Monday, July 24, 2017

Cases of rank unethical scientific practice

June 30-2017
In the current scientific environment, where life runs by the maxim “publish or perish” we see an enormous uptick in new journals, publication of short but poorly documented papers, and the culture of the minimal publishable unit. This has greatly contributed to the swelling bulk of scientific literature while diminishing its quality. Further, it is has resulted in it becoming difficult to keep up with all the scientific literature even in one’s own field. Hence, it is conceivable that one misses key papers pertaining to research one is seeking to publish. Yet, when one fails to cite key papers germane to one’s own publication it raises serious questions. This is especially serious if the primary novel idea or finding being presented in a publication has previously been presented elsewhere. Instructional resources pertaining to scientific plagiarism provided by the Department of Health and Human Services, USA, (https://ori.hhs.gov/images/ddblock/plagiarism.pdf ) have the following to say regarding plagiarism of ideas:

 “Appropriating an idea (e.g., an explanation, a theory, a conclusion, a hypothesis, a metaphor) in whole or in part, or with superficial modifications without giving credit to its originator.” 

We believe that this is precisely what has happened in two cases pertaining to discoveries we have formerly published and outline the situation below:  Recently, two papers examining the active CRISPR polymerase domain of Type III CRISPR systems have become public. One was published in the Science magazine and the other was deposited in bioRxiv, a preprint archive for biological sciences (Jul-24-2017-- see update appended below). Both papers carry out a set of experiments which test hypotheses that were exactingly reached as part of a rigorous computational study published by our group in late 2015. The new papers confirm the predictions down to very minute details, and the conclusions they reach and discuss adopt almost exactly the same language as our computational paper. Thus, experimental researchers, have contributed to the understanding of Type III CRISPR systems, firmly establish a concept first explicitly laid out in our paper, resolving the mystery and the very origins of a key arm of prokaryotic counter-nucleic acid immunity along with implications for parallel animal immunity mechanisms.

There’s only one problem: absent from either paper is any mention, let alone citation, of our original paper which was the first to lay out this concept. There can be absolutely no doubt that our computational paper was the sole source of the authors’ “inspiration”. The current literature is rife with misunderstanding regarding the role of the Type III CRISPR polymerase, with various dubious assertions linking it to various kinds of activities, most extraordinarily, nuclease activity. Prior to a week ago, our paper was the only paper to provide a unifying functional hypothesis for the role of the Type III CRISPR polymerase which was supported by several lines of consilient evolutionary and genomic evidence. From this starting point, it is impossible to excuse the lack of reference to the paper, but it becomes even harder when considering that the paper was published in a high-profile journal (Nucleic Acids Research), which one would assume any supposed CRISPR specialist with the capacity to do something known as PubMed Search, a basic tool of biological research, could access. Further, the work has been presented as a lecture in several high-profile conferences and other venues, and was extensively described from more of a layperson’s perspective in a detailed blog post.

Unethical citation takes many forms and we have been very frequently victims of such. There is a general tendency in the community of wet-lab workers to extensively use computationally derived ideas and predictions while failing to acknowledge or even disparaging them when it comes to actual acknowledgement of prior research in their own publications. This would be rather unthinkable in certain other sciences, such as physics, where a clearly published preexisting prediction cannot be ignored by experimental workers who subsequently publish confirmation. In the same paper of ours we also had several other (in our opinion) important predictions concerning nucleotide recognition in various signaling networks, including immunity systems. One of these was the first prediction for the TIR domain being an enzyme which potentially hydrolyzes the base-sugar linkage. A subsequent experimental verification of this hypothesis has been published with due citation of our prior prediction. This shows that ethical practice does not preclude high-profile publication. Hence, we see the actions of non-citation by the above-mentioned authors pertaining to the other discoveries described in the same paper as an act of blatant unethical scientific practice, which in our eyes is no less than plagiarism. This continues with a point we made in a previous post regarding the inability of the peer-review and the editorial system at the scientific magazines and other journals to prevent bad scientific practice. Since the paper deposited in bioRxiv has not been formally published we still hope that the authors might take corrective steps prior to the final publication of their work and hope that this represents an example of the preprints helping to reform the publishing system in biology. 

Finally, we have circumstantial evidence that the authors of the Science paper from Lithuania have accessed our paper and blog well before they submitted their article for review to Science. Their article was received for publication June 8, 2017 and accepted for publication June 22, 2017. We have visitor logs for our blog (presented below) that visitors from the same university using the same mail serve have accessed our blog over 14 times on March 7 and March 8th 2017. Further, as can be seen below we notice that they have accessed our original paper in Nucleic Acids Research, as well as the key figure in post that essentially forms the basis of the discoveries which they fail to cite. We find this as further reason to suspect their scientific ethics in regard to this publication.











Additionally, below is a screen shot of a google search with some elementary related keywords that would have trivially retrieved our previous publication for a reviewer/editor.



Update (Jul-24-2017): After publishing the above entry, we directly contacted the authors of the bioRxiv preprint, briefly outlining the above concerns. To their credit the authors have properly cited our work in their final released draft which was published last week in the Nature magazine (click to read paper). This is a good illustration of the value of the preprint movement in “reforming” scientific practices.