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. From the same paper (and same paragraph) as the first sentence that Sal quoted above:

    By functional priori-tization of many MS-based PTMs studies, which was based on
    cross-regulatory events, domain activity and protein–protein
    interactions, Beltrao et al. analyzed their evolutionary conserva-
    tion and functionality. They confirmed the assumption that
    phosphorylation sites with known biological functions, as well
    as phosphorylation sites that have been shown to be regulated
    in MS-based experiments, are more likely to be evolutionary
    conserved [105]. They, moreover, found an increase of evolu-
    tionary conservation of phosphorylation sites [105], which occur
    in close proximity to other PTMs, hinting toward the impor-
    tance of PTM-crosstalk [106], as discussed below. A later study
    of co-occurring phosphorylation and ubiquitylation events in
    yeast confirmed higher evolutionary conservation of phosphory-
    lation sites, which co-occur together with ubiquitylation
    events [107]. A high-resolution temporal analysis of phosphoryla-
    tion signaling after osmotic shock in yeast further hinted
    toward evolutional conservation of fast-occurring versus slow-
    occurring phosphorylation events [91].

    The authors then go on to explicitly recommend that evolutionary conservation be used in prioritizing research studies. I guess phylogeny is not so useless to molecular biology after all.

  2. Look carefully now at this cytochrome-c diagram in light of the articles on the phosphoproteome I just highlighted.

    The phosphorolatable sites alone could be those with

    Eukaryotes: Serine, Tyroinse, Arginine or the letters S, Y,R
    Prokaryotes: Histidine and Aspartate or the letters H, D

    Eukaryotic difference in Cytochrome C:
    http://images.slideplayer.com/24/6969676/slides/slide_7.jpg

    Now do you see the different ways the letters are in different positions? If those are phosphorylated sites, then that’s a different network and machines and addresses for each creature. Like I said, the assumption that the proteins have mostly functionless portions in the 88% that is variable is likely an untrue assumption. They may indeed be functional, and if so, they can’t be monkeyed with just by random mutation and be expected to be so optimized for function and functional redundancy.

  3. The authors then go on to explicitly recommend that evolutionary conservation be used in prioritizing research studies. I guess phylogeny is not so useless to molecular biology after all.

    It should be “common design” not evolutionary conservation. You’ll get the same result for molecular biology with that assumption, so therefore the assumption of phylogeny is totally superfluous. The Nested “conserved” features are by God, not by common descent.

  4. colewd: Whale design is above my pay grade but in the case of macintosh laptops some versions have only silicon memory and some have hard disc memory depending on the tradeoff between total memory, memory cost and footprint.

    What does that have to do with a nested hiearchy? You said common design with a “well planned design” explains the nested hiearchy. Are you saying this is true for laptops? So are you saying I could make a phylogeny from some set of laptop characteristics, and this phylogeny would be highly congruent with another phylogeny built from another set of laptop characteristics?

    I hope you don’t really believe this.

  5. Transposons are distinctive because of their structure. That’s how you find them. They are also distinctive because that structure often codes for proteins that actually cause the transposon to move (or copy-paste) from one location to another. They often break on landing – one can tell whether a transposon is active or not. So, the Design explanation would have it that God has placed a sequence at the same site in multiple species which has all the hallmarks of being a ‘dead’ transposon. It did not transpose, it’s just been disguised to look as if it did. Not only is it in disguise, it’s there to provide a misleading phylogenetic marker. Or maybe it provides a vital function to all its possessors – even though those possessors may be as unalike as pig, whale and deer.

    Then, within a narrower clade all possessing the first, He’s done it again. And again. And again.

    Same pattern in any species with transposons. What a guy!

  6. colewd:
    Allan Miller,

    Whale design is above my pay grade but in the case of macintosh laptops some versions have only silicon memory and some have hard disc memory depending on the tradeoff between total memory, memory cost and footprint.

    So you’re “discussing” what’s clearly above your pay-grade, but that’s okay because you’re right no matter how little you know.

    I’m wondering if you actually know of any organism with divergent instruction sets (as in operating systems) and yet the same brain (central processor) as that organism with a very different instruction set. You know, like Apple computers and Dell computers using the same Intel chips.

    Because that’s quite possible with designed objects, while not the sort of thing that evolution could produce or that is ever found in organisms. As usual, you’re just saying whatever makes you feel good about your beliefs, without bothering to think about how really differently design makes things than anything that we see in life..

    Glen Davidson

  7. stcordova: It should be “common design” not evolutionary conservation. You’ll get the same result for molecular biology with that assumption, so therefore the assumption of phylogeny is totally superfluous. The Nested “conserved” features are by God, not by common descent.

    You’re confused again. Conservation comes in degrees, it is almost never absolute except at the single-residue level. In some enzyme active sites, 2-4 residues might be invariant across the tree of life. The rest of the protein will diverge with increasing distance of relationship. Even then, this does not at all indicate the enzyme’s active site could not have evolved, nor that change to it is impossibly prohibitive.

    It is even worse for your ad-hoc design rationalization at the morphological level, where a “conserved” feature like “has a spine” or “has four limbs” is itself confirming a nesting hiearchical pattern when you look at the actual details of the spine and limbs. What are their actual shapes? How is the shape and distribution of bones in those limbs, and so on? The four limbs of all primates group together, the four limbs of canines group together, etc. etc.

    You keep demonstrating that you literally don’t understand what the pattern you’re asked to account for even is.

  8. stcordova: Now do you see the different ways the letters are in different positions? If those are phosphorylated sites, then that’s a different network and machines and addresses for each creature. Like I said, the assumption that the proteins have mostly functionless portions

    Who are these people who claim these proteins have “functionless portions”? Which proteins in particular?

    They may indeed be functional, and if so, they can’t be monkeyed with just by random mutation and be expected to be so optimized for function and functional redundancy.

    How do you know that? Nothing you’ve said here entails they couldn’t have evolved to be how they are, nor that future evolutionary changes to them are impossible.

  9. Rumraket:

    Yes it does.

    No it doesn't if the nested hierarchy is independently defined by orphan systems and if random mutation can't explain the nested hierarchical differences in proteins are functionally relevant. Funtionality and neutral random mutation don't exactly go hand-in-hand unless there is a miracle and/or intelligent design.

    Theobald's program doesn't deal with the POOFs, it is cherry picked data, which is illegitimate science.

  10. stcordova: More info on phosphorylation of proteins, and more reasons Common Descent needs a miracle.

    More than the zero you have succeeded in showing so far? Will we get to your actual first one then?

    The phosphorylation site has to be distinct, it can’t be randomly assembled much like an address or phone number or url can’t be random and still function.

    Distinct, so it just has to be different enough from another site to prevent or even just reduce cross-talk? Why can’t that evolve? Concrete real-world experiments show that emergence of protein-protein and protein-DNA binding sites and their subsequent change can and do evolve.

    The 88% difference between proteins among species could indicate 88% different function, not random non-functional changes through common descent.

    Where did you pick up this non-functional strawman?

    Look, if you’re going to knock down strawmen, can you at least make them stand upright to begin with?

    The phosphorylation post translational modification is one of several post translational modifications that require specific amino acid sequences to serve as addresses for the phosphorylation site. Eukaryotes have a lot of phosphorylation. Note the difference between Eukaryotes and Prokaryotes.

    It would not surprise me if plants and animals have a different phosphoproteome even for the same proteins.

    That wouldn’t surprise me either. It’s all nice and interesting on it’s own. A shame it doesn’t get you to the conclusion you so desperately seek.

  11. stcordova:

    As usual, Sal, you confuse the cause of nested hierarchy with the cause of mutation. I don’t think you will ever figure this out, because you are determined not to. Please explain why there is a nested hierarchy of life.

  12. stcordova,

    Theobald’s program doesn’t deal with the POOFs, it is cherry picked data, which is illegitimate science.

    Irony.

    Anyway, when you’re looking at the root of a tree, you don’t look at the branches. For a universal model, you need things that are universal.

  13. stcordova: No it doesn’t if the nested hierarchy is independently defined by orphan systems

    What does this even mean “independently defined by orphan systems”? Try to spell it out in some more detail. Give actual examples from the literature.

    and if random mutation can’t explain the nested hierarchical differences in proteins are functionally relevant.

    What does this mean? Why is random mutation required to explain the “functional relevance” (whatever the fuck that even is) of the nesting hiearchical differences in proteins?

    Can you at least try to make sense here? It’s like you’re not even sure what words to use to describe what you’re thinking.

    Are you somehow trying to say that the accumulation of random mutations cannot explain how one protein can change in function and sequence, into another?
    Or, are you trying to say that the phylogeny we can make from a set of orthologous proteins from different species cannot be explained by the independent accumulation of mutations?

    I’m sorry, I just don’t know what you’re saying. Help me out here.

    Funtionality and neutral random mutation don’t exactly go hand-in-hand unless there is a miracle and/or intelligent design.

    They seemed to be doing just fine in the Lenski long-term evolution experiment. Both functionally beneficial and random neutral mutations happened, and both ended up acting in unison to produce the cit+ function after over 20.000 generations had passed.

    Yes yes I know, “They’re still just bacteria”. An elephant didn’t crawl out of one of Lenski’s flasks one morning, so it must all be meaningless and inconsequential right?

    Theobald’s program doesn’t deal with the POOFs, it is cherry picked data, which is illegitimate science.

    He didn’t cherrypick any data at all. He tested exactly the kind of data that actually COULD test whether there is a universal common relationship of extant life on Earth.

  14. Rumraket:

    Why can’t that evolve?

    It can if you invoke miracles of simultaneous change in:

    1. the phosphorylation biding sites
    2. the phospho proteome readers
    3. the pohspho proteome writers
    4. the cell-specific phosphoproteome networks

    http://rstb.royalsocietypublishing.org/content/367/1602/2540

    hosphorylation 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 has been pivotal in the [sic] evolution of new functions required for the development of multi-cellular animals.

    The authors used the word “evolution”, it should be the word “design”.
    not to mention the other Post Tranlational modifications like acetylation, methylation, ubiquitination, simulation, glycol conjugation, etc.

    And that only at the proteomic level, not to mention the transcriptomic level and micro-RNA and who knows what else constraints, and then the genomic level constraints and those binding sites for molecular machines.

    Rumraket:

    Why can’t that evolve?

    POLYCONSTRAINTS!!!! You can’t change one thing without possibly breaking a whole bunch of other things. I just described 3 levels poly constraint. Evolutionists have a Pollyanna viewpoint that evolution can solve things.

    Reminds me of Haeckel:

    Evolution is the magic word by which we shall solve all the riddles that surround us.

    Ernst Haekel

    That’s about as meaningful a mechanistic explanation as abracadabra did it. Which is little different from invoking the miracles of special creation.

  15. Please explain why there is a nested hierarchy of life.

    God did it, common descent didn’t because it couldn’t as demonstrated ad nauseam.

  16. Bill actually thinks that the “traits” of computers yield an objective nested hierarchy.

    Read Theobald, Bill. Until you learn what the rest of us are talking about, you’ll just keep falling flat on your face.

  17. John:

    Please explain why there is a nested hierarchy of life.

    Sal:

    God did it, common descent didn’t because it couldn’t as demonstrated ad nauseam.

    Why did God choose an objective nested hierarchy — which is exactly what you’d expect from unguided evolution — when there were literally trillions of other options available to him?

    Stop dodging the question, Sal.

  18. stcordova: God did it, common descent didn’t because it couldn’t as demonstrated ad nauseam.

    Do you actually believe that “god did it” is an explanation? Please explain why we would expect to see a nested hierarchy resulting from “god did it”. I presume you know why we would expect to see a nested hierarchy resulting from common descent; is that correct?

  19. stcordova:
    Rumraket:

    Why can’t that evolve?

    It can if you invoke miracles of simultaneous change in:

    1. the phosphorylation biding sites
    2. the phospho proteome readers
    3. the pohspho proteome writers
    4. the cell-specific phosphoproteome networks

    Why do they have to be simultaneous?

    The authors used the word “evolution”, it should be the word “design”.
    not to mention the other Post Tranlational modifications like acetylation, methylation, ubiquitination, simulation, glycol conjugation, etc.

    Yes yes, all nice. Why can’t that evolve?

    And that only at the proteomic level, not to mention the transcriptomic level and micro-RNA and who knows what else constraints, and then the genomic level constraints and those binding sites for molecular machines.

    Yes, all of it. Why can’t it evolve?

    Why can’t that evolve?

    POLYCONSTRAINTS!!!! You can’t change one thing without possibly breaking a whole bunch of other things.

    Why not? You say this is the case. Why can’t they emerge and change due to a combination of gene duplications and pleiotropic interactions between different residues?

    Possibly? Some things are now possibly so constrained that subsequent change is unlikely? Does that mean they couldn’t have evolved at all?

    Reminds me of Haeckel:

    Yes it is ironic how much that single sentence of Haeckel’s has been quote-mined by you, who actually and literally believe that “God” is the actual magic word with which you “solve” all the riddles that surround us.

    Why did God make a nested hierarchy as you’d expect from an evolutionary process of branching descent with independent modification?

  20. keiths: Why did God choose an objective nested hierarchy — which is exactly what you’d expect from unguided evolution — when there were literally trillions of other options available to him?

    I take issue with your use of the word “unguided”, which is superfluous and plays into Sal’s false dichotomy. We expect a nested hierarchy from common descent whether evolution is guided or unguided.

  21. Rumraket: Yes it does. What are you blathering about now?

    Your own source says it doesn’t. Don’t you even read what you post?

    Not only that, but evolution is defined as changes in allele frequencies, and changes in allele frequencies do not predict nested hierarchies.

    Enough with your opinions already. I won’t tell you where to put them because from the smell of them you already know at least that much. So stop pulling them out and playing with them.

  22. Mung: Your own source says it doesn’t. Don’t you even read what you post?

    I have posted many things in this thread. Please enlighten me with the specific one you talk about.

    I’m going to predict it doesn’t say what you’re insinuating.

  23. colewd: Whale design is above my pay grade but in the case of macintosh laptops some versions have only silicon memory and some have hard disc memory depending on the tradeoff between total memory, memory cost and footprint.

    Macintosh computers come in desk and laptops, do they form a nested hierarchy?

  24. John:

    I take issue with your use of the word “unguided”..

    I know you do. 🙂

    …which is superfluous and plays into Sal’s false dichotomy. We expect a nested hierarchy from common descent whether evolution is guided or unguided.

    That’s incorrect. I’ve explained this before, but let me try again.

    We expect an inferable, objective nested hierarchy only if change is predominantly gradual and inheritance is primarily vertical.

    Guided evolution is not constrained in those ways. A Designer/Guide could introduce hundreds of mutations at once, for example, and could move complex features from one lineage to another. Unguided evolution can’t do that.

    The word “unguided” belongs where I put it:

    Why did God choose an objective nested hierarchy — which is exactly what you’d expect from unguided evolution — when there were literally trillions of other options available to him?

    Anyway, Sal shouldn’t take any comfort in our disagreement. As a creationist, he’s screwed either way.

  25. Mung:

    Not only that, but evolution is defined as changes in allele frequencies, and changes in allele frequencies do not predict nested hierarchies.

    Poor Mung is confusing a definition of evolution with the theory of evolution.

  26. colewd:
    Allan Miller,

    Whale design is above my pay grade but in the case of macintosh laptops some versions have only silicon memory and some have hard disc memory depending on the tradeoff between total memory, memory cost and footprint.

    So how are the silicon and hard disc storage related?

    Hint: They’re not.

    Early Macs didn’t have flash memory at all. Apple didn’t invent it, either, Toshiba did. Today’s Macs can have either magnetic or flash memory, mix and match, tailor the computer to the needs. This is not what we see in life, where birds have to fuse once-articulated ancestral bones into single rigid wing structures, birds don’t get mammalian ear bones or lactation, while mammals don’t get bird optics or lungs. Why do Macs get to use parts that were invented by an entirely different company, while birds and mammals are stuck with ancestral parts modified for different purposes?

    Your supposed “nested hierarchy” is nothing of the sort, it is a matter of Apple engineers deliberately choosing components based on usefulness without worrying about ancestry at all (other than royalties, of course). But then you’ve never bothered to learn what nested hierarchies are really about, you just repeat what a lot of ignorant folk say in hopes that it will seem to make sense to others in order to “support their case.”

    Glen Davidson

  27. keiths:
    We expect an inferable, objective nested hierarchy only if change is predominantly gradual and inheritance is primarily vertical.

    Vertical, yes. Gradual, no. Why must change be gradual?

    Guided evolution is not constrained in those ways.A Designer/Guide could introduce hundreds of mutations at once, for example, and could move complex features from one lineage to another. Unguided evolution can’t do that.

    I think you have a false view of what guided evolution is supposed to be, but that isn’t important. The question isn’t whether guided evolution could produce what we don’t see. The question is whether unguided evolution is necessary to produce what we do see. And it isn’t. Guided evolution predicts a nested hierarchy as long as it occurs within a context of common descent. Like Sal, you apparently confuse the source of nested hierarchy with the source of mutation.

  28. newton,

    Macintosh computers come in desk and laptops, do they form a nested hierarchy?

    While there are clearly differences in desk and laptops there are many commonalities and so they can arranged in a nested hierarchy with slight exceptions. The shared features are-
    Operating system
    Applications software
    Microprocessor architecture (Intel)
    Printed Circuit boards
    Capacitors
    Resistors
    Inductors
    Ram Memory both Dram and Sram
    Eprom memory
    Logic chips
    Disk Drives when used
    Key boards
    Aski code
    c c++ HTML and other supported languages
    Safari internet interface
    D connectors
    Charging adaptors

    You now have a feel for it. We know for a fact that this is the result of common design.

  29. colewd: You now have a feel for it. We know for a fact that this is the result of common design.

    Sadly, you have no clue about what a nested hierarchy is. You could no more arrange computers into a nested hierarchy than you could comprehend a scientific publication.

  30. GlenDavidson,

    Your supposed “nested hierarchy” is nothing of the sort, it is a matter of Apple engineers deliberately choosing components based on usefulness without worrying about ancestry at all (other than royalties, of course).

    Ancestry is critical for apple with both software, network and cloud compatibility. The engineers don’t just chose any components. Their software is built around the Intel architecture so component selection will follow hard compatibility rules. Software compatibility drives the need for common design.

  31. John Harshman,

    Sadly, you have no clue about what a nested hierarchy is. You could no more arrange computers into a nested hierarchy than you could comprehend a scientific publication.

    Really? Care to back up this claim?

  32. colewd:
    newton,

    While there are clearly differences in desk and laptops there are many commonalities and so they can arranged in a nested hierarchy with slight exceptions.The shared features are-
    Operating system
    Applications software
    Microprocessor architecture (Intel)
    Printed Circuit boards
    Capacitors
    Resistors
    Inductors
    Ram Memory both Dram and Sram
    Eprom memory
    Logic chips
    Disk Drives when used
    Key boards
    Aski code
    c c++ HTML and other supported languages
    Safari internet interface
    D connectors
    Charging adaptors

    You now have a feel for it.We know for a fact that this is the result of common design.

    Uh-huh, and how do these Intel-chip using computers fit with the Macs that used IBM and/or Freescale chips?

    They don’t, there’s simply a break from using the other companies’ chips to the use of Intel chips. It’s like there were brains in one line of computers and separate brains in a different line of computers, then suddenly Apple had the brains that existed in the other lineage. It fits not at all with your claims.

    What do you care? You don’t, because you’re merely indulging your beliefs, rather than noting how very different from biologic evolution the changes made in Apple are. In addition, you’re sticking with one brand trying to make it fit better, and even it is really vastly different from biologic evolution. Put all computers together, and you really can see how mixing and matching parts to fit use occurs, rather than the slavishly derivative nature that life portrays.

    Of course your “analogy” in fact works against your claims, since there really is no nested hierarchy even in Apple brand machines, let alone in all of computers. I’m sure that you’ll keep on making the same idiotic claims regardless, though.

    Glen Davidson

  33. colewd:
    GlenDavidson,

    Ancestry is critical for apple with both software, network and cloud compatibility.The engineers don’t just chose any components.Their software is built around the Intel architecture so component selection will follow hard compatibility rules.Software compatibility drives the need for common design.

    Of course ancestry matters, but you’re ignoring the brain transplant that occurred in Apple when it adopted Intel chips rather than the ones they had been using.

    A lot of things, especially economics, means that much technology is in fact rather derivative and evolutionary much of the time. However, what you get in technology and not in life are the unprecedented, non-derivative, transfers of complex technology in very short times, in biologic terms.

    Glen Davidson

  34. John,

    Like Sal, you apparently confuse the source of nested hierarchy with the source of mutation.

    Besides being false, comparing me to Sal is a low blow. 🙂

    Guided evolution predicts a nested hierarchy as long as it occurs within a context of common descent.

    No, it doesn’t, and that seems to be the root of your confusion. More on this later.

  35. keiths: That’s incorrect.I’ve explained this before, but let me try again.

    We expect an inferable, objective nested hierarchy only if change is predominantly gradual and inheritance is primarily vertical.

    Guided evolution is not constrained in those ways.A Designer/Guide could introduce hundreds of mutations at once, for example, and could move complex features from one lineage to another. Unguided evolution can’t do that.

    The word “unguided” belongs where I put it:

    Only when you define “unguided” the way you do, which strikes me as somewhat idiosyncratic. I think most people would regard selective breeding as guided evolution. Yet it produces nested hierarchies. Quite unavoidably. From context, you seem to equate “unguided” with “patternless and arbitrary.”

    So your use of “unguided” is incompatible with your use of “evolution.”

  36. colewd:
    John Harshman,

    Really?Care to back up this claim?

    Ah, your mantra. I back up the claim by failing to put computers into a nested hierarchy based on the characteristics you name. Now you back up your claim: prove me wrong by actually doing it. Bet you can’t, for a couple of reasons. First, you have no idea how to make a nested hierarchy using characters. Second, the characters you have chosen don’t fit a nested hierarchy anyway. This should be obvious, since a few years ago Apple changed every model from PowerPC to Intel chips and rewrote the whole operating system to be Unix-based. That’s design: no nested hierarchy, just wholesale changes for perceived advantage.

  37. keiths: Besides being false, comparing me to Sal is a low blow. 🙂

    Sure, it’s a low blow. But is it false? Not according to what we’ve seen so far.

  38. GlenDavidson,

    Of course ancestry matters, but you’re ignoring the brain transplant that occurred in Apple when it adopted Intel chips rather than the ones they had been using.

    The brain transplant is the change from Motorola to Intel. A massive pain in the ass because Moto could not invest aggressively enough in next generation fab capability.

    This point is not relevant to the argument.

    The big difference is the living organisms are using molecular level machinery which as far as we know has always been true. Semiconductors are not at that level yet and have been shrinking line widths every 18 months.

    The key point is compatibility is critical to living systems as it is to computers and so the family of mac computers can be arranged in a nested hierarchy according to function and capability and design requirements will drive them in that direction.

    A nested hierarchy is a natural output of a design process. We would also expect occasional convergence in a design process that we would not expect from common descent.

  39. John Harshman,

    Ah, your mantra. I back up the claim by failing to put computers into a nested hierarchy based on the characteristics you name. Now you back up your claim: prove me wrong by actually doing it. Bet you can’t, for a couple of reasons. First, you have no idea how to make a nested hierarchy using characters. Second, the characters you have chosen don’t fit a nested hierarchy anyway. This should be obvious, since a few years ago Apple changed every model from PowerPC to Intel chips and rewrote the whole operating system to be Unix-based. That’s design: no nested hierarchy, just wholesale changes for perceived advantage.

    This is not a relevant argument since after the change to Intel we have a nested hierarchy which was the natural output of a design process.

    Again with design we would expect some level of convergence. Common descent would not predict convergence.

  40. colewd: The brain transplant is the change from Motorola to Intel. A massive pain in the ass because Moto could not invest aggressively enough in next generation fab capability.

    This point is not relevant to the argument.

    It’s entirely relevant. Things appear without precedent or ancestry in designs like they don’t do in life.

    The key point is compatibility is critical to living systems as it is to computers and so the family of mac computers can be arranged in a nested hierarchy according to function and capability and design requirements will drive them in that direction.

    They can be so arranged, but it’s not a “natural” arrangement at all. That’s why we don’t see trees for technological evolution, because there simply isn’t the kind of continuity with basically irreversible changes in technology as there is in life. If you knew biology, rather than pseudoscience, you could actually see this, rather than merely assert the opposite. Anyway, why don’t you show how they fit a nested hierarchy in the same way life does? We know why, maybe you could learn why if you tried.

    A nested hierarchy is a natural output of a design process.

    Mere assertion, contrary to fact.

    We would also expect occasional convergence is a design process that we would not expect from common descent.

    Hold onto that fantasy. It appears to be important to you psychologically, even if it has nothing to do with the science you fail so badly to understand.

    Glen Davidson

  41. colewd: The key point is compatibility is critical to living systems as it is to computers and so the family of mac computers can be arranged in a nested hierarchy according to function and capability and design requirements will drive them in that direction.

    A nested hierarchy is a natural output of a design process. We would also expect occasional convergence is a design process that we would not expect from common descent.

    The word salad above is yet more evidence that you don’t know what a nested hierarchy is, what evidence for it would be, or what sort of process could produce one. You claim that computers are a nested hierarchy. You can show that by producing the hierarchy in the form of a tree, with characteristics distributed on branches, and computers at the tips. Bet you won’t. Bet you can’t.

  42. John Harshman,

    You claim that computers are a nested hierarchy.

    This is not my claim. Two logical fallacies in one post. Creating a straw-man and burden shift. Your claim was that I could not fit mac computers into a nested hierarchy.

  43. colewd: This is not my claim. Two logical fallacies in one post. Creating a straw-man and burden shift. Your claim was that I could not fit mac computers into a nested hierarchy.

    Playing with words is another skill you lack. But OK, I claim that you can’t fit mac computers into a nested hierarchy. Show me I’m wrong by doing it.

  44. colewd,

    Did you ever actually read Theobald’s 29+ Evidences for Macroevolution?

    If so, was the following section too difficult to understand? Do you have questions about it? I ask this because if you actually understood it, you wouldn’t be making so many mistakes regarding the objective nested hierarchy.

    From Prediction 1.2:

    The nested hierarchical organization of species contrasts sharply with other possible biological patterns, such as the continuum of “the great chain of being” and the continuums predicted by Lamarck’s theory of organic progression (Darwin 1872, pp. 552-553; Futuyma 1998, pp. 88-92). Mere similarity between organisms is not enough to support macroevolution; the nested classification pattern produced by a branching evolutionary process, such as common descent, is much more specific than simple similarity. Real world examples that cannot be objectively classified in nested hierarchies are the elementary particles (which are described by quantum chromodynamics), the elements (whose organization is described by quantum mechanics and illustrated by the periodic table), the planets in our Solar System, books in a library, or specially designed objects like buildings, furniture, cars, etc.

    Although it is trivial to classify anything subjectively in a hierarchical manner, only certain things can be classified objectively in a consistent, unique nested hierarchy. The difference drawn here between “subjective” and “objective” is crucial and requires some elaboration, and it is best illustrated by example. Different models of cars certainly could be classified hierarchically—perhaps one could classify cars first by color, then within each color by number of wheels, then within each wheel number by manufacturer, etc. However, another individual may classify the same cars first by manufacturer, then by size, then by year, then by color, etc. The particular classification scheme chosen for the cars is subjective. In contrast, human languages, which have common ancestors and are derived by descent with modification, generally can be classified in objective nested hierarchies (Pei 1949; Ringe 1999). Nobody would reasonably argue that Spanish should be categorized with German instead of with Portugese.

    The difference between classifying cars and classifying languages lies in the fact that, with cars, certain characters (for example, color or manufacturer) must be considered more important than other characters in order for the classification to work. Which types of car characters are more important depends upon the personal preference of the individual who is performing the classification. In other words, certain types of characters must be weighted subjectively in order to classify cars in nested hierarchies; cars do not fall into natural, unique, objective nested hierarchies.

    Because of these facts, a cladistic analysis of cars will not produce a unique, consistent, well-supported tree that displays nested hierarchies. A cladistic analysis of cars (or, alternatively, a cladistic analysis of imaginary organisms with randomly assigned characters) will of course result in a phylogeny, but there will be a very large number of other phylogenies, many of them with very different topologies, that are as well-supported by the same data. In contrast, a cladistic analysis of organisms or languages will generally result in a well-supported nested hierarchy, without arbitrarily weighting certain characters (Ringe 1999). Cladistic analysis of a true genealogical process produces one or relatively few phylogenetic trees that are much more well-supported by the data than the other possible trees.

    Interestingly, Linnaeus, who originally discovered the objective hierarchical classification of living organisms, also tried to classify rocks and minerals hierarchically. However, his classification for non-living objects eventually failed, as it was found to be very subjective. Hierarchical classifications for inanimate objects don’t work for the very reason that unlike organisms, rocks and minerals do not evolve by descent with modification from common ancestors.

    The degree to which a given phylogeny displays a unique, well-supported, objective nested hierarchy can be rigorously quantified. Several different statistical tests have been developed for determining whether a phylogeny has a subjective or objective nested hierarchy, or whether a given nested hierarchy could have been generated by a chance process instead of a genealogical process (Swofford 1996, p. 504). These tests measure the degree of “cladistic hierarchical structure” (also known as the “phylogenetic signal”) in a phylogeny, and phylogenies based upon true genealogical processes give high values of hierarchical structure, whereas subjective phylogenies that have only apparent hierarchical structure (like a phylogeny of cars, for example) give low values (Archie 1989; Faith and Cranston 1991; Farris 1989; Felsenstein 1985; Hillis 1991; Hillis and Huelsenbeck 1992; Huelsenbeck et al. 2001; Klassen et al. 1991).

    There is one caveat to consider with this prediction: if rates of evolution are fast, then cladistic information can be lost over time since it would be essentially randomized. The faster the rate, the less time needed to obliterate information about the historical branching pattern of evolution. Slowly evolving characters let us see farther back into time; faster evolving characters restrict that view to more recent events. If the rate of evolution for a certain character is extremely slow, a nested hierarchy will be observed for that character only for very distantly related taxa. However, “rate of evolution” vs. “time since divergence” is relative; if common descent is true, then in some time frame we will always be able to observe a nested hierarchy for any given character. Furthermore, we know empirically that different characters evolve at different rates (e.g. some genes have higher background mutation rates than others). Thus, if common descent is true, we should observe nested hierarchies over a broad range of time at various biological levels.

    Therefore, since common descent is a genealogical process, common descent should produce organisms that can be organized into objective nested hierarchies. Equivalently, we predict that, in general, cladistic analyses of organisms should produce phylogenies that have large, statistically significant values of hierarchical structure (in standard scientific practice, a result with “high statistical significance” is a result that has a 1% probability or less of occurring by chance [P < 0.01]). As a representation of universal common descent, the universal tree of life should have very high, very significant hierarchical structure and phylogenetic signal.

  45. Flint,

    From context, you seem to equate “unguided” with “patternless and arbitrary.”

    I’m not sure where you got that idea. Quite the contrary. Unguided evolution of the kind we see, with mostly incremental change and primarily vertical inheritance, is expected to produce an objective nested hierarchy. That isn’t “patternless and arbitrary” at all.

    I think most people would regard selective breeding as guided evolution. Yet it produces nested hierarchies. Quite unavoidably.

    Selective breeding is just one form of guided evolution. There are others that don’t produce inferable objective nested hierarchies.

    Guided evolution doesn’t predict an inferable ONH unless you tack on extra unwarranted assumptions. Unguided evolution does predict an inferable ONH, given the kind of variation we actually see in nature.

    Hence the Rain Fairy comparison I made in an earlier exchange with you:

    Flint,

    Sorry, but I don’t understand your explanation. I think we can safely say that IF AND ONLY IF we make a certain set of presumptions about the means, motivations, and goals of the guide, and make sure this set is other than what we observe, we can then say evolution is unguided by THIS guide, according to THESE assumptions.

    It’s the other way around. The only way to rescue ID is to assume that the Designer, by choice or constraint, acts in a way that mimics unguided evolution. However, that assumption is so ad hoc and unjustified that it renders ridiculous the very hypothesis it is intended to support. IDers have no reason to make that assumption, and therefore no reason to favor ID over unguided evolution, a theory that matches the evidence without requiring ridiculous, ad hoc, unjustified assumptions.

    My go-to analogy for this is the Rain Fairy. Here’s a parallel version of the above paragraph, but in terms of the RF:

    It’s the other way around. The only way to rescue the Rain Fairy hypothesis is to assume that the Rain Fairy, by choice or by constraint, acts in a way that mimics unguided meteorology. However, that assumption is so ad hoc and unjustified that it renders ridiculous the very hypothesis it is intended to support. Rain Fairyers have no reason to make that assumption, and therefore no reason to favor the Rain Fairy hypothesis over unguided meteorology, a theory that matches the evidence without requiring ridiculous, ad hoc, unjustified assumptions.

    The nice thing about this analogy is that IDers instantly recognize the absurdity of the Rain Fairy hypothesis. They’re taken aback when it’s pointed out that ID uses the same bad logic.

  46. Flint: Only when you define “unguided” the way you do, which strikes me as somewhat idiosyncratic. I think most people would regard selective breeding as guided evolution. Yet it produces nested hierarchies. Quite unavoidably. From context, you seem to equate “unguided” with “patternless and arbitrary.”

    Exactly. All selection that results in evolutionary change can be considered non-random. In natural selection the guide is the niche. It’s irrelevant to common descent whether one considers the process is guided or not.

  47. Alan,

    It’s irrelevant to common descent whether one considers the process is guided or not.

    If common descent is occurring, it’s occurring, whether or not it’s guided. That’s trivial and obvious.

    The question we’ve been discussing is different: namely, whether guided evolution predicts an inferable ONH. The answer is no, unless you tack on extra, unjustified assumptions about how the designer/guide operates.

  48. colewd: Really? Care to back up this claim?

    Him backing up his claim that you can’t do it, would require that you actually attempt to do it. Sort of like if he had said “you can’t jump 10 meters vertically into the air” and you say “Care to back up that claim?”. Then you’d have to agree to actually do it, try to jump 10 meters into the air vertically. Your failure to then cooperate is not his/i> failure to meet his burden of proof.

    So please, take some mac computers, then arrange them into a nested hiearchy.

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