Home > Human Evolution > Orangs in the family tree

Orangs in the family tree

June 29, 2009

Many readers may be aware of the recent paper (in Journal of Biogeography no less) by Grehan and Schwartz claiming that there is sufficient morphological evidence to support the claim that orangutans are our closest living relatives, while simultaneously dismissing all of the genetic evidence for chimps being the closest living relative. John Hawks offers a succinct reply, one which is supported by my (admittedly rushed) reading of the paper.

Ref: John R. Grehan & Jeffrey H. Schwartz. Evolution of the second orangutan: phylogeny and biogeography of hominid origins. Journal of Biogeography, 2009 DOI: 10.1111/j.1365-2699.2009.02141.x

Update (6/30): The paper is available online here.

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  1. Cuthbert
    June 30, 2009 at 9:23 am

    Not a very objective reply I have to say, especially coming from a scientist. On closer reading of the paper one will find that there is some subjectivity in the human origins debate. The main message is this: morphological evidence for a human-Orang relationship is rejected based on molecular evidence. This implies that molecular data is superior to morphological data. This of course ignores the fossil data that paleoanthropologists use for a majority of their hypotheses.

    An objective way to view this debate is to treat both forms of data as equally relevant. There is only one problem with this: add them together and you get a orang – chimp – human polytomy. This does not help those in human origins research who require a human-chimp relationship in order to make hypotheses about dispersal routes and origins. Furthermore paleoanthropology is based in morphology. Accepting molecular over morphological evidence completely undermines their field (at least any hypothesis dealing with morphological phylogenetics) . But sometimes people like John Hawks, for instance, may need to turn a blind eye to some evidence in order up-hold a pet theory. After all, chimps are very cute and “Out of Asia” doesn’t sound that great.

  2. John Grehan
    June 30, 2009 at 10:02 am

    The Cuthbert comment is pretty much on the money. I have not yet seen Hawks’ response as the web page shows up as blank apart from the title. I an guess that Hawks’ will either repeat the claim that molecular evidence is somehow better, or that our morphological evidence is wrong.

    There are plenty of problems with molecular analyses from a cladistic viewpoint and this problem has gone largely unchallenged. There is often the rhetorical representation of molecular similarity as ‘genetic’ as if morphology is somehow not ‘genetic’, yet molecular comparisons are really about a DNA morphology that amounts to bean counting of objects (bases) for which no one knows their evolutionary replacement.

    Everything is taken at face value in molecular analysis. In morphology one can individually evaluate each homology claim. In this respect morphology is potentially superior as a source of phylogenetic evidence.

  3. June 30, 2009 at 10:06 am

    Schwartz has been banging this drum since the early 80’s – i.e before the advent of many of the advances in molecular data and analysis that strengthen the claim that chimps are our closest living relative. While Hawks’s reply may be “[n]ot a very objective” one, it represents the consensus of the community, both palaeontological and molecular regarding this issue. Schwartz’ use of the morphological evidence has been questioned in the past (see for example, this review). His dismissal of molecular evidence is tenuous and ignores known problems (e.g. homoplasy) with morphological data. It is notable that the editors of J. Biogeog. issued an apologia of sorts for the paper, admitting that the study wasn’t the sort of thing that they normally published and that the methods (even for biogeographers) were controversial.

    As an aside, if paleontologists rely mostly on morphological (fossil) data, and it is the molecular folks (e.g. John Hawks) that support the human-chimp relationship, how come Schwartz has received so little support from paleontologists who should, by your estimate, be all for use of morphology over molecules? How come Grehan & Schwartz could not get the paper published in, for example, Journal of Human Evolution? Is it possibly that the paper would have been unconvincing even to individuals pre-disposed to weighting morphology over molecules? (Let’s leave aside conspiracy theories, shall we? Schwartz is a senior member of the community and has worked with the likes of Ian Tattersall).

    I write the above as a morphologist who has for nearly 20 years argued for the continued relevance of morphological data in testing evolutionary hypotheses. You cannot completely ignore either molecular or morphological data. However, the fossil record is patchy just at the point where we’d like further data and until that data appears, I’m willing to take the molecular data as providing our best current hypothesis.

  4. June 30, 2009 at 10:09 am

    In this respect morphology is potentially superior as a source of phylogenetic evidence.

    The key word here is, of course, “potentially”. The superiority needs to be demonstrated.

  5. June 30, 2009 at 10:29 am

    This post by Brian Switek reminds me of how the issue of whale evolution has become clarified over more-or-less the same time period that Schwartz has been proposing the orang theory.

    During the 1980’s and 1990’s there was a heated “fossils vs. proteins” debate about whale ancestry. Paleontologists favored an extinct group of predatory mammals called mesonychids as whale ancestors based on anatomy while molecular studies consistently grouped whales close to or even within artiodactyls. The debate was resolved with the discovery of more fossil evidence (primarily distinctive ankle bones) such that the fossil evidence confirmed the molecular hypothesis. A new, more complete understanding was reached through this debate.

    So what we have here is that the limited fossil evidence said one thing, while the molecular evidence said another. The debate was resolved with the discovery of further fossils and the molecular evidence was shown to be right all along. Subsequent work in evo-devo then fleshed out these results. It’s a wonderful example and one that I use in class all the time.

    I’m not much of a betting man, but I’m willing to bet that future fossil finds will vindicate our belief in the close relationship between Pan and Homo and our African origins.

  6. John Grehan
    June 30, 2009 at 10:42 am

    Well, the superiority of molecular evidence has yet to be demonstrated either.

  7. John Grehan
    June 30, 2009 at 11:11 am

    Hawks’ reply (which I have not seen) cannot represent the consensus, only the majority. The hominid origins paper goes into the molecular problems in some depth and the ‘dismissal’ (after due consideration) does not ignore ‘known problems’ such as homoplasy. The hominid origins paper deals directly with homoplasy through phylogenetic analysis that demonstrates the human-orangutan relationship as the most congruent set of data. The character relationships that do not fit with this tree are the homoplasies. Quite simple really.
    Yes the methods are controversial, but this has nothing to do with their intrinsic veracity.

    The reason why Schwartz received so little support from the paleontologists is that he came up with the ‘wrong’ answer.

    Paleontologists supporting the molecular theory of human origin are caught up in a paradox. If the molecular claims are the truth, then their field is not science (not independently predictive), so they try to say if morphology is all we have then it is ok (as if some how crap can be turned into gold if it is all there is). Molecular evidence is useless for reconstructing the fossil record if it cannot be integrated, and if morphology of the living AND the fossil gives a different answer, then the molecular evidence is uninformative no matter how much one might prefer it.

    How come we could not get published in the Journal of Human evolution since we never tried? The article was about biogeography and phylogeny and Journal of Biogeography is a major scientific journal with high academic standards and the paper got intensive review by experts in the field of hominid origins (so no need to introduce the possibility of conspiracy).

    Preference for molecular data in the absence of sufficient fossil data (whatever sufficient might be) does not solve the problem that molecular similarity cannot integrate the living with the fossil.

  8. John Grehan
    June 30, 2009 at 11:13 am

    The whale case does not prove anything either way for hominid evolution. While one might bet on the future, there is no shortage of fossil data for the australopiths and so far the evidence clearly places them within a human-orangutan clade. Australopiths even look more like orangutans.

  9. June 30, 2009 at 2:01 pm

    The example was not meant to “prove anything either way”. It was meant to illustrate that history tells us that inferences based on the fossil record can be overturned by future discoveries.

  10. June 30, 2009 at 2:03 pm

    “Everything is taken at face value in molecular analysis”

    That’s a little bit of a sweeping statement, now isn’t it?

  11. June 30, 2009 at 4:56 pm

    John L: Thanks for the quote. If you want more information let me know and I can send you some more details. The use of evo-devo to understand the origin of feathers and the “phase shift” of dinosaur fingers has also been an interesting case of interdisciplinary work and debate.

    John G: Based upon what? Outside of a fleeting reference in the A. afarensis section in “The Last Human” and Schwartz’s work I have never seen anyone suggest that australopithecines point to a human-organ clade. Saying that Australopithecus “looks more like orangs” doesn’t make sense given that you provide no other alternative (more like orangs than what?) and you do not provide any references.

    Contrary to what you said, the whale example is a good fit for the claims of those who maintain a human-orang clade. If the fossil and molecular data are truly in conflict then further discoveries of early hominins/stem hominids will be required to test the competing hypotheses. The problem is that the fossil record of chimpanzees, gorillas, &c. if very poor and we are going to need to understand their history as well as our own to further clarify relationships. That being said, that there is a human-orang clade is an exceptional claim and as such requires exceptional evidence.

  12. June 30, 2009 at 5:02 pm

    John G: Sorry, forgot for a moment that you were one of the authors of the paper, which I have indeed read. Like I said, however, I think this issue is a fair parallel of the debate over whale origins. Those who support an orang-human clade based solely upon anatomical/fossil evidence are making predictions about where transitional fossils might be found that contrast with those based upon molecular or anatomical + molecular evidence. To prove your case, those transitional forms will have to be found (especially if you rule out molecular evidence in supporting your cause).

  13. John Grehan
    June 30, 2009 at 6:43 pm

    Not necessarily – in the sense that DNA bases are taken at face value in the absence of any evidence of their prior condition.

  14. John Grehan
    June 30, 2009 at 6:44 pm

    ok – no worries.

  15. John Grehan
    June 30, 2009 at 6:50 pm

    If you read the hominid origins paper with the details outlined in Table 2 in the appendix you will see that australopiths share several unique features with orangutans and their fossil relatives. Examples include the forwardly directed zygomatic roots, the vertically inclined zygomas, the broad cheekbones, the posterioly thickened posterior palate. The cheekbone characteristics contribute to the overall orangutan appearance which is also evident in the absence of the African ape interorbital torus and sulcus.

    There is nothing intrinsically exceptional in the orangutan claim as it is based on ample morphological evidence. If anything is exceptional it is the molecular claim of infalibility on hominid origins

  16. John Grehan
    June 30, 2009 at 6:54 pm

    No worries. Not sure what a ‘transitional form’ might be (australopiths are transitional in that they represent orangutan relatives that happen to be bipedal. But predictions are part of science, and the orangutan hypothessis leads to the prediction that other hominid fossils will also conform to the human-orangutan clade, and that future earlier hominid fossils will also. In making these novel predictions the orangutan analysis already represents a theoretical progressive research program, and if it is corroborated by future fossil discovery then it will be an empirical progressive research program. By the way, the Taung juvenile has an orangutan-like incisive foramen.

  17. SLPage
    July 1, 2009 at 1:06 pm

    Schwart also recently published a paper attacking the concept of molecular clocks and used this to rail against molecular phylogenetics. His paper was not very good and, to me, indicated a rather shallow grasp of the field. His paper was remarkable in its rather unprofessional attack against some recent molecular-based papers, including an author I consider a personal friend. I contacted him about it, and did not feel that Schwartz’s rant was worth a response. Such is the level of “controvery” Schwart generates in the field.

    News magazines, it seems, make more of it than is warranted.

  18. SLPage
    July 1, 2009 at 1:13 pm

    Perhaps, but that is no reason for a scientist to concoct farcical arguments against the entire field, as Schwartz did in his paper on molecular clocks.

  19. SLPage
    July 1, 2009 at 1:14 pm

    And what is the evidence indicating the prior condition of a morphological character?

  20. John Grehan
    July 1, 2009 at 1:15 pm

    Why not give some details by specifying the paper and exactly what you found objectionable?

  21. John Grehan
    July 1, 2009 at 1:17 pm

    Glad you acknowledge the fact.

    Please specify the paper and what was farcical in your opinion?

  22. SLPage
    July 1, 2009 at 1:18 pm

    John:
    “So what we have here is that the limited fossil evidence said one thing, while the molecular evidence said another. The debate was resolved with the discovery of further fossils and the molecular evidence was shown to be right all along. ”

    The same thing happened in Primate phylogeny. Morphological analyses origially indicated a baboon-mandrill clade and a mangabey clade, molecules said mandrill-terrestrial mangabey, baboon-arboreal mangabey clades. Fleagle re-examined anatomical evidence and found support for what the molecules said.

    I know, I was in on some of the molecular studies. Of note, at no point did we belittle the morphologists or declare the whole field to be unreliable. It seems that only those desperately hanging on to pet notions engage in this sort of unprofessional behavior.

  23. SLPage
    July 1, 2009 at 1:21 pm

    It is at my office, so I don’t recall the specifics, but one the them was the erroneous attribution of the reliance upon the concept of a molecular clock by molecular phylogenetics.

  24. John Grehan
    July 1, 2009 at 1:23 pm

    Out group comparison of the character state (that may ore may not be supplemented by developmental information).

  25. SLPage
    July 1, 2009 at 1:26 pm

    “But sometimes people like John Hawks, for instance, may need to turn a blind eye to some evidence in order up-hold a pet theory.”

    Interesting. The last lines of the review of Schwartz’s ‘The Red Ape’ are apropos:

    The message of The Red Ape will be productive only in inverse relation to the blind allegiance with which its devotees support it. The Red Ape comes close to a case of the pot calling the kettle black.

  26. SLPage
    July 1, 2009 at 1:27 pm

    One can do the same for bases. Huh…

  27. John Grehan
    July 1, 2009 at 1:27 pm

    You said “Of note, at no point did we belittle the morphologists or declare the whole field to be unreliable”. That is great, but that is not what is happening with the human-great ape relationship. Molecular theorists have belittled morphology, calling the orangutan theory “loopy” and perposterous nonsense”.

    I’m not sure if those molecular theorists would being considered as “desperately hanging on to pet notions engage in this sort of unprofessional behavior”

  28. John Grehan
    July 1, 2009 at 1:29 pm

    Yes, but because any one base is replaced by another, rather than showing evidence of a transforamtion, there is no way to individually know if the condition within or outside the ingroup is primitive or derived.

  29. John Grehan
    July 1, 2009 at 1:33 pm

    Where did the quote regarding John Hawks come from?

    What is the point you are tyring to make with the review comment?

  30. July 1, 2009 at 6:09 pm

    Folks,

    I am aware that this thread has gotten a little confusing now that I switched off comment-threading (it wasn’t really working well in any case). Sorry about that. Hopefully some of the discussion can be recreated.

  31. July 3, 2009 at 12:00 pm

    Does someone care to explain to me how (if the molecular phylogeny is fatally flawed by its phenetic nature) Strait & Grine 2004 managed to infer a phylogeny based solely on morphological data using cladistic parsimony analysis that was congruent with the molecular results i.e. what’s the get out of jail free card for their Pan-Homo clade?

    This sort of paper reiterates the problem we have with regarding “character state” morphological approaches. Anyone can decide on some characters, plug them into PAUP and generate a tree that makes no sense- and tell the world that they have real incite unlike all the others.

    No wonder people look at me suspiciously when I tell them I’m interested in morphological phylogenetics.

  32. questionableauthority
    July 3, 2009 at 1:13 pm

    @John Grehan

    Molecular theorists have belittled morphology, calling the orangutan theory “loopy” and perposterous nonsense”.

    Belittling a particular (or peculiar) hypothesis is not the same thing as belittling the use of morphological data in general. And, with all due respect, “preposterous” does not seem to be an excessively harsh criticism under the circumstances.

    Even if we ignore the existence of other morphological analyses that reach different conclusions than yours, this isn’t a case where we’re talking about a dataset that a couple of gene jockeys cooked up with some surplus grant funding.

    The genetic evidence for the human-chimp clade is longstanding. It includes many different studies of many different genetic characters. You’re not dismissing a single study or method; you’re choosing to ignore the results of many studies, conducted at many different labs over several decades, that used different sets of characters and different analytical techniques.

    Given a choice, I’d much rather have our closest relatives be orangs rather than chimps. They’re more fun to watch, my subjective impression is that they’re more intelligent, and I’m a hardcore Pratchett fan. However, even after reading your study, I see no reason to doubt that the chimps are more closely related.

  33. John Grehan
    July 5, 2009 at 6:20 am

    Belittling a particular (or peculiar) hypothesis may not the same thing as belittling the use of morphological data in general, but the context of the responses to the orangtuan evidence is that morphology, in general, is unreliable and phylogenetically meaningless without molecular corroboration (which is another way of science that mohological phylogenetic analysis is not science).

    “And, with all due respect, “preposterous” does not seem to be an excessively harsh criticism under the circumstances.” – I did not infer that it was excessively harsh, but in the absence of a reasoned argument, such responses are tautamount to ‘belittling’ – in my opinion of course.

    “Even if we ignore the existence of other morphological analyses that reach different conclusions than yours” – at least we did not ignore them.

    “this isn’t a case where we’re talking about a dataset that a couple of gene jockeys cooked up with some surplus grant funding.” – We never said it was.

    “The genetic evidence for the human-chimp clade is longstanding.” – Its actually quite recent, from the 1960’s.

    “It includes many different studies of many different genetic characters.” – Yes that is true, but so what?

    “You’re not dismissing a single study or method; you’re choosing to ignore the results of many studies, conducted at many different labs over several decades, that used different sets of characters and different analytical techniques.” We do not ‘ignore’ them, but provide explanations as to why those internally consistent results may get the wrong answer. The analytical techniques are all cluster techniques so it does not matter that they were different. They cannot elimiate the underlying problem of primtive retention.

    “However, even after reading your study, I see no reason to doubt that the chimps are more closely related.” I guess the converse might be that I see no reason do doubt the orangutan theory. But this is just a statement of belief. It is not sceince. Science is all about doubt. Without doubt there is no progress – in my admittedly biased opinion.

  34. July 5, 2009 at 7:43 pm

    @John Grehan

    So I’m just wondering how you account for the distribution of ERVs between Homo, Pan, Gorilla and Pongo. The pattern would seem to indicate that Pan is closer to Homo than Pongo. Or does that get ignored?

  35. slpage
    July 6, 2009 at 3:41 pm

    “Where did the quote regarding John Hawks come from?”

    The first response by “cuthbert.”

    “What is the point you are tyring to make with the review comment?”

    It should have been obvious – it was ironic.

  36. slpage
    July 6, 2009 at 3:43 pm

    “You said “Of note, at no point did we belittle the morphologists or declare the whole field to be unreliable”. That is great, but that is not what is happening with the human-great ape relationship.

    Perhaps it has something to do with the fact that such a position flies in the face of the overwhelming majority of the evidence?

  37. John Grehan
    July 6, 2009 at 4:26 pm

    One often sees reference to the “overwhelming majority of the evidence” but it is a facade that obfuscates the problem of shared primitive retention and shared derived novelty that is the key to systematic relationships. If one fails to restrict analysis to apomorphic conditions in morphology, the “overwhelming majority of the evidence” in morphology will also support the chimpanzee and African ape relationship. The ‘majority’ is of itself not the delineator of relationship, only the majority of apomorphies within the ingroup. It is in this aspect that molecular comparisons are problematic and have so far failed to provide an empirical defense showing that the bases are really apomorphic.

  38. July 6, 2009 at 11:14 pm

    Yes, but because any one base is replaced by another, rather than showing evidence of a transforamtion, there is no way to individually know if the condition within or outside the ingroup is primitive or derived.

    I haven’t been involved in phylogenetics, but I thought most modern methods were likelihood-based and averaged over the possible ancestral states. This criticism would then be irrelevant.

    Would anyone who knows more about phylogenetics be able to comment?

  39. John Grehan
    July 7, 2009 at 5:21 am

    BobOH said “I thought most modern methods were likelihood-based and averaged over the possible ancestral states. This criticism would then be irrelevant.”

    One might thinks so, but this helps make my point. In the absence of having any empirical knowledge of the phylogenetic meaning of individual bases, analyists have to resort to elaborate clustering methods (over which they argue with each other as to which is correct). Maximum likelihood seems to be just a computational way of guessing what the right answer is and then seeing how close the data fits that theory. As an ‘average’ of ancestral states its really just an elaborate measure of overall similarity that generates a result that could be influenced by the overwhelming majority of similarities that are in reality primitive retentions.

    Whether or not one may agree with this perspective, raising the question does show that there are problematic issues in molecular analysis and that it does not necessarily generate self evidence results.

  40. slpage
    July 9, 2009 at 12:02 pm

    But morphologists just guessing as to whether a bony protrusion is pointy or rounded is the best way to assess data.

    Wow…

  41. John Grehan
    July 9, 2009 at 12:22 pm

    Perhaps no worse than trying to figure out whether C was preceded by A, T, G, or even itself an unknown number of times.

    Morphology does involve judgment calls on character comparisons and shape or linear qualities are particularly problematic. There are many examples of poorly described morphological characters in systematics, and hominid systematics is no exception. The test of the future will be whether the unique similarities proposed for humans and orangutans stand up to further scrutiny. So far most have, and the number remaining still far exceed the one or two features for humans and orangutans.

    Wow…

  42. July 9, 2009 at 12:26 pm

    I’ll repeat this again as it may have been lost:

    @John Grehan

    So I’m just wondering how you account for the distribution of ERVs between Homo, Pan, Gorilla and Pongo. The pattern would seem to indicate that Pan is closer to Homo than Pongo. Or does that get ignored?

  43. slpage
    July 9, 2009 at 12:39 pm

    “One often sees reference to the “overwhelming majority of the evidence” but it is a facade that obfuscates the problem of shared primitive retention and shared derived novelty that is the key to systematic relationships.”

    Ah, just a facade. It is amazing how all those folks who pioneered and refined the methodologies employed in molecular phylogenetics just couldn’t see the truth, and how we have had to rely on a handful of non-molecular phylogeneticists (at least one of whom seems to believe that the field relies entirely on the concept of the universal molecular clcock) to reveal the TRUTH.

    But seriously, molecular systematics uses outgroups, too. And we really, really have taken the things you mention into account (hard to believe, I’m sure). Here are a couple papers that have analyzed the Great Ape issue using molecules:

    Catarrhine Phylogeny: Noncoding DNA Evidence for a Diphyletic
    Origin of the Mangabeys and for a Human–Chimpanzee Clade
    http://homopan.wayne.edu/Publications/2001/MPE_page_2001.pdf

    DNA hybridization evidence of hominoid phylogeny: Results from an expanded data set
    http://www.springerlink.com/content/p5570q7703n65593/

    Ribosomal RNA gene sequences and hominoid phylogeny
    http://mbe.oxfordjournals.org/cgi/content/abstract/7/3/203

    All wrong, according to you. Noncoding DNA, coding DNA, mtDNA analyses. MP, ML, NJ methods – all wrong.

    How to explain this then, I wonder:

    Gene trees and the origins of inbred strains of mice
    http://www.sciencemag.org/cgi/content/abstract/254/5031/554
    “Phylogenetic analyses of 144 separate loci reproduce almost exactly the known genealogical relationships among these 24 strains.”

    Just a big coincidence, I suppose, while had a crack team of molecule-rejecting morphologists examined these mice, they could have reproduced the true phylogeny with 100% accuracy, no doubt.

    Pardon my sarcasm, but I find the notion that all techniques and all analyses employing molecules – NONE of which have indicated a closer kinship between orangs and humans than between chimps and humans – must be wrong because Schwartz and his band of merry men, using a carefully selected set of morphological characters, have shown everyone else to be all wrong, and when other morphological studies do not support their claim, those studies myust be bashed, the authors accused of all but engaging in fraud.

    That stinks of… something.

    “If one fails to restrict analysis to apomorphic conditions in morphology, the “overwhelming majority of the evidence” in morphology will also support the chimpanzee and African ape relationship.”

    Funny how one must perform analyses in the way you demand they be done in order to get the same results you do. Reminds me of how IDcreationists claim that you must first accept the notion of Intelligent Design in order to understand their “evidence.” I don’t buy it.

    “The ‘majority’ is of itself not the delineator of relationship, only the majority of apomorphies within the ingroup. It is in this aspect that molecular comparisons are problematic and have so far failed to provide an empirical defense showing that the bases are really apomorphic.”

    Perhaps, and thus it is a good thing that molecular methods do not ignore such things. A serious question – have you or Schwartz ever actually seen a DNA data matrix? Because it really, really, doesn’t seem like you have.
    One can easily spot by a trained eye the patterns of shared apomorphies in such a matrix, just as, I suppose, a trained morphologist can spot such features on a set of fossils.

    And, I suppose Mr.Lynch et al. just don’t get it, either…

    Morphometrics and hominoid phylogeny: Support for a chimpanzee–human clade and differentiation among great ape subspecies
    http://www.pnas.org/content/101/13/4356.abstract

    “Phylogenetic analysis using distance-based methods corroborates the molecular consensus on African ape and human phylogeny, strongly supporting a Pan–Homo clade.”

    And as for the Shoshani paper, in which the authors are accused of just shy of fraud for not coming to the same conclusions you folks did (and since Hezy was killed last year, I don’t suppose he will be able to defend his honor against your unwarranted implications) – their use of 246 characters apparently did not include beard and mustache… If only they had conculted Schwartz first and learned what the BEST characters to use would have been…

  44. slpage
    July 9, 2009 at 12:44 pm

    “Perhaps no worse than trying to figure out whether C was preceded by A, T, G, or even itself an unknown number of times.”

    Like I’ve recently written, I have to wonder if you folks have ever actually seen a DNA data matrix. The polarity of mutation can become quite obvious when taken in a broader context.

    “Morphology does involve judgment calls on character comparisons and shape or linear qualities are particularly problematic. There are many examples of poorly described morphological characters in systematics, and hominid systematics is no exception. The test of the future will be whether the unique similarities proposed for humans and orangutans stand up to further scrutiny. So far most have, and the number remaining still far exceed the one or two features for humans and orangutans.”

    You didn’t read the Shoshani paper, did you?

    “Wow…”

    Wow is reserved for the mind-bending realization that some will, to prop up a pet hypothesis, slander the dead and dismiss decades worth of research performed by hundreds of people.

  45. John Grehan
    July 9, 2009 at 12:49 pm

    It gets a bit silly when I have to be asked if I have read Shoshoni et al 1996. The implication is that I have not, and therefore I am incompetent. The other implication is that slpage regards this paper as providing authoritative evidence. In that case he/she can explain how many of the claimed apomorphies for humans and chimps/African apes are not corrororated (see Schwartz 2005, Grehan 2006 – cited in the hominid paper). One of the authors even admited that two of the few features claimed for humans and chimps were clearly wrong.

    wow…

  46. slpage
    July 9, 2009 at 1:01 pm

    “It gets a bit silly when I have to be asked if I have read Shoshoni et al 1996. The implication is that I have not, and therefore I am incompetent.”

    Not having read a paper is not incomptence. Accusing them of purposefully avoiding using characters that would have grouped orangs with humans is… something.

    ” The other implication is that slpage regards this paper as providing authoritative evidence.”

    No, it is my claim that it is amorphological analysis, a fairly extensive one, that not only does nto group orangs with humans but groups oraqngs as a sister group to a gorilla-chimp-human clade. Which is what molecular alayses do, without exception (providing all of those taxa are used in the analysis).

    “In that case he/she can explain how many of the claimed apomorphies for humans and chimps/African apes are not corrororated (see Schwartz 2005, Grehan 2006 – cited in the hominid paper). One of the authors even admited that two of the few features claimed for humans and chimps were clearly wrong.’

    Fine, toss out those two. Is that going to result in orang jumping over gorilla to join human? Or does one have to only use the characters that you folks did for that to happen?

    “wow…”

    Wow, like, why do you keep ignoring John’s question, for one thing…

    But no, hundreds of geneticists and molecular phylogeneticists researching this issue for decades using all sorts of different loci and many different methods are all just plain wrong because they apparently do not do what you think they should, and your little handful of cherry picked morphological characters trumps eberything.

    Got it.

    Wow…

  47. slpage
    July 9, 2009 at 1:05 pm

    Is it correct that JR Grehan has published in Rivista?

  48. John Grehan
    July 9, 2009 at 1:10 pm

    “No, it is my claim that it is amorphological analysis, a fairly extensive one, that not only does nto group orangs with humans but groups oraqngs as a sister group to a gorilla-chimp-human clade.”

    But my point was that most of their evidence is not corroborated. The fact that two were admitted do not invalidate the rest. The authors have never responsed on the rest.

    What do you mean by cheery picking (I have to ask as your previous response shows that I need to make sure of your meaning first).

    “methods are all just plain wrong because they apparently do not do what you think they should”

    I have never said that. What I have said is that there are systematics principles that provide possible explanations as to why a consistent molecualr result is not necessarily correct and could be wrong (note – not necessarily wrong, just could be) in the face of contradictory morhological evidence.

  49. John Grehan
    July 9, 2009 at 1:15 pm

    What Rivista?

  50. July 9, 2009 at 1:23 pm

    @ slpage

    Your longish comment was held up for moderation due to the number of links. Sorry about the inconvenience. I’ll delete the duplicate.

  51. John Grehan
    July 9, 2009 at 1:39 pm

    “But seriously, molecular systematics uses outgroups, too. And we really, really have taken the things you mention into account (hard to believe, I’m sure).”

    Outgroup analysis is part of the cladistic method, but one also needs a homology criterion for each character and that’s where it gets tricky with bases that replace each other with no transitional information.

    I notice that one of the example citations refers to hybridization – a method acknowledged by molecular theorists to be phenetic.

    “NONE of which have indicated a closer kinship between orangs and humans than between chimps and humans – must be wrong because Schwartz and his band of merry men, using a carefully selected set of morphological characters, have shown everyone else to be all wrong, and when other morphological studies do not support their claim, those studies myust be bashed, the authors accused of all but engaging in fraud.”

    Thank you for acknowledging that our characters have been ‘carefully selected” – yes we did our best to make sure that they were corroborated apomorphies and provide documentation of the evidence (which has been lacking in other studies).

    We do no ‘bashing’ but took the time to go through each character proposed in support of human-chimp and human-African ape relationships and establish whether or not they could be verified.

    distance-based methods – these are also phenetic measures of relationship.

    “Funny how one must perform analyses in the way you demand they be done in order to get the same results you do.”

    No – that is incorrect. One would not necessarily get our results if there were indeed more human-chimp apomorphies than human-orangutan.

    “the authors are accused of just shy of fraud for not coming to the same conclusions you folks did”

    You are insinuating that accusation. I am not.

    (and since Hezy was killed last year”

    I am very sorry to hear that. I did not know. But much of his data came from Colin Groves who is active in the field.

    “their use of 246 characters apparently did not include beard and mustache… If only they had conculted Schwartz first and learned what the BEST characters to use would have been”

    Groves and others can evaluate our charactes and falsify them and counter argue that their features are correct. I welcome and look forward to such a response.

    That’s it for me today.

  52. John Grehan
    July 12, 2009 at 1:13 pm

    John Lynch said “So I’m just wondering how you account for the distribution of ERVs between Homo, Pan, Gorilla and Pongo. The pattern would seem to indicate that Pan is closer to Homo than Pongo. Or does that get ignored?”

    I would be interested to see John Lynch explain how their results indicate that Pan is closer to Homo than Pongo.

    John Grehan

  53. July 12, 2009 at 1:41 pm

    The Gorilla-Pan-Homo clade has two ltr ervs that differentiate that clade from Pongo. That would seem to indicate they form a group excluding Pongo.

    In addition, Carl Zimmer points out that Alu inserts tell a similar story. See the thread I linked to earlier.

  54. July 12, 2009 at 1:43 pm

    It would also be preferable to move the discussion of the erv evidence over to that thread.

  55. July 13, 2009 at 6:57 am

    What Rivista?

    Rivista di Biologia. It has a bad reputation, having published papers by the likes of John A. Davison (an infamous crank).

  56. John Grehan
    July 13, 2009 at 7:49 am

    So everyone who has published in Rivista di Biologia is a crank?

    How did Bob O’H know what jouornal slpage was referring to?

  57. July 13, 2009 at 8:19 am

    The journal has a reputation amongst Darwinoids who follow (and laugh at) creationists. I’m guessing that’s what slpage meant, but I’m pretty sure I’m right. I don’t think publishing in Rivista means you’re a crank, but suggests that your work might not always be of the highest quality. And yes, it is nothing more than a cheap shot.

    P.S. what about the ERVs issue?

  58. John Grehan
    July 13, 2009 at 8:33 am

    Joh Lynch wrote: “The Gorilla-Pan-Homo clade has two ltr ervs that differentiate that clade from Pongo. That would seem to indicate they form a group excluding Pongo.”

    Are these ltr ervs uniquely identical or do they share unique base substitutions?

    By the way, none of the ltr’s listed in this paper support a human-chimp clade.

  59. John Grehan
    July 13, 2009 at 8:37 am

    Bob O’H wrote “The journal has a reputation amongst Darwinoids who follow (and laugh at) creationists. I’m guessing that’s what slpage meant, but I’m pretty sure I’m right. I don’t think publishing in Rivista means you’re a crank, but suggests that your work might not always be of the highest quality. And yes, it is nothing more than a cheap shot.”

    Irony here is that when one mentions publishing in prominent ‘mainstream’ journals as possiblity indicating soemthing about the quality of the work, one then gets the response that the source of publishing has no necessary relationship to the quality. I am inclined to agree.

    “P.S. what about the ERVs issue?” just responded.

  60. sparc
    July 18, 2009 at 10:21 pm

    Isn’t the “blockquote” tag working in the comment section? Its use would make comments more readable.

  61. July 18, 2009 at 10:25 pm

    Yes it does.

    .

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