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. DNA_Jock
    Ignored
    says:

    Mung: Why didn’t you say that in the first place instead of accusing me of a cover-up? So now who is the one changing the subject. I apologize to John for attributing to him a goofy claim he never made.

    What? Why didn’t I say that in the first place?
    Gee, how did I enter this conversation?

    Mung:

    John is claiming that random genetic drift and the neutral theory of molecular evolution are one and the same. To which I say nonsense.

    Completely incorrect characterization of the conversation.
    You need to retract this claim, Mung.
    What actually happened:

    To which you replied:

    You are wrong. Again. Sadly. Context DNA_Jock. Context.

    My claim was ALWAYS about the neutral theory. If you would like the background, the missing context, I’ll be happy to explain it to you.

    Like I said, ‘A simple, “Gee, I didn’t think that through” would suffice.’
    So my apologies for accusing you of a cover-up. I mistakenly assumed that you were smart enough to follow along in a conversation that you were having.
    It won’t happen again.

  2. Mung Mung
    Ignored
    says:

    Allan Miller: Hey, I don’t want to over egg it; it was a brief thought, barely formed!

    You would have to love the irony though if information theory could be used to support common descent!

    It was an interesting proposal. I will keep it in mind and see if I can come up with anything that makes sense from information theory with ancestor as source and descendant as receiver and the intervening path as a communications channel where we can try to recover the signal from the source at the output of the channel.

    It was a sincere cool idea from me to you!

  3. Mung Mung
    Ignored
    says:

    DNA_Jock: You need to retract this claim, Mung.

    Claim retracted.

    But speaking of keeping track of a conversation, it is THIS comment of yours that I have been responding to and that I have been disputing (wasn’t that obvious?):

    DNA_Jock: Mung, you appear to be making a lame-ass attempt to cover your mistake by changing the subject from the PROCESS neutral evolution (which John had in fact covered under ‘mutation’ and ‘drift’) to neutral theory, which AIUI is a CLAIM regarding the relative importance of drift and adaptation in life’s history.
    Please stop it.

    I mistakenly assumed that you were smart enough to follow along in a conversation that you were having. It probably will happen again. Ta.

  4. DNA_Jock
    Ignored
    says:

    Good grief.

    phoodoo:

    What is the process by which regulation is modified, small mutations and natural selection?

    John:

    Small mutations, large mutations, natural selection, and drift. That ought to about cover it. Can you think of any other process that I left out?

    Pretty clear that we are talking about processes here, mechanisms.
    Mung snark:

    Neutral evolution

    Allan

    Covered, under drift

    Mung snark:

    Right. Who needs Kimura anyways

    John snark:

    Do you know what “drift” means?

    Mung snark:

    Yes John, I do. I also know that random genetic drift and neutral theory are two different things.

    Later Mung:

    John is claiming that random genetic drift and the neutral theory of molecular evolution are one and the same. To which I say nonsense.

    Which Mung has conceded was in error. I mean, it’s a rather obvious category error, and it is Mung’s, not John’s.
    I entered the conversation to point out this error.
    John was discussing processes, mechanisms by which gene regulation is modified. Mung wanted to talk about competing schools of thought in evolutionary theory, but he crashed the Segway.
    There’s some unlinked context over at PS that shows that Mung has not completely lost the plot. Apparently.

  5. Entropy Entropy
    Ignored
    says:

    phoodoo:
    I found no less than five attempts by Jerry Coyne writing to try to downplay the significance of recent HGT discoveries.

    Significance in what sense?

    phoodoo:
    And even in his never ending attempt to be the evolutionary head propagandist, he is even forced to admit -“Quammen is right that the horizontal transfer of genetic information does complicate our effort to understand the evolutionary past.”

    Evolutionary head propagandist? HGT facilitates evolution. Why would anybody who actually understand evolution want to deny HGT?

    phoodoo:
    When Jerry Coyne, who spends his entire life’s existence being as disingenuous as he can possibly muster in order to go to bat for his religion, in no less fervor than Republicans praising a drunken frat boy groper, is forced to confront some hard truths for his side, you know even he is feeling the walls closing in.

    I’m still lost. You talk as if HGT was something that went against evolution, when it clearly is a phenomenon that makes it much easier for it to happen.

    phoodoo:
    Quick, quick Jerry, we need a Russian style media diversion campaign, write as many articles as you can in one week trying to deflect, deflect.

    Again, why would anybody deflect? HGT is an interesting mechanism in the evolutionary repertoire.

    phoodoo:
    Be the Alan Fox, the Lizzie Liddle of the academic community, just shout, “But it doesn’t matter, Darwin is strong”, and no one will look too closely.

    Oh! I see! You’re projecting from your religious inclinations and you think that unless it’s some mechanism proposed by Darwin then it’s not evolution. Right? Well phoodoo, you’ve got that very wrong. It’s not about worshipping some figure, even someone as important as Darwin in the development of evolutionary theory. It’s about getting better and better understanding about how things happen.

    phoodoo:
    Hey, it worked for Trump supporters, its gotta be good.The Allan Millers, the DNA Jocks, the KN’s of this world, don’t worry, they will help you hand wave, just get out those pamphlets, NOW!

    Some more projection on your part here phoodoo.

    phoodoo:
    You skeptics are quite the thinkers, huh?

    Enough to notice that you have no idea. You know that HGT is a natural phenomenon, right? That nobody has caught some magical being in the sky puffing genes into existence and then, for example, building them into antibiotic resistance “cassettes” that this being then inserts into all sorts of microbes. That what they catch in the act are plasmids, viruses. You know this, right?

  6. John Harshman John Harshman
    Ignored
    says:

    Mung: What’s to object to John. You are aware of the conversation at Peaceful Science that keep referring to are you not? So I am not making that up, right?

    Did I call it or what? A totally irrelevant objection. The conversation at Peaceful Science has nothing to do with your present misunderstanding.

  7. John Harshman John Harshman
    Ignored
    says:

    DNA_Jock: There’s some unlinked context over at PS that shows that Mung has not completely lost the plot. Apparently.

    As it happens, there isn’t. All it shows is that Mung never had the plot.

  8. CharlieM CharlieM
    Ignored
    says:

    DNA_Jock:

    CharlieM: Why would they be targets? You are assuming that the 63 letter string is aiming for something. Very teleological

    ROFL
    No, I was performing ID-math(tm) and thus using ID-language: the T in P(T|H) stands for “target”. Read Dembski.

    So if you were “performing ID-math(tm)”, can you give us the figures you were using?

    You still have not explained why increased Dpp copy number results in embryonic cells assuming more dorsal fates, under your archetype theory.

    Dpp is “capable of rapid diffusion in all directions, and yet gradients form slower, directionally and independent of morphogen production rates.”

    From the article by Jessica L. Erickson, where I took the above quote from:

    As early as 1964 it was suggested that simple diffusion of morphogens away from their secretion source did not provide an adequate explanation for the formation and maintenance of morphogen gradients. Involvement of the endosome in morphogen distribution models provides an explanation for the slow, directional movement of morphogens, as well as their ability to form intracellular and extracellular gradients independent of morphogen production rates. Drosophila melanogaster morphogens Wg and Dpp form stable, steep, longrange gradients that specify the polarity of the wing disc. The process of endocytosis is imperative to the two central themes in gradient formation: active transport facilitating long-range signaling and degradation of morphogen to sustain gradient shape. This review investigates the endomembrane-mediated processes of re-secretion, degradation and argosome transport of Wg and Dpp in the hope that a better understanding of the endomembrane system will contribute to a more accurate and comprehensive model for morphogen gradient formation and maintenance.

    To say that “Dpp copy number results in embryonic cells assuming more dorsal fates” is a very misleading statement.
    More from the article

    There seems to be a general agreement that active degradation of morphogens must occur to maintain the steep gradients of Wg and Dpp.

    There are several coordinated factors which contribute to the directions of growth and thus the morphology of the individual organism. Every stage of development expresses the archetype in its own unique way. And the correct growth is achieved by maintaining the appropriate balance between production and destruction of proteins such as Dpp.

    And this is an enduring feature of all living systems from the molecular scale to earthly life as a whole, it is sustained by maintaining the balance between growth and decay, life and death. Blind evolution would not take this maintenance of balance over time into account because it has no thought for the future and balance can only be maintained by anticipating the future before it happens.

  9. CharlieM CharlieM
    Ignored
    says:

    John Harshman: That isn’t evolution. Of course mutation, selection, and drift can change DNA sequences that change regulation. But that isn’t what you meant, is it?

    What is wrong with saying that individual cells evolve during the development of a multi-cellular organism?

  10. CharlieM CharlieM
    Ignored
    says:

    Entropy: Then what the heck do you mean by aim Charlie? What do you think that teleological means? In my understanding of those words, both imply intention, so it would be you who introduced the concept, if not the literal term.

    A heat seeking missile is aiming for the source of heat but we do not say that it has the intention to hit its target. The latter has more of an implication of consciousness than the former.

    Leaving aside yet-another-misuse-of-language (natural “selection,” for example, gives evolution a “direction,” only not an “intentional” one), what makes you think this is about fear?

    At least in my case, this is about basic philosophical foundations. We cannot claim that there’s “aims” or “teleology” unless we had the proper evidence for such a thing. In the meantime, what we see is things being what they are, and we should avoid concluding from mere metaphorical language, and/or from mere anthropomorphisms.

    You do have a point in that we should not jump to conclusions without evidence.

    But we do witness aspects of nature where structures are in place in readiness for future use. Eyes before sight, lungs before air breathing, birds nests before eggs and so on.

  11. CharlieM CharlieM
    Ignored
    says:

    Entropy: What do you think that teleological means?

    End-Directed. Directed towards an end. It makes no claim about whether the directedness or the end are natural or not.

  12. CharlieM CharlieM
    Ignored
    says:

    Allan Miller: Still, I don’t know why you feel the need to keep side-stepping my very straightforward question. Regardless of the mechanistic path by which genes are supposed to end up held in common without passing through ‘vertical’ descent, how are these anomalies discovered? What makes them stand out? What are they anomalous with respect to?

    They maybe anomalous with respect to eukaryotes, but are they anomalous in prokaryotes? I would say that its common appearance here makes the species concept that is quite apt for metazoan redundant when it is applied to prokaryotes.

    And I have no problem with agreeing that common descent is a well established feature within eukaryotes. Just how linear and extensive it is I am not so sure.

    The commonality of genes between widely differing species tells me that it is the way genes are organised and not the genes themselves that make the difference.

    I would say our difference of opinion lies in the way we see this organising principle.

  13. DNA_Jock
    Ignored
    says:

    CharlieM: So if you were “performing ID-math(tm)”, can you give us the figures you were using?

    They are right there in the comment I linked to originally.

    CharlieM: To say that “Dpp copy number results in embryonic cells assuming more dorsal fates” is a very misleading statement.

    No, it is not. I even quoted from the review that you cited regarding the effect of injecting Dpp transcripts into the embryo.

    The fact that CharlieM is capable of mindlessly cutting&pasting from yet another article about imaginal wing development is entirely irrelevant to embryonic pattern formation. You are doing it again, and it makes you appear unaware that drosophila pupate…
    If your comment included an attempt to explain why injecting transcripts into embryos leads to more dorsal ectodermal fates, I must have missed it. Could you be more specific?

  14. John Harshman John Harshman
    Ignored
    says:

    CharlieM: What is wrong with saying that individual cells evolve during the development of a multi-cellular organism?

    Impenetrability, that’s what I say.

  15. CharlieM CharlieM
    Ignored
    says:

    Allan Miller:
    CharlieM

    But if there is wisdom involved in evolution then the same sequences could be used by separate organisms because these are the sequences that are most suitable for that particular organism. Physical DNA does not need to be transferred.

    So if, for example, we observe an intracellular parasite/symbiont such as Wolbachia in cells, and also discover Wolbachia genes in the nuclei of the host species, we are not justified in saying that they were physicallytransferred? Somehow, we should prefer the notion that the host and Wolbachia both need the‘most suitable’ genes, despite one being an insect and the other a bacterium?

    I did not say that it cannot be transferred in this way, I said it need not be.

  16. Mung Mung
    Ignored
    says:

    Let’s review:

    John Harshman: Do you know what “drift” means?

    Mung: Yes John, I do. I also know that random genetic drift and neutral theory are two different things.

    John Harshman: Yes, just as dogs and poodles are too different things.

    John is clearly saying that neutral theory is to random genetic drift as poodles are to dogs.

    John Harshman: You were shocked because you don’t know what drift and neutral evolution are; you only know the names.

    Mung: There was no debate or controversy over random genetic drift John. There was one over the neutral theory. Random genetic drift did not kill Darwinism in 1968.

    They are not the same.

    I am rather clearly talking about the neutral theory of evolution.

    John Harshman: First rule of holes: stop digging.

    John reiterates his earlier claim. He certainly appears to be disagreeing with my statement that neutral theory is not the same as random genetic drift.

    Joe Felsenstein: CharlieM asks John Harshman what evolutionary phenomena could account for changes in gene expression. Harshman gives a straightforward list. Mung then says what about neutral theory.

    Even Joe picked up on the fact that I was talking about neutral theory. He probably read what I actually wrote and even understood the reference to 1968.

    John Harshman: To refresh your memory: I said that selection and drift are mechanisms of evolution. You chided me for leaving out neutral evolution. I pointed out that neutral evolution is a subset of drift. You said, apparently, “is not”, or something; it’s unclear.

    John essentially admits he hasn’t been following along all that well and still seems clueless that I am talking about neutral theory, in spite of the repeated mentions and references, and then accuses me of making a claim i never made.

    John Harshman: So what you need to do is support or abandon your claim that neutral evolution is not a subset of genetic drift.

    DNA_Jock, for whatever reason, turns a blind eye.

    It was only after this that I made my comment that sparked off this whole series of exchanges with DNA_Jock. It doesn’t make my comment right or appropriate, I apologized and retracted it, but DNA_Jock needs to consider the importance of context and no be so quick to castigate people for misbehavior.

    DNA_Jock: I entered the conversation to point out this error.

    And you should have left it at that rather than also accusing me of an attempted cover-up followed up by what are very much in essence accusations of lying about whether or not there was an attempted cover-up.

    As you saw, once you pointed that statement about John out to me (admittedly for the second time) I promptly addressed it.

    Your “pointing out this error” was obscured by your other baseless allegations. Keep that in mind for the future.

  17. DNA_Jock
    Ignored
    says:

    Naah, Mung; originally, I only pointed out that you appeared to be trying to cover up your error. A friendly ‘fix this’ heads-up. You promptly doubled down, which provided a basis…
    Yes, John was slow to pick up on your segue from processes (the original topic of the conversation, including your original “Neutral evolution” comment) to schools of evolutionary thought, because it was a total non-sequitur on your part.

  18. John Harshman John Harshman
    Ignored
    says:

    Mung:
    John is clearly saying that neutral theory is to random genetic drift as poodles are to dogs.

    John is clearly aware that you don’t always use the correct words to describe what you mean, and is making allowances, assuming that you have not just changed the subject from neutral evolution.

    John reiterates his earlier claim. He certainly appears to be disagreeing with my statement that neutral theory is not the same as random genetic drift.

    I’m not sure you know what “neutral theory” is; you seem to be confusing it with “the neutral theory”. And confusing both with “neutral evolution”, which was your original statement. I tried to make the differences clear, but you seem to have ignored that. Now of course neutral theory (the mathematical population genetics of neutral evolutiion) is not the same as genetic drift; mathematics is not the same as a phenomenon. But it hardly seems necessary for anyone to say that, and I don’t believe that’s what you were trying to say.

    Even Joe picked up on the fact that I was talking about neutral theory. He probably read what I actually wrote and even understood the reference to 1968.

    You changed the subject. Perhaps you didn’t notice. You started with neutral evolution and changed to neutral theory, by which you possibly mean the neutral theory. Hard to tell what you mean, because there’s always the suspicion that you don’t know what you’re saying.

    John essentially admits he hasn’t been following along all that well and still seems clueless that I am talking about neutral theory, in spite of the repeated mentions and references, and then accuses me of making a claim i never made.

    No, John admits that you aren’t very good at expressing yourself. I think that’s compounded by your desperate attempts to disguise a simple initial error.

  19. Mung Mung
    Ignored
    says:

    John Harshman: Small mutations, large mutations, natural selection, and drift. That ought to about cover it. Can you think of any other process that I left out?

    Mung: Neutral evolution.

    Click the link boys. Then follow the instructions.

    neutral evolution

  20. John Harshman John Harshman
    Ignored
    says:

    Mung:
    Click the link boys. Then follow the instructions.

    neutral evolution

    Please explain what you mean. Please explain why you were not wrong to say that I had left out neutral evolution from a list of evolutionary processes when I did mention drift.

  21. Nonlin.org
    Ignored
    says:

    So what’s the deal with this “directed evolution” oxymoron?
    http://nonlin.org/chemistry-nobel-2018/

    Wasn’t the whole point of “evolution” to separate creation from creator? And now they let the intelligent agent back in? I would not be a happy evolutionist with this interpretation.

    In this case, not only are “random mutations” not entirely random as the mutations desired had to converge towards a clear, specified target, but also “natural selection” has been replaced by Intelligent Selection clearly done by qualified researches pursuing a specific goal. At best this would be called “artificial selection”, but even that is misleading since organism breeding is a human activity that goes well beyond simple ‘selection’.

    The process used is simple organism breeding as done by mankind for thousands of years, in this case sped up by advanced technologies.

    If “evolution” needs “directions”, then IDsts and neo-Darwinists are all a big, happy, continuously quarreling family 🙂

  22. Allan Miller
    Ignored
    says:

    CharlieM: They maybe anomalous with respect to eukaryotes, but are they anomalous in prokaryotes?

    Anomalous means anomalous, regardless what group we are talking about. The point I am trying to get you to grasp is that an anomaly is an anomaly because it goes against the expectation of simple vertical descent. That is, there must be a pattern of vertical descent in the first place against which such deviations stand out. What you are proposing is classically Creationist: to say that because there are anomalies, everything could be ‘anomalous’, and there is no such thing as pattern.

    You almost seem to wish to use the things that can only be discovered by phylogenetic analysis to be an argument against the very techniques of phylogenetic analysis, which is, if you did but know it, quite a paradoxical position to espouse.

    I would say that its common appearance here makes the species concept that is quite apt formetazoan redundant when it is applied to prokaryotes.

    No one mentioned species till you, just now. It’s true, species concepts do not apply well across the boundary. The reason is recombinant sex, but it’s not the reason there is more gene transfer observed in prokaryote lineages. And don’t forget what we were talking about: the relationship of mitochondria to prokaryotes.

    And I have no problem with agreeing that common descent is a well established feature within eukaryotes. Just how linear and extensive it is I am not so sure.

    Well, what does the evidence say? If gene transfer is comparatively rare, and the signal of common descent comparatively strong, what’s the issue? I mean, these are the organisms people particularly agonise over. Especially chimps …

    The commonality of genes between widely differing species tells me that it is the way genes are organised and not the genes themselves that make the difference.

    Is the hierarchic structure of gene relationships at close taxonomic removes not also represented at higher levels? Where does the boundary reside, where sequence commonality stops representing common descent and starts representing some mysterious Other?

  23. Allan Miller
    Ignored
    says:

    CharlieM: said

    I did not say that it cannot be transferred in this way, I said it need not be.

    Well, you were rather dismissive of gene transfer a few posts back, some kind of feeble attempt by Darwinists to keep things ‘blind’. But here’s a phenomenon with some very suggestive characteristics. What would lead us to reject the possibility that the mitochondrion started out as an intracellular parasite, like Wolbachia? Don’t forget, phylogenetic analysis places it in the alpha proteobacteria.

  24. CharlieM CharlieM
    Ignored
    says:

    Allan Miller:

    The extent of a gene is somewhat labile, depending on what one wishes to convey. It’s best not to get too dogmatic about what is or isn’t. The term was, after all, coined long before anyone knew anything about the underlying molecular biology. A gene for fair hair, say, may simply involve a switch (for all I know; it’s just an example).

    So what was Entropy trying to convey when he told me that cell fifferentiation was controlled by the products of a couple of “master” genes? He did not specify which genes exactly.

    He just directed me to this link and I have included this quote from it:

    Homeoprotein transcription factors typically switch on cascades of other genes. The homeodomain binds DNA in a sequence-specific manner. However, the specificity of a single homeodomain protein is usually not enough to recognize only its desired target genes. Most of the time, homeodomain proteins act in the promoter region of their target genes as complexes with other transcription factors. Such complexes have a much higher target specificity than a single homeodomain protein. Homeodomains are encoded both by genes of the Hox gene clusters and by other genes throughout the genome.

    From the same web page it tells us:

    The regulation of Hox genes is highly complex and involves reciprocal interactions, mostly inhibitory.

    The page also lists well over a hundred homeobox genes spread over at least four chromosomes in humans.

    Which pair of “master” genes do you think he was he talking about?

  25. CharlieM CharlieM
    Ignored
    says:

    Allan Miller:
    CharlieM:

    On a related note. where does the initial RNA polymerase come from in the newly fertilized egg?

    It was already there in the egg. The initial copies would have been transcribed from the mother’s DNA. Post fertilisation, in the diploid it is up for grabs depending on dosage, dominance effects etc.

    So the development of the fertilised egg is turning out to be much more complicated than it just being kicked off by a couple of master genes.

    From this article, “The maternal-to-zygotic transition during vertebrate development: a model for reprogramming”.

    The maternal-to-zygotic transition (MZT) is one of the most profound changes in the life of an organism. It involves gene expression remodeling at all levels, including the active clearance of the maternal oocyte program to adopt the embryonic totipotency…

    the chromatin is remodeled to stabilize the pluripotent state, and maternal instructions in the form of mRNAs and proteins are actively cleared to remove the previous cellular identity…

    Together these mRNA features are mechanistically linked to coordinate post-transcriptional gene regulation for individual mRNAs as well as for co-regulated groups of transcripts. This network of mRNA regulation dominates gene control during oogenesis and early embryogenesis, occurring in the absence of transcription…

    So complex regulation is in evidence from the very beginning of fertilisation.

    They continue:

    Cooperativity and redundancy in maternal mRNA clearance mechanisms suggests the existence of a combinatorial code that governs mRNA fate during development (Figure 3). While some elements of this regulatory code have been identified during the MZT (Walser & Lipshitz, 2011) the complexity of this regulatory mechanisms suggest that there are additional elements of this code that likely regulate mRNA stability

    Such organisation cannot come from a point within the system. The control comes from above, from the organism as a whole, which to begin with is a single cell. The organism takes account of all the internal and external signals it receives and it acts accordingly. And this is still happening in each of us as multi-cellular organisms. Our bodies stabilise themselves through homeostasis. And the most fundamental aspect of achieving this is by coordinating the appropriate gene expressions. Genes are expressed on signals coming from the body. During exercise genetic activity activates the production of the appropriate substances and signals to increase our heart rate, produce sweat and so on.

    “Master” control comes from above the genes, not within the genes.

  26. CharlieM CharlieM
    Ignored
    says:

    Entropy: I cannot give you a full course on embryonic development here, right? However, as DNA_jock said, it’s a start.

    What seems to be happening is that you focus too much into those details and lose the thread.

    The point of contention was that you argued that somebody else would get into knots defending the argument that cell differentiation was controlled by a master gene. I said that it’s better to try and figure it out, rather than argue, and that the results from embryology say that it’s a couple master genes.

    The complexity of cell regulation doesn’t tell you whether it’s a couple “master” genes controlling that differentiation or not. It just tells you that there’s complexities to how such regulation happens. Still, from the results in the study of cell differentiation, it’s just a couple “master” genes that start the process of differentiation (and, from what I remember, one was more important than the other).

    In your diagram, you have a generic transcriptional “machinery”complex. What makes the difference between starting a cascade of cell differentiation and expressing a gene whose product is involved in metabolism, for example? The answer is: the specific transcription factor(s) involved in either. So, again, no matter how complex you want to make transcription, cell differentiation is still controlled by a couple “master” genes in many-if-not-all animals (in some organisms it’s just one “master” gene, in some others there might be more, but I haven’t seen such examples yet).

    1. See my replies to Allan above.
    2. Name those genes.

  27. CharlieM CharlieM
    Ignored
    says:

    Here is very thought provoking, informative short video by Denis Noble. In it he explains the limits of mathematical models and why this rules out a belief that biology is just the application of physics and chemistry..

    He formulated the principle of biological relativity which states that there is no privileged level level of causation in biological systems.

    He says:

    It is the .organism as a whole, the complete cell that determines whether or not the DNA is reliable and indeed reproduced accurately.

    He concludes that the central dogma should “never have been used to back up the general theory of evolutionary biology”.

  28. Allan Miller
    Ignored
    says:

    CharlieM,

    Which pair of “master” genes do you think he was he talking about?

    I think questions about other people’s posts are best directed at them. Still, there is no conflict between the initiation of a long cascade of ‘downstream’ consequences – eg SRY in mammalian gender differentiation – and my statement that the molecular biology responsible for given phenotypic alleles may be due to regulatory differences rather than differences in exons.

  29. Allan Miller
    Ignored
    says:

    CharlieM,

    Well, good for Noble. Shall I don the glove puppet of someone who thinks otherwise, and we can have a play-fight via the words of others?

  30. Allan Miller
    Ignored
    says:

    CharlieM,

    So the development of the fertilised egg is turning out to be much more complicated than it just being kicked off by a couple of master genes.

    Maybe, but the source of the original transcript of a given RNA polymerase molecule has little to do with that.

  31. Mung Mung
    Ignored
    says:

    Allan Miller: where sequence commonality stops representing common descent and starts representing some mysterious Other?

    Yes. For those who only accept common descent within created kinds questions like this expose that their acceptance of common descent within created kinds is a priori and not at all based on the evidence for common descent that scientists depend on.

    If I had an answer to that question I might not accept universal common descent. Until then …

  32. CharlieM CharlieM
    Ignored
    says:

    Entropy:

    CharlieM:
    And how do we know that DNA sequences were exchanged between unrelated species by horizontal gene transfer?

    By checking several lines of evidence, from the genes displaying codon-usages foreign to the host cell, to it looking suspiciously-too-similar to the gene in the unrelated species, to our everyday experience with mobile elements. Many of them very well characterized.

    I don’t deny that there are similar genes in unrelated species. What I would not want to do is to assume that they got there by a certain evolutionary pathway just because that pathway strengthened my prior belief in how I think evolution should work.

    I believe that HGT is a process which is common and natural to organisms such as bacteria. Genetic recombination is achieved in bacteria by way of HGT, and genetic recombination is achieved in diploid eukariotes by way of meiosis. This is consistent with my thinking that, not individual bacteria, but groups of bacteria at a higher taxonomic level should be treated as equivalent to individual higher animals. In higher animals individuals are made up of a community of cells concentrated in space, in bacteria individuals are diffused in space. Slime molds are examples of an intermediate level.

    …what else do you think is involved (in HGT), if not “blind” phenomena?

    By “blind” I mean acting in a way that takes no account of the future. Bacterial conjugation is not blind in that it is a purposeful process which allows genetic material to be transferred between bacteria. And bacteria have the ability to also pick up DNA freely from their environment. Once inside the bacteria, the DNA will be used by the cell as appropriate.

    How could we test for such a thing?

    We could compare sequences in as many genomes as possible and think about how plausible it would be for homologous sequences to show up in the organisms that they are found in. With the ever expanding amount of data that is becoming available, researchers are finding more and more sequences which are “out of position” in phylogenic trees. (See the example I have provided below).

    if it’s just your imagination, why should we propose that without the evidence to support it?

    There is evidence. For example, the frequency of convergent evolution points to a higher level of organisation.

    Do you understand that we have to go by what we can test, not by the way you’d like things to be?

    Yes, and testing is difficult in a historical science such as in the study of the evolution of life. A person’s philosophical viewpoint has a great deal of influence on what they are willing to accept as a likely scenario.

    CharlieM: Horizontal gene transfer is a theory invoked to save blind evolutionary theories.

    As I explained, this is false. However, I’m curious: save them from what exactly?

    Save them from the evidence which conflicts with the neat branching tree which I suspect most early evolutionists would have wished for. It has been found to be quite messy and this has to be accounted for by the means of blind evolutionary forces, hence “mistakes” in genomes due to extranious DNA insertions transferred horizontally.

    By what mechanisms would those organisms end up with such almost-identical DNA sequences independently, and within a very short time frame?

    If intelligence is involved there does not need to be a physical transfer mechanism.

    Why would the gene be abundant in one lineage, as if vertically-inherited, while being restricted to one strain in the other lineage as if it came from the lineage where it’s abundant?

    As I said, I believe that HGT is a natural process in prokaryotes.

    How can we test for your proposed mechanism?

    What mechanism? There does not have to be a mechanism.

    How does your mechanism explain that the gene-we-call-transferred is surrounded by sequences betraying mobile element involvement in the transfer if it wasn’t a transfer? Etc.

    Again, there does not have to be a transfer mechanism.

    DNA Jumps Between Vertebrates

    BovB is a retrotransposon, a piece of DNA that can copy and paste itself around the genome to create large swathes of repetitive sequences. It is abundant in the cow genome. Researchers have also found it in the DNA of many other animals, including elephants, horses, platypuses, pythons, sea snakes, geckos, sea urchins, and zebrafish.

    To better understand how BovB found its way into such a diverse range of creatures, researchers at the University of Adelaide used sequences from these animals to construct a phylogenetic tree. If BovB had been passed down from a common ancestor and remained in their genomes as they diversified, then the more closely related species would have more similar versions of the DNA sequence. But that was not the case.

    Instead, the team found that BovB sequences from cows were more closely related to snakes than elephants, for example. The researchers suggest that the only explanation for such unexpected evolutionary relationships is that BovB has jumped between genomes, and they figured that it must have done so at least 9 times.

    Finally, the researchers identified a potential vector. BovB sequences were found in two tick species that suck the blood of lizards and snakes, indicating that parasitic arthropods could be responsible for passing the jumping genes between species.

    So this stretch of DNA can be found in many animals including elephants, horses, platypuses, pythons, sea snakes, geckos, sea urchins, zebrafish and ticks. This is what I mean by using HGT to save the theory.

  33. CharlieM CharlieM
    Ignored
    says:

    Kantian Naturalist: The whole is not a higher level of organization than the parts of which it is comprised.There’s a conceptual muddle in your thinking here.

    Of course it is. An individual termite has a certain level of organisation. A termite nest has a certain level of organisation. The whole system includes the organisation of the individual termites, it also includes the organisation of the termite nest. The termite can be seen as one level of organisation, the nest can be seen as one level of organisation, the whole can be seen as two levels of organisation. Two is a higher number than one.

  34. Rumraket Rumraket
    Ignored
    says:

    CharlieM: By “blind” I mean acting in a way that takes no account of the future. Bacterial conjugation is not blind in that it is a purposeful process which allows genetic material to be transferred between bacteria. And bacteria have the ability to also pick up DNA freely from their environment. Once inside the bacteria, the DNA will be used by the cell as appropriate.

    The sending bacterium has no idea how the DNA will affect the recieving bacterium, and vice versa. That’s the sense in which it is blind. Interestingly bacteria a tendency to expel foreign DNA that turns out to be of no immediate benefit. It is a well-known phenomenon that bacteria will, for example, lose plasmids if they are not under selective pressure to keep them. That’s why when you transform bacteria with plasmids in the lab, the plasmids are usually designed with that in mind so they carry an antibiotic resistance gene, and then you grow the bacteria in the relevant antibiotic such that the bacteria are under selective pressure to keep the plasmid and copy it when they divide.

  35. Rumraket Rumraket
    Ignored
    says:

    CharlieM: So this stretch of DNA can be found in many animals including elephants, horses, platypuses, pythons, sea snakes, geckos, sea urchins, zebrafish and ticks. This is what I mean by using HGT to save the theory.

    And yet there is an immediate and obvious mechanism by which that can happen, the ticks. What you call “save the theory” as if that is somehow an issue is researchers not ignoring relevant data. What would you have them do, deliberately ignore that a known vector exists?

  36. Corneel Corneel
    Ignored
    says:

    CharlieM: in bacteria individuals are diffused in space

  37. Corneel Corneel
    Ignored
    says:

    Myxobacteria

    Yeah, I know. An “extreme example”, right?

  38. CharlieM CharlieM
    Ignored
    says:

    Corneel: So, in what way do the differences between ontogeny and phylogeny argue against your likening of phylogenesis to organismal development?

    They don’t argue against it. The differences are due to the same type of processes taking place within different time and space frames. With this in mind the differences are to be expected.

    Both involve an overall expansion of form being held in balance by the forces of growth and decay. The same forces are at work within these different frameworks.

    I would say that taking the “details” into consideration severely cripples your implied suggestion that phylogenesis is a coordinated affair.

    The coordination lies in the balance of nature. For life on earth to have continuously survived requires that the system be in dynamic equilibrium at every stage. We have seen examples of this equilibrium being disrupted when humans introduce foreign species to an ecosystem without understanding the consequences.

  39. CharlieM CharlieM
    Ignored
    says:

    Corneel:

    CharlieM: It doesn’t actually give any explanation as to how such complexity has arisen other than evolution did it.

    That is true, but it does keep you from wondering why the descendant lineages of a zygote don’t end up all looking the same; They are capable of using positional information to initiate specific patterns of gene expression. And that knowledge in turn equips you with understanding of how genetic mutations are capable of changing the developmental program.

    Or they are capable of individual physical expression of an overarching dynamic pattern rather than forming through a vast series of accidental changes.

  40. CharlieM CharlieM
    Ignored
    says:

    John Harshman to Mung: I said that selection and drift are mechanisms of evolution.

    I would say that selection is a force of individuation and drift allows balance to be maintained.

  41. Rumraket Rumraket
    Ignored
    says:

    CharlieM: in bacteria individuals are diffused in space.

    No that’s actually not the default state of bacteria in the wild, but an artifact of how we grow bacteria in lidquid cultures that are constantly shaken and mixed to ensure more effective mixing of nutrients. In their “natural” state bacteria like to stick together in bacterial mats and colonies.

  42. CharlieM CharlieM
    Ignored
    says:

    DNA_Jock:

    CharlieM: So you think that as in the case of human DNA transcription, a process which is able to select a short stretch of DNA from a tightly wound supercoil of around 3 million base pairs, at the relevant time in the quantities needed is a simple task?

    Are you asking about prokaryotic transcription? Your English is somewhat mangled…
    I guess the answer is yes:…

    Sorry my mistake, typed million when I meant billion.

  43. John Harshman John Harshman
    Ignored
    says:

    CharlieM: I would say that selection is a force of individuation and drift allows balance to be maintained.

    You can say whatever you like. But can you actually support any of it? I think not.

  44. CharlieM CharlieM
    Ignored
    says:

    DNA_Jock: CharlieM: So if you were “performing ID-math(tm)”, can you give us the figures you were using?

    They are right there in the comment I linked to originally.

    Okay, so according to your figures N = “a big number” that you have as the denominator. For the numerator there is either 1 or 8000. And you think that it would make a big difference which one it was. What if N was the number obtained by the amount of combinations in a 63 digit string with 20 choices available in each position? Would it make any significant difference if the numerator was 1 or 8000?

  45. DNA_Jock
    Ignored
    says:

    CharlieM: Would it make any significant difference if the numerator was 1 or 8000?

    Yes, it would make an 8,000-fold difference.
    Whatever the denominator is. This is grade school math.
    But if you want to argue that the denominator should be 20^63, you are going to have to demonstrate that we can ignore the effects of selection.
    Have at it. Make gpuccio and kairosfocus proud.

  46. Mung Mung
    Ignored
    says:

    John Harshman: To refresh your memory: I said that selection and drift are mechanisms of evolution. You chided me for leaving out neutral evolution.

    I wasn’t chiding you John. I was making a joke. Sorry you didn’t get it. It was never about whether you were right or wrong with your list.

    Microevolutionary theories are gradualistic explanatory mechanisms that biologists use to account for the origin and evolution of macroevolutionary adaptations and variation. These mechanisms include such concepts as natural selection, genetic drift, sexual selection, neutral evolution, and theories of speciation.

    http://www.talkorigins.org/faqs/comdesc/

  47. John Harshman John Harshman
    Ignored
    says:

    Mung: I was making a joke.

    Of course you were. That’s why you waited until just now to tell us.

  48. Nonlin.org
    Ignored
    says:

    Allan Miller: No, it’s not a problem for evolution. In fact, it is the result of evolution. The analogy with thermodynamics can be taken too far. The ‘disorder’ I’m talking about is the gradual scrambling of the original ‘message’. This does not mean that resultant ‘messages’ are inviable.

    Isn’t EVERYTHING the magic result of “evolution” (the mystery that no one can see happening)? I hear entropy is not really “disorder”. And how do we get humans and cats when milk and coffee turns invariably light brown with no cats/humans in between?

  49. Nonlin.org
    Ignored
    says:

    Alan Fox:
    1. I know much is made of the influence of On the Origin of Species on Francis Galton (also Darwin’s cousin) who is credited with the idea of eugenics. Galton only went so far as to suggest financial inducements to encourage “able couples” to marry. It was in the US where eugenics was developed into a policy. I’m unaware of anywhere where eugenics policies are still being pursued.

    2. Intelligent Design a scientific theory? I rather think not. I’ve made a bit of an internet career of asking for details about this theory. When I could comment at UD, I used to ask for details of such a theory without receiving any details of such a theory. Paul Nelson visited here at TSZ and he confirmed there still wasn’t one. So I’d be very interested to learn about this Intelligent Design explanation. Please tell me more!

    3. Depends if your objection is semantic. The process is undeniable.

    Selection. Darwin’s big idea. The environment selects successful phenotypes.

    4. But I digress. Please, let’s hear about the explanation from Intelligent Design.

    1. Not about Galton. This nastiness was very strong in the 20th century and is ongoing. Now it’s as simple as IYIs pretending to know what’s “best”. And when the bodies pile up, it’s always someone else’s fault.
    2. Coming up. Next OP. Meanwhile, I keep hearing: “this theory might be illogical, but I believe it because you don’t show me an alternative”. Does this claim make sense to you?
    3. Semantics? ‘Messy mix’ ≠ ‘Modification’ Clear and simple.

    We were talking about “modification”, not “selection”, but that doesn’t work either as shown elsewhere.
    4. Soon enough…

  50. Nonlin.org
    Ignored
    says:

    John Harshman: So all you know about this is that you’re parroting something Swamidass said?

    Did I not make clear that Swamidass made a stupid claim? Read again. Why don’t you two fight it out. I’ll get the popcorn.

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