To what extent should we have confidence in the average published scientific result? The news that Professor Marc Hauser of Harvard University may have been involved in scientific misconduct, yielding irreproducible results, prompts us to reflect on whether irreproducible results are usually caught, or not.

The current system of publishing scientific papers hampers scientific advancement in particular ways. I’d like to diagnose the problems so that new publishing efforts (like PLoS ONE) can be shaped to remedy them. I believe that a major flaw in the modern journal system is that it discourages complete treatments of the literature.

In my graduate school days, we had something called ‘The Scathing Wall’, a small bulletin board which provided some outlet for one of our greatest frustrations—dealing with the reviews that came back from a journal after we had submitted a manuscript.

My scientific workflow includes email between myself and lab members and collaborators, annotations on previously published papers, adding information and ideas to the lab wiki, Python programs to create visual displays and run experiments with them, and Python and R code to plot the results and do the statistical analysis.

The conventional encyclopedia: old and unimproved! Here is a preprint of my entry for the The Sage Encyclopedia of Perception with headword “The Binding Problem”. The hardcopy version of the encyclopedia will be a massive 1100-page tome with hundreds of contributors.

Nature has published a news item by Declan Butler on the finances of one of its competitors: the open-access PLoS journals, using language that puts the organisation and its journals, especially PLoS ONE, in a negative light.

Thanks to Efoundations, I see Elsevier has announced an Article 2.0 contest, in which programmers can create new value by harvesting data from 7500 XML-encoded scientific articles.  This is an exciting opportunity for web 2.0 programmers interested in science. But I hope people keep in mind they’d be giving their software ideas to a publisher that charges exorbitant prices for publicly-funded science.

McDawg says he has four PLoS ONE t-shirts! He must be embarrassed to not have a PLoS Pathogens t-shirt, PLoS Messenger Bag, or PLoS Travel Mug. Support open access by becoming a Public Library of Science member and get the goodies. Or do it for free by posting one of these free signs on your door or website. PLoS ONE has been doing really well, with over 2000 papers published to date.