Thursday, February 26, 2015

Lingham-Soliar's (2015) Galileo complex

Hooo-eeee, Theagarten Lingham-Soliar (2015) just published volume 2 of his work "The Vertebrate Integument."  Sure sounds scholarly, and parts of it are, but the last chapter is something else.

Before the end

The preceding chapter also has some fun parts, such as section 6.4- "Sinosauropteryx, A Basal Theropod."  Well, it's not exactly basal, that would be more like Eodromaeus, or coelophysoids.  He then goes on to say "Given the importance of Sinosauropteryx as a basal dinosaur with alleged protofeathers."  Wait, now it's a basal dinosaur?!  He repeats this again in section 7.4.1.  Try 'basal coelurosaur' if you want the term to be meaningful.

Lingham-Soliar follows this with section 6.5- "Pushing Feathered Dinosaurs into the Mid-Triassic", based on Xu et al.'s (2009) Beipiaosaurus paper.  The Mid-Triassic part is based on a quote in their concluding paragraph where they note the resemblance of coelurosaurian integument to Psittacosaurus' quills and pterosaurian pycnofibers, though Lingham-Soliar conveniently cuts out the pterosaur part from his quote.  Perhaps the greater similarity to pycnofibers and certainty of a Middle Triassic (if not earlier) basal ornithodiran wasn't as insultable as dragging feathers rootward to hypothetical Middle Triassic dinosaurs based solely on quills in one ornithischian?

Notably, Lingham-Soliar doesn't seem to believe in pycnofibers either.  At least he finally realizes the vast majority, if not all, of pterosaur researchers accept fuzzy pterosaurs (unlike his 2003 paper, or Feduccia from 1996 onward*), though in the end he punts the question- "Given the dismal accounts in the literature of so-called protofeathers in non-avian dinosaurs, e.g., Sinosauropteryx (see Chap. 6), the subject of pycnofibers and their alleged functions such as thermo-regulation and warm-bloodedness will not be discussed any further here."

* The funny thing here is he says "Although it was thought to have been based on an unfortunate interpretation of Sharov’s (1971) description of hair-like structures in the pterosaur Sordes pilosus", in reference to the idea of fuzzy pterosaurs, he leaves out who thought that.  The answer is himself and Feduccia.  But instead of taking responsibility and admitting the BANDits and himself were so grossly ignorant of the pterosaur literature that they misunderstood fuzzy pterosaurs as being based on a misunderstanding of a 1971 paper, he uses the passive "it was thought."  "Mistakes were made..."

I'm being oppressed! (these titles write themselves)

Anyway, on to chapter 7- "The Last Best Hope."  Lingham-Soliar actually begins by retelling the story of Galileo's persecution by the Catholic church and of Nazis excluding Jews from scientific research in 1930s Germany.  Because Larry Martin died while under house arrest for his views and Alan Feduccia was kicked out of his position at the University of North Carolina, amirite?

A section on peer review follows, bemoaning the bias that can exist in the system.  The ironic thing here is that I completely agree, but what I find disturbing are all of the falsehoods that slip through peer review in Feduccia's papers.  And where are many of those published?  In The Auk, published by the American Ornithologist' Union, where Feduccia is a fellow.  And who is credited with reviewing e.g. Feduccia's (2013) "Bird origins anew" paper in that journal?  Burnham, Czerkas, James, Ruben, Lingham-Soliar, Zhou, and two I haven't heard of.  What an unbiased lot!  There's some phrase about pots and kettles that seems appropriate here...

Page 302 is where things start to get silly- the first figure in this chapter is a cartoon of The Emporer's New Clothes.  Because Prum's (2003) statement "current critics of the theropod origin of birds are not doing science" is analogous to telling Feduccia he needs to see a nonexistent item, or something.  Several figures follow using redrawn scenes from Tim Burton's Alice in Wonderland movie, with quotes changed to deride cladistics.  Well if that's not convincing, I don't know what is.  Lingham-Soliar then scolds Nature senior editor Henry Gee for a post on the vrtpaleo mailing list where he accurately criticized BAND for not using cladistics, correctly stated to be the accepted form of phylogenetic inference in the scientific community.  Little did I realize this is "pure censorship."  What's especially ironic is Lingham-Soliar's description of this as an inappropriate "outburst" with "purple prose", when Gee wrote that post in reply to Storrs Olson.  Has he ever read Olson's writing?!  I can't think of anyone in paleontology who writes less professional pieces and gets them published- cladistics was "elevated to a religion years ago", one has to "to suppress one's gag reflex" to read about living dinosaurs, the whole story of Chinese feathered dinosaurs "is essentially a hoax" and "the information has been suppressed" regarding Jehol non-theropods with filaments.  

But Lingham-Soliar is not to be outdone by Olson.  Having already implicitly compared the situation to Galileo and Nazi Germany, he now writes BADists "then state that most scientists support their view, which ironically dominates "primetime" magazines. The regime in apartheid South Africa also said that most people in the country supported its ideology - the fact that most opponents were prevented a voice seemed a tiny, insignificant detail not worth considering."  Does he really think there's some population of theropod and basal bird workers out there who believe in BAND but are being prevented from publishing that opinion?  All of the theropod workers I know must be very good actors.  He even follows Olson's penchant for referring to BAD in religious terms- "people like Dr. Padian with their reduction of science to evangelical preaching and biblical-like hell and damnation for nonbelievers."  Who knew BANDits get thrown into an eternal lake of fire?

In addition to the Peters-esque conspiracy vibe, Lingham-Soliar is similar to David in claiming his own studies as definitive evidence against Big Paleontology.  The following would fit right in on Pterosaur Heresies- "can there be at least some level of justification for Gee’s (2010) euphoric editorial, i.e., if the finding of melanosomes is correct then the filaments are indeed protofeathers? Alas, it seems not as we discovered in Chap. 6 - the notion of melanosomes in the filaments of Sinosauropteryx was shown to be "without scientific merit" (Lingham-Soliar 2011)."  Ah yes, 'we' discovered it was shown to be wrong- by me!  Also amusing is Lingham-Soliar's constant use of positive adjectives to describe those whose view he supports.  Olson is "Curator of Birds (now Emeritus Curator) at The National Museum of Natural History and one of the most eminent ornithologists in the world", while Norell is "curator of dinosaurs at the AMNH."  A bit better than a janitor, really.  The capitalization, the lack of abbreviation, it's just too good. Similarly, Lingham-Soliar has a penchant for describing his own work with superlatives- "detailed", "rigorous ... which received global attention", "the most revolutionary and explicit images of fiber microstructure in the feather."

BADistics

Lingham-Soliar writes at length about how cladistics is supposedly unfalsifiable, but that's simply untrue.  Any given phylogenetic hypothesis found via cladistic analysis can be falsified by the discovery of a different relationship once new taxa or characters are added.  Bullatosauria was popular for a while, the joining of ornithomimosaurs and troodontids recovered in analyses like Holtz (1994).  What falsified that?  The cladistic analyses of a newly discovered series of basal troodontids (e.g. Sinovenator, Mei) that were more Archaeopteryx-like, not more ornithomimosaur-like.  Indeed, we now have taxa like Anchiornis that blur the line so much that some analyses recover them as troodontids and others as birds.  The last time I checked the parsimony of alternative hypotheses in the Lori matrix, Bullatosauria was actually the least parsimonious of any previously suggested maniraptoriform topology I could think of.  

You want falsifiability?  If Lingham-Soliar is correct that the filaments of non-bird ornithodirans are collagen (and I agree in a minority of cases they are), then where are all of the fuzzy Jehol fish, frogs, lizards, choristoderes, etc.?  These all had collagen in life, so at least a few should be preserved this way if coelurosaurs, pterosaurs and small ornithischians are.  No doubt they've been suppressed as Olson claimed. :|  Or alternatively, present a repeatable method for distinguishing Jehol feathers on birds/maniraptorans from collagen on other ornithodirans.  As far as I know, neither Lingham-Soliar nor anyone else has ever tried to demonstrate Jehol bird filaments are collagen and BANDits have always interpreted them as feathers.

To continue the hyperbole, did you know that because Ernst Mayr drew attention to pitfalls in cladistics, "he was defamed by supporters of cladistics and the dinosaurian origin of birds in a manner reminiscent of Lysenkoism in the Soviet Union."  I must have been too young to remember Mayr being imprisoned in a labor camp and executed.  Similarly, "Erik Jarvik had been the butt of the attack by the cladists in the search for tetrapod ancestors" because he had lungfish closer to tetrapods than coelacanths.  "It turned out Jarvik was subsequently shown to have been right and the cladists at the time, who were highly critical of him, wrong."  So to this day, cladistic analyses of sarcopterygian relationships must be untrusted, right?  No, actually what changed the consensus were better cladistic analyses.  The more extensive cladistic analyses falsified the hypothesis found in the earlier analyses.  Astounding.  And you know what's further tested those analyses?  Cladistic molecular analyses, which used a completely different character set.

In case you're wondering, "the Achilles heel of cladistics" was discovered by Jarvik- "cladists arbitrarily pick out unreliable characters from a list without checking their reliability."  Of course!  Why don't I fire up my objective reliabilitometer more often?!  Or if only there were some method to delete and replace random characters then rerun these permutations multiple times, in order to test the strength of each node if certain characters are deleted and other characters are weighted more strongly.  But that would be as impossible as pulling yourself up by your own bootstraps!

The only good analysis is a BAND analysis

Repeating the ridiculous notion of Feduccia et al. (2005)- "To take one powerful alleged line of support for the theropod origin of birds namely Caudipteryx, Maryanska et al. (2002) in an exhaustive cladistic analysis showed that rather than a theropod dinosaur as proposed by some cladistics studies, Caudipteryx is a flightless bird. This finding remains undisputed."  Undisputed!  Except that Lingham-Soliar is blatantly lying, since Maryanska et al. placed Caudipteryx within Theropoda, even using undisputed(!) theropods such as Coelophysis and Allosaurus.  And except that the result of placing Caudipteryx closer to Aves than Archaeopteryx was disputed by Rauhut (2003), Holtz (2004), Ji et al. (2005), Choiniere et al. (2010) and its variations, Turner et al. (2012), Cau's analysis in Godefroit et al. (2013), Foth et al. (2014), all of the 60+ variants of the TWG matrix published over the last decade and a half, and even James and Pourtless' (2009) terrible BAND analysis.  Indeed, I don't think any other analysis has ever recovered that result.  As for "exhaustive", Maryanska et al. had 20 taxa and 195 characters, so 3,900 total codings.  The analysis of Godefroit et al. had a similar purview but used 101 taxa and 992 characters, resulting in 100,192 codings.  Over 25 times the size, and just to make Jarvik happy, it was reweighted two different ways to emphasize those "reliable" characters.

Needless to say, Lingham-Soliar's discussion of James and Pourtless' analysis is completely uncritical.  I just went over why that analysis was so bad, so no need to repeat it here.  It's ironic that he complains so often about BAD being 'verificationist' yet just accepts that James and Pourtless had valid, meaningful results despite claiming cladistics is "a discipline I am familiar with as a "working scientist" i.e. when I was involved in taxonomy."  What about that pseudosuchian nested sister to ornithomimosaurs?  You didn't notice that because the authors chose not to mention or figure it and you never examined the actual data yourself?  I see, I see...

Lingham-Soliar then complains about a rejection he got, where the reviewer wrote "The author of this paper might be taken more seriously if he did not show such contempt for all other work done on the subject, if he did not ignore all other lines of evidence that he pretends his particular investigation is overthrowing, and if he did not appear so injured by the refusal of the scientific community to recognize his genius."  Haha, that describes Theagarten to a tee.  "That this was a personal assault did not concern the referee and shamefully was wholly supported by the editor-in-chief of a notable US biological/science journal, with the words, "referees are only human." So was Jack the Ripper!"  Why, rejecting poor Lingham-Soliar's manuscript was just like serial murder!  Nazis, Stalin, the Inquisition... what evil characters are left for Lingham-Soliar to equate BADists to?  I got it!  We're the Galactic Empire and Padian is just like Emperor Palpatine, crushing rebellion and silencing dissenters with his force lightning of parsimony!

BranchingGate... no wait, Branchgazi

Alas, that guess was incorrect.  Instead, Xu, Prum and Zhao get compared to Richard Nixon and accused of fraud in the next section.  Why fraud, you ask?  Because Lingham-Soliar doesn't understand how citations work.  In the description of Sinornithosaurus' feathers (Xu et al., 2001), they state "the shorter, unbranched integumental appendages of Sinosauropteryx^2, a basal coelurosaur, are also congruent with the predicted Stage I feather morphology."  Lingham-Soliar thinks "the superscripted 2 refers to Chen et al. (1998) who they cite as making that critical description namely that feather morphology in Sinosauropteryx are "UNBRANCHED" [my emphasis] as support for their model."  And because one line of Chen et al.'s discussion calls the feathers "multibranched", and the last line in the paper suggests feathers evolved from "simpler, branched structures", the authors are "falsifying (OED, misrepresent, distort, (a fact, etc.)) another author’s work."  Here's an innocent explanation- that superscript 2 just refers to citing Sinosauropteryx's latest description, not to any particular interpretation in that description.  Why describe its feathers as unbranched?  Because Prum (1999) in the paper establishing that model wrote "From my direct observations of the two specimens of Sinosauropteryx (Chen et al., ’98), the integumentary structures appear to consist of unbranched filaments about 20 mm long."  Here again, Chen et al. is merely cited as the description, and we can see Prum has his own interpretation of the morphology.  He then says "Additional
examination of the integumental structures of Sinosauropteryx and Beipiaosaurus is required to establish: (1) whether the filaments are branched, unbranched, or hollow."  The truth is that there's still ambiguity, and even the eventual osteology (Currie and Chen, 2001) merely concluded that several features "suggest a feather-like structure with central shafts and plumulaceous barbs" and that "the evidence does favour the interpretation that each has a simple branching structure", but that there was no direct observation of such.  Notable is that Lingham-Soliar later quotes this paper in a way I would describe as misleading as it removes the caveats of uncertainty- "They stated that the integumentary structures comprise "central shafts and plumulaceous barbs" and have a "simple branching structure."  Who's lying now?


It just gets worse from here based on that one misunderstanding of what Xu et al. were citing Chen et al. for in 2001.  Xu et al. (2009) claimed Beipiaosaurus' EBFFs were the first unambiguous unbranched feather, yet they "quite astonishingly" cited the 2001 paper as evidence for prior examples being branched!  Yeah, because the 2001 paper was primarily describing branched feathers of Sinornithosaurus.  The 2001 noting of unbranched feathers in Sinosauropteryx was likely from Prum's 1999 observation, but by 2009 that had been overridden by Currie and Chen's 2001 osteology of the genus, which is indeed cited by Xu et al. in 2009 too.

But wait!  In the slightly later Zheng et al. (2009) description of Tianyulong, "Xing Xu along with his present PNAS co-author Xiaoting Zheng" wrote "In both Tianyulong and Sinosauropteryx, the filamentous structures are singular and unbranched."  Ha!  They can't keep their story straight!  Well, no again.  You see, Theagarten, coauthors sometimes disagree about details and even conclusions, and often have different responsibilities.  If we check the contributions of each paper, Xu wrote the Beipiaosaurus manuscript, and You wrote the Tianyulong one.  Maybe You thinks Sinosauropteryx's feathers are unbranched and thus disagrees with Currie and Chen but agrees with Prum?

So this whole thing is due to Lingham-Soliar not knowing how scientific papers work.  It's not fraud.  There's no massive coverup.  How surprising!

Beating a dead Yanornis-Microraptor chimaera

The next section is a tired recounting of the "Archaeoraptor" story, which Lingham-Soliar should actually be happy about.  Nature and Science both rejected manuscripts of the would-be official "Archaeoraptor" description, and the name and chimaerical misinterpretation only made it into the popular press.  He writes "Archaeoraptor" "has joined the ranks
of paleontological folklore notoriety on a par with Piltdown man", but Eoanthropus (Piltdown man) was accepted by some of the literature for years.  Lingham-Soliar further simply believes Olson's statements that Sloan "decided first, that it was appropriate for a journalist to differentiate a taxon new to science and second that evidence claiming to support the new taxon could be presented in a nonpeer reviewed magazine" and that "the name Archaeoraptor liaoningensis Sloan is now
available for purposes of zoological nomenclature."  Neither is true, as Creisler showed in 2001 on the DML.  If you're thinking citing a mailing list would be problematic, Lingham-Soliar is referencing in part a post by Olson on vrtpaleo here, so DML posts would be up for grabs too.  Next time check The Theropod Database, Theagarten!  I covered the whole story there, with references.  Yet due to his misplaced trust in Olson's accuracy, Lingham-Soliar says "one might think it would have spelt the end of Sloan’s days as an editor of NGM."  Ouch.


Apples to... um... microapples

Believe it or not, in this supposedly technical treatise of vertebrate integument, the penultimate section is "Education and Freedom in Apartheid South Africa."  That's what it's about too.  No paleontology or biology here.  Might I humbly suggest that any comparison between BAD vs. BAND and Apartheid is terribly disrespectful to the victims of the latter?

Theagarten ends the book with a chapter on freedom of press/speech and an appendix which lists the Universal Declaration of Human Rights.  If you want yet more irony, recall what I wrote above about the reviewers of Feduccia (2013).  Yet Lingham-Soliar has the gall to write "All the evidence points to the fact that in Birds are Dinosaurs only potentially favorable referees are chosen."  There's that pot and kettle again.

Actually, it turns out that's not quite how he ends this book.  You see, I didn't read ahead when writing this post.  I've been writing responses as I read the sections in Lingham-Soliar's book.  Remember above, when I guessed "what evil characters are left for Lingham-Soliar to equate BADists to?"  My first thought of a remaining evil was Islamic militants.  But that was too contemporary for me to feel comfortable joking about, so I went with Star Wars.  Yet Lingham-Soliar actually goes there with his Note in Press- "The tragic events in France concerning Charlie Hebdo and Press Freedom is a reminder of those who put their lives on the line for the rights we enjoy in democratic and secular societies - in the words of the children of Soweto [part of his Apartheid section],"the struggle continues." France’s stance against being blackmailed by totalitarian states and terrorists must be applauded lest we become like them."

Wow.

Conclusion

The sad part here is that Lingham-Soliar actually has a very good point about how crappy many peer reviews are.  You don't have to look further than this blog to find examples of miscoding, not coding, poor procedure, etc..  It's in desperate need of revision.  But this is hardly unique to BAD.  Just look at my recent posts- James and Pourtless' paper is sympathetic to BAND and has terrible flaws, Xu et al.'s 2015 defense of a dromaeosaurid species' validity was conceptually flawed and didn't involve birds, Carrano et al.'s ICZN petition seems shady but is about an actual basal theropod with no bearing on bird origins, Norman's 2014 paper with poor understanding and utilization of phylogenetic nomenclature was about ornithischians, etc..  It's not even unique to dinosaurs.  In a manuscript I wrote with David Marjanovic criticizing papers that don't code taxa for characters that are known for those taxa, I wrote about dinosaurian examples, and he wrote about basal tetrapod examples.  I would bet the issue pervades all of science.  Peer reviewers are unpaid, busy themselves, and often not specialists in what they're reviewing.  So they don't check some important things, often don't know what to check for, and are probably often too trusting the author's 'done the work.'  It's a problem.

But what an unhelpful way to present this problem!  It proposes a bias in the rigor of peer review, but any BAD supporter who has read a paper by a BANDit would laugh.  Even ignoring any methodological problems with BANDits, they simply don't know much about dinosaurs.  As a brief example, here are a couple statements made by Feduccia et al. (2005)- which had Lingham-Soliar as a coauthor.  "To illustrate the difficulty of defining the various dinosaur groups, Carroll (1988, p. 290) pointed out that "The 'carnosaur' families may each have evolved separately from different groups that have been classified as coelurosaurs."" "Like the term "thecodont," a collective term to describe Triassic basal archosaurs, coelurosaur and carnosaur describe, respectively, small and large theropod dinosaurs."  Did you realize, Theagarten, that these concepts are so obsolete that no one in the 90s, let alone the 2000s, would take them seriously?  Carroll's cited work is a general vertebrate paleontology textbook written 17(!) years earlier.  Who would ever think that's a valid source for contemporary taxonomy?!  Past the 80s, Coelurosauria has basically always been recognized as the clade of theropods closer to birds than to carnosaurs, including Compsognathus, Ornitholestes, ornithomimosaurs, oviraptorosaurs, dromaeosaurids and troodontids.  Even if you dispute birds belong there, the concept of the group has remained consistent.  The idea that carnosaurs are big theropods and coelurosaurs are small theropods is the kind of simplification of 1920-1970s phylogeny that you read in old childrens books.  So how did such a blatant misrepresentation make it through peer review into your paper?  And there are endless examples like this in BANDit works.  I could say that you and Feduccia are maliciously misrepresenting how well established the consensus of dinosaur phylogeny/taxonomy is.  The same paper also says "the question of whether birds are derived from dinosaurs depends on what one defines as dinosaur, or the Dinosauromorpha", even though the concept of Dinosauromorpha has never been controversial, nor is contingent on the definition of Dinosauria, which itself hasn't been controversial since dinosaur monophyly was established in the 70s.  Is this because the BANDits have peer reviewers that are in cahoots to let bad information through?  No.  It's just that peer reviews are sometimes poor and that you and Feduccia don't know much about dinosaurs.  "Basal dinosaur" Sinosauropteryx... "undisputed" Maryanska et al. 2002...

Next up is your mischaracterization of Prum's (2003) "not doing science" critique as being focused on cladistics.  Far from it.  Prum was criticizing Feduccia for- not explicitly proposing an alternative phylogenetic position for birds (e.g. why or why not are they in Avemetatarsalia, or Archosauria, or Archosauriformes); ignoring how character evidence works together to support or refute hypotheses, instead only taking single characters and disputing their homology, stating a single character is homoplasious, and ignoring the fact convergence can only be shown if the majority of characters support the real relationship; and most importantly for completely contradicting all of his previous work which disputed similarity between dromaeosaurids and birds without any sort of explanation for how he got things so wrong before, and why we should trust his methods now that they've been disproven.  Was your mischaracterization malicious or merely ignorant?

Your paper has continual complaints about free speech, free press, censorship!  But BANDits get tons of media presence.  If we look at everything since Gee's 1999 "censorship" mailing list post, Feduccia's gotten published on the topic of bird origins...
- a 2000 American Zoologist article. 
- a 2001 Journal of Ornithology article.
- a 2001 rebuttal in TREE.
- a 2002 Auk article. 
- a 2002 Naturwissenschaften article.
- a 2003 TREE letter.
- a 2003 Auk book review.
- a 2005 Journal of Morphology article.
- a 2007 Auk article.
- a 2007 Proceedings B article.
- a 2013 Auk article.
- a 2014 Journal of Ornithology Article.
And more, no doubt.  There is an article published almost every year.  He also wrote the book "Riddle of the Feathered Dragons: Hidden Birds of China" from New Yale University Press.  How is Feduccia being prevented from airing his views?  That's not an outlier either.  Martin got plenty of publications, as did Czerkas.  And just look at yourself, Theagarten.  You've had numerous articles published disputing BAD interpretations.  Some were rejected, but EVERYONE gets many manuscripts rejected.  And you got this entire present volume published!  You got to air your accusatory views of a conspiracy in science, via a scholarly publisher.  How is this being censored?  Freedom of speech means you're allowed to say what you want without being a criminal, freedom of press means you're allowed to publish what you want without being a criminal.  Neither means any particular platform, e.g. Nature, has to host your views.


You want to accuse BADists of fraud, but in this very volume you frame the Sinosauropteryx media rush in 1996 as if it preceded  its description ("Soon after [in 1996], without any scientific investigation, a pen-and-ink sketch of the sensational specimen appeared on the front page of The New York Times, as support for the theory.  In 1998, a description of Sinosauropteryx appeared in the journal Nature (Chen et al. 1998).").  You know Sinosauropteryx was officially described, as feathered, in 1996 by Ji and Ji, right?  You falsely state Maryanska et al. (2002) did not recover Caudipteryx as a theropod, and that its results are undisputed more than a decade later.  You conveniently cut out reference to pterosaurs in Xu et al.'s (2009) quote.  You repeat Olson's incorrect allegations "Archaeoraptor" was intended to be established by Sloan in National Geographic and that his article was valid under the ICZN.  Should I accuse you of fraud, or are you just very ignorant of dinosaur research, and never bothered to look up Sinosauropteryx's Chinese description, don't follow theropod phylogenetics papers, didn't bother researching "Archaeoraptor" past what Olson said, etc.?

Finally, it turns out I was wrong.  I wrote in reference to Olson that "I can't think of anyone in paleontology who writes less professional pieces and gets them published."  That was before I read the rest of this document.  Feduccia and Martin display gross ignorance of dinosaur knowledge, Olson has a sharp tongue and tedious fondness for religious analogies, but it's only you, Theagarten, who has compared BAD researchers to the Inquisition, Nazis, Apartheid, Stalin and Al-Qaeda.  That's beyond the pale and completely unprofessional.  Even if everything you wrote were true and there was some massive conspiracy to only allow BAD ideas into Nature/Science/PNAS and the popular media, that would be insignificant compared to the evil of those parties.  Shame on you.  And a hearty **** you on behalf of Xu, Prum and Zhao who you directly accuse of fraud.  Grow up and get serious.

Reference- Lingham-Soliar, 2015. The Vertebrate Integument Volume 2: Structure, Design and Function. Springer, Heidelberg New York Dordrecht London. 348 pp.

18 comments:

  1. I read Volume 2 last weekend and you've written up a splendid summary Mickey.

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  2. Part 1 of 2:

    Lingham-Soliar reminds me strongly of the many, many people on the Internet who completely fail to distinguish criticism from censorship, "that's wrong" from "I'm coming to lock you up".

    Similarly, "Erik Jarvik had been the butt of the attack by the cladists in the search for tetrapod ancestors" because he had lungfish closer to tetrapods than coelacanths.

    Well. Jarvik was the last survivor (quite literally) of the Swedish School (Säve-Söderbergh, Stensiö) which had diphyletic tetrapods: salamanders derived from porolepiforms (thus very close to lungfish), "eutetrapods" including Ichthyostega derived from "osteolepiforms".

    For an astonishingly long time, there was an unrelated controversy over whether the closest relatives of the monophyletic Tetrapoda were the lungfish or the "crossopterygians". Then "Crossopterygii" turned out – by phylogenetic analysis, duh – to be grossly paraphyletic, and the coelacanths turned out to be the sister-group to all other extant sarcopterygians rather than close to the "osteolepiforms" (such as Eusthenopteron). Given how extremely little Lingham-Soliar (and indeed every other BANDit, including people who only ever comment on the Internet and write e-mails) knows about dinosaurs, I bet he has mixed those two controversies up.

    I got it! We're the Galactic Empire and Padian is just like Emperor Palpatine, crushing rebellion and silencing dissenters with his force lightning of parsimony!

    ...the force lightning branching out of his hands like two cladograms...

    BranchingGate... no wait, Branchgazi

    So, -gate is for real scandals and -ghazi for fake ones? I heartily approve. :-)

    "the name Archaeoraptor liaoningensis Sloan is now available for purposes of zoological nomenclature."

    Let's see... just off the top of my head, there's no diagnosis, no explicit declaration of a type specimen, and no explicit declaration of the name as new, right? All of those have been required since 2000, the first two for longer.

    Also, although Lingham-Soliar is in good company on this, the authors' names are not part of a scientific name (at least in Zoology). The year can be cited to show which names have priority, and at such occasions it is customary to also cite the authors in order to provide a rudimentary bibliographic reference. The Code makes quite clear that there's no basis for citing authors without years in order to glorify the authors.

    The sad part here is that Lingham-Soliar actually has a very good point about how crappy many peer reviews are. You don't have to look further than this blog to find examples of miscoding, not coding, poor procedure, etc.. It's in desperate need of revision.

    The greatest problem may be one of the simplest ones: the silly custom of inviting only two reviewers per manuscript*. Even the historical linguists have gone to three. It's really not an uncommon occurrence that the strengths and weaknesses of both reviewers overlap so much that both overlook the same glaring problem which lies just outside their discipline. It's also not an uncommon occurrence that a reviewer spends a total of five minutes skimming the manuscript and writing the review, so instead of two reviews you get a review and a worthless paragraph that tells the authors to do exactly what they did anyway.

    * Except in very rare cases, like when the two reviewers disagree profoundly with each other and the editor can't decide, or of course when a revised manuscript is sent to new reviewers because the old ones happen to be unavailable – my first paper was reviewed by a total of four people.

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    1. Ah, I didn't know about the diphyletic tetrapod thing. Lingham-Soliar only says "Jarvik had been the butt of the attack by the cladists in the search for tetrapod ancestors and was scathingly blamed for a failure to see lungfish relationships developed directly from comparisons among living gnathostomes without as they put it “interruption by futile paleontological searches for ancestors” and delaying the solution to the problem by decades" and "As it turned out Jarvik was subsequently shown to have been right and the cladists at the time, who were highly critical of him, wrong, something considerably downplayed today." He apparently discussed Jarvik in detail in Volume 1, which I don't have. It would be hilarious if Lingham-Soliar got the whole thing wrong.

      "Let's see... just off the top of my head, there's no diagnosis, no explicit declaration of a type specimen, and no explicit declaration of the name as new, right?"

      It didn't even get that far. Sloan explicitly stated the taxon was to be described formally in an later publication, so this runs afoul of ICZN article 8.3- "Names and acts may be disclaimed. If a work contains a statement to the effect that all or any of the names or nomenclatural acts in it are disclaimed for nomenclatural purposes, the disclaimed names or acts are not available."

      "although Lingham-Soliar is in good company on this"

      That was a quote of Olson's Lingham-Soliar believed, so Olson's at fault for listing the author afterward. It does get confusing quoting people who are quoting other people.

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    2. Lingham-Soliar may not have got the whole thing wrong; there were, before Gauthier et al. trounced them in 1988, cladists who believed in all seriousness that fossils are completely useless and that only extant taxa (without SHOCK HORROR missing data) should be used in phylogenetic analysis.

      I don't know where exactly Jarvik thought lungfish go; the discovery that they're close to Porolepiformes is fairly recent.

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  3. Part 2 of 2:

    In a manuscript I wrote with David Marjanovic criticizing papers that don't code taxa for characters that are known for those taxa, I wrote about dinosaurian examples, and he wrote about basal tetrapod examples.

    Does that sentence belong higher up, in the paragraph about disagreements between authors of the same paper? Anyway, I should have time to work on that manuscript again in just a few weeks. :-) There is hope!

    Something funny did happen in the peer review of the previous version of that manuscript, though. After we got the rejection (the manuscript wasn't deemed interesting enough), I noticed that the whole first line was missing from a matrix (a table in the manuscript, not even a supplementary-information file!), so it began with character 46 instead of character 1. I had fixed this problem several times earlier, because our two Word versions somehow couldn't deal with the tables, and evidently I had overlooked that the problem was back when I submitted the manuscript. Neither the reviewers nor the editor noticed. Even when matrices are presented as new, discussion-worthy interpretations, many people treat them like a mass of measurements they couldn't evaluate without repeating all of the work, so they ignore it, and matrices thoroughly infested with typos and similar mistakes are published.

    any BAD supporter who has read a paper by a BANDit would laugh. Even ignoring any methodological problems with BANDits, they simply don't know much about dinosaurs.

    And they're completely unwilling to inform themselves! They're like those Internet creationists who firmly believe that any bit of knowledge they personally don't have cannot possibly exist. And there was desking of heads and palming of faces.

    Did you realize, Theagarten, that these concepts are so obsolete that no one in the 90s, let alone the 2000s, would take them seriously?

    The names Carnosauria and Coelurosauria completely changed their meanings around 1990; before that, they referred to poorly delimited wastebasket taxa, while nowadays they refer to clades. Carroll (1988) was before that. The BANDits, having been asleep since the mid-70s*, haven't noticed the change.

    * ...as shown by everything they say about hadrosaurs, for example.

    the concept of Dinosauromorpha has never been controversial [I'm not allowed to underline]

    That's because it was coined in the context of phylogenetic nomenclature. It comes with an explicit phylogenetic definition. There simply is no question about how to define it.

    not explicitly proposing an alternative phylogenetic position for birds

    Aaah, the "avimorph thecodonts", the first taxon united by common descendants rather than common ancestors. :-) Was it Prum (2003) who put it that way?

    a 2007 Proceedings B article

    Wow.

    Should I accuse you of fraud, or are you just very ignorant of dinosaur research, and never bothered to look up Sinosauropteryx's Chinese description, don't follow theropod phylogenetics papers, didn't bother researching "Archaeoraptor" past what Olson said, etc.?

    Ignorant – and seemingly unable to consider the very idea that he might be ignorant; like the more annoying Internet creationists.

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    1. "Does that sentence belong higher up, in the paragraph about disagreements between authors of the same paper?"

      Nah, it was supposed to be an example of bad peer review outside Dinosauria, with you finding Ruta et al. and Ruta and Coates didn't code codable characters in Ventastega, and their peer reviewers didn't catch that.

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    2. Spoiler alert: now that I got my grubby little paws on Williston (1909) and Douthitt (1917), I just found they also ignored a lot of codable characters in Diplocaulus which haven't been redescribed or illustrated since 1917 (except that a largely useless version of Douthitt's skeletal restoration in dorsal view, without the indications of which bones are actually known, has been reproduced again and again). I don't know how easy those publications were to get in different places around the turn of the millennium... nowadays, Williston (1909) is on JSTOR, and Douthitt (1917) seems to have been scanned by the U of Chicago, which originally published it. Both publications were cited in the Lepospondyli volume of the Handbuch (which dates from 1998 and of course contains the useless version Douthitt's restoration, but doesn't cite a source for it), so it's hardly possible that Ruta & Coates didn't know they exist.

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  4. I wrote:

    Anyway, I should have time to work on that manuscript again in just a few weeks. :-) There is hope!

    Actually... I should look into a few things next week or even tomorrow, while I have the literature I used to lack at arm's length.

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  5. Sinosauropteryx a basal theropod? How does one even think that, even with that view on "Carnosauria" and "Coelurosauria"? That's just baffling.

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  6. Just a note: we may try to establish a way to define what "basal" and "derived" terms mean. While "crown" and "stem" have clear meaning (although often misunderstood...), "basal" and "derived" have not. For example, I don't consider Carnotaurus a "basal theropod", while other may consider it as such.
    Ironically, I consider Homo sapiens as a "basal amniote", as it belongs to the basalmost amniote branch (using a cladogram of the crown amniotes). The fact it's very apomorphic compared to the last common ancestor of amniotes does not affect the fact it's a mammal, thus a member of the first branch diverging among the main amniote crowns: (mammals (turtles, lepidosaurs (crocs, birds))).
    I suspect "basal" and "derived" should be used exclusively as reference terms: for example, stating that "in clade A, X is more basal than Y relative to Z (that is, Y is closer to Z than X)", not "X is a basal A".

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    1. I agree Andrea - I think "basal" and "derived" are just being as more modern-sounding "primitive" and "advanced". There's no conceptual difference that I can make out most times I see it used.

      Sometimes people might be better off just saying "early".

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    2. Yes, I had this dispute in mind as I typed the post. I'll have you know sauropsids are the basalmost amniotes (assuming archosauromorph turtles). ;) The point was that no dinosaur worker calls Sinosauropteryx a basal theropod or a basal dinosaur, whereas Lingham-Soliar does and uses it as a point in his arguments- e.g. "What made this so potentially pivotal was as
      mentioned above Sinosauropteryx’s basal theropod status", "it is Sinosauropteryx’s basal theropod status as well as the apparently primitive nature of the alleged feathers that has made this dinosaur so critical with respect to both bird and feather evolution", "Given Sinosauropteryx’s basal dinosaur status this is probably the most critical part of Xu et al.’s (2001) model." In actuality, BADists are still fine with basally unfeathered theropods and/or dinosaurs, as intriguing as Tianyulong and Kulindadromeus are.

      BTW: I just noticed Lingham-Soliar's figure 5.10 "A reconstruction of Sinosauropteryx, a basal theropod dinosaur" is actually a redrawn picture of Ellison's NGMC 91 illustration, the young possible Sinornithosaurus. Such similar names, right? :|

      BTW part 2, the BTWening- Lingham-Soliar emailed me back after I sent him a link to this, so we may get some explanation or clarification.

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    3. John,

      in fact we may separate the terms referring to position on (atemporal) cladograms to terms referring to timing of divergence (that is linked to branching pattern in cladograms), to terms just related to stratigraphic positions, to term referring to amount of morphological divergence from ancestors. These different concepts are often termed with the same words (basal/derived), but are not necessarily linked: Carnotaurus is both late and apomorphic compared to basalmost theropods, about the same as Tyrannosaurus is, but is more basal than the latter using relationships. The latter also is linked to what we assume is "the derived condition". For example, the widespread (and implicitly assumed) concept that birds are "the most derived theropods" may perhaps be correct assuming the number of branching events we obtain from current theropod cladograms, or the amount of morphological divergence from the root (although I suspect this is biased by accuracy of characters used to test hypotheses more than "reality"), but is misleading if we consider that "Theropoda" was coined for Allosaurus (and two synonyms of Allosaurus), not for birds. Thus, based on both relationships and historical origin of the term, Sinraptor is a theropod more derived than birds, being it closer to the taxon always anchored to the theropod word since its erection (Allosaurus).

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    4. "Basal" means "far away from the clade(s) I'm most interested in at the moment". Nothing less, nothing more.

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    5. I'll have you know sauropsids are the basalmost amniotes (assuming archosauromorph turtles).

      That assumption is unnecessary; it's been a long time since anybody thought the turtles are the sister-group to all other amniotes.

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  7. By the way, this isn't just restricted to BANDits - I've been sitting in an ornithology class where it was (rather begrudgingly) concluded that theropods are probably the ancestors or birds, but while teaching the "controversy" a multi-decade old phyletic diagram was trotted out that "basically everyone would agree with, except for where birds go". The diagram had pterosaurs, dinosaurs, and crocodiles emerging from "thecodonts", and in theropoda it was just carnosauria and coelurosauria, with tyrannosaurs in carnosauria and Coelophysis in coelurosaurs.

    Along those lines, it was also repeated as a mantra that the fossil record is very incomplete so we "can't know the answer for sure". While obviously no one would dispute the lack of completeness in the fossil record, it seems that this has become more of an excuse to not bother learning what fossil evidence there actually is available.

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  8. Mickey, this is great stuff. I really hope that you consider publishing this (and, indeed, many of your other excellent rebuttals) in a more formal venue.

    I prob should no longer be surprised at the amount of poor (non-) science performed by Feduccia, Lingham-Soliar, and their ilk but I am still occasionally gob-smacked by how much of it reads more as wilful ignorance rather than simply a more excusable lack of knowledge of the relevant literature. The comparison of the position of mainstream palaeontologists with everything from the Renaissance Catholic Church to the Nazis to Apartheid is not only offensive and unprofessional, it is just laughable. It has no place in the formal literature.

    Scott, sadly, the situation you describe appears to be all-too-common. We've learned that ostriches don't really hide their heads in the sand but it would seem that the same can not be said of some ornithologists.

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