Common Design vs. Common Descent

I promised John Harshman for several months that I would start a discussion about common design vs. common descent, and I’d like to keep my word to him as best as possible.

Strictly the speaking common design and common descent aren’t mutually exclusive, but if one invokes the possibility of recent special creation of all life, the two being mutually exclusive would be inevitable.

If one believes in a young fossil record (YFR) and thus likely believes life is young and therefore recently created, then one is a Young Life Creationist (YLC). YEC (young earth creationists) are automatically YLCs but there are a few YLCs who believe the Earth is old. So evidence in favor of YFR is evidence in favor of common design over common descent.

One can assume for the sake of argument the mainstream geological timelines of billions of years on planet Earth. If that is the case, special creation would have to happen likely in a progressive manner. I believe Stephen Meyer and many of the original ID proponents like Walter Bradley were progressive creationists.

Since I think there is promising evidence for YFR, I don’t think too much about common design vs. common descent. If the Earth is old, but the fossil record is young, as far as I’m concerned the nested hierarchical patterns of similarity are due to common design.

That said, for the sake of this discussion I will assume the fossil record is old. But even under that assumption, I don’t see how phylogenetics solves the problem of orphan features found distributed in the nested hierarchical patterns of similarity. I should point out, there is an important distinction between taxonomic nested hierarchies and phylogenetic nested hierarchies. The nested hierarchies I refer to are taxonomic, not phylogenetic. Phylogeneticsits insist the phylogenetic trees are good explanations for the taxonomic “trees”, but it doesn’t look that way to me at all. I find it revolting to think giraffes, apes, birds and turtles are under the Sarcopterygii clade (which looks more like a coelacanth).

Phylogeny is a nice superficial explanation for the pattern of taxonomic nested hierarchy in sets of proteins, DNA, whatever so long as a feature is actually shared among the creatures. That all breaks down however when we have orphan features that are not shared by sets of creatures.

The orphan features most evident to me are those associated with Eukaryotes. Phylogeny doesn’t do a good job of accounting for those. In fact, to assume common ancestry in that case, “poof” or some unknown mechanism is indicated. If the mechanism is unknown, then why claim universal common ancestry is a fact? Wouldn’t “we don’t know for sure, but we believe” be a more accurate statement of the state of affairs rather than saying “universal common ancestry is fact.”

So whenever orphan features sort of poof into existence, that suggests to me the patterns of nested hierarchy are explained better by common design. In fact there are lots of orphan features that define major groups of creatures. Off the top of my head, eukaryotes are divided into unicellular and multicellular creatures. There are vetebrates and a variety of invertebrates. Mammals have the orphan feature of mammary glands. The list could go on and on for orphan features and the groups they define. Now I use the phrase “orphan features” because I’m not comfortable using formal terms like autapomorphy or whatever. I actually don’t know what would be a good phrase.

So whenever I see an orphan feature that isn’t readily evolvable (like say a nervous system), I presume God did it, and therefore the similarities among creatures that have different orphan features is a the result of miraculous common design not ordinary common descent.

3,738 thoughts on “Common Design vs. Common Descent

  1. John Harshman claims I’m incoherent. So let the evolutionary biologist, John Harshman argue whether Rhipidistia is real or not. He wants to say I don’t understand, here’s his chance to engage the data rather than just sit on the sidelines and whine.

    Whichever way John argues will show that claidistic categories come and go, they are imaginary, and that is why they are debatable.

    In contrast, patterns of similarity and diversity are real. That is TAXNOMY not PHYLOGENY.

    You confuse distances with cladistic relationship

    No I’m not, but maybe you need to set Corneel straight on that. 🙂

  2. stcordova,

    Freaking too funny. You guys bash colewd over the head with cytochrome-c and now that the favor is returned and I bash your arguments with cytochrome-c, you complain I’m using cytochrome-c.

    I’m complaining that you’re over-reaching the conclusions, by concentrating solely on one gene. By cherry-picking, indeed. The only reason cytochrome c was so extensively discussed with Bill was because of his obsession with it, and its role in apoptosis, and his apparent belief that this needs to be just-a-bit-different in each organism. It has a significant historic role because it was the first to be subject to molecular phylogeny, but things did not end there.

    Other genes are available.

    Did you notice the Smithsonian article suggests the anomalies are geneome wide? How the heck did all the lungfish AND coelecanth genes conspire this way?

    Dunno what you mean.

  3. stcordova: 99.9999…% possible ones don’t as a matter of principle.

    Refer to this paper and connect the dots:
    https://academic.oup.com/sysbio/article-abstract/27/1/27/1626689?redirectedFrom=PDF

    So, your belief in the phylogenetic tree rests on that hypothetical .0000……01% of the population of hypothetical trees.So what is the necessary condition for that tree to be real? Common descent. But common descent is the premise you are wishing to prove, soooo, without recourse to circular reasoning phylogeny is not formally provable.

    Your logic escapes me here. Of course science doesn’t deal with the “formally provable”; that’s mathematics. Science deals with inference from observation. Common descent isn’t a premise, it’s a conclusion; it explains why the observed data fit a nested hierarchy. So much for circularity. The number of possible trees is irrelevant except that it makes a match between trees from different data sets very improbable to be due to chance.

    However taxonomic relationships, such as the fact we are more morphologically similar to chimps than to blades of grass..That is real.

    Sorry, but “morphologically similar” isn’t the proper criterion. Only derived similarities count. You seem hung up on raw similarity. There once was a school of systematics that you would like, the pheneticists, but they’re extinct now. Here’s the question you should be answering: why should derived similarities fit a nested hierarchy?

    Don’t you see you are conflating concepts in desperate attempt to justify phylogeny.Taxonomy and phylogeny may correlate, but they are not the same thing.

    You are correct, but not in the way you think. Phylogeny explains taxonomy, and these days taxonomy attempts to conform to phylogeny. In general, the changes needed to conform are minor. Now why should that be?

  4. Mung,

    I don’t know. Are they? Does similarity mean shared ancestry?

    I’d say so, yes. That is, at least, the only cause I know of that leads to such swathes of … well actually, identity. We say ‘similar’ but we mean a certain percentage is identical. It’s not 100% were-you-there conclusive of shared ancestry, but I ‘d like to see a viable alternative.

    What does that even mean given a hypothesis of universal common descent, where even dissimilar DNA sequences share a common ancestor?

    There’s that word ‘universal’ again … eventually, due to mutation, two initially identical sequences can become steadily less identical – to the point of being completely unrelated on observation. They really are commonly descended, but you can’t tell. UCD does not rest on that – it does not take sequences with absolutely no relationship to each other and declare them commonly descended.

  5. stcordova:
    John Harshman claims I’m incoherent.

    That’s because you are. A little knowledge is a dangerous thing, and all.

    So let the evolutionary biologist, John Harshman argue whether Rhipidistia is real or not.He wants to say I don’t understand, here’s his chance to engage the data rather than just sit on the sidelines and whine.

    Some relationships are easy to resolve, others are not. Relationships among the three clades of living sarcopterygians are in the difficult bin. But the question is unimportant to your claim that mammals aren’t fish. It’s the monophyly of Sarcopterygii that matters, and that happens to be one of the easier questions. Even cytochrome c will show it, I suspect, if you sample a few more species. Note that the paper you cited in your support also has a monophyletic Sarcopterygii.

    Whichever way John argues will show that claidistic categories come and go, they are imaginary, and that is why they are debatable.

    Ah, the old creationist mantra: if we don’t know everything, therefore we know nothing. Not all clades are created equal. Some have been stable for hundreds of years, some have been stable only since molecular data became available, and some are still not stable. Some are imaginary (i.e. shown not to exist on the true tree) and have been abandoned, but most are not and are only confirmed by new data.

    In contrast, patterns of similarity and diversity are real.That is TAXNOMY not PHYLOGENY.

    I’m not sure you know what those words mean, even if you put them in all caps. And I would still like an answer for why those patterns of similarity fit a nested hierarchy. That’s what this thread is supposedly about, yet you have never advanced a hypothesis. (“God did it that way for unknown reasons” is not a hypothesis.)

    No I’m not, but maybe you need to set Corneel straight on that. 🙂

  6. John Harshman:

    Phylogeny explains taxonomy

    No it does not because it doesn’t explain TREGs and other orphan systems that define taxonomies.

    3,300 comments, you don’t even deal with orphans.

  7. John Harshman:

    Not all clades are created equal. Some have been stable for hundreds of years,

    Like the ones creationists like Linnaeus defined. Agree, because those were based on taxonomy, not on the assumption of common descent which create abominations like Rhipidistia.

  8. stcordova: 3,300 comments, you don’t even deal with orphans.

    I have dealt with them something like twenty times. Both by explaining why they aren’t a problem for common descent (without them common descent couldn’t even be inferred for fucks sake), and by giving detailed accounts of how some of them evolved.

  9. stcordova: So, your belief in the phylogenetic tree rests on that hypothetical .0000……01% of the population of hypothetical trees. So what is the necessary condition for that tree to be real? Common descent. But common descent is the premise you are wishing to prove, soooo, without recourse to circular reasoning phylogeny is not formally provable.

    That is completely backwards. Phylogenetic analysis indicates one (or a few, depending on the quality of your data) tree to be more likely than any of the others. Only one tree correctly describes the real phylogeny. Whereas there are numerous ways to build your “taxonomic” trees, all of which are equally valid. That just depends on which characters you arbitrarily prioritize for your classification.

    stcordova: However taxonomic relationships, such as the fact we are more morphologically similar to chimps than to blades of grass.. That is real.

    It definitely is, the explanation being that we share a more recent common ancestor with chimps than with grasses. Or did you forget that we are also closer to chimps in a phylogenetic sense? No difference there. A more interesting question would be whether rhinoceroses should be grouped with elephants or with horses. Phylogenetics says the latter, but they used to be lumped in with elephants and hippopotamus (pachyderms). So what is the “real” relationship according to you?

  10. stcordova: 3,300 comments, you don’t even deal with orphans.

    Because it is the distribution of derived characters that matters, not the origin.

    People might have told you this before.

  11. stcordova: No it does not because it doesn’t explain TREGs and other orphan systems that define taxonomies.

    3,300 comments, you don’t even deal with orphans.

    Again, I don’t think you know what “taxonomy” means. Then again, I don’t know what “TREGs” means, so perhaps we’re even. 3,300 comments, and you still don’t understand what phylogeny is supposed to explain or why orphans are not an argument against common descent. Why should orphan systems, whatever those are, be organized in a nested hierarchy?

    Like the ones creationists like Linnaeus defined. Agree, because those were based on taxonomy, not on the assumption of common descent which create abominations like Rhipidistia.

    “Based on taxonomy” is a fine example of incoherence as well as evidence you don’t know what the word means. I can see why it might be wrong, but why is Rhipidistia an abomination? And of course it isn’t based on any “assumption of common descent”.

    No I’m not, but maybe you need to set Corneel straight on that.

    What was that even a response to? You reproduced a long post of mine and added that to the end. Did you mean that you aren’t incoherent? Because that post all by itself is good evidence that you are. What am I supposed to set Corneel straight on? And perhaps you could respond to a few of the points in that comment you ineptly tried to quote from. Have you forgotten how to use the “quote” button?

  12. John Harshman: God did it that way for unknown reasons” is not a hypothesis

    yeah, “unknown reasons”:

    “11 Therefore God sends them a strong delusion, so that they may believe what is false, 12 in order that all may be condemned who did not believe the truth but had pleasure in unrighteousness.”

  13. Corneel: yeah, “unknown reasons”:

    “11 Therefore God sends them a strong delusion, so that they may believe what is false, 12 in order that all may be condemned who did not believe the truth but had pleasure in unrighteousness.”

    Yeah, I don’t think Sal has really owned this notion or considered the implications. It seems pointless to argue against a claim that he may not take seriously and isn’t willing to discuss.

  14. Corneel,

    Here is an example where there is a taxonomic tree. The phylogeny is non-existence because I designed the peptide sequences. I put the sequences in FASTA format:

    >AARK
    MFAD AARK

    >AARL
    MFAD AARL

    >AAQA
    MFAD AAQA

    >AAQI
    MFAD AAQI

    >ATKN
    MFAD ATKN

    >ATKW
    MFAD ATKW

    >ATTY
    MFAD ATTY

    >ATTZ
    MFAD ATTZ

    Now I used Phylogenetic Software, Mega 6.0 with Maximum Likelihood, 150 boostraps, Jone-Taylor_Thornton modeling with Nearest Neighbor-Interchange and strong Branch Swap filtering, blah blah blah….

    Does the fact it can build a phylogenetic tree mean the patterns of similarity and diversity which I designed were the result of common descent from an ancestor via random mutation and natural selection? Heck no, but it doesn’t stop the software from making a tree out of it.

    That said the peptide sequence “MFAD AARK” is more similar to “MFAD AARL” than to “MFAD ATTZ”, that is a TAXONOMIC fact. The generated phylogeny is totally bogus since the sequences weren’t created through a process of common descent with random variation and natural selection. It was created by intelligent design. Nevertheless, the phylogenetic software makes a nice conceptual organization of the taxon, so it’s really good for something.

    By way of extension, this would be awesome software to lead creationists to the promised land of Baraminology!

  15. Corneel (continued):

    The moral of the story is TAXONOMY is real, whereas PHYLOGENY may or may not be real. Here is the “phylogenetic” diagram generated by the run of Mega as described in the previous comment:

  16. stcordova: Does the fact it can build a phylogenetic tree mean the patterns of similarity and diversity which I designed were the result of common descent from an ancestor via random mutation and natural selection? Heck no, but it doesn’t stop the software from making a tree out of it.

    I mentioned some of the ways that exercise was inept the last time you posted it. It isn’t clear why you thought you needed to post it again. It isn’t clear what lesson you think this teaches. That it’s possible to fake phylogeny on purpose? That a tree-building algorithm will build a tree even given non-structured data? You are very bad at making whatever point this is supposed to be. Yes, you are indeed incoherent.

    That said the peptide sequence “MFAD AARK” is more similar to “MFAD AARL” than to “MFAD ATTZ”, that is a TAXONOMIC fact.

    Once again, you seem not to know what “taxonomic” means.

    By way of extension, this would be awesome software to lead creationists to the promised land of Baraminology!

    How would it do that?

  17. Rumraket:

    stcordova: 3,300 comments, you don’t even deal with orphans.

    I have dealt with them something like twenty times. Both by explaining why they aren’t a problem for common descent (without them common descent couldn’t even be inferred for fucks sake), and by giving detailed accounts of how some of them evolved.

    I disagree with the statement that without “orphans” common descent couldn’t even be inferred. We can infer it just fine from the sequences of genes that are present in all of the species being studied.

  18. Joe Felsenstein: I disagree with the statement that without “orphans” common descent couldn’t even be inferred. We can infer it just fine from the sequences of genes that are present in all of the species being studied.

    Ah, but every nucleotide substitution is an orphan base. It appears that Sal defines “orphan system” as anything that hasn’t always existed, and he doesn’t care whether there are well-known mechanisms and/or evidence for how it arose. You may recall his “flower”, which he supposed was full of orphan genes, even after it was explained that most of those “orphans” had homologs in other taxa.

  19. John Harshman:

    That it’s possible to fake phylogeny on purpose?

    Nope. It shows it’s possible for you to fool yourself a designed set of architectures are the result of common descent if you’re willing to persuade yourself it is.

    http://theskepticalzone.com/wp/common-design-vs-common-descent/comment-page-65/#comment-199226

    You yourself show you’ll believe common descent, even if something has no ancestors, so then even if common design is true, and something has no ancestors, merely because you can arrange them in a hierarchy, as is the case with the sequences I created, you’ll believe it doesn’t falsify common descent.

    something without ancestors doesn’t falsify common descent

    –John Harshman

    You keep cherry picking data (as in ignoring the problem of mechanistically evolving orphan systems). You pointed out some Phyla have been defined for hundreds of years. Did they need all the fancy phylogenetic techniques? Nope, it was obvious from the organs that some creatures had that others didn’t — eh, you know, orphan systems.

    The assumption of phylogeny does not give a mechanistically credible explanation for such orphan systems like the TREGs which Dr. Tan discusses.

    The issue with Rhipidistia is easily settled by noting tetrapods have systems that Lungfish don’t have, that Lungfish have more in common taxonomically with Coelecanths than tetrapods. This is confirmed by cytochrome-c and the 43 other genes in the study I cited earlier.

    Hypothetically, the pattern of similarity that might have suggested to me tetropods descended from something between a Lungfish and Coelecanth would have been:

    Lungfish vs. Human : 3%
    Coelecanth vs. Human : 3%
    Coelecanth vs. Lungfish: 6%

    or

    Lungfish vs. Human : 1%
    Coelecanth vs. Human : 5%
    Coelecanth vs. Lungfish: 6%

    But that’s not the pattern is it? Therefore you can’t claim very easily humans are descendants of fish, or as Axel Meyer put it “evolutionarily speaking we are Sarcopterygian fish”. Instead to make this claim you have to stretch and over interpret the data because the data say:

    Lungfish vs. Human : 14%
    Coelecanth vs. Human : 15%
    Coelecanth vs. Lungfish: 7%

    How some dudes concocted the Rhipidistia clade composed of Lungfish and Tetrapodamorpha in light of the molecular data (such as that above) is beyond me. Oh, I know, they must have really strained to over-interpret the data and rely on mangled poorly informative dead creatures like the one pictured below to make up a story (Note the imaginary Tiktaalik that was concocted from the mangled remains of whatever poor creature(s) became a fossil).

    Truthfully speaking, we are taxonomically mammals, and unless there is a mechanistic explanation as to how taxonomically structured fish become taxonomically structured mammals, there is no formal proof of common descent of humans from fish. You can accept it as an article of faith, but let’s not pretend you have anything resembling a real mechanistic explanation on par with well established mechanistic theories like celestial mechanics.

    And all your straining might be in vain if the fossil record is young as attested by the physical data.

  20. Sal, to John:

    Nope. It shows it’s possible for you to fool yourself a designed set of architectures are the result of common descent if you’re willing to persuade yourself it is.

    The elephant, Sal:

    Don’t kid yourself, Sal. The elephant is still in the room. Would you care to explain to us why, out of the more than 10^38 possible trees for the taxa in Theobald’s Figure 1, we infer the same exact tree from the morphological and molecular data?

    Coincidence? The Designer just happens to be an anal-retentive evolution mimic? He hates the eggheads and wants to fool them into accepting common descent?

    Be brave and answer the question.

    Or admit that you can’t.

    Have you informed your “subscribers” that you are unable to answer this simple question?

  21. A reminder:

    Sal,

    The designer made it easy for Darwinists to ignore evidence, and difficult for the truth to be perceived. Those wanting the truth have to examine the data with less bias.

    Have you explained to Behe, whom you fawned over in this segment of the “Apologetics Academy” Youtube video, that he needs to examine the data with less bias?

    Since he is not a Darwinist, how do you explain his acceptance of common descent? Why is he ignoring the Designer’s message? Why doesn’t he “want the truth”, like you and Bill? (LMAO)

  22. There are in principle testable predictions relating to the molecular clocks.

    The following relationship has bothered me for a long time and I’ve alluded to it in various forms and other genes and species such as the aaRS gene in bacteria:

    Lungfish vs. Human : 14%
    Coelecanth vs. Human : 15%
    Coelecanth vs. Lungfish: 7%

    It did not surprise me at all that it dawned on someone that there is clocking problem in Coelecanths in light of such data. What surprised me is so few noticed it and reported it! It was plain as day to me. The problem also occurs with Lungfish.

    The one thing no one will consider is the creatures were created recently!

    So what is the testable prediction? This may or may not be feasible, but in principle, we could estimate actual clock rates by comparing the genomes of parents and offspring. Are our sequencing techniques free of enough noise and sensitive enough to detect the actual clock rate? I don’t know. Plus we probably don’t have the money to do this until sequencing technology becomes even cheaper.

    So what is the testable prediction? I predict the actual clock rate will be faster than people think. The Coelecanth isn’t slow in evolving it’s genome. It was created recently and its divergence from other creatures is by design, not random mutation.

    I should mention, creationists I’ve talked to say they think they are seeing codon bias erode in certain microbes which scientists havebeen able to track for a sufficient amount of time to notice it.

    I’m seeing revisions to clock rates of mutation here and there, and it superficially suggests many species are young because their INTRA-group divergence is too small. There are situations coalescence theory would be inapplicable to explain the lack of divergence, hence my interest in the relative lack of INTRA-species and INTRA-group divergence.

    For the coelacanth being a living fossil for hundreds of millions of years, one would think all the extant coelecanths that have been sequenced would show more divergence. They don’t, they look all like they came from a recent common ancestor rather than an ancestor hundreds of millions of years in the past. Coelescence may explain that, but coalescence may not explain other situations…

    I saw the same pattern with other living fossils like cycads….

    The problem I saw in the Lungfish and Coelecanths is one I’m seeing in essential genes in bacteria, but a substantially bigger problem. The aaRS gene in bacteria is supposedly ancient, so why is there not the same INTRA-group divergence?

    Sooo, creationists have reasons to try to learn phylogenetic methods because of these issues, even though they reject Universal Common Ancestry.

  23. Once an ‘orphan event’ has happened, it flows down the mainline of DNA copying, and becomes evidence for common descent of that clade.

    If a single ‘orphan event’ is enough to disbar common descent of the rest of the genome (for no clearly articulated reason), what are we to make of a situation such as this:

    Clade 1 has ‘orphan gene’ A. Clade 2 has both ‘orphan gene A’ and ‘orphan gene B’. Conventional analysis by people not shitting themselves over eternal damnation for getting it wrong would have it that A happened, was inherited by all descendant species and then, in one descendant lineage, B happened. Clade 2 would be a subclade of Clade 1. Seems simple enough, and not really something one would fight tooth and nail against if less depended on it.

    But no, both ‘orphan events’ indicate (per Sal), specific acts of Creation. Clade 1 has no ancestors. But – curiously – neither does Clade 2, though it nests within. Without B, we’d maybe have Clade 1 as a baramin, created with A then commonly descended from that point on. But no. The B-less members of Clade 1 can be commonly descended, because there are no more magic events. But those with both A and B – it’s a nested baramin. The creation of the first, parentless Clade 2 individual required that it additionally be furnished with, not just ‘orphan B’, but a copy of ‘orphan A(nnie)’ as well (and a whole host of the rest of Clade 1’s genomic complement, of course, otherwise it wouldn’t nest).

    A nested hierarchy of baramins. It’s pointlessly esoteric.

  24. stcordova,

    Let’s try something else. I have rearranged your little set of sequences:

    >AARK
    MFAD AARK

    >AARL
    MFAD AARL

    >AAQK
    MFAD AAQK

    >AAQL
    MFAD AAQL

    >ATRK
    MFAD ATRK

    >ATRL
    MFAD ATRL

    >ATQK
    MFAD ATQK

    >ATQL
    MFAD ATQL

    I have no idea what Mega will do to it, or whether it will even parse. That isn’t the point. But I sure am curious what real TAXONOMY you are going to tell me this one has.
    Note that it is also designed, like yours. Note also that you can build several equally valid hierarchical trees, depending on which amino acid position you prioritize.

    So the burning question here is: Why didn’t God design organisms according to this distribution? If you want to make common design fly, that is what you need to explain.

    ETA: corrected the sequences. getting late, I guess.

  25. stcordova,

    For the coelacanth being a living fossil for hundreds of millions of years, one would think all the extant coelecanths that have been sequenced would show more divergence.

    Grurgh. Suppose you had a population of just 100 individuals of a ‘living fossil’. How much divergence do you really think you’d find, despite a squillion years of change? Your grasp of population genetics is dire.

  26. stcordova: Nope. It shows it’s possible for you to fool yourself a designed set of architectures are the result of common descent if you’re willing to persuade yourself it is.

    Again you are incoherent. What is “a designed set of architectures”? In the current case, you created a perfect nested hierarchy. In what way does that differ from faking common descent?

    You yourself show you’ll believe common descent, even if something has no ancestors, so then even if common design is true, and something has no ancestors, merely because you can arrange them in a hierarchy, as is the case with the sequences I created, you’ll believe it doesn’t falsify common descent.

    something without ancestors doesn’t falsify common descent

    –John Harshman

    You’re quote-mining me to me? That’s a new low. Do I have to explain what that means, or will you admit to the quote mine?

    You keep cherry picking data (as in ignoring the problem of mechanistically evolving orphan systems). You pointed out some Phyla have been defined for hundreds of years. Did they need all the fancy phylogenetic techniques? Nope, it was obvious from the organs that some creatures had that others didn’t — eh, you know, orphan systems.

    I don’t think you have a very clear definition of “orphan systems”. Most of these so-called orphans are clear transformations of pre-existing organs. Now of course one doesn’t need “fancy phylogenetic techniques” to recognize some clades. As I’ve said, some are easy using morphology, some are easy only using molecular data, and some are just plain difficult. But there is no difference in kind. And you still have not come up with any explanation for why this nested hierarchy should exist.

    The assumption of phylogeny does not give a mechanistically credible explanation for such orphan systems like the TREGs which Dr. Tan discusses.

    I don’t know what TREGs are or who Dr. Tan is. You don’t seem interested in explaining. But again, phylogeny is not intended to explain the origin of systems, though it may assist in deriving an explanation. Nor is phylogeny an assumption. As someone may have mentioned once or twice, it’s a conclusion from data for which you have not attempted an alternative explanation.

    The issue with Rhipidistia is easily settled by noting tetrapods have systems that Lungfish don’t have, that Lungfish have more in common taxonomically with Coelecanths than tetrapods. This is confirmed by cytochrome-c and the 43 other genes in the study I cited earlier.

    What systems do tetrapods have that lungfish don’t? I still don’t think you know what “taxonomically” means; you seem to use it as a mantra. But if you are backing off your original claim that “fish” are a group separate from tetrapods in favor of the claim that lungfish + coelacanths are a group separate from tetrapods, I see this as a positive development and have no quarrel with you.

    Hypothetically, the pattern of similarity that might have suggested to me tetropods descended from something between a Lungfish and Coelecanth would have been

    I’ll just stop you right there. All this does is reveal your ignorance of phylogenetic analysis and the interpretation of trees.

    But that’s not the pattern is it? Therefore you can’t claim very easily humans are descendants of fish, or as Axel Meyer put it “evolutionarily speaking we are Sarcopterygian fish”.

    You still fail to comprehend. Regardless of the relationships among tetrapods, lungfish, and coelacanths, the data show that they are a clade, separate from actinopterygians, sharks, lampreys, hagfish, and various extinct groups. (We call that clade “Sarcopterygii”.) The very paper you cite in your support shows that tetrapods are descended from “fish”, if you can manage to understand the tree it contains.

    And all your straining might be in vain if the fossil record is young as attested by the physical data.

    The physical data attest no such thing. You have pointed to what are at best a few minor anomalies and at worst (and the worst is correct) PRATTs. Even at best, you have to cherry-pick your anomalies and ignore all we know about geology, paleontology, radiometric dating, and phylogeny. Typical Gish Gallop.

  27. Allan:

    Grurgh. Suppose you had a population of just 100 individuals of a ‘living fossil’. How much divergence do you really think you’d find, despite a squillion years of change? Your grasp of population genetics is dire.

    I mentioned coalescence, but that won’t work too well half the population is on one side of the world and the other half on the other.

    It’s not my lack of grasping population genetics or any other topic but a general tendency on your part to render the most uncharitable interpretation to what I say.

  28. stcordova:
    There are in principle testable predictions relating to the molecular clocks.

    True. What you have done is falsify the notion that cytochrome c follows a universal molecular clock. Different taxa apparently are evolving at different rates. So how does that render phylogeny invalid?

    It did not surprise me at all that it dawned on someone that there is clocking problem in Coelecanths in light of such data.What surprised me is so few noticed it and reported it!It was plain as day to me.The problem also occurs with Lungfish.

    Again, your inability to interpret the trees you construct by rote is the real lesson here. If you will just look, you will see that it’s the mammals that are the odd ones, not the coelacanths and lungfish. Mammals must have considerably longer branches than the other taxa in the tree, which means a faster evolutionary rate than the other vertebrates included.

    The one thing no one will consider is the creatures were created recently!

    You will have to explain the reasoning on that one. What about any of this tells you “recent creation”?

    So what is the testable prediction?This may or may not be feasible, but in principle, we could estimate actual clock rates by comparing the genomes of parents and offspring. Are our sequencing techniques free of enough noise and sensitive enough to detect the actual clock rate? I don’t know.

    I know. The answer is “yes”, and those rates are similar to the rates calculated from phylogeny.

    So what is the testable prediction? I predict the actual clock rate will be faster than people think. The Coelecanth isn’t slow in evolving it’s genome. It was created recently and its divergence from other creatures is by design, not random mutation.

    Care to quantify that? How recently, and what mutation rate do you predict? Will it be faster than the human mutation rate?

    I’m seeing revisions to clock rates of mutation here and there, and it superficially suggests many species are young because their INTRA-group divergence is too small.

    Please present a case. Which species?

    For the coelacanth being a living fossil for hundreds of millions of years, one would think all the extant coelecanths that have been sequenced would show more divergence.

    Why would one think this? Why wouldn’t it be much more likely that the two living species are recently diverged but coelacanths as a clade stretch way, way back? Suppose all mammals went extinct except for mule deer and white-tailed deer. Would you claim that their low amount of divergence suggested that mammals were created recently?

    Sooo, creationists have reasons to try to learn phylogenetic methods because of these issues, even though they reject Universal Common Ancestry.

    That too is incoherent. You have made no case for creationists learning phylogenetic methods.

  29. stcordova,

    I mentioned coalescence, but that won’t work too well half the population is on one side of the world and the other half on the other.

    And is it?

    It’s not my lack of grasping population genetics or any other topic but a general tendency on your part to render the most uncharitable interpretation to what I say.

    What you say is wrong, that’s the problem. You didn’t get it in the Adam and Eve thread either – my view of your population genetics is not merely based on this one data point. A population cannot hold more divergence than its size permits, nor can it retain divergence in excess indefinitely – it moves towards an equilibrium of mutation and loss, and if it has more than the equilibrium value, it will shed it. The age of the lineage has much less to do with it.

  30. John Harshman:

    I don’t know what TREGs are or who Dr. Tan is. You don’t seem interested in explaining.

    I provided a link earlier, but you don’t seem interested in the topic anyway.

    Dr. Tan is an associate professor of cellular biology in Missouri. Her PhD is from an Ivy League school, UPenn. She wrote an article that expresses some of my views about orphan systems. I found the article by accident googling Orphan and taxonomy. I learned of Tan also by accident just googling. I later found out she was a student of Paul Nelson at the Discovery Institute.

    The reason I’m doubtful you’ll give it any consideration is you’ve never conceded how difficult it is for some of the systems I’ve described to evolved, like say, spliceosomal introns, chromatin modifications, histone-mediated double-stranded break repair, the differing position so Initiation Factors, etc. etc.

    Instead, I just get a litany of “look at that nested hierarchy” as if that’s a mechanistic solution to the problem of orphan systems. I pointed out the non-sequiturs of you using that line of argument. You refuse to correct your error, so I don’t bother too much trying to fix the way you conceive of things. If that line of illogic makes you happy, then I’m not going to exert to much effort to rob you of your happiness. That would be kind of mean.

    Anyway: TREG is Taxonomically Restricted Essential Genes

    I spelled out the acronym a few times already for you.
    https://answersingenesis.org/creation-science/baraminology/taxonomically-restricted-essential-genes-organisms-family-tree/

    but a highlight:

    C. Taxonomically Restricted Essential Genes

    Three things should be kept in mind when considering essential genes. First, even the simplest prokaryotic cells require hundreds of essential genes. For example, the organism with the smallest known genome that can constitute a cell, the parasitic bacterium Mycoplasma genitalium, contains 381 essential genes, 79% of its annotated 482 proteincoding genes (Glass et al. 2006). Note that to die is not the most interesting phenotype; rather, it is an extreme phenotype. Thus, to survive is only the minimum. Second, there are many genes that are not essential on their own but are essential when deleted along with another nonessential gene. This well-known genetic phenomenon is called synthetic lethality (Tucker and Fields 2003). Therefore, we do not know how many additional genes in the M. genitalium genome are required for its survival, once synthetic lethality is considered. Studies in yeast show that synthetic lethal is a common phenomenon (Baryshnikova et al. 2013; Costanzo et al. 2010; Kaboli et al. 2014; Tong et al. 2001, 2004). Of the 6200 Saccharomyces cerevisiae genes, about 5100 are non-essential for cell viability. In contrast, a study covering ~30% of the genome identified 10,000 synthetic lethal pairs, and it is estimated that S. cerevisiae contains over 200,000 synthetic lethal combinations, 200-fold more than the number of yeast essential genes (Baryshnikova et al. 2013; Costanzo et al. 2010). Third, not all essential genes are required for the survival of its host organisms at all growth conditions, i.e. some genes are only conditionally essential (Hillenmeyer et al. 2008; Ramani et al. 2012). For example, yeast genes involved in galactose metabolism are essential only when the sole carbon source of yeast is galactose. Thus, the exact list of essential genes for an organism may change depending on the experimental conditions. Normally, when determining what genes are essential for an organism, the organism is provided with an optimal growth environment with all necessary nutrients, a non-stressful situation that is least demanding for the organism. Thus, we will limit the essential gene lists to those required for the survival of organisms under their optimal growth conditions.

    To determine whether there are TREGs, essential genes from several model organisms are grouped according to their taxonomic distribution, or apparent evolutionary age—the proposed “evolutionary origin of a gene, defined by the evolutionarily most distant species where homologs can be found” (Chen et al. 2012a; Wolf et al. 2009), based on the online gene essentiality database (OGEE, http://ogeedb.embl.de/, [Chen et al. 2012a]) (figs. 1 and 2, table 1). For example, the Escherichia coli genes were divided into six groups: 1) Cellular organism group, which can be found in both bacteria and eukaryotes (note that archaea was not counted as a domain separate from bacteria in the analysis); 2) Bacteria group, which can be found in proteobacteria and some non-proteobacteria bacteria but not outside bacteria; 3) Proteobacteria group, which can be found in gammaproteobacteria and some non-gammaproteobacteria proteobacteria but not outside proteobacteria; 4) Gammaproteobacteria group, which can be found in enterobacteriaceae and some non-enterobacteriaceae gammaproteobacteria but not outside gammaproteobacteria; 5) Enterobacteriaceae group, which can be found in E. coli and some non-E. coli enterobacteriaceae but not outside enterobacteriaceae; and 6) Not assigned group. The sixth group includes those genes of which no homologs could be found in other organisms at the time the OGEE database was generated. Some genes of this group are E. coli specific. Therefore, group one E. coli genes are shared between bacteria and eukaryotes; groups two to six are specific to the bacteria domain (fig. 1A, boxed with dash-dot-dot line); groups three to six are specific to the proteobacteria phylum (fig. 1A, boxed with dash-dot line); group four to six are specific to the gammaproteobacteria class (fig. 1A, boxed with dotted line); group five to six are specific to the enterobacteriaceae family. Note that a family-restricted TREG is also an order-restricted TREG, which is also a class-restricted TREG, which is also a phylum-restricted TREG, which is also a domain-restricted TREG.

  31. stcordova: I provided a link earlier, but you don’t seem interested in the topic anyway.

    So far I don’t know what the topic is.

    Dr. Tan is an associate professor of cellular biology in Missouri.Her PhD is from an Ivy League school, UPenn.

    Why should anyone care where her PhD is from?

    She wrote an article that expresses some of my views about orphan systems. I found the article by accident googling Orphan and taxonomy.I learned of Tan also by accident just googling.I later found out she was a student of Paul Nelson at the Discovery Institute.

    Why should anyone care how you found the article or about Paul Nelson? Please exercise some self-discipline.

    The reason I’m doubtful you’ll give it any consideration is you’ve never conceded how difficult it is for some of the systems I’ve described to evolved, like say, spliceosomal introns, chromatin modifications, histone-mediated double-stranded break repair, the differing position so Initiation Factors, etc. etc.

    No, I’ve never conceded that any of this is relevant to common descent. And it isn’t. Are you saying that all these are orphan systems? What is your definition of “orphan system”?

    Instead, I just get a litany of “look at that nested hierarchy” as if that’s a mechanistic solution to the problem of orphan systems.

    You persist in completely misunderstanding. No, it isn’t a mechanistic (or otherwise) solution to the problem of orphan systems. Nested hierarchy isn’t a solution to anything. It’s just evidence for common descent, and will remain so until you can explain the hierarchy by some other mechanism.

    I pointed out the non-sequiturs of you using that line of argument.

    That’s a problem for you, because you don’t seem to understand what my line of argument is.

    Anyway:TREG is Taxonomically Restricted Essential Genes

    Finally. I presume that these are important to you because you think that such things can’t evolve. Why do you think so? I also presume that you think each taxonomically restricted essential gene shows that all species with it must belong to a separate baramin from all species without it, and thus the most restricted genes define baramins (though, oddly, the less restricted ones don’t). Can you identify any taxonomically restricted essential genes that separate humans from chimps? Or any other species pair you would care to discuss.

    I have to say that lengthy quote seemed pointless with regard to anything we’re talking about; as usual you fail to explain any point.

  32. John Harshman,

    So you ask who Dr. Tan is, and when he answers you, you say, “Why should I care where she went to school, why should I care how you discovered her, or who she worked with…”

    You are quite a charmer John.

  33. Joe Felsenstein: I disagree with the statement that without “orphans” common descent couldn’t even be inferred. We can infer it just fine from the sequences of genes that are present in all of the species being studied.

    That’s just vague enough to be useless. But thanks anyways.

  34. Corneel: “11 Therefore God sends them a strong delusion, so that they may believe what is false, 12 in order that all may be condemned who did not believe the truth but had pleasure in unrighteousness.”

    Them who? What truth did they not believe?

  35. Corneel: Only one tree correctly describes the real phylogeny.

    If only “common descent” or “unguided evolution” actually predicted that one true tree.

    But sadly, “common descent” and “unguided evolution” predict far more false trees than the one true tree.

    By keiths logic, common descent and unguided evolution are false.

  36. Allan Miller: How could one construct a phylogeny, given no differences?

    Similarities are indicative of common descent. Except when they aren’t. And now you are telling us that differences are also indicative of common descent. Except when they aren’t.

  37. Allan Miller: There’s that word ‘universal’ again … eventually, due to mutation, two initially identical sequences can become steadily less identical – to the point of being completely unrelated on observation. They really are commonly descended, but you can’t tell. UCD does not rest on that – it does not take sequences with absolutely no relationship to each other and declare them commonly descended.

    Is there a specific percentage of dissimilarity at which shared ancestry can no longer be inferred? If so, what is it? 50%?

    Is there a specific percentage of similarity at which shared ancestry can now be inferred? If so, what is it? 51%?

    The inference is supposed to be objective, isn’t it?

  38. keiths: Are you able to tie your shoes?

    I used to be able to. It was a required skill when I was in the military. But now I wear shoes without shoe laces, just in case I’ve forgotten how.

    I have to admire how you manage to find time off from admiring your own magnificence to post yet another content-less post here at TSZ.

    kudos

  39. I used to be able to. It was a required skill when I was in the military. But now I wear shoes without shoe laces, just in case I’ve forgotten how.

    Good. Best to keep things simple for yourself.

  40. One of the challenges is the gene annotation. So many genes are annotated as cytochrome-c, but they are clearly not the same thing as the size ranges from about 100-500 even in the same organism. I chose the ones that were about 520 residues across species. That said, the shark data looked not very alignable so I dropped it. I put in some more fish. When I tried chicken and frogs, it gave some interesting results that didn’t look quite right. It is possible I picked the wrong cytochrome-c.

    I could go to the ortholog database to draw my sequences. At least those are precomputed to be better quality sets and presumably it picks the correct genes.

    The published studies used other genes like RAG1. That analysis can be done in principle.
    Anyway, here are the added fish sequences

    >Oncorhynchus nerka (Sockeye salmon) (Salmo nerka)
    MAITRWFFST NHKDIGTLYL VFGAWAGMVG TALSLLIRAE LSQPGALLGD
    DQIYNVIVTA HAFVMIFFMV MPIMIGGFGN WLIPLMIGAP DMAFPRMNNM
    SFWLLPPSFL LLLSSSGVEA GAGTGWTVYP PLAGNLAHAG ASVDLTIFSL
    HLAGISSILG AINFITTIIN MKPPAISQYQ TPLFVWAVLI TAVLLLLSLP
    VLAAGITMLL TDRNLNTTFF DPAGGGDPIL YQHLFWFFGH PEVYILILPG
    FGMISHIVAY YSGKKEPFGY MGMVWAMMAI GLLGFIVWAH HMFTVGMDVD
    TRAYFTSATM IIAIPTGVKV FSWLATLHGG SIKWETPLLW ALGFIFLFTV
    GGLTGIVLAN SSLDIVLHDT YYVVAHFHYV LSMGAVFAIM GAFVHWFPLF
    TGYSLHSTWT KIHFGIMFIG VNLTFFPQHF LGLAGMPRRY SDYPDAYTLW
    NTVSSIGSLV SLVAVIMFLF ILWEAFAAKR EVASIELTST NVEWLHGCPP
    PYHTFEEPAF VQVRTN

    >Acipenser gueldenstaedtii (Russian sturgeon) (Danube sturgeon)
    MAITRWFFST NHKDIGTLYL VFGAWAGMVG TALSLLIRAE LSQPGALLGD
    DQIYNVIVTA HAFVMIFFMV MPIMIGGFGN WLVPLMIGAP DMAFPRMNNM
    SFWLLPPSFL LLLASSGVEA GAGTGWTVYP PLAGNLAHAG ASVDLTIFSL
    HLAGVSSILG AINFITTIIN MKPPAVSQYQ TPLFVWSVLI TAVLLLLSLP
    VLAAGITMLL TDRNLNTTFF DPAGGGDPIL YQHLFWFFGH PEVYILILPG
    FGMISHIVAY YAGKKEPFGY MGMVWAMMAI GLLGFIVWAH HMFTVGMDVD
    TRAYFTSATM IIAIPTGVKV FSWLATLHGG SIKWDTPLLW ALGFIFLFTV
    GGLTGIVLAN SSLDIVLHDT YYVVAHFHYV LSMGAVFAIM GAFVHWFPLF
    TGYTLHGTWS KIHFAVMFVG VNLTFFPQHF LGLAGMPRRY SDYPDAYALW
    NTVSSIGSLI SLVAVIMFLF ILWEAFAAKR EVMSVELTTT NVEWLHGCPP
    PYHTYEEPAF VQVQSTS

    When I put these in and used a minimum evolution tree (it was the faster algorithm), I got the diagram below.

    [click link below to enlarge]
    http://theskepticalzone.com/wp/wp-content/uploads/2017/11/more_fish.png

  41. The diagram I generated recovers the Teleostomi clade quite nicely:

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

    EXCEPT, the mammals don’t nest inside Teleostomi! Just like I said, mammals aren’t fish! The TYPOLOGICAL classification nicely agrees with the Molecular phylogeny in this case, and I expected as much, but what is embarrassing is the paleontologists are thrown under the bus who claim we evolved from fish. If we evolved at all, it was some ancestor who was not a fish.

    One might still argue we evolved from fish, and that the extant organisms aren’t representative of the ancestor since the fish were evolving, so the molecular data can’t be interpreted the way I’m interpreting it. Well then, if that is the case, how do you know we evolved from fish, not to mention, it creates a clocking problem which I pointed out earlier.

  42. stcordova: When I put these in and used a minimum evolution tree (it was the faster algorithm), I got the diagram below.

    Sal, you have unfortunately dropped the outgroup (shark), so there’s no way to tell from your tree whether you have recovered Sarcopterygia. You need an outgroup. Also, you need some tetrapods that aren’t mammals.

    Now, you’re using midpoint rooting, but that assumes a molecular clock, which is clearly unwarranted. You can at least see from this tree that the mammals are evolving more quickly than the other species.

  43. John Harshman:

    but that assumes a molecular clock, which is clearly unwarranted.

    Well, thank you for your response. Why is a molecular clock unwarranted, just because it doesn’t agree with a foregone conclusion? You do see the epicycles and ad hoc rationalizations piling up don’t you?

    But in any case, we can do this more methodically than the haphazard way I’m doing it now. We could use, for example the 43 genes used in the study that at least looks in agreement with what I’ve been saying.

    So to humor you, I’ll search for a shark gene with an Entrez querry, we’ll put it in the outgroup. Fair enough? I’ll put a frog xenopus in too.

  44. While Mega is computing, I used the NCBI Entrez query to get higher quality sequences for Shark and Frog (xenopus), but the thing exploded on Gallus gallus (chicken) and sent me to the NCBI help desk!

    But here are the sequences I recovered as the most homologous to the Australian lungfish sequence I was using. This time I also added the accession numbers:

    >Scoliodon macrorhynchos (Pacific spadenose shark) YP_006460407.1
    mainrwlfst nhkdigtlyl ifgawagmvg talsllirae lgqpgsllgd dqiynvivta
    hafvmiffmv mpimiggfgn wlvplmigap dmafprmnnm sfwllppsfi lllasagvea
    gagtgwtvyp plasnlahag psvdlaifsl hlagvssila sinfittiin mkppaisqyq
    tplfvwsilv ttvllllslp vlaagitmll tdrnlnttff dpagggdpil yqhlfwffgh
    pevyililpg fgmishvvay ysgkkepfgy mgmvwammai gllgfivwah hmftvgmdvd
    trayftsatm iiaiptgvkv fswlatlhgg sikwdtpllw algfiflftv ggltgivlan
    ssldivlhdt yyvvahfhyv lsmgavfaim agfihwfpli sgftlhqtwt kiqftvmfig
    vnltffpqhf lglagmprry sdypdaytlw nvissigsli slvavimllf iiweafaskr
    evlsvelpyt niewlhgcpp pyhtyeepaf vqvqrspf

    >Xenopus victorianus (Lake Victoria clawed frog) YP_006883487.1
    maitrwlfst nhkdigtlyl vfgawagmvg talsllirae lsqpgtllgd dqiynvivta
    hafimiffmv mpimiggfgn wlvplmigap dmafprmnnm sfwllppsfl lllassgvea
    gagtgwtvyp plagnlahag asvdltifsl hlagvssilg ainfitttin mkppamsqyq
    tplfvwsvli tavllllslp vlaagitmll tdrnlnttff dpagggdpvl yqhlfwffgh
    pevyililpg fgmishivty ysgkkepfgy mgmvwammsi gllgfivwah hmftvdlnvd
    trayftsatm iiaiptgvkv fswlatmhgg tikwdapmlw algfiflftv ggltgivlan
    ssldimlhdt yyvvahfhyv lsmgavfaim ggfihwfplf tgytlhetwa kihfgvmfag
    vnltffpqhf lglagmprry sdypdaytlw ntvssvgsli slvavimmmf iiweafaakr
    evtlteltst niewlhgcpp pyhtfeepaf vqiqssnn

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