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.

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

  1. Rumraket: In other words: Things that came later depended on things that happened before.

    Well yes! In order for things to happen in the future things have to be put in place first. For example, for you have become a free thinking adult you had to begin as an unconscious, single celled organism with the ability to develop.

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  2. OMagain: Sure it’s an accident. Otherwise it would matter if they appeared “together” or in a “specific order”. As formulated currently your position is that “whatever happened was no accident”.

    If consciousness is to develop it does matter in which way things develop. The plant world is not developing towards individual consciousness but it has developed in a way that prepared the earthly environment to allow for the evolution of animals which do attain consciousness.

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  3. CharlieM: The plant world is not developing towards individual consciousness

    Plant’s talk to each other, they warn each other of nearby predators, they excrete chemicals designed to make themselves unattractive and if you watch their actions speeded up 1000x you’d think they were as conscious as any lower animal.

    https://www.youtube.com/watch?v=CrrSAc-vjG4

    In short, you are disregarding the reality of the world in favour of a position you find attractive.

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  4. Rumraket: Even more ironically, while phoodoo requires that some things must be observed, to be believable, (morphological change due to evolution), he’s fine accepting that morphological change takes place due to an invisible designer working behind the scenes.

    What morphological change?

    So you think chihuahuas and St. Bernards are indeed examples of change then huh? This is how stupid your idea of change is. Variation isn’t change.

    You show all those different skulls and they all look different don’t they? Boy, they sure do. So why don’t we call these all different animals then? They are not all dogs, some must be poodles, and some must be pekinese, and some must be mastiffs, they can’t be the same animal! I mean heck, those skulls look more different from each other than all the hominids do. So if we found a pug skull and a wolf skull, and we didn’t know what they were, you can bet your ass we would call these completely different animals.

    So that’s what change is to you. You believe one day, if we wait long enough, pugs will become like whales sharks, and Irish setters will become like termites.

    Variation isn’t change dufus. 50,000 generations of e.coli ought to tell you that.

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  5. Allan Miller: This is actually nicely illustrative of the problem one has talking to Creationists – there are just so many, disunited Creationist positions! They unite only in thinking evolution a load of tosh.

    Evolution is ok. It’s evolutionists that I can’t stand.

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  6. Allan Miller: Consider a retroviral insert found in rats and mice but in no other taxa.

    Consider retroviral inserts found in all other primates, but not in humans. Is it a miracle?

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  7. phoodoo: So you think chihuahuas and St. Bernards are indeed examples of change then huh? This is how stupid your idea of change is. Variation isn’t change.

    How did that variation come to exist phoodoo?

    No wolf looks like a St Bernards, or a poodle, or a Chihuahua.

    Variation isn’t change dufus. 50,000 generations of e.coli ought to tell you that.

    Of course it’s change you fool. Just because they’re called E coli doesn’t mean no change has happened. That’s just a label. Really, that’s your argument? They’re still called E coli so nothing has changed? Isn’t that a really stupid thing to say?

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  8. OMagain: Plant’s talk to each other, they warn each other of nearby predators, they excrete chemicals designed to make themselves unattractive and if you watch their actions speeded up 1000x you’d think they were as conscious as any lower animal.

    https://www.youtube.com/watch?v=CrrSAc-vjG4

    In short, you are disregarding the reality of the world in favour of a position you find attractive.

    Thanks for the interesting video. It will take me a while before I’m able to watch it all.

    Meanwhile, do you believe that in order for plants to function in the way shown in the video they need to be conscious in the same way that animals are? For instance do you believe that they feel pain?

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  9. Mung: Consider retroviral inserts found in all other primates, but not in humans. Is it a miracle?

    Why would it be? What is a miracle?

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  10. Mung,

    Consider retroviral inserts found in all other primates, but not in humans. Is it a miracle?

    Not necessarily. Do you have a specific example?

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  11. Mung,

    Evolution is ok. It’s evolutionists that I can’t stand.

    They is sad. They all speak so highly of you.

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  12. John Harshman:

    Mammals are nested within Sarcopterygii because The common ancestor of all Sarcopterygii (not just the living ones) is also an ancestor of mammals.

    That’s circular phylogenetic reasoning, that isn’t structural reasoning. You conflate the two as if they are the same thing, they aren’t. One is speculative (phylogeny on the assumption of common descent), the other is empirical (taxnomic/typological/structural).

    Vertebrates can be structurally defined by:

    The defining characteristic of a vertebrate is the vertebral column, in which the notochord (a stiff rod of uniform composition) found in all chordates has been replaced by a segmented series of stiffer elements (vertebrae) separated by mobile joints (intervertebral discs, derived embryonically and evolutionarily from the notochord).

    You don’t need circularly reasoned Phylogenetic Phantasies to classify a vertebrate as a vertebrate.

    The vertebrates can be sub divided into other groups. Creatures with beaks and feathered wings can be called birds. Creatrues with mammary glands mammals. Aquatic creatures that can respirate with gills can be called fish. You don’t need Phylogenetic Phantasies to make such classifications.

    In fact, Phylogenetic Phantasies make a mess of intuitive classification. Phylogenetic Phantasy says “tetrapods are Sarcopterygiian fish” — which in effect says: parrots are fish, giraffes are fish, elephants are fish, kangaroos are fish, frogs are fish, penguins are fish, bears are fish, buffalo are fish, horses are fish, lions are fish, dogs are fish, cats are fish, turtles are fish.

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  13. Allan Miller:

    Sal would have it that the presence of this insert is an ‘incongruity’ that actually means that rats and mice do not nest in the Rodentia.

    No, because when nesting is based on structure, not phylogentic phantasies, rats and mice will nest together.

    Have you been to a grocery store? Did you notice they label things : fish, poultry (birds), meats (cow meat, lamb meat). These are structural classifications. They existed long before Darwin and phylogenetic phantasies. One can construct a real nested hierarchy based on structure. This is true morphologically and also at the molecular level.

    Linnaeus was among those who formalized and systematized structural classification. The evolutionist came along trying to make themselves relevant, and reclassified birds as fish with their phylogenetic phantasies rather than resorting to the more naturally intuitive taxonomic/typological/structural classification.

    Chemists don’t classify things on phylogeny but on structure and function (chemical activity). To the extent biology can be defined by chemical systems, it only makes sense to extend the chemical system of classification to complex arrangements of matter.

    Because of HGT, we don’t define bacteria by their gene trees, we essentially do a structural comparison. There are relatively discrete properties that distinguish them even after HGT.

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  14. John Harshman:

    Since the origin of characters is irrelevant to the subject of this thread

    Says who? You or the author of this thread (me). What I said in the OP:

    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 you’re trying to redefine the terms of the OP because it apparently makes your position quite indefensible. Common descent assumes that over N-generations, one thing can evolve to another, and that one feature can change to another in mechanistic terms.

    There is not much of a barrier to evolving one gene to have some allelic variants by point mutation. One can build gene trees on such alleles-like variants. Creationists would have no problem with that, and instead of clades, they would believe the phylogeny defines clans and nations just like in Genesis 10.

    It becomes harder however when the allele-like variants within a gene family imply -omic changes like phospho proteome, acetyl proteome, methyl proteome, glyco conjugation and other postranslation modifications.

    Variation becomes a gargantuan problem when it requires simultaneous coordinated change — a POOF. At that point, such transformations become a problem for common descent because ordinary mechanisms won’t explain how a prokaryote-like creature will give rise to a eukaryote. Therefore if a transformation can’t happen during a process of common descent, common descent stops being a viable explanation for the existence of diversity. If common descent is falsified, then the patterns of similarities are common design.

    So, the question you may or may not have answered, but worth setting the record straight on. “Hypothetically, what structure in a species would persuade you common descent was false?” If you say there would be no such structure in principle, then even if God made life with a set of miracles, you’d never be able to infer it. I asked the same question (in a different way) Rumraket, and I don’t think he answered. I think I’d like to hear Allan Miller’s response.

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  15. Some house keeping:

    http://theskepticalzone.com/wp/common-design-vs-common-descent/comment-page-85/#comment-203381
    Dr. Entropy:

    Must be too hard for an illiterate like yourself.

    I’d explain this in Spanish, but I think your problem is not the language, but the lack of an appropriate educational background.

    You can criticize my educational background, but you’re pointing to my ethnicity here based on my name. That’s an insulting racist slur.

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  16. I mentioned the phospho proteome and other -omes as being barriers to mutation to genes between species. Evolutionists build their gene tree phylogenies on simplistic assumptions that there isn’t much functional compromise in changing amino acid residues, that there may not be very much species-specific function associated with the difference in amino acids on the same gene across species. I think that is a simplistic and inaccurate view of the importance of amino acid sequences on a species-specific basis.

    I’ve argued that this is a highly pre-mature simplification. To see the importance of the species-specific phosphoproteome, acetyl proteome, methyl proteome, etc. consider the importance of a single amino acid or even the amino acids near them.

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2813771/

    There are a number of cases in which mutations of the post-translational target sites were found to be directly involved in disease. One example is a loss of N-linked glycosylation in the prion protein (PRNP), where amino acid substitution T183A was shown to be involved in autosomal dominant spongiform encephalopathy [8]. This particular variant causes numerous clinical symptoms such as early-onset dementia, cerebral atrophy, and hypometabolism. Interestingly, a wild-type form of PRNP was also found to be protease-resistant in the presence of the mutant. N-linked glycosylation occurs on asparagine residues in NX[ST] motifs, thus the loss of the threonine in the consensus sequence prevents the attachment of a carbohydrate. Modifications of the NX[ST] motif have previously been implicated in intracellular accumulation of PRNP in vitro [9]. Another example is a loss of acetylation sites in androgen receptor (AR). Loss of AR acetylation has been implicated in Kennedy’s disease, an inherited neurodegenerative disorder. Here, amino acid substitution K630A or both K632A and K633A have been shown to cause a significant slowdown of ligand-dependent nuclear translocation [10]. Furthermore, the non-acetylated mutants misfold and form aggregates with several other proteins, including ubiquitin ligase E3, thus affecting proteosomal degradation. And yet another example involves serine phosphorylation in the period circadian protein homolog 2 protein (PER2). Mutation of S662 is associated with the familial advanced sleep phase syndrome, an autosomal dominant disorder with early sleep onset (around 7:30pm) and early awakening (around 4:30am), but normal sleep duration [11]. Biochemical studies have shown that phosphorylation of S662 affects phosphorylation (by casein kinase CKIε) of several other residues in PER2, resulting in an overall hypophosphorylation of PER2. Interestingly, creation of a negative charge by S662D or an excess of CKIε restores the phosphorylation patterns of PER2. The current working hypothesis regarding PER2 is that phosphorylation of S662 likely creates a recognition site for CKIε and triggers a cascade of downstream effects.

    Recall, I said, there has to be an addressing scheme so the right Serine is modified on the right protein. This addressing scheme can be compromised if the amino acid sequence is changed since the amino acid sequence serves as a street sign of sorts:

    One such situation occurs with mutation R16C, which diminishes phosphorylation of S19, in human PTP synthase and causes hyperphenylalaninemia [32–34]. The situation where a substitution site and the modification site are at the same position is referred to as the direct match. A substitution site that is no more than 3 residues away from the modification site is referred to as the neighborhood match.

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  17. stcordova: That’s circular phylogenetic reasoning, that isn’t structural reasoning.

    Sal, don’t quote-mine me to me. It’s too easy to get caught. That wasn’t phylogenetic reasoning, it was an attempt to explain clades to you. Mammals are nested within Sarcopterygii on the basis of molecular and morphological characters that place them on the phylogenetic tree. You think possession of a spinal column is just fine, but you don’t think the characters that diagnose Sarcopterygii (e.g. four lobed appendages connected to the body by a single bone, tooth enamel, paired choanae) are fine. What’s the difference? Talk about cherry-picking.

    You don’t need circularly reasoned Phylogenetic Phantasies to classify a vertebrate as a vertebrate.

    True. Fortunately “circularly reasoned Phylogenetic Phantasies” is your own invention and doesn’t describe what any scientist actually does. So why is there such a thing as “vertebrate”? Why are there groups within groups in a nested hierarchy?

    In fact, Phylogenetic Phantasies make a mess of intuitive classification. Phylogenetic Phantasy says “tetrapods are Sarcopterygiian fish” — which in effect says:parrots are fish, giraffes are fish, elephants are fish, kangaroos are fish, frogs are fish, penguins are fish, bears are fish, buffalo are fish, horses are fish, lions are fish, dogs are fish, cats are fish, turtles are fish.

    Why do you feel so threatened by that? How is it different from saying that they’re all vertebrates? Why aren’t they all gnathostomes (intuitively distinguished by having jaws) as well as vertebrates, or osteichthyans (intuitively distinguished by having endochondral bone), or any of the myriad groups you don’t like but that have the same morphological support as the ones you do?

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  18. stcordova: Says who? You or the author of this thread (me). What I said in the OP:

    Says me. If you will note, the thread was intended as a response to my challenge, so presumably I would be the one to determine the nature of that challenge.

    So, the question you may or may not have answered, but worth setting the record straight on. “Hypothetically, what structure in a species would persuade you common descent was false?” If you say there would be no such structure in principle, then even if God made life with a set of miracles, you’d never be able to infer it.

    Yep, you’re still conflating common descent with the origin of novelty. The answer to the question is indeed that there would be no such structure in principle, because the evidence for common descent is not the existence of any particular structure but the nested hierarchy in which species are organized. If god made life with a set of miracles outside the context of common descent, we would not expect a nested hierarchy. If you want to give me evidence of separate creation, you’re going to have to show me that life doesn’t form a nested hierarchy.This will be difficult since you have already agreed that it does, though sometimes you do waffle. Is your argument going to be based entirely on waffles?

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  19. John Harshman,

    Yep, you’re still conflating common descent with the origin of novelty. The answer to the question is indeed that there would be no such structure in principle, because the evidence for common descent is not the existence of any particular structure but the nested hierarchy in which species are organized. If god made life with a set of miracles outside the context of common descent, we would not expect a nested hierarchy.

    If life was created by a common designer then why would we not expect the morphological and genetic patterns that we see. You say that it would not form a nested hierarchy but how would you know until you identified the specific process?

    How much does your claim of “common descent” really explain if it cannot account for the origin of novel features?

    Are you making the claim that the diversity we see was a result of reproduction that was either divinely guided or not. How do you really know that reproduction was the mechanism if divine intervention was involved? Just because you can group organisms by some shared characteristics and some share more than others.

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  20. colewd: If life was created by a common designer then why would we not expect the morphological and genetic patterns that we see.

    I explained that to you in the post where I showed to you that it doesn’t yield hiearchical structure in the data, nor does it yield convergence of independent phylogenies.

    That’s why. Remember all the excuses you tried to dream up that would somehow result in nesting hiearchies? They consistently didn’t.

    Go read all those posts again. It starts here.

    Again. All the rationalizations you could think of FAILED to produce a nesting hiearchy.

    The designer is re-using designed genes and “parts” in new organisms? Doesn’t yield a nested heirchy.
    The designer is re-using designed genes and “parts”, but this time slightly tweaking them for functional reasons, in every new organism?
    Doesn’t yield a nested heirchy.
    The designer is re-using designed genes and parts, but this time they’re interdependent (“like a software program”) and have to bind to each other and interact like multi-protein complexes?
    Doesn’t yield a nested heirchy.

    Then you ran out of excuses and tried to reverse the whole situation and started claiming that because evolution involves random mutations and random deaths, common descent would NOT yield convergence of independent phylogenies.

    Then I did exactly that, produced a genealogical history of common descent by copying, random deaths and random mutations, and it did yield a nesting hiearchy and convergence of independent phylogenies.

    Then you ran away from the thread and didn’t respond for weeks. Now you’re back, and your brain seems to have completely reset and you’re asking all the same questions again.

    Are you truly suffering from dementia Bill? You hinted that you are a few months ago. Is that true?

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  21. colewd: How much does your claim of “common descent” really explain

    The nested hiearchy. And the convergence of independent phylogenies.

    None of which ANY falsifiable creationist “hypothesis” has ever been able to explain.

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  22. John Harshman keeps trying to define the nested hierarchy in terms of phylogeny. The problem is that when one is arguing common design vs. common descent, one can’t assume the premise one is trying to prove (except in the case of a proof by contradiction, or assumption for the sake of argument).

    By assuming phylogeny, one is already assuming common descent, thus by invoking phylogenetically defined hierarchies, one is already assuming the premise one is trying to prove, and that is circular reasoning!

    In contrast, whether one accepts common descent and/or common design, the taxonomic/typological/structural hierarchy is intuitively evident. Structural hierarchies are present in chemistry from the atomic level up to macro molecules and assemblages of macro molecules. One does not need to invoke phylogeny to conceptualize a structure based hierarchy of chemical systems. Biology is full of chemical structures!

    I already showed how in principle one can construct a nested hierarchy purely on structure without having to assume common design nor common descent.

    John’s insistence on building hierarchy on phylogeny is circular reasoning with respect to the question of common design vs. common descent.

    Of course it is understandable John may not like the structural approach because it doesn’t accord with the notion that creatures with beaks and feathered wings aren’t fish. For someone who has invested so much time studying birds, it’s rather ironic John want’s to insist birds be described as fish. Birds breath with an Avian lung, they don’t breath with gills. One might argue lungfish also have primitive lungs, but they also breathe partially with gills. Furthermore lungfish don’t have legs nor feathered wings nor as far as I can tell an Avian lung. Birds also have a certain kind of thermos regulation not found in fish.

    But I guess, if one neglects such salient differences between a bird and fish, one can even convince themselves an eagle that flies is a fish that swims. But one really doesn’t need a PhD in evolutionary biology to see the world like that. If psychedelic drugs were legal, a dose of LSD-25 will make one see all sorts of things, even more far out.

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  23. stcordova,

    When you hit 10000 (ten thousand) comments on this OP, which you will, I would like to take you and Harshman out to dinner…Sea food place if you both don’t mind, so that we are not forced to eat birds… you probably know what I mean…

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  24. J-mac:

    When you hit 1000 comments on this OP

    Actually your comment was number 4,524. I guess we’re having a wonderful time in this discussion since it’s been going on for a few months now.

    I would like to take you and Harshman out to dinner

    That’s very kind of you. Speaking of get togethers, I’m planning to go the the International Conference of Creationism 2018 in Pittsburg July 29 – Aug 1.

    I actually had lunch with an evolutionary biologist at the 2013 conference.
    This guy:
    https://www.researchgate.net/profile/Erik_Hanschen

    But anyway here is the 2018 conference.

    http://www.creationicc.org/

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  25. colewd: If life was created by a common designer then why would we not expect the morphological and genetic patterns that we see.

    You have the question backwards. Why would we expect the patterns that we see? If you know of a reason, present it now. I don’t think there is one. On the other hand, it’s exactly what we would expect from common descent.

    How much does your claim of “common descent” really explain if it cannot account for the origin of novel features?

    It explains the nested hierarchy in which morphological and molecular features are organized. That’s all it has ever been supposed to explain.

    Are you making the claim that the diversity we see was a result of reproduction that was either divinely guided or not.

    It’s unclear what you mean, but as far as I can tell I’m not making the claim. Common descent isn’t about diversity or about presence or absence of divine guidance. “Common descent” sums it up quite well.

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  26. stcordova: Actually your comment was number 4,524.I guess we’re having a wonderful time in this discussion since it’s been going on for a few months now.

    That’s very kind of you.Speaking of get togethers, I’m planning to go the the International Conference of Creationism 2018 in Pittsburg July 29 – Aug 1.

    I actually had lunch with an evolutionary biologist at the 2013 conference.
    This guy:
    https://www.researchgate.net/profile/Erik_Hanschen

    But anyway here is the 2018 conference.

    http://www.creationicc.org/

    Sal,
    You are my favorite YEC… It doesn’t mean I agree with you most of the time but I respect you for who you are…
    It is the same way I respect other contributes to this blog…

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  27. stcordova:
    John Harshman keeps trying to define the nested hierarchy in terms of phylogeny.

    No, he doesn’t. He keeps trying to explain the nested hierarchy in terms of phylogeny, which is quite different. Most of what you wrote after that is therefor moot.

    In contrast, whether one accepts common descent and/or common design, the taxonomic/typological/structural hierarchy is intuitively evident.

    It most certainly is not. You are just picking a handful of characters you like and ignoring all the rest. There is as much reason, in “structural” terms, to accept Gnathostomata and Osteichthyes and Sarcopterygii as there is to accept Vertebrata or Mammalia, yet you reject the first three and accept the last two. Cherry-picking. Now, I could speculate on the reasons: your ability to understand classification is stuck at a kindergarten level; you like stuff that’s visible from a distance; don’t know what else.

    Structural hierarchies are present in chemistry from the atomic level up to macro molecules and assemblages of macro molecules.One does not need to invoke phylogeny to conceptualize a structure based hierarchy of chemical systems.Biology is full of chemical structures!

    Now you’re just playing with the term “hierarchy” and indulging in non sequiturs. Are you proposing that last sentence as an explanation for the nested hierarchy of life? If so, we can discuss why it’s among your sillier pronouncements.

    I already showed how in principle one can construct a nested hierarchy purely on structure without having to assume common design nor common descent.

    Well, of course you can, if the data actually are organized into a nested hierarchy. But that doesn’t explain how they came to be organized that way, which is what we’re supposedly talking about.

    John’s insistence on building hierarchy on phylogeny is circular reasoning with respect to the question of common design vs. common descent.

    It’s hard to tell what you mean by “building hierarchy on phylogeny”, so I can’t comment on this except to say that I have never indulged in circular reasoning. You are mistaken about something, but I can’t say what.

    Of course it is understandable John may not like the structural approach because it doesn’t accord with the notion that creatures with beaks and feathered wings aren’t fish.

    I have mercifully deleted the remainder of your kindergarten systematics. Why are you so obsessed with this “birds are not fish” thing? How can you possibly make the argument that “X is different from Y, therefore X is unrelated to Y”? That’s a denial that any sort of change can occur by any mechanism at all. Even you must realize that’s absurd. Mustn’t you?

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  28. colewd: If life was created by a common designer then why would we not expect the morphological and genetic patterns that we see.

    Because a common designer would have a brain able to think better than unintelligent processes do[n’t].

    Glen Davidson

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  29. If all these brilliant people here can’t convince a bright guy like Salvador of the truth of common descent maybe I should be a little more skeptical of it myself.

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  30. Mung:
    If all these brilliant people here can’t convince a bright guy like Salvador of the truth of common descent maybe I should be a little more skeptical of it myself.

    Maybe you should be a little more skeptical of Sal instead. It’s impossible to convince someone who desperately wants not to be convinced. Perhaps a better course would be to pay attention to the arguments, and let them convince you or not.

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  31. John Harshman:

    There is as much reason, in “structural” terms, to accept Gnathostomata and Osteichthyes and Sarcopterygii as there is to accept Vertebrata or Mammalia, yet you reject the first three and accept the last two. Cherry-picking. Now

    Really? Let’s talk about your specialty Aves.

    We can start with major systems like say the skeletal structure. I’d say the skeletal structure is hardly a minor thing to cherry pick. You tell the readers if the following skeleton looks like a fish skeleton and why.

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  32. Here is the best lungfish skeleton example I could find. It’ doesn’t look like a bird skeleton to me. Anyone can add a better picture if they have one.

    The bottom line is John is arguing that structurally a bird nests within such a fish.

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  33. Allan Miller: Not necessarily. Do you have a specific example?

    Sure. I’m too dumb to make something like that up. 🙂

    All nonhuman primates, in fact most mammals, carry endemic infectious retroviruses … There are two kinds, simian foamy viruses (SFVs) and simian infectious retroviruses (SIVs) that are shared among most nonhuman primates. Among humans, we have only the newly introduced HIV and human T leukemia virus, and no others. If we were descended from a common ancestral population with chimpanzees, we should carry the SIV and SFVs viruses also, but we don’t. Either we were purged of the viruses or we never had them.

    – Theistic Evolution. p. 489

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  34. stcordova: Here is the best lungfish skeleton example I could find. It’ doesn’t look like a bird skeleton to me.

    It’s obvious to me that it is a feather with a head attached. Being that water is just another fluid, the feather obviously evolved for flight in water.

    HT: Glen Davidson

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  35. stcordova,

    Sal, your kindergarten taxonomy isn’t helping you. Rather than argue seriously, you attempt to convince me that a bird isn’t a lungfish. I agree that a bird isn’t a lungfish. But you agree they’re both vertebrates despite their differences, so how is that significantly different from agreeing they’re both sarcopterygians despite their differences? You don’t seem to have any comprehension of how nested hierarchy works.

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  36. John Harshman,

    You have the question backwards. Why would we expect the patterns that we see? If you know of a reason, present it now. I don’t think there is one. On the other hand, it’s exactly what we would expect from common descent.

    The patterns we see consist of common genes and common morphology. I would expect this from a common design. If you look at the family of MacIntosh computers this is exactly what we see down to the transistor level. Unlike common ancestry common design explains the evolution of new capability like lithography that is smaller and faster.

    It explains the nested hierarchy in which morphological and molecular features are organized. That’s all it has ever been supposed to explain.

    Does it really explain this if it does not explain new features? As Mung said new features are an important part of the nested hierachy.

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  37. colewd:
    John Harshman,

    The patterns we see consist of common genes and common morphology.I would expect this from a common design.If you look at the family of MacIntosh computers this is exactly what we see down to the transistor level. Unlike common ancestry common design explains the evolution of new capability like lithography that is smaller and faster.

    Bill, you just are not equipped to discuss this subject. I’ve tried. Think: nested hierarchy. That’s all common descent explains. That’s what common design doesn’t explain. How can it be that I still have to tell you this?

    Does it really explain this if it does not explain new features? As Mung said new features are an important part of the nested hierachy.

    Mung is confused. The pattern made by the distribution of new features is an important part of the nested hierarchy. The new features themselves are not. The nested hierarchy is a pattern. That’s all it is. Common descent explains nested hierarchy. Common descent doesn’t explain the origin of new features. It only explains the nested hierarchy, and there is nothing else that explains it.

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  38. colewd: The patterns we see consist of common genes and common morphology.

    And uncommon genes and uncommon morphology in quite separate lines. That is what is so very different from technology, as Apple gets much the same technology as Hewlett-Packard or Dell.

    I would expect this from a common design.

    That’s because you ignore how different the uncommon accumulations of genes and morphology are in different lines.

    If you look at the family of MacIntosh computers this is exactly what we see down to the transistor level.

    It is very different from what we see in life. Once upon a time all computers with monitors had CRT monitors. Then came flat screens, and all of the smaller computers of nearly all brands started shifting toward flat screens. Once aluminum wires were in computer chips, then came the technology to use copper with its better conductivity, and while it took some time, eventually nearly all chips are now made with copper wires. Silicon dioxide was the very convenient insulator for silicon transistors for a long time, now hafnium dioxide is used in different brands. 32 bit chips were the norm once, now 64 bits are common.

    These things occur across computer brands, unlike what we see in life. Birds have feathers, bats have hair/fur, both stuck with their ancestral limitations. Nerves in vertebrates become myelinated in many cases, cephalopods get none of this “technology.” Why don’t you have bird lungs, bird vision, or bird testes that can take high temperatures? Common descent explains this, “common design” is no explanation at all.

    Unlike common ancestry common design explains the evolution of new capability like lithography that is smaller and faster.

    Yes, changes are so much less limited by design than they are by the evolution of life.

    Glen Davidson

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  39. I think nested hierarchies are especially fortuitous for us humans.

    It’s interesting that nature is especially conducive to being broken down into ever smaller units like that.

    Domain
    Kingdom
    Phylum
    Class
    Order
    Family
    Genus
    Species

    here is another

    book
    chapter
    paragraph
    sentence
    phrase
    word
    syllable
    letter

    …….or……….

    mixtures
    compounds
    elements
    molecules
    atoms
    nucleons and electrons
    quarks

    How lucky we are that things just seem to work that way.
    If the biological world was not organized so that we could categorize things from the general to the more specific I’m not sure how we could ever make sense of it.

    peace

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  40. colewd: The patterns we see consist of common genes and common morphology. I would expect this from a common design.

    No, you wouldn’t. You saw this with your own eyes in this very thread.

    At this stage you are either lying or revealing some sort of intense cognitive impairment. Which one is it?

    If you look at the family of MacIntosh computers this is exactly what we see down to the transistor level.

    This is simply false. There is no nested of any attributes of Mac Computers, and even more importantly, there is no no convergence of independent phylogenies.

    If you disagree, then please tell me how to sort and group macintosh computers by character states, pick three of them, and then we will see if there are really groups within groups and whether those three characters yield similar trees.

    You say one of the characters that yield nested hiearchies for mac computers is at “the tranistor level”. Please elaborate. What is it about transistors in mac computers that yield a hiearchy of groups within groups? Be specific.

    You will fail this challenge completely.

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  41. Mung,

    Yes, you absolutely should be sceptical of it. Indeed, if your reasons for accepting it are as feeble as they appear to be, then I don’t really know why you accept it at all.

    I am mystified as to why the arguments themselves aren’t persuasive, rather than you simply going along with groupthink, but then I don’t know what it’s like to be religious, so maybe that gets in the way.

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  42. Mung,

    And the only explanation you can come up with for the distribution of viral families is a miracle? That’s a strange, infective miracle right there.

    Obviously I know nothing about it, but a few possibilities present themselves: infection does not neatly follow vertical descent, there may be differential immunity, and incomplete lineage sorting can cause an absence in a descendant line while fixation runs to completion in sister groups.

    An interesting case study though, because you seem happy to accept common descent of the viral sequences, in their families, but perhaps not the organisms in which they reside – despite the overwhelming pattern which makes these anomalies anomalies in the first place.

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  43. fifthmonarchyman:
    I think nested hierarchies are especially fortuitous for us humans.

    It’s interesting that nature is especially conducive to being broken down into ever smaller units like that.

    Domain
    Kingdom
    Phylum
    Class
    Order
    Family
    Genus
    Species

    here is another

    book
    chapter
    paragraph
    sentence
    phrase
    word
    syllable
    letter

    …….or……….

    mixtures
    compounds
    elements
    molecules
    atoms
    nucleons and electrons
    quarks

    How lucky we are that things just seem to work that way.
    If the biological world was not organized so that we could categorize things from the general to the more specificI’m not sure how we could ever make sense of it.

    peace

    Your latter two lists don’t yield objective nesting hiearchies. To pick an example, your book chapters will contain words and letters found everywhere in the book. The same is true for paragraphs, sentences, phrases, words and syllables.

    The copying of books(by hand or some other error-prone process) go through a branching genealogical process, so you can sort books into nesting hiearchies. But notice here that if you do that, you are implicitly admitting that books share common descent. And that we can infer this from the fact that they sort into nesting hiearchies.

    With respect to the arrangements of matter into mixtures, compunds, molecules and so on, there are no nesting hiearchies here either. The group of molecules that contain carbon will not form a clade to the exclusion of molecules that contain nitrogen, or oxygen, or sulfur etc. etc. Nor does the group of carbon molecules contain within it the group of all hydrogen, or oxygen, or iron, or molybdenum-containing molecules. Because the group of all sulfur-containing molecules will overlap with pretty much everything else, including carbon and so on. Again there are no true groups within groups.

    How about a group defined by all man-made tables. Will that form a clade that excludes all other objects? Well, are tables the only entities made of molecules? No. Of elements? No. Of atoms? No. Of mixtures? No. Of compounds? No. Can we define the table-clade by the sort of molecules they’re made of? Can we think of an exclusively table-fitted type of material or a molecule only used in tables? No. There’s no material of which tables are made, that is not also used in some other object.

    You can categorize these things in groups, yes, but they will not form nesting hiearchies. Only entities that go through a branching genealogical process will form nesting hiearchies.

    All life can be sorted in an objectively verifiable manner into nesting hiearchies. A trait shared only and entirely with other things also known to go through a branching genealogical process. Hence, these things share common descent. You evolved, you’re an ape. Tough shit, get over it.

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  44. stcordova,

    No, because when nesting is based on structure, not phylogentic phantasies, rats and mice will nest together.

    I don’t know why you think molecular character states are somehow ‘phantasies’. Turn the clock back 50 years, folks, Creationist in the house!

    But OK, what about when we add shrews, dormice, hamsters, gerbils, guinea pigs? Do they nest with rats and mice? If not, why not? And why can different genes be arranged into a nested hierarchy, with something of a fractal character regardless whether you zoom in or out?

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  45. stcordova,

    I mentioned the phospho proteome*** and other -omes as being barriers to mutation to genes between species. Evolutionists build their gene tree phylogenies on simplistic assumptions that there isn’t much functional compromise in changing amino acid residues,

    *** [-ome! -ome! -ome! -ome nama Shiva ya!]

    The refutation of this remains the same as the other few dozen times you’ve tried it. Constraint at some sites does not equal constraint at all. And, indeed, gene trees are frequently built on noncoding sequence – introns, SINEs, etc. It depends on the depth you wish to probe. Genes that change but little – are under stronger constraint – are actually just the job for probing deep branches. You would have it – without proof – that due to the very constraint that one requires at that depth, genes cannot change at all.

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  46. Mung:
    If all these brilliant people here can’t convince a bright guy like Salvador of the truth of common descent maybe I should be a little more skeptical of it myself.

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  47. fifthmonarchyman: If the biological world was not organized so that we could categorize things from the general to the more specific I’m not sure how we could ever make sense of it.

    How about as well-engineered entities in which the better structures (or whatever, like maybe better chemistry) are chosen for particular needs, rather than as entities heavily constrained by past evolution? You know, maybe like good autos, or computers.

    We seem capable of dealing with engineering choices that aren’t beholden to inheritance.

    Glen Davidson

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