Common Design vs. Common Descent

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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. keiths
    Theobald: 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.

    This part is very important.

    Check out this video where John van Wyhe mentions how it looks when organisms were first attempted categorized: How we found out evolution is true: John van Wyhe at TEDxNTU. The part about categorization starts at around 11:20.

    Btw, Sal should watch that whole video. It gives a nice introduction to how the first christian creationist geologists discovered that the Earth had to be old, extremely old. Even before they knew anything at all about evolution, they were still forced by the data (stratigraphic order of layers and the fossils they contain) to think that God had made an extremely long series of successive creations of different organisms over time.

  2. keiths: 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.

    Here are a couple of questions:

    All body cells can be traced back to an original common ancestral cell, so is it true that they can be arranged in an objective nested hierarchy?

    And.

    From the moment of your conception have your bodily cells developed and combined in such a way as to achieve and maintain a particular recognised form?

    If your answer to both these questions is yes then then you must agree that within life on earth we have examples of nested hierarchies culminating in specific recognised forms.

  3. colewd: I agree they all can be categorized as mammals because of similar features. Some live in the ocean, some on land, and some can fly. Some of the ones that live in the ocean and fly have echo location capability. The hierarchy does not seem very nested.

    You are not being consistent, or maybe I misunderstand your position. If you reject the nested hierarchy of life, there is no requirement for you to defend common design.

  4. colewd: I agree they all can be categorized as mammals because of similar features. Some live in the ocean, some on land, and some can fly. Some of the ones that live in the ocean and fly have echo location capability. The hierarchy does not seem very nested.

    So do you accept the objective nested hierarchy for animals or not? If there was none, I could say this:

    I agree they all can be categorized as mammals fish because of similar features. Some on land, and some can fly have mammary glands, and some lay eggs. Some of the ones that live in the ocean and fly have echo location capability become really big and burrow in the mud have lungs. The hierarchy does not seem very nested.

    You were instantly able to recognise that whales are mammals, but could I not also group them with fishes*? If there is no nested hierarchy both appraisals would be equally valid, because any grouping would be arbitrary.

    * Yes, I know.

  5. CharlieM: All body cells can be traced back to an original common ancestral cell, so is it true that they can be arranged in an objective nested hierarchy?

    If differentiation is irreversible, yes. A phenomenon known as stereotypical development. Caenorhabditis elegans nematode worms have it, for example.
    Cell differentiation is not genetic change. Not sure how well your analogy will fare 🙂

    ETA: remove typo

  6. Corneel: If differentiation is irreversible, yes. A phenomenon known as stereotypical development. Caenorhabditis elegans nematode worms have it, for example.
    Cell differentiation is not genetic change. Not sure how well your analogy will fare

    ETA: remove typo

    Sorry, I omitted the fact that I was talking about normal human development. But anyway here is a diagram of C elegans development which is a fine example of a nested hierarchy. (from here)

  8. dazz:
    The day Bill Cole learns something I’ll have no choice but to believe in miracles

    Didn’t he mention he had dementia at some point? I don’t know if he was joking, but it explains a lot.

  9. CharlieM: Sorry, I omitted the fact that I was talking about normal human development. But anyway here is a diagram of C elegans development which is a fine example of a nested hierarchy. (from here)

    Sure, it’s fine, but isn’t that just inevitable? Yes, liver cells developed from other liver cells, etc. There are stem cells and the like that complicate the matter to some degree in humans, but mostly you’re going to have the familiar inheritance patterns arise.

    Erik would just say that we know it happens because we can see it happen, as if we would otherwise have no idea what patterns to expect from the evolution of organisms (rather counter to the history of evolutionary thought, of course). Bill would just say that such patterns arise with design, and that convergence is a problem for evolution–which is entirely contrary to what is expected from the pressures of natural selection (I think it’s a problem for evolution in his mind merely because it’s a tired old trope at UD and other creationist sites).

    For you, I think there’s some kind of mystical connection between development and evolution, but it’s really just what you get from common descent.

    Glen Davidson

  10. Allan Miller:

    How many sites in a typical protein are under this assumed constraint? I think you’re reaching a bit if you want this to be a general constraint on the entirety of evolution.

    Why a typical protein? How about the histones for starters since they are well chracterized.

    Half of eukaryotic proteins are glycosylated for starters, 1/10 to 1/2 are phosphorylated, who knows what else. Until we study each cell type we’re only scratching the surface. This is the tip of the ice berg.

    The lack of conservation suggests that there is not even much of a constraint in any case.

    The usual evolutionary balderdash just like the junkDNA hypothesis. Jump to conclusions to defend a theory in the absence of all the facts. Rush to conclusions, just like evolutionist had slobbered all over the supposed nylonase evolultion for decades and still promote, so it is with the complexity of proteins and how function is defined.

    You see, I don’t exactly take the angle Doug Axe takes, I look at the polyconstraints of MULTIPLE functions of the protein residues.

    All that docking on parking lots is not trivial. Stuff has to dock and release, dock and release. How’s that going to happen in an orchestrated fashion. You have to have all these sites there and it can’t interfere with the other functioning of the protein! How is the timing worked out?

    There are now in the present day a lot of mechanistc challenges that evolutionists weren’t even aware of in the past.

    So how many sites, you ask? YOU should be the one asking and answering those question before you assert there is no constraint. I pointed out, it might not be as trivial as you suppose.

    I talked to a topoisomerase rearcher recently. He was doing mass spec, and the thing was chock full of likely phosphorylation sites. We really don’t know for all proteins. Heck we don’t even know what all the proteins are, but it doesn’t stop evolutionists from claiming “evolution did it without miracles.”

    And phosphorylation is only one class of modification! There is also mythylation, acetylation, sumulation, ubiquitination, glyco conjugation, who the heck knows what else is out there. The Postranlational markings are also cell-type specific and cell-phase specific to boot.

    I may look at histones and compare them. You hopefully can see the problem of re-arranging residues in histone proteins as seen in the diagram below, right? 🙂
    You don’t need Doug Axe arguing for improbability of such complexity being transformed from one creature to the next in light of such diagrams I hope:

  11. dazz:
    The day Bill Cole learns something I’ll have no choice but to believe in miracles

    I think unlearning some things might be as miraculous for him.

    So might learning what an adequate basis for making claims is. “There are differences” seems to be all that he understands about nested hierarchies, so different Mac products are for him a “nested hierarchy.” Kind of left out understanding anything about the whole matter.

    What does he think biologists do, mistake model differences for evolutionary change? Wouldn’t somebody notice? Or is this just another fantasy about how evilutionists ignore something so obvious, yet something that he still cannot support in any meaningful way at all?

    I don’t think he’s ever realized how clades, and thus nested hierarchies, depend upon derived characters, and not upon the choices that engineers make. True, there is derivation in design evolution, but the plasticity of intelligence, and thus of design, degrades such signals rather quickly, and the portability of ideas prevents meaningful hierarchical arrangement according to derived characters.

    To a considerable degree, evolution splits, while design combines. Bill seems not to understand this.

    Glen Davidson

  12. keiths: 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.

    The unjustified assumptions are the commonly understood definition of “guided evolution”, that the designer adds some of the mutations at various points in each lineage. They might be big mutations or several mutations at once. And he doesn’t add the same set of mutations in multiple places. Would you agree that given these constraints we expect a nested hierarchy? Then we can’t say that a nested hierarchy demonstrates unguided evolution. We can only say that if there is guided evolution it follows certain constraints. There’s no need to suppose that all conceivable forms of guided evolution produce a nested hierarchy but also no reason to reject guided evolution because we see a nested hierarchy. I don’t see a problem with that, but you apparently do. Why?

    (I will suggest that the particular nested hierarchy we see — what looks like a random walk buffeted by changing environments — does argue against guided evolution, but that’s another matter.)

  13. In the interest of fairness, ironically, it was Michael Behe who wrote this paper on Histone Deletion mutants. What Brenda Andrews discovered years later was that the deletion mutants don’t have immediate effect on yeast because of the deep redundancy, what she calls “highly buffered” architecture of eukaryotes.

    http://www.cell.com/trends/biochemical-sciences/pdf/0968-0004(90)90231-Y.pdf

    A basic tenet of the molecular clock hypothesis is that the rate of
    sequence drift for a protein depends on the number of amino acid
    residues that are critical for its function. However, recent experiments
    have determined that, although core histone sequences are highly
    conserved among eukaryotes, large regions of the proteins are
    dispensable for growth in yeast.

    Michale Behe

    They might bee dispensible in single knockout experiments, Brenda Andrews should they might not be in double or triple or N-knockout experiments.

    Behe mentions the possibility the histone N-termini are actually functional but redundant and therefore deletable in single knockout experiments.

    That paper was 27 years ago!

  14. Here is Brenda Andrews at the NIH NHGRI ENCODE 2015 planning workshop (not the 2015 ENCODE Users meeting that I had the privilege of attending earlier in 2015):

    She explains the existence of “highly buffered” eukaroytic genomes. It thus invalidates Theobald’s citation of variants of proteins not having clinical effect. Theobald’s citation were of experiments not comprehensive enough in light of Andrews work. Hence, function is not easily deduced by single-layer knockout experiments as I also pointed 11 years ago below:

    Airplane magnetos, contingency designs, and reasons ID will prevail

    One way Darwinists conclude something is evolutionary junk, a vestigial feature, or an otherwise useless biological artifact is to apply “knock-out” experiments on an organism. If a piece of the organism is knocked out, and the organism still functions well and is otherwise “fit”, then the knocked-out piece is deemed useless, an evolutionary leftover, junk, or even bad design.

    What’s wrong with such logic you ask? Well allow me to clarify. Imagine if one applies this line of reasoning to the architecture of a magneto-fired airplane engine:

    We knocked out the left magneto system on Airplane X and determined the airplane flies just as well without it. We knocked out the right magneto system on Airplane Y and determined the airplane flies just as well without it. We conclude therefore from these knockout experiments that neither the left magneto nor the right magneto have any functional significance since the airplanes were clearly fit without them. Magnetos are therefore unneeded vestigial artifacts, junk, and evidence poor design, totally useless to the airplane. Furthermore this is further evidence that airplanes are made by blind watchmakers.

    Think I’m kidding, and evolutionary biologists don’t make these kinds of obviously bad inferences?

    See:
    Minimal genome should be twice the size, study shows

    “Previous attempts to work out the minimal genome have relied on deleting individual genes in order to infer which genes are essential for maintaining life,” said Professor Laurence Hurst from the Department of Biology and Biochemistry at the University of Bath.

    “This knock out approach misses the fact that there are alternative genetic routes, or pathways, to the production of the same cellular product.

    When you knock out one gene, the genome can compensate by using an alternative gene.

    But when you repeat the knock out experiment by deleting the alternative, the genome can revert to the original gene instead.

    Using the knock-out approach you could infer that both genes are expendable from the genome because there appears to be no deleterious effect in both experiments.”

    PS
    Larry Moran mentions he knew Brenda Andrews as a graduate student when he was teaching.

  15. stcordova: What Brenda Andrews discovered years later was that the deletion mutants don’t have immediate effect on yeast because of the deep redundancy, what she calls “highly buffered” architecture of eukaryotes.

    All the more reason such systems are evolvable, as redundancy leaves other parts free to change. Think about it.

    This is such a typical indication that these systems evolve by gene duplication and epistasis.

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

    HERE

    As with any investigational scientific method, certain conditions must hold in order for the results to be reliable. A common premise of many molecular phylogenetic methods is that genes are transmitted via vertical, lineal inheritance, i.e. from parent to offspring. If this premise is violated, gene trees will not recapitulate an organismic or species phylogeny. This assumption is violated in instances of horizontal transfer, e.g. in transformation of a bacterium by a DNA plasmid, or in retroviral insertion into a host’s genome. During the early evolution of life, before the advent of multicellular organisms, horizontal transfer was likely very frequent (as it is today in the observed evolution of bacteria and other unicellular organisms). Thus, it is questionable whether molecular phylogenetic methods are applicable, even in principle, to resolving the evolutionary patterns of many microbes, including early evolution near the most recent common ancestor of all living organisms (Doolittle 1999; Doolittle 2000; Woese 1998).

    Evolution predicts a nested hierarchy except when it doesn’t.

    That’s what you have, and it’s pure hogwash.

    The best you can say is that if certain conditions hold, then evolution predicts a nested hierarchy, and then go on to show that those conditions do in fact hold, and that is something no one has done yet in this thread.

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

    Even keiths gets it.

    Guided evolution is not constrained in those ways.

    Neither is unguided evolution. So now what boy phylogenist?

  19. John Harshman: Why must change be gradual?

    Because changes must be “small” enough to occur by random chance so that we can exclude the miraculous as a possibility. It’s silly, I know. But how else are you going to rule out a divine guiding hand?

  20. stcordova,

    Half of eukaryotic proteins are glycosylated for starters, 1/10 to 1/2 are phosphorylated, who knows what else. Until we study each cell type we’re only scratching the surface. This is the tip of the ice berg.

    Your argument appears to be that, because of phosphorylation/glycosylation, these cause a constraint that prevents proteins from evolving at all. That’s nonsense. Even if there were an evolutionary brake at certain sites, the entire protein repertoire of every organism – every segment of what you love to term the ‘proteome’ to sound fancy – would need to consist solely of phosphorylation/glycosylation sites for your argument to have any merit.

  21. Alan Fox: All selection that results in evolutionary change can be considered non-random.

    I’m sorry, but this exhibits a fundamental misunderstanding of the nature of natural selection. It also helps highlight the difference between artificial selection and natural selection.

    Natural selection is a stochastic process. Random.

  22. Rumraket: Btw, Sal should watch that whole video. It gives a nice introduction to how the first christian creationist geologists discovered that the Earth had to be old, extremely old.

    But Salvador is a Young Life Creationist not a Young Earth Creationist. 🙂

  23. CharlieM: All body cells can be traced back to an original common ancestral cell, so is it true that they can be arranged in an objective nested hierarchy?

    Having a common ancestor and lineal vertical descent is not enough. We require more epicycles.

  25. John,

    There is no canonical definition of “guided evolution”, and the assumptions you are tacking on are indeed unjustified and arbitrary. For example, you write:

    And he [the Designer/Guide] doesn’t add the same set of mutations in multiple places.

    Says who? And if he does, are you going to argue that it isn’t guided evolution?

    Same thing with Bill Cole’s bugaboo, the gene that disappears and reappears. If the designer/guide chooses to do that, will you argue that it’s no longer guided evolution? That makes no sense.

    Your statement is false:

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

    John:

    There’s no need to suppose that all conceivable forms of guided evolution produce a nested hierarchy but also no reason to reject guided evolution because we see a nested hierarchy.

    Would you agree with the following, then?

    There’s no need to suppose that all conceivable forms of guided meteorology match the predictions of unguided meteorology, but also no reason to reject guided meteorology merely because the evidence matches those predictions.

    In other words, do you think that the Rain Fairy is a viable explanation for the weather? I don’t, and I reject guided evolution for the same reason. Both can be force-fitted to the data, but only through the imposition of unwarranted assumptions.

  27. Mung: The best you can say is that if certain conditions hold, then evolution predicts a nested hierarchy, and then go on to show that those conditions do in fact hold, and that is something no one has done yet in this thread.

    That actually seems correct. if there really had been massive amounts of horizontal gene transfer, the phylogenetic signal would have been lost. Yet usually the phylogenetic signal is present. So isn’t it fair to say that, absent an alternative explanation, the conditions were most likely fulfilled?

  28. Corneel: Yet usually the phylogenetic signal is present. So isn’t it fair to say that, absent an alternative explanation, the conditions were most likely fulfilled?

    The terms “usually” and “most likely” are just hanging out there in thin air. And if we talk only of single-celled organisms does that still hold?

    I’m only challenging the claim that an objective nested hierarchy is predicted by evolution. I say it is not.

  29. 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.

    A what design purpose is served by designing computers that fit within a nested hierarchy?

  31. Mung,

    John Harshman: We can only say that if there is guided evolution it follows certain constraints.

    Which is just what he says about unguided evolution. 🙂

    The constraints are built into the basic design architecture of transcription translation and alternative splicing along with control mechanisms like protein destruction.

    As with computers constraints are built with transistor architecture micro processor architecture and the software operating system etc.

    I think the integrity of the of ONH depends of the basic system architecture and its longevity depends on the ability to improve function and add features without fundamental change.

    The prokaryotic cell was severely limited but the eukaryotic cell had the design legs to get from yeast to humans with minimum fundamental architectural change.

    We have no idea how DNA changed to create the diversity of life but thinking about computers maybe it was a remote download 🙂

  32. newton,

    A what design purpose is served by designing computers that fit within a nested hierarchy?

    Compatibility. The same software can operate all devices and your software carries forward with new or different models.

    Other issues like cost control but compatibility is the biggy, Biology interestingly enough has the same issues like how living organisms convert organic substances to energy.

    Off to visit two of my children and my grandson 🙂

  33. Alan Fox: All selection that results in evolutionary change can be considered non-random.

    Mung: I’m sorry

    You’re picking up Brit habits 🙂

    …but this exhibits a fundamental misunderstanding of the nature of natural selection. It also helps highlight the difference between artificial selection and natural selection.

    There is no difference between artificial and natural selection. The difference is, well, artificial. In selective breeding, humans (or ants with their fungus gardens) are just an additional component of the niche.

    Natural selection is a stochastic process. Random.

    Oh no. If the process were not biased, there would be no cumulative change.

  35. colewd,

    I think the integrity of the of ONH depends of the basic system architecture and its longevity depends on the ability to improve function and add features without fundamental change.

    You have no idea what you’re talking about.

    Did you read and understand the Theobald excerpt I posted? If not, what is puzzling you about it?

  36. keiths: In other words, do you think that the Rain Fairy is a viable explanation for the weather? I don’t, and I reject guided evolution for the same reason. Both can be force-fitted to the data, but only through the imposition of unwarranted assumptions.

    No, the Rain Fairy isn’t a viable explanation for the weather, but not because we would expect a different weather pattern if the Rain Fairy existed. Your arguments have nothing at all to do with your claim that “unguided” is a necessary element in the idea of common descent.

  37. newton:

    A what design purpose is served by designing computers that fit within a nested hierarchy?

    colewd:

    Compatibility. The same software can operate all devices and your software carries forward with new or different models.

    Again, you don’t know what you’re talking about, Bill. Compatibility can easily be achieved with computers that do not conform to an objective nested hierarchy.

  38. colewd: newton,

    A what design purpose is served by designing computers that fit within a nested hierarchy?

    Compatibility. The same software can operate all devices and your software carries forward with new or different models.

    Ah yes, the opposite of what actually obtains in biologic nested hierarchies. The latter are about the derivative, splitting, divergence, reproductive incompatibility (whether infertility, hybrid disadvantage, or simply a disinclination to interbreed). There is considerable similarity, of course, but divergence occurs that prevents reproductive compatibility.

    You really just don’t get any of this, do you? Life doesn’t have the kind of compatibility that is often designed into quite different products. You don’t know the difference between design and biologic evolution, as if this weren’t all too obvious previously.

    Other issues like cost control but compatibility is the biggy, Biology interestingly enough has the same issues like how living organisms convert organic substances to energy.

    Wow, what a meaningless claim.

    Off to visit two of my children and my grandson

    Designed for compatibility, were they?

    Glen Davidson

  39. John,

    Your arguments have nothing at all to do with your claim that “unguided” is a necessary element in the idea of common descent.

    That isn’t even close to what I’ve been claiming. You’re making the same mistake as Alan.

    I’m taking issue with your assertion that

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

    That isn’t true. Guided common descent doesn’t predict an objective nested hierarchy, just as guided meteorology doesn’t predict the weather we see.

    Can you get an objective nested hierarchy from guided common descent? Sure, if you add a bunch of unwarranted assumptions.

    Can you get the weather we see from guided meteorology, aka the Rain Fairy? Sure, if you add a bunch of unwarranted assumptions.

    Why do either? Nothing justifies those assumptions other than a desire to force fit the hypothesis to the evidence.

    Your earlier statement is a perfect example of this:

    And he [the Designer/Guide] doesn’t add the same set of mutations in multiple places.

    Why restrict the Designer/Guide that way? It isn’t as if we’re talking about a known Designer/Guide who has certain characteristics and behaves in certain known ways. Your statement is an assumption made solely for the purpose of forcing the hypothesis to agree with the observed data.

  40. Alan Fox: If the process were not biased, there would be no cumulative change.

    I’m sorry, but this is simply false. 🙂

    Changes can accumulate solely with random genetic drift. Also, you are arguing that a stochastic process cannot be biased, which is likewise nonsense.

  41. Alan,

    Mung is right on both counts. Cumulative change does not depend on selection, and stochastic processes can be biased.

    Also, you wrote earlier that

    In natural selection the guide is the niche.

    To the extent that there is “guidance” at all, it comes from selective pressures, not from niches.

  42. Alan Fox: If the process were not biased, there would be no cumulative change.

    Mung: I’m sorry, but this is simply false. 🙂

    You can be as sorry as you like. I’d prefer more detail regarding why you think my statement is false.

    Changes can accumulate solely with random genetic drift.

    In the absence of selective bias, yes.

    Also, you are arguing that a stochastic process cannot be biased

    I don’t think so. I don’t think I used the word “stochastic”

    … which is likewise nonsense.

    Example. Roulette wheel. The roulette wheel as used in casinos has 38 (US cheats with two zeros) slots of equal size; just under 10 degrees of sector. The niche has slots that are of unequal size (and that vary). There’s still an element of chance but there is bias.

  43. Alan,

    I don’t think so. I don’t think I used the word “stochastic”

    Mung did, and you disputed his statement:

    Mung:

    Natural selection is a stochastic process. Random.

    Alan:

    Oh no. If the process were not biased, there would be no cumulative change.

    Stochastic processes can be biased.

  44. keiths: Stochastic processes can be biased.

    Where have I disputed that? That was rather my point with the biased roulette wheel. It really is a waste of time engaging with you.

  45. keiths:

    Stochastic processes can be biased.

    Alan:

    Where have I disputed that?

    Right here:

    Mung:

    Natural selection is a stochastic process. Random.

    Alan:

    Oh no. If the process were not biased, there would be no cumulative change.

    It was just a mistake, Alan. Mung corrected you. Accept it and move on.

  46. keiths: Why restrict the Designer/Guide that way?

    Why not? Are not particular sorts of guided evolution still examples of guided evolution? If the designer chooses to introduce particular innovations only in one species, why not? My point is that the source of mutation is irrelevant. So why add “unguided”, which makes particular assumptions about the source of mutation?

  47. Mung: Evolution predicts a nested hierarchy except when it doesn’t.

    Ahh so we’re back to your silly retort that because there are possible conditions under which the predictions change, that means there’s effectively no prediciton at all, it’s all up for grabs and we can’t know anything.

    You do this “except when it doesn’t” line over and over again, and it never stops being unfathomably stupid.

    Let’s see how we can also use it:
    You should go to the doctor with your rash/broken leg/swelling in your armpit, he can fix it, except when he can’t.
    Oh well then I guess you shouldn’t go to the doctor.

    That’s where your thinking takes you.

    Let’s try some more of these:
    Remember to lock your bike or it will probably get stolen, except when it doesn’t.
    Oh well then I guess you should just leave it unlocked.

    Getting a good night’s sleep before a long drive helps prevent accidents, except when it doesn’t.
    Mung has just proven sleep is superflous. Great.

    You should study before a test or you’ll probably flunk it, except when you don’t.
    Bah, homework. Who wants that anyway?

    I trust that I have made it clear already, to any rational observer, why your constant usage of that shitty “..except when it doesn’t” line is really fucking dumb.

    This idea you have that because there are some time exceptions to rules, means the rule is meaningless or usless, or can’t be systematically used to make predictions, is absolute fucking horseshit.

    No Mung, evolution still predicts a nested hiearchy. Just that it doesn’t necessarily hold for all possible data sets and here are the reasons why. That’s what that says.

    So you were wrong about my source, as predicted.

    That’s what you have, and it’s pure hogwash.

    No actually it makes perfect logical sense.

    The best you can say is that if certain conditions hold, then evolution predicts a nested hierarchy, and then go on to show that those conditions do in fact hold, and that is something no one has done yet in this thread.

    All theories that make predictions operate under this metric. If certain conditions Y hold, then X is predicted. If X, then Y. That’s how prediction works. Are you just realizing this now? Holy fuck, buddy.

    Now, those conditions do in fact hold. How do we know? Because we HAVE a nested hiarchy of life. If those conditions didn’t hold, then we WOULDN’T have the nested hiearchy. That’s how predictions work. The very fact that we have a nested hierarchy of life means the conditions obtained. The states of affairs were such that we got a nested hiearchy of life. Which means life evolved. Get over it.

  48. John,

    Are not particular sorts of guided evolution still examples of guided evolution? If the designer chooses to introduce particular innovations only in one species, why not?

    Are not particular sorts of guided meteorology still examples of guided meteorology? If the Rain Fairy chooses to behave in a way that matches what we’d expect from unguided meteorology, why not?

    The extra assumptions are unjustified. It’s dumb when you do it on behalf of the Rain Fairy, and it’s dumb when you do it on behalf of guided evolution.

  49. Rumraket, to Mung:

    I trust that I have made it clear already, to any rational observer, why your constant usage of that shitty “..except when it doesn’t” line is really fucking dumb.

    Amen.

    But that’s Mung.

  50. Guidance usually means taking a system or object along a trajectory that isn’t natural toward a specific destination or goal.

    For example a sailing ship could be blown by the wind to all sorts of places, but guidance will help it toward a goal.

    A nested hierarchy in a protein sequence is hypothetically possible if there aren’t many functional constraints on the sequence and large parts are free to mutate and the mutation doesn’t progress so far as to totally erase phylogenetic relationships. So in that sense a nested hierarchy is possible via common descent and random mutation.

    A nested hierarchy is not possible by common descent without miracles when there are complex integrated Orphan Systems and Features. Nested Taxonomic Hierarchies can be even better described by Orphan Systems than protein phylogenies especially when looking only at a limited set of proteins. For example Chimp and Human cytochrome-C is identical, so it’s not much use in and of itself for building a complete nested hierarchy. It is better to use Orphan Systems (salient characteristics) to build taxonomic nested hierarchies.

    But such systems are also a barrier to common descent.

    Furthermore, I’ve provided data on why protein phylogenies can’t be the result of common descent with random mutation on the sequences since the sequences are often under functional constraint.

    NOTE: functional constraint doesn’t necessarily mean under selection, because redundant functions are usually not visible to selection, and are often selected against because of metabolic cost.

    There is more to the protein sequence changing than the sequence itself because a lot of machinery is dependent on that sequence as illustrated with the histones and the phosphoproteome, etc.

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