Fork me on GitHub

The onslaught against scientific publication

By Deepak Singh | Published: September 20, 2006

Well not quite that, but it makes for a better headline. The scientific paper and the process of peer review as you and I have known all of our scientific lives is facing something of a grassroots revolt. The Scientist is carrying an article on the subject by Mark Gerstein and Michael Seringhaus, with an equally provocative title.

They argue that the science of today, with its mountains of data and ambitious scale, has outgrown the traditional scientific manuscript. Since scientific information today comes in multiple levels and in different guises, they believe that the paper is somewhat optional. Betraying their bioinformatics roots, they strongly favor databases and other repositories as sources of scientific information. In their opinion, the “paper” must be just one part of a submission, data deposition should be required and a unified nomenclature should be enforced. They go on to make numerous other suggestions, all leaning towards open and complete access of data, web-centric access and formats, and believe that a publication should be a living document with all its entities in complete sync.

In general I agree with them that the article model of scientific publication is somewhat outmoded. To me a paper should be concise, with a list of goals, methods, results and analysis. The supporting data and data analysis should be included and accessible online. The peer-review process is the other side of the coin, one that Seringhaus and Gerstein do not not discuss in significant detail, but the experiment currently underway at Nature has received more coverage lately, as noted by Timo, including an article in Wired. In the Pipeline also has an interesting take on the project.  People should have the right to, within editorial guidelines, debate the authors, offer counterargments, etc.  When a rebuttal, update or counteropinion is published, a web presence means that the reference should be directly to the original article.  Hyperlinking would make life so much easier.  I also think a wiki format is a great idea as instead of padding their paper count, researchers could publish updates right with the original paper.  A mechanism I like is the online submission of a paper to a pre-print server.  There the paper can be read, but not commented upon.  The peer reviewer selection process should be random and from a database which would evolve with time.  Following publication, the paper should be opened up for public debate.  Seems like a good starting point at least.

Whatever the merits or demerits of the Nature efforts, the fact remains that it is a step in the right direction. Is it the right model? I don’t think its perfect. That will take time, but it will work itself out. Whether it is Nature or PLoS ONE, something will work out in the end. How quickly depends a lot on the community. Most people are happy being consumers and not participants.

Technorati Tags: , , , , ,

powered by performancing firefox

This entry was posted in Admin. Bookmark the permalink. Post a comment or leave a trackback: Trackback URL.
  • Strangely enough, so is Microsoft. They are actively thinking about adding scientific semantics into the Office products.
  • New ways of doing things are definitely on the minds of the NSF folks. See the new call for a plant science cyberinfrastructure (PSCIC). I don't think we all need (or can) be information scientists. I talked on the phone today with a group of "links"(wha?!&$@) and ontology experts and I certaintly don't talk their talk! However, by bringing together such experts and a dabble of domain expertise - I'll bet these teams can build great tools for biological knowledge discovery and management. Heck - I'm sure the GooglePlex is thinking along these lines.
  • I would take it one step further. This is not the kind of traning left for graduate school, but should be part of a students training right from the get go (undergrad or earlier). After all, when science advances we retrain ourselves. As someone said somewhere, this is not sexy science, in the long run "knowledge management" is as much a part of 21st century science as anything else. If we fail to do something about it, then we are only hampering our own efforts.

    Let's take something very simple. I have a whole bunch of PDFs. I organize them somewhat in folders etc, but when I want to search for a specific term, I don't open every file, but rather run google desktop to find appropriate search terms. Now this is crude, but if microformats and metadata were supported, it would make life even more easier. Everyone knows how to use google (to some extent). The same for Pubmed. Why not empower that mode of search and exchange. The bioinformatics community is at the early adopter part of the curve, so I don't see why the community cannot create the framework and tools that might one day become ubiquitous.
  • ALl of this begs the question, how many of our scientists today especially in the lifesciences receive any training whatsoever in electronic archival and other computational skills. The academic lifescience community will not move away from the paper and pen notebook. Its all well for some overly-computer literate bioinformaticians and omics-practicioners to talk about moving away from the traditional peer reviewed paper.
    With the budget squeeze it is hard enough to get money to do reserach the old way , and how I wonder will organizations like the NIH and NSF start bringing about a new way of doing things?
  • Couldn't agree more. One thing I forgot to stress in my commentary was the fact that web-based publication gives you the added ability of using microformats and other forms of semantic communication. How much better would all our searchengines get if one could search all that meta information.
  • I'm a huge fan of open access publishing - I think it's really got the potential to level the playing field - along with blogs and other websites and even wikis - as you mention. Surprisingly Seringhaus and Gerstein really did gloss over the relative ease of FINDING things you care about in the literature vs. an open world publishing environment (they write, "a scientist in search of genomic data or bioinformatics software need look no further than online databases or laboratory Web sites"). Personally, I think it's still HARD to find the "best of breed" tools and databases even using Google or the yearly Nucleic Acids compendiums. Grand Challenge? Using tags, metadata, links, ontologies (gasp!), and even comments, mixed with semantic searches to find what you care about in some future open access/ open world publishing environment.
blog comments powered by Disqus

  • Archives

  • Disclaimer

    All opinions on this blog are my own and do not reflect those of my employers, past or present