Common Descent Munged

I come from the Michael Behe school if ID. I accept common descent, by which I mean universal common ancestry. It seems to be the consensus view in science, it seems reasonable to me, and I don’t have any compelling reasons to doubt it.

But could I actually defend my belief in common ancestry if asked? All living organisms share certain features in common. Organisms leave offspring. Therefore, universal common ancestry. That sounds pretty weak, I admit. I need to do better.

I don’t believe that new organisms appear out of thin air, so to speak. I accept that the organisms of today are the offspring of prior organisms. Even young earth creationists accept common descent prior to the flood and common decent after the flood, though they resist the idea of universal common ancestry. I still haven’t figured out how and where they draw the lines though, so why should I draw a line that I cannot defend. Therefore common ancestry. That still sounds pretty weak, I admit. I still need to do better.

So time to hit the books. What are the arguments for universal common ancestry in the books on evolution that I have. Erm… Halp!

Why do folks believe in universal common ancestry and what is the best book on “the evidence for evolution” to refer to in order to find the best arguments in favor of universal common ancestry?

What if it’s not the evidence for the theory of common descent per se that leads people to accept it, but rather how the theory of common descent provides an explanatory framework. Does its explanatory power outweigh the need for evidence for it and do people confuse what it can explain with what constitutes evidence for the theory?

What is the evidence for universal common ancestry and why is it considered evidence for universal common ancestry?

263 thoughts on “Common Descent Munged

  1. RodW: I guess one way of describing it is that IDers always look to the facts of nature that don’t tell us anything so they can use their default explanation as opposed to the facts that do tell us something because those always point to evolution

    That’s a caricature!

  2. J-Mac: The study raises questions over why mRNA expression levels differ between species if they do not necessarily cause protein differences. Although further study is needed, Gilad believes this study suggests that protein expression levels evolve under greater evolutionary constraint than mRNA levels, via a yet-uncharacterized compensation or buffering mechanism.
    And there you go…by using a Darwin of the gaps argument you keep your job, possibly the funding, and the Darwinian bullies will leave you alone…

    Thanks for the paper JMac. It doesn’t show what you suggest it shows however. This is not a case where an evolutionary model predicted one thing but they found another. Although there are some general predictions made based on an evolutionary understanding ( such as where to find particular transition fossils) most people know you cant predict things in minute detail. The prediction they make here is not even relevant to evolution but what they find is somewhat supportive ( and instructive) about evolution and somewhat contradictory to ID – especially the Common Design argument.

    The vast majority of genes found in humans are also found in chimps with a sequence identity of ( I think) greater than 99%. They looked at all the genes and found a bunch that had very different mRNA levels but a large fraction of these had a similar protein level. They assumed, because of the basic facts of molecular biology that more mRNA meant more protein and vice versa and were hoping that these differing protein levels were involved in creating the differences between human and chimps. They explain the discrepancy by saying there are compensatory mutations that would, say, decrease the protein levels. if mRNA levels go up. There was no need to invoke this. Many protein levels are maintained by feedback loops that would automatically adjust the protein levels despite differing mRNA levels.

    This is relevant for evolution because it is just another example among many of how the function and ‘appearance’ of an organism can remain the same while mutation generates diversity and essentially changes the underlying complexity. This makes it easier for different lineages to change rapidly in response to change. If it weren’t for this the only way organisms could evolve would be by plodding through and endless series of point mutations, each of which would change the organism slight in a way that had to be selected for.

    Its pretty obvious that Common Design it out the window on this one ..but I need to get back to work………

  3. I’m still interested in hearing a Darwin of the Gaps argument.

    Over the years I’ve gone back and forth on whether God of the Gaps arguments ultimately the way IDers debate. At first I though they were. Then I thought Steven Meyer made a convincing argument that ID was based on a positive argument. Then I concluded most of ID is a God of the Gaps argument with only superficial positive arguments layered over it. Now I’d have to say I’m neutral.

  4. RodW: It doesn’t show what you suggest it shows however.

    If it did, you would be the first one to admit it…and we all here believe it…
    Thanks for your obviously unbiased statement…;-)

  5. J-Mac: If it did, you would be the first one to admit it…and we all here believe it…
    Thanks for your obviously unbiased statement…;-)

    I would admit it. I admit now that there are bits of evidence if viewed in isolation might suggest ID rather than evolution, although I cant think of any examples at the moment
    You keep saying the people are biased against ID but you never present any evidence for ID that would reveal that bias When people shoot down your arguments you attribute it to bias and it never occurs to you that maybe your arguments just don’t hold water.
    I suggest you set aside some of the time you use for posting for reading biology texts. You might come to accept evolution but even if you don’t at least you’ll start to understand the arguments your opponents are using.

  6. Mung:
    Do snakes literally eat dirt?

    God and the audience would understand the snake eating dust is a byp[roduct of being close to the ground. not that the snake has a dirt diet. they all would know snakes eat rodents etc.
    By the way some of the great snakes have vestigial evidence of once having had legs. Very rare in creatures to have vestigal parts showing former body plans.
    Although if evolution was true it should not just be common but the rule and on every bit of a present body plan.

  7. Allan Miller: Ah, typical word-gaming. Never mind the concepts, peck at the words. Try ‘argument’ then. Or ‘case’. I dunno. Is this vital to your understanding?

    I was not just pecking on the word (viz. supposition). The problem is that which you supposed: “One can make a perfectly reasonable supposition that wholeseale substitution would be more damaging than a terminal tail, without having to watch it happening to ‘prove’ it.”

    Sorry, but yes you have to either see it or it has to be directly derivable from things seen, without any missing links. By supposing what you are here you are presupposing your own conclusion.

    But I don’t blame you. Theobald does the same thing, so you can say you are in good company.

  8. John Harshman: OK, you sure can cling to a metaphor. But now suppose you see the Wycliff translation, or some other translation with slightly different wording. Or suppose you see a translation into Frisian. Related languages? Leaving the metaphor, the point is that many features of organisms have detailed similarity that goes way beyond “they have vowels. Your analogy was a bad one.

    My analogy never was with just vowels. It was vowels and consonants and words and sentences etc. Note the etc. You can expand it to books and it applies all the way.

    The problem is: How do you know that the other book is Frisian (and that Frisian is not English)? There are many features of organisms with detailed similarity that make you infer “common descent”, but this inference can only make sense if you (a) have a way to distinguish descent from a species and (b) you know by some other means, such as observation, that species (meaningfully defined so that intra-species variation is excluded, i.e. by analogy that the books are really in English versus Frisian, not copies of the same text with spelling variation) are indeed able to do the thing called common descent, particularly universal common descent.

    In linguistics, such observation and standard of evidence exists. Both Semitic and Indo-European languages have a good historical track record. From that track record it can be seen how both families changed and diverged. At the same time it cannot be admitted that IE and Semitic are related by common descent, even though both have vowels, consonants, words, sentences, books, etc.

  9. Rumraket:
    But this is where I argue that, if we really go with that sense of common design, it still turns out not to make sense. There are a few things we can sort of invoke common design to make sense of, but there are so many other discrepancies that, when we try to account for all of the data we have, it stops making sense. That common design as an explanation for similarities, doesn’t actually explain them, both because there are patterns in the similarities and dissimilarities, and there’d be no reason for them to be merely similar instead of outright identical, in many situations.
    That if we really go with the common design rationalization, things shouldn’t actually be merely similar, they should be virtually identical down to the last atom. And the only deviations should be due to funtional necessity.

    Yes common design, as you say, can be invoked easily to explain likeness in biology.
    You say there is more that can’t. Wait a minute.
    The design easily can have within it flexibility to respond to needs.
    For example human colour.
    We can easily have a design in the body that upon crossing a threshold allows the colour og the body to change. So you have extreme black colour for Africans and Southern Indians. yet they are unrelated biologicaly and changed independently but with like results.
    likewise original “brown I guess” segregated Indo -european speaking tribes, upon moving to cloudly europe independenly changed to a white colour. yet unrelated to being related to each other. it was independent. including white Finnish people speaking a non indo-euro language. just also were triggered to white upon migration.
    The likeness of these colours does not demand common descent as the origin. a common design easily explains it too and more accurately.
    Anyways its a 19th century intellectual failing that they couldn’t imagine a common design, from a creator, accounting for biology patterns. They to easily/quickly saw common patterns as proof for common descent.
    If i or you or anyone was a creator I am sure a common design to biology, including its need to constantly organize itself , would be our plan.
    Everything would be just a twist off everything else.
    A curve, a spectrum curve.
    The common descent conclusion would be a special error made if only believing there is one option for likeness.
    Evolutionism and society must reject common descent as the only option. They must allow the common design option or lose credibility for scientific investigative integrity.

  10. Byers, quoting Genesis:

    So the LORD God said to the serpent, “Because you have done this, “Cursed are you above all livestock and all wild animals! You will crawl on your belly and you will eat dust all the days of your life.

    Mung:

    Do snakes literally eat dirt?

    Byers:

    God and the audience would understand the snake eating dust is a byp[roduct of being close to the ground. not that the snake has a dirt diet. they all would know snakes eat rodents etc.
    By the way some of the great snakes have vestigial evidence of once having had legs. Very rare in creatures to have vestigal parts showing former body plans.

    What about speech organs? Were those part of the “former body plan”? That serpent was sure talkative.

  11. Erik: My analogy never was with just vowels. It was vowels and consonants and words and sentences etc. Note the etc. You can expand it to books and it applies all the way.

    You do have a tendency to pick at particular wordings, as if my failure to mention consonants, etc. in that sentence invalidated my point. Is it unconscious desperation? Again, I’m talking about detailed similarity that goes way beyond possession of sentences and books. If we really must retain this analogy, it’s about books that tell the same story with similar but not identical words.

    The problem is: How do you know that the other book is Frisian (and that Frisian is not English)? There are many features of organisms with detailed similarity that make you infer “common descent”, but this inference can only make sense if you (a) have a way to distinguish descent from a species and (b) you know by some other means, such as observation, that species (meaningfully defined so that intra-species variation is excluded, i.e. by analogy that the books are really in English versus Frisian, not copies of the same text with spelling variation) are indeed able to do the thing called common descent, particularly universal common descent.

    I don’t understand the difference. Is there not common descent within species? If the whole biota were considered a single species, how would that affect inferences of common descent? Not at all.

    In linguistics, such observation and standard of evidence exists. Both Semitic and Indo-European languages have a good historical track record.

    If we must keep the metaphor, we have that standard of evidence in fossils. And as I have pointed out many times, we do not have that standard of evidence for a great many language families. You don’t have such evidence for Algonquian or Bantu, yet you presumably believe there are relationships within those families, perhaps even Amerind or Niger-Congo. You really can’t point to Indo-European as evidence for that. You apply quite a different standard to languages than to species. I suppose that’s because you’re a creatonist. Are you a creationist?

  12. John Harshman: You do have a tendency to pick at particular wordings, as if my failure to mention consonants, etc. in that sentence invalidated my point. Is it unconscious desperation? Again, I’m talking about detailed similarity that goes way beyond possession of sentences and books. If we really must retain this analogy, it’s about books that tell the same story with similar but not identical words.

    You have been grasping at straws since day one. It doesn’t matter a zilch if the languages have books, words, sentences, etc. It doesn’t matter a zilch if the words are “similar but not identical”. This is not how descent is established.

    The words do not have to be similar. They have to be related! In linguistics, it’s not the similarity of the words that determines relatedness. It’s regular correspondences of whatever current shapes the words have. The current shapes may be completely divergent, but if there are groups of words that systematically correspond the same way, then those are related languages. Whereas unsystematic correspondence – e.g. phonetics is a fair match, but morphology is not, and the common vocabulary does not reflect the same grammatical subsystem in the languages – tells that these are borrowings, contact phenomena, not organic relations.

    So you are consistently failing to understand what is at stake. It is not enough for you to point to similarities. Everybody agrees that there are similarities. Sand castles all over the world are similar and they are of the same material, but it does not mean that they have a common ancestor whose descendants migrated all over the world. Sand castles arise independently in different parts of the world. You are not making any effort to prove that species can do common descent the way evolution requires.

    John Harshman: . And as I have pointed out many times, we do not have that standard of evidence for a great many language families. You don’t have such evidence for Algonquian or Bantu, yet you presumably believe there are relationships within those families, perhaps even Amerind or Niger-Congo. You really can’t point to Indo-European as evidence for that.

    Standard of evidence does not mean track record. Uralic languages lack the track record comparable to IE, but Uralic was identified as one family almost half a century before IE – by looking at the vocabulary in the way I just described. The very same evidence demonstrates that Uralic is not related to IE. That was the standard of evidence back then and it’s the same now, just the details have been considerably enhanced.

    The standard of evidence means to have a method to distinguish between organic relatedness on one hand and borrowings and unrelated chance resemblances on the other. From you I have seen nothing but assertion of common descent due to similarity all along – if not always immediate, then a more remote one down the line.

  13. John Harshman: I suppose that’s because you’re a creatonist. Are you a creationist?

    Apparently this is the only thing that really matters to John. This is the same John who thinks that The Modern Synthesis is just population genetics.

  14. Erik: You have been grasping at straws since day one. It doesn’t matter a zilch if the languages have books, words, sentences, etc. It doesn’t matter a zilch if the words are “similar but not identical”. This is not how descent is established.

    Of course it is, especially once you’re in stemmatics, rather than linguistics. And that’s actually what is much closer to biologic phylogenies. So why bring up languages? Two good reasons. You have fairly extensive phylogenetic relationships between language families, hence a better analogy, better graphics for didactic purposes (actually, manuscript familes may also be quite extensive, but people aren’t familiar with them, so not great for teaching). And, people often do have a glancing knowledge of related languages, while few have any real knowledge of manuscript families.

    The words do not have to be similar. They have to be related!

    Yes, we know that. That’s why statistical measures are used. You seem to take analogies far too literally, hence you demand in biology what is necessary in linguistic phylogenetics. But the differences are rather large, in fact, and languages are in fact a good deal more problematic than biologic relationships are. We actually have very nearly the same sorts of system across organisms, and even the same “word forms,” somewhat mutated.

    In linguistics, it’s not the similarity of the words that determines relatedness. It’s regular correspondences of whatever current shapes the words have.

    And biology is not language. What is remarkable is how different linguistic evolution and biologic evolution are, yet with fairly similar nested hierarchies. But languages change in systematic ways, while biology does not. That’s why similarities of genes matter in biology in a way that they do not (at least not in the same way) in linguistics.

    The current shapes may be completely divergent, but if there are groups of words that systematically correspond the same way, then those are related languages.

    Yes, that’s because languages don’t change like biology does. Also, languages change a great deal more than do the genes in biology.

    Whereas unsystematic correspondence – e.g. phonetics is a fair match, but morphology is not, and the common vocabulary does not reflect the same grammatical subsystem in the languages – tells that these are borrowings, contact phenomena, not organic relations.

    But there isn’t any question at all about systematic correspondences in biology. It’s virtually the same code throughout, and quite similar biochemistry as well. The systematic correspondences are already so well established that it doesn’t come up, and cannot be what distinguishes clades from each other. Oh, true, there are small variations in the genetic code, and these can be used for phylogenetics, but I don’t think they would even be analogous to dialects, and we certainly wouldn’t try to hang the whole case for evolution on solely those.

    Really, the systematic similarity in biology–almost identical in several important aspects–could itself be considered adequate evidence for evolution, in context. Unless one had even a small case for design, which has not been proven to be the case, the systematic similarities are overwhelming.

    The problem comes when we’re discussing these issues with people who already think that God made life similar by design, and who are not about to accept the fact that we have no evidence for that hypothesis. And then if we’re going to engage, how many times can we bring up the fact that life has nearly the same genetic code throughout? It both gets boring, and there is a certain logic to the idea that common design could do it (although the small variants in it seem problematic for that scenario). By contrast, it makes no sense that life would have the kind of derivation that is found in manuscript families, albeit minus the sometimes considerable additions and deletions, hence we tend to argue more on that level instead.

    So you are consistently failing to understand what is at stake.

    No, he doesn’t, he just isn’t hung up about the linguistic analogy that you want to force biology into. The analogy is the nested hierarchies that indicate derivation, not the systematic changes that occur in languages, because biology is not all that much like language.

    It is not enough for you to point to similarities.

    It’s similarities in context. It’s more like manuscript families and plagiarism detection, similarities in words and in structure matter, as they do in phylogeny.

    Everybody agrees that there are similarities. Sand castles all over the world are similar and they are of the same material, but it does not mean that they have a common ancestor whose descendants migrated all over the world. Sand castles arise independently in different parts of the world.

    Oh, you don’t think that sand castles have mental “ancestors”? Of course they do.

    You are not making any effort to prove that species can do common descent the way evolution requires.

    Maybe you should learn a bit about biology, rather than assuming that the analogy with language decides everything.

    Standard of evidence does not mean track record. Uralic languages lack the track record comparable to IE, but Uralic was identified as one family almost half a century before IE – by looking at the vocabulary in the way I just described. The very same evidence demonstrates that Uralic is not related to IE. That was the standard of evidence back then and it’s the same now, just the details have been considerably enhanced.

    What if Uralic changed via random mutation plus natural selection (yes, and the rest)? You really don’t get to fault phylogenetic methods in biology for not fitting your insistence that biology agree with linguistics.

    The standard of evidence means to have a method to distinguish between organic relatedness on one hand and borrowings and unrelated chance resemblances on the other. From you I have seen nothing but assertion of common descent due to similarity all along – if not always immediate, then a more remote one down the line.

    No, he’s mentioned the nested hierarchy. But that wasn’t so much borrowed from linguistic phylogenetics as it was from stemmatics for use in cladistics:

    Willi Hennig, whose Phylogenetic Systematics (1966) set up modern phylogenetics, took some of his ideas out of the discipline of stemmatics, or tracking manuscripts by differences in transcription (Platnick and Cameron 1977, Atkinson and Gray 2005). Phylogeny and the history of language and culture

    You’ve got much the same sort of nested hierarchies there. As typical with analogies, the correspondence isn’t perfect, but it’s pretty good.

    Glen Davidson

  15. GlenDavidson: Of course it is, especially once you’re in stemmatics, rather than linguistics. And that’s actually what is much closer to biologic phylogenies. So why bring up languages?

    Are you saying that Harshman’s (and Theobald’s) arguments bear resemblance to stemmatics? Elaborate.

    GlenDavidson: You seem to take analogies far too literally, hence you demand in biology what is necessary in linguistic phylogenetics.But the differences are rather large, in fact, and languages are in fact a good deal more problematic than biologic relationships are. […] But languages change in systematic ways, while biology does not.

    So relationships of languages are problematic (due to contact phenomena, I guess) while biologic relationships are not. At the same time, biology does not change in systematic ways. Shouldn’t this be a problem for biology?

    In linguistics, even though contact phenomena contaminate the data, the contamination can be identified as such by means of systematic analysis. If biology changes in unsystematic ways, then what justifies saying that the changes are due to evolution from universal common descent rather than that they are, for example, insurmountable differences?

    GlenDavidson: Yes, that’s because languages don’t change like biology does. Also, languages change a great deal more than do the genes in biology.

    I know. So it should be easy for you to prove your case, or what? Or is it perhaps so that relevant genetic changes are called changes a la evolution from universal common descent only by convention, while in actual observable reality species look rather sticky.

    GlenDavidson: But there isn’t any question at all about systematic correspondences in biology.It’s virtually the same code throughout, and quite similar biochemistry as well.The systematic correspondences are already so well established that it doesn’t come up, and cannot be what distinguishes clades from each other.Oh, true, there are small variations in the genetic code, and these can be used for phylogenetics, but I don’t think they would even be analogous to dialects, and we certainly wouldn’t try to hang the whole case for evolution on solely those.

    What does the case for evolution hang on?

    GlenDavidson: Really, the systematic similarity in biology–almost identical in several important aspects–could itself be considered adequate evidence for evolution, in context.Unless one had even a small case for design, which has not been proven to be the case, the systematic similarities are overwhelming.

    Again, why would systematic similarity serve as evidence for evolution? Evolution is, from what I have heard, one species evolving into another, and all species evolving from common ancestors by universal common descent. Similarity versus evolution – completely different things.

    We know how manuscripts evolve. The fact that all manuscripts have written text in them does not in itself justify classifying them into lineages. Knowing that generations of copyists copy them with errors and other changes does. Manuscripts have “mental ancestors” as you say – except that they are actually creators. The history of manuscripts is importantly the history of copyists.

    What do we know about species? Some of them, once they appear in the fossil record, stay the same until today, while others go extinct some time after they appear. What else do we know about them? Are you sure they don’t have mental ancestors like sand castles?

  16. keiths:
    Byers, quoting Genesis:

    Mung:

    Byers:

    What about speech organs?Were those part of the “former body plan”?That serpent was sure talkative.

    yes speech can be done by creatures. Why not? Balaams horse spoke too.
    However it was understood by the author/audience of the story that aa being was speaking through the snake.
    Thats why the prophecy was made the SNAKES head would be crushed by someone the SNAKE bit on the heel.
    Not this actual snake of snakes in general. Instead the one speaking through the snake SATAN.

  17. Erik: Are you saying that Harshman’s (and Theobald’s) arguments bear resemblance to stemmatics? Elaborate.

    Obviously Harshman has skated toward stemmatics, bringing up texts like the Lord’s Prayer. More importantly, Willi Hennig reportedly took some of the ideas for modern phylogenetics from stemmatics, as I noted and linked.

    So relationships of languages are problematic (due to contact phenomena, I guess) while biologic relationships are not.

    Well, there just is a number of reasons why relationships in languages can be problematic, the tendency to having the contact problem much more than biology being one of them.

    At the same time, biology does not change in systematic ways. Shouldn’t this be a problem for biology?

    No. I don’t know why it should be. Of course whether the change is “systematic” depends on what is meant by that word, and “Systematic Phylogenetics” could only be systematic because there are systematic effects occurring during evolution. But I gather that you mean “systematic” in linguistics to mean something other than there being some systematic results, like the nested hierarchy, which seems right to me. I write this because I don’t want to be seen to be claiming that there is nothing systematic about evolution in all senses.

    In linguistics, even though contact phenomena contaminate the data, the contamination can be identified as such by means of systematic analysis. If biology changes in unsystematic ways, then what justifies saying that the changes are due to evolution from universal common descent rather than that they are, for example, insurmountable differences?

    I don’t think that you can say that biology changes in “unsystematic ways,” it’s that there aren’t the systematic causes like there are in languages, the latter due to minds being involved.

    I know. So it should be easy for you to prove your case, or what?

    Doesn’t follow. The point is to expect changes to produce different effects in biology, due to different causes.

    Or is it perhaps so that relevant genetic changes are called changes a la evolution from universal common descent only by convention, while in actual observable reality species look rather sticky.

    No, are manuscripts “rather sticky”? Why would the evidence of common descent of manuscript families be good and descent of life not be good? You’re busily faulting analogies for not being exact, while you’re ignoring the fact that common descent is actually quite detectable even when the causes differ quite noticeably. No idea why you’re resisting the analogy where it’s meaningful and demanding that it be similar where no expectations for similarity is appropriate.

    What does the case for evolution hang on?

    The evidence of slavish derivation, the “tree” found in linguistics. Also on the fossil record being proper to the sequence necessary to evolution, such as single cells first, then multicellular organisms, with the peak of complexity tending to increase over time, at least thus far.

    Again, why would systematic similarity serve as evidence for evolution? Evolution is, from what I have heard, one species evolving into another, and all species evolving from common ancestors by universal common descent. Similarity versus evolution – completely different things.

    If manuscripts evolve while the language remains largely unchanged, that’s certainly no argument against their evolving. But there are many languages in the human world, just one “language” in life. Because of the centrality of information to reproducing life, there is good reason to suppose that the DNA code would not change much, which it hasn’t.

    We know how manuscripts evolve. The fact that all manuscripts have written text in them does not in itself justify classifying them into lineages. Knowing that generations of copyists copy them with errors and other changes does.

    Well you were the one who was making something of systematic effects. I discussed them briefly, as it makes sense that the same DNA code would be reproduced throughout all descendants. My point is simply that we don’t even have to look for systematic changes in the DNA code, it’s all one reproduced system, or “language” if you will.

    Then I pointed out that we usually move on to derivation, since that’s more obviously due to evolutionary changes.

    Manuscripts have “mental ancestors” as you say – except that they are actually creators. The history of manuscripts is importantly the history of copyists.

    It’s not especially important to systematics. It will matter some, since copyist “accidents” are not random in the same way that mutations are random with respect to fitness, but that the patterns of derivation are visible either way means that the analogy is fairly good with respect to the “nested hierarchies.”

    What do we know about species? Some of them, once they appear in the fossil record, stay the same until today,

    Do they? You mean from relatively recent times? I don’t know of any species remaining the same from, say, the Cambrian.

    while others go extinct some time after they appear. What else do we know about them?

    That they group much like evolving manuscripts do. Something you manage to avoid, while throwing up irrelevancies.

    Are you sure they don’t have mental ancestors like sand castles?

    No one’s sure of that, of course. But it would be very strange, as the resulting patterns are very different from those of manufactured goods. Minds tend to take ideas from various sources and combine them, while life seems not to, with horizontal changes apparently being due to actual transfer of genetic material (or of material easily read into an organism’s genetic material, at least).

    I just thought I’d include a link to an article that covers a number of the differences between linguistic analogies and biologic phylogenies.

    Glen Davidson

  18. GlenDavidson: Obviously Harshman has skated toward stemmatics, bringing up texts like the Lord’s Prayer. More importantly, Willi Hennig reportedly took some of the ideas for modern phylogenetics from stemmatics, as I noted and linked.

    Obviously Harshman did no such thing, if we go by the actual terms he used, namely “similar but not identical”. Manuscripts, in order to form a lineage, must contain, not a similar, but the same text with differences small enough so that the text can still be called the same. Harshman’s terms indicate that he was not implying parallels to stemmatics.

    As to the link to Hennig, that’s you, not Harshman. This makes you a better guy to discuss these issues with than Harshman.

    GlenDavidson: Of course whether the change is “systematic” depends on what is meant by that word, and “Systematic Phylogenetics” could only be systematic because there are systematic effects occurring during evolution.

    This would be a profound difference (either difference of approach and method or difference of the subject matter itself; or both) in comparison to linguistics. In linguistic, a change is said to be systematic because language itself is regarded as a system. As a system, a language is structured to different parts of grammar like phonology, morphology, syntax, all of which must coexist at all times with each their respective typological categories and subcategories. An organic change is an effect that uniformly affects a (sub)category. That the effects are uniform can be revealed by internal reconstruction and comparative analysis with related languages. Other kinds of changes are either due to contact or extra-linguistic reasons.

    I assumed that the analogy would hold, because biological organisms could also be viewed as a system, an irreducible whole with a specific structure where systemic change would normally be fatal. But apparently biologists view organisms as formless play-doh that can take any shape as so-called natural selection may dictate.

    GlenDavidson: The point is to expect changes to produce different effects in biology, due to different causes.

    I understand quite well that biology is its own subject matter with its own nature. It’s what I keep saying: We know that languages evolve not from the trees we draw, but from observations of language throughout time. What is that in biology that justifies the assumption that evolution occurs (of one species into another, ultimately from universal common descent) by our ability to draw trees? What sort of facts (as distinguished from assumptions and suppositions) demonstrate this? Still no answer. “Similarity”, “nested hierarchies” and “we can draw a tree” are the wrong answers.

    GlenDavidson: No, are manuscripts “rather sticky”?

    Every manuscript is rather sticky when left to its own devices. No manuscript comes about without extra-manuscriptal (specifically human) creative effort. Manuscript lineages are not the result of unguided evolution. They are very much guided by collective human collaboration across generations.

    GlenDavidson: Why would the evidence of common descent of manuscript families be good and descent of life not be good?

    Depends on what the evidence for descent of life is. Still waiting for it.

    GlenDavidson: The [case for evolution hang on the] evidence of slavish derivation, the “tree” found in linguistics. Also on the fossil record being proper to the sequence necessary to evolution, such as single cells first, then multicellular organisms, with the peak of complexity tending to increase over time, at least thus far.

    “We can draw a tree.” Wrong answer, because the exact same applies to the track record of historical texts, but we know for a fact that they didn’t evolve by themselves unguided. They were actively developed by humans. If we go by analogy, why should the analogy stop at this point? What is that in the nature of biological organisms that permits their treatment as play-doh that by itself becomes the nested hierarchy of species, families, and kingdoms that we observe today?

    GlenDavidson: Well you were the one who was making something of systematic effects. I discussed them briefly, as it makes sense that the same DNA code would be reproduced throughout all descendants. My point is simply that we don’t even have to look for systematic changes in the DNA code, it’s all one reproduced system, or “language” if you will.

    Agreed. This is a good description of biosphere as we see it. Not an argument for its evolution though.

    GlenDavidson: Then I pointed out that we usually move on to derivation, since that’s more obviously due to evolutionary changes.

    “Obviously”???

    GlenDavidson: I don’t know of any species remaining the same from, say, the Cambrian.

    Here’s what I did:

    1. Google “cambrian living fossils”
    2. Two examples here
    https://io9.gizmodo.com/12-of-the-most-astounding-living-fossils-known-to-sci-1506539384

    GlenDavidson: That they group much like evolving manuscripts do.Something you manage to avoid, while throwing up irrelevancies.

    It’s no problem for me that they group like that. We humans are good at grouping stuff. But when you assume that the way we group stuff says all we need to know about the origin of the stuff, we part ways.

    GlenDavidson: I just thought I’d include a link to an article that covers a number of the differences between linguistic analogies and biologic phylogenies.

    Glen Davidson

    Thanks for the link. Looks interesting, maybe even relevant. I’ll give it a read.

  19. Erik might also be interested in Dawkins’ Ancestor’s Tale, pages 133 -139 (in my edition) where he discusses cladograms applied to analysing the earliest manuscripts of The Canterbury Tales. Not sure if someone already linked to this 2011 paper by Howe et al

  20. Glen:

    Then I pointed out that we usually move on to derivation, since that’s more obviously due to evolutionary changes.

    Erik:

    “Obviously”???

    Yes, obviously. The case for common descent is a slam dunk, Erik, due to the observed patterns of derivation. That isn’t in any doubt. Glen and John are simply trying to help you understand why that is. Theobald explains it nicely in 29+ Evidences for Macroevolution. Did you find it difficult to follow?

    My own impression is that the linguistic and stemmatic analogies are confusing you more than they’re helping. You might want to consider tossing away the crutches and trying to understand the biological case on its own terms.

  21. One difficulty I find in conversing with Erik is that he seems unwilling to even try to understand the genetic case. The analogy holds water best (should one insist on analogising) when considering the digital sequences of letters on the one hand and bases/amino acid residues on the other. But no, we get stuff like this:

    I assumed that the analogy would hold, because biological organisms could also be viewed as a system, an irreducible whole with a specific structure where systemic change would normally be fatal. But apparently biologists view organisms as formless play-doh that can take any shape as so-called natural selection may dictate.

    The form and integrity of entire organisms is quite irrelevant to the construction of cladograms based upon digital sequence. Likewise, the overall form and meaning of a text, and whether changes were deliberate or accidental, are irrelevant to the tracking of differences among instances of it.

  22. Alan Fox,
    Good one, much more relevant read than Glen’s. Thanks.

    Allan Miller: The form and integrity of entire organisms is quite irrelevant to the construction of cladograms based upon digital sequence. Likewise, the overall form and meaning of a text, and whether changes were deliberate or accidental, are irrelevant to the tracking of differences among instances of it.

    Yup, let’s abstract the data, draw trees on it, and say the trees represent what we want them to represent, nevermind how biological organisms behave in the actual world.

    I would hope biologists don’t think like you do.

  23. Erik,

    Yup, let’s abstract the data, draw trees on it, and say the trees represent what we want them to represent, nevermind how biological organisms behave in the actual world.

    What a strange approach. You want to argue by analogy, but don’t wish to make it more apposite.

    I would hope biologists don’t think like you do.

    They do – I got this from them, not the other way around. My possibly forlorn hope is that most people don’t think like you do.

  24. Allan, to Erik:

    My possibly forlorn hope is that most people don’t think like you do.

    Amen.

  25. Allan Miller: What a strange approach. You want to argue by analogy, but don’t wish to make it more apposite.

    I got that approach from philologists. Philologists don’t argue, “We can draw a tree, therefore common descent.” They argue, “The track record of languages has such-and-such nature and, given such-and-such nature, demonstrates common descent, which can be illustrated by a tree.”

    Now, sorry but I have a really hard time reconciling this with biologists who argue, “We can draw a tree, therefore common descent.”

  26. Erik,

    Why is the observed fact of common descent of genes not admissible? You don’t really say, beyond ‘it isn’t’. Genes are copied. If we see sequences with a high degree of digital commonality, we are reasonably entitled to infer that they arise from the same template, much like variant texts. What other cause for digital commonality would you like to invoke? And at what point does it take over from common descent (observed within species, and to some extent between depending on the rabidness of one’s ‘species-immutablism’). How do we tell them apart?

  27. Erik,
    I’ll admit I’m not familiar with the term “stemmatics”, but I’m certainly familiar with the idea of manuscript descent and with the analogy to phylogenetics. I wasn’t exactly talking about that, but I was edging toward it.

    Here, try this one: Howe C.J., Barbrook A.C., Spencer M., Robinson P., Bordalejo B., Mooney L.R. Manuscript evolution. Trends in Genetics 2001; 17:147-152.

    What is that in the nature of biological organisms that permits their treatment as play-doh that by itself becomes the nested hierarchy of species, families, and kingdoms that we observe today?

    That’s simple enough. Unlike manuscripts, organisms copy themselves, and the copies contain changes. That would seem to be the evidence you demand that such things do happen.

  28. John Harshman: That’s simple enough. Unlike manuscripts, organisms copy themselves, and the copies contain changes. That would seem to be the evidence you demand that such things do happen.

    Good for the observation that offspring is not identical to their immediate parents. However, the offspring is always within the same species as their parents, so the inductive inference is not good for macroevolution. Macroevolution requires separate evidence.

    By analogy, two manuscripts that do not contain the same text cannot be aligned together. Ever.

  29. Erik: However, the offspring is always within the same species as their parents, so the inductive inference is not good for macroevolution

    Doesn’t this same inductive argument apply to languages too? Parents always shared the same language with their kids.

  30. dazz,

    Sure. So?

    Language is the kind of thing that can change radically within a generation. It can be replaced if the population is conquered by someone determined to extinguish them. All this we know not by drawing trees, but by having eyes open to the facts of the world.

    Are species the kind of thing that morph into each other and diverge into more species every once in a while? To determine this, it is not enough to draw a tree.

  31. Erik: Language is the kind of thing that can change radically within a generation. It can be replaced if the population is conquered by someone determined to extinguish them.

    But that doesn’t produce a new language, it replaces one with another existing language. The inductive inference still suggests languages cant descend from one another

  32. dazz,

    You are not getting the point. It’s okay. To each his own.

    By the way, Alan Fox’s linked article was very interesting. No evidence for evolution, but interesting anyway. The article references the following book https://archive.org/details/cu31924026439350

    Most interesting to see that this debate has been going on since day one. I will read that book too. It’s a shortie.

  33. Erik: You are not getting the point

    I think I do. You believe organisms, unlike languages, aren’t the kind of things that can “evolve” into one another.

    There’s still the inductive inference you mention, which when applied to languages, suggests languages shouldn’t “evolve”.

    One final question: if we had good reasons to believe that there’s no significant horizontal flow between languages, would a nested hierarchy of similarities between languages imply common descent?

  34. dazz: One final question: if we had good reasons to believe that there’s no significant horizontal flow between languages, would a nested hierarchy of similarities between languages imply common descent?

    By itself? No.

    Compare: Vases, cups, bowls. They have similarities so that you can arrange them into a nested hierarchy, but it does not mean they emerged at a single place and have been morphing into one another ever since. Neither does it say which shape was the first. As far as evidence goes, whichever of these you dig up in the oldest archeological layer can be said to be the first. But going just by the tree you can draw on their shapes, there’s no way to decide.

  35. Erik: Good for the observation that offspring is not identical to their immediate parents. However, the offspring is always within the same species as their parents, so the inductive inference is not good for macroevolution. Macroevolution requires separate evidence.

    Yes, and one generation always speaks the same language as its parents, so the inductive inference is not good for macrolinguistics. We have no evidence that one language can transform into another. In other words, despite my giving you exactly what you asked for, it isn’t enough, because you just don’t want to believe that evolution is possible.

    By analogy, two manuscripts that do not contain the same text cannot be aligned together. Ever.

    Why do you suppose that two species don’t contain the same “text”? We can indeed align the genomes of different species. So now is that evidence for macroevolution?

  36. John Harshman: Why do you suppose that two species don’t contain the same “text”?

    Because they are two species, not one.

    Two manuscripts on the same material, written in the same hand, but containing a different text cannot be placed in the same lineage. The same text on whatever material is the same lineage.

    Two species may be very much alike, as if two books of the same size and color, but if they do not interbreed, there is no reason to assume that one arose from the other (because that’s what *offspring* and *parents* mean). The superficial material would be the same, but there’s something inside them that seems to block the offspring-parents relationship. So probably not quite the same text, even though similar looks.

  37. Erik: But apparently biologists view organisms as formless play-doh that can take any shape as so-called natural selection may dictate.

    Evolution for children.

  38. dazz: You believe organisms, unlike languages, aren’t the kind of things that can “evolve” into one another.

    No, he’s saying that languages and texts don’t “evolve” into one another. Organisms don’t evolve into one another either.

    #PlayDoh!

  39. I simply fail to grasp how people can so grossly fail to understand what is so plainly written.

  40. Erik,

    Two species may be very much alike, as if two books of the same size and color, […]

    Ach … recourse to bad analogy once more. It is the text that counts, certainly when talking of molecular phylogeny. You have given no mechanism other than common descent to account for a high degree of sequence alignment. In the absence of such an alternative, why exclude common descent? “They cannot interbreed” doesn’t work, because nor can any two bacteria.

  41. Erik: By itself? No.

    Compare: Vases, cups, bowls. They have similarities so that you can arrange them into a nested hierarchy, but it does not mean they emerged at a single place and have been morphing into one another ever since. Neither does it say which shape was the first. As far as evidence goes, whichever of these you dig up in the oldest archeological layer can be said to be the first. But going just by the tree you can draw on their shapes, there’s no way to decide.

    Unlike bowls, language is transmitted from one generation to the next, and it’s observed to change ever so slightly between generations. With that in mind, and the nested hierarchy, it would be silly to doubt common descent between languages

  42. Allan Miller: Ach … recourse to bad analogy once more. It is the text that counts, certainly when talking of molecular phylogeny.

    But we are not talking molecules. We are talking species. Biology, not chemistry.

    Are species the same thing as genes or are species more like populations of live bodies with certain properties, carrying specific genes among other things? Now, you cannot say the genes are the same text across the entire biosphere because if you say so then how do you distinguish between different species? Apparently you don’t, so to me it looks like a sloppy standard of evidence permits drawing the universal tree of life. But if different species have specific differences in genes (which is what makes them different species), then by what reasoning are the genes the same text?

    Allan Miller: “They cannot interbreed” doesn’t work, because nor can any two bacteria.

    Are you saying that whatever applies to bacteria applies to the animal kingdom too? It should, because the same text, right? So let cattle germinate instead of breed!

    The different domains of biosphere seem to me to have very important differences, despite the similarity on the genetic level. Just like castles are not the only thing you can build from sand. On the micro-level, it would always be sand, but on the macro-level it can be very different shapes that should not be taken for the same thing for all purposes.

  43. dazz: Unlike bowls, language is transmitted from one generation to the next, and it’s observed to change ever so slightly between generations.

    Correct. But note that this is an empirical observation, a categorically different thing than drawing trees on abstract data. The tree serves as an illustration after the fact, not as evidence in itself when observations are absent.

  44. Erik: Correct. But note that this is an empirical observation, a categorically different thing than drawing trees on abstract data. The tree serves as an illustration after the fact, not as evidence in itself when observations are absent.

    Are you saying that the tree is not an empirical observation? Once again, if languages form a nested hierarchy, and multiple nested hierarchies using different elements in the languages all converge into the same tree, and you know these elements don’t transfer from one language to another, but are transmitted from one generation to the next instead… wouldn’t it be reasonable, even unavoidable to conclude that the tree counts as powerful evidence of common descent in languages?

  45. dazz: Are you saying that the tree is not an empirical observation?

    I have been very clear on this. The tree by itself proves nothing. The tree is drawn on some thing, but what that thing *does* is a matter of independent empirical observation. The tree may illustrate what that thing has been observed doing. The ability to draw the tree is not in itself evidence for that the thing can do this or that.

    You can draw lineages of manuscripts. This does not mean that manuscripts can replicate themselves. Copyists are required to replicate manuscripts. This is the nature of manuscripts.

    Species are known to reproduce themselves with minor variations. This seems to be the nature of species. Species replicating into other species with major variations a la macroevolution and (universal) common descent have not been observed, so drawing trees about it is wishful thinking.

  46. Erik: The ability to draw the tree is not in itself evidence for that the thing can do this or that

    But the tree is not all we’ve got, you keep ignoring #2:

    1. Multiple studies based on different independent words produce the same language tree for every word
    2. Words are observed to only be transmitted from one generation to the next, never between languages “horizontally”

    There’s no reason why one should not conclude common descent of languages under those circumstances.

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