Common Design vs. Common Descent

I promised John Harshman for several months that I would start a discussion about common design vs. common descent, and I’d like to keep my word to him as best as possible.

Strictly the speaking common design and common descent aren’t mutually exclusive, but if one invokes the possibility of recent special creation of all life, the two being mutually exclusive would be inevitable.

If one believes in a young fossil record (YFR) and thus likely believes life is young and therefore recently created, then one is a Young Life Creationist (YLC). YEC (young earth creationists) are automatically YLCs but there are a few YLCs who believe the Earth is old. So evidence in favor of YFR is evidence in favor of common design over common descent.

One can assume for the sake of argument the mainstream geological timelines of billions of years on planet Earth. If that is the case, special creation would have to happen likely in a progressive manner. I believe Stephen Meyer and many of the original ID proponents like Walter Bradley were progressive creationists.

Since I think there is promising evidence for YFR, I don’t think too much about common design vs. common descent. If the Earth is old, but the fossil record is young, as far as I’m concerned the nested hierarchical patterns of similarity are due to common design.

That said, for the sake of this discussion I will assume the fossil record is old. But even under that assumption, I don’t see how phylogenetics solves the problem of orphan features found distributed in the nested hierarchical patterns of similarity. I should point out, there is an important distinction between taxonomic nested hierarchies and phylogenetic nested hierarchies. The nested hierarchies I refer to are taxonomic, not phylogenetic. Phylogeneticsits insist the phylogenetic trees are good explanations for the taxonomic “trees”, but it doesn’t look that way to me at all. I find it revolting to think giraffes, apes, birds and turtles are under the Sarcopterygii clade (which looks more like a coelacanth).

Phylogeny is a nice superficial explanation for the pattern of taxonomic nested hierarchy in sets of proteins, DNA, whatever so long as a feature is actually shared among the creatures. That all breaks down however when we have orphan features that are not shared by sets of creatures.

The orphan features most evident to me are those associated with Eukaryotes. Phylogeny doesn’t do a good job of accounting for those. In fact, to assume common ancestry in that case, “poof” or some unknown mechanism is indicated. If the mechanism is unknown, then why claim universal common ancestry is a fact? Wouldn’t “we don’t know for sure, but we believe” be a more accurate statement of the state of affairs rather than saying “universal common ancestry is fact.”

So whenever orphan features sort of poof into existence, that suggests to me the patterns of nested hierarchy are explained better by common design. In fact there are lots of orphan features that define major groups of creatures. Off the top of my head, eukaryotes are divided into unicellular and multicellular creatures. There are vetebrates and a variety of invertebrates. Mammals have the orphan feature of mammary glands. The list could go on and on for orphan features and the groups they define. Now I use the phrase “orphan features” because I’m not comfortable using formal terms like autapomorphy or whatever. I actually don’t know what would be a good phrase.

So whenever I see an orphan feature that isn’t readily evolvable (like say a nervous system), I presume God did it, and therefore the similarities among creatures that have different orphan features is a the result of miraculous common design not ordinary common descent.

3,738 thoughts on “Common Design vs. Common Descent

  1. keiths: Bill, study John’s explanation, along with the trees, until you understand what’s going on.

    In other words, go away and never come back?

  2. John:

    In other words, go away and never come back?

    That is indeed the most likely outcome, if Bill actually follows my instructions. 🙂

  3. colewd: In every case in the Berkeley diagram the common ancestor is not identified.

    Common ancestors are never identified. If they did, they might be susceptible to testing. Isn’t that convenient?

  4. colewd: Does this mean you believe that all the diversity of life is the result of reproduction with random change driving diversity … ?

    No, it does not mean that. But neither does it exclude the Wagner Effect. To the everlasting horror of Petrushka and keiths.

    … or is their room for guided mutations?

    Yes, the actions or influence of a guiding intelligence cannot be excluded.

  5. I counted more than 15 areas.

    Jesus, Mung. How did you manage to fuck that up?

    You can even figure out, from first principles, that the number must be 15.

  6. keiths: You can even figure out, from first principles, that the number must be 15.

    Maybe you should learn how to count before appealing to first principles!

    Here’s how I managed, since you’ll probably never figure it out on your own. I counted as an area everything that met the definition of an area.

    Still confused?

  7. Mung,

    It doesn’t take a genius to figure out that John was talking about the numbered areas within Sal’s flower.

    But it’s well beyond you, apparently.

  8. keiths: It doesn’t take a genius to figure out that John was talking about the numbered areas within Sal’s flower.

    I am beyond genius. 🙂

    It doesn’t take a genius to figure out that the numbers within Sal’s flower aren’t there to number the areas. If that were the case there would be at least 10,660 areas. Duh.

    If we wanted to number the areas all we’d need is to number them 1 through 15, according to your theory. But your theory stinks.

    You counted the number of numbers, I counted the number of areas. I am beyond genius. You’re not even an abacus.

  9. Mung,

    You are subtracting value from the discussion, as usual, by raising dumb (and bogus) objections that completely miss the point.

    Why bother?

  10. keiths: Why bother?

    Intellectual honesty. There are, in fact, more than 15 areas in the diagram.

    Instead of arguing against what is so blazingly obvious to anyone who is not a slow fourth grader, why not agree that there are more than 15 areas and then argue that the fact that there are more than 15 areas is irrelevant?

  11. keiths: LMFAO.

    I knew you would appreciate that!

    You’re arguing with John over who is the most honest. As if it matters.

    You won’t go to hell for being a liar. Trust me. 🙂

  12. You’re arguing with John over who is the most honest.

    Huh? You’re arguing with all the people who knew exactly what John was talking about, without any help.

  13. Mung: You’re arguing with John over who is the most honest.

    keiths: Huh?

    wow. you simply can’t be this clueless. It took place right here in this thread. You had honesty on your side. John’s position, somehow, was less honest than yours.

    Have you forgotten already?

  14. Mung,

    It is stupid, and very Munglike, to appeal to “intellectual honesty” to explain why you disagreed with John, who was correctly (and honestly) talking about the 15 numbered areas within Sal’s flower.

    Give it up. You’re only subtracting more value from the discussion.

  15. keiths: Give it up. You’re only subtracting more value from the discussion.

    But as someone who appreciates intellectual honesty, I must continue to point out that the numbers do not number the areas. The numbers number something else. And even John knows what the numbers number. But not keiths. He thinks the numbers number the areas. Absurd.

    There are areas that contain more than one number. All an honest person needs to do is look at the colors and the borders which the diagram uses to delineate the areas. The colors and the borders delineate the areas, not the numbers.

    Each number is in at least one area. But there are numbers which are within more than one area. It’s so freaking obvious that it ought to go without saying.

  16. Mung: I really wish you’d make up your mind. That imperfect reproduction just is evolution was your earlier claim. Are you now walking that back, having understood how silly it is?

    My two claims are not in any way in conflict.

    Rumraket: Evolution happens because organisms imperfectly reproduce.
    Rumraket: Imperfect reproduction is an instance of evolution.

    At no point did me saying one of these imply the other was not the case, or contradict it in any way.

    Traveling happens because people move from location A to location B by whatever means.
    People moving by car from location A to location B is an instance of traveling.

    No conflict.

  17. stcordova: A phylogenetic tree may not be real! For all you know it is an artifact of your imagination, not reality.

    That’s why you can test phylogenies by constructing more of them from independent data sets. If the same method keeps coming up with a very similar tree using an entirely different set of data, chances are the phylogeny is real. And by “chances are”, with a 36 taxon phylogeny there are 3,3×10^49 possible ways to arrange a tree that connects them. If you keep coming up with a similar tree for different data sets, that is an unfathomable statistical confirmation that the tree is a reality.

    Back to Theobald: http://www.talkorigins.org/faqs/comdesc/section1.html#independent_convergence
    “Prediction 1.3: Consilience of independent phylogenies
    Here we commence to beat Pauling’s poor 40-year dead horse. If there is one historical phylogenetic tree which unites all species in an objective genealogy, all separate lines of evidence should converge on the same tree (Penny et al. 1982; Penny et al. 1991; Zuckerkandl and Pauling 1965). Independently derived phylogenetic trees of all organisms should match each other with a high degree of statistical significance.

    Well-determined phylogenetic trees inferred from the independent evidence of morphology and molecular sequences match with an extremely high degree of statistical significance. Many genes with very basic cellular functions are ubiquitous—they occur in the genomes of most or all organisms. An oft-cited example is the cytochrome c gene. Since all eukaryotes contain the gene for this essential protein, neither its presence nor its function correlates with organismal morphology. Additionally, because of the fact of DNA coding redundancy, parts of certain DNA sequences have absolutely no correlation with phenotype (e.g. certain introns or the four-fold degenerate third-base position of most DNA codons). Due to these two aspects of certain DNA sequences, ubiquity and redundancy, DNA sequences can be carefully chosen that constitute completely independent data from morphology. (See point 17 and 18 for more background about the molecular sequence evidence and for more detail about how it is independent of morphology.) The degree of phylogenetic congruence between these independent data sets is nothing short of incredible.”

  18. stcordova: Genes poof into existence in your model

    Sal, they’re mostly gene duplications. In the paper from which you got that diagram, the authors count a duplication as a gene-gain.

  19. Rumraket,

    No conflict.

    And a typical instance of Mung’s value subtraction. It didn’t advance the discussion in any way. It was just Mung trying, and failing, to find a gotcha.

    Sometimes I actually feel sorry for Mung. Imagine how desperate you’d need to be to raise objections like that one, or to pretend that John had miscounted the numbered areas in Sal’s flower.

    Meanwhile evolutionary theory keeps winning, and ID keeps losing.

  20. Rumraket, to Sal:

    And by “chances are”, with a 36 taxon phylogeny there are 3,3×10^49 possible ways to arrange a tree that connects them. If you keep coming up with a similar tree for different data sets, that is an unfathomable statistical confirmation that the tree is a reality.

    It’s amusing to see Sal — a self-styled gambling expert — betting against such stupendous odds.

  21. Mung: Common ancestors are never identified. If they did, they might be susceptible to testing. Isn’t that convenient?

    What does that even mean, to test a common ancestor? Suppose we found some fossil species that was a good candidate for the common ancestor of humans and chimpanzees. What kind of “test” would you do with it?

    Common ancestors are not identified, not because they don’t exist, but because that sort of relationship status cannot be inferred from a fossil. If scientists simply claimed some fossil to be an ancestor, that would actually be dishonest. Because we have no way of knowing that. If you look around you in the world, most species that exist are just one among a huge set of very similar-looking organisms. With a random and very small fraction of them turning fossils from this diversity, it would be very unlikely that among it there was an actual ancestor to a species living 30 million years later. And then combining this with the gradual loss of fossils to erosion, and the odds of a paleontologist finding any particular fossil organism exposed on the surface, the odds of finding an actual ancestor becomes astronomical.

    So it’s not that they don’t exist. They probably do. We might even have some in museums. We just can’t claim to know that they really are on the lineage that lead to anything that exists today. The odds are against it, so the most honest thing you can do is just to depict them as extinct sister taxons in a cladogram.

    With regards to “testing” ancestors: Did you know scientists can reconstruct ancestor gene-sets using phylogenetics, and even ancestral molecules from which entire families of proteins have evolved? And from these, they can some times even infer the sort of metabolism it had. And with the inferred molecular sequences, the ancestral molecules can be re-made in the laboratory and tested for function, stability and so on? And with that data, combined with information about their metabolism and their relationships to other organisms, scientists can infer what kind of environments the species lived in and what it ate.

    This data can then be compared to geological and astronomical data. What was the Earth like hundreds of millions to billions of years ago? How much oxygen was there? What was the average temperature? What was the local climate? And so on and so forth. IIRC a well known example is that the rise in oxygen in Earth’s atmosphere has been correlated with the rise of oxygenic photosynthesis, for example.

    These are ways to test inferences from phylogenetics, by comparing data from different fields of investigation. Even without having the actual direct ancestor

  22. John Harshman,

    With you diagram of gene loss and gene addition, you act as if I didn’t even address that point earlier, and I even used fashionable jargon like “Incomplete Lineage Sort”! Did you miss addressing the problem with that explanation which I pointed out? Err, as in the larger the number of species sampled, the larger the gene the ancestors had to carry.

    In view of the the other problems I identified which you never addressed, it looks like common descent is defended by hand waves and avoidance of contrary data points.

    But you yourself expressed the sentiment. There is not gap of difficulty that would persuade you common descent is false because some cherry picked data points form a nested hierarchical structure that can be hypothetically generated by random mutation and common descent provided the pattern is consistent with random mutation which I pointed out is naïve given that genes are functionally polyconstrained. The cherry picking avoids the necessary POOF of orphan systems that are needed.

    One can create nested hierarchies based on POOFED orphan systems just as easily. Linnaeus essentially did as much long before Darwin.

  23. stcordova,

    One can create nested hierarchies based on POOFED orphan systems just as easily. Linnaeus essentially did as much long before Darwin.

    Good grief! You mean the pattern existed already? I’m shocked, shocked I tell you.

  24. colewd,

    Thanks. In every case in the Berkeley diagram the common ancestor is not identified. What are your thoughts here?

    It doesn’t need to be.

    That one existed is strongly supported by the data – particularly, to repeat my tedious refrain, if one looks at molecular data. If all members of a given clade share a SINE insert at a given position, do I need the ancestor with the SINE insert at that position in order to infer that the ancestor in fact had the SINE insert at that position? It’s a ‘nice-to-have’, but even without it one has a reasonable hypothesis, with no viable rivals, that what one is looking at at that site in that clade is, in fact, the ancestor’s DNA sequence, give or take a mutation or two.

  25. stcordova,

    Unlike the real thing. 🙂 Remember this:

    Yes, that’s a Venn diagram that isn’t a nested hierarchy. The claim is not that the only way to draw sets in biology is by nesting.

    Consider: could you draw a nested hierarchy, or any other set of subsets, if there were no differences between organisms? You wish to deny the hierarchy based upon the fact that there is change – an interesting gambit.

  26. stcordova:
    With you diagram of gene loss and gene addition, you act as if I didn’t even address that point earlier, and I even used fashionable jargon like “Incomplete Lineage Sort”!Did you miss addressing the problem with that explanation which I pointed out?Err, as in the larger the number of species sampled, the larger the gene the ancestors had to carry.

    That’s right, you didn’t address the point earlier, at least not sensibly. Your use of incomplete lineage sorting was incorrect, and it isn’t true that the ancestral genome had to be large. You had forgotten that genes are gained as well as lost.

    In view of thethe other problems I identified which you never addressed, it looks like common descent is defended by hand waves and avoidance of contrary data points.

    You never identified any problems. All your supposed problems are either imaginary or irrelevant to the question.

    But you yourself expressed the sentiment.There is not gap of difficulty that would persuade you common descent is false because some cherry picked data points form a nested hierarchical structure that can be hypothetically generated by random mutation and common descent provided the pattern is consistent with random mutation which I pointed out is naïve given that genes are functionally polyconstrained.The cherry picking avoids the necessary POOF of orphan systems that are needed.

    I don’t know what sentiment you think I expressed, but none of that is relevant to common descent. As usual, you have confused the source of mutation with the source of nested hierarchy. We could go into why your claims about the source of mutation are wrong, but I prefer not to encourage your irrelevancies.

    One can create nested hierarchies based on POOFED orphan systems just as easily.Linnaeus essentially did as much long before Darwin.

    “Create”? Are you now denying that the hierarchy is real? And of course Linnaeus did it, but can you explain why that hierarchy existed for Linnaeus to find? That’s the supposed subject here, you know.

  27. stcordova: One can create nested hierarchies based on POOFED orphan systems just as easily. Linnaeus essentially did as much long before Darwin.

    I guess he was just dogmatically committed to evolution.

    Or what?

    It’s bizarre how you have to deny the patterns that other creationists discovered.

    Glen Davidson

  28. The best thing about Sal’s comment is his pride at having used a bit of technical jargon:

    …and I even used fashionable jargon like “Incomplete Lineage Sort”!

    And he got it wrong.

  29. Mung,

    Sure it did, by pointing to Sal’s failed “dazzle them with jargon and diagrams” approach. That might work with his “subscribers”, but not with folks who actually understand the science.

  30. Mung:
    So, to recap, just to keep the record straight.

    I accept a nested hierarchy. I accept common descent. I think “common design” as an explanation for the nested hierarchy is silly and pretty much meaningless. I’ve seen nothing in this thread to change my mind. Sorry Sal.

    I don’t know whether the nested hierarchy is universal. I don’t think that evolution “predicts” a nested hierarchy. And neither of those is necessary for life to still share a common ancestor. I don’t therefore see anything internally inconsistent in my position.

    Comments?

    You’ve agreed that reproduction with variation (descent with modification) produces branching
    reproduction with variation, as already pointed out, is evolution, and branching produces binary trees and nested hierarchies.

    Ergo, evolution predicts the nested hierarchy, and a nested hierarchy of organisms that are the result of reproduction with variation (descent with modification) implies common descent so you are indeed a conventional evolutionist.

  31. dazz: You’ve agreed that reproduction with variation (descent with modification) produces branching
    reproduction with variation, as already pointed out, is evolution, and branching produces binary trees and nested hierarchies.

    Ergo, evolution predicts the nested hierarchy, and a nested hierarchy of organisms that are the result of reproduction with variation (descent with modification) implies common descent so you are indeed a conventional evolutionist.

    I have to disagree. HGT is quite real. So ONLY a mechanism of inheritance produces a nested hierarchy. Start introducing not only HGT, but various CRISPR gene splicing, direct DNA modification, etc. violate that mechanism. And even if you insist that human gene manipulation isn’t “evolution”, nonetheless not all phenotypical changes result from inheritance alone.

  32. Flint: I have to disagree. HGT is quite real. So ONLY a mechanism of inheritance produces a nested hierarchy. Start introducing not only HGT, but various CRISPR gene splicing, direct DNA modification, etc. violate that mechanism. And even if you insist that human gene manipulation isn’t “evolution”, nonetheless not all phenotypical changes result from inheritance alone.

    I know there’s more to evolution than just vertical inheritance, not like that hasn’t been addressed by those in the know here already.

  33. dazz: I know there’s more to evolution than just vertical inheritance, not like that hasn’t been addressed by those in the know here already.

    I know. But non-vertical inheritance doesn’t produce nesting.

  34. dazz, to Mung:

    You’ve agreed that reproduction with variation (descent with modification) produces branching reproduction with variation, as already pointed out, is evolution, and branching produces binary trees and nested hierarchies.

    Ergo, evolution predicts the nested hierarchy, and a nested hierarchy of organisms that are the result of reproduction with variation (descent with modification) implies common descent so you are indeed a conventional evolutionist.

    The failure to distinguish between the actual nested hierarchy and inferred nested hierarchies creates a lot of confusion in these discussions. Branching descent does indeed generate a nested hierarchy, as a simple matter of logic. That hierarchy may or may not be inferable, however. Whether it’s inferable depends on other things such as the amount of horizontal transfer and the rate and nature of the genetic changes.

    This is at the root of my disagreement with John, who writes:

    Guided evolution predicts a nested hierarchy as long as it occurs within a context of common descent.

    Common descent will produce a nested hierarchy, by its very nature. But John is talking about an inferable nested hierarchy, and it’s not true that guided evolution by common descent necessarily predicts one of those.

    In fact a devious Guider, by carefully inserting the appropriate mutations at the right times and places, could cause us to infer a nested hierarchy that is completely at odds with the actual one.

  35. Even HGT events give rise to nested gene trees. There is no requirement that the nested hierarchy proceed only through whole-genome replication (vertical inheritance). A nested hierarchy is a prediction of template-directed DNA synthesis (which one may or may not choose to see as ‘nothing to do with evolution’, I guess!), which can pass through vertical inheritance, HGT, gene duplication or transposition.

    It’s copying that is at the root of the expectation, and copying is not always mediated by gametes or their equivalent. Obviously, Darwin was unaware of this; vertical inheritance is a reasonable first approximation.

  36. Allan Miller: A nested hierarchy is a prediction of template-directed DNA synthesis (which one may or may not choose to see as ‘nothing to do with evolution’, I guess!),

    After being informed that you misinterpreted what I wrote why would you repeat this silly nonsense?

    In case you missed it:

    Mung: Except that I did not say that DNA replication has nothing to do with evolution.

    But nice try.

    Do try to keep up Allan.

  37. Allan Miller: Even lower-level, it’s an inevitable consequence of semiconservative replication of DNA. When a DNA molecule replicates, the two new molecules are commonly descended from the first. When each of those replicates … hard to draw without drawing a tree.

    So DNA replication is an inevitable consequence of semiconservative replication of DNA. Just brilliant. Any more gems of wisdom?

  38. dazz: This is ridiculous

    I agree. Next time Allan should exercise more caution.

    When someone writes “it,” it is often useful to figure out what “it” refers to.

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