Common Descent Munged

I come from the Michael Behe school if ID. I accept common descent, by which I mean universal common ancestry. It seems to be the consensus view in science, it seems reasonable to me, and I don’t have any compelling reasons to doubt it.

But could I actually defend my belief in common ancestry if asked? All living organisms share certain features in common. Organisms leave offspring. Therefore, universal common ancestry. That sounds pretty weak, I admit. I need to do better.

I don’t believe that new organisms appear out of thin air, so to speak. I accept that the organisms of today are the offspring of prior organisms. Even young earth creationists accept common descent prior to the flood and common decent after the flood, though they resist the idea of universal common ancestry. I still haven’t figured out how and where they draw the lines though, so why should I draw a line that I cannot defend. Therefore common ancestry. That still sounds pretty weak, I admit. I still need to do better.

So time to hit the books. What are the arguments for universal common ancestry in the books on evolution that I have. Erm… Halp!

Why do folks believe in universal common ancestry and what is the best book on “the evidence for evolution” to refer to in order to find the best arguments in favor of universal common ancestry?

What if it’s not the evidence for the theory of common descent per se that leads people to accept it, but rather how the theory of common descent provides an explanatory framework. Does its explanatory power outweigh the need for evidence for it and do people confuse what it can explain with what constitutes evidence for the theory?

What is the evidence for universal common ancestry and why is it considered evidence for universal common ancestry?

263 thoughts on “Common Descent Munged

  1. This is a very general view…
    What are the common features that make you the believer in universal common ancestry? Be more specific…

  2. J-Mac: What are the common features that make you believer in universal common ancestry? Be more specific…

    DNA. RNA. Protein. The genetic code. Cell membranes. Cell division. Cell metabolism. Cell machinery. To name a few.

    ETA: Transcription. Translation.

  3. But could I actually defend my belief in common ancestry if asked? All living organisms share certain features in common. Organisms leave offspring. Therefore, universal common ancestry. That sounds pretty weak, I admit. I need to do better.

    Yes, it’s amazing how poor your understanding is after over a decade on these issues. It isn’t a matter of “living organisms share certain features in common,” it’s the derivative nature of the clades branching off and sharing homologies that aren’t shared with separated clades. The nested hierarchy, in other words, that would crucify common descent if it didn’t exist, and that no intelligence need observe (and would be expected not to do, generally). It’s birds having eyes that mammals don’t get, and mammals having earbones that birds don’t get, that kind of thing, that an intelligent designer (or more) shouldn’t be stuck with.

    Of course there’s the progression of life in a manner that is essential for evolution, moving from single cells to multicellular marine organisms, later terrestrial organisms, etc., complete with transitionals like the cynodonts.

    I have no idea why Behe thinks it makes sense that life would be limited by evolutionary processes that his Designer transcends.

    It’s basic stuff, that Mung still doesn’t get after being presented with it repeatedly. He’s stuck with weak stuff, mainly because he doesn’t get the most basic facts of evolution.

    Glen Davidson

  4. J-Mac: You are kidding…right?

    Nope. If you know of unique processes that call into question universal ancestry I’m all ears.

  5. Glen, to Mung:

    Yes, it’s amazing how poor your understanding is after over a decade on these issues…

    It’s basic stuff, that Mung still doesn’t get after being presented with it repeatedly.

    That’s the part that fascinates me. How could he be so impervious to learning?

    Mung:

    It seems to be the consensus view in science, it seems reasonable to me, and I don’t have any compelling reasons to doubt it.

    It never occurred to you to learn why it’s the consensus view in science, or to pay attention when others here have explained that, repeatedly, to the Sals, the J-Macs, and the colewds?

  6. Mung,

    You may have noticed us recommending Douglas Theobald’s

    29+ Evidences for Macroevolution

    The Scientific Case for Common Descent

    …oh, about a hundred times or so. Have you ever thought of actually reading it?

    Give it a go. Then, as a bonus, you can read this OP to learn that

    Since common descent IDers accept the reality of common descent, you might be surprised that the evidence for common descent is a problem for them, but it is — and it’s a serious one. Read on for details.

  7. Let’s try to remember that each group of taxa has different evidence of its common descent, though the categories of evidence are mostly the same. For some groups, the evidence is easier to see than for others. This evidence is mostly found not in books but in scientific papers. If you’re interested in some particular group, I could probably suggest what to read.

    As for universal common descent in particular, here’s the one people keep citing every time this comes up. I assume you have never bothered to look at it:

    Theobald D.L. A formal test of the theory of universal common ancestry. Nature 2010; 465:219-223.

  8. John Harshman: As for universal common descent in particular, here’s the one people keep citing every time this comes up. I assume you have never bothered to look at it:

    Theobald D.L. A formal test of the theory of universal common ancestry. Nature 2010; 465:219-223.

    You meant this? http://theobald.brandeis.edu/pdfs/Theobald_2010_Nature_all.pdf

    When you link properly, you are making it less of a bother. Guess you don’t care.

    My objection remains the same. Theobald up front, “However, the ‘universal’ in universal common ancestry is primarily supported by two further lines of evidence: various key commonalities at the molecular level6 (including fundamental biological polymers, nucleic acid genetic material, L-amino acids, and core metabolism) and the near universality of the genetic code.”

    This is like saying: All languages have vowels and consonants (and words and sentences etc.), therefore universal common descent. Kinda demotivates strongly from reading further. But I have read all of it anyway.

  9. J-Mac: If you believe in UCA, you should start with this first…the fundamentals…
    Eukaryotic Cell vs Prokaryotic Cell comparison:

    Or perhaps start reading the paper you yourself once linked to:

    Certain prokaryotes classified as bacteria might look like bacteria but, he insisted,were genetically much different. In fact, their rRNA supported an early separation. Many of these species had already been noted for displaying unusual behavior, such as favoring extreme environments, but no one had disputed their status as bacteria. Now Woese claimed that they formed a third primary group —the archaea- as different from bacteria as bacteria are from eukaryotes.

    then accept deep phylogeny has THREE domains at the bottom , and never use the word prokaryote again.

    If you please

  10. Erik: You meant this? http://theobald.brandeis.edu/pdfs/Theobald_2010_Nature_all.pdf

    When you link properly, you are making it less of a bother. Guess you don’t care.

    My objection remains the same. Theobald up front, “However, the ‘universal’ in universal common ancestry is primarily supported by two further lines of evidence: various key commonalities at the molecular level6 (including fundamental biological polymers, nucleic acid genetic material, L-amino acids, and core metabolism) and the near universality of the genetic code.”

    This is like saying: All languages have vowels and consonants (and words and sentences etc.), therefore universal common descent. Kinda demotivates strongly from reading further. But I have read all of it anyway.

    Good for you. Then you must have realized that a sentence in the introduction is not the test of common descent he’s talking about.

    Still, what he describes in that sentence is not at all similar to “vowels and consonants”. You might say that of DNA and L-amino acids, but certainly not of the fundamental polymers and core metabolism, which are more like particular words or books.

  11. keiths: 29+ Evidences for Macroevolution

    “Joe Felsenstein Joe Felsenstein Post authorAugust 23, 2017 at 1:45 am
    J-Mac: All of them, all the time.

    You seem to think that it takes some special category of change to make a new species. And that “ordinary” change isn’t that.

    It’s the old “microevolution is different from macroevolution” argument

    http://theskepticalzone.com/wp/betting-on-the-weasel/comment-page-13/

    Who to believe, if 2 evolutionists are confused what constitutes evolution and can’t agree on what evolution is?

    That’s why I took up this hobby…to try to find 2 evolutionists that agree on 2 major things about evolution other than evolution itself…

    And evolution is apparently alive and well…apparently

    https://www.youtube.com/watch?v=FdghRwWfaOQ

  12. Argumentum ad Badanalogium

    I don’t know what the linguistic equivalent is for the universal assignment of, say, UUA and Leucine, but it doesn’t much matter if there is one or not.

    50+ positions of the genetic code are invariant. Most of the variants are STOPs in at least one species – a fact which is susceptible to an evolutionary explanation, assuming common descent, but no equivalent explanation suggests itself on common design.

    It’s not just the assignments per se. The enzymes underlying the assignment fall into two structural and reaction-type classes, taking 10 acids each. Again, supports common descent, at least from LUCA onwards. There is no clear Design reason for two enzymatic solutions. There’s no particular evolutionary one either, but one can see how, having arisen (by magic or ‘chance’), common descent might preserve it.

    One can say all these are compatible with ‘common design’. But that’s just saying ‘anything I see is compatible with Design’. There is no reason for it to be associated with common design (other than a requirement for an alternative to descent with the word ‘common’ in it). But there are reasons one can associate with common descent.

  13. J-Mac,

    That’s why I took up this hobby…to try to find 2 evolutionists that agree on 2 major things about evolution other than evolution itself…

    Whereas any two ID/Creationist/frontloaded quantum hooplaists are in absolute agreement on what happened instead.

  14. John Harshman: Then you must have realized that a sentence in the introduction is not the test of common descent he’s talking about.

    Yes, except that this particular sentence is employed as particular proof in its own right.

    John Harshman: Still, what he describes in that sentence is not at all similar to “vowels and consonants”. You might say that of DNA and L-amino acids, but certainly not of the fundamental polymers and core metabolism, which are more like particular words or books.

    “Languages that have books have common descent.” How is this any better?

  15. Allan Miller: I don’t know what the linguistic equivalent is for the universal assignment of, say, UUA and Leucine, but it doesn’t much matter if there is one or not.

    To keep to things that matter, maybe try to make some connection to Theobald’s article. None of the terms you employ appears in his article, so it looks like you are making stuff up as you go. Theobald has a Harshman-approved article out, so maybe you can summarize what he proved in your opinion and how.

    Allan Miller: One can say all these are compatible with ‘common design’. But that’s just saying ‘anything I see is compatible with Design’. There is no reason for it to be associated with common design (other than a requirement for an alternative to descent with the word ‘common’ in it). But there are reasons one can associate with common descent.

    Reasons such as?

  16. Theobald D.L. A formal test of the theory of universal common ancestry. Nature 2010; 465:219-223.

    So where is the explanation for the evolution of orphan systems? Does he only look at sequences common to all organisms? That’s sampling bias, and sampling bias is junk science.

  17. Allan Miller:
    J-Mac,

    Whereas any two ID/Creationist/frontloaded quantum hooplaists are in absolute agreement on what happened instead.

    Don’t you claim that evolution is science? So why is there so much contradictory beliefs?

    BTW: If you can’t defend what you think is science…counterattack on creationism make your own beliefs look impotent…not to mention unscientific…lol

  18. Erik,

    To keep to things that matter, maybe try to make some connection to Theobald’s article. None of the terms you employ appears in his article, so it looks like you are making stuff up as you go.

    I think you’ll find that my observations on the genetic code are not made up. What a ridiculous slur! I suspect an attempt to goad, as you do. Nor am I obliged only to link it to Theobald, since his reference to the universal code is in passing.

    Reasons such as?

    Oh, so now you want to talk about it. Make your mind up.

    Substitution anywhere other than at a STOP would lead to wholesale replacement of that codon. That would be far more damaging to an organism than reassignment of a STOP, which would merely add a ‘tail’ to the protein of a length dependent upon the extent to which the codon matrix is occupied by remaining non-STOPs.

  19. J-Mac,

    Don’t you claim that evolution is science? So why is there so much contradictory beliefs?

    There isn’t – at least nowhere near to the extent you imagine.

    BTW: If you can’t defend what you think is science…counterattack on creationism make your own beliefs look impotent…not to mention unscientific…lol

    Oh, how rich. Someone whose whole schtick is attack, rather than defence, whines when someone else questions their own ‘science’.

  20. stcordova,

    sampling bias is junk science.

    Let’s apply that to the distribution of C14 in carbon-bearing deposits then, shall we?

  21. Allan Miller: Substitution anywhere other than at a STOP would lead to wholesale replacement of that codon. That would be far more damaging to an organism than reassignment of a STOP, which would merely add a ‘tail’ to the protein of a length dependent upon the extent to which the codon matrix is occupied by remaining non-STOPs.

    So you take it that design or creation (or any other non-evolutionary mechanism) must operate by replacement of codons?

    It would be nice to see if you have a concrete example – an observably reassigned STOP during a chain of speciations, reasonably lengthy enough chain in order to qualify as common descent, not mere variation of (the same) species.

  22. Rumraket: That doesn’t call it into question, it is another line of evidence in favor of it. In fact, for some of the code variants with their minor differences, we can see evolutionary remnants of how those minor code differences evolved.

    The genetic code evolved…huh? You don’t say…?

    “…the genetic code is universal, all but identical across animals, plants, fungi, bacteria, archaea and viruses. The 64-word dictionary, by which three letter DNA words are translated into 20 amino acids and one punctuation mark, which means ‘start reading here’ or ‘stop reading here,’ is the same 64-word dictionary wherever you look in the living kingdoms (with one or two exceptions too minor to undermine the generalization)…”

    The reason is interesting. Any mutation in the genetic code itself (as opposed to mutations in the genes that it encodes) would have an instantly catastrophic effect, not just in one place but throughout the whole organism. If any word in the 64-word dictionary changed its meaning, so that it came to specify a different amino acid, just about every protein in the body would instantaneously change, probably in many places along its length. Unlike an ordinary mutation…this would spell disaster…”-Richard Dawkins The Greatest Show On Earth (2009, p. 409):

    So far we have 31 different genetic codes and counting…Since according to Joe Felsenstein we have 10 billion (not 10 million) species on the earth, how many more genetic code variants are we expecting to find if we continue to go at this pace?

    I think we are going to have to look for a new evolutionary mechanism for the genetic code itself…since the current one “…would have an instantly catastrophic effect..” as the god of evolution Richard Dawkins pointed it out himself lol

    All we can do is watch Darwin’s faithful to continue to pretend that all is well and continue to keep on the respirator the long-dead-theory that atheism-driven materialism needs it so much for their faithful…

  23. Erik,

    So you take it that design or creation (or any other non-evolutionary mechanism) must operate by replacement of codons?

    No. But replacement of codons by STOP is susceptible to an evolutionary explanation (given above). If you have a ‘design’ explanation for variant codes, and their clustering of differences on STOP, by all means present it.

    It would be nice to see if you have a concrete example – an observably reassigned STOP during a chain of speciations, reasonably lengthy enough in order to qualify as common descent, not mere variation of (the same) species.

    How would that affect the argument? One can make a perfectly reasonable supposition that wholeseale substitution would be more damaging than a terminal tail, without having to watch it happening to ‘prove’ it. After all, this is right up the Creationist’s alley when they argue that proteins are unevolvably ‘brittle’.

  24. J-Mac,

    I think we are going to have to look for a new evolutionary mechanism for the genetic code itself…since the current one “…would have an instantly catastrophic effect..” as the god of evolution Richard Dawkins pointed it out himself lol

    Nope, we don’t need a ‘new mechanism’. Gradual assignment of STOPs is a perfectly feasible mechanism that circumvents Dawkins’s ‘catastrophe’ (the catastrophe which Erik now wants me to demonstrate before he’ll accept it even in principle. A curious state of affairs: you accept it without murmur, Erik wants it to happen before his very eyes. Both because those contradictory positions suit your particular respective purposes: disagreeing with evolutionists. Funny.)

    It explains the clustering of modern variants around STOP into the bargain.

  25. Allan Miller: No. But replacement of codons by STOP is susceptible to an evolutionary explanation (given above). If you have a ‘design’ explanation for variant codes, and their clustering of differences on STOP, by all means present it.

    Small steps, please. First tell me how you tell the difference between a reassignment and a substitution.

    Allan Miller: How would that affect the argument? One can make a perfectly reasonable supposition that…

    Supposition? This makes all the difference to the argument. If all you have is supposition, you don’t even have an argument.

  26. phoodoo,

    Oh bullshit, support that statement.

    Don’t be stupid. I have to find out the precise extent to which J-Mac imagines there is dispute, then prove for every instance that there is a sufficiency of consensus to avoid the charge? What’s the threshold? I’m a busy man, you know.

    It is perfectly possible for me to make that assertion, because that is how I perceive the matter. You and J-Mac perceive the matter differently … so what? You don’t buy any of it anyway, so what’s it matter?

  27. J-Mac,

    Yea, I had this drawn out conversation with Rumraket, challenging that same claim, that the genetic code evolves. Rumraket event tried to provide specific examples of the code evolving, wouldn’t you know. He made all kinds of amazing claims in that thread, along with a good deal of attempts at literature bluffing hoping that no one would notice, if he buried his point deep enough in uninteresting and irrelevant technical data on bacteria.

    But I noticed.

    There is no evidence for the evolution of the genetic code. But I do love one of the theories, they call it The Frozen Accident Theory. Its a perfect name, especially for the regulars here at TSZ, who positively bust a nut anytime you refer to the mechanisms of evolution as an accident.

    “No one believes in accidents, that is a caricature!” *

    *Quote-Every evolutionist on this site, at one time or another.

  28. Allan Miller,

    Then why, when J Mac asked why there are so many contradictory beliefs, did you claim there aren’t?

    Allan Miller:
    phoodoo,

    Don’t be stupid. I have to find out the precise extent to which J-Mac imagines there is dispute, then prove for every instance that there is a sufficiency of consensus to avoid the charge? What’s the threshold? I’m a busy man, you know.

    It is perfectly possible for me to make that assertion, because that is how I perceive the matter. You and J-Mac perceive the matter differently … so what? You don’t buy any of it anyway, so what’s it matter?

  29. phoodoo,

    Then why, when J Mac asked why there are so many contradictory beliefs, did you claim there aren’t?

    I said the extent of dispute is not nearly as great as he clearly imagines. That is a more subtle position than your phrasing. You want me to go on some fool’s errand to gather data in support of something I did not even say. And again: why? It’s how I perceive the matter.

  30. Mung,

    Nope. If you know of unique processes that call into question universal ancestry I’m all ears.

    The accuracy of DNA repair mechanisms. How is the variation generated to get the diversity we see? If we measure 2 randomly selected humans we get .1% commonality in DNA. Where is the genetic variation coming from?

  31. Erik,

    Small steps, please. First tell me how you tell the difference between a reassignment and a substitution.

    A substitution is a change of one codon’s amino acid to another.
    A reassignment would be changing an unassigned codon – functionally, a STOP – to code for an amino acid.

    Supposition? This makes all the difference to the argument. If all you have is supposition, you don’t even have an argument.

    Ah, typical word-gaming. Never mind the concepts, peck at the words. Try ‘argument’ then. Or ‘case’. I dunno. Is this vital to your understanding?

    Or chew on this; synonyms of ‘supposition’ are: belief, surmise, idea, notion, suspicion, conjecture, speculation, view, inference, theory, thesis, hypothesis, postulation, guess, guesswork, feeling, hunch, assumption, presumption.

    Some of those senses are less applicable than others. But If one truly feels that one cannot make an argument without any of those senses, one is probably going to prove to be too much like hard work to converse with.

    One word. Jeez, this place!

  32. If you know of unique processes that call into question universal ancestry I’m all ears.

    I don’t, but I believe a process exists. In contrast UCA-ists (Universal Common Ancestry believers) claim they know, when in fact it is only a belief that ignores the need of miracles to make UCA feasible.

    Regarding the genes in Theobald’s analysis, did he bother to try to explain the presence on complex processing of splicesomal introns unique to one group of genes. Did he just “cherry pick” or should I say “exon pick” sequences and then run his computation. Cherry picking is junk science.

    Splicesomal introns need spliceosomes to make them work.

    https://evolutionnews.org/2013/09/the_spliceosome_1/

    The spliceosome has been described as one of “the most complex macromolecular machines known,” “composed of as many as 300 distinct proteins and five RNAs” (Nilsen, 2003). The animation above reveals this astonishing machine at work on the precursor mRNA, cutting out the non-coding introns and splicing together the protein-coding exons.
    Spliceosome.jpgIntrons (which, unlike exons, do not code for proteins) can be of considerable length in higher eukaryotes, even spanning many thousands of bases and sometimes comprising some 90% of the precursor mRNA. In contrast, lower eukaryotes such as yeast possess fewer and shorter introns, which are typically fewer than 300 bases in length. Since introns are the non-coding segments of genes, they are removed from the mRNA before it is translated into a protein. This is not to say, of course, that introns are without important function in the cell (as I discuss here).
    Comprising the spliceosome, shown at right (excerpted from Frankenstein et al., 2012)[1] are several small nuclear ribonucleoproteins (snRNPs) — called U1, U2, U4, U5 and U6 — each of which contains an RNA known as an snRNA (typically 100-300 nucleotides in length) — and many other proteins that each contribute to the process of splicing by recognizing sequences in the mRNA or promoting rearrangements in spliceosome conformation. The spliceosome catalyzes a reaction that results in intron removal and the “gluing” together of the protein-coding exons.

  33. I think I am ready to believe in Darwinian evolution, when someone can just give a detailed description of the random mutations that go from a creature with arms, to a lobster with two snapping claws, and the joints and muscles to make it work. That isn’t asking much from the theory is it?

    What does the first accident look like? How much advantage do you get from it?

  34. Corneel: then accept deep phylogeny has THREE domains at the bottom , and never use the word prokaryote again.

    So what’s the evidence for shared ancestry among the three domains at the bottom? IOW, what’s underneath the bottom, or holding up the bottom, if anything?

  35. John Harshman: Let’s try to remember that each group of taxa has different evidence of its common descent, though the categories of evidence are mostly the same. For some groups, the evidence is easier to see than for others.

    John, even young earth creationists accept common descent within groups. I’m talking about UNIVERSAL common ancestry.

    John Harshman: As for universal common descent in particular, here’s the one people keep citing every time this comes up. I assume you have never bothered to look at it:

    I ask for books that cover the evidence for universal common ancestry and you give me a paper. Gee thanks.

    Is it just not covered in books on the evidence for evolution? Does Coyne cover it in Why Evolution is True?

  36. The relationship of the exon with the spliceosomal intron is like this with the “X” for the exon and the “i” for the intron. 1 part exon to 10 parts intron is a good ballpark figure in terms of the number of DNA bases:

    iiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiii

    So how did Theobald account for this “poof” entry in his computation. The ancestor gene would have looked like:

    XXXXXXXXXX

    that suddenly evolved into

    iiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiiiiiiiiXiiiii

    That doesn’t look like the gene gradually evolved with a few mutations here and there does it? So much for the gradually branching tree. Cherry picking indeed!

    Like I said, UCAists only pretend their theory doesn’t require statistical miracles.

  37. stcordova,

    That doesn’t look like the gene gradually evolved with a few mutations here and there does it?

    No, it doesn’t. It looks like insertion of ‘selfish’ sequence, and gradual elongation in the gap, protected from mutational effect by the splicing mechanism.

    But its not relevant to Theobald anyway, any more than the genes that make a redshank’s legs red.

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