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. So dazz is going to write an algorithm that is constructed in such a way as to create a set of sequences that if analyzed by some other piece of software, will produce a nested hierarchy. And if it fails to do so, he’ll tweak it until it does.

    And this will be proof that an algorithm written to produce a nested hierarchy will in fact produce a nested hierarchy.

    That about capture it dazz?

  2. Mung: if analyzed by some other piece of software, will produce a nested hierarchy

    not just “a nested hierarchy”. The same one

  3. dazz: not just “a nested hierarchy”. The same one

    The same one as what?

    And do you dispute that you will have to write the program in a particular way in order to get it to produce a nested hierarchy? IOW, you will have to write a program that generates a nested hierarchy in order to have a program that generates a nested hierarchy. So what’s the point?

    So already we know you’ll have to tweak [aka “fine tune”] the mutation rate.

    How about the length of the sequence that you start with, your initial LUCA sequence? For example, how long with it be? Do you think 5 characters will be enough? 10? 20?

    If a nested hierarchy is “entailed” then what are the principles that are involved? I mean, trying out various pieces of code until you get a nested hierarchy from the algorithm isn’t really what you had in mind is it?

  4. John Harshman,

    That isn’t true. You are demanding an auxiliary and unnecessary hypothesis of clocklike gene loss, which is not connected to the common descent hypothesis. The data don’t support the auxiliary hypothesis, which nobody has advanced, but they do support the main hypothesis of common descent.

    If the clock has no restriction then what is the data telling us? You predict a nested hierarchy supporting inheritance as a hypothesis and when the data conflicts you invoke variable gene loss so you have protected the theory from any contrary data which smells of an unfalsifiable theory incapable of prediction.

    Of the 13,172 genes that Sal’s flower identified as being inherited by future species
    -12897 made it to humans
    -12718 made it mice
    -10983 made it to chickens

    Call me crazy but I would expect order of dissension to be reversed. The further down the evolutionary trip the more opportunity to lose genes yet the greatest number of genes made the longest trip. The genes going down that path experienced a gene loss time warp. Inheritance seems an unlikely cause of this pattern.

  5. keiths, a while back:

    We are using ‘guided evolution’ to refer to evolution that is guided by an intelligent agent.

    Alan, more recently:

    And this qualification makes what difference, exactly?

    keiths:

    It maintains a useful and desired distinction, while your suggested usage erases that distinction.

    Alan:

    Can your [sic] support those assertions?

    Of course.

    PS what usage did I suggest?

    See here:

    What do you mean by “guided”? Evolution is guided by the niche. If God created the universe, he created the niches. Such guidance produces a nested hierarchy.

    The ‘useful distinction’ I referred to above is the distinction between unguided and guided evolution, where ‘guided evolution’ refers to an evolutionary process in which an intelligent agent actively intervenes, while ‘unguided evolution’ refers to an evolutionary process that unfolds on its own without active interventions.

    Whether evolution requires this sort of active guidance is a separate question from whether the universe was created by God in such a way that evolution would passively unfold in a desired direction.

  6. Moved some comments to guano that broke the rule on attacking ideas, not members and also ones that should have been posted in “Moderation Issues” or “Noyau”. Please use “Noyau” for flaming and “Moderation Issues” for complaints about moderation.

  7. keiths: The ‘useful distinction’ I referred to above is the distinction between unguided and guided evolution…

    But that distinction is impossible to establish – it’s simply a matter of personal belief or lack of it.

    … where ‘guided evolution’ refers to an evolutionary process in which an intelligent agent actively intervenes, while ‘unguided evolution’ refers to an evolutionary process that unfolds on its own without active interventions.

    So, you observe a process and then you decide whether an intelligent agent actively intervenes or the process is determined from causality (the principle of sufficient reason) or the process is undetermined because the universe is not strictly determined. How do you do this?

    Whether evolution requires this sort of active guidance is a separate question from whether the universe was created by God in such a way that evolution would passively unfold in a desired direction.

    Unless you are a determinist and believe the PSR is true for our reality.

  8. Don’t know if anyone else has read The Universe in a Single Atom: The Convergence of Science and Spirituality by the Dalai Lama where he writes:

    Buddhism must accept the facts — whether found by science or found by contemplative insights. If, when we investigate something, we find there is reason and proof for it, we must acknowledge that as reality — even if it is in contradiction with a literal scriptural explanation that has held sway for many centuries or with a deeply held opinion or view.

    Seems a very pragmatic way of dealing with reality versus belief.

  9. dazz,

    Would it? I’d be interested to see a mathematical or computer model for the process of common descent. Perhaps others are too.

  10. Mung: And do you dispute that you will have to write the program in a particular way in order to get it to produce a nested hierarchy? IOW, you will have to write a program that generates a nested hierarchy in order to have a program that generates a nested hierarchy. So what’s the point?

    Well of course that is the point. Making the model forces you to make your hidden assumptions explicit. It also shows which decisions and parameter values (such as the mutation rate) are required to get certain results, so others can decide whether they deem those values biologically plausible.

    I suspect such simulation programs already exist, and have been used for exactly this purpose.

  11. Mung: Mice are rather obviously the least devolved.

    Yea but fish are higher in the scale of nature, although chickens are top of the pecking order.

  12. CharlieM: Yea but fish are higher in the scale of nature, although chickens are top of the pecking order.

    Pleased to see you’ve managed to quell your anthropomorphism. 😉

  13. Alan Fox: Seems a very pragmatic way of dealing with reality versus belief.

    If only this very principle could be applied by those what can’t seem to see that it does apply to them… I called it bias blindness…others call it cant…
    No need to list endless examples…they are all not hidden from an inquiring mind…that is if one possess such…or has the courage to investigate what may not be aligned with what is expected to find…

    Well…this is what I teach my kids… Investigate the natural world (without any bias) wherever it leads you…

  14. keiths:

    The ‘useful distinction’ I referred to above is the distinction between unguided and guided evolution…

    Alan:

    But that distinction is impossible to establish – it’s simply a matter of personal belief or lack of it.

    No, it isn’t. That’s the point I’ve been making in this thread. We can reject guided evolution based on the biological evidence, just as we can reject the Rain Fairy hypothesis on the basis of the meteorological evidence.

    So, you observe a process and then you decide whether an intelligent agent actively intervenes or the process is determined from causality (the principle of sufficient reason) or the process is undetermined because the universe is not strictly determined. How do you do this?

    Your question is confused, because those categories are not mutually exclusive.

    If you want to learn about my argument for unguided evolution, read the thread.

    keiths:

    Whether evolution requires this sort of active guidance is a separate question from whether the universe was created by God in such a way that evolution would passively unfold in a desired direction.

    Alan:

    Unless you are a determinist and believe the PSR is true for our reality.

    No, the questions are still separate, even for determinists.

  15. keiths:

    But that distinction is impossible to establish – it’s simply a matter of personal belief or lack of it.

    No, it isn’t.

    Yes it is. Unless you can support your claim, it’s your opinion, my opinion, anyone else’s opinion.

    That’s the point I’ve been making in this thread. We can reject guided evolution based on the biological evidence…

    But unless you can distinguish between a guided process where the guidance is not apparent and an unguided process you are just choosing the option that suits your opinion.

    …just as we can reject the Rain Fairy hypothesis on the basis of the meteorological evidence.

    What causes weather? If you are a determinist and accept the PSR, you don’t really have an answer. No-one does, as far as I can see. I generally look out of the window.

  16. Alan Fox,

    Sorry for the delay in responding old friend…..

    At the BLAST site?

    No, but I’m embarrassed to say I don’t know exactly where since some of the full genome sequence data are spread around. When I was grabbing full genomes, they were the sort that could fit on my computer like say, E. Coli. And I just grabbed a full genome where I could find it on the net from some laboratory website that was offering it for free…

    The full human genome can be downloaded chromosome by chromosome in a variety of places.

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

    There are places where lists of genes for organisms are published.

    A caution however is in order. Gene identification isn’t a 100% science if it is done by solely by computational inference. Genes can be mis-labeled, etc. The Gold Standard of labeling a gene a real gene is of course sequencing the proteins in an organism and confirming it, the silver standard is looking at the mRNA expressed sequences. The problem is that some genes are expressed only for a few hours out of an entire lifetime of the organism, so there is a lot of guesswork, and we can miss the existence of genes, etc.

    The phylogeny of the nylonases earlier I depicted shows yet another issue in gene idenfication. In some cases, the nylonase protein sequences shared less than 2% sequence identity even though they were classified as the same protein!!!!! A published study by Rost said many proteins deemed to be homologous share only 12% sequence identity.

    The Hidden Markov models which Theobald’s work is based on are also used to infer these weak similarities. The similarities are above random, but they are weak. We know experimentally they are generally legitimate because of things like X-Ray crystallography confirming similaity in 3D folding or (in the case of enzymes) similar catalytic function.

    One nice things is so many of the tools have now been codified and made into software, BLAST and MUSCLE being and example, and so doing business these days is so much easier.

    I hope to publish some videos to teach creationists how to use some of these tools including the phylogenetic ones. The phylogenetic one is of interest in the nylonase project Dr. Sanford and I are working on since it establishes the conservation of the nylonase NylB fold, and thus falsifies a paper Ohno published in 1984 on which Ken Miller, Dennis Venema and the NCSE relied on to make their case against ID. Papers are still citing Ohno’s work as correct. It’s not. The phylogenetic diagram I put together is worth a thousand words against Ohno’s claims.

  17. keiths: Your question is confused, because those categories are not mutually exclusive.

    Yes, I think the law of the excluded middle is a bit simplistic for reality. I omitted another option; the “I don’t know and suspect no-one else does either” option.

  18. stcordova: Papers are still citing Ohno’s work as correct. It’s not. The phylogenetic diagram I put together is worth a thousand words against Ohno’s claims.

    I see another Japanese researcher Seiji Negoro has published work that indicates another evolutionary path from a beta-lactamase via two amino acid changes.

    PS, I’ve no objection to you referring to me as “friend” but “old”? Steady on!

  19. Alan:

    I see another Japanese researcher Seiji Negoro has published work that indicates another evolutionary path from a beta-lactamase via two amino acid changes.

    I concur with aspects of Negoro’s work. I actually used some the Hidden Markov-like (not exactly the same model, but same result) software called muscle. I independently arrived at some of his conclusions here:

    http://theskepticalzone.com/wp/invited-responses-to-my-nylonase-research-and-the-question-of-new-proteins-without-gods-help/comment-page-4/#comment-197874

    There is a subtle but important distinction. Ohno is essentially arguing an Orphan Gene can easily pop out of nowhere (a change of 400+ amino acids instantaneously via frame shift). Negoro, et. al, myself included think a 2 amino acid change is what really happened, maybe even less if any at all.

    Although, I think Dr. Sanford and I have falsified the post-1935 gene duplication hypothesis. We think there was gene duplication, but not the way they think!

  20. Alan:

    PS, I’ve no objection to you referring to me as “friend” but “old”? Steady on!

    Yes of course, my long time friend. How’s that. 🙂

  21. stcordova,
    Don’t get me wrong, I think it is perfectly reasonable to attack someone’s scientific hypothesis by presenting a better scientific alternative. But don’t you then take the same path of Dennis Venema and his colleagues at BioLogos. Once you allow science in the door, you must also take the same pragmatic approach to dates — and the reductio ad absurdam is Deism.

  22. Alan:

    But that distinction is impossible to establish – it’s simply a matter of personal belief or lack of it.

    keiths:

    No, it isn’t. That’s the point I’ve been making in this thread. We can reject guided evolution based on the biological evidence, just as we can reject the Rain Fairy hypothesis on the basis of the meteorological evidence.

    Alan:

    Yes it is. Unless you can support your claim, it’s your opinion, my opinion, anyone else’s opinion.

    I have supported it. That’s the purpose of the argument I’ve been making. You’re welcome to present a counterargument, if you have one.

  23. Alan:

    But unless you can distinguish between a guided process where the guidance is not apparent and an unguided process you are just choosing the option that suits your opinion.

    You think that to reject Rain Fairyism in favor of modern meteorology is a matter of mere preference and opinion, and not of scientific validity?

    Wow.

    What causes weather? If you are a determinist and accept the PSR, you don’t really have an answer. No-one does, as far as I can see. I generally look out of the window.

    Your last sentence is a non sequitur, and the rest of the quote doesn’t make sense either. Meteorologists do have an answer, and if you respond that it isn’t a real answer unless it identifies an ultimate cause, then you’re making the same mistake that Vincent did in the “Five Proofs” thread.

  24. Alan:

    So, you observe a process and then you decide whether an intelligent agent actively intervenes or the process is determined from causality (the principle of sufficient reason) or the process is undetermined because the universe is not strictly determined. How do you do this?

    keiths:

    Your question is confused, because those categories are not mutually exclusive.

    Alan:

    Yes, I think the law of the excluded middle is a bit simplistic for reality.

    Another non sequitur. The issue isn’t whether the LEM is true; it’s whether your categories are mutually exclusive. They aren’t.

    Do you see why?

  25. keiths:

    I have supported it. That’s the purpose of the argument I’ve been making. You’re welcome to present a counterargument, if you have one.

    Alan:

    I disagree. All I’ve seen are assertions.

    If so, then your reading has been highly selective. Take another look.

  26. keiths:
    Alan:

    You think that to reject Rain Fairyism in favor of modern meteorology is a matter of mere preference and opinion, and not of scientific validity?

    I’m sorry! Was I meant to take that seriously? As a pragmatist, I use what works. In my part of the world, the meteo is not all that reliable. It’s limited by the density of measuring stations so the most reliable way of gauging the weather is having a look out of the window

    Your last sentence is a non sequitur, and the rest of the quote doesn’t make sense either.Meteorologists do have an answer, and if you respond that it isn’t a real answer unless it identifies an ultimate cause, then you’re making the same mistake that Vincent did in the “Five Proofs” thread.

    Well, if we’re discussing meteorology, I’m not dismissing their predictions. As to “have an answer”, well that’s open to wide interpretation. If you want to use meteorology as a metaphor for something else, fine. I remain unimpressed.

  27. keiths: The issue isn’t whether the LEM is true; it’s whether your categories are mutually exclusive. They aren’t.

    Another assertion! 🙂

  28. keiths:

    You think that to reject Rain Fairyism in favor of modern meteorology is a matter of mere preference and opinion, and not of scientific validity?

    Alan:

    I’m sorry! Was I meant to take that seriously? As a pragmatist, I use what works. In my part of the world, the meteo is not all that reliable. It’s limited by the density of measuring stations so the most reliable way of gauging the weather is having a look out of the window

    None of that answers my question:

    You think that to reject Rain Fairyism in favor of modern meteorology is a matter of mere preference and opinion, and not of scientific validity?

  29. Alan:

    Yes, clearly, it does.

    Just to eliminate possible misunderstanding, do you mean “Yes, clearly it is a matter of mere preference and opinion?”

    Or are you saying “Yes, it does answer your question?” Because it doesn’t.

  30. Alan:

    Well, if we’re discussing meteorology, I’m not dismissing their predictions. As to “have an answer”, well that’s open to wide interpretation.

    I addressed that:

    Your last sentence is a non sequitur, and the rest of the quote doesn’t make sense either. Meteorologists do have an answer, and if you respond that it isn’t a real answer unless it identifies an ultimate cause, then you’re making the same mistake that Vincent did in the “Five Proofs” thread.

    Meteorologists have an actual answer in terms of physics. All the Rain Fairyists have is “the Rain Fairy did it that way.”

    If you want to use meteorology as a metaphor for something else, fine. I remain unimpressed.

    You’re unimpressed with lots of things you don’t understand. It’s one of your flaws. You don’t understand my argument, which makes sense given that you claim not to have seen it. Instead of dismissing it from a state of incomprehension, why not take a look at it instead, and offer a rebuttal if you can come up with one?

  31. Alan,

    Nope, I was just asserting that I’d answered your question about Rain Fairies.

    You didn’t.

    Here’s my question:

    You think that to reject Rain Fairyism in favor of modern meteorology is a matter of mere preference and opinion, and not of scientific validity?

    Do you think that?

  32. Anyway, I’m puzzled. Aren’t there loftier matters for you to deal with? There’s a question from DNA_Jock upthread that you haven’t responded to.

  33. keiths:

    Another non sequitur. The issue isn’t whether the LEM is true; it’s whether your categories are mutually exclusive. They aren’t.

    Alan:

    Another assertion!

    Hence my very next sentence:

    Do you see why?

    If you see your mistake, I won’t bother explaining it. If you don’t, I will.

  34. keiths: You think that to reject Rain Fairyism in favor of modern meteorology is a matter of mere preference and opinion, and not of scientific validity?

    Neither do I think that Rainfairyism is a hypothesis worth considering, scientifically or otherwise (you should realise this, following on from North Sentinel Island) nor do I think there is such a thing as scientific validity.

  35. keiths:

    If you see your mistake, I won’t bother explaining it. If you don’t, I will.

    Alan:

    You decide.

    I can’t decide, because you haven’t written anything that would indicate whether or not you see your mistake. Do you?

  36. keiths: You’re unimpressed with lots of things you don’t understand.

    That’s not true. I’m in awe of the universe, which I certainly don’t understand.

  37. keiths: I can’t decide, because you haven’t written anything that would indicate whether or not you see your mistake.

    Just assume it and carry on.

  38. Why are you afraid of such a simple question? Just answer it honestly.

    Do you see your mistake, or do you think you were correct?

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