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.

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

  1. Rumraket:

    All you do is assert. You make claims about facts that you never back up.

    I backed up the fact that phosphorylation sites on the protein are writable, readable, and erasable.

    This was in response to your apparent view that phosphorylation sites were static (unchangeable) rather than dynamic (changeable). You objected and said:

    By the way Sal, your whole argument from “RAM” here is completely nonsensical. RAM can only function as RAM if it is editable and rewritable. It has to be possible to change it basically on the fly, as memories are stored, deleted, rewritten and so on.

    To which I pointed out:

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3415845/

    Phosphorylation sites are formed by protein kinases (‘writers’), frequently exert their effects following recognition by phospho-binding proteins (‘readers’) and are removed by protein phosphatases (‘erasers’). This writer–reader–eraser toolkit allows phosphorylation events to control a broad range of regulatory processes,

    And it is exactly this kind of writing and reading that goes on with Histone Proteins that motivated this:

    http://theskepticalzone.com/wp/epigenetic-memory-changes-during-embryogenesis/comment-page-7/#comment-123513

    http://link.springer.com/chapter/10.1007/978-1-4614-7696-2_4?no-access=true

    Epigenetic memory may be defined as a set of gene product concentrations and gene activity by levels in the cell. This information is analogous to random access memory of computers (RAM)… The discrete genome has analogy to read-only memory of computer devices (ROM)

    As to the never ending litany of “Sal doesn’t understand”, actually it looks like I was like minded with some pretty smart researchers. Get a load of the diagram! Confirms the OP:

    DNA is not just a static read-only memory (ROM) for coding proteins, but hosts dynamic random access memory (RAM) in the form of methylations and histone modifications for regulation of gene expression, cellular differentiation, learning and cognition, and who knows what else.

    In other words, I backed up my point.

    From “Quantitative Approaches to model Pluripotency and Differentiation in Stem Cells”:

  2. For colewd:

    This publication describes only one set of proteins among many thousands. The proteins described below are histones. See how even these histones implement a computer Random Access Memory (RAM):

    http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0035703

    In living cells, DNA is packaged along with protein and RNA into chromatin. DNA methylation has long been associated with control, and particularly repression, of gene transcription [28], [29]. In 2000, the term “histone code” was coined to capture the idea that post-translational modifications on histone proteins might have specific functions, and be read, erased and written by specific modifiers and effectors [30], [31]. A related term, “epigenetic code”, emphasized the idea that these molecular modifications were stable enough to encode information, apart from DNA sequence, that could be transmitted, in some cases, from parent to daughter cells [32]. In the years since the proposal of this paradigm, biologists have indeed elucidated the specific <b.read/erase/write functionality of many histone modifying protein domains [33], [34], [35].

    Chromatin-reading and -writing proteins operate as components of molecular complexes that read and write multiple marks in a combinatorial fashion. These complexes often include transcription factors that recognize specific DNA sequences, as well as effector units that carry out gene transcription or other functions, and scaffolding proteins or RNA to bring the right components together into the complex. The phenomenon of engaging multiple marks at once is often referred to as “multivalency” of chromatin modifiers, or “cross-talk” between combinatorial marks [32], [36], [37], [38]. Reading units within one complex may target marks within one histone, in different histones in the same nucleosome, or even across multiple nucleosomes [39]. The same protein may take part in different complexes depending on which subunits are currently available. Thus, a chromatin-modifying complex can be thought of as a read-write rule with the following form: “Find a nucleosome adjacent to DNA sequence AGCCAT; if it is marked with H3K4me3 and H3K27ac, and the DNA is not methylated, then mark the next nucleosome with H3K4me3 and start transcription of a gene.”

    These rules may operate sequentially on chromatin at a particular location. For example, in animal development, the DNA methylation pattern is erased in the early embryo [40], a new pattern established by the time of implantation, and further altered over the course of somatic development. Gametogenesis also involves coordinated erasing and rewriting of DNA methylation. These developments are carried out in a series of steps involving chromatin modification read-write rules implemented by complexes [41].

    An idealized model of chromatin

    Here I present a new computational system, in which chromatin is the writable memory and chemical modifications are the written symbols. Read-write rules model the molecular complexes that recognize and place specific combinations of DNA and histone modifications. The formalism can be easily “programmed” to solve problems such as the NP-complete Hamiltonian path problem, either by the same massively parallel guess-and-check approach of Adleman, or by a more deterministic algorithm that traverses the search tree, with backtracking.

    I prove that chromatin computers are Turing-complete by using one to simulate a Turing machine. The mapping to a Turing machine is not forced, but uses components whose complexity is no greater than that of biological chromatin. I implement a script to simulate execution of chromatin computer programs. I show that biological chromatin has many features that provide computational efficiency, such as parallelism, nondeterminism, addressable memory, modification of the program during computation, and topological shortcuts. The chromatin computer formalism is thus both a natural model of biological chromatin, and a powerful language in which to write computer programs.

    ….

    I calculate that each human cell contains at least 80 megabytes of writeable chromatin – a plentiful amount compared to, say, the 150,000 bytes of onboard memory in the Apollo mission that got astronauts to the moon.

    This compares with the figure I arrived at here:
    http://theskepticalzone.com/wp/thorp-shannon-inspiration-for-alternative-perspectives-on-the-id-vs-naturalism-debate/

    16.5 million nucleosomes per cell, and at least 40 bits

    stcordova’s estimate as published at Amazon in the book
    https://www.amazon.com/Naturalism-Alternatives-Scientific-Methodologies-Methodological-ebook/dp/B01N9WGRUZ

    Which is 16,500,000 x 40 bits x 1 byte/8 bits = 82.5 ~ 80 megabytes

    I was spot on baby! So much for the endless litany by my detractors at TSZ that I don’t understand.

  3. stcordova: Rumraket:

    All you do is assert. You make claims about facts that you never back up.

    I backed up the fact that phosphorylation sites on the protein are writable, readable, and erasable.

    Who the fuck said otherwise?

    YOU are the one who says they can’t evolve because changing them would be detrimental to biological function.

    You keep bringing up this RAM thing as if it is some sort of barrier to evolution. I’m merely pointing out that you can’t have your cake and eat it too. You’re going to have to decide whether you believe they can change, in which case they can evolve, or whether they can’t change, in which case you need 10 million species on the Ark, at least.

    Either way it is you who have a problem with editable phosphorylation sites.

    This was in response to your apparent view that phosphorylation sites were static (unchangeable) rather than dynamic (changeable). You objected and said:

    By the way Sal, your whole argument from “RAM” here is completely nonsensical. RAM can only function as RAM if it is editable and rewritable. It has to be possible to change it basically on the fly, as memories are stored, deleted, rewritten and so on.

    YES, that’s me saying that if it really is RAM, then they have to be able to change. But that would mean they can evolve.

    To which I pointed out:

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3415845/

    Phosphorylation sites are formed by protein kinases (‘writers’), frequently exert their effects following recognition by phospho-binding proteins (‘readers’) and are removed by protein phosphatases (‘erasers’). This writer–reader–eraser toolkit allows phosphorylation events to control a broad range of regulatory processes,

    What did you point out? What are the implications of this irrelevant factoid?

    Make an actual argument here.

    And it is exactly this kind of writing and reading that goes on with Histone Proteins that motivated this:

    Epigenetic memory may be defined as a set of gene product concentrations and gene activity by levels in the cell. This information is analogous to random access memory of computers (RAM)… The discrete genome has analogy to read-only memory of computer devices (ROM)

    And so what?

    Once again you’re just spamming with irrelevancies.

    As to the never ending litany of “Sal doesn’t understand”, actually it looks like I was like minded with some pretty smart researchers. Get a load of the diagram! Confirms the OP:

    It confirms the OP? How does it confirm the OP?

    You claim it does, but you don’t explain anything about how or why. You’re just spamming and flailing with random irrelevant facts.

    Most of your participation in this thread amounts to the Chewbacca-defense.

    “A Chewbacca defense is the name in the United States given to a legal strategy in which the aim of the argument seems to be to deliberately confuse the jury rather than to factually refute the case of the other side. This term was used in an episode of the animated series South Park, “Chef Aid”, which premiered on October 7, 1998. This episode satirized attorney Johnnie Cochran’s closing argument defending O. J. Simpson in his murder trial. The term has since been commonly used in describing legal cases, especially criminal ones. The concept of disguising a flaw in one’s argument by presenting large amounts of irrelevant information has previously been described as the modern-day equivalent of a red herring or the fallacy ignoratio elenchi (irrelevant conclusion).

    That’s you Sal, constantly doing the Chewbacca defense.

    DNA is not just a static read-only memory (ROM) for coding proteins, but hosts dynamic random access memory (RAM) in the form of methylations and histone modifications for regulation of gene expression, cellular differentiation, learning and cognition, and who knows what else.

    In other words, I backed up my point.

    What point? You still haven’t made a coherent point. You’ve just spammed with random technoblather of zero relevance. You’ve still not gotten around to making any actual arguments where you give any supporting reasoning.

  4. stcordova:
    For colewd:

    This publication describes only one set of proteins among many thousands.The proteins described below are histones.See how even these histones implement a computer Random Access Memory (RAM):

    http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0035703

    This compares with the figure I arrived at here:
    http://theskepticalzone.com/wp/thorp-shannon-inspiration-for-alternative-perspectives-on-the-id-vs-naturalism-debate/

    Which is 16,500,000 x 40 bits x 1 byte/8 bits = 82.5 ~ 80 megabytes

    I was spot on baby! So much for the endless litany by my detractors at TSZ that I don’t understand.

    What’s this “for colewd” bullshit? Are you actively relying on this man’s inability to make sense of the things you say? Doesn’t that make you something of a sociopath that you are exploiting this man? He probably even thinks of you as a friend.

    Also, how in the flying fuck are you demonstrating that you understand anything? You can do basic arithmetic, copy-paste diagrams and figures, and quote irrelevant technical factoids without ever bothering to explain what their implications are for the subject of this thread? Yeah man you’re really showing how you totally “get” all this.

    Bill and/or whoever is reading this thread, don’t let Sal confuse you with his voluminous spam about irrelevant fancy-sounding technobabble. What he lacks in argument and reasoning he makes up for in technical-sounding spam.

  5. Rumraket:

    What point?

    Phoshporylation sites on proteins are like RAM. Each species has a slightly different implementation of coordinated RAM (including readers, writers, erasers, positioners of read/write/erasing heads), therefore the variation in genes between is not a random walk from copy-error mutations, but a COORDINATED variation on a basic theme, not a random variation — somewhat like the different models of computers colewd was discussing.

    These computer models can be arranged also in a nested hierarchy. The nested hierarchy is one of common design, not common descent. Ergo, with a little bit of extended thinking, one could see that that common design could be a better explanation for the patterns of similarity diversity that created nested hierarchies of structure (not phylogeny) in biology.

    In the discipline of music, there is theme and variation. There were some masterpieces written based on theme and variation. The most famous variation on a theme is played in the Bellagio Fountains of Las Vegas, Rachmaninoff’s 18th Variation on a theme of Paganini:

    https://www.youtube.com/watch?v=p1wN2W6IiL0

    Rachmaninoff wrote 24 variations on a Theme. John Harshman should need no explanation as to why a composer, a “creator” if you will, would want to express himself by writing 24 variations on a basic theme. The composer did this because he wanted to. Simple as that. The composer wrote it because it was a beautiful idea….

    There is even a bit of a nested-hierarchical structure in the music, not to mention repetitive elements (ah, yes biologists hate that, but tis a musician’s delight):
    https://en.wikipedia.org/wiki/Rhapsody_on_a_Theme_of_Paganini

    Yet when God creates a theme with variation, John suddenly demands I explain why God would do it that way. Well, I don’t ask why Rachmaninoff wrote the 24 variations on a theme of Paganini, which the 18th is THE most famous, it’s easy to simply accept it as true and beautiful. For me to understand why Rachmaninoff did what he did, it would be necessary to have his mind!

    He probably even thinks of you as a friend.

    I hope so.

    Doesn’t that make you something of a sociopath that you are exploiting this man?

    How am I exploiting him? I’m giving him all this free-of-charge entertainment, and so are you.

    If anything, you’re the one I’m exploiting, not Bill. Thanks for letting me exploit all your free-of-charge editorial reviews of my ideas.

  6. stcordova: So what are you going to build it on, the order of evolution which assumes common descent? In that case you’re defining nested hierarchy based on your evolutionary assumptions, not direct structural evaluation. The problem is your circular reasoning and circularly reasoned definitions.Structural comparison minimizes assumptions about evolution.

    I’m surprised that you still have no idea how phylogenetic analysis works, even after blithely pushing buttons in CLUSTAL and reading some unknown portion of Joe’s book. The nested hierarchy is present (or not) in the data, and phylogenetic algorithms discover it based on some measure or other of fit to a tree. If there is no particular fit, various tests of structure will show that. Nothing to do with assumed order of evolution or any other fantasies you may have.

    You’re trying to force your definition of nested hierarchy (phylogenetic) on me and argue there is one and only one way to build a nested hierarchy.That’s false. A conceptual nested hierarchy can be built based on structure with no assumption of common descent. If it disagrees with your phylogenetic nested hierarchy, then all the better for the claim of common design.

    Once more, you need to pay at least some attention. Phylogenetic analysis does not assume nested hierarchy or common descent. It doesn’t even assume phylogeny. Nested hierarchy is not “built” but discovered. Common descent is not an assumption but an explanation, the only explanation anyone has for the existence of nested hierarchy in the data. The methods by which “conceptual nested hierarchy” is “built” do not differ from phylogenetic analyses.

    Now, what is the prediction of common design for the data? How does common design explain nested hierarchy?

  7. John Harshman:

    Phylogenetic analysis does not assume nested hierarchy or common descent.

    You want to go on record as saying “Phylogenetic analysis does not assume common descent.” Can I attribute that assertion to you now?

  8. Rumraket: What’s this “for colewd” bullshit?

    That’s for the bits you would not understand. Don’t take it all personal. We can’t all know everything.

  9. stcordova: Phoshporylation sites on proteins are like RAM. Each species has a slightly different implementation of coordinated RAM (including readers, writers, erasers, positioners of read/write/erasing heads), therefore the variation in genes between is not a random walk from copy-error mutations, but a COORDINATED variation on a basic theme, not a random variation — somewhat like the different models of computers colewd was discussing.

    Please demonstrate the truth of everything that follows your use of the word ‘therefore’. Because what you wrote before it, does not entail what you wrote after it.

    The premise: “Each species has a slightly different implementation of coordinated RAM”

    Does not entail the conclusion:
    “therefore the variation in genes between is not a random walk from copy-error mutations”

    Nor that:
    “but a COORDINATED variation on a basic theme, not a random variation — somewhat like the different models of computers colewd was discussing.”

    NONE of what you write there follow the opening premise.

    Also, what IS a “random walk from copy-error mutations” and how does natural selection factor into that?

    These computer models can be arranged also in a nested hierarchy.

    What computer models? Please show me this nested hiearchy of computer models.

    The nested hierarchy is one of common design, not common descent.

    What does common design even mean? You keep using a term you have never defined. Be specific and quantitative.

    Ergo, with a little bit of extended thinking, one could see that that common design could be a better explanation for the patterns of similarity diversity that created nested hierarchies of structure (not phylogeny) in biology.

    Since NONE of the conclusions you state, follow from ANY of the premises you invoke, you can’t use the word ‘ergo’.

    You really don’t understand how any of this works do you? And I mean this thing with debate and discussion. You never really make any arguments. You just state irrelevant facts, and then you state conclusions that don’t follow from your irrelevant facts.

    Even worse, when you some times try to make it seems as if one of your irrelevant facts contradicts the theory of evolution, or common descent, you invariably use some idiotic strawman of the process that involves strange ideas and basic misconceptions, like that the frequency of bases, or the occurence and fixation of mutations, must be equiprobable.

    And you always completely neglect to consider the effect of selection on anything.

    In the discipline of music, there is theme and variation There were some masterpieces written based on theme and variation. The most famous variation on a theme is played in the Bellagio Fountains of Las Vegas, Rachmaninoff’s 18th Variation on a theme of Paganini:

    Rachmaninoff wrote 24 variations on a Theme. John Harshman should need no explanation as to why a composer, a “creator” if you will, would want to express himself by writing 24 variations on a basic theme.The composer did this because he wanted to. Simple as that.The composer wrote it because it was a beautiful idea….

    Cochran: ” …ladies and gentlemen of this supposed jury, I have one final thing I want you to consider. Ladies and gentlemen, this is Chewbacca. Chewbacca is a Wookiee from the planet Kashyyyk. But Chewbacca lives on the planet Endor. Now think about it; that does not make sense!The Chewbacca Defense

    There is even a bit of a nested-hierarchical structure in the music

    There is? Where?

    not to mention repetitive elements (ah, yes biologists hate that

    Which biologists? Where? Why would they hate that? Cite them.

    Yet when God creates a theme with variation, John suddenly demands I explain why God would do it that way.

    Are we to take this as your concession that yes, you really do believe that God deceptlively made the nesting hiearchies of life which would be expected by a branching genealogical process, just because he could?

    How am I exploiting him?
    By being knowlingly full of shit simply because you don’t have any actual arguments? You’re just deflecting. This whole thread is basically you deflecting the central points with irrelevant blather. And it’s getting increasingly incoherent.

    If anything, you’re the one I’m exploiting, not Bill. Thanks for letting me exploit all our free-of-charge editorial reviews of my ideas.

    You don’t even have any ideas.

  10. stcordova: You want to go on record as saying “Phylogenetic analysis does not assume common descent.”Can I attribute that assertion to you now?

    Sure. But I’ll expect you will quote-mine it to imply something I wouldn’t agree with.

  11. Rumraket,

    Are we to take this as your concession that yes, you really do believe that God deceptlively made the nesting hiearchies of life which would be expected by a branching genealogical process, just because he could?

    You are asserting a branching genealogical process however significant new innovation like sight and flight occurred. John will claim that this is not part of common descent because the common descent conclusion only address the nesting of the data but as we showed with Mac computers designers will also create nesting. The nesting itself is only marginally supportive of the common descent claim.

    If common descent is true between reptiles and birds the innovation of feathered flight must be explained. What also must be explained is how the MYC gene can vary by 14% (per John’s paper) without the animals going extinct.

    If the claim is that common descent is true but where descent stops and creation takes over is unknown, then I think we agree. John’s two papers are a good case study as one appears to support the common ancestor claim where the other does not.

  12. colewd:
    Rumraket,

    You are asserting a branching genealogical process however significant new innovation like sight and flight occurred.

    That sentence is incoherent. Can you put that in another way?

    John will claim that this is not part of common descent because the common descent conclusion only address the nesting of the data but as we showed with Mac computers designers will also create nesting.

    You showed no such thing. You never SHOW these things, you just CLAIM these things.

    So where is this objective nested hiearchy of mac computers?

    The nesting itself is only marginally supportive of the common descent claim.

    What is “marginally”? State that in quantitative terms. Give numbers.

    If common descent is true between reptiles and birds the innovation of feathered flight must be explained.

    The evolution of feathered flight does have a potential explanation in the process of evolution, but that isn’t actually necessary to be able to infer common descent.

    What also must be explained is how the MYC gene can vary by 14% (per John’s paper) without the animals going extinct.

    But it is a manifest fact that it varies. Are you saying that the fact that the gene is not identical between species makes it a fundamental mystery how they can even live?
    If it is mysterious to you how these species can even exist with the gene being different in different species, how is that not also a problem you need to explain on “design”? Are these species being kept alive by a sustained divine intervention or what?

    Wouldn’t the gene being different actually be evidence of evolution?

    What’s funny about your comment here is that to someone like Sal, orthologous genes (different versions of the same gene, in different species), are apparently fine as an indication of common descent. He seems to draw the line at taxonomically restricted genes. But you seem to disagree here? It isn’t even clear why.

    If the claim is that common descent is true but where descent stops and creation takes over is unknown, then I think we agree.

    That’s not a claim I remember me or anyone else here making. I don’t even know what that really means.

    John’s two papers are a good case study as one appears to support the common ancestor claim where the other does not.

    Why?

  13. Rumraket,

    You are asserting a branching genealogical process however significant new innovation like sight and flight occurred.

    That sentence is incoherent. Can you put that in another way?

    Simply put, more occurred then would be expected from reproduction. We have never seen a major innovation resulting from reproduction such a sight or flight. Yet to claim common descent between yeast and vertebrates these innovations must have occurred.

    Bill: John will claim that this is not part of common descent because the common descent conclusion only address the nesting of the data but as we showed with Mac computers designers will also create nesting.

    Rum: You showed no such thing. You never SHOW these things, you just CLAIM these things.

    I showed how there are similarity and differences between two similar but separate designs, the Mac book air and the Mac book pro. In this case the similarities and differences are result of similar design not inheritance.

    But it is a manifest fact that it varies. Are you saying that the fact that the gene is not identical between species makes it a fundamental mystery how they can even live?

    The sequence variation is probably not from random change. This is a nuclear protein which must bind with several proteins and has a specific phosphorylation pattern as Sal mentioned.

    What’s funny about your comment here is that to someone like Sal, orthologous genes (different versions of the same gene, in different species), are apparently fine as an indication of common descent. He seems to draw the line at taxonomically restricted genes. But you seem to disagree here? It isn’t even clear why.

    We may disagree here but nuclear proteins are mutation sensitive especially a protein that is mission critical to the cell cycle. Mutation to this protein probably requires mutation to some proteins that bind with it.

    That’s not a claim I remember me or anyone else here making. I don’t even know what that really means.

    Unless the claim is universal common descent then there is some line of demarkation.

    John’s two papers are a good case study as one appears to support the common ancestor claim where the other does not.

    Why?

    With the limited data we have on group (crocks) MYC genes are very close with the sequences measured <.5%. The flightless birds have greater then 10% sequence variation with the limited sequence data compared.

  14. colewd:

    I previously did not either and was blind to new evidence that was around me which only started to exist when I opened my eyes.

    LOL.

    Common descent alone does not explain the extreme difference in sequence variation between nested flightless birds and nested crocks.

    “Nested crocks” is a pretty good description of creationism.

  15. I said:

    stcordova: You want to go on record as saying “Phylogenetic analysis does not assume common descent.”Can I attribute that assertion to you now?

    To which John Harshman Responded:

    Sure. But I’ll expect you will quote-mine it to imply something I wouldn’t agree with.

    So why would a phylogenetic insist there is one and only one proper way to group things?

    Here are pictures of 3 skeletons here:

    Lungfish (a Sarcopyterygiian fish)
    http://theskepticalzone.com/wp/wp-content/uploads/2017/10/04_African-lungfish_Skeleton1.jpg

    Tuna (an Actinogypteriian fish):
    http://theskepticalzone.com/wp/wp-content/uploads/2017/10/caljsiol_sio1ca175_060_118a1-1024×689.gif

    Pigeon (a bird, a tetrapod):
    http://theskepticalzone.com/wp/wp-content/uploads/2017/10/bird_skeleton1.jpg

    State the reasons why to the readers, why it is illegitimate to say the most structurally similar skeletons are

    1. Tuna and Lungfish

    instead of:

    2. Tuna and Pigeon
    3. Lungfish and Pigeon

    Couldn’t I decide conceptually that I want to group things close together in terms of skeletal structure to make the nested hierarchy according to geometric principles? Why is that wrong, why do I have to adopt your phylogenetic methods? Why is the phylogenetic way the right way to make a nested hierarchy? What is illegitimate about using an old school structural comparison?

    After all, if we aren’t assuming common descent, we can just group things conceptually according to our utility, and not try to force fit a nested hierarchy that supports a forgone conclusion about historical origins.

    For eons, people distinguished creatures like cats from fish. That is based on structure, not phylogeny. That’s something phylogenists have serious difficulty coming to terms with, the problem of the conceptual nested hierarchies that naturally come to people’s minds based on unprejudiced comparisons of similarity and diversity.

  16. John Harshman:

    Now, what is the prediction of common design for the data? How does common design explain nested hierarchy?

    There is no prediction. Why does there have to be a prediction to assert a claim is true? There is common design in the 24 variations on a theme of Paganini by Rachmaninoff. Why do I have to make a prediction to assert there is common design by Rachmaninoff in all 24 variations of a basic theme for you to accept common design? Why do I have to explain Rachmaninoff’s reasons for making 24 variations on a melody in order for you to accept the common design in his 24 works of art. Hypothetically, you could put the notes through a phylogeny software program and create a nested hierarchy. Would that silly exercise make you then believe the designer (Rachmaninoff) was being deceptive, that he faked a phylogeny, that there is no common design? Of course not.

    Yet, you will apply a different standard to God. You do so because you see Rachmaninoff, but you don’t see God. Ok, I respect that.

    But the point remains, if the Designer created creatures such that one could not evolve from another, that should count as evidence of creation, and therefore common design, should it not? Like the issue with accepting the common design of Rachmaninoff’s 24 variations on the same melody, you don’t need predictions, you don’t need to explain the designer’s rationale for making the designs in order to hypothesize something has common designs.

    The assumption of evolution by mutation and natural selection does not explain the structural nested hierarchy defined by un-evolvable features. We don’t see any experimental evidence that a fish will make coordinated changes to become a bird through random copying errors and differential reproductive success, actually quite the opposite.

    Therefore common design is suggested because “God must have done it, because evolution can’t.”

  17. stcordova: Therefore common design is suggested because “God must have done it, because evolution can’t.”

    So God made life look like it evolved because nature couldn’t do it.

    I guess the creationist rule is, ‘anything but evolution,’ so making sense is hardly needed, let alone achieved.

    Why do I have to make a prediction to assert there is common design by Rachmaninoff in all 24 variations of a basic theme for you to accept common design?

    You must, and do, have a prediction for design by Rachmaninoff, or it might just be random marks or some such thing. The basic prediction is that you’ll have the evidence for rationality, for intelligence, in his work. He will not be impeded by some strange adherence to past works, so that there could only be derivations of information inherited by some kind of reproduction. Of course Rachmaninoff’s works are not much like evolution, and the evolutionary productions in life are not much like what intelligent beings make.

    Real theories require real evidence for them, and don’t merely rely on the pretense that if nothing else explains it, then it does.
    That’s prejudging and nothing better. Evolutionary theory, of course, does have real evidence, while intelligent design avoids honesty about the issue because life is really constrained by unintelligent factors–ones that a fairly intelligent mind (and it would require a very intelligent mind to design life) would not obey–unless for some joke or fraud (etc.). Your only hope would be to find evidence of the joke or fraud or whatever, and of course that’s hardly anything anyone has come up with. Barring that, life constraints and patterns are simply not those that exist among known intelligent beings.

    It’s just possible that something other than evolution made life, but it wasn’t by any kind of design that makes sense of life. Design wouldn’t be a good option even if evolution were to fail, as life’s patterns and limites would simply not match up with what we actually see in human design, the only design of consequence that has been observed.

    Glen Davidson

  18. stcordova: Couldn’t I decide conceptually that I want to group things close together in terms of skeletal structure to make the nested hierarchy according to geometric principles? Why is that wrong, why do I have to adopt your phylogenetic methods? Why is the phylogenetic way the right way to make a nested hierarchy? What is illegitimate about using an old school structural comparison?

    The problem here is the definition of nested hierarchy. Nested hierarchy doesn’t mean group by similarity. Something must get “nested.” Some patterns of things shared by all groups would be seen at the base of the tree, some sub-patterns shared by each group would be seen in the “branches,” and the same for subgroups, etc.

    Another problem is the amount of information in the structures you’ve decided to use for your grouping. The lungfish skeleton seems lacking in terms of enough bones to decide where it goes (the link to the tuna does not work). Here I’d need to learn anatomical stuff better, perhaps follow the development of the lungfish skeleton to decide if those protruding things near the “neck” correspond to, say, clavicles, or to something else, then check the development of other bones, whether some bones disintegrate, or fuse, during development, etc, etc. Either way, if there’s not enough information in the skeletons, I’d risk making the wrong groups based on a shallow analysis.

    Even “old school” structural comparisons rely on sufficiently informative features. Not shallow resemblances.

  19. stcordova: There is no prediction. Why does there have to be a prediction to assert a claim is true?

    There must be evidence to assert a claim is true. If you don’t like “prediction”, how about “expectation”? From common descent we expect a nested hierarchy, which is to say that the data will fit a tree. From common design we expect…what? That’s your problem here. How do you explain the nested hierarchy of life? Lately you seem to be claiming that the nested hierarchy doesn’t exist and is a matter of convenience only, but that won’t fly.

    There is common design in the 24 variations on a theme of Paganini by Rachmaninoff. Why do I have to make a prediction to assert there is common design by Rachmaninoff in all 24 variations of a basic theme for you to accept common design?

    What does “common design” mean here? Merely that Rachmaninoff produced all the variations? What is the evidence of common design, other than that we know the variations were all composed by Rachmaninoff?

    Why do I have to explain Rachmaninoff’s reasons for making 24 variations on a melody in order for you to accept the common design in his 24 works of art. Hypothetically, you could put the notes through a phylogeny software program and create a nested hierarchy. Would that silly exercise make you then believe the designer (Rachmaninoff) was being deceptive, that he faked a phylogeny, that there is no common design? Of course not.

    My prediction is that you could not do that silly exercise and that the variations do not form a nested hierarchy. You can’t use a hypothetical and contrary to fact exercise as evidence of common design.

    Yet, you will apply a different standard to God.You do so because you see Rachmaninoff, but you don’t see God.Ok, I respect that.

    I doubt you respect anything, and that certainly isn’t my reasoning process. Your bad analogy doesn’t explain why life displays nested hierarchy. Note that the argument here isn’t even over whether god had anything to do with life; it’s over common descent vs. separate creation. “Common design” is supposed to be an attempt at explaining the nested hierarchy given the absence of common descent. So far there has been no such explanation, and the attempted Rachmaninoff analogy certainly isn’t one.

    But the point remains, if the Designer created creatures such that one could not evolve from another, that should count as evidence of creation, and therefore common design, should it not?

    No. Once again you confuse the origin of variation with the origin of the nested hierarchy. You mean “could not evolve from another by unguided processes”; there’s always the unstated qualifier.

    Like the issue with accepting the common design of Rachmaninoff’s 24 variations on the same melody, you don’t need predictions, you don’t need to explain the designer’s rationale for making the designs in order to hypothesize something has common designs.

    We aren’t talking about the designer’s rationale. Focus. The question is what explains the nested hierarchy displayed by the data. Common descent explains it, and you have offered no alternative.

    The assumption of evolution by mutation and natural selection does not explain the structural nested hierarchy defined by un-evolvable features.We don’t see any experimental evidence that a fish will make coordinated changes to become a bird through random copying errors and differential reproductive success, actually quite the opposite.

    Once again, you focus on the mechanism of variation rather than the explanation of nested hierarchy. That isn’t the topic. If you want to argue for guided evolution, you need another thread. Now we do in fact have copious evidence of the transitional stages between fish and bird, which you want to ignore, and they even form a fairly good temporal sequence. In other words, the sequence of the fossil record is a much better fit to the phylogenetic tree than would be expected by chance, and the consilience of these two independent forms of evidence reinformces both the temporal sequence in the record (contradicting flood geology) and common descent.

    Therefore common design is suggested because “God must have done it, because evolution can’t.”

    Accepting that claim for the sake of argument, how is common descent ruled out? Why couldn’t god have done it through guided evolution and common descent? That would at least explain the nested hierarchy, which you have otherwise not done.

  20. GlenDavidson: So God made life look like it evolved because nature couldn’t do it.

    No Glen. You still don’t get it. But I am patient with you, so I will explain it to you again.

    Men attributed the works of God to “Nature.”

  21. Who trusted God was love indeed
    And love Creation’s final law
    Tho’ Nature, red in tooth and claw
    With ravine, shriek’d against his creed

  22. John Harshman: Why couldn’t god have done it through guided evolution and common descent?

    The god of the old testament is not one for subtlety. Sal is convinced that the signature of his deity will be found in the clear, not inferred.

  23. John Harshman:

    There must be evidence to assert a claim is true. If you don’t like “prediction”, how about “expectation”?

    Creative intelligent agencies do not have to follow a predictable pattern. Could anyone on the planet predicted the 24 variations of a basic theme that Rachmaninoff made of the same basic melody by Paganini (another intelligent designer). No. But no one will deny the 24 variations are intelligently designed. So as a matter of principle, and intelligent agency’s work does not have to be predictable to be asserted as intelligently designed. Evidence of intelligent agency can come via another route.

    There must be evidence to assert a claim is true.

    Agreed, and that is actually something common descent doesn’t have because even as you said, it doesn’t explain the origin of novel features that look miraculously designed. It is these miraculously designed features that define the nested hierarchy defined by structural novelties.

    A poof is evidence of creative ability and genius at the same time, but one that doesn’t follow prediction. God-of-the gaps is valid enough for me, maybe not for you. But I pointed out several times, if you won’t accept God-of-the gaps, even if a miracle happened, you wouldn’t accept it as evidence of God. So if you won’t accept miracles as evidence of God, what will you accept?

    Ok, so you say you’ll accept something that is predictable. Ok, so if it’s predictable, then it is law like physics, in which case it’s not an intelligent God, it is a law of physics. Thus, by your epistemological policy, even if an Intelligent God exists, even if he has left a trail of miracles that you could reconstruct by inference if you were willing to do so, you’ll guarantee you’ll miss the correct answer. That is of course your choice to decide what you’ll believe in a world where we always have far less facts than we would like. It is, like so many things, like wagering in a casino on what is true based on very incomplete data…

    And one thing we’re learning, the differences in genes and the proteins they code do not look like random variations. Much like the notes in the 24 variations by Rachmaninoff of Paganini’s melody, they are non-random, but rather coordinated.

    I demonstrated the coordinated changes associated with Serine and Threonine residues (the phosphorylations). In prokaryotes the phosphorylations happen on Histidine, but in eukaryotes, on Serine, and in higher more sophisticated eukaryotes on Threonine. There are even more coordinated patterns likely to be discovered such as those associated with protein methylation, acetylation, palmitylation, ubiquitination, glycoconjugatin, etc.

    An example that no one here except me wanted to discuss was the different eye Rhodopsin architectures. Rhodopsin is a protein important to vision. Different species attach the glycans to different locations on their Rhodopsin. That difference is necessary for the way the creature sees.

    Speaking of which, species specific difference in proteins that result in species specific glyco conjugations is worth a separate comment. Just like the species-specific RAM of phosphorylation, there is species specific glyconjugation that constrains the sequences on proteins. So again, as before, the presumption of random mutation copy errors being a mechanism for generating the variations in genes between species is falsified.

    Finally, phylogenists only pretend common descent predicts the patterns found in biology. It didn’t predict the emergence of spliceosomal introns did it?

    PS
    Here is a video of the full 24 variations by Rachmaninoff on a theme of Paganini, the 18th is the most famous and the one that is featured in the Las Vegas Bellagio Casino fountains every night as shown earlier.

    https://youtu.be/BRKZAxStvQo

  24. Variations on a theme can be intelligently designed. The issue is, how can we determine a variation is random vs. intelligently designed.

    Rachmaninoff’s 18th variation on a basic theme of Paganini is featured in this movie clip with Christopher Reeves seeing the face of Jane Seymour for the first time. How do we know the 18th variation is not the result of random variation, but rather design? As I argued with John, it’s not about predictable variation (random variation with a mean and distribution) following expectation. If anything, there a subtle violations of expectation in designed variation which are deliberately designed to violate random expectation.

    So, without the additional facts of humans knowing Rachmaninoff was a real person, how do we know the 18th Variation was NOT the product of a Random Number Generator?

    The species on the planet are variations on a theme. How do we know the variations are random or designed? Those are some interesting questions aren’t they?

    In the meantime, Christopher Reeves sees Jane Seymour for the first time with Rachmaninoff’s 18th variation on a theme of Paganini playing in the background. Intelligent Design is often sublime in its beauty:

    https://youtu.be/h4N1mxN5JbU

  25. Here is Santana and the Dave Mathews Band performing “you’re the love of my life”:
    https://youtu.be/IV83Q-okrMs

    Santana’s song has “homologous” sections with Brahms 3rd symphony 3rd movement:
    https://www.youtube.com/watch?v=VCpvp2LDsWY

    If we didn’t know that Santana and Brahms were intelligent designers, but only had access to the sound clips, how could we know the variations on a basic theme are intelligently designed vs. the product of random variation?

  26. Phylogenetic analysis is somewhat like signal processing and correlation. Signal processing is taken to the state-of-the art in audio comparisons and reconstruction. Our ability to hear and appreciate music is a phenomenally sophisticated signal processing system.

    At about 1:34 in the following video of Billy Joel one will hear the “homologous” signal in his tune with the 2nd movement of Beethoven’s Pathetique Sonata:

    https://youtu.be/Dnn_Tv5KebQ

    Here is the 2nd movement of Beethoven’s Pathetique Sonata:

    If we only had statistics and signal processing, rather than access to the designers like Billy Joel and Ludwig van Beethoven, how do we know the “homologous” constructs aren’t the product of random variation, but rather intelligent design? This is a compelling problem in statistical signal processing, the realm of Electrical Engineers. 🙂

    Anyway, the 2nd movement of Beethoven’s Pathetique Sonata:
    https://youtu.be/vGq3-Fi_zQY

  27. stcordova: Creative intelligent agencies do not have to follow a predictable pattern.

    True. And yet the nested hierarchy of life follows the pattern predicted by common descent. Why?

    Agreed, and that is actually something common descent doesn’t have because even as you said, it doesn’t explain the origin of novel features that look miraculously designed. It is these miraculously designed features that define the nested hierarchy defined by structural novelties.

    You persist in ignoring the nested hierarchy, which common descent explains, and in introducing the origins of various features, which common descent does not explain and was never intended to explain. This is like objecting to Newton’s law of universal gravitation by complaining that it doesn’t explain the different sizes and compositions of the planets. Since gravitation doesn’t explain those facts, the planets must have been poofed into their positions and carried about on the backs of angels. QED.

    Your music analogy and everything that follows is irrelevant and pointless. Nor is this in any way an argument about whether god exists or has acted in the world. It’s about common descent, nothing more. You have never once addressed the point, in however many thousands of posts.

  28. You persist in ignoring the nested hierarchy

    No I don’t.

    And which nested hierarchy are you talking about, the one that is constructed to support you foregone conclusions of common descent or other nested hierarchies that are based on structure and anatomical similarities (like skeletal similarity).

    Multiple possible nested hierarchies don’t exactly common descent do they? They do fit well with common design where shared motifs and convergences are very well permissible.

    I posed a question to you about the skeletal structures, which it seems you feel uncomfortable giving a straightforward answer. When I ask which are more similar, you say, “it’s not about similarity.” Then what is about???? I’ll tell you what it’s about, it’s building and force fitting a nested hierarchy to support the foregone conclusion common descent even when it doesn’t fit, such as with the skeletal structures of Tuna, Lungfish, and Pigeon’s.

    So I don’t ignore nested hierarchy, in fact I suggested a few myself that should be structurally obvious. But then you argue, nested hierarchy “it’s not about similarity.” Then what’s it about then? Supporting common descent? That’s fudging and cherry picking toward a foregone conclusion. So you’re building your framework on circular reasoning, fudging and cherry picking.

  29. This is nice title from the journal of Molecular Biology and Evolution. The author tries to label his opponents with the worst possible label, he insinuates they are creationists! LOL!

    https://academic.oup.com/mbe/article/33/8/1902/2579327

    How Common Is Parallel Intron Gain? Rapid Evolution Versus Independent Creation in Recently Created Introns in Daphnia

    Oh can he be more obvious? Ok let me evolve the phrases:

    1. Evolution vs. Creation
    2. Evolution vs. Independent Creation
    3. Rapid Evolution vs. Indpendent Creation

    N. Rapid >Evolution Versus Independent Creation in Recently Created Introns in Daphnia

    The author of the article didn’t like the implications that introns apparently popped up independently unrelated lines.

    A series of articles in this and other journals reported evidence for a strikingly high degree of parallel insertion of introns in different alleles of the water flea Daphnia pulex .

    .. authors favoring recent intron creation.
    ….
    In a series of papers in this journal, Science and Genome Biology and Evolution , Omilian and Li and their coauthors have reported an exciting set of cases in which new introns have been created in very recent times in the water flea Daphnia pulex

    Ah yes, Roy putting insinuating the creationist label to his rivals.

    But that paper had some nice references to other papers:
    https://www.sciencedirect.com/science/article/pii/S096098220300558X

    Remarkable Interkingdom Conservation of Intron Positions and Massive, Lineage-Specific Intron Loss and Gain in Eukaryotic Evolution

    Sequencing of eukaryotic genomes allows one to address major evolutionary problems, such as the evolution of gene structure. We compared the intron positions in 684 orthologous gene sets from 8 complete genomes of animals, plants, fungi, and protists and constructed parsimonious scenarios of evolution of the exon-intron structure for the respective genes. Approximately one-third of the introns in the malaria parasite Plasmodium falciparum are shared with at least one crown group eukaryote; this number indicates that these introns have been conserved through >1.5 billion years of evolution that separate Plasmodium from the crown group. Paradoxically, humans share many more introns with the plant Arabidopsis thaliana than with the fly or nematode. The inferred evolutionary scenario holds that the common ancestor of Plasmodium and the crown group and, especially, the common ancestor of animals, plants, and fungi had numerous introns. Most of these ancestral introns, which are retained in the genomes of vertebrates and plants, have been lost in fungi, nematodes, arthropods, and probably Plasmodium. In addition, numerous introns have been inserted into vertebrate and plant genes, whereas, in other lineages, intron gain was much less prominent.

    Remember the example above of Billy Joel’s “This Night” having some motif insertions of Beethoven’s Pathetique Sonata? This is the problem with humans sharing more introns with a plant than with fruit fly!!!!

    Rapid Evolution Versus Independent Recent Creation indeed!

    This is that hated “flower diagram” x2, bwahaha! It’s a pan-genome/pan-intron diagram.

  30. stcordova: No I don’t.

    Yes you do. You have no explanation for it. You’ve never tried to explain it.

    And which nested hierarchy are you talking about, the one that is constructed to support you foregone conclusions of common descent or other nested hierarchies that are based on structure and anatomical similarities (like skeletal similarity).

    Neither of these exists as you imagine. The nested hierarchy isn’t constructed; it’s discovered in the data. The one based on “structure and anatomical similarities” doesn’t generally differ from the one based on molecular data. I don’t think you understand what hierarchies you’re referring to, how analyses show them, or pretty much anything you’re talking about.

    Multiple possible nested hierarchies don’t exactly common descent do they? They do fit well with common design where shared motifs and convergences are very well permissible.

    You will need to explain what you’re talking about. Also, your first sentence needs a verb to be at all intelligible.

    I posed a question to you about the skeletal structures, which it seems you feel uncomfortable giving a straightforward answer. When I ask which are more similar, you say, “it’s not about similarity.”Then what is about????I’ll tell you what it’s about, it’s building and force fitting a nested hierarchy to support the foregone conclusion common descent even when it doesn’t fit, such as with the skeletal structures of Tuna, Lungfish, and Pigeon’s.

    You can tell me anything you like, but have you understood nothing about all the phylogenetic analyses you have performed so cavalierly in CLUSTAL as well as read about, supposedly, in various papers? Those skeletal structures most certainly do fit a nested hierarchy, though to make sense of lungfish you need to incorporate a great many fossils.

    So I don’t ignore nested hierarchy, in fact I suggested a few myself that should be structurally obvious.

    I don’t think you understand what a nested hierarchy is, even now. Nor do you have any real clue about how to analyze structure.

    But then you argue, nested hierarchy “it’s not about similarity.” Then what’s it about then? Supporting common descent? That’s fudging and cherry picking toward a foregone conclusion. So you’re building your framework on circular reasoning, fudging and cherry picking.

    When you put an argument from me in quotes, I will ask you to quote something I have actually said. Nested hierarchy is a particular pattern in the data, not just varying degrees of similarity. You seem to have no idea what that pattern looks like or how to find it. It’s hard to talk with you about things you don’t understand, won’t understand, and refuse to understand.

    I would also ask you to respond to my posts, not just to some single sentence while ignoring the rest.

  31. stcordova: This is that hated “flower diagram”

    Nobody hates the “flower diagram”. You just fail to understand its implications. And I think your emphasis on the word “created” as if it actually refers to creationism is hopelessly naive.

  32. Below is a picture of the plant Arabidopsis Thaliana. The paper I just cited says humans are more similar intron-wise to this plant than they are to animals like fruit flies and nematodes.

  33. John Harshman,

    John Harshman: Why couldn’t god have done it through guided evolution and common descent?

    He could have. Or there are other ways he could have that don’t involve common descent. You have failed to show that the data we see that shows a nested hierarchy could not simply be the result of design with an unknown implementation and some limited common descent as we see in crocks.

    Your flightless bird paper is very damming evidence against common descent being responsible for all species; even a guided version. Your explanation of loss of flight is very problematic. The evidence favors special creation in a specific location.

  34. John Harshman:

    Nested hierarchy is a particular pattern in the data, not just varying degrees of similarity

    “A particular pattern” as in a pattern that assumes common descent and ignores the problems posed by other possible hierarchies like the ones where lung fish skeletons are put together by more similar skeletons like that of tuna instead of pigeons. It pretends their isn’t incongruence between these other reasonable conceptual hierarchies when there is definitely incongruence. The way the myth of phylogeny is perpetuated is by arguing for a congruence of phylogenetic nested hiearchies based on ignoring incongruence posed by structural nested hierarchies.

    I don’t think you understand what a nested hierarchy is, even now. Nor do you have any real clue about how to analyze structure.

    Don’t misinterpret my resistance to accept your definition of nested hierarchy with me not understanding. You’re the one not realizing you’ve created a circularly reasoned definition of nested hierarchy based on the implicit assumption of common descent. I show exactly why.

    As far as me not understanding structure, explain to the readers which pair of skeletons are more structurally similar:

    1. tuna and lungfish
    2. tuna and pigeon
    3. lungfish and pigeon

    Go ahead. You said I don’t understand. Explain which pair of skeletons are more similar. You said I don’t understand structure. So explain to the readers which pair of skeletons is more structurally similar.

    The reason you have problems dealing with this simple question is that it highlights the cherry picking nature of phylogenetic methods in constructing phylogenetic nested hierarchies. That’s why I’m not defining nested hierarchy by phylogeny like you do.

    I’m not ignoring what you say, I’m pointing out you’re dead wrong. There’s a difference.

  35. John Harshman: And yet the nested hierarchy of life follows the pattern predicted by common descent.

    Which nested hierarchy does common descent predict? Please be as specific as possible.

    John Harshman: The nested hierarchy isn’t constructed; it’s discovered in the data.

    It has to be discovered in the data because it cannot be predicted.

  36. stcordova: one could see that that common design could be a better explanation for the patterns of similarity diversity that created nested hierarchies of structure (not phylogeny) in biology

    Yes, anything I think of “could be” a better explanation. That you can be granted. It’s just that “common design” so far simply means “god did it” and if “god did it” is an “explanation” then you’ve already lost. And given you’ve explicitly said that you are happy with “god did it” I’m not sure what you have to offer other then peer reviewing real scientists real work without really understanding it in the first place.

    If “common design” meant something other then “it looks just like evolution because the designer liked reusing components and refused to pass innovations around like human designers but just like evolution is constrained but god still did it so that’s alright” then perhaps it could be a better explanation in reality as well as possibility.

    But you can’t even name a single way we could tell the difference between the two, many thousands of words later. And you’ve already said if evolution did not do it then common design did. But common design is not a mechanism like evolution is. So you’ve literally said nothing in tens of thousands of words Sal.

  37. Mung: Which nested hierarchy does common descent predict? Please be as specific as possible.

    Which nested hierarchy does common design predict? Please be as specific as possible.

  38. stcordova: It pretends their isn’t incongruence between these other reasonable conceptual hierarchies when there is definitely incongruence. The way the myth of phylogeny is perpetuated is by arguing for a congruence of phylogenetic nested hiearchies based on ignoring incongruence posed by structural nested hierarchies.

    You should write a paper and expose this scandal!

  39. colewd:
    John Harshman,

    He could have.Or there are other ways he could have that don’t involve common descent.You have failed to show that the data we see that shows a nested hierarchy could not simply be the result of design with an unknown implementation and some limited common descent as we see in crocks.

    Well of course it could be the result of design with an unknown implementation, as that hypothesis would allow for anything at all. And yet common descent predicts nested hierarchy. So why would this unknown implementation so exactly match the expectation of common descent? You have given no reason. Why does common descent in crocs look exactly like unknown implementation of common design in birds? Why can’t we tell where common descent leaves off and common design begins?

    Your flightless bird paper is very damming evidence against common descent being responsible for all species; even a guided version.Your explanation of loss of flight is very problematic.The evidence favors special creation in a specific location.

    You will have to explain what you mean by that.

  40. stcordova: “A particular pattern” as in a pattern that assumes common descent

    No, the pattern is there regardless of the cause. Common descent is just the only cause anyone has proposed so far that makes any sense. Feel free to come up with another.
    and ignores the problems posed by other possible hierarchies like the ones where lung fish skeletons are put together by more similar skeletons like that of tuna instead of pigeons.
    Sorry, but that isn’t a nested hierarchy.
    It pretends their isn’t incongruence between these other reasonable conceptual hierarchies when there is definitely incongruence. The way the myth of phylogeny is perpetuated is by arguing for a congruence of phylogenetic nested hiearchies based on ignoring incongruence posed by structural nested hierarchies.

    I don’t think you even read my posts. You keep on repeating the same points I have refuted over and over without addressing my refutations. Have you even read this far into this post? Hi, Sal.

    Don’t misinterpret my resistance to accept your definition of nested hierarchy with me not understanding.

    Don’t worry, I’m not misinterpreting. My definition isn’t mine. It’s just the real one.

    As far as me not understanding structure, explain to the readers which pair of skeletons are more structurally similar:
    1. tuna and lungfish
    2. tuna and pigeon
    3. lungfish and pigeon

    See? You still don’t understand what a nested hierarchy is, and asking that question just underlines it. Sorting by degree of overall similarity isn’t how you recognize one.

    I’m not ignoring what you say, I’m pointing out you’re dead wrong.There’s a difference.

    But it happens that you’re ignoring what I say. You have no idea how to discover hierarchical structure in data, whether molecular or morphological. Asking which of three skeletons looks more similar to you isn’t it. And in fact your only method for discerning even similarity is to say something like “hey, it looks more similar to me”.

  41. Mung: Which nested hierarchy does common descent predict? Please be as specific as possible.

    What point are you trying to make? Common descent predicts no particular nested hierarchy. It just predicts that the data will have hierarchical structure and that different partitions of the data will have similar hierarchical structure. Is this not something you already knew?

    It has to be discovered in the data because it cannot be predicted.

    What, if anything, is the point you are trying to make here? Are you doing any more than playing around with words? The prediction is that hierarchical structure will be present in the data, ready to be discovered when you look.

  42. stcordova: The reason you have problems dealing with this simple question is that it highlights the cherry picking nature of phylogenetic methods in constructing phylogenetic nested hierarchies. That’s why I’m not defining nested hierarchy by phylogeny like you do.

    We’ve clearly dealt with your loaded question. It’s you who’s having problems reading our answers, which highlights your inability to reading for comprehension. How many sentences can you actually read and understand before your brain quits?

  43. John Harshman,

    So why would this unknown implementation so exactly match the expectation of common descent?

    I don’t think it does across the board. In the case of crocs it matches close the variation we see where we know ancestry has occurred like dogs. In the case of flightless birds the variation is much higher and it does not look like ancestry is shared.

    Why does common descent in crocs look exactly like unknown implementation of common design in birds?

    Not sure what you mean here.

    Why can’t we tell where common descent leaves off and common design begins?

    I don’t think we have enough experience and data yet but your two papers are an excellent case study as they maybe a representation of a line of demarkation between design and descent.

    The fact that the birds are geographically diverse is evidence of separate design so again these papers are an interesting case study.

  44. colewd:Me: So why would this unknown implementation so exactly match the expectation of common descent?

    I don’t think it does across the board. In the case of crocs it matches close the variation we see where we know ancestry has occurred like dogs. In the case of flightless birds the variation is much higher and it does not look like ancestry is shared.

    The only difference between the one and the other is that the distances across birds are greater than those across crocs. And the variation within crocs is many times that across dogs. So why does it look like ancestry is shared among crocs but not in birds? Just because of the distances? I think you’re confused about distances.

    Me: Why does common descent in crocs look exactly like unknown implementation of common design in birds?

    Not sure what you mean here.

    I mean that there is no difference in the pattern except for a greater level of distance, yet you interpret them differently. What is your justification for that difference?

    Me: Why can’t we tell where common descent leaves off and common design begins?

    I don’t think we have enough experience and data yet but your two papers are an excellent case study as they maybe a representation of a line of demarkation between design and descent.

    The fact that the birds are geographically diverse is evidence of separate design so again these papers are an interesting case study.

    This is not an explanation. What suggests a line of demarcation to you? Aren’t crocs equally geographically diverse, if not more so?

  45. colewd,

    Regarding percent differences in DNA, to the extent some DNA is like driving directions, this is like saying two sets of driving directions are 98% identical minus a left turn here, a right turn there!

    A good example of this, as you pointed out many times is the alternative splices.

    Even supposing we are 98% similar to Chimps, do humans have capabilities that are so novel that we wouldn’t expect them to arise naturally and ordinarily from a common ancestor? I think there is a lot we don’t know as far as the Chimp human divide except large scale things like the amount of alternative splicing and Alu RNA editing going on.

    For someone like myself who believes the fossil record is young, I doubt chimps and humans could evolve from a common ancestor in so short of a time.

    The reason creationists suspect some crocodiles descended from a common ancestor isn’t because of pure phylogenetic studies, it’s because it’s been shown some crocs that were believed to have evolved into two separate lineages 10 million years ago were able to interbreed in the present day! That’s sufficient evidence for me for common ancestry, I wouldn’t have to use John Harshman’s papers in that case to assume common ancestry! Whether this applies to all crocs and alligators is an open question. We simply don’t know enough.

  46. John Harshman:

    Don’t worry, I’m not misinterpreting. My definition isn’t mine. It’s just the real one.

    https://en.wikipedia.org/wiki/Hierarchy#Nested_hierarchy

    Nested hierarchy

    Matryoshka dolls, also known as nesting dolls or Russian dolls. Each doll is encompassed inside another until the smallest one is reached. This is the concept of nesting. When the concept is applied to sets, the resulting ordering is a nested hierarchy.

    A nested hierarchy or inclusion hierarchy is a hierarchical ordering of nested sets.[8] The concept of nesting is exemplified in Russian matryoshka dolls. Each doll is encompassed by another doll, all the way to the outer doll. The outer doll holds all of the inner dolls, the next outer doll holds all the remaining inner dolls, and so on. Matryoshkas represent a nested hierarchy where each level contains only one object, i.e., there is only one of each size of doll; a generalized nested hierarchy allows for multiple objects within levels but with each object having only one parent at each level. The general concept is both demonstrated and mathematically formulated in the following example:
    square ⊂ quadrilateral ⊂ polygon ⊂ shape

    A square can always also be referred to as a quadrilateral, polygon or shape. In this way, it is a hierarchy. However, consider the set of polygons using this classification. A square can only be a quadrilateral; it can never be a triangle, hexagon, etc.

    Nested hierarchies are the organizational schemes behind taxonomies and systematic classifications. For example, using the original Linnaean taxonomy (the version he laid out in the 10th edition of Systema Naturae), a human can be formulated as:[9]
    H. sapiens ⊂ Homo ⊂ Primates ⊂ Mammalia ⊂ Animalia

    taxonomies may change frequently (as seen in biological taxonomy), but the underlying concept of nested hierarchies is always the same.

    In many programming taxonomies and syntax models (as well as fractals in mathematics), nested hierarchies, including Russian dolls, are also used to illustrate the properties of self-similarity and recursion. Recursion itself is included as a subset of hierarchical programming, and recursive thinking can be synonymous with a form of hierarchical thinking and logic.[10]

    I don’t see the author of that article defining nested hierarchy in terms of common descent like phylogenists do.

    I’m not ignoring you, I’m telling you your wrong, or at the very least other people don’t define nested hierarchy like you do. Someone who builds nested hierarchies from mathematical constructs will balk at defining nested hierarchies the way you’re trying to.

    So there you go again, you assume just because we disagree that I don’t understand. That’s ok, I just proved my point like I proved my points about phosphorylations to Rumraket even though he insists I don’t understand or that my claim that phosphorylations were like RAM were non-sensical.

  47. I posted this also in the phylogenetics systematics thread:

    Matryoshka dolls, also known as nesting dolls or Russian dolls. Each doll is encompassed inside another until the smallest one is reached. This is the concept of nesting. When the concept is applied to sets, the resulting ordering is a nested hierarchy.

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