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. Entropy Entropy
    Ignored
    says:

    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. colewd
    Ignored
    says:

    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. Allan Miller
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    says:

    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. Allan Miller
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    says:

    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. CharlieM CharlieM
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    says:

    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. Allan Miller
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    says:

    CharlieM,

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

  7. Allan Miller
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    says:

    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?

  8. CharlieM CharlieM
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    says:

    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!

  9. CharlieM CharlieM
    Ignored
    says:

    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.

  10. CharlieM CharlieM
    Ignored
    says:

    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.

  11. John Harshman John Harshman
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    says:

    CharlieM: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.

    Conveniently, that means you can express your disagreement with mainstream science, provide your own theory, and then completely avoid defending that theory or presenting any evidence in its favor. Again, well played, sir.

    How strong is the case for endosymbiosis?

    Very strong. Even the little bits you found on the internet and then quote here help to show that, if you would only read them instead of presenting them triumphantly as support for some unstated doubts.

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

    None of that is relevant to the point, which is that cyanobacteria were present in ancient stromatolites and that they long precede eukaryotes.

    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.

    Wrong theory. Mitochndria clearly began as intracellular parasites, just like their closest “free” relatives. What about the membrane?

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

    I don’t believe your source even says that. Even if it did, so what?

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

    Quite so. Nothing you quoted or cited casts any doubt on the theory. That you appear to think so merely suggests that you have problems with reading comprehension.

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

    In what way is it interesting in connection with what we’re talking about?

  12. OMagain
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    says:

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

    “Atoms are designed”: what’s the testable hypothesis?

  13. CharlieM CharlieM
    Ignored
    says:

    John Harshman: Conveniently, that means you can express your disagreement with mainstream science, provide your own theory, and then completely avoid defending that theory or presenting any evidence in its favor. Again, well played, sir.

    I don’t have a disagreement with mainstream science. I have a problem with individuals passing theory off as fact and with what I believe are inflated claims for the creative forces of natural selection acting on stochastic changes.

    I have not presented any theories. I have stated some of my beliefs in the hope that they will be challenged. I can put up with ridicule as long as there is some constructive criticism to go along with it.

  14. Allan Miller
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    says:

    CharlieM,

    You think this paper is total garbage?

    No, your statement was total garbage. The one I blockquoted and said “this is total garbage” beneath; the one that said people follow what they are told at Uni because it fits their ‘materialist’ worldview.

    The paper, I can’t read because it is behind a paywall and I don’t have a subscription or institutional acces. I’m willing to bet you are in the same position. We’ve both read the abstract; whoop-te-doo.

    There is a deep technical discusion behind all this – long branch attraction, the relative merits of RNA vs protein coding genes, the spectre of gene transfer … what I don’t see is these separate university-educated people going along with what they are told because it ‘fits their materialist worldview’.

    Allan: Which is the one materialists are supposed to believe?

    Charlie: The one with the most compelling evidence.

    Thereby flatly contradicting yourself. I would agree.

    Allan: Which support an origin of prokaryotes in eukaryotes?

    Charlie: Which rules out the possibility and why?

    Both of them. If one says mitochondria are a sister group to Rickettsiales, another that they are a sister group to the entirety of alphaproteobacteria, both are implicitly arguing against the entirety of the prokaryotes being derived from eukaryotes.

    I am not putting forward that theory, I am looking for evidence which would rule it out.

    You need to grasp the rationale better then, I would suggest.

  15. CharlieM CharlieM
    Ignored
    says:

    John Harshman:

    CharlieM: How strong is the case for endosymbiosis?

    Very strong. Even the little bits you found on the internet and then quote here help to show that, if you would only read them instead of presenting them triumphantly as support for some unstated doubts.

    From a previous link:

    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

    So they are suggesting that mitochondria belong to a branch that appeared before the existence of alphaproteobacteria. I would like to know the genetic relationship between mitochondria and bacteria. I don’t want to take anything for granted just because it is a commonly held view. Maybe you could go into more detail about why you think the evidence is strong..

  16. Entropy Entropy
    Ignored
    says:

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

    I can explain ways for testing, but first I want to make sure that you understood that it cannot be falsified for something it is not supposed to explain. Like those “transitions” you keep taking about.

  17. John Harshman John Harshman
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    says:

    CharlieM: So they are suggesting that mitochondria belong to a branch that appeared before the existence of alphaproteobacteria.

    No, that isn’t what it says. It says “before the divergence of all sampled alpha proteobacteria”. Do you understand the difference? The evidence for endosymbiosis, incidentally, doesn’t depend on the exact relationship between mitochondria and either any particular alpha proteobacterium or to all the ones that paper sampled. This is just you being unwilling to believe anything you don’t want to, and demanding more and more evidence forever, vs. your acceptance of anything, no matter how tenuous, that agrees with what you do want to believe.

  18. John Harshman John Harshman
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    says:

    CharlieM: I don’t have a disagreement with mainstream science. I have a problem with individuals passing theory off as fact and with what I believe are inflated claims for the creative forces of natural selection acting on stochastic changes.

    So far natural selection hasn’t come into it. Why are you introducing it? And it’s a typical creationist tactic to denigrate evolution as “just a theory”. You can’t evaluate the evidence, you won’t look at the evidence, and you do indeed have a disagreement with mainstream science.

    I have not presented any theories. I have stated some of my beliefs in the hope that they will be challenged. I can put up with ridicule as long as there is some constructive criticism to go along with it.

    Your beliefs can’t be challenged and there can be no constructive criticism until you give us something to criticize. “I feel this” is undebatable. “Why I feel this” might be. But you are unwilling to defend your ideas.

  19. CharlieM CharlieM
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    says:

    John Harshman: None of that is relevant to the point, which is that cyanobacteria were present in ancient stromatolites and that they long precede eukaryotes.

    Cyanobacteria were just one example of organisms assumed to contribute to the formation of ancient stromatolites. I would say that relying on the fossil record to determine the constituents of very ancient biota can be misleading. Fossilization is a very rare event and even more so in these very ancient times.

    CharlieM: 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.

    Wrong theory. Mitochndria clearly began as intracellular parasites, just like their closest “free” relatives.

    It is not at all clear that they began as intracellular parasites. Here is a very comprehensive review of the multiple proposals for the origin of mitochondria in eukaryotes.

    From the paper:

    The origin of mitochondria is a unique and hard evolutionary problem, embedded within the origin of eukaryotes. The puzzle is challenging due to the egalitarian nature of the transition where lower-level units took over energy metabolism. Contending theories widely disagree on ancestral partners, initial conditions and unfolding of events. There are many open questions but there is no comparative examination of hypotheses. We have specified twelve questions about the observable facts and hidden processes leading to the establishment of the endosymbiont that a valid hypothesis must address.

    I think it shows the difficulty involved in integrating mitochondria into a functioning cell.

    What about the membrane?

    The paper examines the problems with membranes:

    ⦁ The chimaeric nature of eukaryotes and membrane conversion.

    The host either originated as an archaeon or as a bacterium. In case of an archaeal host, one has to explain the origin of both bacterial membranes and bacterial metabolic enzymes. In case of a bacterial host, archaeal information machinery needs an explanation.

    And they go on to discuss the various proposed solutions to the problem.

  20. CharlieM CharlieM
    Ignored
    says:

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

    I don’t believe your source even says that. Even if it did, so what?

    This is from the abstract:

    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.

    What do you think they mean by these words?

    Your ask, “so what?”. A cell gains a nucleus and the mitochondria together and has the organisational ability to incorporate them in its overall function, and you don’t see this as a problem for Darwinian evolution? The organisational, creative power of the blind forces is quite amazing. Darwinian evolution seems to have no limits to its ability.

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

    Quite so.

    You are happy to accept this theory with all its problems as listed here as a fact?

  21. CharlieM CharlieM
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    says:

    John Harshman:

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

    In what way is it interesting in connection with what we’re talking about?

    Well if you are correct in your view that bacteria preceded eukaryotes then it means that the proteins necessary for the production of cytoskeletons were in effect prepared in advance in bacteria. That is very fortunate for the future evolution of multicellular organisms. Thinking further along these lines is it not possible that prokaryotes were created in preparation for their vital role in eukaryotes? A house cannot be built without the necessary foundations and eukaryotes cannot exist without their prokaryote partners. The reverse cannot be said to be true.

    We have seen the very complex steps needed to bring about multicellular eukaryotes. IMO this is far too much for blind, chance processes to achieve. And the more science progresses the more complexity we find. Our understanding of the complexities involved is only just beginning. The number of circles within circles is growing exponentially. Just look at any protein interaction network.

  22. Rumraket Rumraket
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    says:

    CharlieM: That is very fortunate for the future evolution of multicellular organisms. Thinking further along these lines is it not possible that prokaryotes were created in preparation for their vital role in eukaryotes?

    This is a silly way to think about things. Any particular chain of events can be thought of in that fashion. The animals and plants in bygone geological epochs died and became tars and oils so so that one day bitumen could be extracted and used to make asphalt was laid down on the roads so that one day in the future children could fall and scrape their knees on them. That’s me thinking in that way. There isn’t any series of historical events that can’t be put to such an analysis. The past happened so that the future could be built upon it. But it is just an unfalsifiable interpretation, a conjecture with zero actual evidential merit.

  23. colewd
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    says:

    Entropy,

    I can explain ways for testing, but first I want to make sure that you understood that it cannot be falsified for something it is not supposed to explain. Like those “transitions” you keep taking about.

    Sure. If you can show a coherent hypothesis that does not require transitions to fully test the claim. I am not sure this hypothesis will mean much.

    Darwins original concept of all life originated from a single ancestor required explaining transitions.

  24. Alan Fox Alan Fox
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    says:

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

    Well, the central concept is quite simple. All extant and extinct* life descends parent-to-offspring in an unbroken line from a common ancestor. It’s a big target to shoot at. Yet you manage to miss quite spectacularly! 🙂

    * No direct evidence yet has been found regarding “false starts”

  25. CharlieM CharlieM
    Ignored
    says:

    Allan Miller: what I don’t see is these separate university-educated people going along with what they are told because it ‘fits their materialist worldview’.

    The authors of the paper I previously linked to have given a thorough critique of all the major contending hypotheses on the appearance mitochondria. These authors have one thing in common with all the other authors they are critiquing. Every one of them are starting out from a position where it is assumed that eukaryotes are the result of blind forces, no teleology is involved. Nature is full of teleology but any thoughts of teleology in the every increasing complexity observed in evolution is not even entertained.

    Living organisms are a byproduct of physical and chemical forces and that is the only way to look at it if you want to be taken seriously by orthodox scientific establishments.

  26. CharlieM CharlieM
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    says:

    John Harshman: So far natural selection hasn’t come into it. Why are you introducing it?

    From this paper that I have been discussing, selection features quite prominently. Indeed one of the twelve questions that the authors say need to be answered in the process of mitochondrial appearance is: Does the hypothesis give the organism an early selective advantage?

    I don’t see how we can discuss endosymbiosis without natural selection being in the background at the very least.

  27. John Harshman John Harshman
    Ignored
    says:

    CharlieM: Cyanobacteria were just one example of organisms assumed to contribute to the formation of ancient stromatolites. I would say that relying on the fossil record to determine the constituents of very ancient biota can be misleading. Fossilization is a very rare event and even more so in these very ancient times.

    How is that relevant to whether cyanobacteria precede eukaryotes? Are you claiming that eukaryotes were present before cyanobacteria but produced no fossils for several billion years? Or will you retreat into the proposition that you are making no claims at all, just trying to learn? The problem with that is if you aren’t making a claim in the paragraph above, it serves no purpose. If you think there is any doubt that chloroplasts are descended from free-living cyanobacteria, you must be able to make some kind of case, which you have not done.

    It is not at all clear that they began as intracellular parasites. Here is a very comprehensive review of the multiple proposals for the origin of mitochondria in eukaryotes.

    Note that every one of those proposal involves endosymbiotic origin, so if you like that review, we’re just arguing about details. Nothing supports your claim, which you deny making, that bacteria are descended from mitochondria, not the other way around.

    I think it shows the difficulty involved in integrating mitochondria into a functioning cell.

    I think it shows the difficulty involved in deciding how mitochondria became integrated.

  28. John Harshman John Harshman
    Ignored
    says:

    CharlieM: A cell gains a nucleus and the mitochondria together and has the organisational ability to incorporate them in its overall function, and you don’t see this as a problem for Darwinian evolution? The organisational, creative power of the blind forces is quite amazing. Darwinian evolution seems to have no limits to its ability.

    I think you misunderstand what “at the same time” means; you aren’t thinking about deep time. “At the same time” can cover millions of years.

  29. John Harshman John Harshman
    Ignored
    says:

    CharlieM: Living organisms are a byproduct of physical and chemical forces and that is the only way to look at it if you want to be taken seriously by orthodox scientific establishments.

    What’s your alternative? What other forces do you propose and what’s your evidence that they exist?

  30. Entropy Entropy
    Ignored
    says:

    colewd:
    Sure. If you can show a coherent hypothesis that does not require transitions to fully test the claim.

    How could “transitions” test for common ancestry? That doesn’t make any sense.

    colewd:
    I am not sure this hypothesis will mean much.

    For not testing for what common ancestry isn’t about?

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

    I suspect that you’re mistaking common ancestry and evolution. Common ancestry is a component of the theory of evolution, but it’s not a synonym with it.

  31. Allan Miller
    Ignored
    says:

    CharlieM: The authors of thepaper I previously linked to have given a thorough critique of all the major contending hypotheses on the appearance mitochondria. These authors have one thing in common with all the other authors they are critiquing. Every one of them are starting out from a position where it is assumed that eukaryotes are the result of blind forces, no teleology is involved. Nature is full of teleology but any thoughts of teleology in the every increasing complexity observed in evolution is not even entertained.

    Living organisms are a byproduct of physical and chemical forces and that is the only way to look at it if you want to be taken seriously by orthodox scientific establishments.

    What would you offer them to persuade them that teleology was involved? All very well having a marvellous new notion that everyone is just too blinkered to accept; you have to do some persuadin’.

    Not sure what brought this tangent on though. The discussion was but recently about the weight of evidence for the direction of the phylogenetic arrow.

  32. Allan Miller
    Ignored
    says:

    I find it a bit peculiar that someone with a scala naturae view would prefer the idea that prokaryotes arose from eukaryotes. Isn’t the reverse what you’d expect? Are you just being contrarian for the hell of it, because if evolutionists say it it must be the blinkers talking?

  33. John Harshman John Harshman
    Ignored
    says:

    Allan Miller:
    I find it a bit peculiar that someone with a scala naturae view would prefer the idea that prokaryotes arose from eukaryotes. Isn’t the reverse what you’d expect? Are you just being contrarian for the hell of it, because if evolutionists say it it must be the blinkers talking?

    I believe I can deal with that. Charlie believes in a reverse scala naturae, in which all other life is an imperfect representation of the human archetype. That archetype is spirit and as such leaves no fossils, but has over time become increasingly good at representing itself in matter. In short, wackitude.

  34. colewd
    Ignored
    says:

    Entropy,

    I suspect that you’re mistaking common ancestry and evolution. Common ancestry is a component of the theory of evolution, but it’s not a synonym with it.

    It (common ancestry) appears to be a trivial claim so it really is not worth discussing.

  35. Entropy Entropy
    Ignored
    says:

    colewd:
    It (common ancestry) appears to be a trivial claim so it really is not worth discussing.

    I find it fascinating, but if you lost interest that’s all right. Sorry that I insisted on that one single point, but, if we let go of misunderstanding go on unchecked, then they pile up and there can never be any advance in these conversations.

  36. colewd
    Ignored
    says:

    Entropy,

    I find it fascinating, but if you lost interest that’s all right. Sorry that I insisted on that one single point, but, if we let go of misunderstanding go on unchecked, then they pile up and there can never be any advance in these conversations.

    I think you have been consistent with your claim so I am good. While you are consistent with your claim others are not. If you say universal common descent explains some similarities of all life on earth I think it is a claim that is reasonable.

    The only issue is the word universal common descent implies more to other people.

  37. Allan Miller
    Ignored
    says:

    colewd:
    Entropy,

    It (common ancestry) appears to be a trivial claim so it really is not worth discussing.

    [blink]

  38. CharlieM CharlieM
    Ignored
    says:

    Rumraket:

    CharlieM: That is very fortunate for the future evolution of multicellular organisms. Thinking further along these lines is it not possible that prokaryotes were created in preparation for their vital role in eukaryotes?

    This is a silly way to think about things. Any particular chain of events can be thought of in that fashion. The animals and plants in bygone geological epochs died and became tars and oils so so that one day bitumen could be extracted and used to make asphalt was laid down on the roads so that one day in the future children could fall and scrape their knees on them. That’s me thinking in that way. There isn’t any series of historical events that can’t be put to such an analysis. The past happened so that the future could be built upon it. But it is just an unfalsifiable interpretation, a conjecture with zero actual evidential merit.

    Children fall and scrape their knees without the presence of bitumen but multicellular organisms cannot exist without the presence of prokaryotes. Reductionist thinking does not make the connections, it only sees the separate parts. For example the human organism is a whole in space and time, perfectly adapted to its natural environment at every stage from the moment of conception until its death.
    In the words of Goethe from Faust:

    How everything weaves itself into the whole,
    One part in the other acting its role.

    The whole human organism contains the essence of all forms of life within itself. It contains prokaryotes within itself in the form of mitochondria. There does not have to be a chain link of cause and effect between these two. That is the result of thinking borrowed from physics which deals with lifeless matter. This “cause and effect” thinking is justified in that domain, but not if we are trying to understand the kingdoms of life. Look at a protein network, its workings cannot be separated into cause and effect. In order to understand it, it must be thought of as a functioning whole.

    It is the same in life as a whole. Regarding prokaryotes and mitochondria, one did not cause the other, they are just similar beings suited to their own environment. And the link between prokaryotes, protists, fish, amphibians, reptiles, and mammals is not a causal one, they are just aspects within the whole. In the same way that the various forms of leaf along the stem of a buttercup plant do not have a causal relationship, they are just similar organs with a form suited to their position. I have referred to this example previously which I have taken from the work of Ronald Brady

  39. Allan Miller
    Ignored
    says:

    CharlieM,

    There remains the fact that mitochondria, on phylogenetic analysis, nest within or near the alpha proteobacteria. This means that, on a dispassionate view of the evidence, one must conclude that eukaryotes arose from prokaryotes, and not the other way around. Or, one presents an alternative explanation for the data.

  40. Allan Miller
    Ignored
    says:

    Anyone else noticed how well designed ears are for the perching of spectacles?

  41. CharlieM CharlieM
    Ignored
    says:

    John Harshman: CharlieM: Cyanobacteria were just one example of organisms assumed to contribute to the formation of ancient stromatolites. I would say that relying on the fossil record to determine the constituents of very ancient biota can be misleading. Fossilization is a very rare event and even more so in these very ancient times.

    How is that relevant to whether cyanobacteria precede eukaryotes? Are you claiming that eukaryotes were present before cyanobacteria but produced no fossils for several billion years? Or will you retreat into the proposition that you are making no claims at all, just trying to learn? The problem with that is if you aren’t making a claim in the paragraph above, it serves no purpose. If you think there is any doubt that chloroplasts are descended from free-living cyanobacteria, you must be able to make some kind of case, which you have not done.

    If you understand the example of the buttercup leaves I referred to in my last post you will see that I don’t believe that one caused the other. They are both entities which have come from the same source. Which one appeared first is incidental. It is fine with me if cyanobacteria appeared first, but I do not claim to know which came first because the fossil record is so incomplete. From Wikipedia:

    Organisms are only rarely preserved as fossils in the best of circumstances, and only a fraction of such fossils have been discovered. This is illustrated by the fact that the number of species known through the fossil record is less than 5% of the number of known living species, suggesting that the number of species known through fossils must be far less than 1% of all the species that have ever lived.

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

  42. Corneel Corneel
    Ignored
    says:

    CharlieM: The whole human organism contains the essence of all forms of life within itself. It contains prokaryotes within itself in the form of mitochondria.

    But not in the form of chloroplasts, so the human organism does NOT contain the essence of all forms of life within itself.

    I propose instead that buttercups are the universal archetype of all life.

  43. CharlieM CharlieM
    Ignored
    says:

    John Harshman:

    CharlieM: It is not at all clear that they began as intracellular parasites. Here is a very comprehensive review of the multiple proposals for the origin of mitochondria in eukaryotes.

    Note that every one of those proposal involves endosymbiotic origin, so if you like that review, we’re just arguing about details.

    I am precisely arguing that every one of those proposals begin with the assumption that blind evolutionary forces are at work. And from the arguments it can be seen how difficult it is to align the endosymbiotic scenario with the observed facts. Not one of them consider that the evolution of life as a whole could proceed along the same lines as the development of individual organisms. Individual development certainly doesn’t proceed by blind forces.

    The arguments in the research from that link only have meaning in a Darwinian framework.

    Nothing supports your claim, which you deny making, that bacteria are descended from mitochondria, not the other way around.

    I deny making it because I have not made that claim. As can be seen from my recent posts they need not originate by descent of one from the other. There are other options to consider.

  44. John Harshman John Harshman
    Ignored
    says:

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

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

    Which one appeared first is incidental. It is fine with me if cyanobacteria appeared first, but I do not claim to know which came first because the fossil record is so incomplete.

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

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

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

  45. John Harshman John Harshman
    Ignored
    says:

    CharlieM: I deny making it because I have not made that claim. As can be seen from my recent posts they need not originate by descent of one from the other. There are other options to consider.

    What options are you considering? Do you have any evidence favoring any of those options? Or will you just retreat from any claims at all?

  46. CharlieM CharlieM
    Ignored
    says:

    Allan Miller:

    There remains the fact that mitochondria, on phylogenetic analysis, nest within or near the alpha proteobacteria. This means that, on a dispassionate view of the evidence, one must conclude that eukaryotes arose from prokaryotes, and not the other way around. Or, one presents an alternative explanation for the data.

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

  47. dazz dazz
    Ignored
    says:

    CharlieM: If you understand the example of the buttercup leaves I referred to in my last post you will see that I don’t believe that one caused the other. They are both entities which have come from the same source

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

  48. CharlieM CharlieM
    Ignored
    says:

    Allan Miller:
    Anyone else noticed how well designed ears are for the perching of spectacles?

    And for stopping your hat falling over your eyes, don’t forget that 🙂

  49. CharlieM CharlieM
    Ignored
    says:

    Corneel: But not in the form of chloroplasts, so the human organism does NOT contain the essence of all forms of life within itself.

    I propose instead that buttercups are the universal archetype of all life.

    There are two opposing views on life and the world, One where matter is primal and the other where consciousness is. Obviously I follow the second view and my opinions below reflect this.

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

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

  50. John Harshman John Harshman
    Ignored
    says:

    CharlieM,

    Now who can argue with that? I think we’re all indebted to Gabby Johnson for clearly stating what needed to be said. I’m particulary glad that these lovely children were here today to hear that speech. Not only was it authentic frontier gibberish, it expressed a courage little seen in this day and age.

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