What’s wrong with this paper?

Taking a new tack with the common descent/common design theme, I’d like to sneak up on it. As Sal Cordova likes to do, I offer a hypothesis for critique. Here’s an old phyogenetic analysis of mine. Does it show common descent? If not, what’s wrong with it?

Harshman J., Huddleston C.J., Bollback J., Parsons T.M., Braun M.J. True and false gharials: A nuclear gene phylogeny of Crocodylia. Systematic Biology 2003;  52:386-402.

This one is about crocodiles. Are crocodiles all the same kind? How do you know? If they aren’t how many kinds are there within the group and how do you know? If they are, are they a whole kind or just part of a larger kind? And if the latter, what is the larger kind?

216 thoughts on “What’s wrong with this paper?

  1. Corneel: My understanding of kinds are specially created groups of organisms.

    No argument there.

    Obviously that means they must be independent and cannot be nested within each other.

    That does not follow at all. Nesting can be based on something other than common ancestry. But I think I understand what you meant now.

    There does not have to be a “eukaryote kind” in order to for there to be different “kinds of eukaryotes.” And these different “kinds of eukaryotes” can be nested within the “eukaryote kind” but the “eukaryote kind” is not a real kind but it’s not something that was itself specially created. It’s just a way of grouping the created kinds.

    So I withdraw my objection. 🙂

  2. Corneel:

    It is? What about the polyconstrained phosphoproteome you have been going on about? In humans, MYC is a proto-oncogene protein and has multiple phosphorylation sites:

    Phosphorylated by PRKDC. Phosphorylation at Ser-329 by PIM2 leads to the stabilization of MYC (By similarity). Phosphorylation at Ser-62 by CDK2 prevents Ras-induced senescence. Phosphorylated at Ser-62 by DYRK2; this primes the protein for subsequent phosphorylation by GSK3B at Thr-58. Phosphorylation at Thr-58 and Ser-62 by GSK3 is required for ubiquitination and degradation by the proteasome.

    Friggin awesome find. Merry Christmas to you.

    Regarding your question, I should have said, “perfectly believable that in 6,000 years, random mutation can create all those alleles before too much damage is done.” That is the hypothesis of Genetic Entropy by John Sanford. Apparently the lower organisms don’t have the constraints the Humans are under. We’re special.

    Anyway, that was an awesome studly find on phosphorylation sites. That was very kind of you. That made my day. Merry Christmas, Corneel! 🙂

  3. John Harshman:

    Can we agree that accepting the biblical timeline takes you outside science?

    No, we can accept it as a working hypothesis. The anomalies you are so quick to dismiss are much bigger than you’re giving them credit for. The helium in Zircons may put a limit on the age of the Earth to around 6,000 years. We really don’t know very much at all. Why the rush to judgement to eliminate the possibility that God did it?

    Are we agreed on common descent of crocodylians yet?

    No, maybe gharials, but it would be nice if Crocodylians are a created kind. It would save a little room on the ark if they weren’t swimming out there in the waters of the great flood for a year.

    I’ll be a believer in the Crocodylian created kind if there is a hybridization experiment proving they can interbreed, just like the LiPons and LiGers, etc. hybridizations proved to creationists Lions, Tigers, Leopards, Panthers, and other big cats descended from a created kinds. Same goes for the canine kind, which even YLC/YECs believe were on the ark as illustrated by this phylogeny tree provided by YEC (presumably taken from evolutionists):

    (from the earlier link
    http://nwcreation.net/evolution_creation.html)

    Like I said, there is a hate/love relationship among the YLC/YECs over common descent. A little bit of common descent goes a long way to solving the problems of Noah’s Ark.

  4. Mung: There does not have to be a “eukaryote kind” in order to for there to be different “kinds of eukaryotes.” And these different “kinds of eukaryotes” can be nested within the “eukaryote kind” but the “eukaryote kind” is not a real kind but it’s not something that was itself specially created. It’s just a way of grouping the created kinds.

    I had to read that several times, but yes that is what I meant.

  5. John Harshman:

    Are we agreed on common descent of crocodylians yet?

    It would be a good thing for the Noah’s Ark advocates if you are right. See, you and Joe Felsenstein are helping lead us to the promised land of creationism with all your work on common descent. Merry Christmas!

  6. stcordova: Apparently the lower organisms don’t have the constraints the Humans are under. We’re special.

    And a Merry Christmas to you as well, Sal.

    Crocodiles are lower organisms? And this allows them to evolve? That is a mighty interesting proposition. Any ideas how to test that perchance?

  7. stcordova: It would be a good thing for the Noah’s Ark advocates if you are right.

    Why, does it make flood geology work, for once?

    Does it explain why the same sort of evidence for common descent in one case is evidence for common design in another? Does it explain the weird derivative developmental processes (rigid bird wing bones fused out of many bones, say) that make sense only in common descent and are senseless with either good or bad design?

    Anomalies are supposed by the pseudoscientists to be fatal to real science, yet the total lack of coherent causal models in ID/creationism are supposed to be fine. Meaning that even IDists/creationists have no confidence in their own “science.”

    Glen Davidson

  8. Mung,

    Can phylogenetic analysis tell us that two species are not related? If so, please provide an example.

    Not definitively, since the signal of relationship is eroded by time. A test does not necessarily have to yield a binary answer: definitively yea or nay. It could be yes or don’t know. That’s hardly a problem for a hypothesis of common descent, is it, the fact that it could be confirmed but not definitively eliminated?

  9. stcordova,

    Why the rush to judgement to eliminate the possibility that God did it?

    What, you think with a couple of hundred years of accumulated evidence on the actual age of the earth, and the grotesque ludicrousness of the Ark/Flood story, we should withhold judgement just a little longer?

  10. stcordova: Why the rush to judgement to eliminate the possibility that God did it?

    Rush to eliminate? The “possibility” that “God” did it doesn’t even enter the equation. You’ve got it backwards Chava, it’s the possibility that “God” did it that needs a lot, but really a lot, of support before being entertained. It’s not as if “God” is right there, unambiguously within our grasp, and all we had to do was check if She had anything to do with anything, or if She left it to natural processes. Nature on the other hand is right here. So what options do we have other than nature?

    Anyway, way out of the OP, so I’m out.

  11. stcordova: Why the rush to judgement to eliminate the possibility that God did it?

    Why the rush to judgment that the earth is spherical (spheroidal, for the pedants), rather than flat?

    Not that science at large is trying to eliminate the possibility that God did it, but the “rush” is to base the models on the evidence. A foreign concept to IDists/creationists.

    Glen Davidson

  12. Corneel:

    Crocodiles are lower organisms? And this allows them to evolve? That is a mighty interesting proposition. Any ideas how to test that perchance?

    Yes, but we don’t have the technology nor money to do it — yet. 🙂

    But, I should have specified the “lower organisms” were definitely the microbes.

    But regarding the crocks and the humans, we could compare the number of post-translational modifications per protein for starters. We’ll see then if we are “higher” than crocs in that regard.

    I think in the case of random mutation creating “alleles,” many are disease associated as it’s possible many alleles now are functionally compromising who we were 6,000 years ago. 6,000 years ago we live longer, stronger, and smarter. There is some evidence to that effect.

    Having seen some psuedo genes in humans, like INFL3, some human “alleles” (using the term loosley) are the pseudo gene, some are the active gene.

    There are paralogs of INFL3 in the human. One working paralog is NG_042193.1, the paralogous pseudo gene I’m not sure is annotated, but you can find the first exon starting at coordinate 45,136 and the end of the last exon at 46,919 in AC011445.6. A mutation in the Adenine at coordinate 45,633 in AC011445.6 converts the pre-mature stop codon (TAA) to a Tyrosine (TAC). Individuals who get this nice back mutation “allele” have better immune defense as this paralog interferon is active in them and they don’t catch colds and other viral infections as easily.

    That is an example of what I meant of how even we humans can tolerate some mutation, suffer, but not immediately not go extinct by these new disease associated alleles. That hopefully reconciles that apparent contradiction with random mutation creating new alleles, and yet the human (and other genomes) also having sophisticated proteomic “-omes”.

    The species specific “-omes” were created with species specific functions, but many of the new alleles that weren’t created heterozygously into the kinds but were added by mutation are probably function-compromising alleles. Sadly we see the effect of the function compromising alleles that are damaged -omes in various human heritable diseases. Random mutation created these alleles — almost no question, and people are suffering the consequences of the new alleles. That is Genetic Entropy.

  13. If crocs didn’t swim during the great flood, but were on the ark, but if they all descended from one ancestral set of crocs as John insists, and as some YEC might even speculate, look at all the room that will be saved on the ark!

    https://wiki.shanti.virginia.edu/download/attachments/41287861/Screen%20Shot%202014-10-07%20at%207.24.54%20PM.png?version=1&modificationDate=1412734225641&api=v2

    If any of these extant form can interbreed that would be interesting, like take some extant species from lineages that split from the cretaceous era. That would be totally awesome. After all we have living fossil sharks, lungfish, and horseshoe crabs, it would be so cool to see these living fossil crocs breed too.

  14. One reported example supporting the common descent of crocs that even a YLC/YEC would love to hear:

    https://en.wikipedia.org/wiki/List_of_genetic_hybrids

    Saltwater crocodiles (Crocodylus porosus) have mated with Siamese crocodiles (Crocodylus siamensis) in captivity producing offspring which in many cases have grown over 20 feet (6.1 metres) in length. It is likely that wild hybridization occurred historically in parts of southeast Asia.

    Ok, so according to the phylogenetic diagram in the previous comment, the two lineages split 10 million years ago, and yet one hybridization experiment undoes 10 million years of evolution in a snap. Freaking amazing! Let’s do more experiments like this.

    Merry Christmas!

  15. Mung: Did you means to say guided common descent? Because you are using evolution and common descent inter-changeably.

    No, I’m not. Like Sal, you seem to be confusing the origin of innovation with the explanation of nested hierarchy. Common descent doesn’t need any guidance. It just happens. I don’t think evolution (the origin and spread of innovations) needs any guideance either, but if it did then Sal would be free to use it.

  16. Mung: There’s no law that says that kinds cannot be nested. They would just not be nested due to common descent.

    Then we’re back to trying to explain why there is a nested hierarchy. Have you come up with an alternative to common descent for that?

  17. Mung: Can phylogenetic analysis tell us that two species are not related? If so, please provide an example.

    There is no example, because all species are related. But one can assume non-relationship and test it. That’s what Theobald did. Remember Theobald 2010?

  18. Allan Miller: Not definitively, since the signal of relationship is eroded by time. A test does not necessarily have to yield a binary answer: definitively yea or nay. It could be yes or don’t know. That’s hardly a problem for a hypothesis of common descent, is it, the fact that it could be confirmed but not definitively eliminated?

    So non relationship cannot be tested?

    John Harshman: There is no example, because all species are related. But one can assume non-relationship and test it. That’s what Theobald did. Remember Theobald 2010?

    Except when it can be tested.

  19. stcordova: Me: Can we agree that accepting the biblical timeline takes you outside science?

    No, we can accept it as a working hypothesis.

    But that isn’t how you accept it. You are unwilling to consider that it isn’t true.

    The anomalies you are so quick to dismiss are much bigger than you’re giving them credit for. The helium in Zircons may put a limit on the age of the Earth to around 6,000 years. We really don’t know very much at all. Why the rush to judgement to eliminate the possibility that God did it?

    Ah, when in doubt, do the Gish Gallop. I thought you were an Old Earth, Young Life creationists. Now you’re going back to YEC? How about the universe?

    Me: Are we agreed on common descent of crocodylians yet?

    No, maybe gharials, but it would be nice if Crocodylians are a created kind. It would save a little room on the ark if they weren’t swimming out there in the waters of the great flood for a year.

    If you don’t accept that they’re a single kind, how do you explain the nested hierarchy within crocodylians? Also, can we agree that “it would be nice” is not a good reason to believe something?

    I’ll be a believer in the Crocodylian created kind if there is a hybridization experiment proving they can interbreed

    You won’t believe it without hybridization? Why? Are you saying that ability to hybridize can’t be lost within a kind? Are you saying that different kinds should be unable to hybridize? In either case, what’s your argument?

    (from the earlier link http://nwcreation.net/evolution_creation.html)

    I will note that your diagram includes hyenas, which are feloids. So the claim here would seem to be that Carnivora is a single kind. Though perhaps that was unintentional.

    Like I said, there is a hate/love relationship among the YLC/YECs over common descent. A little bit of common descent goes a long way to solving the problems of Noah’s Ark.

    Why should we care about solving the problems of a fictional event? The number of species on the ark is hardly the greatest of its problems. And this “solution” requires evolution far beyond what you are willing to believe. Think of all the orphan genes!

  20. Mung: So non relationship cannot be tested?

    Except when it can be tested.

    I will charitably assume that you are misunderstanding on purpose for humorous effect. The effect is not humorous but merely annoying. Keep up the word games and I’ll put you back on “ignore”.

  21. stcordova,

    There are some species (maples come to mind) that are interfertile despite 20 million years of separation. It’s not the big deal you seem to think it is.

  22. Allan Miller:

    There are some species (maples come to mind) that are interfertile despite 20
    million years of separation. It’s not the big deal you seem to think it is.

    Awh c’mon Allan, John Harshman’s got me excited at the prospect of the common descent of crocodiles. The joke among the YLC/YECs at the creationists conferences is that we’re all closet hyper-evolutionists because of the need to cram all the creatures into Noah’s ark.

    But even for creatures not on the Ark, like say Sharks, the living fossils, wouldn’t it be cool to interbreed these creatures. This would accord with YECs Nathaniel Jeason and Rob Carter’s hypothesis of created heterozygosity. If hybridization is carried out successfully on hundred million year old “living fossils” it will lend credence to Carter and Jeanson’s theories and the mechanism of sub-speciation from a created kind.

    Btw, Merry Christmas, Allan.

  23. Mung,

    So non relationship cannot be tested?

    […]

    Except when it can be tested.

    Do you understand what ‘not definitively, no’ means? Is Theobald’s test a definitive test of non-relationship?

  24. stcordova,

    Interbreeding is not much of a test of anything beyond the extent of genetic identity in the diploid. It’s a practical barrier to gene flow, and so its absence aids divergence, but I don’t see why it should be a dividing line between Kinds (effectively, Kinds=BSC). Its absence doesn’t prove a species pair is not commonly descended; its presence simply indicates that divergence is not yet far enough along.

    Merry Christmas to you too.

  25. Allan:

    I don’t see why it should be a dividing line between Kinds (effectively, Kinds=BSC). Its absence doesn’t prove a species pair is not commonly descended

    It’s not, it’s trying to erase supposed dividing lines. The more educated creationists (like Kurt Wise who was Stephen Gould’s student), are quite interested in erasing supposed barriers between species. Once the question of cramming creatures into the ark came to the forefront, a lot of anti-evolutionists did an about face. It’s not well known except in the more educated ranks of YECs like Kurt Wise and others.

    But because of the timeline this creates a whole new set of problems, the problem of hyperevolution. If there is hyperevolution due to heterozygosity of an ancestral population, this will create a little anarchy and confusion, and for now that would be good for the YECs to see wreak some havoc and confusions using accepted data.

    Jeanson argues much of what we call speciation is really mixing of pre-existing alleles. He studied horse hyper-evolution a lot. I may see him at the International Creationism Conference in July/August. I may ask him more about these things then….

  26. stcordova: Yes, but “evidence for” is not “proof of”. A common genetic code is evidence in favor of universal common descent, but not absolute proof.

    However, Complex novel features is evidence against universal common descent.

    And here it is revealed that Sal doesn’t actually understand what evidence is, or what it means to say that there is evidence for or evidence against something.

    In order to have evidence against a hypothesis, you have to have data that is explicitly predicted to be different than what you have. Common descent does not predict that there should not be taxonomically restricted characters, or genes, or organs, or bio-systems. So finding these things can’t be evidence against common descent. At worst you could argue that their existence are facts that common descen’t doesn’t explain. What it does explain is their distribution in groups within groups, as that is how they would sort (however they manage to arise in the first place) through a branching genealogical process.

    It is not enough merely to have data that the hypothesis does not predict. After all, the hypothesis could be compatible with that data but being neither for or against it. For example, common descent could be happening but guided by God, or a designer that is creating complex phenotypes or structures in the sense that Michael Behe thinks, as in a designer that some times intervenes to create a flagellum, or the blood clotting cascade.

  27. Rumraket: Common descent does not predict that there should not be taxonomically restricted characters, or genes, or organs, or bio-systems.

    And common descent does not predict that there should be taxonomically restricted characters, or genes, or organs, or bio-systems.

  28. Allan Miller: Is Theobald’s test a definitive test of non-relationship?

    John seems to think so.

    John Harshman: There is no example, because all species are related. But one can assume non-relationship and test it [non relationship – Mung]. That’s what Theobald did. Remember Theobald 2010?

  29. Allan Miller: What we do have is the situation in which an analysis on one set of character states (be they morphological, molecular or a combination) maps pretty well on the analysis on another, otherwise uncorrelated set (be they etc etc etc).

    John Harshman: Just to make this clear. In the current case, the argument is over the position on the tree of a single species, Gavialis gangeticus. Doug Theobald has a web page that discusses exactly this case and shows how unlikely that little disagreement is by chance.

    Mung: ok, so we’ve eliminated the chance hypothesis. God does not play dice.

    Right.

    I think something more needs to be said here. It is the chance congruence of trees that is being rejected in favor of the congruence of trees being due to common descent.

    But that does not mean a design hypothesis has to involve a designer deliberately and knowingly involving chance as a step or factor in Her design-process, in order to be rejected with the the chance hypothesis. Sounds paradoxical so I will elaborate.

    The designer could be designing individual genes with an eye for function. As in every single nucleotide is deliberately chosen because of it’s potential effect on the function of some gene in question. That it is either the best possible gene for it’s job, or at least that it is good enough to perform that job. That means sequences are constrained towards what they do, rather than being constrained towards yielding some particular phylogenetic tree if future biologists submit putative orthologous genes to phylogenetic analysis.
    That would mean that, whatever phylogenetic tree these genes which were designed and constructed to yield particular functions, nevertheless happens to yield, when they are subjected to phylogenetic analysis, is an unintended byproduct of the sorts of sequences that were designed for their functions.

    In other words, it is a possibility that the phylogenetic trees the genes yield would STILL be chance byproducts of a deliberate design process.

    But the statistics says that a situation where multiple such genes corroborate a similar overall branching structure, is unfathomably unlikely even should such genes have been designed for their functions if the phylogenetic trees they yield was not a factor in that design process.

    Which raises the question of course, given that the trees overwhelmingly corroborate each other, to those who reject common descent and believe in design, why would the trees do so?
    You pretty much have to assume the designer is forcing them to corroborate each other, either in spite of function, or at least simultaneously with constraining function, because designing them towards function alone would still not yield consilience of independent phylogenies.

    So to someone like Sal to who rejects common descent, he HAS to assume that God is being deliberately deceptive.

    It is either common descent, or a deceptive designer that is deliberately making the gene trees agree. Because designing towards function alone simply does not explain it, the odds are so overwhelmingly against it.

  30. Mung: And common descent does not predict that there should be taxonomically restricted characters, or genes, or organs, or bio-systems.

    No it explains why it is possible to sort them objectively in groups within groups. To explain how they arise in the first place requires a theory of their origin, something that invokes a mechanism that produces changes and novelties over time. There are evolutionary theories for such things.

  31. John Harshman: Why should we care about solving the problems of a fictional event? The number of species on the ark is hardly the greatest of its problems. And this “solution” requires evolution far beyond what you are willing to believe. Think of all the orphan genes!

    Heh, it would be interesting to know the number of orphan genes in all species of crocodylians.

    Sal seems to be solidly in the camp of “orphan genes can’t evolve”, which could either put him back on having to insist there were 10 million species on the Ark, or force him to invoke the “front loading” rationalization with unbelievable levels of selective gene-loss.

    But if Sal is okay with unbelievable levels of selective gene-loss, he can’t complain about his favorite venn diagram as evidence against common descent without being massively hypocritical (not that that will stop him).

    Stuck between a rock and a hard place.

  32. Mung: John seems to think so.

    If I took Allan’s point I think the key word was definitive. As in “formal axiomatic proof”.

  33. Mung: And common descent does not predict that there should be taxonomically restricted characters, or genes, or organs, or bio-systems.

    Exactly. So they can’t be evidence for or against common descent. The evidence is, of course, the nested hierarchy, of which taxonomically restricted characters, etc. are a part.

  34. John Harshman: Why should we care about solving the problems of a fictional event?

    Harshman must be referring to abiogenesis again 😉 I’m glad he got one of his senses back…lol

  35. Mung,

    Theobald gives a statistic that favours common descent much more strongly than alternative models. I see that as a test of relationship, not of non-relationship. If one failed to establish common descent, one has not – definitively – established separate origin, because of the possibility of complete signal erasure. John may or may not agree, but what would be your own view?

  36. Allan Miller:
    Mung,

    Theobald gives a statistic that favours common descent much more strongly than alternative models. I see that as a test of relationship, not of non-relationship. If one failed to establish common descent, one has not – definitively – established separate origin, because of the possibility of complete signal erasure. John may or may not agree, but what would be your own view?

    Does Theobald mention utricularia in his statistics? I can’t seem to find it and every Darwinist on earth, including him, runs away from this issue…. any idea why?

  37. Rumraket: No it explains why it is possible to sort them objectively in groups within groups. To explain how they arise in the first place requires a theory of their origin, something that invokes a mechanism that produces changes and novelties over time. There are evolutionary theories for such things.

    Since when is common descent not a theory that requires a mechanism?

  38. Rumraket: Heh, it would be interesting to know the number of orphan genes in all species of crocodylians.

    It would also be interesting to know if all species of crocodylians share the same embryonic development. We could create trees based on similarities and differences in embryonic development too can’t we?

  39. Rumraket: There are evolutionary theories for such things.

    Yea, like random mutations plus natural selection equals all of life we see. That kind of theory?

    Evolutionist: Random mutations plus natural selection explains all of life.

    Doubter: Eggshells?

    Evolutionist: Just because we don’t have a step by step guide….Yes, everything. I don’t know. One day…

  40. John Harshman: Exactly. So they can’t be evidence for or against common descent.

    I don’t believe I have argued that they are evidence against common descent.

    It’s amazing to me that you will go post after endless post with Salvador but I have to walk on eggshells around you. Perhaps you could reflect on why that is.

  41. Rumraket: If I took Allan’s point I think the key word was definitive. As in “formal axiomatic proof”.

    No, I don’t think so. Science doesn’t offer us proofs, after all.

  42. Allan Miller: I just can’t take the Ark seriously. It’s silly, and I am always nonplussed when fully-grown adults try and rationalise it.

    I bet that’s what the people watching Noah build it thought. 😉

  43. Allan Miller: Theobald gives a statistic that favours common descent much more strongly than alternative models. I see that as a test of relationship, not of non-relationship. If one failed to establish common descent, one has not – definitively – established separate origin, because of the possibility of complete signal erasure. John may or may not agree, but what would be your own view?

    I think that the issues with Theobald’s paper are publicly available.

    But I agree that one has to compare the probability of an independent origin to an alternative theory, but given that everyone and her sister is arguing that common descent does not explain origins it appears that there is quite a disconnect between the two things being compared.

    A statistic that favors common descent would mean that we know what to expect from common descent, but we don’t know what to expect from common descent. You cannot predict the outcomes of “common descent.” You cannot say which outcomes of “common descent” are more probable than others.

    What we see is what we would expect under common descent. Here’s what we would expect under a separate origins hypothesis. We don’t see what we would expect under an independent origins model. Therefore, what we see confirms common descent. Well, duh.

    So I would question whether the random origins hypothesis represent the separate origins model that most creationists have in mind.

    Everything is related. So how is any given tree a test of relatedness?

  44. Mung: It’s amazing to me that you will go post after endless post with Salvador but I have to walk on eggshells around you. Perhaps you could reflect on why that is.

    Pretty simple. Sal generally makes what he imagines to be a serious contribution and a serious argument. You generally don’t.

  45. John Harshman: Pretty simple. Sal generally makes what he imagines to be a serious contribution and a serious argument. You generally don’t.

    Salvador will be pleased to hear that. 🙂

    I fully understand how little serious argumentation actually goes on around here and don’t try to pretend otherwise. Take for example your recent response to Erik:

    John Harshman: Erik,

    I can’t really do anything for you. You seem unable to interpret ordinary language. How odd for a linguist.

    And why should I take seriously anyone who claims that feathers evolved for insulation and that feathers also evolved for flight? Do they sound like they are really putting forth a serious argument?

  46. Mung: But I agree that one has to compare the probability of an independent origin to an alternative theory, but given that everyone and her sister is arguing that common descent does not explain origins it appears that there is quite a disconnect between the two things being compared.

    Here, the trick lies in your tacit equivocation of the wordk “origins”. Common descent explains the pattern of distribution of character states. That’s one sort of origin. What everyone is saying it doesn’t explain are the origins of character states, quite a different sort of origin. And common descent is a single origin in a third meaning. No idea what disconnect you think there is.

    A statistic that favors common descent would mean that we know what to expect from common descent, but we don’t know what to expect from common descent. You cannot predict the outcomes of “common descent.” You cannot say which outcomes of “common descent” are more probable than others.

    Actually, you can say which outcomes are more probable than others. Likelihood analysis determines the probability of the data given a particular tree. You may be confused because the probability of any particular data is very small, since there are incredible numbers of data sets that would be equally probable. However, this doesn’t matter when comparing the data that do exist against different trees.

    So I would question whether the random origins hypothesis represent the separate origins model that most creationists have in mind.

    In my experience, most creationists have no model in mind. I’ve certainly had no success in getting any creationist to articulate a model. What do you know?

    Everything is related. So how is any given tree a test of relatedness?

    I do not understand those two sentences. Could you explain?

  47. Allan Miller:

    I just can’t take the Ark seriously. It’s silly, and I am always nonplussed when fully-grown adults try and rationalise it.

    Yes, even when I talk about it myself, it seems comical, as if foolishness of a child’s fairy tales….

    However, there was something that struck me in Dave Raup’s book, Bad Genes or bad luck. Raup was hailed by Stephen Gould as “the best of the best” and yet ironically Raup really did very little field work, he was mostly a computer type paleontologist! 🙂

    Raup was troubled that entire orders were wiped out rapidly in mass extinctions, but could quite reconcile why so many otherwise vulnerable creatures survived. The YEC/YLCs believe, based on evidence like the Colorodo Mines experiment on stratification, that the fossil records is mostly a record of a single cataclysm, and combined with the Faint Young Sun Paradox, this confirms the fossil record was through a cataclysm that was global and wiped out life.

    So why then did such vulnerable creatures as humans and things that couldn’t swim survive? We don’t have to postulate an ark to postulate a miracle preserved their life. That is close enough for me to believe in a miracle akin to an ark.

    Some of the work of Sanford, Carter, Jeanson is to now tie the immense and growing bioinformatics databases to prove a common bottle neck for all the varieties of creatures. Jeanson’s work on the horses shows a lot of promise in confirming this bottle neck.

    The spectrum of YLC/YECism spans pure anti-evolutionism to Baraminology/model building. Most creationists are on the anti-evolution side of the spectrum, however the model builders are now coming into prominence, and Jeanson is one of the few model builders I actually get along with (I never could quite jive with the Baraminologists, God bless them).

    Jeanson has argued there is a genetic signature for domesticated animals that shows a bottle neck from a foundry population less than 10,000 years ago. If we see the same pattern in other animals, this would be consistent with Noah’s ark, or some comparable miracle. The data might not confirm Noah’s ark directly, but it would confirm a global bottle neck, just as was suggested by Raup’s paradox.

    The International Conference on Creationism (ICC) in Pittsburgh, PA July/August 2018 should be a lot of fun as creationists from all over the world will meet to discuss the latest and greatest. I expect Carter and Jeanson to be there, and it would be great to hang out with them again. I had the honor of Jeanson’s time at the Lipscomb conference this past June.

    At ICC 2018, Geologist Stephen Austin will give a big presentation on the various stratification experiments that are being conducted that show the stratification in the geological record were the result of a massive global cataclysm involving water….

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