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. Corneel: Mung shouldn’t pick features that are shared by every single creature on the planet.

    I obviously failed to read the rules. Heh.

    In order to be convergent, they first need to be different.

    That was my claim. Many warm little ponds or many deep sea vents or many different RNA “worlds” with many different origins of life with those which converged on these specific features being the ones that survived and became the diversity of life we observe today.

    What, you think life only got started once at a single spot on the planet? Are you a creationist? 😉

  2. Mung: Rumraket: You won’t get branching if there’s no accumulation of change.

    Then why did you write the following?

    Rumraket: Branching is inevitable for any situation where more than one offspring survives.

    Because now you are saying branching is not inevitable.

    Make up your mind please.

    I concede that every time I post, I have a bad habit of assuming you know at least the most basic thing about biology. It’s hard for me to get used to having to explain literally everything we know about molecular and cell biology before we even get to arguments about evolutionary biology and it’s predictions.

    In this situation, I assumed you knew that reproduction entails the accumulation of mutations over generations. Simply put, the DNA replication process makes errors, it does not have perfect replication fidelity.

  3. Mung: Now if you can just demonstrate that evolution predicts cladogenesis. Or even anagenesis for that matter.

    You seem to misunderstand. At this point evolution is defined as anagenesis plus cladogenesis, and the nested hierarchy is a prediction that follows from that.
    This is also why John keeps repeating that he doesn’t need to explain the origin of “orphan features”; they are subsumed under the process of lineage change (anagenesis)..

    Of course both anagenesis and cladogenesis are well explained by the micro-evolutionary processes of selection, drift, migration and mutation but that’s for another thread.

  4. Mung: That was my claim. Many warm little ponds or many deep sea vents or many different RNA “worlds” with many different origins of life with those which converged on these specific features being the ones that survived and became the diversity of life we observe today.

    What, you think life only got started once at a single spot on the planet? Are you a creationist?

    I suggest you browse back a bit and find the part about coalescence.

  5. Mung: That was my claim. Many warm little ponds or many deep sea vents or many different RNA “worlds” with many different origins of life with those which converged on these specific features being the ones that survived and became the diversity of life we observe today.

    What, you think life only got started once at a single spot on the planet? Are you a creationist?

    No, but I think that’s very very unlikely at least from the perspective of chance convergence alone. Somebody has actually tested that theory:

    W. Timothy J. White, Bojian Zhong, David Penny. Beyond Reasonable Doubt: Evolution from DNA Sequences
    PLoS One. 2013 Aug 8;8(8):e69924. https://doi.org/10.1371/journal.pone.0069924

    As the authors state, it’s not that what you suggest is impossible, and there could be another source of extreme convergence rather than convergence due to mere chance. But you have to come up with a testable model that explains why there would be such extreme levels of convergence. The key word is testable. And as they also note, in order for such a model to account for all the data we have, it would have to be so unfathomably complicated it can’t even be meaningfully said to make predictions.

  6. Rumraket: In this situation, I assumed you knew that reproduction entails the accumulation of mutations over generations. Simply put, the DNA replication process makes errors, it does not have perfect replication fidelity.

    Yes. Regardless of evolution. Or do you claim that the DNA replication process and it’s lack of perfect replication fidelity is a prediction of evolution too?

    IOW, we’d have a nested hierarchy even without evolution, simply as a product of reproduction. So it’s not a prediction of evolution.

  7. Mung: Yes. Regardless of evolution. Or do you claim that the DNA replication process and it’s lack of perfect replication fidelity is a prediction of evolution too?

    No I would claim it is an instance of evolution.

  8. Rumraket: Mung: Yes. Regardless of evolution. Or do you claim that the DNA replication process and it’s lack of perfect replication fidelity is a prediction of evolution too?

    No I would claim it is an instance of evolution.

    Imperfect replication was observed long before Darwin. It was an observed fact which Darwin incorporated into his theory.

  9. Corneel,

    For the personal stuff; I would say a nested hierarchy is the nested ordering of species into successively more inclusive taxa (thought that one up myself just now, so use at your own peril). Yes, I think species are ordered that way and that common ancestry neatly explains why this is so

    Thanks. Can you add a personal definition of common ancestry?

    I don’t have any comment on why most branches have “an ancestor with no identify”, because I don’t have the faintest idea what you mean.

    If you look at the tree of whales posted earlier all the species are connected on a branch. The node of the branch is only identified with a letter and not an animal. So the common ancestor is not identified.

    Humans and chimps share a common ancestor. The ancestor is not identified.

  10. colewd,

    Can you give me a clear definition of a nested hierarchy? Do you think living organisms fit perfectly into that definition? If you think this pattern clearly points to common ancestry, please explain how. Do you have any comment on why most branches have an ancestor with no identify?

    Christ, Bill. Every single one of those questions is answered in Theobald’s 29+ Evidences for Macroevolution.

    Which you claim to have read.

    Are you actually telling us that you read the following…

    As seen from the phylogeny in Figure 1, the predicted pattern of organisms at any given point in time can be described as “groups within groups”, otherwise known as a nested hierarchy.

    …and missed the fact that it defines the term “nested hierarchy”? How is it possible for a (supposed) college graduate to read that without realizing that it answers the question?

    Get off your ass and read — actually read — Theobald. Then, if you’re still confused, come to us with questions about the specific parts of his essay that you don’t understand.

  11. Mung,

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

    Confusing as ever. Here’s where I got that impression:

    Allan: Even lower-level, it’s an inevitable consequence of semiconservative replication of DNA.

    Mung: So it has nothing to do with evolution, and claiming it’s a prediction of evolution is utterly gratuitous.

    It has nothing to do with evolution, it has to do with semiconservative replication of DNA instead. I can only conclude from the bare words that you think that if it is a consequence of semiconservative replication of DNA, then that has nothing to do with evolution.

  12. colewd: Can you add a personal definition of common ancestry?

    You’re not seriously asking that, are you? In a sense I can understand why someone could at least be confused about what a nesting hiearchy really is and how it applies to biology. But common ancestry? C’mon Bill. It’s in the name.

  13. keiths,

    Get off your ass and read — actually read — Theobald. Then, if you’re still confused, come to us with questions about the specific parts of his essay that you don’t understand.

    Do you think Cornels definition is inadequate?

  14. Rumraket,

    You’re not seriously asking that, are you? In a sense I can understand why someone could at least be confused about what a nesting hiearchy really is and how it applies to biology. But common ancestry? C’mon Bill. It’s in the name.

    Do you personally support Keiths definition or John’s definition?

  15. colewd,

    Here is an illustration, rather than a definition, of a nested hierarchy. You’ll have to move your mouse and raise your finger a smidge, then bring it down when your cursor is over the link, I’m afraid.

    It can be viewed in set-theoretical terms. If you think of Venn diagrams, a nested hierarchy would show concentric circles with no overlap, similar to contour lines on a map – sets within sets.

  16. Allan Miller:
    colewd,

    Here is an illustration, rather than a definition, of a nested hierarchy. You’ll have to move your mouse and raise your finger a smidge, then bring it down when your cursor is over the link, I’m afraid.

    Money on the discussion switching to snakalizacrocabird ancestors or the equivalent…

  17. dazz: Reproduction with DNA variation, AKA descent with modification, AKA evolution.

    It’s really apparent that the evolution critics here have never understood a thing that’s been said. Nothing said about evolution since 1859 has made the slightest dent in their cranial armor.

    Their entire effort has been devoted to finding snippets to quote mine.

  18. Mung:
    Wow, and for all these years I never realized that I was arguing against the theory of reproduction.

    Congratulations. You have now discovered that evolution happens because organisms imperfectly reproduce. This is progress.

  19. I think Mung makes a great point. Let’s rename the theory to Reproduction and let creationists reject that too

  20. dazz: I think Mung makes a great point. Let’s rename the theory to Reproduction and let creationists reject that too

    Well, they do advocate abstinence don’t they? 😀

  21. Allan Miller:

    If you think of Venn diagrams, a nested hierarchy would show concentric circles with no overlap, similar to contour lines on a map – sets within sets.

    Unlike the real thing. 🙂 Remember this:

  22. colewd: Me: I don’t have any comment on why most branches have “an ancestor with no identify”, because I don’t have the faintest idea what you mean.

    Bill: If you look at the tree of whales posted earlier all the species are connected on a branch. The node of the branch is only identified with a letter and not an animal. So the common ancestor is not identified.

    Ah, I see.

    The most parsimonuous explanation would be that this is because they are all dead. Note that it’s not just the nodes. The branches themselves are also all filled with ancestral species. All dead.
    That makes them kinda hard to identify, don’t you agree?

  23. Rumraket: Congratulations. You have now discovered that evolution happens because organisms imperfectly reproduce. This is progress.

    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?

    Why not just do like Corneel and define evolution to be what you need it to be.

  24. stcordova: Unlike the real thing.🙂Remember this:

    One does have to wonder whether you have any idea of what the figure you keep posting actually represents or shows, or what a phylogenetic tree actually represents or shows.

  25. Corneel: The branches themselves are also all filled with ancestral species. All dead. That makes them kinda hard to identify, don’t you agree?

    How convenient. 🙂

    Evolution wipes out the evidence for evolution.

  26. John Harshaman:

    One does have to wonder whether you have any idea of what the figure you keep posting actually represents or shows, or what a phylogenetic tree actually represents or shows.

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

    The diagram I posted is real.

    You keep confusing your imagination with reality.

  27. stcordova: The diagram I posted is real.

    Yes, and it shows the patterns expected from evolutionary processes. Like that we share only 73 genes with zebrafish that we don’t share with the other two species, and we share a whopping 1602 genes with mice that we don’t share with the other two species.

    On account of having diverged from mice much later.

    Sure would be nice if you knew how to read diagrams properly.

    Glen Davidson

  28. Here is an explanation of Sal’s favorite figure. The trees each represent one of the areas in the Venn diagram, with the most parsimonious interpretation (or one of them if there are several) represented for each. I only had room for 8 of the 15 areas, but the others are similar. A red bar represents gene loss and a green bar represents gene gain. Every tree with only one bar fits the tree perfectly and supports the nested hierarchy. Every tree with two bars doesn’t fit the tree perfectly. Note, however, that the one-bar trees all have many more genes than the two-bar trees, as if the probability of two events on a tree is much less than the probability of one event. Of course that only makes sense if there’s a tree. Otherwise there is no explanation for the differences in number among areas of the diagram. See, phylogeny does explain stuff.

  29. John Harshman:

    See, phylogeny does explain stuff.

    Wrong, like epicycles explain retrograde motion.

    Genes poof into existence in your model, a problem I pointed out doesn’t count as an actual mechanistic explanation.

    Sure your phylogeny works if you allow miracles.

  30. 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?

  31. Allan Miller,

    Here is an illustration, rather than a definition, of a nested hierarchy. You’ll have to move your mouse and raise your finger a smidge, then bring it down when your cursor is over the link, I’m afraid.

    It can be viewed in set-theoretical terms. If you think of Venn diagrams, a nested hierarchy would show concentric circles with no overlap, similar to contour lines on a map – sets within sets.

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

  32. Mung,

    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.

    What does it mean for all life to share a common ancestor. Does this mean you believe that all the diversity of life is the result of reproduction with random change driving diversity or is their room for guided mutations?

    I thought Keiths and John differed here but I might be wrong.

  33. stcordova: Wrong, like epicycles explain retrograde motion.

    Genes poof into existence in your model, a problem I pointed out doesn’t count as an actual mechanistic explanation.

    Sure your phylogeny works if you allow miracles.

    This is you failing to understand what phylogeny explains, yet again. It doesn’t explain the origin of mutations, including new genes. It explains why those mutations, including new genes, are organized into a nested hierarchy. Can you explain why there are way more genes in categories requiring one change on the tree than in categories requiring two changes on the tree? No? But I can. See, phylogeny explains data.

    And I’ll bet that if you look at the individual genes you will likely find evidence that they neither poofed into nor out of existence. I bet most of them arise from gene duplication and you will be able to locate paralogous genes, and that most losses begin with inactivation, leaving pseudogenes in many lineages. Have you looked?

  34. colewd: I thought Keiths and John differed here but I might be wrong.

    Oh no, my young Jedi. You will find that it is you who are mistaken, about a great many things.

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

    I swear we’ve been over this before. There is no way to identify any fossil as ancestral, no way to distinguish it from a close relative of the ancestral species. That’s why only tips have real taxa. Of course we can say that some species are pretty close to the ancestral morphotype, but that doesn’t mean they’re ancestors. And yet this inability to identify ancestors does not lessen the value of a phylogenetic tree. And we can use phylogeny to determine the states at ancestral nodes.

  36. John, to Bill:

    Oh no, my young Jedi. You will find that it is you who are mistaken, about a great many things.

    It’s a shame that Bill can’t actually use youth as an excuse.

  37. John,

    Here is an explanation of Sal’s favorite figure.

    Thanks for drawing out those trees, John.

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

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