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. Erik: The Very Long Time argument is still as bad as it was when it was presented the first time in this thread. Possibly the very worst.

    Why bad? If a small change can occur within a particular time-frame, why cannot successive change accumulate with time, when there is selective pressure for that change? You seem to dismiss the idea out of hand.

  2. colewd:
    Alan Fox, How would you support this claim?

    Feathers might be a good example. The leap from theropod ancestors to birds, covered in feathers and capable of sustained flight might be considered a macro-evolutionary barrier, except that they appear to have evolved from scales in a documented sequence, with their initial role being in as an insulated covering, i. e. in thermoregulation.

  3. Alan Fox: Why bad?

    Not observed, that’s why. Unverifiable and unfalsifiable claims don’t count as evidence in empirical science. It’s another matter if you henceforth explicitly acknowledge that you are actually doing philosophy.

    Alan Fox: I don’t claim any great in-depth knowledge (a little out-of-date biochemistry) but so far, your ignorance is what has impressed me. That can be fixed if you want.

    It can be fixed by pointing out what exactly I am misunderstanding. My understanding happens to come from, among other sources, reading Darwin directly. That’s advanced level, not recommended to everyone, because Darwin’s mind is not pretty to look at. Too muddled thinking concerning central terms and methodological principles.

    It cannot be fixed by repeating irrelevancies that have nothing to do with the principal claims of Darwin. But if modern biology indeed has nothing to do with common descent and has no concern with macroevolution, then we can all move on to some other thread.

  4. Allan Miller: [Macroevolution ]generally ‘evolution above the species level’. That does depend somewhat on the species concept in use, but it does provide an occasionally useful distinction between evolution inside a gene pool, and those processes that subdivide such a pool and diverge the components.

    Actually, I now recall Nick Matzke getting tetchy with me over this (but not well enough to recall where, possibly at UD a while ago). I still think it is a distinction of convenience rather than one of different processes.

  5. Erik: It can be fixed by pointing out what exactly I am misunderstanding.

    That’s a tough one. Not being a mid-reader, I can only judge from what you have written so far.

  6. Alan Fox,

    Actually, I now recall Nick Matzke getting tetchy with me over this (but not well enough to recall where, possibly at UD a while ago).

    Yeah, I recall Larry Moran getting more than a little tetchy with someone at Talk.Origins!

    I still think it is a distinction of convenience rather than one of different processes.

    It’s convenient to make that distinction! But there is something different going on (as well as more of the same).

  7. Alan Fox: As I said, all evolutionary processes are covered by adaptation speciation, and extinction.

    Motoo Kimura would be interested in that claim, were he not extinct.

  8. Allan Miller: It’s convenient to make that distinction! But there is something different going on (as well as more of the same).

    I have to ask!
    That something different is?

  9. Dave Carlson: Breeding is most definitely not just an intra-species thing.There are multitudes of examples of plants hybridizing across species boundaries.In some cases the plants need not even be extremely closely related.In fact, this is one way in which speciation happens.

    …and let’s not forgot animal hybrids like sparred owls, ligers, the three-toed and red-cockaded woodpecker hybrids, black and mallard duck hybrids, beefalos, coywolfs (which I’ve actually encountered here in Virginia), and so forth…

    ETA: Oh…almost forgot: one of my personal favorites is the King Cob (heh!), a fertile hybrid of corn snakes and king snakes.

  10. Erik,
    Why don’t you just go away and study for a month or two, educate yourself then you might be able to have a real conversation with some actual experts in the field.

    I’m sure you’d laugh if someone in your own field acted as you are acting here, thinking they can demolish many years of work by many people without even a basic understanding of what they are talking about.

    I read a starter book on linguistics, and now I know that all existing theories of language origin and acquisition are bunk.

    Crack a book Erik. Come back in a year or two.

  11. colewd: Alan Fox: Those that claim there is a macro-evolutionary barrier are mistaken.

    How would you support this claim?

    Perhaps by the observation that the hypothetical barrier has been crossed countless times in the past, every time one species becomes two or more. For example, in the paleognaths, a group of many species that you agree are descended from a common ancestor.

  12. Alan Fox: Feathers might be a good example. The leap from theropod ancestors to birds, covered in feathers and capable of sustained flight might be considered a macro-evolutionary barrier, except that they appear to have evolved from scales in a documented sequence, with their initial role being in as an insulated covering, i. e. in thermoregulation.

    http://people.eku.edu/ritchisong/554images/Feather_scale_v2.jpg

    This is a hypothetical intermediate stage in the evolution of feathers from scales, from Regal, P. J. 1975. The evolutionary origin of feathers. Quarterly Review of Biology 50: 35-66.

    Basically you are saying that because it’s possible to draw something hypothetical like this between scales and feathers, this proves there are no barriers to macroevolution.

  13. Alan Fox: That something different is?

    Any macroevolutionary process that can’t be reduced to change in allele frequencies within populations. Differential speciation and extinction (species selection) is the most often mentioned.

  14. OMagain: Crack a book Erik. Come back in a year or two.

    I did. I read On the Origin of Species. By Darwin. Darwin says that common descent is the only possible conclusion because there’s something similar in linguistics. Then I came here to see if there’s anything else to back this up besides this failed analogy.

  15. Erik: Basically you are saying that because it’s possible to draw something hypothetical like this between scales and feathers, this proves there are no barriers to macroevolution.

    Not hypothetical. There is fossil evidence of feathers on dinosaurs that were more primitive in form than modern bird feathers and borne by small theropod dinosaurs that couldn’t have flown. Are interested enough to consider specific examples in detail?

  16. Alan Fox: Not hypothetical. There is fossil evidence of feathers on dinosaurs that were more primitive in form than modern bird feathers and borne by small theropod dinosaurs that couldn’t have flown. Are interested enough to consider specific examples in detail?

    I already went online to see the evidence for myself. If you have anything better, be my guest.

  17. Erik: This is a hypothetical intermediate stage in the evolution of feathers from scales, from Regal, P. J. 1975. The evolutionary origin of feathers. Quarterly Review of Biology 50: 35-66.

    Basically you are saying that because it’s possible to draw something hypothetical like this between scales and feathers, this proves there are no barriers to macroevolution.

    No, that isn’t what he’s saying. First, that model is both speculative and out of date. A better model can be found in Prum R.O., Brush A.H. The evolutionary origin and diversification of feathers. Quarterly Review of Biology 2002; 77:261-295. Second, shortly after that paper was written, there began to be found theropods with structures resembling several of the evolutionary stages hypothesized by Prum & Brush, for example Sinosauropteryx.

  18. Erik,
    I see your reference is 1975. There is a lot of fossil evidence that has turned up more recently.

    ETA, I see John Harshman picked up on this.

  19. John Harshman,

    Perhaps by the observation that the hypothetical barrier has been crossed countless times in the past, every time one species becomes two or more. For example, in the paleognaths, a group of many species that you agree are descended from a common ancestor.

    What is the hypothetical barrier? Is the origin of a new breed of dog crossing the barrier?

  20. @ Erik

    Some might describe what you are doing as a Gish gallop. It’s superficially a successful debating strategy but not ultimately intellectually satisfying. Biology and palaeontology are fascinating subjects if you give yourself a little more time.

  21. colewd:
    John Harshman,

    What is the hypothetical barrier?Is the origin of a new breed of dog crossing the barrier?

    The rapid results from artificial selection in dogs is more to do with selection of existing alleles (already in the gene pool).

  22. Alan Fox: Some might describe what you are doing as a Gish gallop. It’s superficially a successful debating strategy but not ultimately intellectually satisfying. Biology and palaeontology are fascinating subjects if you give yourself a little more time.

    Some might describe what you are doing as a non-answer.

    I don’t have many questions. They were stated up front in the OP and the rest of the discussion is small variation on that theme. And we have world-leading experts here. So I guess I have gotten the best answers now.

  23. John Harshman: A better model can be found

    I think this is a key point.
    When Erik says

    (3) Rough correspondence of expansion and extinction of species – when a species or group multiplies and commands many ecosystems, other species go extinct, because the number of souls should remain roughly the same

    Then that is the last word on the matter. There is no way to get to a better model, there is nothing that can be examined, no experiments can be run. You literally have nothing but the words themselves.

    It’s like Charlie’s stuff. His “etheric stuff” can account for any observation it can ‘explain’ anything at all. It can account for anything at all.

    Hey, Erik, it can be observed that at some point there is no life on planet earth. And it is also observed that at a later point there is life on earth.

    Could you reach into the place you are pulling this stuff from and find an explanation for the apparent contradiction between the number of souls staying roughly the same and there being no souls at all, then an increasing number of them until we reach whatever number it is you think is the “staying the same” number?

    Can you do that for me? Can you? I’m quite sure you can. And that’s actually the problem Erik.

  24. colewd: What is the hypothetical barrier? Is the origin of a new breed of dog crossing the barrier?

    I doubt that those who believe in barriers think so. Since you believe in barriers, you will have to tell me where it is and why you think it exists. Erik thinks that the barrier is between each pair of species, and the paleognath paper refutes that. If you think the barrier is elsewhere, let me know and I’ll find an example that refutes that too.

  25. Erik: You mean this? https://fcmdsc.files.wordpress.com/2010/01/fossil-feather.jpg

    No. Look up Sinosauropteryx.

    If my eyes were blurrier, if I squinted harder, maybe I would see something scale-like there. The previous pic did not require any such effort.

    If you could read, and if you bothered to read things people cited for you, you would know that the Prum & Brush model doesn’t feature evolution from scales.

  26. It seems an impossible task to get people to even hypothetically (just to confront the opposing argument) see speciation as a bifurcating process with divergence.

    So you get all this pompous “I understand evolution perfectly well ta very much”. Comedy gold.

  27. John Harshman: No. Look up Sinosauropteryx.

    I did. You will either find a better picture or I can determine you are just throwing words around, not really interested.

    John Harshman: If you could read, and if you bothered to read things people cited for you, you would know that the Prum & Brush model doesn’t feature evolution from scales.

    So you are not even addressing the question at hand, namely evolution of feathers from scales, brought up by Alan Fox and you chimed in to support him.

    It was cool as long as this little topic lasted.

  28. Allan Miller: So you get all this pompous “I understand evolution perfectly well ta very much”. Comedy gold.

    One wonders why someone would go to the trouble of understanding something perfectly they also thought was utterly wrong from top to bottom.

  29. OMagain: Can you do that for me? Can you? I’m quite sure you can. And that’s actually the problem Erik.

    Noted.

    That works both ways, by the way.

  30. Erik: So you are not even addressing the question at hand, namely evolution of feathers from scales

    Feathers didn’t evolve from scales, so that’s a bit of a problem. Read Prum & Brush. And you really can’t find a picture of Sinosauropteryx feathers? Must you be spoon-fed? I have no interest in doing so, because you’ll just say it’s spinach and to hell with it. (The analogy with trying to feed a baby is compelling.)

  31. John Harshman: Feathers didn’t evolve from scales, so that’s a bit of a problem.

    Yes, it is. Because it makes Darwinian evolution look terribly similar to ID – everybody, even the fiercest proponents, are under misconceptions and unable to defend it in orthodox manner.

    Somebody owes an apology (and correction) to Alan. He thought he was dumbing things down to correct those who were mistaken, but it turned out he was mistaken himself.

  32. Somebody owes an apology (and correction) to Alan. He thought he was dumbing things down to correct those who were mistaken, but it turned out he was mistaken himself.

    Divide and conquer already is it? Very Mungish.

  33. Erik: Ah, so there really are no specific claims and no specific concepts in the theory of evolution. And that’s why it predicts things very well. Got it!

    Maybe that’s a plants thing.

    It is, though it’s not only just a plant thing.

    Or maybe it’s just the way the concept of species is used in Darwinian theory. To quote Darwin, “I look at the term species, as one arbitrarily given for the sake of convenience to a set of individuals closely resembling each other, and that it does not essentially differ from the term variety, which is given to less distinct and more fluctuating forms.”

    If you’d like to dismiss mountains of evidence (much of which is available to you from a simple google scholar search) based on an out-of-context quote that is more than 150 years old, that is certainly your perogative. It does, however, seem like an especially peculiar way to go about learning a new subject.

    Species or variety, closely resembling individuals or fluctuating forms, all the same thing. That’s why it works!

    I have no idea what this means. What is the “it” referring to here?

  34. Dave Carlson: If you’d like to dismiss mountains of evidence (much of which is available to you from a simple google scholar search) based on an out-of-context quote that is more than 150 years old, that is certainly your perogative.

    I have read the whole book (and some of the current “mountains of evidence” too). In that particular passage, Darwin first considers – and dismisses – the definition of species that actually defines species as distinct from other species. And then he opts for what I quoted.

    Dave Carlson: I have no idea what this means. What is the “it” referring to here?

    Darwin’s theory of evolution. The most salient points of it are in the OP. This is what you came to discuss here, right?

  35. Alan Fox,

    I have to ask!
    That something different is?

    Essentially, the processes that divide gene pools can be conceptually separated from those that keep each in step. Although one of the things that drives this is divergence, ie microveolution in 2 streams, there are other mechanisms and phenomena not fully captured by the single gene pool approach (micro).

    I think confusion can arise because there is a kind of (non-bifurcating) speciation going on within a pool too – chronospecies. That really is ‘lots of micro’.

  36. Erik,

    The “mountains of evidence” I was referring to is in regard to the fact that interspecific hybridization is something that occurs quite regularly.

    In any case, the fact that you seem to think that evolutionary biologists, following Darwin, define species in such a way that species are not distinct from each other is evidence of how little you’ve apparently learned from your reading.

    It is true that when dealing with recently separated lineages, it may be difficult to determine whether different populations are best treated as species or some other more inclusive taxonomic grouping. This is a natural outcome of evolutionary processes. That fact does not in any way mean that all discussions of species are arbitrary, or that evolutionary biologists don’t think species are generally distinct from one another.

  37. Erik: The Very Long Time argument is still as bad as it was when it was presented the first time in this thread. Possibly the very worst.

    All that bluster yet you can’t tell us why it is bad.

    Doesn’t make you look very bright, ya know?

  38. Adapa: All that bluster yet you can’t tell us why it is bad.

    Again: Because not observed and there are obvious observed counterexamples.

  39. Erik: and there are obvious observed counterexamples.

    Well, if you are just going to go around mentioning all the counter evidence, now you are intentionally just being difficult.

    Can’t we just stick to speculation?

  40. phoodoo,

    Well, if you are just going to go around mentioning all the counter evidence, now you are intentionally just being difficult.

    ‘Mentioning’ all the counter evidence? As in saying ‘obvious observed counterexamples’. OK, can I just mention that there are all these obvious observed examples? Thanks. Debate, the easy way.

  41. Allan Miller: As in saying ‘obvious observed counterexamples’. OK, can I just mention that there are all these obvious observed examples? Thanks. Debate, the easy way.

    I said a bit more than that, namely “currently extant species that emerged in Jurassic era (and we know they are the same species because they didn’t evolve a single bit meanwhile)”, but nobody of course remembers anything when the page has been turned.

  42. Dave Carlson: In any case, the fact that you seem to think that evolutionary biologists, following Darwin, define species in such a way that species are not distinct from each other is evidence of how little you’ve apparently learned from your reading.

    I’ve learned this thing: Trust nobody, not even Darwin (particularly not Darwin!), in anything what is said about the theory of evolution, whether it’s the most central matter to the theory or some sort of example presented as evidence. Yet the theory is true regardless, because of “mountains of evidence” that, when it comes to specifying it, is neither mountains or evidence.

    The supposed evidence is either “things change over Very Long Time” or “there are common traits in different species that can be arranged as nested hierarchies” which can serve as evidence for all sorts of speculations, applicable to Genesis as well as On the Origin of Species. The whole range of speculations was already covered prior to Darwin. He didn’t contribute any improvement whatsoever.

    Some overviews of common descent make it very compelling at first glance, for example at Rationalwiki.org. But when you look closer, the first things on the list – anatomical homologies and DNA and RNA – are completely irrelevant to common descent. When things are made of the same material, it usually means just that – they are made of the same material. It doesn’t say that one species came from another species, which is the actual claim of common descent.

    Next they say there are “endogenous retroviral insertions”. The description sounds like a virus inserts something into the genome at some random point in the past and then this can be traced throughout the evolutionary tree. This seems very compelling, until you arrive at the last sentence of the section, “This rare event is usually species specific.” i.e. it is NOT traced throughout the evolutionary tree. It is carried along only by the descendants of the same species, so it is not evidence for common descent at all, because it is not occurring on the scale relevant to the evolutionary theory.

    Next thing on the list,

    Pseudogenes — Shared errors are a powerful argument for a common source. If two books describe the same concept in similar language, it’s possible they just both converged on the same wording. However, if they both share the same grammar or spelling errors it becomes improbable to assume that they did not derive from a common source. There are genes that no longer code for a protein due to a mutation or error. Species often share the same pseudogene with the same inactivating mutation. A famous example of this is the L-gulonolactone oxidase that synthesizes vitamin C. All simians including humans share one pseudogene of inactivated L-gulonolactone oxidase, but the guinea pig has a different pseudogene indicating a different mutation.

    This is way more compelling than “Endogenous retroviral insertions”, right? The facts/statements:

    *** Pseudogenes are errors because they underwent an “inactivating mutation” in the sense that they “no longer code for a protein”
    *** “L-gulonolactone oxidase” is a pseudogene shared by all simians (monkeys, apes, humans), but not by guinea pigs
    *** As a sidenote, it so happens that “L-gulonolactone oxidase” synthesizes vitamin C

    All this ends up saying is that monkeys, apes, and humans are more similar to each other than to guinea pigs (eureka!) and, incidentally, pseudogenes are not errors in the relevant sense. Instead of undergoing an “inactivating mutation” there’s another useful purpose that they serve.

    And so on down the list: Either completely irrelevant to common descent (even to macroevolution) or self-defeating when you think along with what’s being said.

    It should not be like this. I thought that common descent had a better case for itself.

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