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,”

19 thoughts on “Would you like to read a rejection notice, or two?

  1. William Joyce:: “basic tenants of sound cladistic analysis..” Sounds like you’re living on the ground floor, if that was his malapro

  2. This is, I expect, a common problem in any specialised field. The pool of referees will be small and largely include people with a reputation to defend, even if unconsciously. This is why we have scientific ‘revolutions’ from time to time, the system resists change until the weight of evidence against the status quo becomes overwhelming. And of course your average research student needs to tow the accepted line for the most part if she or he is to advance his/her career and climb the institutional ladder. Apart from anything else it takes a lot more time and effort to advance a new viewpoint than to simply follow a well-worn path, and there is a greater risk of simply being misunderstood by your referee/examiner.
    As I’m not a specialist in your field, I’m unable to judge the validity of your approach, although I see nothing inherently silly or impossible in the idea that turtles are not monophyletic. Parallel evolution is hardly a rare or unknown phenomenon after all, at the end of the day it simply comes down to how persuasive the evidence is when viewed dispassionately (if that’s actually humanly possible — lol!)
    I certainly admire your persistence and attention to detail, two very valuable gifts, so don’t let the bastards grind you down. (And fwiw, I do have a PhD …)

    • Marcomatrix…. Agreed! David does not get a fair review from most “scientists” in the field because of the reasons he has given and because, the further he is kept back, the easier it is for someone to jump on his bandwagon and take over the reins. And that…is a sorry state of affairs.

  3. “My take on the peer-review system is not sanguine. In my geologic youth, conventional wisdom, and accordingly peer reviewers, strongly favored permanent and stable continents and oceans, whereas nowadays collective hunches stretch plate-tectonic models (and mythical plumes) to cover all occasions. I have run the peer-review gauntlet a hundred times or so. My papers describing and interpreting geology in conventional terms have moved smoothly through, whereas my manuscripts challenging consensus concepts often have had heavy going. I gave up on several manuscripts that I still regard as among my best after a year or so each of sequential nitpicking by consensus-supporting reviewers. Other geoscientists for whose work I have a very high regard, and who have challenged groupthink assumptions, report similar experiences.

    “‘There are times when the working definition of truth is taken to be the consensus of one’s scientific intimates, the ‘good old boys.’ Anything outside that limited horizon is discomforting and improper and is to be barred from consideration.’ Parker (1997)”

    — Warren B. Hamilton, 1998, “Archean magmatism and deformation were not products of plate tectonics”

  4. There’s no bias or conspiracy against David here. David doesn’t understand how to do phylogenetic analysis correctly. Its that simple. He doesn’t understand the terminology and what they mean. He doesn’t understand how to form characters correctly, or how to weight them or why or when to do so, or to properly order them and when and why to do so. He doesn’t understand how to check his analysis for homoplasy or any other basic analysis. All of these things have been explained to David , extremly patiently i might add many, many times over by people such as David Marjanovic, Mickey Mortimer, and many others. Indeed Mickey has said numerous times that David’s critique of the major phylogenies lack of taxon inclusion is very worthy of serious consideration, were it not for the major flaws of David’s methodologies. David, of course, ignores all of their advice and continues on doing the same thing he’s always done. Before either of these reviewers could even approach anything close to resembling a bias towards one particular theory or the other, David would need learn how to properly do a phylogenetic analysis first.

    • Would you care to explain to ME, what you are talking about? I don’t mean explaining by pointing out David has made mistakes nor that he has disagreed with other workers in the field. Nor does the fact he uses different means to his ends.

      • Bryan, seriously, go back and read any comment left by Mickey Mortimer or David Marjanovic. I specified these two because they have put in the most time and effort into patiently trying to teach David the basics. Also read the posts regarding David Peters on Mickey’s own blog, where he specifically tests David’s hypothesis using the established methodology. David doesn’t just use “different means to his ends.” I’m not talking about, for example, his use of DGS or interphalangeal lines, those are separate issues entirely. What I and both reviewers here are saying is that he uses Phylogenetic analysis, which has an established methodology understood and used by everyone in the field, and David throws all that out the window makes up his own ideas. Yes, there are specific disagreements between researchers as to the best way to analyse the resulting cladograms, ie parsimony vs. maximum likelihood ,etc. But they all start with the same understanding of, just for an example here, what exactly is meant by “sister taxa.”

      • What IS meant by sister taxa? Educate me. I like Mickey Mortimer a lot, and have talked with him at length about the Habib quad launch theory. Since I asked you personally, I need an answer from you. I am not David’s friend because I think he’s perfect. I do respect his views though, even when I disagree with them.

        He and I DO agree on a number of things, but, so far, all I’ve ever seen from his critics is that David uses different methods and has different views and gets more Google hits…not joking at all there…so he must be shunned. Not disagreed with but shunned. Disagreed with to the point, if David Peters says it it’s wrong. No need to even look at his data.

        Don’t bother telling me your or anyone else’s opinions on David’s modus operandi, on his theories, on his audacity. I want a kindergartener’s view of your definitions. I will ask David for more detail on his methods.

        I mentioned the quad launch hypothesis. I agree with David Peters entirely on his stance. We can discuss this right now, or at any time in the future, if you are interested.

      • @ Christopher above.
        Having wandered in rather late to this discussion, I’d appreciate some links to the comments etc. you’ve mentioned. Thanks.

      • Try this for a start: https://www.youtube.com/watch?v=ALziqtuLxBQ

        And here… https://search.yahoo.com/search?fr=mcafee&type=C111US714D20170207&p=darren+naish+smithsonian+david+peters

        I’ve had conversations by the boatload with people who wholesale reject David Peters’ views on anything. No links will be provided. They were private correspondences which are none of anybody’s business but mine. Let’s just say I was warned I’d better never support David or his views. I can give names, but go to many of the links above to find out for yourself. Look up Habib’s paper on the pterosaur launch subject. I am positive David will direct you to his objections; they are objections which cover the subject quite well and I agree with David’s views on this subject. Period.

        If you want to discuss this particular subject, please read the pertinent materials and get back to us here.

      • Thanks, Bryan. I added a comment to the quad launch video. re: Naish, if he wants to disrespect the work at ReptileEvolution.com he should not be bringing in cartoons from others. Take the presented work apart. Present better alternatives. That’s all fair and expected. When others confirm findings here (Chilesaurus is a great example), then ease off. The problem is Naish black washes the whole effort, which means there are other issues present, as I read it.

      • @ Brian R.
        Thanks for the links which I will look into. No need to name names, indeed I’d like to keep any discussions factual/logical rather than ad hominem. Better to create light than heat :-)

  5. Chris and Bryan, thank you for your comments. For all its faults, and I rescored several dozen data points over the last week, the present phylogenetic analysis is working well, judging by results. Like all other analyses, there is a taxon list and a character list. The software creates the tree. When you say “I throw all that out the window,” you may not realize that objection leaves us all guessing what you mean, or what to do different. That’s why blackwashing does no one any good. Every critic of the analysis has been invited to indicate specifically where the results could be improved, by shifting taxa to more parsimonious topologies, but few have come forth. If they know what is wrong, they need to put their finger on the problem, and so do you. You are invited to do so. Small arguments over time work better than a long list of several paragraphs that invite a similar long-winded response. That way everyone can enjoy each point as if it’s a collegial conversation.

    By the way, what are your thoughts regarding that growing list of taxa that follow earlier discoveries in the LRT?

  6. “If anything, this phylogeny should receive full peer review in a standalone publication”.
    A fair point on the face of it, don’t you think? Have you tried, or do you maintain that the ‘establishment’ have all closed ranks to exclude your ideas? At the very least, given all the work you’ve clearly put in, they deserve detailed testing before being refuted.

  7. It is very odd that you wrote a response to a rejection. There is no point. It’s called “submission” for a reason. ;-)

    It is, however, odder still that an author of the paper you were replying to was sent the manuscript for review. That is downright bizarre. The potential conflict of interest is glaringly obvious, and I’m not aware of that having ever been done before.

    That said, I can’t find anything wrong in Joyce’s review, and I note he’s been honest enough to sign it.

    The data presented has to be good. Otherwise there is no way for the cladogram to have high Bootstrap scores throughout.

    Of course there are several other ways for that to happen. For instance, the data could be cherry-picked instead of good. Or, and that’s what I’ve actually seen in your matrix, the data could contain heaps of redundant characters: the same few characters coded over and over again under different names. I made a list over a year ago; you’ve barely begun to reply.

    Given a constant number of characters, bootstrap percentages correlate (on average) negatively to the number of taxa. More taxa, lower bootstrap values for most nodes. This is an inherent, unavoidable feature of the bootstrap, indeed one of its greatest flaws.

    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.

    I would not make this kind of psychological speculations lightly. Really, not everyone cares about status questions, and not everyone is afraid of criticism.

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