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:

    I think information, and ‘similarity’ at the organismal level, are distractions from the question of UCD. When you are looking at the entire diversity of life, genetics, undreamt of by Darwin, is the way to go. The genetic evidence is powerful, even at the sequence level.

    But more than that is the fact that those sequences have ‘meaning’ which is independent of their organismal context. Take any sequence (shorn of introns if necessary) and process it in any other organism’s translation machinery and it will create a very close facsimile of the native protein, even if the genetic codes differ. If I went to another life bearing planet and dipped a pond I might expect to find nucleic acid genomes, possibly protein catalysis, but not the earthly system – there are base pairs other than AT/CG, including their own stereoisomers, there are hundreds of possible amino acids beyond our 20 (again including isomers), and there are millions of possible codon assignments in a triplet based system. That’s the kind of variation I would expect given separate origin, not a system where ‘well-formed strings’ can be passed around ad hoc and processed consistently. So on those grounds alone, I favour a single surviving lineage, granted that competing systems may have existed historically. The rest are Betamax.

  2. Corneel Corneel
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    says:

    Allan Miller: gene homologues rooted in [..] alpha (not gamma, not delta,etc) proteobacteria

    @Bill

    Like the ATP synthase beta subunit. Are you familiar with that one, perchance?

  3. Corneel Corneel
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    says:

    Alan Fox: Functional information […] Don’t think this is what Bill Cole is talking about.

    Functional Information sensu Bill Cole needs to be created from scratch, which means that it is not allowed to require the pre existence of another sequence. Indeed, neither natural selection nor mutation can produce this type of functional information. In fact, it could be argued that most of the intelligently produced human output does not qualify either.

    ETA: @Bill. At least that is how I understood your argument, but correct me if you think that’s incorrect.

  4. CharlieM CharlieM
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    Kantian Naturalist:

    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.

    My mistake, I have misinterpreted your use of the word “Naturalist”. I am glad that you believe in the possibility of higher realities unknown to present day science.

    It is from this higher form of reality that I believe the physical world has condensed so to speak. Therefore the history of life and the fossil record shows, not a common descent gradually appearing through material processes alone but a gradual process of materialisation from a more subtle field-like realm. So it is a common descent from above and not from below. And it is not just a condensation of life into earthly matter, but the whole earth itself is undergoing the same process of densification.

    The famous “Face of a frog” video gives us a hint of this type of process. The physical form follows a pattern of an overarching field. We can see the pattern forming but we cannot see the field from which it forms. Our scientific instruments may be able to detect the field in this case but we can see that it is too subtle to be sensed directly. The descent of life that I have described in the previous paragraph is a descent from realms which are even above the range of our scientific instruments. These realms are outwith the limits which Western thinking has imposed on reality. So if you agree that it is a strong possibility that this higher reality exists then we are in agreement.

  5. Joe Felsenstein Joe Felsenstein
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    Alan Fox: 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.

    The Szostak/Hazen FI is minus the log of a fraction, where the fraction is the proportion of all sequences that have function better than, or equal to, the observed sequence. To evaluate a change you need to know the fraction before and the fraction after. So you do need the full distribution, or at least a big sample from it.

    Yes, that is a barrier to its use in practice. but no, that does not prevent us from thinking about whether natural selection could change the F.I.

    For a similar situation, imagine talking about planetary motion. Someone claims that in general, planets cannot move in a particular motion X. You think about that and realize that the equations of motion can sometimes produce motion X. So you say “Well consider a planet whose mass is m …” and the other person says “Do you actually know the mass of the planet?” You say no, in practice we don’t, and the other person then dismisses your argument.

    Not all arguments in science need to make use of actual empirical measurements. Particularly when one is evaluating a proposed general impossibility of something.

  6. Kantian Naturalist Kantian Naturalist
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    says:

    CharlieM: . I am glad that you believe in the possibility of higher realities unknown to present day science.

    I don’t. How you got there from my casual allusion to Nagarjuna is utterly baffling.

  7. Mung Mung
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    says:

    dazz: So what?

    So pointing to similarities does not justify a conclusion that they are present due to common descent. One might also mention convergence.

    The reason so many people can so easily question common descent is because it is improperly argued. So please improve your arguments.

    tyvm

  8. Mung Mung
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    says:

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

    Given that you are in no way qualified to judge whether the mind of another person is “dysfunctional” or not you’d best avoid making such comments.

    Consider this a gentle reminder that comments should remain within the rules.

  9. CharlieM CharlieM
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    says:

    Kantian Naturalist: I don’t. How you got there from my casual allusion to Nagarjuna is utterly baffling.

    You don’t believe that reality is limited by the conscious everyday experience of current Western thinking humans, and you don’t seem to believe in any reality outwith of these limits.

    I understand that you believe nothing has ultimate and substantial independence. I would agree with that. Just because higher reality is not bounded by the limits I have mentioned above does not mean that it is ultimately and substantially independent. I too believe that ultimate reality is a unity. Any independence we perceive is the result of our limited cognition and has nothing to do with actual reality.

  10. Mung Mung
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    says:

    Joe Felsenstein: The Szostak/Hazen FI is minus the log of a fraction, where the fraction is the proportion of all sequences that have function better than, or equal to, the observed sequence.

    So the sequences that do not have function better than or equal to the observed sequence could theoretically have no function at all relative to the specific function under consideration?

  11. Allan Miller
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    says:

    Mung: So pointing to similarities does not justify a conclusion that they are present due to common descent. One might also mention convergence.

    The reason so many people can so easily question common descent is because it is improperly argued. So please improve your arguments.

    tyvm

    I’m not sure it’s all down to improper argumentation. There seems a massive blind spot on the part of interlocutors with respect to digital data – gene sequence – where large scale convergence is virtually absent, and side-issues such as function or subjectivity wrt character states can be largely ignored.

    The other common blind spot is in the arena of tree building. It is precisely by combining those approaches – the digital, and tree topologies – that permits putative convergences (and other exceptions to simple vertical descent) to be detected.

  12. dazz dazz
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    says:

    What a coincidence that it’s almost always creotards who find arguments and evidence for common descent unconvincing

  13. Kantian Naturalist Kantian Naturalist
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    CharlieM: You don’t believe that reality is limited by the conscious everyday experience of current Western thinking humans, and you don’t seem to believe in any reality outwith of these limits.

    That’s because I don’t identify the metaphysics we get from our best current science with the metaphysics of “the conscious everyday experience of current Western thinking humans.”

    The latter — what I would call “the descriptive metaphysics of everyday life” — is certainly in tension with, and perhaps incompatible with — the metaphysics of science or a scientific metaphysics. I say that primarily because the best scientific metaphysics (that I know of) points towards an ontology of processes and systems, not an ontology of determinate things with determinate properties.

    I understand that you believe nothing has ultimate and substantial independence. I would agree with that. Just because higher reality is not bounded by the limits I have mentioned above does not mean that it is ultimately and substantially independent. I too believe that ultimate reality is a unity. Any independence we perceive is the result of our limited cognition and has nothing to do with actual reality.

    The cardinal difference between our views, for what it’s worth — and it might not be worth very much — is that I think the process ontology that we get out of a scientific metaphysics confirms the insights of Nagarjuna and (in a closely related way) Spinoza: nothing has ontological independence, or (if Spinoza is right) only the universe as a whole is ontologically independent. (This is what motivates his pantheism: only nature as a whole has the ontological independence that the theological tradition ascribes to God.)

    So rather than think about this in terms of “everyday reality” and “higher reality” as you do — a distinction between kinds or realms of reality — I think of this as a distinction between ways of knowing — ordinary or everyday cognition and scientific knowledge.

  14. Nonlin.org
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    says:

    faded_Glory: You post an OP titles ‘Common Descent Dilemma’. A dilemma is a difficult choice between alternative options. Therefore, one would reasonably assume that you would present at least one alternative to CD.

    Dilemma refers to two parts of the CD scenario that are incompatible with each other. You are not presenting any alternative so the dilemma stands.

  15. Nonlin.org
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    says:

    OMagain: And yet those failed scenarios are the current paradigm.

    It must distress you greatly to know that your superior alternative cannot defeat something that has self-evidently failed.

    What does that even mean? No, a collective delusion does not distress me. It has happened before many times.

  16. Alan Fox Alan Fox
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    says:

    Joe Felsenstein,

    Thanks, Joe. I appreciate the mildness of your reproof! 😉

  17. Nonlin.org
    Ignored
    says:

    OMagain: I ask once more. What makes you think you are worth the effort required for disproving your claims?

    Why don’t you publish your “material” in an actual scientific journal?

    You are here to support your dogma, not to discuss fashion, kittens, or Justin Bieber. Yet you cannot present any logical counterarguments to this OP and that’s telling.

    I will publish, don’t you worry. But unlike others, I just want to make sure it’s rock solid before that.

  18. Alan Fox Alan Fox
    Ignored
    says:

    Nonlin.org: Dilemma refers to two parts of the CD scenario that are incompatible with each other. You are not presenting any alternative so the dilemma stands.

    You haven’t established any incompatibility! UCD is a well-supported explanation for the observed data. For there to be a dilemma, an alternative theory needs proposing. No other theory, no dilemma. And your straw men need work.

  19. Nonlin.org
    Ignored
    says:

    Alan Fox: This seems very fair comment, nonlin. Do you have an alternative explanation for the raw data and evidence we have regarding universal common descent? Or do you just not like the idea of universal common descent for… I dunno… personal reasons?

    This particular OP is not about CD in general, but about CD being incompatible with those four origin scenarios for the reasons shown.
    You must either:
    a) show incompatibility is not true,
    b) come up with a different, compatible scenario, or
    c) agree with this OP’s conclusions.

  20. Nonlin.org
    Ignored
    says:

    Allan Miller: Alan Fox: Though I guess we can’t exclude the possibility that there were multiple origin events. But there was only one winner and all life we see descends from that winner with the losers all becoming extinct, leaving no trace

    True. I think there almost certainly were separate origin events – lots of opportunities on a sterile earth. But there is no remaining evidence pointing in that direction – only one surviving, branching lineage: a deep-rooted genetic relationship among all extant life.

    That’s scenario d) in the OP and it relies on TWO unexplained singularities. Hence the dilemma. Let’s move on.

  21. Nonlin.org
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    says:

    Allan Miller: But rooting it all is the highly conserved genetic encoding. 51 out of 64 codons are invariant; nearly all the remainder are STOPs in at least one species – one would expect codons at protein ends to be more labile than those scattered inside, so even the variations make evolutionary sense.

    Debatable. More importantly, what has that to do with this OP?

  22. Joe Felsenstein Joe Felsenstein
    Ignored
    says:

    Mung: So the sequences that do not have function better than or equal to the observed sequence could theoretically have no function at all relative to the specific function under consideration?

    Sure, that’s possible, but it’s not necessary. Cases where level of function ramps smoothly up from least to most are possible too.

  23. Nonlin.org
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    says:

    Rumraket: Can you support this claim?

    Consilience of independent phylogenies.

    “There’s an app for that”: http://theskepticalzone.com/wp/nested-hierarchies-tree-of-life/

  24. Nonlin.org
    Ignored
    says:

    Allan Miller: 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.

    Who are you calling “separate creation”? Would intelligent breeding of dogs into cats (if we had the technology) be evidence for “evolution” or creation?

  25. Alan Fox Alan Fox
    Ignored
    says:

    Nonlin.org: This particular OP is not about CD in general, but about CD being incompatible with those four origin scenarios for the reasons shown.
    You must either:
    a) show incompatibility is not true

    That’s a burden shift. Your strawmen don’t need refuting.

    b) come up with a different, compatible scenario

    UCD fits the evidence. Why do I need another scenario when UCD fits the evidence?

    or
    c) agree with this OP’s conclusions.

    You are joking!

  26. colewd
    Ignored
    says:

    Joe Felsenstein,

    Sure, that’s possible, but it’s not necessary. Cases where level of function ramps smoothly up from least to most are possible too.

    For evolution to work it needs to be more then possible it must be repeatable.

  27. Nonlin.org
    Ignored
    says:

    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.

    Very much in question. You know what would help? A successful experiment. Too bad LTEE ended up with eColi (the starting point) and nothing else.

  28. Alan Fox Alan Fox
    Ignored
    says:

    Nonlin.org: Would intelligent breeding of dogs into cats (if we had the technology) be evidence for “evolution” or creation?

    That would be evidence for intelligent breeding, I guess. Another straw man.

  29. Alan Fox Alan Fox
    Ignored
    says:

    Nonlin.org: Too bad LTEE ended up with eColi (the starting point) and nothing else.

    Good grief! Strawmen, strawmen, everywhere!

  30. colewd
    Ignored
    says:

    Alan Fox,

    UCD fits the evidence.

    How much does this need to be repeated in order for it to be true. 🙂

  31. Alan Fox Alan Fox
    Ignored
    says:

    colewd:
    Alan Fox,

    How much does this need to be repeated in order for it to be true.

    Until it sinks in, Bill. On the other hand you could always propose a viable alternative explanation. That would be an interesting change.

  32. Nonlin.org
    Ignored
    says:

    Allan Miller: 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).

    “Endosymbiosis” is another singularity that begs for experimental evidence. Without that, it’s just a story… or a “just so story”.

  33. Nonlin.org
    Ignored
    says:

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

    Doesn’t work. There’s an app for that too: http://theskepticalzone.com/wp/natural-selection-evolution-magic/

  34. Nonlin.org
    Ignored
    says:

    Alan Fox: You haven’t established any incompatibility! UCD is a well-supported explanation for the observed data. For there to be a dilemma, an alternative theory needs proposing. No other theory, no dilemma. And your straw men need work.

    di·lem·ma
    [diˈlemə, dīˈlemə]
    NOUN
    a situation in which a difficult choice has to be made between two or more alternatives, especially equally undesirable ones.

    I presented four UCD scenarios equally undesirable for the reasons discussed. You have not even selected and supported your favorite from those scenarios, or presented an alternative or accepted the conclusions of this OP. Let’s make some progress here.

  35. Nonlin.org
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    says:

    Alan Fox: That’s a burden shift. Your strawmen don’t need refuting.

    Now YOU are joking. Good one 🙂

  36. Nonlin.org
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    says:

    Alan Fox: That would be evidence for intelligent breeding, I guess. Another straw man.

    Then there is no evidence you would ever accept.

  37. Alan Fox Alan Fox
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    says:

    Nonlin.org: Then there is no evidence you would ever accept.

    Present some evidence that falsifies UCD. I promise I’ll look at it.

  38. colewd
    Ignored
    says:

    Alan Fox,

    Present some evidence that falsifies UCD. I promise I’ll look at it.

    The appearance of the cell nucleus without a step by step path.

  39. Alan Fox Alan Fox
    Ignored
    says:

    colewd,

    What?

  40. Rumraket Rumraket
    Ignored
    says:

    colewd: How much does this need to be repeated in order for it to be true.

    It doesn’t need repeating. It’s truth is not contingent on you being convinced.

  41. Rumraket Rumraket
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    says:

    colewd: The appearance of the cell nucleus without a step by step path.

    That doesn’t falsify common descent. How can you KEEP not getting this?

    The fact that something might be unexplained does not mean it is evidence against common descent. We are not required to know how every organismal property evolved to be able to infer a common genealogical relationship.

    There was a time at which we had no idea what caused blue or brown eyes, yet we still knew that people with blue and brown eyes could be directly related through descent.

    Bill will you EVER get this super basic logical principle? Ever?

  42. colewd
    Ignored
    says:

    Rumraket,

    The fact that something might be unexplained does not mean it is evidence against common descent.

    .

    The falsification is universal common descent. Unless you can explain the first major transition what strength does the claim really have?

  43. Joe Felsenstein Joe Felsenstein
    Ignored
    says:

    colewd: Joe Felsenstein,

    Sure, that’s possible, but it’s not necessary. Cases where level of function ramps smoothly up from least to most are possible too.

    For evolution to work it needs to be more then possible it must be repeatable.

    The whole FI discussion was about a different issue, whether natural selection could result in increased FI. When we are talking about Szostak and Hagen’s FI the answer is that there is no general reason that it is impossible for that to happen.

    Whether evolution “works” is not the issue in that discussion.

  44. Alan Fox Alan Fox
    Ignored
    says:

    colewd: The falsification is universal common descent. Unless you can explain the first major transition what strength does the claim really have?

    Bill, what does this even mean? OK, you don’t like the idea of common descent. Fine, science can manage without you. The theory of evolution is an explanation for the diversity of extent and extinct life on Earth. It is incomplete, doesn’t explain origins (nor is it supposed to) but it is the best working model we have.

    If you want to criticize it, go ahead, but you’d be less ineffective if you grasped the essentials of the theory. And you’d be somewhat less ineffective if you were to suggest some credible alternative that fitted the evidence and made testable predictions.

  45. Entropy Entropy
    Ignored
    says:

    colewd:
    The appearance of the cell nucleus without a step by step path.

    Do you have evidence that the nucleus appeared without any step by step path?

    Even better, is there any evidence that the nucleus appeared with no precursors? (I’m guessing that’s what you mean).

    If you have no evidence, or if I didn’t understand your claim, and you have evidence for whatever you’re claiming, then explain, and make sure that it falsifies UCD.

    colewd:
    The falsification is universal common descent. Unless you can explain the first major transition what strength does the claim really have?

    As I said, UCD is not supposed to explain everything. How could it being nothing but the relationship among organisms, namely, having common ancestors? It still has lots of strength since it explains, in a single stroke, the similarities. Again, that’s called progress.

    I don’t understand why would anybody claim that something is false because it doesn’t explain everything. More importantly when, by definition, it’s not supposed to do so. This is like claiming that US and UK English do not share roots because that doesn’t explain their spelling differences, the different idioms, or any other differences for that matter.

  46. Rumraket Rumraket
    Ignored
    says:

    colewd: The falsification is universal common descent.

    The falsifaction of what is universal common descent? You’re not making any sense.

    Unless you can explain the first major transition what strength does the claim really have?

    Whether I can explain it or not (and I actually can, but it’s irrelevant) does nothing to take away from the fact that common descent happened. I already gave you an analogy that explains why this is so.

    Let me try again:
    There was a point in time at which we could not explain why it is that some people have blue eyes and others have brown (or green, or grey, and so on). Yet we still knew, despite these apparently mysterious differences, that people with different eye colors shared common genealogical relationships. Some times directly. The fact that different organisms might have inexplicable difference therefore does not constitute a reason to think they do not share a genealogical relationship.

  47. colewd
    Ignored
    says:

    Rumraket,

    does nothing to take away from the fact that common descent happened.

    You cant explain the first transition but the hole theory is a fact 🙂

  48. colewd
    Ignored
    says:

    Entropy,

    I don’t understand why would anybody claim that something is false because it doesn’t explain everything.

    I am claiming it is false because it doesn’t explain the first transition in any believable way. That is universal common descent. Common descent has a much smaller hill to climb.

  49. colewd
    Ignored
    says:

    Joe Felsenstein,

    Whether evolution “works” is not the issue in that discussion.

    Fair enough.

  50. dazz dazz
    Ignored
    says:

    colewd: it doesn’t explain the first transition in any believable way

    Jesus fucking christ, Bill. Common descent is not about explaining transitions. How can that be so hard to grasp? Common descent explains the hierarchical pattern of similarities and differences in all living forms, present in many different, independent lines of evidence.

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