The soft underbelly of a phylogenetic analysis

Here’s another rejection letter
that sees things the way the editors want to see it, not the way things need to be seen. I post these reviews and replies because someday you may want to publish a paper yourself and you need to see what editors are willing to say and do to keep, in this case, the origin of pterosaurs a mystery, and to keep amateurs from embarrassing the academic community by reporting that all they need do is add a few more relevant taxa.

Associate Editor Comments:

The intro: “The manuscript argues for a hypothesis that places Longisquama, Sharovipteryx, Cosesaurus, and a small number of other taxa as being especially closely related to pterosaurs, with their respective morphologies informing the long sought-after origin of characteristic pterosaur traits. The manuscript quite correctly identifies its preferred hypothesis as a minority viewpoint, lamenting the fact that its previous versions continue to be widely ignored by other pterosaur and archosaur workers. The hypothesis is based on a phylogenetic analysis of 231 multistate characters and 1090 taxa — from which the tree topology of 24 taxa relevant to the arguments of the paper were figured and discussed. The results of the entire analysis are available only on the author’s website and to my knowledge have never been published in a peer-reviewed platform.” That will change when one editor and one reviewer let the work see publication, but apparently not on this editor’s watch. 

Where the teeth are bared: “It is an understatement to say that these results differ significantly from those of other studies, with every major reptile clade, as typically recognized, being extensively paraphyletic.” All clades presented in the LRT are monophyletic and fully resolved. This editor is working from an old textbook. Taxon exclusion led to errors in prior studies. This can be readily checked by simply adding taxa and checking that all taxa document a gradual accumulation of derived traits in competing cladograms. That’s why the large reptile tree is so large, to minimize taxon exclusion problems that plague smaller studies. 

There is only one way to get published: “The author states that his character matrix is not really drawn from existing studies but rather was “largely built from scratch.” One could interpret this as an admirable attempt to shed the existing assumptions that burden other studies, but ultimately this hypothesis will never overturn existing paradigms until it demonstrates that it better explains the totality of the existing data. This study certainly does not do that. Simply disregarding a large percentage of the characters that the larger community of workers has decided are important for resolving reptile phylogeny in favor of those the author deems relevant is never going to accomplish this goal.” See below.

Sidenote: “The criticisms of the author’s approach by Hone and Benton 2007 still appear to be relevant – at least they have never been directly addressed, nor are they addressed in this manuscript.” Yes, they are. Hone and Benton excluded the fenestrasaur taxa that overturn the pterosaur origin question in Peters 2000, after promising to test them. Why is every paleo colleague afraid of Cosesaurus (the subject of the submitted manuscript)?

Case closed: “Until the author explicitly demonstrates why the characters he omits should not be included or how adding taxa and characters to an existing matrix, such as that found in the Nesbitt (2011) study, produces the promoted tree topology, I cannot recommend publishing this work or sending it out for further review.”  Problem 1: Nesbitt’s 2011 paper was on archosauriforms. Pterosaurs were thrown into that study, but they are not archosauriforms, as documented 11 years earlier. Problem 2: Adding taxa or characters to an existing matrix assumes the existing matrix is faultless. It is not. Nesbitt 2011 suffers from some inappropriate taxon inclusion and a great deal of taxon exclusion, along with some bad scoring that we looked at in a nine-part series ending here. Problem 3: Peters 2000 added taxa to four prior phylogenetic analyses and recovered the same results each time. None of those four were built on prior analyses. Now let’s move forward 11 years. Why was Nesbitt 2011 published when it mentioned, but did not include relevant taxa reported by Peters 2000? Editors and referees let that pass. Why? Have the rules changed?

Evidently it matters who the author is, and how well they are connected in the academic community, not how well a project is researched.

Editors and referees are only human. They have an agenda and a world view, like everyone does. They see what they want to see, comment on what they want to comment on and maintain whatever status quo they currently follow. How do we know this in this case? Note how little was said in this review (not one sentence) about the new pterosaur traits found in Cosesaurus, which formed the subject of this paper.

My reply:

Dear [Editors]:

Thank you for your kind reply and review.

Ultimately the number of characters or their publication history means little, since one set of two hundred characters will result in the same tree topology as another set of two hundred characters. The character list is the soft underbelly of any analysis, the part editors and reviewers go to when they cannot argue against the demonstrated gradual accumulation of derived traits shown by the included taxa, universally excluded from other studies that include pterosaurs. 

Maintaining the majority view will only keep the origin of pterosaurs in the dark. 

Best regards,

References
Nesbitt SJ 2011. The early evolution of archosaurs: relationships and the origin of major clades. Bulletin of the American Museum of Natural History 352: 292 pp.
Peters D 2000b. A reexamination of four prolacertiforms with implications for pterosaur phylogenesis. Rivista Italiana di Paleontologia e Stratigrafia 106: 293–336.

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Happy Holidays, Everyone!

I wish you all the best!
Here at the David Peters Studio I have not kept up with my usual one-a-day posts (and feeling guilty about it). Having already covered just about every clade out there, I’m reduced to commenting about the paleo news as it comes out and rechecking all the links and data at ReptileEvolution.com, which this blog post supports.

I’ve also managed to squeeze out
a few papers. Digging deeper into various subjects always brings up some dirt and some gold. There’s no reward in publishing a paper, other than the personal satisfaction in knowing you’ve shed a little light on the dark corners of a subject.

It’s important for all of us to be life-long learners.

Thank you
for your readership.

Would you like to read a rejection notice, or two?

In the past week
I submitted a comment to Royal Society Proceeedings B on Foth and Joyce 2017. In it I suggested that the origin of turtles was diphyletic and that would affect the placement of the basalmost turtle in the work of Foth and Joyce.

Referee number 1 wrote:
“This paper is unsuitable for Proceedings B (or any scientific journal) and should be rejected. It is ostensibly a response to a recent paper by Foth & Joyce on the disparity of the turtle skull over time, but in reality it doesn’t address this study at all, but is a back-handed attempt by the author to publish an iconoclastic phylogenetic analysis based on an inadequate dataset riddled with errors and methodological flaws. Sorry, there is no way to be kind about this manuscript.”

Referee number 2 (Walter Joyce, one of the original authors) wrote:
“the attached manuscript by David Peters is a response to an article I published earlier this year with Christian Foth in Proceedings B regarding the evolution of cranial disparity in turtles (Foth and Joyce 2017). Although I welcome any scientific debate regarding this paper, I would like to suggest outright rejecting this contribution for one single reason: It is an open trade secret that David Peters has been developing an enormous phylogeny of reptiles that produces highly outlandish results. One such outlandish result is the polyphyletic origin of turtles. This undertaking has been submitted to many journals over the years and has been rejected every time, as basic tenants of sound cladistic analysis are not followed therein, mostly an adherence to the use of character observations that can be reproduced by people who are not David Peters. I am certain that countless scientists invested countless hours in providing sound arguments why this tree should be rejected and I will therefore save myself the work here. If anything, this phylogeny should receive full peer review in a standalone publication, and not be slipped into the sphere of published scientific literature as part of a not-quite appropriate criticism of Foth and Joyce (2017).”

And here is my reply to the editors:
“Critical thinking is a requirement in science and I’ve had a few hours now to critically think about the replies I received from the two referees. I hope these comments will help you in future endeavors.

1. You already know that referees should be unbiased when they approach a manuscript. Asking Dr. Joyce to be a referee runs counter to that ideal. After all, I was commenting on his paper. His comments should have been requested only after two unbiased referees had ok’d the manuscript for publication.

2. Some referees like to accept manuscripts knowing ahead of time they will reject them. Is there any method you use to prevent this?

3. Whenever I review a manuscript I review some of the details within the manuscript, pointing out errors, if any, congratulating insights, if any. This was not done by either referee. There is no indication that either referee actually read the manuscript, let alone tested the hypotheses that resulted with the matrix provided.

4. The paper was about taxon exclusion. Foth and Joyce excluded taxa pertinent to the origin of turtles, which affected their basalmost taxon and the rest of their phylogram. That point was ignored by both referees who described ‘an inadequate data set’ (did they actually see the dataset, or go by rumors?). No specifics were put forth. No testing of the analysis was described. That’s what I do in such cases. I run the matrix looking for mismatches. Anyone who has the same taxon list, no matter what their character list, will come to the same results as I did, unless they omit certain pertinent taxa, as Foth and Joyce did.

5. Joyce wrote: “It is an open trade secret that David Peters has been developing an enormous phylogeny of reptiles that produces highly outlandish results.”

To that point, many results of my studies follow traditional topologies: birds nest with birds, turtles with turtles, etc. When topologies shift it is virtually always because the large size of the cladogram allows taxa that have not been tested together to be tested together. That the results upset untested traditions and paradigms are THE reason why this work should be published. The origin of turtles could have been known for the last fifty years. I just included taxa that were previously excluded.

Joyce may be upset because i pointed out this oversight, after all the hours he put into his project. That’s never welcome news, especially when that correction comes from someone without a PhD. It is potentially embarassing. Nevertheless, even if the hypotheses comes from an obscure patent clerk, this is how we build our science. The present facts should be central to the case, not any disparaging rumors about the scientist.

The data presented has to be good. Otherwise there is no way for the cladogram to have high Bootstrap scores throughout. The software is unbiased with regard to output. Unfortunately, pride, shame and other emotions are involved here when it comes to the referees. Some don’t like change.

Thank you for reading this. I don’t ask for any revision to the status of my manuscript, only that you review your policies so bias does not influence the next few incoming manuscripts.

Best regards,”

Dinosaur books

At one time
I wanted to write and illustrate a dinosaur book. I had an idea for one (Fig. 1) and was inspired by the writers and artists of the Dinosaur Renaissance. It took several years…

Figure 1. The cover of Giants, the book that launched my adult interest in dinosaurs, pterosaurs and everything inbetween.

Figure 1. The cover of Giants, the book that launched my adult interest in dinosaurs, pterosaurs and everything inbetween.

Then
I got a contract to do my first book. That begat another and another. The shelf life was no more than one year for any of them. None went to second editions, though several had foreign versions. Reviews were good. Libraries stocked them. Book signings were fun, when there was advanced publicity. Every so often there was a big or small check in the mail. Now Amazon keeps them alive, if just barely. Reviews are still good…

Nowadays
I would not want to write and illustrate another dinosaur book. New discoveries make at least part of the text and part of the depiction of its subjects obsolete, sometimes before shelf life is over. The amount of data needed to be covered is staggering. More pages mean the price the book rises out of the ability to pay for many potential readers. With book publication, there are no ‘do-overs’ or ‘updates.’ What’s done is done. And then there are always the nagging typos. There’s a lot of work involved. And it has to be polished perfect. Editors, working for publishers, have their say. So do collaborators, if any. You have to put your life on hold to get the thing done by deadline. And when it’s done, it sits on a bookstore shelf, just one more Christmas or birthday present vying for the consumer’s eye.

It’s much better to post blogs
and nurture growing websites, like ReptileEvolution.com. These can be updated at will in one’s spare time. There are no paper or printing costs. No ships and trucks to distribute them. No bookstores to deal with. No deadlines. News can be reviewed within a day, while it’s still fresh. Everyone in the world has free access to your work. They can focus in on what they really like and ignore the rest at no cost. And one more thing (quoting Steve Jobs) that books can’t provide: animation. There’s no profit in web publishing, but money was never the front and center issue.

Figure 2. Sample animation you’ll never see in a book. The Vienna specimen of Pterodactylus (wings folded). Animation opens the wings and legs to reveal the true shape of pterosaur wings, stretched between the elbow and wingtip with a short fuselage fillet extending from elbow to mid femur.

Even so
I’m glad I went through that book phase. It had its time and place. The process led me to interact with others of like interest. Some of them are PhDs. Others are fellow artists and writers. Everyone should have a hobby to keep in touch with the world and vice versa.

I was inspired to write this blog post
after seeing parts of Walking with Dinosaurs 3D on YouTube. Click here to see it. So much talent and effort went into this— truly outstanding visuals …but the dialog was horrible, as most others agree. And there are a few new dinosaur books out now, updating older dino books. I wish them all well. Someday, perhaps decades from now, those books will either be considered cherished classics or outdated, ready to be updated. It’s all good.

References
www.DavidPetersStudio.com/books
www.ReptileEvolution.com

Coincidence? Or Discovery?

A recent reply (see below) to an earlier post bears noting:

Diandongosuchus nests as a basal phytosaur when choristoderes and basal younginoids are included, far from Qianosuchus, which also does not nest with poposaurs, which are all bipedal (or formerly bipedal) herbivores, a far cry from Diandongosuchus.

Figure 1. Diandongosuchus nests as a basal phytosaur when choristoderes and basal younginoids are included, far from Qianosuchus, which also does not nest with poposaurs, which are all bipedal (or formerly bipedal) herbivores, a far cry from Diandongosuchus.

David Marjanović on April 12, 2017 at 3:16 am said: 
“The redescription of Diandongosuchus (Fig. 1) has now been published in open access. I’m afraid I can’t congratulate you. The new paper, and the SVP abstract before it, uses data you didn’t (and couldn’t) use – you were right for the wrong reasons. No congratulations for coincidences. :-|  “

Reply ↓
davidpeters1954 on May 22, 2017 at 8:31 pm said:
“So, phylogenetic analysis and expanding the inclusion set are the wrong reasons? Tsk, tsk, David. Your bias is showing.”

Back story:
Diandongosuchus (Li et al. 2012) was originally nested with poposaurs. Within a few days of its publication, Diandongosuchus was added as a taxon to the large reptile tree (LRT) and it nested not with poposaurs, but at the base of the phytosaurs. Several other blog posts here, here and here further illustrated the link.

Recently 
Stocker et al. 2016 also nested Diandongosuchus with phytosaurs and shortly thereafter news of that publication was posted here,

Botton line:
Stocker et al. did not recognize the earlier discovery. It was easy to Google. It would have been appropriate to add the original discoverer to the list of authors. This is common practice, even when that person is deceased. More recently Dr. Marjanović withheld congratulations and demeaned the scientific method by which the discovery was attained (an expanded taxon list employed in phylogenetic analysis) as “the wrong reasons.”

 

Carl Sagan once wrote:
“In a lot of scientists, the ratio of wonder to skepticism declines in time. That may be connected with the fact that in some fields—mathematics, physics, some others—the great discoveries are almost entirely made by youngsters.”

“The suppression of uncomfortable ideas may be common in religion or in politics, but it is not the path to knowledge; it has no in the endeavor of science. We do not know in advance who will discover fundamental insights.”

“There are many hypotheses in science which are wrong. That’s perfectly all right; they’re the aperture to finding out what’s right. Science is a self-correcting process. To be accepted, new ideas must survive the most rigorous standards of evidence and scrutiny.”

The hypothesis
that Diandongosuchus is more closely related to phytosaurs than to poposaurs originally appeared here in 2012 and was confirmed four years later by Stocker et al. That Dr. Marjanović does not approve of the earlier discovery tell us more about professional biases against ‘outsiders’, which we’ve seen before, than it does about the ‘coincidence’ he conjures.

 

References
Li C, Wu X-C, Zhao L-J, Sato T and Wang LT 2012. A new archosaur (Diapsida, Archosauriformes) from the marine Triassic of China, Journal of Vertebrate Paleontology, 32:5, 1064-1081.
Stocker MR, Nesbitt SJ, Zhao L-J, Wu X-C and Li C 2016. Mosaic evolution in phytosauria: the origin of longsnouted morphologies based on a complete skeleton of a phytosaur from the Middle Triassic of China. Abstracts of the Society of Vertebtate Paleontology meeting 2016.

 

Some things you learn are not found in any textbooks…yet.

No current discoveries are found in the latest textbooks. 
That’s because it takes time (years typically) for textbooks to be (in reverse order) assigned, accepted, distributed, printed, edited, written and illustrated, researched and concepted. Textbook publishers are out to sell the maximum number of books, so they write to the current consensus, which may be in flux on several points and hypotheses. The current consensus may also be wrong–but it remains the consensus.

There are no courses
at any colleges entitled, PTEROSAURS 101, 102 or 103. Who would attend? There are only two dozen people in the world who have an interest, who study them, or contribute to what we know about them. And where is the consensus? On some points, there is no consensus!! And all too often “the consensus” is holding on to outmoded, invalid and unverifiable paradigms (see below).

Every new fossil specimen is really a new chapter
in an ever expanding textbook on paleontology. And all paleontologists who publish are contributing authors to that future textbook.

Striiving for veracity
It is important for all workers to see things as they are in specimens, and not to reinterpret them to fit an established paradigm, no matter the temptation to do otherwise. For instance, narrow chord wing preservation in pterosaurs is not the result of ‘shrinkage’ as some workers report. Rather it is what it is, universal. All pterosaur specimens have narrow chord wings. If you know one that is different, please tell me. I know one that appears different, but that’s because part of its arm was ripped away and displaced. Look closely. That’s the way it is.

If Galileo
went to school as a teenager and found the following question on a test: “If object A at ten pounds and object B at 10 ounces both fall from 1000 feet at the precisely the same moment, how many seconds ahead of B will A strike the ground?” He’d would not have even had the opportunity to choose answer E. “zero seconds.” Common knowledge at the time, based on Aristotle, would not have allowed it, no matter the facts of this case, proven by experiment. This went on for centuries.

Similarly,
if you were in college today and were given the multiple choice question, “Which one of the following taxa is most closely related to pterosaurs? A. Dinosaurs. B. Scleromochlus. C. Proterochampsids (including Lagerpeton). D. Euparkeria. E. Erythrosucids. F. We don’t know.” You would have to pick “F” to get a good score, because that’s the current consensus… unless your professor had recently written a paper espousing one of the other answers (see below). “G. None of the above” is the better answer according to the large reptile tree where fenestrasaurs are more closely related to pterosaurs. But each one of the above (A-E) has been proposed by recent authors, not caring if they made sense or not.

Imagine the plight of the poor student in Paleontology 101 today
when he or she asks the professor about that website, “repitleevoluton.com” The professor is going to have to say, “If you want a good grade, you’ll ignore that website and provide the same answers that are in your textbook.” That’s what Dr. Darren Naish  reported online. Don’t consider, test or discuss other possibilities. Best to ignore them — if you want to advance in paleontology and get your Masters or PhD.

Take, as an example,
David Hone’s dissertation that was later published in two papers in which he proposed comparing two competing pterosaur origin hypotheses, one by Peters 2000 (Cosesaurus, Sharovipteryx, Longiasquama) and one by Bennett 1996 (Scleromochlus) using the supertree method of analysis (combining several published analyses without actually examining any fossil specimens). Aware that his professor, Michael Benton, had earlier written a paper (Benton 1999) celebrating Scleromochlus as the sister to pterosaurs, Hone decided to delete and diminish the taxa proposed by Peters. He somehow created several typos in the Peters data and then deleted the entire Peters dataset because of those typos (references and the full story here). Then Hone and Benton (2008) gave credit for both competing hypotheses to Bennett while deleting all reference to Peters 2000. As a result, Hone received his PhD, two associated papers (Hone and Benton 2007, 2008) were published and Hone gained the ability to referee pterosaur manuscripts (like mine) submitted to academic journals. I wrote to Dr. Benton about the inconsistencies and leaps of logic between the two parts of their two part paper. His reply was a sheepish, “whoops. :  )”

See how it works? 
That’s how you crush an opposing hypothesis. And that’s just the tip of the iceberg of current readily solvable problems, as Pterosaur Heresies readers are well aware. No PhD wants to admit he/she was wrong. On some problems consensus will likely never be achieved — because in order to do so all invalid candidate hypothesis writers would have to admit they were wrong.

And that’s just not going to happen.
Not without a fight or a dismissal. Let me know if you know of any instances of someone admitting they were wrong (I know of one semi-wrong situation regarding Dr. Padian and his fight with pterosaur tracks). In the origin of snakes, pterosaurs, turtles and dinosaurs there are lots of ‘right’ answers out there, but few challenges to the weaker hypothesis and no one admits to being wrong.

As history tells us, in paleontology it takes decades to turn the boat around. And paleontologists don’t want anyone else, even other paleontologists, solving their mysteries for them… even when solutions are published in the literature.

Thanks for your interest.
I will continue to study and make informed comment on new fossil specimens, (many that haven’t made the textbooks yet). I will throw a spotlight on problems and celebrate solutions as they are verified or not in the large reptile tree. And I encourage you to do the same. If I can do it, anyone can do it.

There are too many paleontologists who
follow
matrices, textbooks and papers blindly
and not enough paleontologists who have the balls to say, “Hey, there’s something wrong here.”

We’ll help fix the world of paleontology someday.
Unfortunately, it’s not going to happen this year. After four years of working with the large reptile tree, and improving it, and enlarging it year after year, it still has not been accepted for publication or gained intrigue among basal reptile workers. They don’t like it. It rocks the boat.

References
Bennett SC 1996. The phylogenetic position of the Pterosauria within the Archosauromorpha. Zoolological Journal of the Linnean Society 118: 261–308.
Benton MJ 1999. Scleromochlus taylori and the origin of the pterosaurs. Philosophical Transactions of the Royal Society London, Series B 354 1423-1446. Online pdf
Hone DWE and Benton MJ 2007. An evaluation of the phylogenetic relationships of the pterosaurs to the archosauromorph reptiles. Journal of Systematic Palaeontology 5:465–469.
Hone DWE and Benton MJ 2008. Contrasting supertree and total evidence methods: the origin of the pterosaurs. Zitteliana B28:35–60.
Peters D 2000. A Redescription of Four Prolacertiform Genera and Implications for Pterosaur Phylogenesis. Rivista Italiana di Paleontologia e Stratigrafia 106 (3): 293–336.

Wikipedia ignoring published literature

I’ve had the honor and privilege
of having several of my manuscripts and figures published in academic journals. But when the authors of Wikipedia wish to describe pterosaurs or the various fenestrasaurs like Cosesaurus and Sharovipteryx all references to my work are deleted or ignored. Worse yet, when it comes to Longisquama, I and my work are described as’ idiosyncratic’ and “strongly denounced.” Such attacks are not found on the pages of other prehistoric reptiles and they don’t belong on the pages of Wikipedia.

Figure 1. Scene from "It's a wonderful life" directed by Frank Capra in which Clarence tells Jimmy Stewart, "You never were born." When the authors of Wikipedia ignore published literature on pterosaurs and fenestrasaurs, this is what they are trying to do.

Figure 1. Scene from “It’s a wonderful life” directed by Frank Capra in which Clarence tells Jimmy Stewart, “You never were born.” When the authors of Wikipedia ignore published literature on pterosaurs and fenestrasaurs, this is what they are trying to do. Click to view a few minutes from this movie.

So, it’s not enough
to view the fossils first-hand, pass peer-review and enter the literature. Evidently some observations, findings and workers are to be shunned, maligned and marginalized. It’s not the first time this has happened in the history of Science. And it probably won’t be the last.

I recently added
my work on pteroid origin and articulation (Peters 2009) to the Wikipedia page on pterosaurs. Let’s see how long it stays up. In the literature these observations and hypotheses have not yet been falsified or questioned, but confirmed.

References
Peters D 2009. A reinterpretation of pteroid articulation in pterosaurs. Journal of Vertebrate Paleontology 29:1327-1330.