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 analogy with linguistics can be easily extended, “All languages have vowels and consonants that appear in pronounceable sequences. […]

    A forlorn plea I find myself making repeatedly: how about dropping the analogies altogether? They are an illustrative tool; an attempt to give people a flavour of something that may be unfamiliar by reference to something that is familiar. They are not prescriptive or to be dogmatically pursued to the nth degree – they clearly can’t be: it ought to be obvious that, to be an analogy, they must differ in some respect from the thing being compared to. Otherwise (eg see Hume) they would be the same thing. So gnawing at some aspect of the analogous system isn’t really getting you anywhere (do you actually want to get anywhere? That is unclear, despite the OP being framed as a question).

    The basic data available to an intelligent human, even one who admits to knowing nothing of genetics, is that the DNA of an offspring is an almost exact copy of that of its parent(s). You need to know little more than that to grasp the basics of the arguments on molecular phylogeny and common descent. The ‘almost’ and the ‘exact’ are both significant. Instead, like many another here, you retreat into obtuseness. “Oh, that’s like saying you can classify cups with spoons ‘cos …”. Forget it. Look at biology, and screw the analogies.

  2. Joe Felsenstein: Look Erik, I have worked for over half a century on the logic of methods for inferring phylogenies. Since back when there were about 6 people in that field. Up to today, when one of my papers is the 41st most-cited paper in all of science. I wrote the standard book on inferring phylogenies. And I distributed the first widely-distributed package of programs for inferring phylogenies.

    So I know how the algorithms for reconstructing phylogenies work.

    Thank you for gracing this thread with your presence, Sir.

    Joe Felsenstein: And no, they contain no step that tells the program to make sure to put anything called “chimpanzee” in the tree near anything called human. And yet, they keep doing that. Owing to the evidence.

    Evidence such as some specific features of chimpanzees and humans? On the genetic molecular level and/or across more levels?

    Based on such data, naturally they would land near each other in the tree. Wouldn’t a ceramic cup and a ceramic vase do the same in your sophisticated program? I suspect they would, given that they are made from the same material in a similar manner. It would be astonishing if they wouldn’t.

    If the proximity in the tree is your sole point, then with all due respect you are missing the point again. Proximity in the tree by itself does not tell that the one thing came from the other or that they had a common ancestor. An attested unbroken chain of one species evolving into another would say that. Is there such a chain?

    Compare: In linguistics, you may have a group of languages geographically close by, sharing a certain set of features. If there were no literary record at all tracing the evolution of any language group whatsoever, it would be impossible to tell if the similarities are due to common descent or due to contact. Because the similarities can occur either way, due to a break-up of a proto-language or due to areal convergence. Fortunately we have literary records, most notably in Indo-European and Semitic families, so we have material evidence for how a language evolves, what organic evolution looks like and what happens with language contact, and this way we can tell what features to look for when inferring organic evolution as opposed to contact and borrowing. And then this knowledge can be used to classify languages with no literary record.

    In biology, is there anything beyond microevolution to tell that a single species can breed an indefinite variety of species? Unfortunately, what I got from you was reluctance to fix the boundary between microevolution and macroevolution. I don’t see how this can be permissible. It’s like Darwin’s reluctance to define species, “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…” The terms species and variety do not essentially differ? It’s as bad as a linguist saying a specific language and the sum total of all languages over the globe do not essentially differ. And that the difference between a borrowing and a sound law is not too important. Hence common descent, or something.

    People keep telling me I confuse linguistics and biology unnecessarily. But actually I am comparing the scientific standard for evidence across the sciences, fully aware of their different subject matter. The closer I look, the less respect I see for the subject matter when biologists make conclusions based on their classification.

    Joe Felsenstein: If you have problems, ask an expert.

    Well, you are the expert. Feel free to show where I went wrong. This is what this thread is for. It will be most appreciated. Thank you.

  3. Allan Miller: The basic data available to an intelligent human, even one who admits to knowing nothing of genetics, is that the DNA of an offspring is an almost exact copy of that of its parent(s).

    And this proves common descent how? To me it looks like telling that breeding is an intra-species thing. Am I not intelligent or what?

  4. Hi everyone,

    I have a quick question for the biologists. Alternative definitions notwithstanding, the biological concept of a species is fairly well-defined. What about higher taxa? Is there anything objective corresponding to the concept of a genus, family, order, class, phylum or kingdom? I’ve heard it argued that animal phyla correspond to body plans, and I seem to remember reading a remark made by Jerry Coyne over at WEIT some years ago (which I haven’t been able to locate, unfortunately), to the effect that if anything corresponds to the notion of animal “kinds,” then the taxon of “order” would be the best candidate, but don’t quote me on that. More recently, I’ve heard people argue that the cladists are right, and that there is nothing objective whatsoever corresponding to these taxa, which would imply that when species A and B from phylum X are classed in the same genus, and when species C and D from phylum Y are classed in the same genus, all that means is that A and B diverged at about the same time as C and D. That would presumably entail that organisms in any kingdom of organisms belonging to the same genus, family, order, class and phylum would have separated 3 million, 15 million, 60 million, 300 million and about 700 million years ago, respectively (using the times for the first appearance of Homo, hominids, primates, mammaliformes, and chordates). On the other hand, the molecular clock hypothesis has come in for some criticism, too. So what’s the latest thinking on the subject? Thanks in advance.

  5. Erik: Rumraket: No. That is one aspect of one of the predictions. Which is necessary, but not sufficient, to infer common descent.

    I know, which is why it would have been important for the text to have stated so. Instead, the text says, “At a very minimum, these four functions are required to generate a physical historical process that can be described by a phylogenetic tree.” Without nothing further required, it very much leaves the impression that they are saying that those functions are minimally sufficient for common descent.

    For fucks sake nobody says nothing further is required. Can you even fucking read?

  6. Erik: From the other thread.

    Rumraket: (…I stated and you ignored), there was never an organism born that wasn’t the same species as it’s parent, yet evolution happens anyway.

    So reproduction has nothing to do with proving evolution and the evidence for evolution must be something totally different.

    No Erik. No. That doesn’t follow.

    I brought up the point about any organism being born, belonging to the same species as it’s parent, IN THE CONTEXT of YOU asserting that reproduction entails no evolution, because you infer that it is always “within species”.

    I explained why that simple observation is NOT a barrier to evolution.

    So to make it even more clear. I took a principle that you tried to use to argue against evolution, and I explained why it is COMPATIBLE with evolution.

    I’m NOT saying reproduction is irrelevant to inferring common descent. For fucks sake. Take your blinders off. You’r reading with tunnel vision.

    Then why did you (and why does Theobald) bring up reproduction as required evidence for common descent?

    Because it IS relevant you fucking dolt. READ FOR COMPREHENSION, THERE IS A CONTEXT.

    Let’s get relevant.

    PLEASE, let’s.

    So I’m henceforth justified to ignore your references to reproduction?

    No, you aren’t.

    Rumraket: It is that the commonalities can be objectively sorted into nesting hierarchies, and that we know from direct observation that the entities in question(organisms) produce nesting hierarchical patterns over multiple generations when they reproduce .

    Yes, things form patterns when you categorize them. It does not prove common descent though.

    The pattern is a PREDICTION from the mechanism of reproduction, isolation and divergence. The pattern is NOT a prediction by any other process.
    So when we FIND such patterns, that implies they were produced by the mechanism of reproduction.

    The similarity of a cup and a vase tells nothing about which one evolved into the other one, and if they did so at all.

    It is not about mere similarity. For the fifth fucking time.

    Are you cognitively equipped to understand that sentence? Don’t bring it up again or you just go straight to ignore as an ignoramus and idiot-troll. If you feel compelled to bring it up again, remember that it has now been EXPLICITLY STATED that NOBODY says you can infer common descent from MERE SIMILARITY.

    CAN YOU FATHOM IT?

    The relevant proof would be either a direct line of traceable intermediate forms or the general knowledge that those kinds of things morph into each other all the time.

    NO, that would NOT be the “proof”. That might make the case stronger than it already is, but it is not necessary to infer common descent.

    We have a mechanism, and that mechanism makes predictions about what we should find if the mechanism happened in the past too.

    We analyzing living organisms, and it turns out we find what the mechanism predicts. So we infer that, in fact, the mechanism produced the predicted pattern.

    That’s really at it’s most basic level what is going on.

    This does not quite apply to biological species, does it?

    Yes it does. Actually. It just takes longer than single human lifetimes for the changes to become so large that they are intuitively obvious.

    In the same way that some trees grow tall, but it takes really long. Much longer than human lifetimes, for them to reach their full height. That’s an analogy about change and time, not an analogy about reproduction. So don’t tell me now that I think the slow growth of trees is used to infer common descent. I’m making a point about some processes being slow. Get it? I predict you don’t.

  7. Erik:As I have quoted already (emphasis mine),

    In 1950, taxonomist Willi Hennig proposed a method for determining phylogenetic trees based on morphology by classifying organisms according to their shared derived characters, which are called synapomorphies (Hennig 1966). This method, now called cladistics, does not assume genealogical relatedness a priori, since it can be used to classify anything in principle, even things like books, cars, or chairs that are obviously not genealogically related in a biological sense (Kitching et al. 1998, Ch. 1, p. 26; ). Using firm evolutionary arguments, however, Hennig justified this method as the most appropriate classification technique for estimating evolutionary relationships generated by lineal descent.

    What are those firm evolutionary arguments? Did they presuppose common descent or did they argue for it and lay out what proves it?

    Why don’t you read the fucking references? How much of the work YOU should be doing are we required to do, to “convince” somebody obviously hellbent on not being convinced? Go fuck yourself you ignorant sack of shit. Do your own fucking reading, and don’t expect random strangers on the internet to provide you an education for free, or hold your fucking hands through the most obviously basic logical inferences.

  8. Rumraket: If you feel compelled to bring it up again, remember that it has now been EXPLICITLY STATED that NOBODY says you can infer common descent from MERE SIMILARITY.

    Okay. How is it inferred then? Because Darwin said similar this and similar that, even *trifling* similar, and that’s ALL he said.

    Rumraket: NO, that would NOT be the “proof”. That might make the case stronger than it already is, but it is not necessary to infer common descent.

    What we actually need to establish is what is sufficient for common descent, not just necessary.

    Rumraket: Yes [the general knowledge that those kinds of things morph into each other] does [apply to species]. Actually. It just takes longer than single human lifetimes for the changes to become so large that they are intuitively obvious.

    Any evidence for species morphing into another species other than Very Long Time? Any attested unbroken chain of a species morphing into another? Such as between chimpanzees and humans that Felsenstein mentioned? Hopefully the evidence is indeed something other than “this one is similar enough in some ways to that one, therefore it came from that one”.

  9. I would like to take this opportunity to put forward my own Theory of Gravity depending on Magical Monkeys (TGMM). I think the effects we call gravity are caused by magic invisible monkeys holding on to everything and pulling them together. Thus planets, stars, and even galaxies are held together by long chains of these monkeys, who live in a giant invisible barrel in the sky. This is my theory, AND NO ONE CAN PROVE ME WRONG!

    THIS is the standard of evidence that Erik and Mr. Byers would hold us to; demanding proof to eliminate the imaginary, and meanwhile offering no evidence of their own.

    Now I must go, I’m meeting Bertrand Russell for tea somewhere between Earth and Mars.

  10. Rumraket: Yes [the general knowledge that those kinds of things morph into each other] does [apply to species]. Actually. It just takes longer than single human lifetimes for the changes to become so large that they are intuitively obvious.

    When things evolve, they change. A lawful (as in laws of nature) change is regular. What are the attested regularities of biological evolution? Such as, when this sort of thing evolves into that sort of thing, such-and-such changes occur, enabling us to tell apart chance resemblances from natural organic evolution. What is the attested stock example of evolution?

    That done, how does this support universal common descent? Because, in comparison, in linguistics there are sound laws, such as affrication (e.g. from kaesar to caesar) that have been attested independently in different groups of languages. Thus it is a plausibly natural sound law that can indicate organic evolution of a language, but this does nothing to support the common descent of all languages.

  11. vjtorley: Is there anything objective corresponding to the concept of a genus, family, order, class, phylum or kingdom?

    No. Age of divergence, as you note, has been proposed as a criterion, but as you imply there are severe operational problems with that.

  12. vjtorley,

    There is no reason to expect that equivalent ranks (e.g., genus, family, order etc.) are going to be comparable across different groups of organisms with respect to number of taxa or divergence times. For example the order Araneae (the spiders) contains more than 40,000 described species and is probably more than 300 million years old. Conversely, the primates are also grouped in to a single order, but the clade is well under 100 million years old and contains only a few hundred species.

    There have been some recent papers suggesting that particular developmental patterns line up well with phylum classifications, but I’m not sure how much that generalization applies outside of animals.

  13. Erik: Okay. How is it inferred then? Because Darwin said similar this and similar that, even *trifling* similar, and that’s ALL he said.

    God, you’re incompetent at everything, aren’t you? You read the analogy to language, and instead of understanding its purpose you cavilled at an inessential mistake. Meanwhile, in that very area of Origins Darwin actually had quite a discussion about which similarities are meaningful to classification and which are not. The upshot:

    As descent has universally been used in classing together the individuals of the same species, though the males and females and larvæ are sometimes extremely different; and as it has been used in classing varieties which have undergone a certain, and sometimes a considerable amount of modification, may not this same element of descent have been unconsciously used in grouping species under genera, and genera under higher groups, all under the so-called natural system? I believe it has been unconsciously used; and thus only can I understand the several rules and guides which have been followed by our best systematists. As we have no written pedigrees, we are forced to trace community of descent by resemblances of any kind. Therefore we choose those characters which are the least likely to have been modified, in relation to the conditions of life to which each species has been recently exposed. Rudimentary structures on this view are as good as, or even sometimes better than, other parts of the organisation. We care not how trifling a character may be—let it be the mere inflection of the angle of the jaw, the manner in which an insect’s wing is folded, whether the skin be covered by hair or feathers—if it prevail throughout many and different species, especially those having very different habits of life, it assumes high value; for we can account

    [page] 373

    for its presence in so many forms with such different habits, only by inheritance from a common parent. We may err in this respect in regard to single points of structure, but when several characters, let them be ever so trifling, concur throughout a large group of beings having different habits, we may feel almost sure, on the theory of descent, that these characters have been inherited from a common ancestor; and we know that such aggregated characters have especial value in classification.

    Source

    What we actually need to establish is what is sufficient for common descent, not just necessary.

    Why don’t you learn about it, rather than ignoring everything that is brought up only to repeat your ignorant attacks? You seem not to like ID, and yet you write the same idiotic nonsense that the IDiots do.

    Any evidence for species morphing into another species other than Very Long Time? Any attested unbroken chain of a species morphing into another?

    Any evidence of, say, the original Indo-European language, other than the descendants and their patterns of preservation of that language? Can we actually infer ancestry where there is no unbroken chain? The thing is, you have utterly failed to comprehend the language analogy with biologic evolution because all you care about is tearing down evolution, not in understanding how one rightfully infers common descent.

    Such as between chimpanzees and humans that Felsenstein mentioned?

    No, incompetent bozo, Felsenstein is far too intelligent and knowledgeable to write the stupid tripe you do. Humans did not evolve from chimps, nor vice-versa.
    Learn to read properly, Darwin, Felsenstein, and all who took on the hopeless task of educating someone as ineducable as you, and you might learn something for once. Doubtful, of course.

    Hopefully the evidence is indeed something other than “this one is similar enough in some ways to that one, therefore it came from that one”.

    Since it never was that, and you managed to bypass all of the discussion by Darwin of how the evidence actually does matter, it’s unlikely that you’ll ever stray from your caricature of what evolution is.

    Glen Davidson

  14. Erik,

    And this proves common descent how? To me it looks like telling that breeding is an intra-species thing. Am I not intelligent or what?

    I reserve judgement. Sequence commonality certainly does not imply interbreeding capacity.

    If you take two ‘blind’ genomes that are almost fully aligned, it is impossible to tell whether they can interbreed or not – ie, if they belong to the same biological species. The DNA lays out as a series of bases, as you know. If you have AGCTGTCCT … (1 million bases omitted) … CTAGGAT in one alignment, and AGCTGTCCT … (1 million bases omitted) … CTACGAT in the other, they could both be Spotted Sandpipers, or one could be Spotted and the other Common.

    Now, if given the additional info they were both Spotted, would you be happy to say that the sequences are probably commonly descended? If, alternatively, one was Spotted and the other Common, what would your preferred explanation of the near-identity be (which is, in fact, digital identity except for base 1,000,013)?

  15. Guys, whilst I understand the exasperation, could I ask we wind back on the insults please!

  16. Alan Fox:
    Guys, whilst I understand the exasperation, could I ask we wind back on the insults please!

    Agreed, Erik WILL not understand, not because of insufficiency of evidence or clarity of explanation, but for ideological reasons lying outside the nominal scope of this discussion. For him, common descent is defined as wrong, and definitions are impervious to logic or evidence. I’d guess the underlying source of his willful ignorance is inaccessible to us. Ironically, it rests on bad faith discussion, which we aren’t supposed to address even though it’s the for this thread.

    Nonetheless, my own knowledge is minimal enough so that even determinedly stupid questions elicit responses I find useful and educational. I’m glad those able to know what their ideology permits them to know, are so patient and willing to explain to me.

  17. GlenDavidson: Any evidence of, say, the original Indo-European language, other than the descendants and their patterns of preservation of that language?

    There are attested unbroken chains of development in several important branches: From Sanskrit, Ancient Latin, Ancient Greek etc. to their modern daughter languages. Same for Semitic languages. This is how we know (1) that languages can evolve gradually over time and (2) precisely how that happens.

    Anything like that in biology? Seems like you are saying no.

    The thing you quote from Darwin, I quoted the very same thing earlier and stated my objections. Perhaps you missed it.

    GlenDavidson: No, incompetent bozo, Felsenstein is far too intelligent and knowledgeable to write the stupid tripe you do. Humans did not evolve from chimps, nor vice-versa.

    Neither did I say they did. What I actually said to Felsenstein, “Proximity in the tree by itself does not tell that the one thing came from the other or that they had a common ancestor.”

    By now I have clicked around behind the link that Felsenstein gave and bookmarked three potentially interesting papers. It seems to be molecular genetics only, with occasional references to fossils very far and wide. So I was right. The only thing that biological evolution has in its support is genetics. Darwin is totally outdated and forgotten. It should not be called Darwinism anymore, even though his false assumptions seem to be live and well.

    Allan Miller: I reserve judgement. Sequence commonality certainly does not imply interbreeding capacity.

    Interbreeding is as irrelevant as are hybridization and cloning. One species morphing into another is relevant. Very Long Time by itself is not evidence. A track record is.

  18. Erik: There are attested unbroken chains of development in several important branches: From Sanskrit, Ancient Latin, Ancient Greek etc. to their modern daughter languages. Same for Semitic languages. This is how we know (1) that languages can evolve gradually over time and (2) precisely how that happens.

    Didn’t answer the question, did you? How do we know that they all came from the original proto-Indo-European? See, inference works, and you try to deny it by changing the subject.

    Anything like that in biology? Seems like you are saying no.

    Of course there is. Virus evolution, breeding experiments, Lenski, etc. But to really get very far, like to proto-Indo-European, you have to rely on the evidence of what has happened. Like real linguists do.

    The thing you quote from Darwin, I quoted the very same thing earlier and stated my objections. Perhaps you missed it.

    Apparently you missed it, or you wouldn’t have written “Because Darwin said similar this and similar that, even *trifling* similar, and that’s ALL he said.” Complete nonsense, easily shown to be false. You blither on as if you hadn’t written something entirely false, though.

    Neither did I say they did. What I actually said to Felsenstein, “Proximity in the tree by itself does not tell that the one thing came from the other or that they had a common ancestor.”

    Yeah, you wrote:

    Any attested unbroken chain of a species morphing into another? Such as between chimpanzees and humans that Felsenstein mentioned?

    I don’t care what you wrote about your “understanding,” which is meaningless, but your mischaracterization of Felsenstein’s point. Which I’m sure you know.

    By now I have clicked around behind the link that Felsenstein gave and bookmarked three potentially interesting papers. It seems to be molecular genetics only, with occasional references to fossils very far and wide. So I was right. The only thing that biological evolution has in its support is genetics.

    No, you’re wrong about almost everything involved with evolution. Fossils are crucial for certain aspects, although there are hugely more genetic data out there.
    Frequency of reference isn’t the issue, although I wouldn’t expect you to know that.

    Darwin is totally outdated and forgotten.

    Oh, now you say that, long after we called you on your pathetic attacks on Darwin as an authority figure. Yes, no one does or should care about your meaningless attacks on Darwin.

    It should not be called Darwinism anymore,

    First off, it isn’t. You don’t even get that right, but follow the lead of IDists, etc. In the UK they still often stick to that term, true, but scientists in most other places typically don’t bother with that name. “Darwinian” is a little more common, as an adjective denoting natural selection.

    even though his false assumptions seem to be live and well.

    You haven’t shown any of his “assumptions” to be false, except according to your own lack of understanding.

    Glen Davidson

  19. Douglas Theobald: If all known species were completely genetically isolated from one another, and there were no instances of hybrids, it would be very difficult to reasonably justify the postulation of millions upon millions of gradual speciation events in the past.
    Prediction 5.6: Speciations

    The standard phylogenetic tree illustrates countless speciation events; each common ancestor also represents at least one speciation event. Thus we should be able to observe actual speciation, if even only very rarely. Current estimates from the fossil record and measured mutational rates place the time required for full reproductive isolation in the wild at ~3 million years on average (Futuyma 1998, p. 510). Consequently, observation of speciation in nature should be a possible but rare phenomenon. However, evolutionary rates in laboratory organisms can be much more rapid than rates inferred from the fossil record, so it is still possible that speciation may be observed in common lab organisms (Gingerich 1983).

    Confirmation:

    Speciation of numerous plants, both angiosperms and ferns (such as hemp nettle, primrose, radish and cabbage, and various fern species) has been seen via hybridization and polyploidization since the early 20th century. Several speciation events in plants have been observed that did not involve hybridization or polyploidization (such as maize and S. malheurensis).

    Some of the most studied organisms in all of genetics are the Drosophila species, which are commonly known as fruitflies. Many Drosophila speciation events have been extensively documented since the seventies. Speciation in Drosophila has occurred by spatial separation, by habitat specialization in the same location, by change in courtship behavior, by disruptive natural selection, and by bottlenecking populations (founder-flush experiments), among other mechanisms.

    Several speciation events have also been seen in laboratory populations of houseflies, gall former flies, apple maggot flies, flour beetles, Nereis acuminata (a worm), mosquitoes, and various other insects. Green algae and bacteria have been classified as speciated due to change from unicellularity to multicellularity and due to morphological changes from short rods to long rods, all the result of selection pressures.

    Speciation has also been observed in mammals. Six instances of speciation in house mice on Madeira within the past 500 years have been the consequence of only geographic isolation, genetic drift, and chromosomal fusions. A single chromosomal fusion is the sole major genomic difference between humans and chimps, and some of these Madeiran mice have survived nine fusions in the past 500 years (Britton-Davidian et al. 2000).

  20. Erik: Okay. How is it inferred then? Because Darwin said similar this and similar that, even *trifling* similar, and that’s ALL he said.

    No, that’s not how. All of this was explained in the 29+ Evidences for macroevolution by Theobald.

    Again. If all of life shares common descent, then we should be able to arrange multiple, independent, genetic, molecular, and morphological characteristics into highly congruent nesting patterns (the individual trees constructed from different data, must match to a high degree of significance).

    And the reason why this WOULD imply common descent is because the mechanism of reproduction PREDICTS such a pattern. That’s why the inference on the basis of trees works for LIFE, but not for Ceramics, or cars, or other man-made objects that don’t imperfectly reproduce themselves.

    In so far as an organism’s genetic, molecular, and morphological characteristics are not highly congruent and fits into the standard phylogenetic tree, we cannot infer that it shares descent with the rest of life.

    What we actually need to establish is what is sufficient for common descent, not just necessary.

    Yes, we need both.

    Any evidence for species morphing into another species other than Very Long Time?

    Very Long Time is not erected as evidence for anything. Very Long Time, if we had no genetic or fossil data to build trees from, would only be an extrapolation. An entirely reasonable and rational one. If small change takes little time, more change takes more time, and lots of change takes lots of time. This inference is so basic and reasonable only a psychotic and religious individual would deny it. It’s basically like saying that if you can walk 10 steps in 10 minutes, you can walk 20 in 20.

    In other words, what we know from direct observation is that species change over time. But we’ve only been around for a short time to observe it. Like with Very Large trees that grow very slowly. No single human being has witnessed the General Sherman tree grow to it’s present size. Yet it is a trivial inference that it did, because we have seen trees grow.

    It’s the same with evolutionary change of species. What we have seen is enough to infer that, if they can change a small amount in a short time, they can change a lot in a long time. That’s just from the observation of evolution happening in the here and now. If that inference about the tree is reaonable, then the inference about evolutionary change is reasonable. Because the logic supporting it is basically identical.

    Now, we can throw fossil data on top, and demonstrate through that, that large-scale morphological change has happened in the past, and that said large-scale morpholgical change is what gave rise to extant biodiversity.

    Any attested unbroken chain of a species morphing into another?

    You first need to define what an “attested unbroken chain of a species morphing into another” actually is. What does it mean to be unbroken? How fine-grained must the resolution be? Must we have have a photo of a direct ancestor from every single generation? If so, why? Why is THAT the standard of evidence you require to accept large-scale morphological evolution, and what OTHER topic of science or history do you demand a similar standard of evidence for? Were you around to see the General Sherman tree grow from a seed to it’s present size? Do you have a photo of it in 10, or 100 year intervals?

    You wouldn’t want, I presume, to be erecting hypocritical standards of evidence you don’t consistently apply for all your beliefs about science and history.

  21. Erik: When things evolve, they change. A lawful (as in laws of nature) change is regular. What are the attested regularities of biological evolution? Such as, when this sort of thing evolves into that sort of thing, such-and-such changes occur, enabling us to tell apart chance resemblances from natural organic evolution.

    Mutations. The biochemical causes of mutations are known, and happen universally in all life.

    That done, how does this support universal common descent? Because, in comparison, in linguistics there are sound laws, such as affrication (e.g. from kaesar to caesar) that have been attested independently in different groups of languages. Thus it is a plausibly natural sound law that can indicate organic evolution of a language, but this does nothing to support the common descent of all languages.

    The fact that mutations happen aren’t invoked as an indication which alone implies that all life presently known to exist on Earth, shares common descent.

  22. GlenDavidson: Virus evolution, breeding experiments, Lenski, etc. But to really get very far, like to proto-Indo-European, you have to rely on the evidence of what has happened. Like real linguists do.

    So nothing beyond microevolution?

    Because, you see, from Ancient Latin to modern Romance languages etc. is not comparable to microevolution. It’s macroevolution. Indo-European proto-language was well established before Lithuanian became common knowledge. Lithuanian confirmed the reconstructions in such a manner that it’s called the living dinosaur in the Indo-European family.

    So there’s nothing like that in biology.

  23. dazz:

    So Theobald said we should be able to observe speciation, even if very rarely. Then he lists hemp nettle, primrose, radish and cabbage, maize, fruitflies and even house mice. The thing missing in this list: Into what other species did all those species turn to?

  24. Rumraket: You first need to define what an “attested unbroken chain of a species morphing into another” actually is. What does it mean to be unbroken? How fine-grained must the resolution be?

    This is something we are sorting out in this thread: What is the standard for evidence in biology?

    Rumraket: Mutations. The biochemical causes of mutations are known, and happen universally in all life.

    I know. And all living organisms are cellular and they reproduce.

    Any mutations beyond microevolution so that you could say speciation is observable?

    And, as I have pointed out earlier, even this would not prove common descent, just like the mere fact that languages change, sometimes radically and rapidly, they diverge, converge, pidginize etc., but none of this implies common descent.

    There is no common descent in linguistics. Darwin thought he knew better and you agree. What’s the evidence?

  25. Erik: So nothing beyond microevolution?

    Whatever. The fact is that we’d know about the language evolution without texts, too. Because some of us don’t deny the evidence left from it.

    Because, you see, from Ancient Latin to modern Romance languages etc. is not comparable to microevolution. It’s macroevolution.

    I actually don’t care, you know, even though one could quibble over the matter. The point is that we have copious evidence of Greek and Latin evolving from a common ancestor without any textual evidence, and an intelligent linguist would acknowledge that with or without textual evidence of other languages evolving. That you dance around the fact to stick to your unreasonable demands in biology only shows that you’re not willing to accept what the evidence of common descent shows where you don’t like it.

    Indo-European proto-language was well established before Lithuanian became common knowledge. Lithuanian confirmed the reconstructions in such a manner that it’s called the living dinosaur in the Indo-European family.

    Yes, and evolution was well established before genetics confirmed it, too. That’s what happens with good theories.

    So there’s nothing like that in biology.

    Sure there is, there are fossils. You didn’t hear any language change to another one, did you? You’re relying on “fossil evidence” to indicate certain changes in language, and we have similar (though not as clear-cut, to be sure) evidence from fossils. But the fossils can go back to a kind of “proto-Indo-European,” at least in lines that fossilize reasonably well, like most vertebrates do. Language evolution lacks similar evidence of the larger scale of changes

    Glen Davidson

  26. Erik: There is no common descent in linguistics.

    No, you don’t even know the difference between common descent and universal common descent. There’s lots of common descent in linguistics, something you should know. Universal common descent is argued, but the evidence for universality of common descent that exists in biology is lacking from languages.

    The important fact is that real linguists would be open to the sort of evidence of universal common descent that exists in biology, if it existed in languages.

    That’s another fact that you keep ignoring, the whole point of you blowing up the mistake Darwin made is that if the evidence of derivation from a common ancestor that we find in life existed in language, real linguists would accept that evidence. You could only do so by applying a double standard. Indeed, you can only argue as you do because you are using a double standard, since you use the fact that languages lack the kind of evidence needed to show universal common descent in order to disparage the fact that life actually does have evidence for universal common descent. The trouble is that if you used the same standard for both you’d have to admit that there is great evidence for universal common ancestry in life but not in languages.

    Glen Davidson

  27. Rumraket: If all of life shares common descent, then we should be able to arrange multiple, independent, genetic, molecular, and morphological characteristics into highly congruent nesting patterns (the individual trees constructed from different data, must match to a high degree of significance).

    Yes, we should. And that would be sufficient? In addition, I would expect a track record of gradual speciation, some indication that species can actually evolve into other species, that it’s a natural thing for them across kingdoms, plants into animals no problem.

    Rumraket: And the reason why this WOULD imply common descent is because the mechanism of reproduction PREDICTS such a pattern.

    Predicts in what sense? I expect something like: There were those two-or-more such-and-such species that implied such-and-such common ancestor and that ancestor was found in the fossil record or so. Or, there were those two-or-more such-and-such species that implied such-and-such other species and those other species were found.

    Predicted in this sense, like Mendeleev predicted germanium? Any such cases in the literature?

    GlenDavidson: You didn’t hear any language change to another one, did you?

    Actually, I have. Where I live, the language change has been rapid within two decades. There was a pidginization effect with two neighboring languages.

    And so have you seen at least, e.g. new words formed, perhaps a morphological feature altered so that an aspect of grammar is realigned. Has happened where I live.

  28. Erik: GlenDavidson: ou didn’t hear any language change to another one, did you?

    Actually, I have. Where I live, the language change has been rapid within two decades.

    And so have you seen at least, e.g. new words formed, perhaps a morphological feature altered so that an aspect of grammar is realigned. Has happened where I live.

    So, not a different language?

    Thought not.

    Glen Davidson

  29. Erik: So nothing beyond microevolution?

    Because, you see, from Ancient Latin to modern Romance languages etc. is not comparable to microevolution. It’s macroevolution. Indo-European proto-language was well established before Lithuanian became common knowledge. Lithuanian confirmed the reconstructions in such a manner that it’s called the living dinosaur in the Indo-European family.

    So there’s nothing like that in biology.

    Nobody has been alive to witness the entire transition from Ancient Latin to Modern Roman. The transition is inferred from snapshots in time.

    So, in fact, biologic and linguistic macro-evolution on that scale is inferred, not directly observed. In this way, they are analogous.

  30. Erik: So Theobald said we should be able to observe speciation, even if very rarely. Then he lists hemp nettle, primrose, radish and cabbage, maize, fruitflies and even house mice. The thing missing in this list: Into what other species did all those species turn to?

    They evolved from ancestors and became the modern species we see. Cabbage (for example) is not a single species, it is an entire family. There are many known species of cabbage that evolved from a common ancestral species.

  31. Erik: This is something we are sorting out in this thread: What is the standard for evidence in biology?

    So answer my question. You brought up the concept of an unbroken chain, now you’re running away from explaining exactly what that is. You want me, instead, obviously as a diversion, to try to answer what the “standard of evidence” is in biology.
    A question so broad it is practically meaningless.

    I know. And all living organisms are cellular and they reproduce.

    And you asked for what the cause of change is, and I answered. I didn’t say that the mere fact that mutations happen proves that all life shares common descent.

    I have already explained what it is that makes it possible to infer common descent.

    Any mutations beyond microevolution so that you could say speciation is observable?

    You’re very confused. It is becoming clear that you can’t keep track of the multiple discussions here. Nobody said mutations prove common descent. Or that mutations are macroevolutionary events.

    You just asked about what-it-is, that makes species A change into species B.

    The answer is mutations. Nobody has claimed, or implied, that the mere fact that mutations is the cause of species A changing into species B, proves that all life that is known to exist on Earth shares common descent. Nobody makes such an inference.

    I truly have your best interest at heart when I say you should probably take a small break and try to sort out exactly what you’re asking, and exactly what people who respond to you, are responding to. Instead of, apparently as you do, think every sentence anyone writes is supposed to constitute a standalone proof of common descent.

    And, as I have pointed out earlier, even this would not prove common descent

    Nobody cares, because nobody disagrees.

    Mutations happen therefore all known life shares common descent is an inference NOBODY makes.

    And when I brought up mutations, I was not answering the question “what is the proof of common descent”? I was answering your question about the general cause of change, if and when speciation happens.

    There is no common descent in linguistics. Darwin thought he knew better and you agree.

    I agree with what, specifically? Don’t speak to me in generalities, or make vague unferenced hints to Darwin’s putative thoughts. Tell me exactly what it is Darwin said, with a quote of Darwin. And then ask me if I agree. I don’t take your word for it about what Darwin thought he knew. Give me openly accessible references, or direct quotes, or shut up about Darwin.

    What’s the evidence?

    For what, specifically? Common descent? If so, this: 29+ Evidences for Macroevolution
    The Scientific Case for Common Descent
    .

  32. Erik: Rumraket: If all of life shares common descent, then we should be able to arrange multiple, independent, genetic, molecular, and morphological characteristics into highly congruent nesting patterns (the individual trees constructed from different data, must match to a high degree of significance).

    Yes, we should. And that would be sufficient?

    In combination with the known fact that the mechanism of reproduction inexorably leads to data that can be objectively sorted into multiple, independent but highly congruent nesting patterns of genetic, molecular and morphological characteristics (aka phylogenetic trees). Yes. That would be sufficient.

    In addition, I would expect a track record of gradual speciation, some indication that species can actually evolve into other species, that it’s a natural thing for them across kingdoms, plants into animals no problem.

    All of those would be bonuses, but are not necessary.

    The last one is nonsensical. Why would plants become animals? That never happened even once in the entire history of life, as far as we are aware. Plants and animals share a common ancestor, but it was neither a plant nor an animal. In the same way that mammals and birds share ancestry, but their common ancestor was neither a bird nor a mammal.

    Rumraket: And the reason why this WOULD imply common descent is because the mechanism of reproduction PREDICTS such a pattern.

    Predicts in what sense?

    Is there multiple senses of predict?

    I expect something like: There were those two-or-more such-and-such species that implied such-and-such common ancestor and that ancestor was found in the fossil record or so. Or, there were those two-or-more such-and-such species that implied such-and-such other species and those other species were found.

    I can barely parse out what you’re asking for here. Is it predicted fossils?

    Predicted in this sense, like Mendeleev predicted germanium? Any such cases in the literature?

    So fossils, you want predicted fossils. Yes, there are cases of those in the literature. Off the top of my head, Archeopteryx.

    Predicted by none other than Charles fucking Darwin .

  33. J-Mac

    Write it, post it, then go to Moderation Issues and request that it be approved.

    You may already have posting privileges.

  34. J-Mac,

    I wrote this for you, here a while ago. It might be helpful to you if you followed the link and read the comment.

  35. Mung:
    Fun thread.

    You find the evidence for common descent compelling. Is there some unwritten law by which believers can’t set other believers straight on evolution related stuff?
    Just curious

  36. Erik, the questions here may have escaped notice. I’m trying to concentrate on molecular phylogeny – sequence data – in order to establish where you place your razor between reasonable and unreasonable inference, based on sequence commonality.

    The only known mechanism generating long stretches of sequence identity is template copying of DNA, as occurs during reproduction. Would you rule this out in the case where the 2 sequences came from different species? If so, on what grounds? And what would you replace it with?

    Do we need 2 causes for sequence identity, one within species and one between?

  37. dazz: You find the evidence for common descent compelling. Is there some unwritten law by which believers can’t set other believers straight on evolution related stuff?

    In what sense is Erik “a believer.” Just curious.

    Yes I find common descent compelling. But is there some unwritten law by which “skeptics” can’t challenge their beliefs and the beliefs of other “skeptics”?

    Is there a standard for evidence in biology, and if so what is it?

  38. Allan Miller, who doesn’t care for analogy, appears to prefer metaphor instead. What is the advantage that metaphor has over analogy? Just wondering.

  39. Mung: In what sense is Erik “a believer.” Just curious.

    Call him a theist if you will

    Mung: Yes I find common descent compelling

    OK, go ahead then. Why is that?

    Mung: But is there some unwritten law by which “skeptics” can’t challenge their beliefs and the beliefs of other “skeptics”?

    I’ve seen that happen here multiple times. Do you need examples?

    Mung: Is there a standard for evidence in biology, and if so what is it?

    Erik asks in this post “Specifically, what is the evidence for common descent?”

    So will you help shed some light on the topic at hand?

  40. petrushka: In both biology and language the inferences are probabilistic.

    Fortunately there’s only one single right way to do probabilities, therefore common descent is a fact.

  41. Mung,

    Allan Miller, who doesn’t care for analogy, appears to prefer metaphor instead. What is the advantage that metaphor has over analogy? Just wondering.

    You could perhaps wonder with a little more clarity. I don’t know what you mean.

  42. dazz, to Mung:

    Erik asks in this post “Specifically, what is the evidence for common descent?”

    So will you help shed some light on the topic at hand?

    Ooh, yes. Mung, tell us in your own words why you accept common descent.

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