Notes from the Biomass

Gregory Petsko's editorial in Genome Biology compares the current practice of stuffing all data into tables and ill-formated text files as supplementary material and only giving an introduction and a discussion in the main paper with fighting a land war in Asia. I don't particularly like the analogy and the tone of the editorial in general but largely agree.
Currently, we attach complex data to a document style that is not much different from way science was communicated in 1950 despite advance in IT technology that make data sharing possible. However, we need to come up with better formats, not longer papers that include more data.

[Via Keats' telescope]

The recently launched Biology Direct differs from the vast majority of scientific journals in that it publishes under an open peer review scheme. The names of the reviewers and their reports are published alongside the original publication. Announced in October 2005 it focusses on genomics and bioinformatics and is backed by an impressive line up of scientists. The first publications went online yesterday, accompanied by a editorial that underlines the experimental nature of the journal.

Launching a new research journal in biology in the year 2006 takes a lot
of hubris…and/or a clearly defined goal. The crucial open access niche has been taken by
the highly successful and still proliferating BMC and PLoS journals, so a new journal
hardly would stand a chance and be worth the efforts of the editors and the publisher
unless it defines itself in a fundamentally new way. Thus, our goals with this new journal,
Biology Direct, are unapologetically ambitious: to establish a new, perhaps, better system
of peer review and, in the process, bolster productive scientific debate, and provide
scientists with useful guides to the literature.


Are peer reviewed publications really a good way to foster scientific debate? Peer review is beneficial to the point of being unmissable for primary research publications but I am not convinced that it enhances debates. For Biology Direct, the facility to comment on the work is included for most BMC titles anyway, though I fail to see widespread use of it, and I don't see where Biology Direct provides additional means. A system that would not require peer review but imposes more structures than blogs, wikis of news forums could provide more to discussion by many different scientists - not that I would know what exactly to implement.

I had hoped for publications with higher profile - the four current papers are somewhat interesting but I would have expected that Landweber, Lipman, and Koonin would have been able to pull higher impact papers into the new journal. Probably, most scientists submitted rather solid but not controversial work and reserve their high profile papers for journals with higher impact (or with an impact factor to begin with).

Still, the direction that Biology Direct will take in the next couple of years will tell us how flexible the publishing scheme really is. PLoS changed quite a bit of it already and there's undoubtedly more coming.


[via F&L]

If you compare the reactions to publications in PLoS Biology (10 e-letters in the last 30days) or the Nature-blogs (3 comments on Free Associationin the same time frame) to the responses in theBritish Medical Journal, you start wondering why the clinical side of the life sciences finds so many more comments than the experimental end. Just the number of comments could be explained by the number of readers but the quality of the contributions is much higher in BMJ, too.

I am a little disappointed by the lack of participation but do not think that it is the fault of journals. The comment functions are as easily accessible in BMJ as in PLoS for instance. Many publications are discussed in journal clubs or on conferences in great length. Why not take the time to share your thoughts? And if you're one of the kind who doesn't like MDs - do you want *them* to be more internet-savvy and future-ready than you whose middle name is 'high-throughput'?

The current cloning scam is taking its toll on the publishers. I was surprised how outspoken Benjamin Lewin (the one with the book), founder and former editor of Cell, critized Science recently. From the NY Times article:

"It sounds as though their processes were rather sloppy," said Dr. Benjamin Lewin, the founder and former editor of Cell, a biology journal known for its rigor. "At a minimum, Science should have been more careful and should never have reached the stage of publishing a paper with identical photos," he said, referring to the fact that some photos of cell colonies in Dr. Hwang's 2005 article were duplicates of one another.

Dr. Lewin said that a journal editor needed to develop an intimate knowledge of his reviewers' strengths and weaknesses, and that "Nature and Science don't have the reputation for rigorous review."

However, digging a little I realized that this is not the first time that Lewin critizes Science harshly. It seems as if the quarrel is going back more than 20 years as can see from this discussion on press embargoes in Science from 1998. Lewin also appeared as an outspoken critic of the publication of the first cloned sheep Dolly a year earlier.
Unfortunately, Cell too has had to retract research publications due to fraud in 2004.

Any publication process has to compromise relevance, timeliness and thoroughness and I don't see a one size fits all approach to the problem - even if it leads to occasional publication of oversold or fabricated results.

[Update: In the Pipeline hast the story too, providing additional view points.]

While many of the readers of this blog will have realized that blogging scientists provided their opinion on Google Base for Nature's coverage thereof, most readers of Nature are probably not aware that PZ Myers, who runs the widely read Pharyngula and Greg Tyrelle, who started nodalpoint.org were most likely selected for comment due to their engagement on the Web.

It seems noteworthy to point out that bloggers are considered as serious source of input for science journalists on one hand but are not credited for their work on the other as neither their blogs nor their activities as bloggers were mentioned.

As far as Google Base is concerned, I largely disagree with the article and think that it's impact on scientific information distribution for the life sciences will be minimal, as was discussed on Pedro Beltrao's blog. However, the format prevents from covering the subject in great depth, so I won't complain about the superficial selection of quotes, which were also referred to in the podcast.

Text mining the biomedical literature has matured from a peculiar idea towards a respectable niche in bioinformatics. In a letter to the editor of Bioinformatics, Blaschke, Valencia and others, themselves pioneers in the field summarize recent advances. They note that the crucial task of relating gene and protein names to normalized identifiers is now producing reliable results, even if they still somewhat lacking in precision compared to other fields of computer linguistics. I am positively surprised about the high numbers. The tasks of identifying the correct sequence of a gene from a paper is sometimes still complicated even if you do it "manually" despite working with fully sequenced bacterial genomes and extensive set of synonyms. Hopefully, we such parses will make it to the desktop soon.

If you think about this from a high-level perspective, the way we work with biomedical information seems absurd. It would be simpler and useful if the names of proteins and genes would be identified as such in the publication using some simple markup like for references to other publications; one could extend reference managers like Endnote or Bibtex. Clearly, we need mnemonic names for spots on a gel, phenotypes or ORFs in sequenced genome for readability but why don't we disambiguate them in a consistent manner now that the majority of important genome sequences are at hand? Other "stable" constituents of a paper -strains, protocolls, chemicals, antibodies- could also be referenced in such manner, directly linking to resources such as the Registry of Standard Biological Parts at the MIT or catalogs (if stable identifiers will be maintained). After all, the method sections often name the supplier of agents - would it not be a logical extension to submit all information?

However, if the publishers support these advancements, text mining methods will be required to identify such information in the tome of fundamental biological information that we have compiled in the last 100 years now that it is slowly becoming digitalized. This will stay an interesting field for years too come.

To many younger scientists the review process appears as an heavily biased, unfair process played by a set of clandestine rules (and established scientists feel the same way but rather play Dr. Seen-it-all). In the current issue of EMBO Journal, Pernille Rørth, its current executive editor presents a detailed, personal view of his her work and challenges to it such as full time editors vs part time editors. Recommended, even if EMBO Journal is not your target journal for submissions.

Sigh. I was drafting a post, enthusiastically sketching the need to non-peer reviewed scientific communication using web technologies, when a friend of mine notified me that work that was carried out in our department was featured on Slashdot. I was not involved in the project now published in PLoS Pathogens other than donating blood once (my poor neutrophils ...) but got curious and paused. So, I went to find out how a technologically and scientifically open and informed group of people would take on the publication. As Bacillus anthracis was studied I was already expecting little interesting considerations of the actual work. I guess, most readers missed the point that we study host-pathogen interaction and that the discoveries are made more on the host side than the bug side. I still was very disappointed with the responses and scrapped my sketch.
I don't want to start bashing Slashdot - it's an interesting place and it's a fairly informed audience. However, I wonder how a "serious" open scientific discussion would work and I am less surprised about the strict rules that for instance PLoS imposes on scientific comments.
What do we need to do to ensure high quality discussion? - moderation only won't work in the very diverse field of the modern sciences as you would have to have editors that are very much skilled in their field and one would practically introduce peer review.
Also, the short-lived comment wave is not stimulating a real discussion. Science blogs and related community pages, in particular those running longer discussions must develop longer threads and thinking to deliver a value that is worth reading and live with small numbers of informed readers. I wonder, whether the reason why there are so few life science blogs about science (not life in the lab or creationists) is caused in part by the need for slower but more thorough formats that are not served by blogs and news groups currently.

Free Association is a blog, accompanying Nature Genetics with commentaries in papers therein and in other journals, editorial policies, announcements of editors at meetings, and covering genetics in the media, including blogs. The commentaries by authors are really required for the usual Nature Genetics two-pager that solely consists of numbers and links to the supplementary material.

Free Association is a "real blog", with identifiable authors, trackbacks, comments and a very clean, unNatural layout free of advertisment, all powered by Movable Type. I appreciate its low tone really and prefer this way of commenting to the letters to the editor at BMJ or PLoS Biology.

Comments are reviewed as most publishers gone blogging do. Let's see what happens when things go controversial. I hope that the editors pick up good traditions from the blogs, such as identifying your sources and providing links to content other than your own, which I often miss in the media coverage.

Most likely, this is one of the first blogs that many geneticists will see - and it will a powerful influence for the A-list of science blogs. It might also be helpful in establishing blogs as a serious form of communication in science - that alone would be a good thing.

[Via nodalpoint.org]

A review of the current state of open access publishing concludes that Peer review and copy-editing may be less rigorous with Full Open Access journals, amongst other controversial findings.
In the light that many of the organizations who requested the report publish under the traditional model one might want to question the independence of Kaufman-Wills, a consulting firm specializing in electronic publishing. The Scientist's feature (which notified me of the report) lists other questions and perspectives on the report, including the opinions of open access activists.