What is the standard for evidence in biology?

Specifically, what is the evidence for common descent?(Not quite) famously, Darwin mused about the similarities of taxonomic hierarchies in linguistics and biology and asserted that the hierarchies must ultimately point to common descent. (Chapter XIV, On the Origin of Species) That’s common descent as distinguished from microevolution.

The linguistic equivalent is the single origin of all languages (eminently unproven and deemed unprovable) as distinguished from a language family (with demonstrable relevant organic shared features).

Darwinists are welcome to present their evidence. From Rumraket, we have the observation that all organisms can reproduce, “Nesting hierarchies are evidence of common descent if you know that the entities sorted into hierarchies can reproduce themselves. And that particular fact is true of all living organisms.” Good start.

From Joe Felsenstein we have the doubt that the border between micro- and macroevolution can be determined, “OK, so for you the boundary between Macro/Micro is somewhere above the species level. How far above? Could all sparrows be the same “kind”? All birds?” Not very promising.

From Alan Fox, “Darwin predicted heritable traits. Later discoveries confirmed his prediction.” Questions: Which heritable traits specifically? Was there a principled improvement over Mendel? And how does this lend credence to common descent?

Thanks to all contributors.

706 thoughts on “What is the standard for evidence in biology?

  1. Allan Miller: But they aren’t identical, which is why they are given separate names. How did they come to be different?

    Some people have blond hair, some don’t. Are they different species?

  2. John Harshman: The data from which the tree is made are “proof”

    If we look at the data available for the evolution of terrestrial vertebrates it is mirrored by the development of humans from birth to adulthood. There is a fair bit of evidence that human line has retained the primal form while other extant tetrapods have derived features. I know you won’t agree with this but it is a good fit for the data and so is an interpretation that can be defended.

    As in the proposed evolution of terrestrial quadrupeds, individual human development begins from a horizontal position through a quadruped stage to the upright, bipedal characteristic of humans.

    Examples of derived features are limblessness in snakes, specialist mouthparts derived from teeth and specialist limbs derived from the pentadactyl limb. All features retained by the human form.

  3. phoodoo,

    Some people have blond hair, some don’t. Are they different species?

    No. Still, as is well known, there is no categorical definition of species that suits all purposes. There is a reason for that.

  4. Allan Miller:
    phoodoo,

    No. Still, as is well known, there is no categorical definition of species that suits all purposes. There is a reason for that.

    So maybe they are different species?

  5. phoodoo,

    So maybe they are different species?

    If someone chooses to call them different species, they are different species according to their private definition. It shows the futility of expecting Nature to give a damn about conforming to our categories.

    Interbreeding is the closest to a ‘natural’ delimiter, but then you get excessive lumping, because polar bears can breed with grizzlies, lions with tigers, European and US maples etc. The offspring of such distant cousins are often infertile themselves – but by no means always.

  6. Daft thing being, when people look for introgression (gene flow between putatively isolated populations, ie possible species), they don’t usually stick them in a room with mood music, oysters and a velvet throw, they look for genes in the one that don’t ‘belong’ there. They use genetic analysis – the thing that some seem to argue can’t be used until after interbreeding is established – to establish it.

  7. CharlieM: If we look at the data available for the evolution of terrestrial vertebrates it is mirrored by the development of humans from birth to adulthood. There is a fair bit of evidence that human line has retained the primal form while other extant tetrapods have derived features. I know you won’t agree with this but it is a good fit for the data and so is an interpretation that can be defended.

    No, it can’t. And I’m quite sure you won’t try. Nor would it be an alternative explanation for nested hierarchy in the data, even if it were true, so I see no need to discuss it here.

    As in the proposed evolution of terrestrial quadrupeds, individual human development begins from a horizontal position through a quadruped stage to the upright, bipedal characteristic of humans.

    That isn’t human development, it’s one cherry-picked feature of human development. It would also seem to directly contradict your claim that humans retain the primal form.

    Examples of derived features are limblessness in snakes, specialist mouthparts derived from teeth and specialist limbs derived from the pentadactyl limb. All features retained by the human form.

    What “specialist mouthparts” are “derived from teeth”? Do you just mean different sorts of teeth? Yes, humans have teeth. Of course they’re teeth specially adapted for the human, generalist diet and look nothing like the teeth of primitive tetrapods. And humans have many derived features, one of which — bipedality — you have already mentioned. The evolution of those derived features is scattered all about the lineage from the tetrapod ancestor to humans.

    And once again, this has nothing to do with whether a nested hierarchy is evidence for common descent.

  8. Anyway, to state the obvious, Erik’s criterion of interbreeding for where “microevolution” ends, is completely useless for bacteria and archaea, who don’t interbreed in any case.

    It’s pretty meaningless anyway with respect to the evidence of derivation, but there doesn’t even exist the interbreeding excuse for claiming microevolution vs. macroevolution among asexual reproducers. So with E. coli there’s only evidence of evolution, along with the only reasonable classification system supported by the evidence, the branching clades that form a “tree.”

    Glen Davidson

  9. GlenDavidson,

    Anyway, to state the obvious, Erik’s criterion of interbreeding for where “microevolution” ends, is completely useless for bacteria and archaea, who don’t interbreed in any case.

    True enough, and the very many asexual eukaryotes. The biology-blindness one must espouse just to service an obsession with chimps!

  10. Allan Miller: If someone chooses to call them different species, they are different species according to their private definition

    So EVERY definition of species is a private one.

    And every claim that speciation has occurred is specious.

  11. phoodoo,

    So EVERY definition of species is a private one.

    Not every definition of species is held by only one person. But there is general agreement that there is no definition that fits all purposes. The Common and Spotted Sandpipers are given different binomial names, despite occasional introgression. So they are different species on some criteria, but not on others.

    And every claim that speciation has occurred is specious.

    No. You are trying to confuse different definitions. If gene flow has ceased, even through hybrids, that is a real thing in the world, whatever we call the two populations that result. We call it speciation, and it conforms to one of the definitions of species in common use – though given that it is a drawn-out process, it is not the dichotomoous category Creationists seem to think it ought to be. Examples of every step of the assumed continuum can readily be found.

    But setting aside the semantic bollocks that dogs every single discussion here, are you saying that reproductive incompatibility in a divided population cannot occur, as a matter of principle?

  12. Allan Miller: But setting aside the semantic bollocks that dogs every single discussion here, are you saying that reproductive incompatibility in a divided population cannot occur, as a matter of principle?

    No, I agree that St. Bernards don’t mate with chihuahuas.

    I think they are still both wolves.

  13. phoodoo,

    No, I agree that St. Bernards don’t mate with chihuahuas.

    I think they are still both wolves.

    Confusing two species concepts again.

    Is there a possibility of two populations emerging by a process of division and divergence from one, where none of the genes of population A can flow by any mating path into the members of population B or vice versa? If the answer is ‘yes’, that is what is known as speciation. Whether you choose to call them the same species as their common ancestor or not is immaterial.

  14. So if we take some fleas to mars and they manage to reproduce then we’ll have a new species of flea and Darwin is fully vindicated!

    Got that phoodoo?

  15. phoodoo: No, I agree that St. Bernards don’t mate with chihuahuas.

    It’s not like the chihuahua was unwilling …

  16. Allan Miller: You have an actual point to make?

    Not one that you’d understand. But for other’s, just look at the title of Darwin’s famous epic. Taking a group of fleas off to mars and declaring a new species seems to fall just a bit short of the Master’s Thesis.

  17. Mung,

    Not one that you’d understand. But for other’s, just look at the title of Darwin’s famous epic. Taking a group of fleas off to mars and declaring a new species seems to fall just a bit short of the Master’s Thesis.

    Ah. You have an excellent point to make but I, and possibly others, too thick to understand it if you were to trouble yourself to put it into words. Gotcha.

  18. The point you are struggling with, I think, is that speciation is not just the conceptual equivalent of a condom. Speciation’s eventual result relates to the inability to reproduce even if the condom (or whatever rhetorical equivalent you think most hi-la-rious) were removed.

  19. Allan Miller: The point you are struggling with, I think, is that reproductive isolation is not just the conceptual equivalent of a condom.

    You overestimate me. But aside from that, sperm in a condom do not reproduce. So they are not analogous to fleas on mars.

  20. Mung,

    You overestimate me. But aside from that, sperm in a condom do not reproduce. So they are not analogous to fleas on mars.

    The condom is analogous to the space between Earth and Mars – a barrier to gamete fusion in both cases. But hey, analogies, eh? Let’s talk about the real thing. Is it impossible for reproductive isolation to evolve?

  21. Allan Miller,

    I am pretty sure that a simple house cats genome could be mated with every other type of cat on the planet, lions, tigers, leopards…if science wanted to try it bad enough. I believe a saber toothed tiger’s genome could as well.

    So I don’t think a billion years seems enough time for speciation. If this whole Darwin system doesn’t speed up, our history books are going to run out of time.

  22. phoodoo,

    I am pretty sure that a simple house cats genome could be mated with every other type of cat on the planet, lions, tigers, leopards…if science wanted to try it bad enough.

    I am doubtful about that. It is not simply a matter of getting a zygote in a petri dish.

    I believe a saber toothed tiger’s genome could as well.

    Do you have one to hand?

    So I don’t think a billion years seems enough time for speciation.

    That’s a leap. The cats diverged a few million years ago, not a billion.

    If this whole Darwin system doesn’t speed up, our history books are going to run out of time.

    That’s what you’re pinning your money on? Speciation is feasible but there hasn’t been enough time for it? I don’t think a squillion years is time enough for French and Spanish to diverge from a common language. Why? Because I said.

  23. Phoodoo believes something to be true.

    Matter: settled.

    It was fun knowing you all. See you in hell.

  24. John Harshman: No, it can’t. And I’m quite sure you won’t try. Nor would it be an alternative explanation for nested hierarchy in the data, even if it were true, so I see no need to discuss it here.

    It would be an alternative explanation, but one that you are not even willing to consider or think about in any objective way. What we see is a line of descent towards the production of individual conscious awareness with specialised forms radiating off along the way and remaining relatively fixed at an earlier stage.

    That isn’t human development, it’s one cherry-picked feature of human development.

    Do you not think that bipedalism is an important, major distinguishing feature of humans?

    It would also seem to directly contradict your claim that humans retain the primal form.

    You need to realise what I mean by form. No doubt for you it is static physical shape, but what I am talking about is a dynamic feature. The human form encompasses everything from a single globular cell to the adult.

    What “specialist mouthparts” are “derived from teeth”? Do you just mean different sorts of teeth?

    Highly specialised structures such as tusks which no longer serve the primary function of holding and/or breaking up food before it is swallowed.

    Yes, humans have teeth. Of course they’re teeth specially adapted for the human, generalist diet and look nothing like the teeth of primitive tetrapods.

    The teeth that we possess have changed from the original teeth that the early tetrapod ancestors of present day humans as I would expect. Keeping in mind that human ancestors were early tetrapods too. And as you will admit human eating habits are very eclectic. Unlike the eating habits of say, an aardvark.

    And humans have many derived features, one of which — bipedality — you have already mentioned. The evolution of those derived features is scattered all about the lineage from the tetrapod ancestor to humans.

    Yes there is a general trend towards bipedalism throughout vertebrate life. But only humans coupled the freeing of the forelimbs with unique dexterity, flexibility and the thinking power to go along with it.

    And once again, this has nothing to do with whether a nested hierarchy is evidence for common descent.

    Well at least we are in agreement that common descent from a single source will produce a nested hierarchy.

  25. I can’t get myself through Charlie’s posts. Honestly. I fall asleep with boredom. It’s just this vague deepity-babble.

  26. CharlieM: It would be an alternative explanation, but one that you are not even willing to consider or think about in any objective way. What we see is a line of descent towards the production of individual conscious awareness with specialised forms radiating off along the way and remaining relatively fixed at an earlier stage.

    It isn’t an alternative explanation because it apparently is still common descent that produces the nested hierarchy. It’s the same explanation. You seem confused about what we’re talking about in this thread. You seem to be trying to talk about the driving force in evolution, which is not the subject here.

    Now, what you’re doing is taking an arbitrary lineage on the tree, which by pure coincidence happens to be yours, and calling that the main line of evolution, while everything else is a side branch. And you seem to be taking an extreme view of Haeckel’s recapitulation, in which human development passes through the adult stage of every ancestor in the human lineage. That’s just wrong. Human features are specializations no more an no less than are tusks, loss of limbs in snakes, or anything else you call “radiating off”. There is no objective reason to single out your lineage or to call other lineages “relatively fixed at an earlier stage”. All that really means is “unlike you”.

    Yes there is a general trend towards bipedalism throughout vertebrate life. But only humans coupled the freeing of the forelimbs with unique dexterity, flexibility and the thinking power to go along with it.

    There is no such trend. Some species have become bipedal, others have not. Some bipedal species have quadrupedal descendants. Some vertebrates never got legs at all. Others turned their legs back into fins (flippers),while still others lost them entirely. There is no “main line”, no side branch, no universal trend, no special evolutionary direction of which you are the pinnacle. You can’t defend that claim, and as I predicted you don’t even try.

  27. John Harshman: There is no “main line”, no side branch, no universal trend, no special evolutionary direction of which you are the pinnacle. You can’t defend that claim, and as I predicted you don’t even try.

    Buzzkill

  28. John Harshman,

    There is no such trend. Some species have become bipedal, others have not. Some bipedal species have quadrupedal descendants. Some vertebrates never got legs at all. Others turned their legs back into fins (flippers),while still others lost them entirely. There is no “main line”, no side branch, no universal trend, no special evolutionary direction of which you are the pinnacle.

    You cannot test anything you have claimed here. How do you know legs turned back into flippers? This is based on your assumption of universal common descent. The same as your assumption that birds historically lost flight.

  29. colewd: You cannot test anything you have claimed here. How do you know legs turned back into flippers? This is based on your assumption of universal common descent. The same as your assumption that birds historically lost flight.

    One step forward, two steps back. You had once admitted that the various species of paleognath birds were related, now you take it back. No, nothing is based on an assumption of universal common descent. We’ve been over this. First, common descent doesn’t depend on universality. Mammals can be related even if not all life is related. Second, common descent is a conclusion from the data, not an assumption going in. I don’t assume that birds lost flight. It’s a conclusion based on the common descent of birds. And common descent of birds is a conclusion based on vast amounts of evidence, from DNA sequences, fossils, and morphology of extant species. I’ve shown you the evidence. Why have you ignored it?

  30. John Harshman: I’ve shown you the evidence. Why have you ignored it?

    If he did not ignore evidence he’d not have the position he has. It’s catch 22.

  31. John Harshman,

    I don’t assume that birds lost flight. It’s a conclusion based on the common descent of birds. And common descent of birds is a conclusion based on vast amounts of evidence, from DNA sequences, fossils, and morphology of extant species. I’ve shown you the evidence. Why have you ignored it?

    Because this data validates similarities and your claim is about transitions.

    I agree with Eric on this point that you have made hypothesis A that certain animals are maternally related and supported the claim with similar DNA and other evidence.

    What has not been done is correlating maternal relationship (ancestry) with DNA similarity. You are assuming maternal relationship without validation of your hypothesis. Until you do this you are reasoning in circles.

  32. OMagain,

    If he did not ignore evidence he’d not have the position he has. It’s catch 22.

    The evidence needs to validate the specific claim. Common descent is a claim about transitions not similarities.

  33. colewd: The evidence needs to validate the specific claim. Common descent is a claim about transitions not similarities.

    What sort of evidence would you expect to see supporting such a claim then?

  34. If it’s not DNA sequences, fossils, and morphology of extant species, what’s left? Do tell.

  35. colewd:
    OMagain,

    The evidence needs to validate the specific claim.Common descent is a claim about transitions not similarities.

    How do you explain hereditary patterns without heredity, including transitions (some of which are documented by relatives of ancestors)?

    Oh, that’s right, you don’t explain, you just try to poke holes in real explanations while explaining nothing.

    Glen Davidson

  36. colewd:
    John Harshman,

    Because this data validates similarities and your claim is about transitions.

    I agree with Eric on this point that you have made hypothesis A that certain animals are maternally related and supported the claim with similar DNA and other evidence.

    What has not been done is correlating maternal relationship (ancestry) with DNA similarity.You are assuming maternal relationship without validation of your hypothesis.Until you do this you are reasoning in circles.

    So you’re definitely retracting your prior admission that paleognaths are related?

    What exactly do you propose I do to validate the hypothesis that DNA similarity (actually, nested hierarchy, which is something different, but never mind) results from ancestry?

  37. colewd,

    What has not been done is correlating maternal relationship (ancestry) with DNA similarity. You are assuming maternal relationship without validation of your hypothesis. Until you do this you are reasoning in circles.

    Oh FFS. Talk about going round in circles.

    Is it circular to infer relationship in, say, DNA fingerprinting? If not, what makes it different?
    What other cause of extensive DNA identity are you proposing?
    Can you nominate a specific taxal node at which you are proposing it?

  38. OMagain,

    If it’s not DNA sequences, fossils, and morphology of extant species, what’s left? Do tell.

    You need something independent of the organisms and everything about them. 🙂

  39. John Harshman: What exactly do you propose I do to validate the hypothesis that DNA similarity (actually, nested hierarchy, which is something different, but never mind) results from ancestry?

    Evidence doesn’t answer anything, it just raises questions.

    Unless it’s “it looks designed.” That’s the final answer. Because it’s the right one.

    Glen Davidson

  40. Allan Miller,

    Is it circular to infer relationship in, say, DNA fingerprinting? If not, what makes it different?
    What other cause of extensive DNA identity are you proposing?
    Can you nominate a specific taxal node at which you are proposing it?

    In the case of paternity testing the correlation has been made between parent and child DNA. The standard for a positive or negative result has been characterized based on data from parents and children.

    If this type of standard was developed to test common descent then the ball game changes. The challenges is the drop in accuracy as you move further away in relation.

  41. colewd,

    In the case of paternity testing the correlation has been made between parent and child DNA. The standard for a positive or negative result has been characterized based on data from parents and children.

    If this type of standard was developed to test common descent then the ball game changes. The challenges is the drop in accuracy as you move further away in relation.

    The ‘drop in accuracy’ is a steady accumulation of difference, entirely in accord with the difference being correlated with the time since branching, an expectation of common descent with modification. It is not clear where you propose to place the divider between an amount of difference that is not circular, and one that is.

    Give an example, preferably one not involving your favourite primate, and explain your method, and what causes the sequence identity if not common descent.

  42. colewd:
    Allan Miller,

    In the case of paternity testing the correlation has been made between parent and child DNA.The standard for a positive or negative result has been characterized based on data from parents and children.

    If this type of standard was developed to test common descent then the ball game changes.

    Sorry, that is “proof of principle” of the evidence for common descent.

    The challenges is the drop in accuracy as you move further away in relation.

    Not exactly a grave difficulty.

    Glen Davidson

  43. Allan Miller,

    Give an example, preferably one not involving your favourite primate, and explain your method, and what causes the sequence identity if not common descent.

    I don’t know the cause of sequence identity. As I don’t know the cause of sequence differences or splicing code differences or gene expression differences.

  44. colewd: I don’t know the cause of sequence identity. As I don’t know the cause of sequence differences or splicing code differences or gene expression differences.

    Clearly you don’t. But why can’t you accept that some of us do?

  45. Allan Miller: Is it impossible for reproductive isolation to evolve?

    That’s an entirely too vague question. How many species of dogs are there?

    If we take a population of fleas to mars, they are reproductively isolated from species of fleas on earth. Are they therefore a new species? According to your analogy the answer would be yes. But that fails to distinguish between spatial isolation and whatever term evolutionists use to indicate groups of organisms that cannot interbreed for genetic reasons that have nothing to do with location/geography.

  46. John Harshman:

    CharlieM: It would be an alternative explanation, but one that you are not even willing to consider or think about in any objective way. What we see is a line of descent towards the production of individual conscious awareness with specialised forms radiating off along the way and remaining relatively fixed at an earlier stage.

    It isn’t an alternative explanation because it apparently is still common descent that produces the nested hierarchy. It’s the same explanation. You seem confused about what we’re talking about in this thread. You seem to be trying to talk about the driving force in evolution, which is not the subject here.

    In the article, On the Independence of Systematics, Ron Brady has this to say:

    Mayr has reiterated this same point in so many different works that I take the passage to be a fair representation of his views, yet it clearly confuses the condition to be explained with the explanation.
    The fact that this confusion is hardly unique to Mayr, but almost ubiquitous in systematics, should make no difference to the argument — the province of science is not a democracy. When Remane (1952) used the classical criteria for homology as a definition of the same, he did so because he was defining a condition found within the data — a pattern of form exhibited by organisms. The “definition” advanced above is a hypothetical account, however true we may think it to be, of the process by which such a condition could come about. It is technically the explanans, while the empirically discovered pattern is the explanandum (thing to be explained). Remane is one of the authors Mayr complains of, but Remane is not guilty of any misunderstanding. He has simply noticed that the definition of a pattern is interchangeable with the criteria used to recognize it (since those ‛criteria’ are actually the very relations that constitute the pattern), and he has avoided the error expressed above — i.e., that our explanation of empirical condition can define the condition.

    Once the problem above is recognized, it becomes obvious that the strategy by which we replace a description of an empirical condition with its explanatory hypothesis is self-defeating. We must still advance an account of the empirical conditions to be explained — we still need a name for the relation of identity (common position in a common plan) found within the data. If we fail to supply this, we fail to distinguish empirical problem from explanatory hypothesis, and once this has happened, we have no independent evidence with which to test, or support, that hypothesis. By making our explanation into the definition of the condition to be explained, we express not scientific hypothesis but belief. We are so convinced that our explanation is true that we no longer see any need to distinguish it from the situation we were trying to explain. Dogmatic endeavors of this kind must eventually leave the realm of science.

    The confusion Brady is talking about is that Mayr uses the hypothetical account of homology to define the empirical fact of homology which was observed long before Darwin produced his theory. To get the full context it would be best to read Brady’s article in full.

    The point is that both you and I are looking at the nested hierarchies which are observed in nature and coming up with a different explanation. But both of our explanations are based on our beliefs on what the driving force is that creates the observed pattern.

    But we cannot use our belief in common descent to justify the nested hierarchies we observe by stating that nested hierarchies are evidence for common descent. in other words Eric has a good point.

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