Common Design vs. Common Descent

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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.

5,163 thoughts on “Common Design vs. Common Descent”

  1. Sal, let’s try another tack for a second. How much common descent do you think actually happens? Do you, like many creationists, accept the idea that the “kind” typically lies at the level of taxonomic family? Like others, do you accept that it’s at the level of suborder or even order? Or do you suppose that each species was created separately?

  2. Allan,

    I don’t need an explanation for the mechanism of a miracle, if indeed a miracle happened. In fact, for mere mortals an explanation of the mechanism might be beyond us.

    On the other hand, you all keep equating nested hierarchical patterns in genes between species as the product of a random walk. The if genes were free to mutate, no big deal, even I would buy that, but the problem is I’ve shown that assumption doesn’t square with the facts that the genes aren’t free to mutate but must mutate along with simultaneous changes in the organisms at the genomic, transcriptomic, and proteomic level. Thus a fundamental assumption of a common ancestral giving rise to copies with slight mutation due mostly to random variation is shown to be suspect.

    All this in addition to me showing the other miracles necessary to make common descent happen.

    You want to believe “evolution did it without miracles” that’s fine, but let’s not pretend you have a mechanistic explanation in any sufficient detail either. You have a faith belief in the face of many opposing facts.

    “Evolution did it without miracles” is not a real scientific theory of science like say, classical electromagnetics, celestial mechanics, quantum mechnanics, thermodynamics, etc.

  3. stcordova: I don’t need an explanation for the mechanism of a miracle, if indeed a miracle happened. In fact, for mere mortals an explanation of the mechanism might be beyond us.

    How is that not anything but an excuse for completely stopping any sceintific investigation or questioning? Once you start taking the idea of miraculous divine interventions seriously to account for patterns observed in nature, where do you draw the line?
    As soon as it becomes even a little bit difficult to figure out the how, someone like you could come along and just declare it can’t be figured out because a fundamentally incomprehensible divine entity is making it happen.

    We would have gone nowhere if that had been the prevailing attitude in history. There are dusins of historical examples of scientific stumbling blocks being declared the exclusive arena of the will of God, when the top thinkers of the time couldn’t figure it out. A famous example is Isaac Newton giving up before discovering pertubation theory (which explains the cohesion of the solar system with the many separate tugs and pulls of different centres of mass). Newton simply gave up and declared it was held together by the will of God.

    Then along came LaPlace and took up the challenge where Newton had given up.
    http://www.naturalhistorymag.com/universe/211420/the-perimeter-of-ignorance

    The Perimeter of Ignorance
    Scientists face a choice: invoke a deity or continue the quest for knowledge
    By Neil deGrasse Tyson

    Writing in centuries past, many scientists felt compelled to wax poetic about cosmic mysteries and God’s handiwork. Perhaps one should not be surprised at this: most scientists back then, as well as many scientists today, identify themselves as spiritually devout.

    But a careful reading of older texts, particularly those concerned with the universe itself, shows that the authors invoke divinity only when they reach the boundaries of their understanding. They appeal to a higher power only when staring into the ocean of their own ignorance. They call on God only from the lonely and precarious edge of incomprehension. Where they feel certain about their explanations, however, God gets hardly a mention.
    (…)

    You posit God to account for what appear to you as gaps in the nested hiearchy of life. Sorry to tell you, but we have no need of that hypothesis. The origin and change of taxonomically restricted genes, whether at the level of multi-constrained regulatory elements or systems, just isn’t the gap you think it is. Molecular evolution has had it’s Laplace here, your difficulties here are entirely imagined.

    And you’ve still not explained the nested hiearchy other than with a vacuous placeholder that actually has no explanatory power: God could have made it.
    Yes, but notice it doesn’t actually explain why there is a nested hiearchy. God could have made it, but… why would you believe he did? It is not enough to just declare that God COULD have made it, when God could also have NOT made it.

    Again, evolution absolutely demands nested hiearchies. God could have simply decided on any other concievable pattern. So you have no reason to expect God to choose the one that evolution absolutely requires. If anything, that just makes God appear deceptive.

  4. Allan,

    I have just twigged that Mung may be simply talking of the fact that the components of the endosymbiotic pairing came from different places.

    I suspected the same, but he says he mean separate ancestry:

    Mung

    Aren’t mitochondria though to have a separate origin?

    keiths:

    No. They are thought to have shared a common ancestor with the organism that engulfed them. Which ought to be obvious, given that their genetic code differs by only 3 codons out of 64.

    Mung:

    How many differences more would there need to be, exactly, to support the hypothesis of an un-shared ancestry between the “host” and the symbiont?

  5. stcordova: but the problem is I’ve shown that assumption doesn’t square with the facts that the genes aren’t free to mutate

    You have shown no such thing. You have tried to argue this by saying the contraints exist at multiple levels. At no point have you gathered these facts into a coherent argument that validly concludes from a set of uncontroversial premises, that these genes can’t mutate.

    You don’t seem to understand what it means to show what you try to argue for. In order to show it, you would have to have data that indicates that every possible, or the vast majority of mutations to these regions, right now are and also were in the past, extremely highly deleterious if not outright lethal.

    Not a single fact have you advanced in that direction. You haven’t even cited a single paper that shows that “this nucleotide right here can’t mutate under any conditions”. You speak in generalities, and handwave towards your conclusion by just using this “constraint” label in reference to several entities (DNA, RNA, protein).

    I’ve explained this now multiple times. You don’t get to establish a conclusion of immutability by vaguely referencing multi-layered constraint. To repeat myself:

    And it still doesn’t get you to your sought conclusion. You have not somehow DEMONSTRATED that they can’t possibly change simply by waving your hands in the general direction of multi-layered constraint.
    Your argument here merely amounts to an insinuation. All that does is explain why they are more conserved over time, than other regions which are less conserved. But they’re still not immutable. We still detect changes between species, and those changes become larger with increasing distance of species relationships. Exactly as you would predict if evolution by common descent was true.
    Multiple levels of constraint just means change is slower, it doesn’t mean the function can’t emerge, or that it can’t change at all over time.

    It. Simply. Doesn’t. Follow.

  6. Rumraket,

    Again, evolution absolutely demands nested hiearchies. God could have simply decided on any other concievably pattern. So you have no reason to expect God to choose the one that evolution absolutely requires. If anything, that just makes God appear deceptive.

    How do you think whale evolution supports the concept of nested hierarchies?

  7. colewd: How do you think whale evolution supports the concept of nested hierarchies?

    So well it that it is irrational to deny it.

  8. Allan Miller: Who cares about Venter?

    Well…you wouldn’t care because, unlike many so called authorities, he is an experimental scientists who has working on artificial genomics…He is one of the most respected experimental scientist in the world

    [Allan Miller] I asked a simple question. The thread title is ‘Common Design vs Common Descent’. So, what is the Common Design explanation for variant codes – the overwhelming commonality, and the reason for variation?

    Venter’s experiments of changing one species of bacteria to another have revealed troubling facts for evolution and common ancestry, which I have already mention earlier…Larry Moran, but many others know that common ancestry doesn’t add up because the tree of life doesn’t exist and the net or bush of life indicates separate life origins…The variations in genetic codes is just one of the nails in the coffin of common ancestry…There is many more…

    Returning to the fundamentals, Veter realized that restriction enzymes are the obstacle to his experiment of changing one species of bacteria to another, which had been know since late 70-ties…

    “Restriction enzyme or restriction endonuclease iare found in bacteria and archaea and provide a defense mechanism against invading viruses.[4][5] Inside a prokaryote, the restriction enzymes selectively cut up foreign DNA in a process called restriction; meanwhile, host DNA is protected by a modification enzyme (a methyltransferase) that modifies the prokaryotic DNA and blocks cleavage. Together, these two processes form the restriction modification system.[6]

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

    I guess I don’t have to ask the question, since the question asks itself, doesn’t it?

  9. keiths: And for extra laughs, tell us why you thought that code differences were more important than sequence differences for the endosymbiotic hypothesis:

    What do sequence differences have to do with it? The discussion was about coding differences, as you well know.

    keiths: Because the discussion is about single vs separate origins of the genetic code(s)…

  10. Allan Miller: I asked a simple question. The thread title is ‘Common Design vs Common Descent’. So, what is the Common Design explanation for variant codes – the overwhelming commonality, and the reason for variation?

    You’ve fallen into the Sal-trap, lol. Common design is meant to explain the similarities, not the differences. 😉

  11. stcordova: All this in addition to me showing the other miracles necessary to make common descent happen.

    The accused’s bloody fingerprint was found on the victim, and the victim’s blood was spattered all over the accused’s clothing and skin. What does the accused have to say in defense?

    Accused: How marvelous are the miracles wrought by God! Sal will explain how God makes evidence appear without the causes occurring.

    Glen Davidson

  12. stcordova,

    I don’t need an explanation for the mechanism of a miracle, if indeed a miracle happened. In fact, for mere mortals an explanation of the mechanism might be beyond us.

    One needs a reason to invoke ‘miracle’. Making it the alternative for ‘lacks-detailed-mechanistic-explanation’ is not warranted. Trying to turn these into symmetrical ‘faith positions’ distills the entire thread: Why is Common Design a better explanation than Common Descent? “Well, it’s just as good”. Which, one might as well express as “it’s just as crap”.

  13. Sal is just repeating the old creationist/ID pattern:

    1. He sees that the objective nested hierarchy overwhelmingly supports the theory of unguided evolution.

    2. He doesn’t like that, so he invents imaginary barriers to evolution, based on personal incredulity.

    3. He needs something to overcome the imaginary barriers, so he invokes an imaginary God.

    4. Now the problem is that the imaginary God behaves just as unguided evolution would if the imaginary barriers weren’t there.

    5. Based on the strength of the evidence, a rational person would conclude that the barriers are imaginary and that evolution really is unguided. Sal instead assumes that the imaginary barriers and the imaginary God are real, and that the imaginary God just happens, for no good reason, to be an unguided evolution mimic, and that his mimicry showcases his “genius”.

    To fully appreciate the stupidity of this thinking, look how it appears when transposed to the Rain Fairy context:

    1a. The Rain Fairyist sees that the evidence overwhelmingly supports the theory of unguided meteorology.

    2a. He doesn’t like that, so he invents imaginary barriers to unguided meteorology, based on personal incredulity.

    3a. He needs something to overcome the imaginary barriers, so he invokes an imaginary Rain Fairy.

    4a. Now the problem is that the imaginary Rain Fairy behaves just as unguided meteorology would if the imaginary barriers weren’t there.

    5a. Based on the strength of the evidence, a rational person would conclude that the barriers are imaginary and that meteorology really is unguided. The Rain Fairyist instead assumes that the imaginary barriers and the imaginary Rain Fairy are real, and that the imaginary Rain Fairy just happens, for no good reason, to be an unguided meteorology mimic, and that her mimicry showcases her “genius”.

    It’s the same bad reasoning in both cases, and it’s dumb as shit.

    Creationism is simply too stupid to be believed.

  14. Allan Miller: You are, I am sure, familiar with the evidence for endosymbiotic theory. You seem to be suggesting above that it is solely based upon the differences in genetic code. I’m puzzled by that, because I know you know that isn’t the case.

    And you would be right to be puzzled. You should perhaps question the interpretation of what I’ve written.

    You seem to be suggesting above that it is solely based upon the differences in genetic code.

    I haven’t even remotely suggested such a thing. I asked if the differences were a factor in the theory. I honestly don’t know if the coding differences factored in, so that is an honest question.

    Some suggested responses:

    1. Yes
    2. No
    3. Maybe
    4. I don’t know
    5. My name is keiths, and I mock your ignorance

  15. colewd,

    How do you think whale evolution supports the concept of nested hierarchies?

    Very well. Why would one make an exception for them?

  17. J-Mac,

    I thought you’d buggered off? Anyway, none of what you wrote has anything to do with a Design explanation for variant codes, which was actually the question.

  18. Mung,

    You’ve fallen into the Sal-trap, lol. Common design is meant to explain the similarities, not the differences

    So the similarities were designed, but not the differences?

  19. Allan Miller: You are, I presume, a grown man, and can evaluate propositions for yourself. If you don’t think 61 invariant assignments is enough to suggest common origin of the code, then that is what you think. It’s not for ‘evolutionary theory’, or me, to tell you what you should think to be a reasonable threshold.

    Is that’s how skeptics do science these days? I’ve fallen behind. Is all of evolutionary theory like this, or only the common descent part?

    I don’t know whether 61 invariant assignments is enough to suggest common origin of the code. I don’t think one way or another. For all I know 1 invariant assignment is enough to suggest common origin of the code. If there is no science of the matter just say so.

  20. Allan Miller: Why is Common Design a better explanation than Common Descent? “Well, it’s just as good”. Which, one might as well express as “it’s just as crap”.

    This actually is one of the intended goals of creationist apologetics. Make it appear as if it is a case of equally rational faith-positions. It’s the good old interpretations-canard. “Oh but we all use the same evidence, we just interpret it differently”. It’s technically not even true, as they really do ignore enormous amounts of it.

    Their explicit position is that there is evidence, and then there is interpretations of that evidence. That no interpretation is superior in any way, to another. They are all equally plausible, all equally likely, all equally rational.

    So while creationists have faith in God, evolutionists have faith in evolution, or naturalism, or whatever. Either way, their position is that the evidence doesn’t lend itself rationally in any more compatible way with one interpretation over another.

    A good example of what that is an utterly fatuous position is the analogy brought up above by GlenDavidson.

    So while it is true that there is no evidence that cannot be in some way rationalized as being at least compatible with some alternative interpretation (little invisible leprechauns teleported into my house and put the drops of blood on my clothes during the night), it simply isn’t true that all interpretations are on an equally rational footing.

    I’ve tried to show this with the “God could have done it” rationalization for the nested hiearchy of life. Yes, God could have done it. But he could also have decided not to. So you have to reason to EXPECT that God did it like that. Whereas, evolution, for the 20th time at least, absolutely requires it.

  25. J-Mac,

    Why are you still here? Your ground-breaking research is calling!

    The disorder I have been studying affects billions of people…However, the related diseases can and often do lead to certain types of cancer… So, the impotence on my research and findings could have some serious implications, if proven right…

    Gotta love the “impotence” bit.

  27. Mung,

    Sorry, don’t understand your beef. I invite you to decide for yourself whether you think 61/64 identical assignments indicates common origin. Of course, convergence is possible, but unlikely. So for me, 61/64 points to common origin. YMMV.

  28. newton,

    That is uncommon design which is also evidence for design by intelligence

    Heh. And with the wordplay out the way, I wonder what Design reason suggests itself for the various variant codes?

  29. Rumraket: Once you start taking the idea of miraculous divine interventions seriously to account for patterns observed in nature, where do you draw the line?

    I personally prefer the line somewhere close to 60/40.

  30. keiths: I suspected the same, but he says he mean separate ancestry:

    I said origin. You even quoted me. Unbelievable.

    ETA: I forgot who I was dealing with. It’s not unbelievable at all.

  31. Allan:

    You seem to be suggesting above that it is solely based upon the differences in genetic code.

    Mung:

    I haven’t even remotely suggested such a thing.

    Sure you did:

    What factored into the symbiotic theory if not differences in the genetic code?

    Don’t worry about it, Mung. People already know that you’re bad at biology.

  32. Allan, to Mung:

    Sorry, don’t understand your beef.

    At this point he’s just trying to cover up his mistakes.

    Don’t bother, Mung. Try to learn something instead.

  33. Allan Miller: So the similarities were designed, but not the differences?

    That’s a separate topic for a different thread.

    newton: That is uncommon design which is also evidence for design by intelligence

    Yes. And a multiplicity of designers. 🙂

  34. Mung,

    That’s a separate topic for a different thread.

    Haha yes! God forbid this tightly focussed one should suffer a derail!

  35. Mung,

    I said origin. You even quoted me. Unbelievable.

    And by ‘origin’, you meant ancestry:

    How many differences more would there need to be, exactly, to support the hypothesis of an un-shared ancestry between the “host” and the symbiont?

    If you disagree with yourself, I’ll let the two of you fight it out.

  36. I’m surprised no-one has picked me up on this – there are 4 differences in mitochondria, not 3. Can’t trust an evolutionist.

  37. keiths: Sure you did:

    What factored into the symbiotic theory if not differences in the genetic code?

    Don’t worry about it, Mung. People already know that you’re bad at biology.

    Even Rumraket understands the meaning of factor. Why don’t you?

    keiths: Don’t bother, Mung. Try to learn something instead.

    Um. That’s why I asked the question about mitochondria.

    I ask questions. They don’t get answered. Then I’m berated for not trying to learn something. I feel like I must be on Sentinal Island.

  38. Allan Miller: I’m surprised no-one has picked me up on this – there are 4 differences in mitochondria, not 3. Can’t trust an evolutionist.

    🙂

    So NOW do you accept that the mitochondria had a separate origin?

  39. Mung:

    I ask questions. They don’t get answered. Then I’m berated for not trying to learn something.

    Mooommmmeeeee! Allan and keiths won’t spoon-feed me!

    Allan had a pertinent suggestion:

    6. Google. An exercise for the student.

  40. Mung,

    The common assignments (and the ribosome/aaRS/tRNA system within which they have context) indicate a common origin for the nuclear and mitochondrial genetic codes. The differences between them indicate a period of evolution separating them from their common ancestor before they encountered each other in endosymbiosis. But, the mitochondrial code differs somewhat from the bacterial, indicating post-endosymbiosis evolution. The plant plastid code is identical to the bacterial, consistent with a more recent endosymbiosis.

    I don’t know what question you want answered, but there is a nutshell summary of the genetic code relations of nuclei and organelles.

    Comparing genetic codes is actually a bit of a hobby of mine. It’s interesting to line them up and note the patterns of variation.

  41. keiths: And by ‘origin’, you meant ancestry:

    You were the one who brought up common ancestry.

    keiths: No. They are thought to have shared a common ancestor with the organism that engulfed them. Which ought to be obvious, given that their genetic code differs by only 3 codons out of 64.

    My response to you was questioning your reasoning about the number of codon differences needed to establish common ancestry, which you still haven’t answered.

    And that’s a different topic from the one I originally raised, which was the origin of the mitochondria.

    Context. Reading comprehension keiths. You’re a big fan of it. Now try doing it.

  42. Mung,

    My response to you was questioning your reasoning about the number of codon differences needed to establish common ancestry, which you still haven’t answered.

    As has been said, it’s not simply the code differences, since the code itself is embedded in a ribosome/aaRS/tRNA system. It’s really that that establishes fundamental common ancestry. But, the 61 60 common assignments indicates the point more forcefully still.

  43. keiths: Mooommmmeeeee! Allan and keiths won’t spoon-feed me!

    If I don’t ask questions I’m not trying to learn anything. If I do ask questions I am not trying to learn anything. And, furthermore, if I do ask questions I’m asking to be spoon fed. I see how it is. 🙂

  44. Allan Miller: As has been said, it’s not simply the code differences…

    So keiths was being overly simplistic. No doubt because he was trying to spoon feed me. 🙂

    keiths: They are thought to have shared a common ancestor with the organism that engulfed them. Which ought to be obvious, given that their genetic code differs by only 3 codons out of 64.

    So there you have it straight from keiths. The simple fact of only three differences should be enough to make common ancestry obvious.

    Pardon me for being skeptical of his claim.

  45. Mung,

    When you try to cover up your mistakes, you just end up tripping over yourself. Is it really worth it?

    If you’re now denying that by ‘origin’ you meant ancestry, then my initial criticism applies. You had no idea what Allan and J-Mac were discussing when you barged into the conversation.

    Reading comprehension, Mung.

  46. Some of my detractors complain I’ve thrown in diversions. Well in this comment I plead guilty.

    Here is Janine playing music. Only God could create something like her. Sublime:

  47. keiths:

    They are thought to have shared a common ancestor with the organism that engulfed them. Which ought to be obvious, given that their genetic code differs by only 3 codons out of 64.

    Mung:

    So there you have it straight from keiths. The simple fact of only three differences should be enough to make common ancestry obvious.

    Because Mung is incapable of inferring that a difference of 3 out of 64 would mean that the remaining 61 are identical.

    It’s a fiendishly difficult inference, Mung, but here goes. I’ll use Allan’s updated figure of 4 different codons.

    1. The codons that are not different are the same.
    2. There are 64 codons total.
    3. 4 are different.
    3. 64 – 4 = 60.
    5. Therefore, 60 are the same.

    Whew. That was hard, wasn’t it, Mung?

  50. Allan Miller:
    newton,

    Heh. And with the wordplay out the way, I wonder what Design reason suggests itself for the various variant codes?

    Whimsical design, it is wordplay all the way down

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