Notes from the Biomass

The publication of a map of the rice genome on August 11th in Nature was echoed in the main stream media. Several of those channels highlighted the global importance of research based on the genome sequence to human nutrition. According to the paper one has to increase the production of rice by 30% in the course of the next 20 years on the same area of arable land. Also, global warming and pollution (amongst others) require other, enhanced rice strains.

Obviously, these facts seem to be more important to the media than all the genes and transposons in the genome. I looked up the references to the facts presented and the statements go back to a paper from 1999, published in Crop Science (impact factor 0.958, #17 in 50 journals in Agronomy [ISI]), and a PNAS publication (contributed), highlighting the impact of global warming. Obviously, the authors had to restrict themselves to a few key publications given the constraints posed by the editors.

After reading the publications and some of that cite them, I find it hard to evaluate the assumptions the researchers make because I am not an expert in crop sciences in asia. However, these publications were only put into the light of the general public in the context of the rice genome and the numbers of citations (60 for the work from 1999) seem low given the potential impact of the work.

Well, read the references yourself. And read the rice genome paper if you are interested what plant genomes look like. It's good solid work and certainly does not require advertising by famine.

As we discuss whether a open, online system could replace how we judge the impact of a publication today, many people question aspects of the current system, run entirely by Thompson ICI.
In the editorial of the current edition of PLoS Biology, Hemai Parthasarathy, its managing editor reviews oddities in the way the impact factor is calculated for PLoS Biology.

Is the impact factor of a journal really that important? We all know that it only captures part of the importance of a journal. I really never understood the scientists who did not want to consider PLoS because the impact factors were not established and I would not be surprised to learn that those will now refrain from publishing in PLoS because of its low impact factor.

Will exaggerating the impact factor ever stop in the awareness driven economy of the sciences? Probably not. How about a more transpararent alternative?

In the interpretation of high-throughout data, we make statements about the number of biological entities. However, the number of genes in a higher eukaryote, of protein domains or folds, or protein complexes is the product of many parameter choices. Because these entities have soft boundaries, we have to make assumptions about their nature that can not be quantified by a confidence interval or other established quantifiers. It would be very useful to label the results with a statement about their validity, expressing the confidence of the researchers, similar to the procedures for annotations in Gene Ontology.
A statement in a publication could read:
The number of protein coding genes in Alosa fallax is 37.387[SEN]. We predict that these proteins form 235.345 splice forms[I50K], arranging themselves into 920 protein complexes[IA<]. 4 protein are involved in fin formation[I5] and 3.454 in cell cycle regulation[I5].

Here are the abbreviations
[I5] Inferred from Perl script. 5 lines of Perl can't be wrong.
[I50K] Inferred from major calculation. 50.000 lines of C++ can't be wrong.
[SEN] Contribution of the senior author.
[REV] Stinking reviewers didn't like our numbers. Have to put them into the acknowledgments.
[IA>] As high as we could get it to meet your expectations
[IA<] As low as we could get it to meet your expectations
[2*] Could be twice as much but who am I
[DUD] Spot on, dude. Seriously!

Isn't blogging great - you can leave semi-random thoughts on the web, get responses and realize that the idea was much better than you initially assumed. After my post on why scientific communication feels static to me, a number of ideas came to my mind as soon as I went cycling that afternoon. Some of them survive to this day. In between, science blogs were exclaimed as the next big thing (the The Scientist article is no longer available to the general public... see?).

My claim still is: Blogging (and other "new" forms of communication over the internet) won't change the way we communicate in the natural sciences. The apparant flaws like the one-dimensional author list, anonymous, unpaid and uncredited peer review and the impact factor craze won't just go away using this "technology".

Would anything be better, if we build a system that would allow everybody to publish without initial peer review on some website/blog and other scientists would transparently comment on it? Citations could be followed easily and trackbacks or similar system would notify us of work in the field.

Much of the system is in place - Pubmed, the Digital Object Identifier, Faculty of 1000 (while not being as comprehensive as one might hope) are there. The conservative nature of sciences will prevent sudden changes, which might be a good thing: As archaic as the Science Citation Index sometimes appears, would you want to replace it with a spamable Google? And what about the information that is stored in paper journals only?

While people spend a considerable amount of time figuring out which journal to publish in to receive the credits they hope for, would anything be better if we replace it with an open system that would make it much harder to be critical? Most contemporary scientists state that they read to little already - we certainly do not want to increase the number of publications without ensuring their quality before they appear.

On the other hand, the internet has already changed the way our communication occurs - PLoS would not have worked without the internet which could reach a large number of scientist quickly. Email and news groups are there without us taking notice and I fail to see a pressing need for blogs to replace anything. I should not forget to add that there seems to be a considerable difference between the mathematics and physics in respect to the biological natural sciences, the prior already publishing much more independently and free on web sites and conferences.

There will be more science blogs - blogs that are used to communicate between scientists rather than communication of scientists with the general public as it happens on esteemed sites like Respectful Insolence or Bad Astronomy. However, they will focus on subjects around the sciences rather than replacing the traditional ways of publishing experimental results or breakthrough findings which undoubtedly will undergo other changes. It's exciting times - I wonder when the first big shots will start their blogs. Only then we'll see a major influx of blogs into the scientific communication anyway.

Friday morning is my regular time to check the scientific RSS-feeds, skim through Nature and Science and empty my mail folder for eTOCs. Being a blogger handicapped in screen-reading, I print more papers than I could ever read. Here's one that I started reading on the way from the printer and continued through: Jan Ihmels et al describe the large scale changes to gene expression after the genome duplication events in the yeasts and the loss of motif in Saccharomyces. Good stuff, I just hope that the differences they see primarliy are not caused by the different sizes and ways the samples from Candida and Saccharomyces were generated in the first place.

The Scientist on scientific blogs. Not that I do see much of it happening if you compare it to what's happing in the pop culture scene.

Two bioinformatics blogs with many hits and one from a pharmaceutics company don't really amount to much yet, eh? Hey, scientists spend there days in front of computers, whereas those pop folk-do no goods spend their time and money partying. How come we produce so few blogs and so little content?


... now back to work.

[Thanks Greg]