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. Erik: They are good at calculating probabilities, but they can’t explain what the probabilities are about.

    When all else fails, just declare something.

    Next step is conspiracy nuttery, where when the evidence goes against you, that evidence must have been faked. Round Earth you say? Satellite pictures are just photoshopped!

  2. Erik: Is there a reason for it or is it just a say-so? Is there something in that combination that makes it lethal or is this all under the umbrella of “let’s suppose”.

    For the examples that I am familiar with, it involves specific interactions between nuclear-encoded mitochondrial genes and the mitochondrial genome. So yes, for some examples the specific molecular mechanism is known. I should probably add that it is not necessary that the combination is lethal. A build-up of many deleterious interactions will result in the same thing.

    Erik: Also, if genetic change occurs incrementally (individual by individual), then why would you say the *population* has fixed alternative genes?

    Because it is the population that is evolving, not the individuals themselves. I thought you had figured that out by now. 🙂

    Erik: But earlier I read about a scenario where two plant species (cross-)bred yielding infertile hybrids, but somehow at some point they began yielding fertile hybrids, which was eventually labeled another species.

    Yes, that is a different mechanism of speciation. Note that there is no lineage split involved, quite the opposite, so not relevant to this discussion (which was about common descent remember?).

    Erik: Given this, how is any of this determined by genes? It more looks like genes go along with the flow just like all the other organs with their shapes and forms and functions go along as “evolution” progresses

    Hmmm, not sure where you are coming from here. Genes don’t determine things, at least not in the sense that you seem to mean. I like the idea of a flow, where occasionaly the stream splits into two. Of course the divergence between two separated gene pools means that at some point, the streams can no longer merge, and this is determined (yes) by the accumulation of genetic differences.

    Erik: The claim of the evolutionary theory is that the variation has no limit, and cross-breeding (perhaps) has no effective barrier, over Very Long Time. The claim appears to be partially experimentally redeemed in the lower orders of nature (insects and plants), but it’s straightforward nonsense insofar as higher animals are concerned.

    I don’t agree with those claims, so I am not going to defend them. I also don’t like the distinction between “lower” and ” higher” animals. Sounds like scala naturae, old-fashioned stuff.

    Erik: So it’s very important to figure out what genes do, how they operate, what function they have for organisms, bearing in mind that just like any other organ may have different forms and functions in different species, so do genes.

    This is of course exactly what biologists have been doing for decades now. When they are not doing statistics of course

  3. Erik: Also, if genetic change occurs incrementally (individual by individual), then why would you say the *population* has fixed alternative genes?

    Corneel: Because it is the population that is evolving, not the individuals themselves. I thought you had figured that out by now.

    Where does the event of a gene change take place? In particular individuals, I assume. They can carry the genes over to the next generation, but when things can change over time, what is the significance of genes being carried over in the first place? On one hand, genes are said to be determining what species we are and what we, as individuals, look like, but on the other, genes can change, while our species and looks remain the same.

    The genes of a population are the sum total of the genes of the individuals that make up the population. Insofar as genes change from individual to individual and generation to generation, how can the genes of the population be said to be *fixed*? It prompts the question – what is the overall causal significance and biological function of genes?

    Corneel: I don’t agree with those claims, so I am not going to defend them.

    As Ernst W. Mayr observes, “transspecific evolution is nothing but an extrapolation and magnification of the events that take place within populations and species…it is misleading to make a distinction between the causes of micro- and macroevolution”.

    Whatever this statement means and entails. My question is what justifies the statement, other than Very Long Time or “we can draw a tree”. “Genes change” by itself does not seem to be enough. It either requires particular important gene changes in particular ways, but if the process of gene change is unguided and mostly causally insignificant, it may require some totally different overriding cause.

    Let’s not forget what I am getting at. I am absolutely NOT interested in how plausible or likely (macro)evolution is. I’m asking how has it been determined that it is the natural course of events that has no effective barriers. Mayr’s answer is “nothing but an extrapolation and magnification of the events that take place within populations and species” even though he incidentally did away with any meaning for the word species.

  4. Erik,

    It turned out that we don’t have biologists here. We have statisticians. They are good at calculating probabilities, but they can’t explain what the probabilities are about.

    So despite several of us giving mechanistic, ‘biological’ answers to questions, your ‘statistician’ viewpoint is now quite firmly lodged in your mind.

  5. Erik,

    Mayr’s answer is “nothing but an extrapolation and magnification of the events that take place within populations and species” […]

    Quote mine. Mayr was summarising the opposing viewpoints of the time.

  6. Erik: It turned out that we don’t have biologists here. We have statisticians. They are good at calculating probabilities, but they can’t explain what the probabilities are about.

    I’ll ask in a different way then. Can you point to a definition of species that you accept?

  7. Erik,

    I’m asking how has it been determined that it is the natural course of events that has no effective barriers.

    If a barrier exists, one would expect it to be manifest. If no barrier is manifest, what persuades us that one exists?

    There is a continuum – genetic differences among broadening taxonomic groups, from race to subspecies to species to genus etc, show differences of degree, not of kind.

  8. Erik: Where does the event of a gene change take place? In particular individuals, I assume. They can carry the genes over to the next generation, but when things can change over time, what is the significance of genes being carried over in the first place? On one hand, genes are said to be determining what species we are and what we, as individuals, look like, but on the other, genes can change, while our species and looks remain the same.
    The genes of a population are the sum total of the genes of the individuals that make up the population. Insofar as genes change from individual to individual and generation to generation, how can the genes of the population be said to be *fixed*? It prompts the question – what is the overall causal significance and biological function of genes?

    We are getting into some pretty basic genetics here, and I submit that your confusion stems from the fact that you are not entirely familiar with that. You seem to be struggling with the fact that genes can change (mutation) and that the genetic composition of a species can change (evolution). Yes, they do. What’s the problem?

    Erik: My question is what justifies the [i.e. Mayr’s ] statement, other than Very Long Time or “we can draw a tree”. “Genes change” by itself does not seem to be enough. It either requires particular important gene changes in particular ways, but if the process of gene change is unguided and mostly causally insignificant, it may require some totally different overriding cause.

    Sorry, but you have lost me here. I am guessing the key word is “unguided”, since I sure don’t know how we arrived here from the original issue (common descent).

  9. Erik: Insofar as genes change from individual to individual and generation to generation, how can the genes of the population be said to be *fixed*?

    Fixation here refers to the process by which the proportion of individuals in the population that carry some allele (particular version of a gene), changes over generations.

    If an allele is “fixed”, it means it has risen to be present in close to 100% of memebers of the population. It doesn’t mean the gene itself can’t change.

    Corneel is right, you need to get some basic terminology down.

  10. Allan Miller: Quote mine. Mayr was summarising the opposing viewpoints of the time.

    I copied the quote from Wikipedia, so Wikipedia was quote-mining.

    Allan Miller: If a barrier exists, one would expect it to be manifest. If no barrier is manifest, what persuades us that one exists?

    *Reproductive barrier* used to be a thing in biology, more or less definitional to species. Beginning with Mayr, it has turned into *reproductive isolation* as a cause of speciation. Speciation also requires barriers, to separate the populations at first, and when the distinct populations lose the ability to interbreed, they will have become distinct species, as indicated by the emerging reproductive barrier. Except that given the ability of genes to change left and right, experimentally achieved speciation might be an illusion. At the same time, no biologist attempts cross-breeding of far-off species. Perhaps they suspect there might be a barrier?

    Corneel: You seem to be struggling with the fact that genes can change (mutation) and that the genetic composition of a species can change (evolution). Yes, they do. What’s the problem?

    The problem: What do genes do and what’s the big deal about it? How come brilliant people like Felsenstein and Harshman think that similarity of genetic material across biosphere demonstrates common descent of it all? For example cytochrome c,

    Me-my dad 100%
    Me-Charlemagne 100% (I’m guessing a bit)
    Me-chimp – 100%
    Me-dog (specifically Sam the black Lab) – 94%

    Okay. Why not use hair or salivation for the same argument? “Look, they all salivate, therefore common descent!” How does this work? Where is the causal link?

  11. Let me quibble a bit with Rumraket’s description of reconstructing genealogies from molecular data.

    Rumraket: But there are such things as high-variability loci in the human genome, where there are measurable changes from one generation to the next. It is regions like these that are used to estimate relationships in DNA-based paternity tests. And they really can be used to built a family-level phylogeny.

    1. For genealogical reconstructions we can use rapidly mutating loci such as STRs (short tandem repeats), but mostly we use sites that vary in the population, and we do not rely on them further mutating during the history of the family.

    2. Yes, the statistical methods used are closely related to those used for inferring phylogenies. But the genealogy reconstructed is not likely to be a tree, because each of us had both a mother and a father, so our individual genealogies branch as one goes back (and also as one goes forward).

    3. To put it all together in one framework, one has to look at coalescent trees of regions of the genome and the phylogenies of species. And also, if you have data from close relatives rather than random samples from a population, at genealogies of families.

    Yes, this is complicated, but the connections between the methods are interesting, and give us good information.

    Now back to teaching elementary genetics.

  12. Erik,

    *Reproductive barrier* used to be a thing in biology, more or less definitional to species.

    You are trying to score silly semantic points on the meaning of ‘barrier’, I suspect. You appeared to demand proof of a barrier to ongoing evolutionary change without limit, a matter not to be confused, apart from in the hands of an inveterate confuser or the irretrievably confused, with a barrier to reproduction.

  13. Erik,

    I copied the quote from Wikipedia, so Wikipedia was quote-mining.

    There is a difference between quoting and quote mining – inability to separate these things being yet another thing which appears distinctive in Creationist debating strategy. I was able to get to primary source material using Google. In the interests of better scholarship, you could do the same.

  14. Erik: Okay. Why not use hair or salivation for the same argument? “Look, they all salivate, therefore common descent!” How does this work? Where is the causal link?

    No one knowledgeable writes “they all ___, therefore common descent.” It’s evident enough that you didn’t like biology in school, as you’re certainly not competent in it.

    But of course hair/fur is actually one of the defining characteristics of mammals at this point. It isn’t some idiotic, well, they have fur so they’re all related like you write, it’s that mammals have a number of features in common, including hair/fur, but also mammary glands, endothermy, etc. The characteristics aren’t necessary exclusively mammalian, as endothermy shared with birds, and I believe hair/fur has been found in pterosaurs, which I believe would be a separately evolved trait.

    How do we end up with salivation and hair? Via descent, of course. If we have a lot of the same characteristics we might be “human,” a few less but still a lot, primates, fewer but still many the same, mammals. Mammals exist via common descent, primates exist via common descent, and humans exist through common descent. Anything else is just creationism, poofs or what-not.

    It’s a matter of consequences, of causes. I know that you don’t accept normal inference of causes in this area, for no reason other than that you can deny it no matter what. Nevetheless, of course hair is an indicator of common descent (although not one wholly exclusive to mammals) just like cytochrome c, unless one is given to made-up stories, like creationists.

    Glen Davidson

  15. Erik: The problem: What do genes do? How come brilliant people like Felsenstein and Harshman think that similarity of genetic material across biosphere demonstrates common descent of it all? For example cytochrome c,

    Me-my dad 100%
    Me-Charlemagne 100% (I’m guessing a bit)
    Me-chimp – 100%
    Me-dog (specifically Sam the black Lab) – 94%

    It is not as simple as “similarity” alone. But just adding one other figure starts to tell the story:


    me-Rhesus monkey 99%

  16. Erik,

    The problem: What do genes do and what’s the big deal about it? How come brilliant people like Felsenstein and Harshman think that similarity of genetic material across biosphere demonstrates common descent of it all? For example cytochrome c,[…]

    It’s not just similarity, but difference. There are differences between cytochrome c’s in different groups, and those differences form a pattern. The same, or very similar, pattern is found when looking at other sequences. A picture starts to emerge, one that is well explained if the cause were common descent with mutation, since a mutation is inherited by all descendants.

    Okay. Why not use hair or salivation for the same argument? “Look, they all salivate, therefore common descent!” How does this work? Where is the causal link?

    You are trying to flip from digital similarity to phenotype. Stick with digital similarity, it’s easier to grasp. You don’t need to know what a stretch of DNA does; you only need to look at the patterns of similarity and difference.

  17. But, I will repeat again for the hard of hearing, my list of cytochrome c differences was not to ‘prove’ that sharing cytochrome c = common descent, but to ask where, in a list of increasing distance, Common Design takes over from Common Descent as the cause of similarity.

  18. Erik: Okay. Why not use hair or salivation for the same argument? “Look, they all salivate, therefore common descent!” How does this work? Where is the causal link?

    Ahhh. Is that it? Why not indeed. If you are uncomfortable with genetics you can use morphological characters. Using morphological characters went out of style at some point because it has several drawbacks compared to genetic characters, but the logic remains the same. Hair, as GlenDavidson already noted, is a synapomorphic (uniquely derived) character of mammals*. We can probably find some more, like lactating and some specific skeletal features.

    Guess what? You will still get a nested hierarchy if you use morphological characters. Convinced yet?

    *I think, not an expert on this. But this is TSZ so I am sure to receive a correction if this mistaken 🙂

  19. Joe Felsenstein: Let me quibble a bit with Rumraket’s description of reconstructing genealogies from molecular data.

    True enough, the reproductive relationships between human individuals, their genealogies, aren’t called phylogenies and they don’t come out as trees.

    On a phylogenetic tree, species (normally) all sit in the crown as individual branches, while in a family genealogy some members are of course directly ancestral to others, so would in some sense have to be nodes in a network of relationships.

    Actually that makes me wonder how extinct species are positioned in phylogenetic trees. How does the algorithm know where to put an ancient extinct lineage? I suppose it’s told in some sense, or what?

  20. Rumraket: True enough, the reproductive relationships between human individuals, their genealogies, aren’t called phylogenies and they don’t come out as trees.

    Ancestry.com might differ, unless I misreading you. About the trees.

  21. petrushka: Ancestry.com might differ, unless I misreading you. About the trees.

    It can’t be a tree if it shows both male and female lineages on the same diagram as any person will have two branches connecting to them, one from each parent.

    The true relationships between family members could easily look like this, with lots of inbreeding:

  22. Erik:
    *Reproductive barrier* used to be a thing in biology, more or less definitional to species. Beginning with Mayr, it has turned into *reproductive isolation* as a cause of speciation. Speciation also requires barriers, to separate the populations at first, and when the distinct populations lose the ability to interbreed, they will have become distinct species, as indicated by the emerging reproductive barrier. Except that given the ability of genes to change left and right, experimentally achieved speciation might be an illusion. At the same time, no biologist attempts cross-breeding of far-off species. Perhaps they suspect there might be a barrier.

    The barrier that Allan is asking you about is a barrier that prevents a species (or population) from evolving over time to become a different species. Evolutionary biologists generally have not found any such barrier. If you accept that speciation is possible, do you think there is some barrier that prevents something like a fish from evolving, over a long time, and through many intermediate forms, into something like a mammal? No such barrier has been found yet.

    As you point out, there is a barrier preventing interbreeding between the original fish species and its descendant mammal species. And also between any descendant fish species and the descendant mammal species. There is no reason under the standard understanding of evolution to think that there is no such barrier. So nobody bothers to try it.

  23. Allan Miller,

    But, I will repeat again for the hard of hearing, my list of cytochrome c differences was not to ‘prove’ that sharing cytochrome c = common descent, but to ask where, in a list of increasing distance, Common Design takes over from Common Descent as the cause of similarity.

    Common design hypothesis may take over where function is added or changed such as with apoptosis.

  24. Walter Kloover,

    As you point out, there is a barrier preventing interbreeding between the original fish species and its descendant mammal species. And also between any descendant fish species and the descendant mammal species. There is no reason under the standard understanding of evolution to think that there is no such barrier. So nobody bothers to try it.

    DNA repair limits variation in the germ line and could be a barrier to speciation occurring.

  25. Joe Felsenstein: It is not as simple as “similarity” alone. But just adding one other figure starts to tell the story:

    Between a cup and a bowl and a vase, put as many numbers as you like, what story do they tell? Can you tell the difference between a thing that actually does something and an abstraction like numbers that do nothing?

  26. I think that, for Erik, the ‘barrier’ preventing interbreeding and the barrier to ongoing evolution may be one and the same. Because he views species as discrete in all directions – genes contained in buckets that can only be transferred to new buckets by ladle – then the idea that a lateral barrier can arise between diverging lineages, without any implication of a comparable ‘forward’ barrier in descent, appears not to compute.

  27. GlenDavidson: But of course hair/fur is actually one of the defining characteristics of mammals at this point. It isn’t some idiotic, well, they have fur so they’re all related like you write, it’s that mammals have a number of features in common, including hair/fur, but also mammary glands, endothermy, etc. The characteristics aren’t necessary exclusively mammalian, as endothermy shared with birds, and I believe hair/fur has been found in pterosaurs, which I believe would be a separately evolved trait.

    Yes, yes. So why mix genes into the story if all those other characteristics supposedly serve as evidence of common descent just fine?

  28. Walter Kloover: If you accept that speciation is possible, do you think there is some barrier that prevents something like a fish from evolving, over a long time, and through many intermediate forms, into something like a mammal? No such barrier has been found yet.

    Who is doing the “something like a fish” to “something like a mammal” experiment? Is it really any wonder then that no barrier has been found?

  29. colewd,

    DNA repair limits variation in the germ line and could be a barrier to speciation occurring.

    As I grow weary of pointing out, the limitation to variation provided by DNA repair does not mean zero mutations.

    It is demonstrable that groups which are not separate biospecies frequently have reduced interfertility beyond the F1 generation (when meiosis is performed for the first time between the parental genomes). What causes that, do you think, if not divergence?

  30. Erik,

    Yes, yes. So why mix genes into the story if all those other characteristics supposedly serve as evidence of common descent just fine?

    Because they allow fine scale resolution, and broader coverage. They aren’t added to provide additional evidence of common descent. As Pauling observed, in that regard molecular characters are ‘beating a dead horse’ – common descent no longer needed to be ‘proved’.

  31. Mung,

    Who is doing the “something like a fish” to “something like a mammal” experiment? Is it really any wonder then that no barrier has been found?

    Get your asses into gear then, Creationists! Put in some work. You think there’s a barrier, find it.

  32. Walter Kloover: The barrier that Allan is asking you about is a barrier that prevents a species (or population) from evolving over time to become a different species. Evolutionary biologists generally have not found any such barrier. If you accept that speciation is possible, do you think there is some barrier that prevents something like a fish from evolving, over a long time, and through many intermediate forms, into something like a mammal? No such barrier has been found yet.

    I see. So it’s like a conceivability argument: Once you have conceded that incremental speciation has brought forth the entirety of the biosphere we observe, can you think of a barrier to it? Indeed, I cannot. The only problem: Why should I concede that incremental speciation operates on that grand scale, rather than on a much more limited scale as mere variation, barely and rarely qualifying as speciation, being fatal when attempted beyond that? Because that’s also what we actually observe.

  33. Erik: Yes, yes. So why mix genes into the story if all those other characteristics supposedly serve as evidence of common descent just fine?

    Because the genes are more specific than the characters that they effect. Plus, you can go beyond just the dna that strongly affects phenotype, and consider pseudogenes, retroviruses, etc. It’s a more full picture of evolutionary changes.

    But one certainly doesn’t have to go to the level of genes and DNA to understand phylogeny fairly well, which is fortunate, since long-extinct organisms (dinosaurs and the like) don’t yield useful DNA.

    Glen Davidson

  34. colewd: Common design hypothesis may take over where function is added or changed such as with apoptosis.

    Why?

    Cytochrome c took on an additional function, therefore common design? Why?

  35. GlenDavidson: Because the genes are more specific than the characters that they effect.

    Good, finally we are getting into what genes do. So, you are saying genes are the cause and characters are the effect. Which gene corresponds to which character? When a gene changes, a character must change? Any other genes beyond that? What do they do? Any good (free) book about this?

    Incidentally, this seems to open a can of worms concerning adaptation. If changes in characters (and perhaps changes in other abilities of the organism) are due to genes and their changes, then what is the effect of an organism trying to adapt to changes in the environment? When the organism changes its behavior due to environmental change, do genes change? Sometimes? Depending on what? Doesn’t this make it so that genes are an effect rather than the cause?

  36. Rumraket,

    Cytochrome c took on an additional function, therefore common design? Why?

    Design is a better explanation for the addition of function especially complex functions in multicellular organisms.

  37. Erik: Similarly, I have no idea why you think the different sparrows you refer to are different species when Chihuahua and St. Bernard’s are one. Despite multiple attempts to get you clarify what species means, you are not even understanding what is being asked. So your question about sparrows remains futile.

    I don’t recall you ever once asking me what “species” means. This is the first time you have managed to articulate that point. There are problems with any species definition, and that is in fact a prediction of speciation theory. If one species becomes two species in anything other than an instant, we should see populations that are intermediate between one species and two. And that would be evidence that speciation happens. If speciation didn’t happen, and each species were separately created, inviolate, there should be no possibility of confusion and no intermediate conditions. But since you ask, I like the so-called biological species concept, the one about interbreeding or potentially interbreeding populations, reproductively isolated from other populations. In order to account for those intermediate cases, I allow some wiggle room. You can’t expect complete absence of hybrids between closely related species, even fertile hybrids. What you can expect is that hybrids will have lesser fitness than non-hybrids, to the extent that there is no long-term gene exchange among species. And you can tell this most easily if two forms have lived in sympatry for a long time while maintaining their distinctness. Since this is true for species within Zonotrichia, I consider them all different species. While there have been extremely rare reports of hybrids between species of the genus (and even between genera), the species have remained distinct in sympatry. (Not every pair of species has overlapping range, but white-crowned sparrow, at least, overlaps all the others.)

    As if your science were the only one. There is a difference between biology (a particular science) and science in general.

    I know. What I’m saying isn’t that you don’t understand biology or the facts of biology (though you don’t). What I’m saying is that you have a basic misunderstanding of the methodology, or perhaps the epistemology, of all science, which is the same in physics, chemistry, and geology as it is in biology. And probably in linguistics too, which suggests you don’t understand the basic epistemology of your own field. There are indications that you don’t, as when you claim that we would be unable to say that languages were related to each other if we didn’t have written records of descent for at least one group.

    The relevant distinction is inference based on a (scientific) model versus observation about reality.

    Yeah, I wasn’t asking you, and that’s just as well because what you say is not in any way helpful.

    What is the causal link that justifies the assumption of common descent?

    There is no need for a causal link to justify common descent, and it isn’t an assumption but a conclusion. Or to put it another way, common descent is the cause of a pattern in the data, and we know that because no other cause explains the pattern in the data, while it’s an obvious prediction of common descent.

    What you’re asking for is actually a cause of speciation, as far as I can tell. But speciation is an unnecessary assumption for common descent, just separation of lineages. Speciation is certainly a reason for separation of lineages, but we don’t need to assume it. Common descent of different species requires that speciation happened, but in that case speciation is a conclusion from common descent, not a necessary prior assumption.

    We actually do know quite a bit about speciation, and I’ve given you some references as well as a summary of the process. You don’t like either of them for some reason, but don’t accuse me of not explaining.

    This is not a statistical question. It is also not strictly a genetics question. It is a question stemming from the biological fact that species breed the same species, so how does the variety of species come about to the point that they lose the ability to interbreed, e.g. apes and humans are said to have common descent, but do they interbreed? Why (not)? What is the cause? This is categorically important in order to figure out what genes do, not just what they look like in different species.

    It doesn’t matter what genes do for the purpose of determining common descent. While speciation and species isolating mechanisms are interesting subjects, they too are irrelevant to determining common descent. We do know that lack of interbreeding between populations can evolve — and that’s what speciation is. Enough of it has happened within historical times, or in the laboratory, that we can study the process.

    But I have basically given up hope to try to find ways to get useful information out of you.

    Your problem here can be summarized by the famous Mark Twain quote, “It ain’t what you don’t know that gets you into trouble. It’s what you know for sure that just ain’t so.” You are going to have to shed all your unconsidered assumptions about biology before you will be able to comprehend what people here are saying. I can help you only so far, because your words don’t necessarily make those assumptions clear. You seem obsessed, for example, with hybridization as a supposedly important factor in evolution, when hybrid species are quite rare, and are only around 5% of species even in plants, and vanishingly rare elsewhere.

  38. Erik: Between a cup and a bowl and a vase, put as many numbers as you like, what story do they tell? Can you tell the difference between a thing that actually does something and an abstraction like numbers that do nothing?

    Cups, bowls and vases are not self-reproducing entities with heritable traits.

    Even so, you could pick some property (like, does it have ornamentation?) of a large collection of cups, vases and bowls, and try to make a tree from that property.

    Then you pick another property (like, how much water can it hold?) and build another phylogeny from that.

    Then you can pick a third property, (like, what type of material is it made of? Ceramics, what type? Metal – what type?) and then built a tree from that.

    Then you can make a tree from their morphology. Overall type (is it a cup, or a vase, or a bowl?), or by shape? (is it round and curved, or square or triangular and has “sides” and “edges”?)

    Then you can compare the trees, what do you get? Four completely different trees.

    The materials-based tree will cluster cups, bowls and vases made of similar materials. You can make it as fine-grained as you want, as you can even sort by listing all the elements and make trees that group by proportion of elements. You’ll probably get something like a ceramics group(subdivided into clusters of different ceramics), a glass-group, a steel-group (sorted by the type of steels, with higher carbon content closer together, higher silicon content closer together) and so on and so forth.

    The tree with water capacity obviously groups them by water capacity, so large capacity cups group with similar capacity vases and bowls. But they’re made of wildly different materials: plastic, metal, ceramics and so on. There will probably be some rough correlation between type and water capacity. Bowls probably hold more water on average than do cups. But does it correlate with the type of material they’re made of? Highly probably no. So the trees are wildly incongruent.

    And how about ornamentation? Does that correlate with the material they’re made of or how much water they hold? Nope.

    No, you can’t do phylogenetics on cups, bowls and vases and get highly congruent phylogenetic trees from an algorithm that sorts by their properties. You’re going to get a conflicting nonsensical mess. Stop bullshitting.

  39. colewd,

    Design is a better explanation for the addition of function especially complex functions in multicellular organisms.

    No, because there is no reason supplied for differences among animals to be attributable to functional differences – that this organism has this cytochrome c isoform for this reason. Saying it is so does not make it so.

    And not forgetting that the vast majority of organisms are not animals. The common feature of all life is DNA replication. Apoptosis is taxonomicallly restricted. If I had a general pattern, which is amenable to a general explanation, I would prefer that over a host of maybes.

  40. colewd: Design is a better explanation for the addition of function especially complex functions in multicellular organisms.

    Why?

  41. John Harshman: There is no need for a causal link to justify common descent, and it isn’t an assumption but a conclusion. Or to put it another way, common descent is the cause of a pattern in the data, and we know that because no other cause explains the pattern in the data, while it’s an obvious prediction of common descent.

    A causal link is absolutely needed. Here’s why. Something like “common descent” also “explains”, for example, manuscript lineages, as we have discussed earlier. Does such “common descent” permit the belief that manuscript text copies itself with changes over time? Not at all. Scribes copy the text. Yet concerning species, you believe they have evolved on their own from bacteria to humans. Pretty far-fetched, to put it mildly. Therefore it’s necessary to see what genes do, how they fit to corroborate the picture, particularly the causal picture. Everybody is not equally gullible.

    You are right about one thing. I haven’t seen the pattern you are talking about. Maybe it’s pretty impressive. However, I have seen the pattern of morphological characters that impressed Darwin. It does not impress me at all, particularly compared to the patterns we deal with in linguistics.

  42. Erik: I see. So it’s like a conceivability argument: Once you have conceded that incremental speciation has brought forth the entirety of the biosphere we observe, can you think of a barrier to it? Indeed, I cannot. The only problem: Why should I concede that incremental speciation operates on that grand scale, rather than on a much more limited scale as mere variation, barely and rarely qualifying as speciation, being fatal when attempted beyond that? Because that’s also what we actually observe.

    Well, you don’t have to concede that he entirety of the biosphere is a result of incremental speciation before trying to think of a barrier. Anyone can try it! People who don’t make that “concession” are the ones with the most incentive to find the barrier, but the only suggestion i see here is DNA repair. I’m not an expert on that but it is not obvious to me how DNA repair could prevent a chain of speciation from fish to mammal. How does the DNA of the intermediate species know that it can only change a little bit more than it has already?

    As to speciation beyond incremental speciation being fatal, I’m not sure what you have in mind. Are you referring to hybridization or saltation? In any case, the mainstream understanding of evolutionary history does not include large amounts (if any) of speciation beyond incremental speciation.
    There was no overnight jump from fish to mammal, which is why Mung’s suggested research project is so impractical.

  43. colewd:
    Rumraket,

    Design is a better explanation for the addition of function especially complex functions in multicellular organisms.

    No. Design typically is more modular and less tangled than are evolutionary changes, which are opportunistic. Conceptually it’s easier to keep causes more modular and separate, but it also makes control a lot easier.

    Organisms are what you’d expect from evolution, conceptually unlikely opportunistic adaptations are rife, and there’s no evidence of conceptual separation and deliberate modularity. Cytochrome c is used in apoptosis merely because it’s there with potent effects that can assist in killing a cell.

    To put it another way, evolution has to use what already exists (or modifications thereof). while a designer might come up with something completely different that didn’t potentially have complex issues of control.

    Of course, while I think that cytochrome c’s “reuse” fits more with evolution than design, by itself it indicates little or nothing. A designer just might use cytochrome c for apoptosis. What one wouldn’t expect is the totality of “reuse” with modification and the extremely tangled relationships of systems and molecules that we see in life, had it been designed.

    What are you doing? Pretty much just taking anything as “evidence for design.” Why not? You have no design criteria or limits coming from observation, just a blind belief in design.

    Glen Davidson

  44. Walter Kloover: I’m not an expert on that but it is not obvious to me how DNA repair could prevent a chain of speciation from fish to mammal. How does the DNA of the intermediate species know that it can only change a little bit more than it has already?

    Indeed. But my questions at this stage are: Is it really all about DNA? Why? How? What the hell is “DNA repair”?

    Walter Kloover: As to speciation beyond incremental speciation being fatal, I’m not sure what you have in mind.

    Most mutations have no causal significance – the successive generations remain within the same species since Cambrian era or whatever you call it. Others are instantly fatal. So where does speciation fit in at all? Being no expert, I am only beginning to find out, time permitting.

  45. Erik: Good, finally we are getting into what genes do. So, you are saying genes are the cause and characters are the effect.

    No I’m not saying that, I said that they effect characters. Not that they did so solely, nor that characters don’t effect selection.

    Which gene corresponds to which character?

    Why don’t you get a basic education? Typically, you don’t have one gene corresponding to one character, you have multiple genes affecting and effecting multiple characters, but even then in response to regulation that often is not due to genes.

    When a gene changes, a character must change?

    Sometimes, but sometimes a gene changes with no obvious character change, and if it does cause change it’s typically in more than one character.

    Any other genes beyond that?

    The old view was that one gene produces one protein, still not a bad rule of thumb. But there are genes that produce RNA regulators, for instance, skipping any protein version.

    What do they do? Any good (free) book about this?

    I don’t know.

    Incidentally, this seems to open a can of worms concerning adaptation. If changes in characters (and perhaps changes in other abilities of the organism) are due to genes and their changes, then what is the effect of an organism trying to adapt to changes in the environment?

    That affects gene expression and regulation.

    When the organism changes its behavior due to environmental change, do genes change?

    No. Mutation can change them, but they’re not themselves changed by behavior. There continues to be some speculation that organism could change genes and/or regulatory sequences beneficially in some manner, however it’s hard to see how this could be caused by known biology, and the evidence for it is at best sparse (looking like none).

    Sometimes? Depending on what? Doesn’t this make it so that genes are an effect rather than the cause?

    Genes clearly are an effect of mutation, and environment can “select” some over others. But they’re certainly far more cause than effect of any individual organism.

    Glen Davidson

  46. Cause and effect are verbal games.

    In a diesel engine, does the rotation of the crankshaft cause combustion, or does combustion cause rotation of the crankshaft?

    Mutation is an event. it may or may not chain to other effects and other causes.

    What needs to be understood is the process and the feedback loops.

  47. petrushka: Cause and effect are verbal games.

    Even when Harshman asserted that common descent is the cause of the pattern in the data? Perhaps he’s been duped about premise and conclusion also.

  48. GlenDavidson: No I’m not saying that, I said that they effect characters. … Typically, you don’t have one gene corresponding to one character, you have multiple genes affecting and effecting multiple characters, but even then in response to regulation that often is not due to genes.

    So not “effect” but “affect”, and just that. This one character changes the whole story to one I am already familiar with.

  49. Erik: A causal link is absolutely needed. Here’s why. Something like “common descent” also “explains”, for example, manuscript lineages, as we have discussed earlier. Does such “common descent” permit the belief that manuscript text copies itself with changes over time? Not at all. Scribes copy the text.

    Sure. But we don’t need to know how the text came to be copied or the process involved in copying in order to determine the common descent of texts. Even a person completely ignorant of how the texts were produced should be able to determine the relationships among texts.

    Yet concerning species, you believe they have evolved on their own from bacteria to humans. Pretty far-fetched, to put it mildly. Therefore it’s necessary to see what genes do, how they fit to corroborate the picture, particularly the causal picture.

    It isn’t even necessary to believe that “they have evolved on their own”. The inference of common descent doesn’t depend on any particular source of variation. It’s possible (though not likely based on other data) that each and every change was injected into each lineage personally by Jesus. That doesn’t change the fact of common descent, since the pattern of injections, if there were any, still shows the nested hierarchy for which descent is the only explanation. Anyway, why is evolution farfetched?

    (Actually, there’s another explanation, but I doubt you would like it: separate creation in such a way as to purposely counterfeit common descent. Do we have to consider that hypothesis?)

    Everybody is not equally gullible.

    Yes, but some people carefully choose what not to be gullible about based on their prejudices.

    You are right about one thing. I haven’t seen the pattern you are talking about. Maybe it’s pretty impressive. However, I have seen the pattern of morphological characters that impressed Darwin. It does not impress me at all, particularly compared to the patterns we deal with in linguistics.

    Perhaps you should look at something more recent, so your opinion is no longer based on complete ignorance. I’ve suggested several references. Here’s one again: Harshman J., Huddleston C.J., Bollback J., Parsons T.M., Braun M.J. True and false gharials: A nuclear gene phylogeny of Crocodylia. Systematic Biology 2003; 52:386-402.

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