Notes from the biomass

Our new paper in BMC Bioinformatics is about the only one that is not “highly accessed”. Next time we’ll take care to put “human cancer interaction” in the title.

The current issue of EMBO Reports contains a short analysis, which shows that the number of retractions of scientific publications increases dramatically. The authors give two possible explanations: Competitions amongst scientists lowers the quality of published research. It might also mean that scientists are more aware of other people’s mistakes and that “the self-correction of science is improving”.

While both alternative are plausible, my favourite suggestion is that online publications have made it feasible to retract papers and there is an incentive for the journals to show that they take care of possible misconduct. A large number of the retractions might be of heavily flawed works rather than fraud (a blogger’s assumption, I have not checked enough retractions myself). Earlier, the community would know that a particular work is not reproducible, but the retraction process was cumbersome and consumed too much time, so it was only pursued in the grossest instances.

There are so many complaints regarding position on the author list that I tend to ignore most of the conversation on the topic unless a journal actually changes something. The PLoS blog features a noteworthy idea by Michael Molla and Tim Gardner. Similar to the roll credits that appear at the end of a movie, they suggest a defined, fine grained roles. Senior author could pose as producers or director, refining their role, and obviously a story can have more than one main character. It’s definitely a step in the right direction but film posters always confuse me in that the names of the actors and the order of their faces in the poster never align. Even if the roles are better defined, the bitching for positions will surely remain.

Most of my dear readers will have either noticed or written about the lack of comments on scientific articles, for instance at the BMC journals and most notably at PLoS ONE, which was designed for interaction of author and reader.
At this point, there’s not too much to add to the conclusions: It’s takes to much time to comment on a scientific article properly, there’s no incentive (can’t put it in your CV) or honor to be gained (no one asked me to review this) and they are not written to be discussed (open/pragmatic) but supposed to discuss the results thoroughly themselves. However, despite all the comments on the matter, trying to study the phenomenon on the web is difficult due to the lack of strong keywords: Searching for “comments on publications” does not take you to very informative resources.
Similar discussions were underway in the Usenet and a particular consideration on the lack of comments made into Wikipedia as Warnock’s dilemma, which I stumbled across by chance. The term did not stick but it’s a worthwhile keyword for research in communication in blogs and scientific publications. Most of the considerations listed can be applied to all forms of written electronic communication.

Next: The careful analysis of the source for the scarcity of my blog output. A killer post.

Philica is an attempt at academic publishing with very few restrictions. Journalology (my source) is critical as is Archaeoastronomy. I too doubt whether the initiators do much good to academic publishing by releasing work on divination methods.

Most of you will have heard of the launch of PLoS ONE, a new publishing platform promising many changes to the way scientific work is communicated. A important aspect distinguishing One from many journals is the strong commitment to increase participation of the readership.
Several bloggers (e.g. Deepak and Pedro) and probably many observers out there are somewhat concerned that the participation of scientists will not be intense, particular in the light of the Nature Peer Review trial that only received few comments.
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If we follow Pedro Beltrao’s proposal to create virtual journals by tagging in Connotea to the end, we should start an online competition to create the journal with the highest impact factor. After all, the fantasy baseball and soccer manager games out there seem to be highly popular.

You probably need to select a minimum number of entries, may be 50 for a year or 5 - 10 a month and limit the subject area. The winner receives free scorn and secret envy from the scientific community.

Despite an explosion of schemes for publishing research, our most important question remains unanswered. What constitutes a significant publication?We could have settled the problem a long time ago. However, evil capitalist publishers for monetary reasons, science magnates (re-styled as revolutionaries) to keep their established position and blue-eyed bloggers for causes they are unsure about all but promote their own style of selecting important works by interaction with other scientists or even the mass media. This only promotes preferential attachment, not absolute importance.
At best, the current discussion wastes trees and electricity in amounts that brings us closer to the entropic death of the universe but does not get us closer to objective publishing criteria. (more…)

Nature Biotech has opened a new section, Community Consultation, which aims to involve the scientific community in the development of standards for publications. The first manuscript for review discusses The Minimum Information required for reporting a Molecular Interaction Experiment (MIMIx).

The authors comprise many important people in the interacting proteins field, both experimentalists and bioinformaticians associated with the development of databases such as DIP, BOND and Intact. One important focus is to enforce unique identifiers for biomolecules; I was pleased to see that the experimental role (such as “bait” in a biochemical purification experiment) is enforced too, as it was missing from many databases and is often neglected in bioinformatics network analysis.

The bioinformatics community will benefit from these standards most. Let’s hope that all publishers will enforce them consistently.
[Via Pedro Beltrao. Nature could really give this broader coverage, they should be proud of it.]

Any sufficiently advanced technology is indistinguishable from magic as long as you don’t use it in your everyday work. In the sciences, there is hardly anything left that I would consider magic devices - instruments that fascinate me because they contradict my daily macroscopic experience. Mass spectrometers are a notable exception. Working in the vicinity of these instruments for several years and probably having understood how some of them work, the results these instruments deliver still fascinate me.

There are other applications to mass spectrometry in biology than identifying proteins, I sometimes have to remind myself. In a recent article in Journal of Biology Claude Lechene and colleagues describe a new instrument that uses stable isotope mass spectrometry for imaging cells in unlabeled samples.

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