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,”