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. Nonlin.org
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    says:

    Allan Miller: It wasn’t even an argument; just pointing out another way to look at divergence. ID-ists are all over Shannon information. Until, that is, we look at signal degradation in a common descent relationship. Then, they blink uncomprehendingly.

    Here we go again with the mysterious allusions. What has ‘signal degradation’ to do with “common descent relationship”? And how are ID-ists “all over Shannon information”?

  2. Nonlin.org
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    Alan Fox: The genotype and thus the phenotype. Monozygotic twins in humans, when one fetilized egg splits, start out as genetically identical but as the embryos develop, mutations can and do occur which result in the genotypes no longer being strictly identical. Although the differences are small enough that identical twins are strikingly similar in appearance as adults. But environmental and developmental factors have an effect where twins environments, exposure to pathogens, education, trauma vary.

    The two essential elements in descent with modification are imperfect reproduction of the genotype and variable success in individuals of a population in getting their particular genotype or part of it into the next generation.

    Darwin used the term “descent with modification” without knowing about genotype and most certainly he was not referring to monozygotic twins diverging after conception. In addition, everyone knew and knows descendants are not identical to either parent but some sort of MESSY mix. Given this “mix” it doesn’t make any sense to talk about “modification” of genotype and/or phenotype.

    Most likely Darwin had in mind populations, not individuals, but even there it doesn’t make much sense given you can’t pin down the “modification”. This is like going to Democritus to learn about nuclear physics. It just doesn’t make any sense.

    My friendly advice is to discard all these concepts that barely make philosophical sense and to stick with the scientific method. However, be prepared to find out that in the end you will have to discard “evolution” too.

  3. Nonlin.org
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    says:

    Mung: ETA: A little back-story for those not following along over at the Peaceful Science blog. The theory of neutral evolution killed off Darwinism back in 1968. So when John failed to mention neutral evolution I was shocked. Shocked I say.

    Yeah, that was a funny one from Swamidass. I am sure everyone here will agree that Darwinism is dead because Haldane and Kimura killed it in the sixties. Meanwhile no experimental evidence whatsoever on either side of neo killing its paleo.

  4. Kantian Naturalist Kantian Naturalist
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    CharlieM: The whole is the termite mound, nest and all the termites, not just the nest. You can’t get away from thinking in terms of the separate parts. When I say whole, I mean whole. From a hierachical point of view the upper levels include the lower levels, they are not exclusive.

    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.

  5. John Harshman John Harshman
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    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.

    First rule of holes: stop digging.

  6. John Harshman John Harshman
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    says:

    Nonlin.org: Haldane and Kimura killed it in the sixties.

    Haldane?

  7. Alan Fox Alan Fox
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    says:

    Nonlin.org: Darwin used the term “descent with modification” without knowing about genotype and most certainly he was not referring to monozygotic twins diverging after conception. In addition, everyone knew and knows descendants are not identical to either parent but some sort of MESSY mix. Given this “mix” it doesn’t make any sense to talk about “modification” of genotype and/or phenotype.

    If you don’t think evolutionary theory, or Darwinian evolution makes sense, then don’t talk about it. As far as I’m concerned, it’s settled science with excellent explanatory power.

    Most likely Darwin had in mind populations, not individuals, but even there it doesn’t make much sense given you can’t pin down the “modification”. This is like going to Democritus to learn about nuclear physics. It just doesn’t make any sense.

    What Darwin had in mind regarding the agency of heritability is not important these days except to those interested in the history. We now know the agent is (for the vast majority of terrestrial organisms) DNA. Darwin’s insight was to propose common descent as an explanation for observed facts and selection as the agency of change within species.

    My friendly advice is to discard all these concepts that barely make philosophical sense and to stick with the scientific method.

    I’d have to discard evolutionary theory as a good explanation for the diversity of life on Earth when someone thinks of a better explanation, one that better fits the evidence. I’m afraid you are not that someone.

    However, be prepared to find out that in the end you will have to discard “evolution” too

    The sorrow at having to discard a well-loved theory would be outweighed by the joy of hearing about a more accurate theory. Think Newton and Einstein!

  8. Allan Miller
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    says:

    Nonlin.org: Here we go again with the mysterious allusions. What has ‘signal degradation’ to do with “common descent relationship”? And how are ID-ists “all over Shannon information”?

    Mysterious allusions? Like I say, you seem unfamiliar with the subject you presume to critique.

    Genetic sequences are subject to mutation, and hence can reasonably be said to undergo an increase in entropy in the Shannon sense, when comparing a present sequence with a particular prior instance. Such as those possessed by the descendants of a given ancestor. It’s not particularly important, I merely noted the connection between the two strands of the thread.

    As to IDists and Shannon, here is but one example.

  9. Allan Miller
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    says:

    Darwinism was killed by neutral evolution in 1968, and again by gene transfer (a long, slow death commencing in 1928 but only really manifest when phoodoo got to hear about it!), and earlier still when Mendel put paid to Darwin’s dubious speculations about the nature of variation. Its zombie corpse lumbers on.

  10. phoodoo
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    says:

    Allan Miller:
    Darwinism was killed by neutral evolution in 1968, and again by gene transfer (a long, slow death commencing in 1928 but only really manifest when phoodoo got to hear about it!), and earlier still when Mendel put paid to Darwin’s dubious speculations about the nature of variation. Its zombie corpse lumbers on.

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

    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.

    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. 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. 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!

    You skeptics are quite the thinkers, huh?

  11. Corneel Corneel
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    CharlieM: No I didn’t mean that the genes should be the same, I meant the cells should be the same.

    Sorry, but I don’t know what you mean by that. In what respect should the cells be the same? If not the phenotype nor the genotype, then what is left?

    CharlieM: Cell differentiation is not the ultimate cause.

    Agreed of course, but I never said it was.

    CharlieM: To call them details is not to dismiss them. What do you think it means to study something in detail?

    Excellent. So, in what way do the differences between ontogeny and phylogeny argue against your likening of phylogenesis to organismal development? I would say that taking the “details” into consideration severely cripples your implied suggestion that phylogenesis is a coordinated affair.

  12. CharlieM CharlieM
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    says:

    Corneel: Oooh, I just love areas of uncertainty.

    Nice vid BTW.

    Yes, I have enjoyed watching both videos.

    Here are your options:
    1) Be a total wimp, keep whining “it’s soooo complex. We will NEVER understand”, and give up.

    It is precisely because we do understand the processes that have been discovered so far that we can see and understand the complexity. And when even further complexity is revealed we will understand that too.

    We have the potential to understand the complexity at every stage. When it was assumed that a single continuous stretch of DNA coded for a single protein, we understood that. When it was realised that further stretches of DNA were required for control purposes, we understood that. When it was realised that a single stretch of DNA could code for multiple proteins, we understood that. When it was realised that exons and introns existed and that a single stretch of DNA could be used in so many ways in the making of proteins, we understood that. I could go on further about how the level of complexity has been slowly revealed and understood but I’m sure you get the point.

    2) Watch Part 2 that explains some of that stuff.

    As in part 1, much of part 2 is taken up by explaining procedures used by researchers to reveal the complexities involved, and in this it does a good job. It doesn’t actually give any explanation as to how such complexity has arisen other than evolution did it.

    Blind evolution could easily have spanned the leap required to go from prokayote to eukaryote! The differences would not have been that difficult to surmount! I beg to differ.

    Your choice

    I have taken up option 2 and watched the video. Option 1 is no option at all as far as I can see.

  13. Corneel Corneel
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    says:

    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.

    CharlieM: Blind evolution could easily have spanned the leap required to go from prokayote to eukaryote! The differences would not have been that difficult to surmount! I beg to differ.

    Sometimes you sound just like a creationist, you know that 😉

    CharlieM: I have taken up option 2 and watched the video. Option 1 is no option at all as far as I can see.

    Excellent!

  14. Neil Rickert
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    says:

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

    I’m not a Coyne fan, but your rant is ridiculous.

    Yes, reality is complex. Yes, the theory oversimplifies. All theories oversimplify. All history oversimplifies.

    So what?

  15. Alan Fox Alan Fox
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    says:

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

    As you didn’t trouble to supply links, I tried tracking them dow. Not to be found recently at Coyne’s website. But googling your quote finds me an article at Uncommon Descent talking about a book review Coyne wrote for the Washington Post.

    You claim in that article that Coyne is forced to admit:

    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.”

    whearas anyone reading the article rather than DeNews’s distortion piece in UD will see Coyne is merely pointing out that HGT/LGT is common in prokaryotes but much less so in eukaryotes.

    So when you write:

    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.

    It’s somewhat hyperbolic. 😉

    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. 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. 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!

    You skeptics are quite the thinkers, huh?

    You should have a lie down in a darkened room after that.

  16. Rumraket Rumraket
    Ignored
    says:

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

    You didn’t find a single one that qualifies for that description. Nobody is “downplaying the significance” of horizontal gene transfer. What they are doing is explaining that they don’t overturn Darwinian evolution, which is the essentially the fact that variation in populations is subject to natural selection. The existence of HGT does nothing to alter that fact.

    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.”

    Yes. Notice how that’s not downplaying, it’s simply explaining that HGT can potentially make it difficult to trace lineage interrelationships if the genes used have been horizontally tranferred. Again, that does nothing to overturn anything about the role of variation in populations being subject to natural selection. Nor does it overturn the fact that life has evolved. All HGT does is to add another potential source of variation. It’s in essence just another mechanism of mutation. Horizontally transferred genes are still subject to natural selection, and once they have been horizontally tranferred, they are vertically passed off to offspring.

    Your lack of familiarity and education in this subject is really decapitating your efforts to stir up some sort of controversy here, and people who know this stuff can only sit back, laugh, and then facepalm.

    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.

    Yeah if only you can keep repeating this convenient story to yourself enough maybe you can even start believing in it yourself.

    You skeptics are quite the thinkers, huh?

    I’ll take that over being as intensely blinded by personal biases as your posting history indicates.

  17. Mung Mung
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    says:

    phoodoo: You skeptics are quite the thinkers, huh?

    Your first time here?

  18. Mung Mung
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    says:

    John Harshman: First rule of holes: stop digging.

    First rule of debate: have an actual argument.

  19. Mung Mung
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    says:

    Allan Miller: Its zombie corpse lumbers on.

    I prefer to think of it as a Frankenstein monster composed of pieces of the dead theories of the past kept alive by the religious fervor of it’s worshipers. 🙂

  20. Mung Mung
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    says:

    Allan Miller: Genetic sequences are subject to mutation, and hence can reasonably be said to undergo an increase in entropy in the Shannon sense, when comparing a present sequence with a particular prior instance. Such as those possessed by the descendants of a given ancestor.

    Could you explain further? I am familiar with the concept of the entropy of the source, which in this case would be the ancestral sequence, right?

    But I am not familiar with the concept of an “increase in entropy” during transmission from source to receiver. Id like to work that out so I understand it.

  21. Rumraket Rumraket
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    says:

    Mung: I prefer to…

    There’s your problem.

  22. Entropy Entropy
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    says:

    Mung: I prefer to think of it as a Frankenstein monster composed of pieces of the dead theories of the past kept alive by the religious fervor of it’s worshipers.

    While I’d love to think of it as a Frankenstein monster, it’s more like a Theseus’ ship of sorts. Old, poorly informed, hypotheses replaced by new, better informed, ones.

  23. Joe Felsenstein Joe Felsenstein
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    says:

    Confusing. 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. Harshman patiently explains that neutral theory uses two of those phenomena, so it is already covered. Mung and phoodoo then decide that the issue is whether “neutral theory” has refuted “Darwinism”.

  24. John Harshman John Harshman
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    says:

    Mung: First rule of debate: have an actual argument.

    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.

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

  25. Joe Felsenstein Joe Felsenstein
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    says:

    Neutral mutation is a combination of two mechanisms, genetic drift and mutation. But those two were already in John’s list.

  26. Mung Mung
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    Joe Felsenstein: Neutral mutation is a combination of two mechanisms, genetic drift and mutation. But those two were already in John’s list.

    Hi Joe,

    We are talking about this:

    https://en.wikipedia.org/wiki/Neutral_theory_of_molecular_evolution

    Some say that it was this theory that killed Darwinism, that Darwinism has been dead since 1968.

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

  27. Entropy Entropy
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    says:

    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.

    I doubt that the wording “is covered by …” means that they’re one and the same.

  28. Mung Mung
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    says:

    Entropy: I doubt that the wording “is covered by …” means that they’re one and the same.

    Fair enough. Perhaps I misunderstood John’s response to my earlier comment that the two are not the same.

    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.

    Surely random genetic drift is accepted by the Darwinians and was not unknown to them prior to 1968.

    Do you think Mootoo Kimura thought his theory was just a subset of drift?

  29. DNA_Jock
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    says:

    Mung: Hi Joe,

    We are talking about this:

    https://en.wikipedia.org/wiki/Neutral_theory_of_molecular_evolution

    Some say that it was this theory that killed Darwinism, that Darwinism has been dead since 1968.

    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:
    Mung:

    John Harshman: Can you think of any other process that I left out?

    Neutral evolution.

    John:

    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.
    ETA: A little back-story for those not following along over at the Peaceful Science blog. The theory of neutral evolution killed off Darwinism back in 1968. So when John failed to mention neutral evolution I was shocked. Shocked I say.

    [emphasis Jock’s]
    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.

    E2fixlink

  30. Allan Miller
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    says:

    phoodoo,

    I really, sincerely and honestly do not know why HGT is supposed to be a problem. But hey, if you say it’s a problem, I’ll start chewing my arm off with frantic worry.

  31. Nonlin.org
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    says:

    Alan Fox: If you don’t think evolutionary theory, or Darwinian evolution makes sense, then don’t talk about it. As far as I’m concerned, it’s settled science with excellent explanatory power.

    I’d have to discard evolutionary theory as a good explanation for the diversity of life on Earth when someone thinks of a better explanation, one that better fits the evidence. I’m afraid you are not that someone.

    The sorrow at having to discard a well-loved theory would be outweighed by the joy of hearing about a more accurate theory. Think Newton and Einstein!

    Don’t talk about a wrong idea that’s being constantly pushed onto society with catastrophic results to date (eugenics++)?

    Intelligent Design is that explanation and is not just better, but also logical in contrast.

    Hey, at least you declare an open mind. Congratulations. Now, let’s work with that 🙂

    So, does it now make sense why “descent with modification” is illogical? No baseline before descent and no modification after, but a messy mix.

  32. Mung Mung
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    says:

    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.

    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.

    It began in a discussion over at Joshua Swamidass’s blog Peaceful Science in which the claim was made that the term Darwinism was out-dated and should no longer be used because Darwinism is dead, has been dead since 1968, and the cause of it’s death was the neutral theory:

    https://en.wikipedia.org/wiki/Neutral_theory_of_molecular_evolution

    You will find numerous mentions of this in my comments here at TSZ in this thread.

    The first clue can be found here:

    http://theskepticalzone.com/wp/universal-common-descent-dilemma/comment-page-11/#comment-234456

    Hint: Kimura

    The second clue can be found here:

    http://theskepticalzone.com/wp/universal-common-descent-dilemma/comment-page-11/#comment-234487

    Hope that clears things up for you.

  33. CharlieM CharlieM
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    DNA_Jock: Prokaryotic transcription is pretty precise, but less complex. Eukaryotic transcription is not so precise at all; it’s more Rube Goldberg-esque. That’s why it’s a good idea to learn the basics before trying to understand the complexities.

    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?

    CharlieM: So when asked how the genes control development, giving an answer that it is initiated by a couple of “master genes” and pointing me to a wikipedia link is no real answer.

    Well, it might not be a complete answer, but at least it is a start.
    Which [jazz hands] “Oh Lordy me, it’s so complicated!” is not.

    I agree that this is no answer, and neither is, “No matter how complex it gets, don’t worry, blind evolution is well up to the task!”

    Prokaryotes are pretty complex organisms, but the gulf in complexity between them and multi-cellular eukaryotes is immense.

  34. Nonlin.org
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    says:

    Allan Miller: Genetic sequences are subject to mutation, and hence can reasonably be said to undergo an increase in entropy in the Shannon sense, when comparing a present sequence with a particular prior instance. Such as those possessed by the descendants of a given ancestor.

    So this should pose a problem for “evolution”, right? Not for ID though given that external interventions from an open system can easily revert the entropy increase in a closed system. This is like some humans constantly intervening to restore one sample of an old car when another identical sample hasn’t been maintained and therefore turned long ago into scrap.

  35. CharlieM CharlieM
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    says:

    Rumraket:

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

    That’s like saying the mutual attraction of opposite charges in magnets is teleological. If that’s teleological to you, then the concept you have in mind when you use the word teleological is vacuous. It is equivalent to saying “some things are more likely to occur than other things”. Oh gee really?

    No its nothing like that. Why would any other 63 string of amino acids found in living organisms be a target for a 63 string of amino acids in one particular organism?

  36. DNA_Jock
    Ignored
    says:

    Mung,

    ROFL

    My apologies that I screwed up the cross-page link. I have fixed it.
    Here’s where it started
    [Comment 234435]

    John Harshman: Can you think of any other process that I left out?

    Neutral evolution.

    The posts that you are citing are, helpfully enough, your subsequent [234456 and 234487] lame-ass attempts to cover your original mistake.
    Like I said.
    How about you stop?

  37. Allan Miller
    Ignored
    says:

    Mung: Could you explain further? I am familiar with the concept of the entropy of the source, which in this case would be the ancestral sequence, right?

    But I am not familiar with the concept of an “increase in entropy” during transmission from source to receiver. Id like to work that out so I understand it.

    Hey, I don’t want to over egg it; it was a brief thought, barely formed! I was just struck by an analogy with thermodynamic entropy, which tends towards increase. The degradation of the ancestral information during a copying series is of similar character, including the possibility of local exceptions, in the form of molecular homoplasy.

    Still, I’m gratified I’m not the only one to think in these terms.

  38. DNA_Jock
    Ignored
    says:

    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: regulating transcription in a ~3 – 5 million bp genome is much simpler than regulating transcription in a 3 billion bp genome (or in a 133 – 150 billion bp genome: hello marbled lungfish and canopy plants!)
    In particular, in prokaryotes it is relatively easy for a repressor to achieve high site-occupancy and thereby turn off a gene (learn about the lac operon, and lambda repressor). In a larger genome, this becomes problematic. See if you can figure out why…

    I agree that this is no answer, and neither is, “No matter how complex it gets, don’t worry, blind evolution is well up to the task!”

    Well thank the Great Green Arkleseizure nobody claimed that! You seem to be projecting there.

  39. Allan Miller
    Ignored
    says:

    Nonlin.org: So this should pose a problem for “evolution”, right? Not for ID though given that external interventions from an open system can easily revert the entropy increase in a closed system. This is like some humans constantly intervening to restore one sample of an old car when another identical sample hasn’t been maintained and therefore turned long ago into scrap.

    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.

  40. Alan Fox Alan Fox
    Ignored
    says:

    Nonlin.org: Don’t talk about a wrong idea that’s being constantly pushed onto society with catastrophic results to date (eugenics++)?

    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.

    But Darwinian evolution and modern evolutionary theory are alive and well.

    Intelligent Design is that explanation and is not just better, but also logical in contrast.

    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!

    Hey, at least you declare an open mind. Congratulations. Now, let’s work with that 🙂

    Have at it!

    So, does it now make sense why “descent with modification” is illogical?

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

    No baseline before descent and no modification after, but a messy mix.

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

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

  41. Mung Mung
    Ignored
    says:

    DNA_Jock: The posts that you are citing are, helpfully enough, your subsequent [234456 and 234487] lame-ass attempts to cover your original mistake.

    Hilarious really. Why don’t you stop. Suffering from a bout of keiths syndrome today?

    I told you I was talking about the neutral theory but you don’t want to take my word for it and turn the evidence I offer into a conspiracy and cover-up. Get a grip.

    The very first post in response was Allan Miller’s and I immediately mentioned Kimura. I even provided you with the back-story which explains my comment to John about what he left out, and it makes sense. But instead, my response to Allan is the beginnings of a cover-up for a dispute between me and John that had not even formed until later in the thread.

    My explanation is far more credible then your cover-up theory.

  42. DNA_Jock
    Ignored
    says:

    Mung,
    True that Allan was the first to point out your error. “Covered, under drift”.
    Cool ETA backstory about some other blog, bro.

    Also true that you wanted to change the subject to talk about Kimura, (although “Right. Who needs Kimura anyways” doesn’t really explain why you think he is relevant…), but your original comment was nonsensical (and not about Kimura’s neutral theory, even if you intended it to be so). Thus you are attributing to John a goofy claim that he never made. THAT is what you need to cut out.
    A simple, “Gee, I didn’t think that through” would suffice.
    Or would you rather try to argue that ‘drift’ and ‘mutation’ does not cover ‘neutral evolution‘? That would be fun.

  43. Rumraket Rumraket
    Ignored
    says:

    CharlieM: Why would any other 63 string of amino acids found in living organisms be a target for a 63 string of amino acids in one particular organism?

    Shape and charge?

  44. John Harshman John Harshman
    Ignored
    says:

    Nonlin.org: At least according to Swamidass: https://discourse.peacefulscience.org/t/is-evolution-speculation/1324/49

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

  45. John Harshman John Harshman
    Ignored
    says:

    DNA_Jock,
    There is a distinction among neutral theory, the neutral theory, and neutral evolution. Neutral theory is the body of mathematical theory dealing with neutral evolution. The neutral theory is the idea that most molecular evolution happens by neutral evolution. Neutral evolution is the process in which alleles on which zero selection is operating can become fixed purely by genetic drift. Neutral evolution, in other words, is drift in which there is no selection acting, and the rate of fixation equals the rate of mutation and is independent of population size. Drift in which selection is acting is called nearly neutral evolution, and depends strongly on population size. Neutral and nearly neutral evolution are both subsets of genetic drift.

    Mung will doubtless make some irrelevant objection. Get on with it.

  46. Mung Mung
    Ignored
    says:

    John Harshman: Mung will doubtless make some irrelevant objection. Get on with it.

    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?

    Don’t you think it remarkable how the existence of that conversation dovetails nicely with what I have claimed. Boy did I just happen to get lucky that it took place before I made my comment here, is that it?

    Or shall we pretend that the two are unrelated like DNA_Jock insists on doing.

  47. Mung Mung
    Ignored
    says:

    DNA_Jock: Thus you are attributing to John a goofy claim that he never made. THAT is what you need to cut out.

    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.

    Now about your goofy claim … going to apologize?

  48. Mung Mung
    Ignored
    says:

    DNA_Jock: Also true that you wanted to change the subject to talk about Kimura, (although “Right. Who needs Kimura anyways” doesn’t really explain why you think he is relevant…), but your original comment was nonsensical (and not about Kimura’s neutral theory, even if you intended it to be so).

    That I was trying to change the subject is not true. You are wrong about that. My comment to John was about the neutral theory of evolution. Why on earth do you think I even responded to John? Got a theory about that? I have a reasonable explanation for my response to him. What’s yours?

    John asked what he had left out. Can we at least agree that he left out the neutral theory of evolution? So it ought to be at least plausible that is what I was referring to.

    Now factor in the recent conversation at Peaceful Science about the importance of the neutral theory in bringing about the demise of Darwinism and it makes even more sense why I would bring it up. Look how important the neutral theory is!

    My story adds up. These’s no good reason not to take my word that I was in fact talking about the neutral theory.

    The backstory from Peaceful Science explains why Kimura was relevant.

    My original comment was not nonsensical if you factor in the context. Your entire case pretty much hinges on my use of neutral evolution rather than neutral theory of evolution. That an a decided unwillingness on your part to trust that I know better than you what I was thinking and why I wrote what I wrote.

  49. Mung Mung
    Ignored
    says:

    Alan Fox: Please, let’s hear about the explanation from Intelligent Design.

    Goddidit.

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