Common Design vs. Common Descent

I promised John Harshman for several months that I would start a discussion about common design vs. common descent, and I’d like to keep my word to him as best as possible.

Strictly the speaking common design and common descent aren’t mutually exclusive, but if one invokes the possibility of recent special creation of all life, the two being mutually exclusive would be inevitable.

If one believes in a young fossil record (YFR) and thus likely believes life is young and therefore recently created, then one is a Young Life Creationist (YLC). YEC (young earth creationists) are automatically YLCs but there are a few YLCs who believe the Earth is old. So evidence in favor of YFR is evidence in favor of common design over common descent.

One can assume for the sake of argument the mainstream geological timelines of billions of years on planet Earth. If that is the case, special creation would have to happen likely in a progressive manner. I believe Stephen Meyer and many of the original ID proponents like Walter Bradley were progressive creationists.

Since I think there is promising evidence for YFR, I don’t think too much about common design vs. common descent. If the Earth is old, but the fossil record is young, as far as I’m concerned the nested hierarchical patterns of similarity are due to common design.

That said, for the sake of this discussion I will assume the fossil record is old. But even under that assumption, I don’t see how phylogenetics solves the problem of orphan features found distributed in the nested hierarchical patterns of similarity. I should point out, there is an important distinction between taxonomic nested hierarchies and phylogenetic nested hierarchies. The nested hierarchies I refer to are taxonomic, not phylogenetic. Phylogeneticsits insist the phylogenetic trees are good explanations for the taxonomic “trees”, but it doesn’t look that way to me at all. I find it revolting to think giraffes, apes, birds and turtles are under the Sarcopterygii clade (which looks more like a coelacanth).

Phylogeny is a nice superficial explanation for the pattern of taxonomic nested hierarchy in sets of proteins, DNA, whatever so long as a feature is actually shared among the creatures. That all breaks down however when we have orphan features that are not shared by sets of creatures.

The orphan features most evident to me are those associated with Eukaryotes. Phylogeny doesn’t do a good job of accounting for those. In fact, to assume common ancestry in that case, “poof” or some unknown mechanism is indicated. If the mechanism is unknown, then why claim universal common ancestry is a fact? Wouldn’t “we don’t know for sure, but we believe” be a more accurate statement of the state of affairs rather than saying “universal common ancestry is fact.”

So whenever orphan features sort of poof into existence, that suggests to me the patterns of nested hierarchy are explained better by common design. In fact there are lots of orphan features that define major groups of creatures. Off the top of my head, eukaryotes are divided into unicellular and multicellular creatures. There are vetebrates and a variety of invertebrates. Mammals have the orphan feature of mammary glands. The list could go on and on for orphan features and the groups they define. Now I use the phrase “orphan features” because I’m not comfortable using formal terms like autapomorphy or whatever. I actually don’t know what would be a good phrase.

So whenever I see an orphan feature that isn’t readily evolvable (like say a nervous system), I presume God did it, and therefore the similarities among creatures that have different orphan features is a the result of miraculous common design not ordinary common descent.

5,163 thoughts on “Common Design vs. Common Descent

  1. Mung,

    People often claim that design explains anything and everything. ok, well then, it explains the nested hierarchy too.

    Just like the Rain Fairy explains the weather. Anyone who is stupid enough to reject common descent in favor of common design should also stupidly reject meteorology in favor of Rain Fairyism, for the sake of consistency.

  2. Erik: I’m the sort of creationist to whom causes matter over probabilities and similarities. That’s why your questions are misguided. I may answer whichever way for the sake of the argument, the real question is if it matters, how and why.

    Not clear on what that all means. But we know the causes of nested hierarchy, we know the causes (or at least most of the causes) of speciation, and we know the causes of mutations. The only thing we don’t generally know the causes of would be what sort of selection, exactly, caused the fixations of particular mutations. Why should the last count and the others not?

    You already conceded that from a little bit of common descent you cannot get more common descent, not to mention UCA. So why do you think your question about sparrows is relevant? Or if it is, then why my answer about dogs and wolves is not relevant? What difference does it make?

    You didn’t have an answer about dogs and wolves, just dogs. Did you forget that? Your answer about dogs wasn’t relevant because it didn’t answer the question I asked, which was about sparrows. Evidence that those sparrows are related is not evidence that all life is related, or even that all sparrows are related. You need different evidence for different things. However, the relevance is the the types of evidence are the same. If you accept that two species are related on the basis of evidence X, and there is evidence Y for two other species, then if X and Y are the same sort of evidence, you ought to accept the conclusions from Y if you accept the conclusions from X. However, since you accept no conclusions from evidence, that isn’t going to work for you.

    So the best evidence for common descent is “Come up with something better!”

    That’s how “inference to best explanation” probably works for you, I guess, but I reject evolution and ID for similar reasons – shift of burden of proof and failure to point to causal links. You think that the ability to draw a tree demonstrates common descent. ID theorists think analogy from man-made artefacts demonstrates ID. Both are wrong.

    Of course I disagree. You don’t have any idea how science works, and that’s clearly one of your problems. All science is inference. All science is comparison of alternative explanatory hypotheses. I didn’t mean that you have to come up with the alternative. I meant that I don’t think there is an alternative that explains the evidence as well or better, and that nobody has ever been able to come up with one, and that there’s a reason nobody has ever been able to come up with one. Nested hierarchy is the simple and obvious expectation from common descent, and it isn’t the expectation from anything else. Remember “If not A then not B = If B then A”? That works. If not common descent then not nested hierarchy; if nested hierarchy then common descent.

  3. Erik,

    I’m the sort of creationist to whom causes matter over probabilities and similarities.

    We wish you were the kind of creationist to whom evidence and rigorous thinking mattered over religious conviction.

    But then again, those people are known as ex-creationists.

  4. Pattern recognition is a big part of science. Find a pattern, then discover what causes this pattern–looking for antecedent events, and determining what might be causal rather than incidental or coincidental.

    That is what happened with evolution, involving both taxonomic patterns (which about all there was when Linnaeus came up with his system) and paleontological patterns. Of course the latter involve the former, but certainly involve a good deal more as well. As one might expect, the same processes were involved in causing both (one should doubt any grand theory that only explained one), and the fact that the patterns of two different sources of information were explicable by the same causes brought the explanation to a high degree of confidence (by those who understood science explanation, anyhow).

    Naturally those who neither understand nor appreciate scientific explanation as producing much better results than inept analogies and easy resorts to anthropomorphic causation like to deny the importance of pattern recognition, and do so piecemeal. Creationsts can explain neither nested hierarchies nor fossil succession, but they can ignore the importance of the interleaved evidence while attacking the foundational nature of pattern recognition and the business of finding causes (not making them up) for those patterns.

    There is no substantial discovery done via ID/creationism for any number of reasons, but especially because they really have to “explain away” the patterns of life to stick to their a priori beliefs, rather than explaining them in any meaningful way at all. ID/creationism is all dead end, plus a lot of demonizing of those who actually care about standards and evidence.

    Glen Davidson

  5. Mung: I find one big poof less preposterous than innumerable little poofs. Occam’s razor and all that.

    The difference is there are no actual “poofs” involved in the origin of ORFan genes. We have evidence from comparative genetics that show how these ORFan genes originate gradually through mutation.
    But over long distances of time, that evidence is gradually erased. When this is the case, it isn’t inferred that the genes then just poofed into existence. They are still inferred to have originated by all the usual mechanisms none of which involve any “poofing”, whether big or small.

  6. GlenDavidson:
    Pattern recognition is a big part of science.

    Some types of sciences. It is not a big part of biological taxonomy, for example. Categorization is. Biologists traditionally recognize both similarities and differences and make taxonomical groupings based on this. With Darwin’s theory of evolution, natural selection and what not, biologists think they have discovered a new exciting all-encompassing pattern that describes all tree of life, allowing to conflate whatever might have caused the differences. But watch it crumble right here right now, yet again.

    John Harshman: You didn’t have an answer about dogs and wolves, just dogs. Did you forget that? Your answer about dogs wasn’t relevant because it didn’t answer the question I asked, which was about sparrows.

    So, what are you saying? Sparrows evolved by common descent, but wolves and dogs didn’t? Or the one has evidence for it that you know about and the other doesn’t? And yes, I mentioned wolves. I think dogs are domesticated wolves.

    John Harshman: Evidence that those sparrows are related is not evidence that all life is related, or even that all sparrows are related. You need different evidence for different things.

    This is what I have been saying. And you have earlier conceded that you have no relevant evidence. What has changed over the last week or so?

    John Harshman: Of course I disagree. You don’t have any idea how science works, and that’s clearly one of your problems. All science is inference.

    We clearly differ at the level of philosophy of science. For me, evidence and inference are different things, but to you they are interchangeable – first you mention evidence, and the next thing is to pretend that inference will do the job. This does not work in any normal science I am aware of.

    I have a very good idea how my science works. If yours works differently, you have some explaining to do. At this stage, I must complain that you are not good at that. For months now, you don’t recognize relevant points at issue and you are unable to clarify your stance in didactical manner.

  7. Mung: People often claim that design explains anything and everything. ok, well then, it explains the nested hierarchy too.

    Yes and therein lies the problem, the potential for design to explain anything and everything. Given that it can do this, we couldn’t imagine an observation even in principle that could falsify it.

    Evolution absolutely requires nesting hierarchies. So we could imagine their absense, and this would then falsify evolution.

    But the same isn’t true for design. There isn’t anything we can imagine that we couldn’t just postulate “is what the designer wanted because His it’s motives are inscrutable”.

    The problem is the ad-hoc-ness of design. It explains everything after the fact, but doesn’t actually predict any particular patterns. And it certainly doesn’t make quantifiable predictions that can be subjected to well-known statistical tests. There isn’t any measures of certainty or likelihood or anything like it. How well should certain patterns match a predicted pattern? Well since no particular pattern is really predicted, how well the patterns we find match the predicted becomes moot.

    Design has zero scientific merit without an actual testable theory. It just exists as some vague idea invoked after the fact.

  8. Erik: Some types of sciences. It is not a big part of biological taxonomy, for example. Categorization is. Biologists traditionally recognize both similarities and differences and make taxonomical groupings based on this. With Darwin’s theory of evolution, natural selection and what not, biologists think they have discovered a new exciting all-encompassing pattern that describes all tree of life, allowing to conflate whatever might have caused the differences. But watch it crumble right here right now, yet again.

    LIke I said, you can’t explain a damned thing, just snipe in your ignorant manner.

    Glen Davidson

  9. Erik,

    Not one helluva coincidence? But on Darwinian evolution, the entire tree of life and its emergence is accidental. On creation, it is the plan of Creator.

    On evolution, cytochrome c is incidental across species, just like clay is incidental to vases, regardless of whether they come from the same potter or not. On creation, it’s decisive what cytochrome c does, so it has a reason to be there.

    Having a reason to be there and having differences follow a tree pattern are not at all the same. The design argument has the potential to explain cytochrome c, but not the pattern of its variants.

  10. Allan Miller: [Erik]Not one helluva coincidence? But on Darwinian evolution, the entire tree of life and its emergence is accidental. On creation, it is the plan of Creator.

    On evolution, cytochrome c is incidental across species, just like clay is incidental to vases, regardless of whether they come from the same potter or not. On creation, it’s decisive what cytochrome c does, so it has a reason to be there.

    On creation there’s supposedly a reason that you don’t know at all (why cytochrome c and not a different protein? Today’s IDists/creationists won’t even demand optimization, since that standard often fails them, so even if cytochrome c were optimal it wouldn’t have any precise fit within today’s wretched creationism). With evolutionary mechanisms there are reasons, many of which will never be known in their details, while reasons for the adaptation itself are often well understood.

    In the end, and without Erik’s equivocations, nothing in creationism has any knowable reason at all, while the adaptations and patterns of life are quite explicable under evolutionary theory. Erik’s “reason” for cytochrome c is no reason at all in the real world.

    Glen Davidson

  11. Given the (pretty low) standard for ‘explanation’ being accepted round here, I would like to offer for consideration my ‘Uncaused Cause’ hypothesis. Everything that we see around us is a direct result of uncaused cause, not design, which requires a somewhat unlikely Intermediate. (It’s actually perturbations in the quantum field, caused by dark matter tripping over dark energy, but I won’t go into details). The result is a regular stream of unlikely events, as regions of Likelihood borrow from regions of Unlikelihood. Tree? Yes, of course it gives a tree! One of the features of Uncaused Cause is that it gives exactly what we see. It doesn’t just explain present observations, but all possible future ones. It is therefore at least as good an explanation as both ‘Common’ Design and Common Descent, at least according to the standards currently being set.

  12. Mung: Corneel: Which reminds me. You accept common descent, right?
    Yes. But I don’t let that keep me from having some fun.

    yes I thought so. 🙂

    Mung: Something that doesn’t end up being reduced to the claim that the creationists lack a better explanation, therefore I win. People often claim that design explains anything and everything. ok, well then, it explains the nested hierarchy too.

    It does, but the Designer needs to work in a specific way to make it work. John has already explained somewhere that the nested hierarchy will still pop up if the Designer lovingly crafts each and every novel feature in his secret laboratory outside time and space, provided that he only inserts them into single lineages and that there is branching evolution. The evolutionists are failing to communicate this message. Conversely the proponents of common design are failing to specify how the Designer does his thing.

  13. A certain faith is being displayed hereabouts that the capacity to interbreed is somehow a test of common descent that is independent of sequence alignments. It is not. The litmus test for successful interbreeding is a successful meiosis in the next generation (otherwise it’s sterile). That very much depends upon sequence alignment.

    The Creationists are arguing that sequences cannot, through divergence, reach a point where they are too dissimilar for successful meiosis, which is rather a foolish position in itself, given an apparent lack of correlation between two diverging populations. But they are also applying a peculiar double standard to the evidence of alignment. As I’ve mentioned, the ability to interbreed would be wrong, as evidence of common ancestry, in the case of Adam and Eve, and all those other pairs that emerged blinking into the Light – if one is that kind of Creationist.

  14. GlenDavidson: Pattern recognition is a big part of science. Find a pattern, then discover what causes this pattern–looking for antecedent events, and determining what might be causal rather than incidental or coincidental.

    Have you read any Darwin? He did not find a pattern and then discover its causes. He moved by inductive leap to overgeneralization. This was very clear when he resorted to analogies. And some of the better students of his bring analogies that repeat the failures, such as Allan Miller’s photocopying analogy. In photocopying, it’s not the sheets of paper that do the copying, but in evolutionary biology the genes are supposed to do it by themselves. Yet in nature, genes do not do it by themselves. Organisms spread genes along the lines of species. What’s the cause of genetic similarities across species (if there is such a cause and not mere correlation) is not known. If there is evidence for it, surely we should have gotten it by now, but all we have is inference from the tree. Just assume that the tree represents causal timeline and that the causes are self-causes and you are all good.

    Come on, all science is inference. Except when it comes to theology, then ask for hard empirical evidence.

  15. What hasn’t been mentioned much is the ‘Common’ part of Common Design. This always puzzles me. The highest degree of sequence alignment is observed among organisms that are accepted by even the most dedicated ‘anti’ as commonly descended. As % alignment goes down – as they become less and less ‘common’ – then it flips to Design. The less ‘Common’ there is, the more Design. It’s the old coattails thing again: Creationism is always playing catchup, but fumbling.

  16. Erik,

    And some of the better students of his bring analogies that repeat the failures, such as Allan Miller’s photocopying analogy. In photocopying, it’s not the sheets of paper that do the copying, but in evolutionary biology the genes are supposed to do it by themselves. Yet in nature, genes do not do it by themselves.

    This is the reddest of herrings. The point is that a process of copying with changes produces a tree pattern, regardless how the copy process is implemented. If, therefore, one finds a tree pattern in the dataset, that is certainly one possible cause one should not dismiss lightly.

  17. Phylogenticists often test their ‘tree-recovery’ programs by generating artificial datasets of copies – they store the true phylogeny as they go, then set the program loose on the end-product to see how well that phylogeny is recovered. The copying is all done in a computer, and not by the data itself.

    Erik would presumably have it that, because this is not self-replication, the program cannot be set loose on organic data and a valid inference made.

  18. Erik: Yet in nature, genes do not do it by themselves. Organisms spread genes along the lines of species.

    What does that even mean, “organisms spread genes along lines of species”? What is a line of species? How do organisms spread genes along them?

    What’s the cause of genetic similarities across species (if there is such a cause and not mere correlation) is not known.

    The cause is descent. They’re similar because they were inherited from common ancestors. They’re different because they also mutate and those accumulate over generations.

    The mechanism of inheritance outright predicts a branching genealogical relationship of divergence from common ancestors. This an observed fact too, not just a theoretical prediction.

    If there is evidence for it, surely we should have gotten it by now, but all we have is inference from the tree.

    The tree is predicted by the theory. If the theory is true, the tree HAS to exist. There is no other testable theory that really REQUIRES the tree. So the tree really is evidence for the theory. If the theory isn’t true, we shouldn’t expect to find the tree.

    And by “the tree” we are talking about multiple independent, highly statistically significantly congruent phylogenetic trees. Multiple nesting hierarchies built from independent data sets, which are nevertheless highly similar. This is the prediction of the theory of common descent, but it isn’t a prediction of anything else. So it can only be evidence for common descent and not evidence for anything else.

    Just assume that the tree represents causal timeline and that the causes are self-causes and you are all good.

    That sentence makes no logical sense and corresponds to nothing done by any person in reality.

    Come on, all science is inference. Except when it comes to theology, then ask for hard empirical evidence.

    You still make inferences FROM hard empirical evidence.

  19. Allan Miller:
    Phylogenticists often test their ‘tree-recovery’ programs by generating artificial datasets of copies – they store the true phylogeny as they go, then set the program loose on the end-product to see how well that phylogeny is recovered. The copying is all done in a computer, and not by the data itself.

    Erik would presumably have it that, because this is not self-replication, the program cannot be set loose on organic data and a valid inference made.

    Besides artifical data sets they also have real phylogenies generated by experimental evolution. All methods of phylogenetic inference have been tested on known real-world phylogenies generated with things like bacteriophages and viruses.

  20. Rumraket,

    Besides artifical data sets they also have real phylogenies generated by experimental evolution. All methods of phylogenetic inference have been tested on known real-world phylogenies generated with things like bacteriophages and viruses.

    Haha, yes! But Common Design is ‘at least as good’ as an explanation for the pattern, because it’s no worse … 🙂

    We should also mention the use of phylogenetic methods in pathology, genealogy and so on. But it’s OK, as long as they can interbreed! Except for bacteria of course, and then … look! A squirrel!

  21. For example, if you’re doing an experiment, you should report everything that you think might make it invalid — not only what you think is right about it; other causes that could possibly explain your results; and things you thought of that you’ve eliminated by some other experiment, and how they worked — to make sure the other fellow can tell they have been eliminated.

    –Richard Feynman

    This is why I like the following exchange:

    Erik: ETA: Another wild guess – “congruence” refers to the trees built on different categories of evidence. E.g. first you take the morphological data from taxa and you build a tree. Then you take the genetic data and you build another tree. Both trees turn out connecting the taxa in the same ways and this is called congruence. Right?

    Rumraket: Pretty much. But congruence comes in degrees though, because you could have a tree that matches on 10 out of 12 branches, and that tree would be more congruent than a tree that only matches on 3 out of 12 branches.

    As I understand it trees can go anywhere from being highly incongruent in the sense that they don’t at all lend any support to a genealogical relationship, through a sort of grey zone where the results are just too uncertain to point one way or the other, to a match that would be perfectly congruent.

    But there’s nothing to like about the following:

    John Harshman: Simple enough. By the standard method of science, which is to ask whether one hypothesis explains the data much better than some other hypothesis. If the data show a strongly nested hierarchical pattern, we infer that the similarities are due to common descent, because we know that common descent would be expected to produce such a pattern and we can’t think of anything else that would be expected to do so.

    Now, this inductive leap of faith plus category error could be perhaps justified, if the trail of data were as uncontroversial as claimed. But what if the reality is that “trees can go anywhere”?

    Rumraket: There is no other testable theory that really REQUIRES the tree…. This is the prediction of the theory of common descent, but it isn’t a prediction of anything else. So it can only be evidence for common descent and not evidence for anything else.

    It’s also the “prediction” of the most trivial gut expectations, such as that purportedly new shapes are variations of the former and existing shapes – cups, bowls, vases, essentially the same thing with variations. It’s not at all specific to evolutionary biology. People are good at noticing “patterns” (some might call it “design”, such as Dawkins does regularly). It’s a whole different matter (a job for the relevant science) to establish that the ability to draw a tree on the similarities indicates causal relations of one morphing into the other by itself as hypothesized. The ability to draw a tree in itself is rather underwhelming.

  22. Erik: Now, this inductive leap of faith plus category error could be perhaps justified, if the trail of data were as uncontroversial as claimed.

    There is no “inductive leap of faith” and no “category error” anywhere in anything said by either myself or John. You’re just bullshitting now.

    But what if the reality is that “trees can go anywhere”?

    What does that even mean, “trees can go anywhere”? Give a concrete example.

    It’s also the “prediction” of the most trivial gut expectations, such as that purportedly new shapes are variations of the former and existing shapes – cups, bowls, vases, essentially the same thing with variations.

    No, it isn’t. There is no prediction that independent data sets from “cups, bowls, and vases” yield highly congruent phylogenetic trees.

    You’re just saying stuff. And it makes zero logical sense.

    It’s nothing special to evolutionary biology. It’s a whole different matter (a job for the relevant science) to establish that the ability to draw a tree on the similarities indicates causal relations of one morphing into the other by itself as hypothesized.

    It does indicate a genealogical relationship for the reasons already explained. Common descent is the only theory that actually predicts that independent data sets used to build phylogenetic trees, should yield highly congruent phylogenetic trees. In other words, that the tree you get from one character set, is highly similar to another tree build from a different data set.

    That is why it indicates a common genealogical relationships, because then the cause of why the tree is the way it is, is that very same common genealogical relationship.

  23. Rumraket: What does that even mean, “trees can go anywhere”? Give a concrete example.

    Just refer to the example you gave yourself. To repeat,

    As I understand it trees can go anywhere from being highly incongruent in the sense that they don’t at all lend any support to a genealogical relationship, through a sort of grey zone where the results are just too uncertain to point one way or the other, to a match that would be perfectly congruent.

    Either you had something concrete in mind or you were just bullshitting. In your own words,

    Rumraket: You’re just saying stuff. And it makes zero logical sense.

  24. Erik: Just refer to the example you gave yourself.

    Ohh, so what you’re saying is that, because it is theoretically possible that independent phylogenetic trees from some genes could fail to corroborate a common genealogical relationship, that means one couldn’t possibly infer a common genealogical relationship in so far as one finds incongruent trees among the congruent ones.

    That it?

  25. Rumraket,

    I’m categorically saying that as long as the tree is the only thing there is, no matter how rigorous, it indicates exactly NOTHING causal in itself. For the tree to indicate true phylogeny, the subject matter of biology (species and organisms) must be such that there are observations of evolutionary events (speciation and common descent) as advertized.

    More theoretically, you were the one who brought up that “trees can go anywhere”, while Harshman has the opinion that the trees are beatifully congruent, giving a clear phylogenetic picture. From my point of view, the details of the in/congruence would be nice to see and the causal significance of the in/congruence would be another thing nice to see along the way.

    These two (in/congruence on the one hand and its causal significance, either mere correlation or actual descent, on the other) are categorically different things. The one is what the thing looks like and the other is what the thing does. Never mix these up, if you are a scientist.

    For example, manuscript lineages form a tree, but manuscripts do not descend by themselves. Scribes generate the manuscripts – this is what “descent” and “lineage” means in this case, due to the nature of the given subject matter. Similarly, “common descent” in biology could entail something totally different from hypothetical assumptions and preconceived notions and this would be interesting to find out.

  26. Erik: For the tree to indicate true phylogeny, the subject matter of biology (species and organisms) must be such that there are observations of evolutionary events (speciation and common descent) as advertized.

    Speciation has been observed. Presumably then common descent has also been observed due to those speciation events. Do you accept that speciation has been observed Erik?

  27. Paul C,

    Just because you say so? No. Whenever I have asked for evidence and references, the answer is something like “we can draw a tree” or “adaptation is speciation” or Very Long Time.

  28. Erik: Just because you say so?

    No, when I say it’s been observed it’s been observed.

    For example, there were the two new species of American goatsbeards (or salsifies, genus Tragopogon) that sprung into existence in the past century. In the early 1900s, three species of these wildflowers – the western salsify (T. dubius), the meadow salsify (T. pratensis), and the oyster plant (T. porrifolius) – were introduced to the United States from Europe. As their populations expanded, the species interacted, often producing sterile hybrids. But by the 1950s, scientists realized that there were two new variations of goatsbeard growing. While they looked like hybrids, they weren’t sterile. They were perfectly capable of reproducing with their own kind but not with any of the original three species – the classic definition of a new species.

    https://blogs.scientificamerican.com/science-sushi/evolution-watching-speciation-occur-observations/

    There are of course other examples. Are you saying that no speciation events have been observed?

  29. Erik’s grandiosity is comical:

    With Darwin’s theory of evolution, natural selection and what not, biologists think they have discovered a new exciting all-encompassing pattern that describes all tree of life, allowing to conflate whatever might have caused the differences. But watch it crumble right here right now, yet again.

    You mean the same way we watched the concept of the empty set crumble when you, with your keen mathematical mind, exposed its incoherence after the mathematical community had embraced it for so many years?

    What would humanity do without you, Erik?

  30. Paul C: As their populations expanded, the species interacted…

    Ah, so to you cross-breeding is common descent. This is something refreshing for a change.

  31. Erik: Ah, so to you cross-breeding is common descent. This is something refreshing for a change.

    I’m not sure what you mean. But perhaps you can clarify by indicating if you think that speciation events have or have not been observed.

  32. Erik:
    Paul C,

    Just because you say so? No. Whenever I have asked for evidence and references, the answer is something like “we can draw a tree” or “adaptation is speciation” or Very Long Time.

    Your ineptitude at understanding is no real objection.

    Glen Davidson

  33. Erik: Ah, so to you cross-breeding is common descent. This is something refreshing for a change.

    Reading through the threads, it becomes mind-boggling to me how monumentally Erik (and other folks like Phoodoo, J-mac, FMM, etc…) misunderstand words and concepts.

    The simple answer is no, Erik. Why? Because cross-breeding is a functional activity (a verb, to be specific). So it can’t be the same thing as common descent, a description of the relationship between species (a noun)? Why would anyone think that? You’re question belies a lack of actually understanding the paragraph.

    The fact that closely related species can cross-breed DOES, however, further support the conclusion of common descent because it helps explain why we see the population offspring (and inheritance) relationships we do.

  34. Erik: Have you read any Darwin?

    Yes, but who cares whether or not I did? Nothing hangs on Darwin per se, and it’s your lack of science competence that leads you to suppose that it does.

    He did not find a pattern and then discover its causes.

    Of course he didn’t, Linnaeus did (though not alone), like I wrote. Reading comprehension would do you a lot of good.

    He moved by inductive leap to overgeneralization.

    Oh, another nugget of wisdom from the ignorant. Fortunately, people who know a lot more than you do looked critically at the theory and found it to explain two very different, but related patterns. Something you can’t begin to address.

    This was very clear when he resorted to analogies.

    Any good scientists is likely to utilize analogies. Your inabililty to think from analogy to reality is what helps you to cling to nonsense.

    If he had stopped with considering just analogies, as you so often do, it would have led to the lack of understanding that you exhibit habitually.

    And some of the better students of his bring analogies that repeat the failures, such as Allan Miller’s photocopying analogy. In photocopying, it’s not the sheets of paper that do the copying, but in evolutionary biology the genes are supposed to do it by themselves.

    Made-up nonsense.

    Yet in nature, genes do not do it by themselves. Organisms spread genes along the lines of species. What’s the cause of genetic similarities across species (if there is such a cause and not mere correlation) is not known.

    Not to those whose comprehension is inadequate. The fact is that we know how genes are duplicated, the patterns that they cause, and we see these patterns. Since we can think from cause to effect, yes, we infer the cause.

    If there is evidence for it, surely we should have gotten it by now

    Yes, and many of us can see it.

    , but all we have is inference from the tree.

    Forget the tree. You never think beyond the mere representation. The whole point is derivation, whose evidence is rampant for those with open eyes.

    Just assume that the tree represents causal timeline and that the causes are self-causes and you are all good.

    That’s the best you can do? Such incompetence.

    Come on, all science is inference. Except when it comes to theology, then ask for hard empirical evidence.

    Life is inference. Theology is speculation, charitably, making things up far more often. But so what? I wasn’t discussing theology, as I’m no anti-theist, just interested in the science that you try to rubbish to make way for your non-explanations.

    Glen Davidson

  35. Erik: I’m categorically saying that as long as the tree is the only thing there is, no matter how rigorous, it indicates exactly NOTHING causal in itself. For the tree to indicate true phylogeny, the subject matter of biology (species and organisms) must be such that there are observations of evolutionary events (speciation and common descent) as advertized.

    No, we technically don’t need to observe speciation. In so far as we have reproduction, and reproduction inexorably produces trees (and it does), finding a tree is enough.

    You’re just categorically wrong, but thanks for making it so clear.

    Erik: More theoretically, you were the one who brought up that “trees can go anywhere”, while Harshman has the opinion that the trees are beatifully congruent, giving a clear phylogenetic picture.

    Yes, it is theoretically possible for the trees to fail to corroborate each other, so I am right when I say that. And John is right when he says they happen to corroborate each other (though I very much doubt he used the term

    Erik: These two (in/congruence on the one hand and its causal significance, either mere correlation or actual descent, on the other) are categorically different things.

    Yes. One is the framework by which common descent is inferred without having observed it happen. And the other is the obsevation of descent itself.

    Sciensts also haven’t observed one generation of stars give rise to the next generation of stars. They infer that this process happens nevertheless, by comparing the predictions of models with observations from astronomy and nuclear physics.

    They also haven’t observed the formation of a mountain range, or a continent. This is also inferred from comparing the predictions of models with observations from geology and physics.

    There isn’t anything unusual about scientifically inferring historical events from patterns in certain data. The fact that you think we need to observe something happen directly, otherwise inference is off the table, is a fantastic position to take, and I very much doubt you really believe this. I’m pretty confident you belive all sorts of things about history without any one person having been alive to directly witness the totality of the transformation in question.

    For example, manuscript lineages form a tree, but manuscripts do not descend by themselves. Scribes generate the manuscripts – this is what “descent” and “lineage” means in this case, due to the nature of the given subject matter. Similarly, “common descent” in biology could entail something totally different from hypothetical assumptions and preconceived notions and this would be interesting to find out.

    This is all well and good, and would be a valid objection if the worlds biologists were postulating the common descent of things that don’t reproduce by passing on their characters to their offspring with mutations in them. Organisms do, so testing the theory of common descent by it’s prediction (congruent trees) is entirely valid.

    From my point of view, the details of the in/congruence would be nice to see and the causal significance of the in/congruence would be another thing nice to see along the way.

    http://www.talkorigins.org/faqs/comdesc/section1.html#independent_convergence

  36. John Harshman,

    I don’t know what that means. Please pay greater attention to clarity. And I don’t think you answered the question, which was “How does the knowledge that some people and dogs share common ancestors tell us that all people and all dogs share common ancestors? You don’t have any evidence that what you know can be extrapolated to cover an entire species.”

    I agree we don’t know.

    We can get a DNA sample from two people or 2 dogs we know are genetically related and see how much variation there is.

  37. GlenDavidson: Nothing hangs on Darwin per se, and it’s your lack of science competence that leads you to suppose that it does.

    Nothing? Like the theory of evolution, that sort of nothing?

    GlenDavidson: Linnaeus did, like I wrote.

    Linnaeus found the pattern. Did he also find the causes?

    GlenDavidson: Forget the tree. You never think beyond the mere representation. The whole point is derivation, whose evidence is rampant for those with open eyes.

    Derivation of what from what? And what’s the rampant evidence? The tree again? Someone mentioned cytochrome c earlier. That’s the evidence? Can you pull yourself together and start making sense?

    Anyway, it was the concisest evidence earlier, very telling, worth repeating,

    Allan Miller:
    OK, where in this continuum of cytochrome c sequence identity does common design kick in, as the alternative to common descent?

    Me-my dad 100%
    Me-Charlemagne 100% (I’m guessing a bit)
    Me-chimp – 100%
    Me-dog (specifically Sam the black Lab) – 94%

    ?

  38. Rumraket: In so far as we have reproduction, and reproduction inexorably produces trees (and it does), finding a tree is enough.

    “Reproduction = macroevolution. Who needs species.” That was quick.

    Rumraket: Sciensts also haven’t observed one generation of stars give rise to the next generation of stars. They infer that this process happens nevertheless, by comparing the predictions of models with observations from astronomy and nuclear physics.

    They also haven’t observed the formation of a mountain range, or a continent. This is also inferred from comparing the predictions of models with observations from geology and physics.

    They also haven’t observed crocoducks or okapis evolving into zebras, but for some reason they are not inferring any. In contrast, they have observed gradual evolution of stone and iron axes, vases, houses, lineages of manuscripts etc. but for some reason they are not inferring those things evolve by themselves.

    It’s not enough to simply infer or not to infer. A good reason for it is required either way. The subject matter of the given science either permits it or it doesn’t; this is the most important reason.

  39. Erik: It’s not enough to simply infer or not to infer.

    Indeed. So do you agree that speciation has been observed, or not?

  40. Erik: Nothing? Like the theory of evolution, that sort of nothing?

    I said nothing “per se,” as historically much hangs on it. But physics doesn’t hang on Newton per se, nor even on Newton plus Einstein plus Planck, etc. Theories hang on the evidence per se, which is certainly the case for evolution. You seem to have no idea of how to get from evidence to good theoretic inferences.

    Linnaeus found the pattern. Did he also find the causes?

    No. Can you begin to follow an argument?

    Derivation of what from what? And what’s the rampant evidence? The tree again? Someone mentioned cytochrome c earlier. That’s the evidence? Can you pull yourself together and start making sense?

    I’ve laid it out, and you’ve ignored it again and again. I don’t think you even get what my examples mean, or can follow what I’ve written about derivation sans tree representation. This whole discussion appears to go over your head, because you’re very intent on rubbishing the evidence for evolution and invested in not actually understanding what it is.

    You blither on, ignoring the congruence of the fossil record with the patterns of extant life that make sense via evolution alone. Yes, you don’t understand derivation, or fossil succession, or really anything about the whole issue. I think you prefer it that way, or your worldview might be threatened.

    Anyway, it was the concisest evidence earlier, very telling, worth repeating,

    Do you have a clue what you’re writing about there? It’s senseless in context.

  41. GlenDavidson: I’ve laid it out, and you’ve ignored it again and again. I don’t think you even get what my examples mean, or can follow what I’ve written about derivation sans tree representation.

    Derivation of what? Where did you lay it out? When? In some other thread a month ago? Find it and we might get back to it. Or not, as you prefer.

  42. Erik: You showed hybrid speciation of plants. What does it demonstrate in your opinion?

    It demonstrates speciation. Hybrid speciation.

    Now, in your opinion, has speciation been observed or not.

  43. Paul C: It demonstrates speciation. Hybrid speciation.

    And where do common descent and (macro)evolution fit in on this scenario? Or is it unnecessary – once cross-breeding and adaptation are conceded, the rest should be a given?

  44. colewd:
    John Harshman,

    I agree we don’t know.

    Well, that’s unexpected. You really don’t know whether all humans are related, or whether all dogs are related? Well, if you can’t go that far, then you’re right that there’s no way I could conceivably convince you that two different species are related.

    We can get a DNA sample from two people or 2 dogs we know are genetically related and see how much variation there is.

    What would that tell us, if anything?

  45. Erik: GlenDavidson:
    Pattern recognition is a big part of science.

    Erik: Some types of sciences. It is not a big part of biological taxonomy, for example.

    Or perhaps you have no idea how biological taxonomy works. Hey, why not ask a professional in the field, me for instance, rather than rely on your own personal ignorance for answers? My answer: yes it is. Classification in modern science is dependent on phylogenetics, which is pattern recognition. But it was even true for Linnaeus, who was trying to create a natural classification, i.e. to recognize the true pattern he thought existed.

    John Harshman: You didn’t have an answer about dogs and wolves, just dogs. Did you forget that? Your answer about dogs wasn’t relevant because it didn’t answer the question I asked, which was about sparrows.

    Erik: So, what are you saying? Sparrows evolved by common descent, but wolves and dogs didn’t? Or the one has evidence for it that you know about and the other doesn’t? And yes, I mentioned wolves. I think dogs are domesticated wolves.

    For a person who claims to be a linguist, you don’t seem to be very good at words. You are constantly ascribing opinions to me that I don’t hold and that my words don’t say. I’m saying you didn’t answer my question. I’m asking why you won’t answer my question. I see you did in fact mention wolves, but what does that have to do with sparrows? And there is in fact evidence for both dogs/wolves and sparrows, but it’s the sort of evidence you appear not to be willing to accept. So why accept one and not the other?

    John Harshman: Evidence that those sparrows are related is not evidence that all life is related, or even that all sparrows are related. You need different evidence for different things.

    Erik: This is what I have been saying. And you have earlier conceded that you have no relevant evidence. What has changed over the last week or so?

    This is you not being good with words again. That’s nothing like what you have been saying. And I have never even hinted that I have no relevant evidence.

    John Harshman: Of course I disagree. You don’t have any idea how science works, and that’s clearly one of your problems. All science is inference.

    Erik: We clearly differ at the level of philosophy of science. For me, evidence and inference are different things, but to you they are interchangeable – first you mention evidence, and the next thing is to pretend that inference will do the job. This does not work in any normal science I am aware of.

    There you are with the word problem once again. Of course evidence and inference are different things. Evidence, by itself, just lies there. Inference is what you have to do to get any sort of conclusion from evidence. You appear not to know much about any normal science.

    I have a very good idea how my science works. If yours works differently, you have some explaining to do. At this stage, I must complain that you are not good at that. For months now, you don’t recognize relevant points at issue and you are unable to clarify your stance in didactical manner.

    I don’t think you have much of a clue about how your science works. I don’t think that if we had no written records of any past languages we would be unable to say that two languages were related. Your science works by inference from evidence, just like any other, though you appear not to understand that.

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