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.

906 thoughts on “Universal Common Descent Dilemma

  1. dazz,

    Common descent explains the hierarchical pattern of similarities and differences

    False

    Common descent explains some the hierarchical pattern of similarities

    True

  2. colewd: False

    Obviously wrong.
    But the point is, do you understand that every time you “challenge” common descent on the basis of supposedly unexplained transitions, you’re just making a fool of yourself? I know the answer to that question is a resonating “no”, but anyway

  3. colewd:
    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.

    I know that’s what you’re saying. Please pay attention: common ancestry cannot explain what it’s not supposed to explain. It only explains the similarities. That’s a direct consequence of what common ancestry means. It doesn’t matter if you’re referring to universal common ancestry in particular, or to common ancestry in general. The point remains the very same.

    Got it now? If so, then you should understand that it cannot be false for failing to explain what it’s not supposed to explain.

  4. Entropy,

    It only explains the similarities.

    I agree with you but you can see Dazz was confused.

    Common descent explains the hierarchical pattern of similarities and differences

    Got it now? If so, then you should understand that it cannot be false for failing to explain what it’s not supposed to explain.

    Give me your current definition of common ancestry and universal common ancestry.

    Some of the definitions clearly make transition claims but if it is modified to not make these I am ok.

  5. colewd: I agree with you but you can see Dazz was confused.

    You’re the only one who’s confused here. Blame your own abysmal reasoning skills

    Consider a “difference” (mutation, trait) arising in a certain branch of the tree of life. If CD is true, that “difference” should propagate as a similarity between members of that branch, but a difference between other branches. That’s what I mean by pattern of similarities and differences, and I’m pretty sure John Harshman and others would agree

  6. Nonlin.org: Debatable. More importantly, what has that to do with this OP?

    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?

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

    Evolution.

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

    Ah, I see you are a fan of Creationist cliche.

  9. 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’?

  10. Kantian Naturalist: 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.

    And this is where we need to go back to our different epistemological points of departure, but, although I would find it interesting, it is probably not a topic for this thread.

  11. 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’?

    Endosymbiosis provides evidence that there is a connection between prokaryotes and eukaryotes. If you are a materialist and believe that complex life is the product of and derives from precursor forms which are less complex then you will believe that endosymbiosis produced eukaryotes. But if you believe the opposite is the case and the material is a product of consciousness then you are not obliged to believe in the complex being totally derived from the simple.

    From this point of view the evidence can have the opposite interpretation. Prokaryotes could be derived from eukaryotes. They could be escapees that have gained the ability to survive outside of the body from which they originated. If they found themselves in an external environment which provided their needs in a similar way to their previous internal environment then they could survive. These relatively simple forms may have arisen from a more complex forebear.

    The evidence can be taken both ways.

  12. colewd:
    Give me your current definition of common ancestry and universal common ancestry.

    Common ancestry is about a set of organisms being related by deriving from a common ancestor. Universal common ancestry makes that set the whole of life in our planet.

    colewd:
    Some of the definitions clearly make transition claims but if it is modified to not make these I am ok.

    There’s no definition that claims “transitions” (whatever that means). As I said, common descent elegantly, parsimoniously, explains the similarities.

    To explain “transitions” we need to go beyond common ancestry, and into the consequences of time (divergence), and into the history of life as documented by whatever evidence we can gather.

  13. CharlieM:

    The evidence can be taken both ways.

    Nope. At least, not on the principle of parsimony. If one accepts a genetic connection between genes in the eukaryotes and the two prokaryote groups, to try reversal one has to imagine a mass transfer of nuclear genes to the separate escapees, somehow concocting viable genomes. In the case of archaea, one has to construct circular replication from a multichromosome nuclear genome, which result remarkably resembles that of all prokaryotes and mitochondria. This is too much of a stretch.

  14. Allan Miller: Nope. At least, not on the principle of parsimony. If one accepts a genetic connection between genes in the eukaryotes and the two prokaryote groups, to try reversal one has to imagine a mass transfer of nuclear genes to the separate escapees, somehow concocting viable genomes. In the case of archaea, one has to construct circular replication from a multichromosome nuclear genome, which result remarkably resembles that of all prokaryotes and mitochondria. This is too much of a stretch.

    I’ll need to look further into this, but meanwhile, how can you be certain of the genomic makeup of the original components at the time of merging/separation?

  15. CharlieM: I’ll need to look further into this, but meanwhile, how can you be certain of the genomic makeup of the original components at the time of merging/separation?

    You can’t. Nonetheless, it is possible to do some reconstruction of ancient genomes, again using parsimony – the minimal number of changes required.

    The other thing to consider is the prokaryote trees themselves. The metabolic genes assumed to come from a bacterium cluster in the alpha proteobacteria – in fact, Rickettsia, a specific group within (not the best news for exceptionalists!). For reversal, one would have to turn the entire bacterial phylogeny on its head. Everything bacterial would be derived from a Rickettsia-like organism, but that would have changed less than they in the meantime. For some reason.

  16. Allan Miller: The other thing to consider is the prokaryote trees themselves.

    Charlie’s notion is in some ways even worse for chloroplasts. Some of the earliest fossils are cyanobacteria, and eukaryotes don’t come around until a couple of billion years later. And then there are the secondary and tertiary acquisitions. Of course Charlie doesn’t care about plants, does he?

  17. Allan Miller: not the best news for exceptionalists!

    Maybe even less attractive is the presence of the other endosymbiont: chloroplasts. In the upside-down scenario all non-photosynthesizing eukaryotes (including humans) are simplified expressions of a more complex chloroplast-bearing forebear. That may not be palatable for human exceptionalists.

  18. Entropy,

    Universal common ancestry makes that set the whole of life in our planet.

    Then you need to explain the origin of the eukaryotic cell and its relation to other life.

  19. John Harshman: Charlie’s notion is in some ways even worse for chloroplasts. Some of the earliest fossils are cyanobacteria, and eukaryotes don’t come around until a couple of billion years later. And then there are the secondary and tertiary acquisitions. Of course Charlie doesn’t care about plants, does he?

    Evidence only suggests that eukaryotes don’t fossilize until a couple of billion years later. Lack of fossilization does not mean lack of existence. Don’t forget in my opinion life descends in gross materiality from a more subtle realm. Fossilization is very rare and denser material fossilizes easier than less dense material.

  20. Joe Felsenstein: Sure, that’s possible, but it’s not necessary.

    Yes, it’s possible. So what then is the basis for your objection to gpuccio on that point?

    Joe Felsenstein: 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”.

    That only a particular set of sequences has function would actually be a subset of the Szostak definition and thus would fit within it and not be contrary to it.

    So as far as I can tell your objection (2) is without merit.

  21. Allan Miller: This is too much of a stretch.

    Oh, so NOW miracles are not allowed?

    The entire materialist narrative is too much of a stretch. Or are materialists the only ones allowed to appeal to “too much of a stretch” as a reason to be skeptical?

    🙂

  22. Mung: Oh, so NOW miracles are not allowed?

    The entire materialist narrative is too much of a stretch. Or are materialists the only ones allowed to appeal to “too much of a stretch” as a reason to be skeptical?

    No, That’s not what I said. But if you want to rely on miracles to account for a phylogeny which is upside down to that inferred on grounds of parsimony, that is your prerogative.

  23. Mung: That only a particular set of sequences has function would actually be a subset of the Szostak definition and thus would fit within it and not be contrary to it.

    So as far as I can tell your objection (2) is without merit.

    Demonstrating, once again, that you don’t understand FI.

    gpuccio places a requirement that a particular subset are the only ones that have function. This is different from the observation that there may exist some subset that lacks function.

    Think of it this way:
    In Dr Keller’s class (n=30), Mung junior has the best GPA. Cool.
    Mung notes that it is possible for students at LHS to have a GPA of zero.
    gpuccio observes Dr. Keller’s class and (since he assumes that the 400 students in other classes must have GPA’s of zero) announces that Mung Jr is in the top 0.25% of ALL students.

    gpuccio is wrong. Whether students with a GPA of zero exist or not.
    gpuccio is also wrong whether Dr. Keller teaches remedial English or B/C Calc. Although in the latter case, he is less wrong…

  24. Mung: No it doesn’t.

    Yes it does. They’re similar because they were inherited from a common ancestor and have not yet changed to the extend that they have lost their similarity.

  25. Mung,

    No it doesn’t.

    Would you support the claim that common descent explains some of the similarities.

    I wonder if the addiction to exaggerated claims will ever end.

  26. colewd:
    Then you need to explain the origin of the eukaryotic cell and its relation to other life.

    Well, I don’t need to do anything, but sure I’d like to do that.
    🙂

    I’m glad, though, that you’re closer to understanding that UCD is not supposed to explain anything but the similarities. Now, we have to think of the consequences of common ancestry. This means that lineages, in the simplest events, would just separate their histories from each other. With time, of course, that would mean that differences would have to accumulate. So, divergence alone (changes with time) would explain some of the differences. Right? In this case, we have the two things coming together to explain something: common ancestry and the fact that with time things change. That means we should see differences accumulating as time goes by after separation from a common ancestor.

    That’s further progress! Now, how about some tests to the above? How about other stuff? Not now. It’s hard enough to get you to understand what UCD is supposed to mean. How’s it going so far?

  27. colewd: Would you support the claim that common descent explains some of the similarities.

    Does he have to or can’t you think for yourself. Take some obvious cases, do you have pets? How did their parents look? How does their offspring look? Do you look like your parents, or siblings, in any way? Why is that Bill?

  28. colewd: You’re attacking a straw-man.

    No he isn’t. It’s what the whole point of Gpuccio’s claim is about, isolating a subset of sequences (such as known sequences), and then insisting that there aren’t any other functional ones out there and therefore this small set of known sequences are too unlikely to have evolved because they’re just an infinitesimal fraction of the total set of possible sequences of equal length.

    It’s even what you said, over and over again. You’re just nay-saying seemingly for the hell of it now Bill, and have apparently forgotten even your own words and arguments.

  29. Rumraket,

    No he isn’t. It’s what the whole point of Gpuccio’s claim is about, isolating a subset of sequences

    You don’t understand his argument and either does Jock. What you are talking about was covered in his TSS op if you care to read it. He fully excepts that there may be other function.

  30. colewd:
    I wonder if the addiction to exaggerated claims will ever end.

    What’s exaggerated about my claim? Sure, a tiny few of the similarities might be explained as independently arising, but writing “most of the similarities” would have worked as nothing but a distraction, while I was trying to get you to understand a simple point that you insisted on missing.

  31. Entropy,

    I was trying to get you to understand a simple point that you insisted on missing.

    Make conservative claims that you can support and we will walk lock step in agreement.

  32. colewd:
    You don’t understand his argument and either does Jock.What you are talking about was covered in his TSS op if you care to read it.He fully excepts that there may be other function.

    But he doesn’t accept that other sequences might be able to perform the same function that other sequences perform.

    His “calculations” as wrong as they are for other reasons, are based on the assumption that only the sequences he’s analyzing, and those sequences alone, would work for a particular function.

    I only saw one comment where he pretended to accept that it was possible that other, independent, sequences might work for some function, only to them dismiss the idea with a hand-wave, claiming that there’d be so few that his calculations would still be spot on.

    For someone pretending to show that god-did-it, scientifically, gpuccio doesn’t consider the enormous jump implied in god-did-it, but doesn’t allow for potential explanations not involving magic because, well, that’s too much of a stretch. But god-did-it? Surely no stretch at all. We see gods walking around all the time. Nothing could be more obvious. Why even try to figure out if other sequences would be able to perform some function? Why even try and figure out if life could be completely different? Complexes completely different? Nah. Reject it without looking. No need. There’s tons of gods all around us! Obvious!

  33. Entropy: But he doesn’t accept that other sequences might be able to perform the same function that other sequences perform.

    This is confusing. What are alleles?

  34. Entropy: I only saw one comment where he pretended to accept that it was possible that other, independent, sequences might work for some function, only to them dismiss the idea with a hand-wave, claiming that there’d be so few that his calculations would still be spot on.

    The similar morphology of bacterial and archaean flagella led researchers to presume there must be some homology connecting the organelles, some shared sequences. Nope. Bacteria and Archaea arrived at their flagellum solutions independently. Totally different sequences – same function.

  35. Entropy: I only saw one comment where he pretended to accept that it was possible that other, independent, sequences might work for some function, only to them dismiss the idea with a hand-wave, claiming that there’d be so few that his calculations would still be spot on.

    Yes, that is what he did.
    But hey, maybe at some point he actually did include ‘other peaks’ in his calculations, but we both missed it. In which case, it should be easy enough for colewd to quote (with a link) gpuccio’s calculation of the effect of other peaks. Remember, for ATP-binding, there’s 10^93 of them…
    Or he can withdraw the ‘strawman’ accusation…

  36. petrushka: This is confusing. What are alleles?

    I know. I tried to use some better description, but the writing became messy, as it happens in most of my posts. Just look at this one.

    “Sequence family” might work though.

    ETA: Ups, and that sentence is horrible! Sorry about that.

  37. Alan Fox,

    Yeah. There’s plenty of examples where the sequences belong to independent families, yet perform the very same functions.

    But people like gpuccio could not care less. They insist on assuming that there’s a single sequence-family solution. They were forced to admit that homologs can perform the same function (though you’ll see plenty of creationists who won’t accept even that), so they have expanded that much. But not entirely. We can see their old thinking (one sequence only for one function) permeating in a new form in the case of gpuccio, since he still assumes that every homolog must be doing something the rest of the family doesn’t. That’s the basis for his claim that FI is added as his “ladder” moves towards humans. He thinks that some function is added at each “step.” A function that could not be performed by anything but by the particular protein with the particular additional “bits.”

  38. colewd:
    Make conservative claims that you can support and we will walk lock step in agreement.

    In which way would my claim, that UCD explains the similarities, conflict with my only point: that you cannot say that UCD is falsified by things it’s not supposed to explain?

    Whether it’s 100% of the similarities, or even if it only explained 0.1% of the similarities (of course it’s much more, but I can see that you’d miss the point and focus on this tiny number), the point would still stand that it cannot be falsified for not explaining what it is not supposed to explain. Right?

  39. CharlieM: Evidence only suggests that eukaryotes don’t fossilize until a couple of billion years later. Lack of fossilization does not mean lack of existence. Don’t forget in my opinion life descends in gross materiality from a more subtle realm. Fossilization is very rare and denser material fossilizes easier than less dense material.

    So, basically, the complete absence of evidence for your theory is the best evidence for it. Well played, sir.

  40. Mung:
    That only a particular set of sequences has function would actually be a subset of the Szostak definition and thus would fit within it and not be contrary to it.

    I think that Joe struggled to try and say what I said very poorly. The likes of gpuccio add the requirement that only a particular subset of a particular protein family would perform whatever function they’re pretending to analyse. This is implied in their, already questionable, way to “measure” functional information. Their measures always refer to a single protein family, with the added “feature” of imagining that as the sequences look more like the human homologue, they add further functions (increasing in FI).

  41. 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?

  42. Mung: That only a particular set of sequences has function would actually be a subset of the Szostak definition and thus would fit within it and not be contrary to it.

    So as far as I can tell your objection (2) is without merit.

    You are mistaken. gpuccio and company add more conditions, and only call it FI if it satisfies those added conditions as well. 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.

  43. Entropy,

    Whether it’s 100% of the similarities, or even if it only explained 0.1% of the similarities (of course it’s much more, but I can see that you’d miss the point and focus on this tiny number), the point would still stand that it cannot be falsified for not explaining what it is not supposed to explain. Right?

    I think it can’t be falsified because it is not a scientific claim or a clear scientific hypothesis stated so it can be tested and thus falsified.

Leave a Reply

This site uses Akismet to reduce spam. Learn how your comment data is processed.