Promiscuous Domains and Motifs Are Better Explained by Common Design than Common Descent, (Sal’s module Hypothesis)

Dr. Winston Ewert put forward his module hypothesis, but I put forward an alternate module hypothesis at the domain and motif level of proteins. It is based actually on papers by evolutionists who have pointed out that the problem of “Promiscuous Domains” remains an unsolved problem in evolutionary biology.

When I put Promiscuous Domains on the table in the Common Design vs. Common Descent thread, the TSZ Darwinists ignored the problem and then declared victory. I viewed their non-response as evidence they didn’t understand the problem and/or preferred to ignore it.

Perhaps pictures are worth ten thousand words. From the NIH, that great source inspiration for the Intelligent Design community, we have the CDART database viewer.

From the CDART viewer, I provide a few of the thousands of diagrams that show the promiscuity of protein domains. The diagrams below show the classical zinc finger ZF-C2H2 “ZF” domain and the Plextrin Homology “PH” domains. Note how the location of domains is “shuffled” to different locations in different proteins. It’s as if proteins are made by different lego-like parts in different order and position. My preliminary look into small 4-amino acid motifs that are the target of phosphorylating kinases suggests the the problem of promiscuity goes all the way down to small motif levels.

Such promiscuity is more consistent with common design than common descent.

Click to Enlarge Classical ZF-C2H2 Zinc Finger Page 5
zf 5

Click to Enlarge Classical ZF-C2H2 Zinc Finger Page 157
cf 157

Click to see all CDART Classical ZF-C2H2 Zinc Finger Architectures

Plextrin Homology Page 1
ph 1

Click to Enlarge Plextrin Homology Page 5
ph 5

Click to see all CDART Plextrin Homology Architectures

920 thoughts on “Promiscuous Domains and Motifs Are Better Explained by Common Design than Common Descent, (Sal’s module Hypothesis)

  1. stcordova,

    I don’t think unguided evolution can randomly shuffle domains and get something coherent.

    The idea that unguided processes are responsible for living organisms is incoherent once you begin to understand life at the cellular level.

  2. stcordova: It’s more subtle than that, what if the Designer wanted to highlight multiple functions, he could do so with a hierarchical arrangement.Random variation will not work, btw, for co-regulated motifs spread across multiple proteins, as I was trying to show with the PhosphoSite motif search.

    There’s a bit of a bind here. Once you start speculating on a designer’s motives it becomes hard to do anything like science with it, but if you don’t, assuming your creator is omnipotent, it’s impossible. It’s a cross you bear, I suppose.

    But the data don’t support your idea. There is no sensible reason for a designer to use a nested hierarchy to achieve the result you have suggested, and we can’t infer that motive from the data. And there’s a real downside: the obvious conclusion from nested hierarchy is common descent, so a creator who didn’t want to deceive would have found some other way to communicate his message.

    Many of the phylogeny programs don’t deal with the creation of “promiscuous” domains either with models of little point mutation and small indel changes,

    Offhand I don’t know of a phylogeny program that deals with indels, except for POI, which nobody uses. What are you thinking of?

    so promiscuous domains and motifs don’t fit most traditional single protein or DNA segment phylogenetic analyses, especially domains and motifs spread across multiple proteins simultaneously in a way that facilitates coherent co-regulation.

    Sorry, but that bit was gibberish. It’s hard to respond other then to mention that fact.

    The evidence of promiscuous functional domains and motifs argues against random mutation. Random variation carries with it expectation values and outcomes, and coordination isn’t an expected outcome.That’s why tornadoes passing through a junkyard don’t create functioning 747 jetliners.

    Are we or are we not talking about common descent vs. separate creation here? How does an argument against random mutation have any relevance?

    In any case, thanks for participating in the discussion.Your objection for the weak taxonomic sample was an excellent one, and so was your complaint about the color scheme of MEGA.

    They’re also things you shouldn’t have needed me to point out. As are my other objections.

  3. John Harshaman:
    Sorry, but that bit was gibberish. It’s hard to respond other then to mention that fact.

    Whether what I said is gibberish or not (I don’t think so), nothing you or any evolutionary biologists have shown that promiscuous domains are the expected outcome of common descent with random mutation, in fact, you’ve totally ignored the difficulties of creating integrated function as you always have. As usual, you remain committed to not engaging the difficulty of random mutations and selection creating integrated systems, several of which systems are alluded to by the components I’ve highlighted like the KRAB proteins and the chromatin writers.

  4. John Harshman: Many of the phylogeny programs don’t deal with the creation of “promiscuous” domains either with models of little point mutation and small indel changes,

    Offhand I don’t know of a phylogeny program that deals with indels, except for POI, which nobody uses. What are you thinking of?

    Sal thinks that if something other than point, aka single nucleotide, mutations / deletions / insertions is involved, then it’s not common ancestry, therefore god-did-it. That recombination produces those patterns, and that recombination is a well established phenomenon, doesn’t matter to him. It’s not single-nucleotide mutations, therefore not common ancestry, therefore god-did-it.

    Yup. As hard as it is to believe it, that’s what he has in mind.

  5. stcordova: Whether what I said is gibberish or not (I don’t think so), nothing you or any evolutionary biologists have shown that promiscuous domains are the expected outcome of common descent with random mutation, in fact, you’ve totally ignored the difficulties of creating integrated function as you always have.

    Don’t you see how you’re conflating “common descent” with “common descent with random mutation”? I have usually argued for the former, not the latter (though I think the latter is also true). You, on the other hand, think that arguing against random mutation is also arguing against common descent, which it is not.

    As usual, you remain committed to not engaging the difficulty of random mutations and selection creating integrated systems, several of which systems are alluded to by the components I’ve highlighted like the KRAB proteins and the chromatin writers.

    The reason I don’t engage with it is that it isn’t relevant to the question of common descent, which is in fact the ostensible subject as mentioned in your title.

    Incidentally, it annoys me that you almost never engage with my entire post, just with a sentence or two that you pick out for reasons that aren’t clear.

  6. Entropy: Sal thinks that if something other than point, aka single nucleotide, mutations / deletions / insertions is involved, then it’s not common ancestry, therefore god-did-it. That recombination produces those patterns, and that recombination is a well established phenomenon, doesn’t matter to him. It’s not single-nucleotide mutations, therefore not common ancestry, therefore god-did-it.

    Yup. As hard as it is to believe it, that’s what he has in mind.

    That isn’t even what I asked about, though Sal seems not to have noticed. I asked which phylogenetic programs he’s thinking about that deal with indels at all.

  7. John Harshman: That isn’t even what I asked about, though Sal seems not to have noticed. I asked which phylogenetic programs he’s thinking about that deal with indels at all.

    I know what you asked. But you asked because you missed Sal’s real problem: it’s not single/small nucleotide changes, therefore god-did-it. Look at his claim. It’s not about whether software deals with indels, it’s that small indels and little point mutations don’t work for explaining domain shuffling. Of course not. That requires larger events, recombinations. But, in Sal’s mind, if it’s not tiny changes, it’s not evolution, therefore it’s magical being in the sky.

  8. John Harshman:

    Incidentally, it annoys me that you almost never engage with my entire post, just with a sentence or two that you pick out for reasons that aren’t clear.

    Some of what you say I simply dismiss as not substantive, nor relevant, or I simply didn’t get around to it. Sorry.

    But quid pro quo, you completely ignore glaring problems that I point out, and blindly assert common descent is the best explanation based on what? Is it first principles of physics and chemistry or a Designer that puts miracles in place to make common descent possible? If you’re going to admit non-random, but rather guided mutations, you may as well be an ID proponent.

    Unless you admit the problems I pointed out with promiscuous domains, I think the rest of your points are pretty minor by comparison.

  9. The classical zinc-finger architecture doesn’t look especially daunting for random mutation to achieve. One needs about 30 amino acids and 2 Cysteines and 2 Histidines in the right place. What’s the odds of that? Well, a rough order guess, 1 out of 20^4 = 160,000. Not astronomical, but there are likely other constraints on the other residues, so maybe 1 in a million?

    But there is another problem, what’s the likelihood it’s going to pop up in a protein that is already functional and not compromise it? If we re-purpose a protein to a different function, we likely break it’s pre-existing function.

    Ok, so we gene duplicate it and then it’s free to MAYBE make a zinc finger. Ok, so it makes a zinc finger, will it be in a protein that’s functionally coherent. For example, the chromatin/histone modifying protein/transcription factors with zinc fingers need to be targeted to the right DNA AND the right histone AND the right amino acid position on the histone tail AND the right post translational modification.

    Sooo, in as much as a random number generator can occasionally spell out a recognizable word, to do so in a context where recognizable sentence come out is highly unlikely.

    Everything I’ve pointed out would mostly apply to shuffled exons somehow transplanting a zinc finger to another protein.

    Finally, zinc fingers are small domains, there are thosands of other domains, many are substantially more complex, such as those that compose the TopoIsomerase family, for example.

  10. John Harshman:

    There is no sensible reason for a designer to use a nested hierarchy to achieve the result you have suggested,

    Well, John, you are dictating how you think God would do business in that case.

    What I have laid out is whether constructions of species allows scientific discovery. As I showed with the metal binding sites in zinc fingers, you can clearly see the conserved regions highlight functionally important amino acid residues. By way of extension, other functionally important regions could be highlighted by conservation, perhaps not by ALL species, but subsets of species. That would clearly seem to be the case with post translational targets restricted to taxonomic groups.

    So, I don’t have to guess necessarily what the Designer had in mind, I just have to observe correlations that are non-random and far beyond expectation. That would be the case with promiscuous motifs, and that would definitely be the case if life is young.

  11. Introducing the SET domain. Acutally, I provided a picture above of some of the proteins with SET domains.

    From wiki:
    https://en.wikipedia.org/wiki/SET_domain

    This describes proteins with SET domains:

    recently there were described three structures of very different proteins with distinct domain compositions:

    Neurospora crassa DIM-5, a member of the Su(var) family of histone lysine methyltransferases (HKMTs)[1] which methylate histone H3 on lysine 9,
    human SET7 (also called SET9), which methylates H3 on lysine 4
    garden pea Rubisco LSMT, an enzyme that does not modify histones, but instead methylates lysine 14 in the flexible tail of the large subunit of the enzyme Rubisco.

    recently there were described three structures of very different proteins with distinct domain compositions:

    recently there were described three structures of very different proteins with distinct domain compositions:

    recently there were described three structures of very different proteins with distinct domain compositions:

    How does common descent explain that?

    And some candy for the eyes. Below is one page out of 20 for the SET domain alone. How does common descent explain that? Answer: it doesn’t.

    Click to ENLARGE

  12. John Harshman:
    What function does “common” have in your title except to mimic the term “common descent”? What does the term “common design” actually mean? You need to flesh out your model before it’s possible to test it. If you refer to separate creation of species, that’s one thing. Separate creation of some nebulous higher taxonomic grouping is another. And how do you rule out common descent with occasional divine intervention to confer particular mutations?

    So far you’re just putting up a bunch of colorful pictures and shouting “wow”. Make some kind of argument for some particular model in contrast to some other particular model.

    Common design was the first hypothesis on biological origins.
    the bible and man presumed a creator created biology on a blueprint.
    thats why all have the same eye styles or almost.
    We all look very much alike just as a creator would do in making a organized universe. not just in physics.
    Evolutionism tries to take physics from biology. Sure it does.
    As if saying physics evolved and is evolving. No one ever says its evolving.

    Common descent is a johnny come lately idea that likeness in biology is PROOF its from a common mother/father.
    In fact evolutionism PROVES it only sees common descent as a exclusive option. Common design is not even a option and so why the wrong idea gets fixed for too long.
    Common design can mean anything from a creator.
    a creator could do that with common designs.
    In groups or parts or left alone but within boundaries.

  13. stcordova: Some of what you say I simply dismiss as not substantive, nor relevant, or I simply didn’t get around to it.Sorry.

    Don’t say “sorry” if you aren’t really sorry. I think you don’t get around to it because you don’t want to think about it and have no sensible answer. But that’s just me.

    But quid pro quo, you completely ignore glaring problems that I point out, and blindly assert common descent is the best explanation based on what? Is it first principles of physics and chemistry or a Designer that puts miracles in place to make common descent possible? If you’re going to admit non-random, but rather guided mutations, you may as well be an ID proponent.

    This is very confused. The glaring problems you point out are not problems for common descent. Why can’t any creationist understand this simple fact? Common descent is a separate issue from the origin of variation. If they’re glaring problems, they are problems for random mutation, natural selection, and such. (I don’t think they actually are, but that isn’t any more relevant to the real issue than the glariing problems themselves are.) I’m not admitting guided mutations; I’m saying that whether they’re random or guided is irrelevant to common descent. Some ID proponents also accept common descent — Behe, for example. He at least understands that these are unrelated issues.

    Now, why common descent? Because it’s the only tenable explanation for nested hierarchy. The explanation you have proposed doesn’t imply nested hierarchy at all.

    Unless you admit the problems I pointed out with promiscuous domains, I think the rest of your points are pretty minor by comparison.

    That might be the case if the issue were not common descent. Would you care to change the title of your post?

    Well, John, you are dictating how you think God would do business in that case.

    As I have already pointed out, it’s necessary to hypothesize God’s motives and methods in order to come up with a testable hypothesis. It’s in fact just what you were doing with your attempted explanation of nested hierarchy and sequence variation. All I did was point out that your claimed motivation doesn’t result in what you think it does. So don’t get huffy.

    What I have laid out is whether constructions of species allows scientific discovery. As I showed with the metal binding sites in zinc fingers, you can clearly see the conserved regions highlight functionally important amino acid residues.

    Wouldn’t purifying selection acting on random mutation achieve the same result? How can you assert that your explanation is better than that? Note, again, that this has zero to do with common descent.

    By way of extension, other functionally important regions could be highlighted by conservation, perhaps not by ALL species, but subsets of species. That would clearly seem to be the case with post translational targets restricted to taxonomic groups.

    Doesn’t this sound to you, just a teeny little bit, like special pleading, applicable post hoc to any observation at all?

    So, I don’t have to guess necessarily what the Designer had in mind, I just have to observe correlations that are non-random and far beyond expectation. That would be the case with promiscuous motifs, and that would definitely be the case if life is young.

    You really need to expand on your reasoning there. Your hypothesis is exactly guessing what the designer had in mind. Correlations of what? Beyond what expectation? What does it have to do with life being young?

    I fully realize you will ignore almost all of this, if not the whole thing. That’s how you work. Yet I find it interesting to point out the gaping holes in your claims, even if you never address them.

  14. stcordova: How does common descent explain that?

    Common descent doesn’t explain that. Common descent is very limited in what it explains. It doesn’t explain the origins of genes, or motifs, or anything other than the pattern of distribution of various characters across species. But it explains that pattern quite well, and you have no explanation for that pattern at all. Well, except for “it pleased god to make it look like that”, which is no explanation.

  15. John Harshman:

    Why can’t any creationist understand this simple fact? Common descent is a separate issue from the origin of variation. If they’re glaring problems, they are problems for random mutation, natural selection, and such.

    Your phylogenetic models are based on lots of random variation to account some (not all) of the hierarchical patterns. There are two components (at least) that may not be consistent with this:

    1. orphan genes or taxonomically restricted genes/proteins, especially those whose transitional forms could be lethal

    2. promiscuous domains and motifs that may contribute to creating hierarchical pattern — that is something I’m looking at now, this is to be determined, but I’ve laid out some of the preliminary findings, such as taxnomically restricted post-translational modifications appearing on ubiquitous proteins across species such as Topoisomerase

    The “promiscuous motifs” and “promiscuous domains” are testable claims. Further, it is worth looking to what extent “promiscuous motifs” and “promiscuous domains” contribute to the hierarchical patterns in individual protein phylogenies.

    In any case, my interaction with you has been very beneficial to extending my thought process and critical thinking.. Apologies if you don’t find this discussion equally valuable to your understanding of reality.

  16. stcordova: Your phylogenetic models are based on lots of random variation to account some (not all) of the hierarchical patterns.

    No, they aren’t. They are based on the existence of variation. Whether it’s random is not relevant.

    There are two components (at least) that may not be consistent with this:

    1. orphan genes or taxonomically restricted genes/proteins, especially those whose transitional forms could be lethal

    2. promiscuous domains and motifs that may contribute to creating hierarchical pattern — that is something I’m looking at now, this is to be determined, but I’ve laid out some of the preliminary findings, such as taxnomically restricted post-translational modifications appearing on ubiquitous proteins across species such as Topoisomerase

    You’re still talking about the origin of variation, which has nothing to do with the pattern of variation. How is it possible you don’t see this?

    The “promiscuous motifs” and “promiscuous domains” are testable claims.Further, it is worth looking to what extent “promiscuous motifs” and “promiscuous domains” contribute to the hierarchical patterns in individual protein phylogenies.

    They contribute to the pattern regardless of their cause. I also think you have confused the testable claim that they exist with the claim of their causes, which may not be testable. At least, so far you have not suggested a testable claim for their causes.

    In any case, my interaction with you has been very beneficial to extending my thought process and critical thinking..Apologies if you don’t find this discussion equally valuable to your understanding of reality.

    Again with the fake apologies. It’s all about you, and you don’t care about anyone else. How very Christian of you.

  17. If common descent needs statistical miracle to make it happen such that the miracle is indistinguishable from acts of special creation, then claiming it’s still common descent is superfluous.

    I just looked ate ZNF136. Which is in the list above which I provide below again.

    It sort of looks taxonomically restricted. That’s one of the multi zinc finger proteins. How do you root that phylogenetic tree for ZNF136 since as far as I can tell it’s restricted to Primates? Don’t you sort of need a common ancestral protein root the thing?

    John Harshman:

    They are based on the existence of variation. Whether it’s random is not relevant.

    So if statistically speaking, if a variation appears like it would take a miraculous act of special creation, just because the pattern can still be force fit into a hierarchical view of biology, you’d still accept common descent because you argue, “since I John Harshman wouldn’t do make hierachical patterns in biology if I created all life through acts of special creation, certainly God wouldn’t, therefore no matter how miraculous looking some of the variations are, I’ll accept common descent.”

    What I mean by “force fit” is that taxnomically restricted features that pop up in a way that is statistically improbable, would still fit in a hierarchical tree, for example taxonomically restricted SETS of genes that are deeply integrated in the systems of the organism are statistically improbable, but the organism can still be force fit into at hierarchical arrangement.

    The best example, and one which you NEVER NEVER NEVER acknowledge is statistically prohibitive is the divide between eukaryotes and prokaryotes.

  18. John Harshman:

    Again with the fake apologies. It’s all about you, and you don’t care about anyone else. How very Christian of you.

    I respect and value your knowledge and expertise, which is more than I can say for Entropy’s “knowledge” and “expertise.” 🙂

  19. stcordova,

    If common descent needs statistical miracle to make it happen such that the miracle is indistinguishable from acts of special creation, then claiming it’s still common descent is superfluous.

    I agree with this. Common descent is at best a partial explanation for the nested pattern.

  20. stcordova:
    If common descent needs statistical miracle to make it happen such that the miracle is indistinguishable from acts of special creation, then claiming it’s still common descent is superfluous.

    You still have no comprehension of the difference between the evidence for common descent and the evidence for random mutation and natural selection. The nested hierarchy is evidence for common descent. Even if a miracle is required to produce each and every mutation, common descent is the best explanation for the taxonomic distribution of those miracles. So in fact, miracles that are organized in a nested hierarchy are not indistinguishable from acts of special creation, if by that you mean creation of species rather than creation of mutations.

    I just looked ate ZNF136.Which is in the list above which I provide below again.

    It sort of looks taxonomically restricted.That’s one of the multi zinc fingerproteins.How do you root that phylogenetic tree for ZNF136 since as far as I can tell it’s restricted to Primates?Don’t you sort of need a common ancestral protein root the thing?

    Well, first, “as far as I can tell” isn’t very far, as far as I can tell. You have not investigated the evolution of that protein at all. But if it is indeed restricted to primates without any clue as to how it arose, that’s not a sign that primates (or the various species of primates) were separately created. At most it’s evidence that the protein was created in the common ancestor of all primates but not the common ancestor of all mammals, etc. You still don’t see the distinction.

    So if statistically speaking, if a variation appears like it would take a miraculous act of special creation, just because the pattern can still be force fit into a hierarchical view of biology, you’d still accept common descent because you argue, “since I John Harshman wouldn’t do make hierachical patterns in biology if I created all life through acts of special creation, certainly God wouldn’t, therefore no matter how miraculous looking some of the variations are, I’ll accept common descent.”

    Again, once you have to decide what the creator’s whims ought to be, you take yourself outside science. You’re the one claiming that the creator would have made a nested hierarchy, which follows from no reasoning at all other than “we see what we see, therefore that’s what god wanted”. The reasoning from nested hierarchy to common descent, on the other hand, is simple and obvious. You now have to present some kind of argument why a creator implies no common descent. Why couldn’t he have worked by tweaking evolving lineages? That would account for the nested hierarchy and your supposed evidence of miracles. So why do you reject that model?

    What I mean by “force fit” is that taxnomically restricted features that pop up in a way that is statistically improbable, would still fit in a hierarchical tree, for example taxonomically restricted SETS of genes that are deeply integrated in the systems of the organism are statistically improbable, but the organism can still be force fit into at hierarchical arrangement.

    You aren’t making much sense here. In what way is the fit forced? What do you mean by “statistically improbable”? You’re being self-contradictory. First you say that you’ve explained nested hierarchy, then you claim that there is no such thing.

    The best example, and one which you NEVER NEVER NEVER acknowledge is statistically prohibitive is the divide between eukaryotes and prokaryotes.

    Please explain what makes this statistically improbable. Are you talking about the necessary mutations? Let’s recall that the origin of mutations has nothing to do with the evidence for common descent. I’ll also point out that this divide has been narrowing considerably since the discovery of various new groups of Archaea.

  21. colewd:
    stcordova,

    I agree with this.Common descent is at best a partial explanation for the nested pattern.

    That’s once again because you and Sal have no comprehension of the difference between nested hierarchy and the changes that make up the hierarchy. Common descent is a complete explanation of the nested pattern. It doesn’t explain the changes themselves. When you conflate the two, you produce confused nonsense like the above.

  22. stcordova: I respect and value your knowledge and expertise, which is more than I can say for Entropy’s “knowledge” and “expertise.”

    Some Christian. You can’t compliment me without insulting a third party.

  23. colewd:
    John Harshman,

    Then support this claim beyond mere assertion.

    This just goes back to the basic idea you can’t understand, which is that the pattern of changes is not the same as the changes themselves. If common descent is incomplete, what about the pattern (not about the changes) does it fail to explain? This isn’t about empirical evidence; it’s about elementary reasoning, about what “explain” means, and about what “nested hierarchy” means. I have fully supported the claim that common descent completely explains nested hierarchy; it’s just another way of saying that nested hierarchy is an expected result of common descent. I can’t see how I could possibly explain this more simply.

    As I’ve said, you will never understand this. But nothing more can be done.

  24. John Harshman,

    I have fully supported the claim that common descent completely explains nested hierarchy; it’s just another way of saying that nested hierarchy is an expected result of common descent. I can’t see how I could possibly explain this more simply.

    Why is it an expected result of common descent?

  25. colewd:
    John Harshman,

    Why is it an expected result of common descent?

    I have explained this many times. Do you truly not understand why sprinkling inherited changes over a tree of branching lineages results in a nested hierarchy of the data extracted from the species at the tips of that tree? I have directed your attention to a diagram showing how that works. Do you remember that? What else could I possibly do?

  26. John Harshman: I have explained this many times. Do you truly not understand why sprinkling inherited changes over a tree of branching lineages results in a nested hierarchy of the data extracted from the species at the tips of that tree? I have directed your attention to a diagram showing how that works. Do you remember that? What else could I possibly do?

    Sprinkling heritable changes? So, in your view, common descent could be compatible with miraculously created and/or intelligently designed heritable changes that were sprinkled into lineages. Is that right?

  27. stcordova:
    I respect and value your knowledge and expertise, which is more than I can say for Entropy’s “knowledge” and “expertise.”

    I’d answer that if I thought that Sal could read for comprehension. But, sadly, he cannot.

  28. stcordova: Sprinkling heritable changes?So, in your view, common descent could be compatible with miraculously created and/or intelligently designed heritable changes that were sprinkled into lineages.Is that right?

    Yes. How is it possible that, after years of discussion, you only now realize this?

  29. colewd:
    John Harshman,

    What are “sprinkled inherited changes”?

    I mean that changes occur, for whatever reason, with whatever cause, at various times in various lineages, and are inherited by their descendants. Was that really unclear or are you stalling?

  30. Entropy posts are reasonable substitutes for Glen Davidson’s vacuuous posts. They serve the purpose of keeping my thread alive.

    Can you provide a few more ad homs and racists comments toward me like have in the past, just to liven things up?

  31. stcordova:
    Can you provide a few more ad homs and racists comments toward me like have in the past, just to liven things up?

    Sorry Sal, but it was you who interpreted my calling you by a Latin-American nickname as racist, when I did that because I’m Latin-American, and that’s the common nickname for my Salvador friends. That you’re ashamed of being called by a Latin-American nickname shows your racism, not mine.

    ETA: Also, calling you illiterate is not ad hominem, it’s a conclusion from your demonstrated inability to read for comprehension.

  32. John Harshman,

    I mean that changes occur, for whatever reason, with whatever cause, at various times in various lineages, and are inherited by their descendants. Was that really unclear or are you stalling?

    How do you determine that all these changes occurred as a result of the reproductive process and are indeed the result of inheritance?

  33. colewd:
    John Harshman,

    How do you determine that all these changes occurred as a result of the reproductive process and are indeed the result of inheritance?

    It’s irrelevant whether they occurred by the reproductive process, whatever you mean by that. The reason they occurred is not relevant to the fact of their having happened at a particular time in a particular lineage. They aren’t the result of inheritance. Inheritance isn’t what causes things to occur; it’s what causes things that are present in ancestors to be present in descendants.

    I’m trying to keep the language as simple as possible here.

  34. John Harshman,

    Inheritance isn’t what causes things to occur; it’s what causes things that are present in ancestors to be present in descendants.

    Ok. Do you agree that the “sprinkled inherited changes” are occurring during the reproductive process?

    How do you isolate it as a cause of the same or similar genes versus special creation where components may be reused?

    How do argue against the claim that we may be observing both in the hierarchal pattern?

  35. colewd:
    John Harshman,

    Ok. Do you agree that the “sprinkled inherited changes” are occurring during the reproductive process?

    How do you isolate it as a cause of the same or similar genes versus special creation where components may be reused?

    How do argue against the claim that we may be observing both in the hierarchal pattern?

    Yeah, John, how’d you do that IN PRINCIPLE?

  36. colewd:
    John Harshman,

    Ok. Do you agree that the “sprinkled inherited changes” are occurring during the reproductive process?

    So near, and yet so far. First, as I have said just above, it’s irrelevant whether they occur during the reproductive process. Second, it’s true that most mutations occur either in DNA replication or in meiosis, but some occur at other times. It’s conceivable (though I doubt it) that some are zapped in directly by god, and if so it hardly matters when.

    How do you isolate it as a cause of the same or similar genes versus special creation where components may be reused?

    What do you mean by “it”? If by “special creation” you refer to separate creation of species, we have no reason to expect a nested hierarchy from that sort of process.

    How do argue against the claim that we may be observing both in the hierarchal pattern?

    Because a nested hierarchy is not expected from separate creation of species. Or do you mean something different by “both”? What in fact are you trying to say?

  37. stcordova: Yeah, John, how’d you do that IN PRINCIPLE?

    Ah, so now there’s a tag team of the clueless operating here. How did I do what IN PRINCIPLE? Please state your question in the form of a coherent sentence.

  38. John Harshman,

    Inheritance isn’t what causes things to occur; it’s what causes things that are present in ancestors to be present in descendants.

    In order for inheritance to explain the hierarchal structure it needs to explain the differences along with the similarities.

    What do you mean by “it”? If by “special creation” you refer to separate creation of species, we have no reason to expect a nested hierarchy from that sort of process.

    A pure assertion.

    Because a nested hierarchy is not expected from separate creation of species. Or do you mean something different by “both”? What in fact are you trying to say?

    Your claim is the pattern is completely explained by common descent. How do you know that it is not a combination of common descent and special creation causing the pattern.

    You claim a hierarchal pattern is caused by ancestry (common descent) yet the only evidence you are claiming that supports ancestry are similar features.

  39. John Harshman: This just goes back to the basic idea you can’t understand, which is that the pattern of changes is not the same as the changes themselves. If common descent is incomplete, what about the pattern (not about the changes) does it fail to explain? This isn’t about empirical evidence; it’s about elementary reasoning, about what “explain” means, and about what “nested hierarchy” means. I have fully supported the claim that common descent completely explains nested hierarchy; it’s just another way of saying that nested hierarchy is an expected result of common descent. I can’t see how I could possibly explain this more simply.

    As I’ve said, you will never understand this. But nothing more can be done.

    It diesn’t explain nests as a mechanism. Nor does it prove there are nests except in minor cases.
    Your imagining nests because of like traits in biolopgy. Your seeing eyeballs everywhere and CONVINCING YOURSELVES SCIENTIFICALLY thats proof of common descent. It isn’t. its proof of likeness.
    YES all mankind comes from common descent of Adam/Eve. YES.
    Yet its a minor point of the nests of humans and not proof of actual lineage. other mechanisms can explain differences without a mere drifting away.
    Nests only matter if they explain common descent of great biology. Not cichlid fishes only.

  40. colewd:
    John Harshman,

    In order for inheritance to explain the hierarchal structure it needs to explain the differences along with the similarities.

    To be more accurate: it needs to explain the pattern of differences and similarities among taxa. And in fact it does.

    [That a nested hierarchy is not expected from separate creation of species is] A pure assertion.

    If that assertion were incorrect, you should be able to explain why we expect a nested hierarchy from separate creation. Please do so now. If you can’t, that’s good evidence for my point.

    Your claim is the pattern is completely explained by common descent.How do you know that it is not a combination of common descent and special creation causing the pattern.

    What do you mean by “a combination”? Please explain the scenario you’re putting forward, and I’ll explain, if I can (and I predict that I can) why it would not produce a nested hierarchy.

    You claim a hierarchal pattern is caused by ancestry (common descent) yet the only evidence you are claiming that supports ancestry are similar features.

    All that tells me is that you don’t actually know what a nested hierarchy is. It’s not “similar features”. It’s a particular pattern of similarities and differences.

  41. John Harshman,

    Bill

    In order for inheritance to explain the hierarchal structure it needs to explain the differences along with the similarities.

    John

    All that tells me is that you don’t actually know what a nested hierarchy is. It’s not “similar features”. It’s a particular pattern of similarities and differences.

    How can you make this statement which is in direct contradiction of what you quoted me saying?

    The problem is your claim nested hierarchy (which includes similarities and differences) is NOT explained by inheritance. Inheritance on its own only explains similarities.

    How do you explain the differences required for a nested hierarchy with inheritance or something else?

  42. colewd:
    John Harshman,

    How can you make this statement which is in direct contradiction of what you quoted me saying?

    Beause what I quoted you saying is wrong. You keep confusing the individual points with the pattern.

    The problem is your claim nested hierarchy (which includes similarities and differences) is NOT explained by inheritance.Inheritance on its own only explains similarities.

    Still more evidence that you don’t understand nested hierarchy. It’s not just inheritance. It’s inheritance from a particular starting point. The species that don’t share the ancestor at that starting point will not have the similarity; they’ll have a difference. See? The tree of common descent explains the pattern of similarities and differences by inheritance in some lineages and lack of inheritance (because they aren’t descended from that ancestor) in others.

    How do you explain the differences required for a nested hierarchy with inheritance or something else?

    It’s really much simpler than you are trying to make it. Just look at the figure in the croc paper.

    Meanwhile, you have ignored everything I asked of you. Let me refresh:

    If that assertion were incorrect [that separate creation does not imply a nested hierarchy], you should be able to explain why we expect a nested hierarchy from separate creation. Please do so now. If you can’t, that’s good evidence for my point.

    What do you mean by “a combination” [of common descent and separate creation]? Please explain the scenario you’re putting forward, and I’ll explain, if I can (and I predict that I can) why it would not produce a nested hierarchy.

  43. John Harshman,

    The species that don’t share the ancestor at that starting point will not have the similarity; they’ll have a difference. See?

    Why will they have a difference?

  44. colewd:
    John Harshman,

    Why will they have a difference?

    Now you’re just being lazy. I invite you to figure this out for yourself. Try looking at that figure in the croc paper if you can’t do it on your own.

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