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. Robin: Such folks really can’t wrap their head around trait blending or recessive vs dominant traits and the like.

    I can just fine. I can even wrap my head around the fact that recessive traits emerge every now and then. If recessive traits of our ancestral past were natural, they should be visible more often, fins or gills occasionally. But actually, whenever they do, it’s unnatural.

  2. Erik: I can just fine. I can even wrap my head around the fact that recessive traits emerge every now and then. If recessive traits of our ancestral past were natural, they should be visible more often, fins or gills occasionally. But actually, whenever they do, it’s unnatural.

    Why?

  3. Allan Miller: Yes. Use molecular data. Then use more of it. That’s what I’ve been talking about all along.

    You observe similarities. Some things are more similar to each other than other things. That’s what I’ve been talking about all along.

    John Harshman: So we agree that the tree is a real thing, not a human construct, and such in need of explanation.

    Yes. And the explanation is that similar things go together. Always did.

    John Harshman: Common descent didn’t change the principle of nested hierarchy.

    Correct.

    John Harshman: What it did was provide an explanation of why that hierarchy exists.

    In some sciences, speculative unobserved explanations don’t count, because one speculative assumption is as good as any other. If there is nothing better, it’s indicative of a science in a crisis – a theoretical or intellectual crisis. It’s not good for anyone to perpetuate the crisis.

    Economics has been in a similar crisis for at least half a century. One way out of it is to recognize the sadly unfounded speculative state of the science and therefore experiment safely and cautiously, counsel lawgivers extremely sparingly, and internally encourage more free speech to find a better theoretical framework.

    John Harshman: It’s been done most often with everyone’s favorite genetics lab animal, Drosophila melanogaster.

    This one? I hope I have the right picture this time https://i.wp.pl/a/f/jpeg/25543/mucha_okladka2.jpeg

    Thanks for the references. Must love Coyne et al.

  4. Erik: Hmm. How about the fact that they are similarities? Wouldn’t a big cup and a small vase, amphoras and bottles also group like “nested identities” in the shape of a tree? Is there a way to avoid this?

    You need to quit with your insipid non-thought, and realize that it’s how organisms fit a tree, which is like languages do, and akin to how family trees exist. Just about any kind of items could be classified into tree order, but vertebrates generally fit into a tree classification according to heredity.

    You certainly should understand how languages branch off into other languages that then share inherited words and other characters. That’s what you should take from Darwin’s analogy with language evolution, not your “gotcha” over universality, that no one with a bit of sense cares about. You simply don’t get the kinds of groupings that you get with languages and organisms without heredity. Only a few manufactured goods have analogous branching, the only ones I know about being highly conservative religious items.

    You could group automobiles into tree classification, but they don’t demand such a classification, as languages and organisms do. That’s because automobile designs are portable, features readily cross manufacturing and other lines. Computer chips didn’t even begin in automobiles, yet they easily “jumped into” cars from Intel or wherever, because design isn’t as limited as heredity is, or as languages generally have been. Languages, of course, are also not as limited in picking up words from unrelated languages as vertebrates generally are limited in their sources of DNA, but until recently languages didn’t pick up too many to obscure the evolutionary patterns (which they may do eventually, though not yet).

    The real point is, creationists, IDists, and whatever Erik is, would certainly be telling us that evolution entails the current trees if it turned out that they didn’t naturally fit into such a classification scheme. They’d be right, for once. But since organisms do have the derivative natures that naturally fit the tree classifications, they have to do everything they can to deny that it is an entailment of evolutionary processes (and certainly not of any kind of intelligence).

    Glen Davidson

  5. Erik: According to Rationalwiki, L-gulonolactone oxidase synthesizes vitamin C.

    Correct. However — and this is crucial — the L-gulonolactone oxidase pseudogene does not. And that’s what the question was about.

  6. Erik: You observe similarities. Some things are more similar to each other than other things. That’s what I’ve been talking about all along.

    John Harshman: So we agree that the tree is a real thing, not a human construct, and such in need of explanation.

    Yes. And the explanation is that similar things go together. Always did.

    That isn’t an explanation. The tree isn’t just about similarities. It’s about a nested hierarchy. Just putting similar things together doesn’t make a nested hierarchy from data. Your idea about cups and vases wouldn’t work in practice, as different people, looking at different aspects of the objects, would come up with different classifications. That’s because there is no objective, real nested hierarchy of pottery.

    John Harshman: Common descent didn’t change the principle of nested hierarchy.

    Correct.

    John Harshman: What it did was provide an explanation of why that hierarchy exists.

    In some sciences, speculative unobserved explanations don’t count, because one speculative assumption is as good as any other. If there is nothing better, it’s indicative of a science in a crisis – a theoretical or intellectual crisis. It’s not good for anyone to perpetuate the crisis.

    There is no such crisis in evolutionary biology. You are very quick to pass judgment on fields you know nothing about, as you admit. And yet you accept that Indo-European is a real language family, with the languages connected by descent from *PIE. Why, since nobody has ever seen a speaker of *PIE or seen an ancient document written in *PIE?

    This one? I hope I have the right picture this time https://i.wp.pl/a/f/jpeg/25543/mucha_okladka2.jpeg

    There are a lot of similar looking species of fruit flies, but I have no reason to doubt that the picture is what you suppose. Why?

  7. Erik,

    According to Rationalwiki, L-gulonolactone oxidase synthesizes vitamin C.

    The claim is that this gene due to the stop condon does not synthesize vitamin c in humans and great apes. A common pseudo gene is seen as evidence for common descent between man and great apes.

    There is evidence (2013) that this gene (expressing the L-gulonolactone oxidase enzyme) is active during embryo development and the stop condon is created by RNA editing after embryo development which puts the common pseudo gene claim in doubt.

  8. GlenDavidson: You simply don’t get the kinds of groupings that you get with languages and organisms without heredity.

    But there’s a catch. With languages we know that there’s heredity, just as a side-effect of being aware of history. So we know about heredity by independent observation. Moreover, we know that to follow the line of descent, we must consciously ignore the most obvious superficial similarities and observe other reconstructed similarities that occasionally have little to do with the superficial output.

    With species, the heredity is not observed. We form big groupings by obvious large-scale constitutional similarities and, in parallel, we *separate* minor groupings by minor differences. The common descent assumption has no effect on the procedure, essentially extraneous. Somewhat of a difference.

  9. How are automobiles classified? Certainly not by trees, even though they could be, because trees would only suggest relationships that don’t exist. They’re classified by make, model, year, that sort of thing. There are some “evolutionary relationships” that sometimes are included into classifications.

    The Corvette has sort of evolved over the years. But what gave rise to carbon fiber in Corvettes? Nothing, it’s just an engineering material that engineers decided to use. You get nothing like that in organisms. Titanium is another material that just gets put into Corvettes, no antecedent whatsoever. And I’ve mentioned computers previously, as I could a host of other revolutionary changes that have no counterparts in organisms. Product “evolution” may well be thought to occur, but it has never been anything as derivative as biologic evolution typically has to be.

    Most any kind of thing could be classified into tree classification, but few are because there is nothing meaningful about such trees, save for hereditary lineages like those of organisms and languages. Trees are used in those cases because they actually make sense of the data.

    Glen Davidson

  10. Erik: But there’s a catch. With languages we know that there’s heredity, just as a side-effect of being aware of history.

    I think we know that about organisms, too.

    So we know about heredity by independent observation. Moreover, we know that to follow the line of descent, we must consciously ignore the most obvious superficial similarities and observe other reconstructed similarities that occasionally have little to do with the superficial output.

    It’s strange that you act like this is something that sets language evolution apart from organic evolution conceptually, rather than it being a great example of how heredity forms the patterns that betray the evolution of both languages and organisms. I can only think that you do so because your opposition to biologic evolution comes first, so instead of using language evolution as confirming that such patterns and retained accidental features must appear in any sort of derivative hereditary scheme, you pretend that the tree pattern only is entailed for languages.

    With species, the heredity is not observed.

    The effects are observed.

    We form big groupings by obvious large-scale constitutional similarities and, in parallel, we *separate* minor groupings by minor differences.

    Yes, this sort of pattern (congruences of homologies) is entailed by organic evolution, as it is with language evolution (the latter with lesser, and different, constraints, but the patterns of hereditary derivation are obvious in both).

    The common descent assumption has no effect on the procedure, essentially extraneous. Somewhat of a difference.

    So we don’t have to know about evolution to find the patterns entailed by evolutionary processes. That’s kind of the point.

    Glen Davidson

  11. GlenDavidson: Yes, this sort of pattern (congruences of homologies) is entailed by organic evolution, as it is with language evolution (the latter with lesser, and different, constraints, but the patterns of hereditary derivation are obvious in both).

    In my view, the procedures are not similar at all. What sort of constraints are observed when doing biological groupings, say on the morphological level? How was it deduced that such constraints should be observed? In linguistics it’s common knowledge on completely independent grounds that there are Wanderwörter like “internet” that must be raked out of the data when tracing heredity. Is there anything like this in biology? And, more crucially, how was such an element first detected?

    The trees on the other hand are similar, yes. Thence my solid impression that you can build a tree on anything and you can project any sort of meaning to it, so in order to truly know what it means you have to go to some independent source. Language trees represent heredity because the evolution of language is documented throughout history and this is how we know that languages can do that sort of thing. How do we know that species do roughly the same sort of thing? It should be clear that the tree by itself proves nothing. The tree is not a prediction, it’s an inevitable consequence when you group things, anything, by some well-specified characteristics.

  12. colewd: There is evidence (2013) that this gene (expressing the L-gulonolactone oxidase enzyme) is active during embryo development and the stop condon is created by RNA editing after embryo development which puts the common pseudo gene claim in doubt.

    Please post a complete citation for this claim. It makes no sense, by the way, since the stop codon is in the DNA, not just the RNA. It’s vaguely possible that RNA editing would turn the stop codon in the mRNA into a sense codon, but I’d like to see that.

  13. Erik: In my view, the procedures are not similar at all. What sort of constraints are observed when doing biological groupings, say on the morphological level? How was it deduced that such constraints should be observed?

    You’d actually have to study into it. Darwin mentioned Owen, the latter did a lot of the work in distinguishing homologies from analogies, which he did not link to evolutionary theory at the time.

    In linguistics it’s common knowledge on completely independent grounds that there are Wanderwörter like “internet” that must be raked out of the data when tracing heredity. Is there anything like this in biology? And, more crucially, how was such an element first detected?

    Horizontal gene transfers were first apparently observed in prokaryotes (presumably bacteria), as relatively unrelated strains had very similar genes in some cases. Later, the transfer of genetic material was observed to have occurred over relatively short periods of times. Unfortunately, drug resistance genes often transfer.

    The trees on the other hand are similar, yes. Thence my solid impression that you can build a tree on anything and you can project any sort of meaning to it,

    Yeah, instead of actually thinking it through and noting that tree classification is not used for manufactured goods (except for some very conservative cases), you just assumed that it was imposed upon biology. Well, it wasn’t. You can impose tree classification, but it’s rarely done outside of phenomena that are hereditary and derived. Why aren’t trees used for classifying cars? It’s because trees are not an informative means of classifying them.

    so in order to truly know what it means you have to go to some independent source.

    Why don’t you try to figure out why trees aren’t used for classifying computer chips, the Osprey, minerals, or the elements? It makes no sense to classify elements according to trees, and it makes eminent sense to classify them in rows and columns, as in the periodic table. Scientific classification is supposed to be meaningful, and generally is, and your assumption that it isn’t is your fault.

    Language trees represent heredity because the evolution of language is documented throughout history and this is how we know that languages can do that sort of thing. How do we know that species do roughly the same sort of thing?

    Because they form the trees without being forced, because accidental features cluster along with congruences in morphologic homologies, because species aren’t hard and fast categories (can’t be, if evolution is true), and because you haven’t in the slightest shown that any kind of classification scheme for life is meaningful except the one that is entailed by derivation of species from ancestral species.

    Glen Davidson

  14. Erik: In my view, the procedures are not similar at all. What sort of constraints are observed when doing biological groupings, say on the morphological level? How was it deduced that such constraints should be observed? In linguistics it’s common knowledge on completely independent grounds that there are Wanderwörter like “internet” that must be raked out of the data when tracing heredity. Is there anything like this in biology? And, more crucially, how was such an element first detected?

    Your view is incorrect. Your Wanderwörter would just create noise if you left them in, and with a big enough data set wouldn’t prevent the true tree from being discerned. And in general you know they’re Wanderwörter because they don’t fit the rest of the data. The analogy in biology would be horizontal transfer. In most cases it’s rare enough that nothing needs to be done to correct for it. And it’s detected in the same way you detect loan words: largely by incongruence with other data. You continue to introduce nonexistent differences between language phylogeny and biological phylogeny, apparently for no purpose other than to allow you to accept one while rejecting the other.

  15. GlenDavidson: Because they form the trees without being forced…

    I know. That’s the problem https://s-media-cache-ak0.pinimg.com/originals/49/d5/66/49d5669cc6ce8a2ec5a461ae32d52f21.jpg See how things evolve from a common ancestor just so, effortlessly?

    Sorry, but the tree is just a way to illustrate the simple fact that you are grouping stuff. This is all it means. Further meanings to the tree require other independent evidence. If ability to draw the tree is all that is required in biology to assert common descent, well, things used to be different. The tree has been there in biological taxonomy all along, but biologists were not overly assumptive and declarative about it.

    John Harshman: Your view is incorrect. Your Wanderwörter would just create noise if you left them in, and with a big enough data set wouldn’t prevent the true tree from being discerned.

    Nope. Your view is incorrect. “Big enough data set” is the noise. Data sorted out by relevant criteria becomes the data set actually worth analyzing. Your way is the sure way via lack of methodological care to random outcomes.

  16. Erik: I know. That’s the problem https://s-media-cache-ak0.pinimg.com/originals/49/d5/66/49d5669cc6ce8a2ec5a461ae32d52f21.jpg See how things evolve from a common ancestor just so, effortlessly?

    No, that’s nothing like a tree, and it indicates nothing with respect to common ancestry (some continuity is suggested, and, of course, exists).

    Sorry, but the tree is just a way to illustrate the simple fact that you are grouping stuff. This is all it means.

    That’s all it did mean, until people figured out what caused it.

    Further meanings to the tree require other independent evidence.

    Independent evidence is what is used to make a proper tree. You seem not to get the most basic aspects phylogeny.

    If ability to draw the tree is all that is required in biology to assert common descent, well, things used to be different.

    That isn’t all that’s required, sound reasons are needed to draw a legitimate tree.

    The tree has been there in biological taxonomy all along, but biologists were not overly assumptive and declarative about it.

    Of course they weren’t, they needed a theory and further evidence to support the derivative nature of the tree. You can’t explain why variations on “ovis” and “fart” exist throughout most of the Indo-European languages without positing an ancestral language we’ve never heard, proto-Indo-European, nor can you explain the variations of genes in chimps and humans without positing an ancestral species we’ve never seen that bequeathed those genes to both branches.

    Glen Davidson

  17. Erik: Your way is the sure way via lack of methodological care to random outcomes.

    And yet in phylogenetics we don’t get random outcomes. How would you explain that?

    Sorry, but the tree is just a way to illustrate the simple fact that you are grouping stuff. This is all it means.

    Not if the tree is a description of the underlying data and those data prefer a particular tree strongly. You are correct that anything can be organized into a tree. But in most cases the data don’t demand to be organized that way, and different people would come up with different trees. That isn’t how it works with languages or species, though. Language trees aren’t just a way to illustrate the simple fact that you are grouping stuff, are they? Once again you make an attempt to introduce spurious differences to allow you to accept the language trees as real but reject the biological trees as unreal.

    And the fact that there were hierarchical classifications before Darwin is not an argument against common descent. An effect can be visible even if you don’t know the cause, but the cause explains the effect. And you have so far been unable to describe any other cause for the nested hierarchy of life.

  18. Erik,

    I can just fine. I can even wrap my head around the fact that recessive traits emerge every now and then. If recessive traits of our ancestral past were natural, they should be visible more often, fins or gills occasionally. But actually, whenever they do, it’s unnatural.

    Oh good grief. That’s not what ‘recessive’ means.

  19. GlenDavidson: That isn’t all that’s required, sound reasons are needed to draw a legitimate tree.

    And hopefully those sound reasons are this time something better than yet another “we can draw a tree”. What are they?

    John Harshman: Not if the tree is a description of the underlying data and those data prefer a particular tree strongly.

    Do you have an argment for this? Logical or scientific, either will do.

    John Harshman: And the fact that there were hierarchical classifications before Darwin is not an argument against common descent.

    Correct. Not for either. Either there is good evidence for common descent completely apart from trees or your argument for “my tree can do better than anyone else’s” is totally mind-blowing and shuts down all skepticism.

  20. If you take a bunch of vessels and arrange them as a tree on one character (why in heck would you choose to arrange them as a tree? … ah, let it pass) there is no expectation you could get the same tree with another character. Say I’ve got a blue Wedgewood cup, yellow amphora with a missing handle, mug saying “World’s Greatest Biologist”, and so on.

    So I arrange them into a tree. Amphora goes here, cup goes there, mug goes there. Now I want to arrange them by colour. OK [shuffle shuffle]. Now by damage [shuffle shuffle]. Each time, I get a different arrangement.

    Now, I take a set of genes from a taxon. I build a tree on the pattern of identities in that set. ‘Cos, y’know, you can make a tree out of anything.

    Now do this with a completely different set of genes from the same taxon. Fuck me, it’s the same tree. Let’s take another. Nope, same. Even looking at ‘scratches’ – the kind of difference that makes no difference, and yes there really are such things – they arrange into the same tree.

    How so? It’s as if the vessel type, and colour, and maker’s marks, and blemishes, all group in the same way. Common descent says why. ‘I can arrange anything into a tree’ doesn’t.

  21. John Harshman: Language trees aren’t just a way to illustrate the simple fact that you are grouping stuff, are they?

    Actually, they are. But the specific way they are drawn when the goal is to demonstrate descent, e.g. how you go about eliminating the frigging noise first (linguistic data is very sensitive to noise and the tree can be anything if you don’t sort out the data properly) leads hopefully to the desired result. And the hope is justified because we know from millennia of written history how language undergoes change. And we acknowledge the fact that the trails stop at some point. To draw trees beyond that is highly speculative, to put it kindly. You can get a “world tree” only if your selection of data is too broad and generous, based on the wrong criteria or irrelevant criteria or hardly any criteria at all.

    By Darwin’s standard, biology does not have such a point. There is always some similarity or another to draw a tree on.

    GlenDavidson: You can’t explain why variations on “ovis” and “fart” exist throughout most of the Indo-European languages without positing an ancestral language

    At the same time, you *cannot* posit an ancestral language for languages that have variations of “internet”. Only core vocabulary matters, the rest is irrelevant for positing common ancestry. Historical sound laws and syntagmatic properties matter more than current superficial resemblance.

    In biology, however, you can go by “homologies”, e.g. both humans and apes have brains in their skulls, therefore common descent, never thinking any further what this means: Something ape-like must have bred bred humans, and earlier something crawled out of the water and began breeding mammals. Can species do this sort of thing? These things cannot just happen. “Natural selection” is insufficient to explain this. There must be some further laws of nature at work that bring about new species by leaps and bounds. Based on the same material, yes, therefore “homologies”, but it’s not those earlier primitive species breeding new species by themselves. Dogs have been around humans for millennia now, so they have had time to observe the survival power of humans. I bet they want to troll the internet like their masters do. So why don’t they evolve in that direction? (it’s just an analogy. Darwin used analogies too. I don’t even have a dog.)

  22. It’s interesting that someone like Erik, who can be seen learning in this thread starts the OP with what seems like a genuine offer

    Darwinists are welcome to present their evidence.

    but we’ve quickly seem that Erik does not start from a neutral position, he’d already decided that common descent is nonsense. And this certainty persists, despite the ongoing education he’s receiving.

    Why such certainty Erik? You’ve already been shown to have insufficient understanding several times during your learning phase. Is it not time to simply say It seems this is more complex then I had assumed, I’ll do some learning on my own and come back. Most people would do so at this point, once their realize their surface understanding is just that.

    You made a claim early in the thread you understood evolution perfectly. No, you don’t.

    But actually, whenever they do, it’s unnatural.

    Some dressing with your salad?

  23. OMagain: Erik does not start from a neutral position, he’d already decided that common descent is nonsense.

    Actually, nonsense responses presented as evidence started to arrive quickly and this led to its logical conclusion. And of course I did not start from a neutral position. As seen from the OP, I had read at least one book, said to be foundational to the topic. Not a good idea to start a discussion completely unprepared.

  24. Erik: And hopefully those sound reasons are this time something better than yet another “we can draw a tree”. What are they?

    One is that I know the difference between what I wrote and the caricature of “we can draw a tree” that you keep recasting it into. You sound a lot like Byers, you know, “it’s just a line of reasoning,” but you really should be thinking better than Byiers does.

    The point is the justification for drawing the tree.

    On the other hand, obviously the data aren’t necessarily about trees per se it’s about derivation. Trees just illustrate the derivation and indicate how it occurs repeatedly. They’re entailed by evolution, so they’re one sort of prediction by which evolutionary theory is tested.

    What would we expect bird wings to be made of? If they evolved from dinosaurs, and even if they evolved from other reptiles, we’d expect bird wings to be formed out of the articulated bones of the forelimbs of their terrestrial ancestors. And what do we find? We find bird wing bones to develop from the bones of their terrestrial ancestors, only the separate bones that became articulated in terrestrial theropods now become fused into rigid bird wing bones.

    Of course then there are the transitionals, like Archaeopteryx with its many articulations that are absent from modern birds, teeth, long bony tail, etc. Chimps would be seen as transitionals were they only known as fossils, albeit not ancestral. Transitional forms must have existed, and they do, from Tiktaalik to the cynodonts, and on to the many hominin fossils.

    This fits the unforced trees (unlike your non-tree), but that’s not necessarily the point. The point is derivation and the evidence it leaves behind. This happens in languages and in life, and between you and Byers, it’s the latter who is more consistent, denying language evolution that isn’t attested to by historical documents.

    Glen Davidson

  25. Erik:

    John Harshman: Language trees aren’t just a way to illustrate the simple fact that you are grouping stuff, are they?

    Actually, they are. But the specific way they are drawn when the goal is to demonstrate descent, e.g. how you go about eliminating the frigging noise first (linguistic data is very sensitive to noise and the tree can be anything if you don’t sort out the data properly) leads hopefully to the desired result.

    Oh, that’s obvious double-speak. First, trees are just about grouping stuff, then when they’re constructed to demonstrate descent it’s entirely different.
    Except that they’re generally illustrated as trees for categorization, and there’s no break from when they’re meant to demonstrate descent. You’re just making up an artificial break.

    And the hope is justified because we know from millennia of written history how language undergoes change.

    Yes, and real linguists can and do go beyond what has been demonstrated by historical data, because they’re not denialists who won’t accept that effects point to very real causes.

    And we acknowledge the fact that the trails stop at some point. To draw trees beyond that is highly speculative, to put it kindly.
    You can get a “world tree” only if your selection of data is too broad and generous, based on the wrong criteria or irrelevant criteria or hardly any criteria at all.

    Uh-huh, and what are these data? Why, they’re the data of related similarities. Not, of course, just any similarities, but of specific derivations from ancestral languages that in many cases don’t still exist. Derivations that lead naturally to tree classifications, although that’s not the point per se, it just illustrates the derivation.

    These are the kinds of data that you won’t accept in biology past your pathetic “microevolution.”

    By Darwin’s standard, biology does not have such a point.

    No, it isn’t “by Darwin’s standard,” it’s by the kind of evidence that you accept for languages we’ve never heard, like proto-Indo-European. Languages are too labile to hold the phylogenetic signature of derivation past a certain point, while life generally is not.

    And life does have such points. Viruses often lack the possibility for phylogenetic relationships to be plotted out, because their genomes are too labile to hold onto phylogenetic signatures.

    There is always some similarity or another to draw a tree on.

    No, there isn’t. But unlike many viruses and languages, the three domains do continue to hold onto the evidence of their common derivation. That’s just what was found via the evidence, quite as languages were found not to have evidence of their common derivation (if true) to persist.

    GlenDavidson: You can’t explain why variations on “ovis” and “fart” exist throughout most of the Indo-European languages without positing an ancestral language

    At the same time, you *cannot* posit an ancestral language for languages that have variations of “internet”. Only core vocabulary matters, the rest is irrelevant for positing common ancestry. Historical sound laws and syntagmatic properties matter more than current superficial resemblance.

    Thanks for the pedantic non-response. That has nothing to do with the fact that you accept the existence of a language we’ve not heard based on the evidence of derivation that is not unlike the evidence of derivation throughout most of life.

    In biology, however, you can go by “homologies”, e.g. both humans and apes have brains in their skulls, therefore common descent, never thinking any further what this means:

    What an idiotic caricature and projection of your insipid non-reasoning.

    Something ape-like must have bred bred humans, and earlier something crawled out of the water and began breeding mammals. Can species do this sort of thing? These things cannot just happen. “Natural selection” is insufficient to explain this. There must be some further laws of nature at work that bring about new species by leaps and bounds.

    Gee, I wish you could make a cogent argument, rather than merely sneering and insisting that your prejudices are the truth.

    Since when has it all been chalked up to “natural selection”? Read something beyond Darwin if you think to be an expert in what you understand so little.

    Based on the same material, yes, therefore “homologies”, but it’s not those earlier primitive species breeding new species by themselves.

    You’re welcome to learn, rather than to despise and misrepresent.

    Dogs have been around humans for millennia now, so they have had time to observe the survival power of humans. I bet they want to troll the internet like their masters do. So why don’t they evolve in that direction? (it’s just an analogy. Darwin used analogies too. I don’t even have a dog.)

    Uh, what? Have you any clue about what evolution entails?

    Glen Davidson

  26. Anyway, it’s not all about currently living organisms and the trees that illustrate the derivation that is demonstrated, it’s also about the history of life. This is not unlike Erik’s “historical documents,” we have the fossils of transitionals and the general “progression” of evolution. Jonathan Wells:

    Why Does the HIstory of Life Give the Appearance of Evolution?

    Fossil evidence suggests that life on earth originated about three and a half billion years ago, starting with prokaryotes (single-celled organisms without nuclei, such as bacteria). Much later came eukaryotes (cells with nuclei), which included algae and single-celled animals (protozoa). Multicellular marine animals appeared long after that. Then came land plants, amphibians, reptiles, mammals, primates, and finally humans. Not only did living things appear in a certain order, but in some cases they also had features intermediate between organisms that preceded them and those that followed them. Kenneth R. Miller challenges critics of Darwinism to explain why we find “one organism after another in places and in sequences… that clearly give the appearance of evolution.”

    Wells quotes some apologetic nonsense that hardly tells us why God couldn’t have poofed everything into existence at once, or created land life first. Archaetypes and other tripe. Clearly nothing to do with the science, or how it really must be that more complex organisms could only evolve after simpler organisms existed, or why transitionals like cynodonts and Archaeopteryx appear at around the right time and with the right derivative aspects to bridge the “gaps” (not that any is necessarily ancestral, and Archaeopteryx has been shown not to be ancestral to modern birds).

    Of course I’ve mentioned things like this before, and Erik simply goes back to his mantra that the trees are everything, along with the equivalent of the claim that we can’t use forensics to find out anything that hasn’t been explicitly seen. Recapping Ken Ham.

    Glen Davidson

  27. Erik: Actually, nonsense responses presented as evidence started to arrive quickly and this led to its logical conclusion. And of course I did not start from a neutral position. As seen from the OP, I had read at least one book, said to be foundational to the topic. Not a good idea to start a discussion completely unprepared.

    Like reading a book on the Wright Brothers then thinking you know enough to intelligently discuss modern jet aircraft design.

    Dunning-Kruger writ large with this one.

  28. Erik: John Harshman: Language trees aren’t just a way to illustrate the simple fact that you are grouping stuff, are they?

    Actually, they are.

    Oh, come on. You know that they’re intended to demonstrate actual relationships among languages, and not just among languages with written ancestors. And you believe that many, though perhaps not all, of those trees are true. Do you actually think that the Algonquian languages have a common ancestor? Why or why not?

    But the specific way they are drawn when the goal is to demonstrate descent, e.g. how you go about eliminating the frigging noise first (linguistic data is very sensitive to noise and the tree can be anything if you don’t sort out the data properly) leads hopefully to the desired result.

    That is also done with phylogenetic data. You have your “core vocabulary”. Theobald 2010 used “core proteins”. Have you ever read any paper on phylogeny published after 1859? Even one?

    And the hope is justified because we know from millennia of written history how language undergoes change.

    Ha! Those are just fossils. Do you have a continuous record? No, just fragments from various times and places. Where’s the missing link between Latin and Greek? You have no evidence that they’re related at all.

    And we acknowledge the fact that the trails stop at some point. To draw trees beyond that is highly speculative, to put it kindly.

    Is there not disagreement on just where the trail stops? And why, if the trail stops in languages, do you think it must stop with life — and at the level of individual species at that?

    A question for you: do you think that there was one origin of language, so that all the world’s languages are related even though there’s no preserved evidence of it? Or do you think there are many independent origins of human language?

    By Darwin’s standard, biology does not have such a point. There is always some similarity or another to draw a tree on.

    You create a strawman caricature of phylogenetics and then scoff at it. It’s not “some similarity or other”. It’s a huge set of similarities objectively assessed. Again, I wonder if you have ever read any of the phylogenetics literature after 1859. If you’re interested in the evidence for universal common descent specifically, you need to read Theobald 2010.

    Theobald D.L. A formal test of the theory of universal common ancestry. Nature 2010; 465:219-223.

    http://theobald.brandeis.edu/pdfs/Theobald_2010_Nature_all.pdf

  29. John Harshman,

    Please post a complete citation for this claim. It makes no sense, by the way, since the stop codon is in the DNA, not just the RNA. It’s vaguely possible that RNA editing would turn the stop codon in the mRNA into a sense codon, but I’d like to see that.

    Here is a partial citation:
    http://dx.doi.org/10.1136/adc.49.4.278
    http://ajcn.nutrition.org/content/40/5/1050.

    full.pdf+htmlVitamin C induces Tet-dependent DNA demethylation and a blastocyst-like state in ES cells

    Kathryn Blaschke, Kevin T. Ebata, Mohammad M. Karimi, Jorge A. Zepeda-Martínez, Preeti Goyal, Sahasransu Mahapatra, Angela Tam, Diana J. Laird, Martin Hirst, Anjana Rao, Matthew C. Lorincz & Miguel Ramalho-Santos
    AffiliationsContributionsCorresponding authors
    Nature 500, 222–226 (08 August 2013) doi:10.1038/nature12362
    Received 10 December 2012 Accepted 10 June 2013 Published online 30 June 2013

  30. colewd:
    John Harshman,

    Here is a partial citation:

    You really can’t do citation, can you?

    http://dx.doi.org/10.1136/adc.49.4.278
    http://ajcn.nutrition.org/content/40/5/1050.

    Nothing in either of those about your claim.

    full.pdf+htmlVitamin C induces Tet-dependent DNA demethylation and a blastocyst-like state in ES cells

    Nothing there about your claim either. In fact even your really bad citations have nothing to do with your claim that the Gulo pseudogene is activated in human fetuses “by RNA editing”.

  31. John Harshman,

    Nothing there about your claim either. In fact even your really bad citations have nothing to do with your claim that the Gulo pseudogene is activated in human fetuses “by RNA editing”.

    The experiment shows elevated vitamin C level in fetuses. The following paper shows that RNA editing can create a premature stop condon. .

    There is real experimental evidence here John, which is woefully missing in your citations such as the Theobald 2010 paper you cited that claims a probability calculation with no experimental evidence to support it.

  32. colewd,

    There is evidence (2013) that this gene (expressing the L-gulonolactone oxidase enzyme) is active during embryo development and the stop condon is created by RNA editing after embryo development which puts the common pseudo gene claim in doubt.

    Wha? It’s only regarded as a pseudogene in humans. If it really isn’t, that’s less of a help than you think to your hope that humans and chimps (again with the chimps! It’s like people are obsessed) aren’t related.

    Even if they were unrelated genes (which they aren’t), only another 3 bilion base pairs to go at!

  33. Allan Miller,

    Wha? It’s only regarded as a pseudogene in humans. If it really isn’t, that’s less of a help than you think to your hope that humans and chimps (again with the chimps! It’s like people are obsessed) aren’t related.

    Even if they were unrelated genes (which they aren’t), only another 3 bilion base pairs to go at!

    The point that Erik is making is that the evidence for common descent is woefully inadequate. I agree with him and don’t believe that you can make a credible case that chimps and humans descended from a common ancestor without the a priori assumption of universal common descent which is assumed in most evolution papers including John’s 2008 paper where he concludes that there are multiple losses of flight in birds yet he has no clue how this flight was lost.

  34. colewd,

    The point that Erik is making is that the evidence for common descent is woefully inadequate.

    And he’s wrong …

    I agree with him and don’t believe that you can make a credible case that chimps and humans descended from a common ancestor without the a priori assumption of universal common descent

    … and so are you.

    Universal common descent has very little to do with the common ancestry of humans and your favourite species. Obviously, if UCD is true, humans and chimps are definitely related, but if UCD is untrue, that doesn’t mean they definitely aren’t.

    That evidence on humans stands completely separate from that on ratites, whales or what have you.

    You think 3 billion base pairs that support common descent are eliminated by the 40 million or so that aren’t identical. How ludicrous.

  35. Adapa: Like reading a book on the Wright Brothers then thinking you know enough to intelligently discuss modern jet aircraft design.

    Dunning-Kruger writ large with this one.

    Yep, that’s pretty much The Skeptical Zone in a nutshell.

  36. colewd:
    John Harshman,

    The experiment shows elevated vitamin C level in fetuses.The following paper shows that RNA editing can create a premature stop condon..

    True. But there’s nothing to connect the two. Anyway, the human Gulo gene isn’t nonfunctional just because it has a premature stop codon (actually several). It’s also missing the majority of its sequence, and it has a number of frame shift mutations. Even if somehow it were expressed it wouldn’t be a functional enzyme.

    There is real experimental evidence here John, which is woefully missing in your citations such as the Theobald 2010 paper you cited that claims a probability calculation with no experimental evidence to support it.

    You understand nothing about the Theobald paper, so don’t try criticizing it. Your real experimental evidence has nothing to do with what you’re trying to claim. And as I’ve tried to explain to you many times, experiments are nothing special in science; they’re just the setting up of conditions under which observations you’re interested in are more likely.

  37. colewd:
    Allan Miller,

    The point that Erik is making is that the evidence for common descent is woefully inadequate.I agree with him and don’t believe that you can make a credible case that chimps and humans descended from a common ancestor without the a priori assumption of universal common descent which is assumed in most evolution papers including John’s 2008 paper where he concludes that there are multiple losses of flight in birds yet he has no clue how this flight was lost.

    Wait, haven’t you previously agreed that there is good evidence for common descent of paleognaths? Are you now backtracking on that? And the evidence for the common descent of primates is much more extensive, because for some reason a lot of scientists are obsessed with them.

    Why would it be necessary to know how flight was lost in order to know that paleognaths are related?

  38. John:
    Notice that this isn’t in humans, isn’t Gulo, isn’t a pseudogene, involves editing of RNA, not DNA, and introduces a stop codon rather than eliminating one. But I’ll grant you it’s your closest yet.

    Bill:
    The experiment shows elevated vitamin C level in fetuses. The following paper shows that RNA editing can create a premature stop condon[sic].

    Applying Bill-logic™, RNA editing creates a functional calcium synthesis gene in fetuses.
    Okaaaay.

  39. Allan Miller,

    You think 3 billion base pairs that support common descent are eliminated by the 40 million or so that aren’t identical. How ludicrous.

    This is the point Erik is making. You are trying to support common descent with similarities. The claim of common descent is much larger then just the DNA similarities. The sharing of an ancestor is a monster claim especially if you have no idea who the ancestor is.

  40. colewd: The sharing of an ancestor is a monster claim especially if you have no idea who the ancestor is.

    I’m convinced! Ancestors are not shared. It’s not been shown.

    Now, what are were proposing as the ancestor-replacement?

    Or do we just say “we don’t know” when asked?

  41. colewd,

    The sharing of an ancestor is a monster claim especially if you have no idea who the ancestor is.

    Are you actually serious?

  42. Erik,
    What would you say to someone who said to you that they had read one book on linguistics, said they understood it (the field) perfectly and then said that the core accomplishments and understandings in the field were incorrect and unsupported, but without proposing something more fit to to replace them?

    Just wondering.

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