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.

310 thoughts on “Universal Common Descent Dilemma

  1. colewd:
    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.

    It can be falsified, only not for not doing what is not supposed to do. Are we clear about the latter yet?

  2. Entropy,

    It can be falsified, only not for not doing what is not supposed to do. Are we clear about the latter yet?

    So state it as a testable hypothesis and how would you falsify it?

  3. Alan Fox: 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.

    An interesting case within the same cells: the (almost) total lack of sequence commonality between Class l and Class ll aminoacyl tRNA synthetases. That is, the genetic code itself has been divvied up between enzymes of apparently separate origin, all doing broadly the same biochemical thing. This happened pre LUCA, on the evidence.

  4. Although ‘information’ is somewhat OT, there is an interesting link between Shannon info and the ‘materialist’ expectation on divergence: the role of entropy. 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?

  5. Allan Miller:

    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.

    This very recent paper challenges your belief in the close relationship between mitochondria and a Rickettsia-like organism:
    Deep mitochondrial origin outside the sampled alphaproteobacteria

    Mitochondria are ATP-generating organelles, the endosymbiotic origin of which was a key event in the evolution of eukaryotic cells. Despite strong phylogenetic evidence that mitochondria had an alphaproteobacterial ancestry, efforts to pinpoint their closest relatives among sampled alphaproteobacteria have generated conflicting results, complicating detailed inferences about the identity and nature of the mitochondrial ancestor. While most studies support the idea that mitochondria evolved from an ancestor related to Rickettsiales, an order that includes several host-associated pathogenic and endosymbiotic lineages, others have suggested that mitochondria evolved from a free-living group. Here we re-evaluate the phylogenetic placement of mitochondria. We used genome-resolved binning of oceanic metagenome datasets and increased the genomic sampling of Alphaproteobacteria with twelve divergent clades, and one clade representing a sister group to all Alphaproteobacteria. Subsequent phylogenomic analyses that specifically address long branch attraction and compositional bias artefacts suggest that mitochondria did not evolve from Rickettsiales or any other currently recognized alphaproteobacterial lineage. Rather, our analyses indicate that mitochondria evolved from a proteobacterial lineage that branched off before the divergence of all sampled alphaproteobacteria. In light of this new result, previous hypotheses on the nature of the mitochondrial ancestor should be re-evaluated.

    Researchers are struggling to find a suitable prokaryote ancestor of mitochondria. And even if they do find suitable candidates how are they going to tell if either was the precursor of the other or if they both developed in parallel?

    The physical origin of the various domains of life are so remote in time that it is very difficult to fathom the sequence of events. Those who go along with the conventional view taught in schools and universities do so because it fits in with their materialist beliefs. For life to develop out of dead matter by a series of fortuitous events it is absolutely essential for it to have had a very simple beginning. Any hint that this may not be the case will not be entertained.

    IMO the earth can be thought of as a living organism with bacteria, archaea, fungi and plants being the equivalent of organelles within the organism, intimately connected with its viability. We humans are more like embryos within the mother organism in the process of a separation the likes of which domains such as archaea and bacteria don’t seem to be undergoing. The habits and abilities of bacteria may change to suit changing conditions (think of antibiotic resistance), but the outcome of this change only allows them to carry on doing the recycling job that they have always done.

    For example:

    From this deep-sea location, a team of researchers collected fossilized sulfur bacteria that was 1.8 billion years old and compared it to bacteria that lived in the same region 2.3 billion years ago. Both sets of microbes were indistinguishable from modern sulfur bacteria found off the coast of Chile.

  6. CharlieM,

    Those who go along with the conventional view taught in schools and universities do so because it fits in with their materialist beliefs.

    This, I must say, is total garbage. Rickettsiales simply happened to be the best fit last time I looked. It favours no particular belief of mine: the data point where they point. You’ve got some researchers favouring one phylogeny, others another, critiquing each others’ assumptions and methodology.

    Which is the one materialists are supposed to believe?

    Which support an origin of prokaryotes in eukaryotes?

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

    I have not proposed any theory about the origin of eukaryote organelles. And that is what I am trying to get people’s views on. I state my beliefs in order to let others know where I am coming from, not to put them forward as something I would expect others to conform to. I am merely exploring the possibilities in the evolution of eukaryote organelles, what research has been carried out, and how they fit in with my beliefs. How strong is the case for endosymbiosis?

    Here is some evidence that the record of the ancient past is not as clear cut as some make it out to be.

    As previously noted, stromatolites are most often described as biogenically-produced structures formed by colonies of photosynthesizing cyanobacteria. However, this is an enormous oversimplification given that the weight of scientific evidence suggests that all three domains of life (the Archaeans, Eubacteria, and Eukaryotes) appeared in the Archaean Era, and thus the so-called microbial mats would have contained representatives among all three domains. Just how and when the base of the tree of life split into the three main branches remains one of the most important questions in all of biology and science, and is the source of constant scientific dispute. Which of the prokaryotes came first, the Archaeans or the Eubacteria remains unresolved, and a consensus has emerged that these primitive microorganisms laterally exchanged genes further confounding attempts to validate what begat what during to course of early evolution on earth. Lateral gene transfer belies the concept of the single common ancestor (see Woese, 1998). While formation by colonies of cyanobacteria is probably the primary mechanism for formation of surviving stromatolites in the deep time of the Archaean and half way through the Proterozoic, it is unlikely to have been the only mechanism…
    some microfossils (actually, putative ancient cellular remnants) indicate that primitive Eukaryotic microorganisms may have appeared prior to 3.5 Bya. Thus, before the end of the Archaean time some 2.5 Ba, all three domains of life (Eubacteria, Archaea, and Eukaryotes) co-existed and were likely already quite diverse.

    And there are various problems with the endosybiosis theory. Questions that need to be answered. Such as if it occurred by phagocytosis how did the organism survive being ingested and broken down which is the normal course of events? And there are problems in explaining the makeup of the mitochondrion membrane.

    There is a suggestion that mitochondria appeared at the same time as the eukaryotic nuclear components.

    The serial endosymbiosis theory is a favored model for explaining the origin of mitochondria, a defining event in the evolution of eukaryotic cells. As usually described, this theory posits that mitochondria are the direct descendants of a bacterial endosymbiont that became established at an early stage in a nucleus-containing (but amitochondriate) host cell. Gene sequence data strongly support a monophyletic origin of the mitochondrion from a eubacterial ancestor shared with a subgroup of the α-Proteobacteria. However, recent studies of unicellular eukaryotes (protists), some of them little known, have provided insights that challenge the traditional serial endosymbiosis–based view of how the eukaryotic cell and its mitochondrion came to be. These data indicate that the mitochondrion arose in a common ancestor of all extant eukaryotes and raise the possibility that this organelle originated at essentially the same time as the nuclear component of the eukaryotic cell rather than in a separate, subsequent event.

    And from “Nature”

    The idea that some eukaryotes primitively lacked mitochondria and were true intermediates in the prokaryote-to-eukaryote transition was an exciting prospect. It spawned major advances in understanding anaerobic and parasitic eukaryotes and those with previously overlooked mitochondria. But the evolutionary gap between prokaryotes and eukaryotes is now deeper, and the nature of the host that acquired the mitochondrion more obscure, than ever before.

    But it is still being stated that the endosymbiotic theory is actually a fact as in the last paragraph of the quote below

    Of course we have known about the profound similarities across the entire phylogenetic tree of life in many of the machines of the central dogma (ribosomes, polymerases, and so on) and the enzymes of central metabolism, but now we’ve also found homologs of the major eukaryotic cytoskeletal proteins in bacteria and many other surprises. But it is still a fundamental observable fact that the vast majority of bacterial cells are physically small and morphologically simple compared with the vast majority of eukaryotic cells. There are certainly exceptions to this – there are bacteria that are large and complicated and there are eukaryotes that are small and simple – but if you just look at any random bacterium versus a random eukaryote, it is clear that there is a fundamental quantitative and qualitative difference in size and complexity. Archaea, which make up the third major domain of life, have some molecular signatures that seem quite similar to those in eukaryotes, but morphologically they look very much like bacteria. Indeed this is the reason that we didn’t recognize them as a distinct domain until very recently . ..

    And of course, eukaryotes have endosymbionts, the mitochondria and chloroplasts that used to be bacteria that the eukaryotes have taken into themselves and tamed for their own purposes

    They have found homologs of the major eukaryotic cytoskeletal proteins in bacteria. That is interesting!

  8. Allan Miller:

    You seem very keen to accept this research, based as it is upon phylogenetic methods. Why is that?

    Because it is very recent and is based on new evidence that was not previously available.

  9. Allan Miller:

    This, I must say, is total garbage. Rickettsiales simply happened to be the best fit last time I looked. It favours no particular belief of mine: the data point where they point. You’ve got some researchers favouring one phylogeny, others another, critiquing each others’ assumptions and methodology.

    You think this paper is total garbage?

    Which is the one materialists are supposed to believe?

    The one with the most compelling evidence.

    Which support an origin of prokaryotes in eukaryotes?

    Which rules out the possibility and why? I am not putting forward that theory, I am looking for evidence which would rule it out.

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