is only in your dysfunctional mind

    See, this is why you are good Dazz.

    I foolishly claimed that Former Moderator (now retired and back as Admin, which also includes being a moderator) Sir Admin Alan Fox was out of his mind. What I should have said was that he was in his mind, but that his mind was simply dysfunctional.

    Learning moment.

  40. dazz:

    Joe Felsenstein:

    You may now have a way to find those out, but you can imagine knowing them, andthan ask whether natural selection could increase the resulting number.For Szostak’s and Hazen’s definition, it can.

    I’m embarrassed. I meant to type “You may not have a way to find those out”.

    And of course “andthan” was supposed to be “and then”.

  41. colewd:
    Allan Miller,

    It’s a mechanism that creates functional information and can explain biological differences.The mechanism you propose is——-?

    I think perhaps first you could answer the question posed. Why do diligent researchers consistently find gene homologues rooted in archaea and alpha (not gamma, not delta,etc) proteobacteria, broadly sorted by function? Ooh! Ooh! I know!

  42. From Hazen’s paper:

    Functional information is defined only in the context of a specific function x.* For example, the functional information of a ribozyme may be greater than zero with respect to its ability to catalyze one specific reaction but will be zero with respect to many other reactions. Functional information therefore depends on both the system and on the specific function under consideration. Furthermore, if no configuration of a system is able to accomplish a specific function x [i.e., M(Ex) = 0], then the functional information corresponding to that function is undefined, no matter how structurally intricate or information-rich the arrangement of its agents.

    Don’t think this is what Bill Cole is talking about.

    ETA *my emphasis.

  43. Mung: Would it be fair to say then that you recognize that common descent alone is insufficient to explain the similarities? The theory of common descent does not say that similarities will be preserved, or what will be preserved, or what will not be preserved.

    It’s not the only possible cause of similarities, but it’s a pretty solid bet. Particularly at the genetic level, when large amounts of sequence identity can only be accounted for by common descent – template based DNA copying in separated lineages deriving from a single molecule in an ancestor. So yes, it is sufficient.

  44. Joe Felsenstein: You may [not] have a way to find those out, but you can imagine knowing them, and than ask whether natural selection could increase the resulting number.

    Well, I see that as something of a barrier to producing “functional information” figures. On the other hand, I see the advantage in being able to say whether a figure (arbitrary as we don’t know the absolute density of function in sequence space) could increase or decrease as a comparison presumably eliminates the unknown estimate of functional density. And Hazen emphasizes it only works for a single precise function.

  45. dazz: I understand that, but I don’t see how the increase in FI can be reasonably quantified without a “good enough” picture of the whole fitness landscape

    Me neither! 🙂

  46. dazz: Pretty sure Joe disagrees. But of course, the creotard version of FI is useless crap

    I see Joe makes the important distinction between Hazen’s FI and gpusccio’s FI as being two different things. Gpuccio’s FI, Joe agrees, is not calculable. Unless I’m misunderstanding Joe Felsenstein, which is entirely possible! 🙂

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