Saturday, July 21, 2018

A Few Notes on Publishing in Science

Image result for peer reviewEnvironmental & Science Education
History of Science
Nature of Science
Edward Hessler

Those of us who do not practice science are quite likely to have heard of peer review, part of the process that leads to the publication of a scientific paper. The traditional process is described on the webpage Scrutinizing Science—Peer Review, from the University of California Museum of Paleontology.

That peer review is being reviewed by many scientific peers may come as a surprise. It is more accurate to say that it has been under scrutiny by scientists for several years.  It is not considered to be the gold standard although it is the most common method used by journal editors. My aim is not to summarize that literature of criticism and research.  It is large and requires more expertise than I have.

In February, NPR’s Richard Harris reported on some of the problems with peer review and some solutions. Here are some of the problems:

--The process is slow, often taking months before the paper is actually published.
--The review process consists of only a few scientists, usually two to three.
--Reviewers may be biased for or against the science and may not have the technical training or experience to properly vet a paper.
--Reviewers are usually anonymous, i.e., the process is not transparent.

“One way forward, “according to Harris’ report, “is to encourage scientists to make their work publicly available on the Internet before it has been peer-reviewed or accepted in a journal” in pre-print journals. I’ve made use of some of these, notably in the physical sciences where the practice has been long established. I want to emphasize that most of my use of pre-print journals in the physical sciences is when I’ve been directed to specific papers. I do not scan them on any regular basis. Harris mentioned a new one for the biological sciences.

Image result for internet
I include the links for the two archives so that you can scan them if you like. On the physical side is arXiv, pronounced “archive.” It is operated by the Cornell University Library and includes sections for physics, mathematics, computer science, quantitative biology, quantitative finance, statistics, electrical engineering, systems science, and economics.  arXiv makes use of moderators to review the submissions.  For more information see the arXiv Wiki entry.

On the biological side is bioRxiv (pronounced bioarchive) the preprint server for biology. It is operated by the Cold Spring Harbor Laboratory.  Articles are screened before being posted and there are more than 30 subject areas. For more information about this archive click on any of the subject area categories and when you are directed to that page there are tabs at the top which answer frequently asked questions.

Harris includes a link to ASAPbio which describes a new system under development by molecular and cell biologist, Michael Eisen, University of California--Berkeley.  Harris quotes Eisen as follows. "What we want to see happen next is to allow the scientists who are reading papers [as part of their normal work] ... to review them. You post a work, people comment on it, you update it, and if it gets better through the process, that's great--now you've produced something good. If, through the process of review and assessment, you and the community realize the work wasn't right, it just sorts of fades and you mark it as such. And I think we'll all be better off if that happens."

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