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On science blogs (cont.)

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.

About this blog

"Notes from the Biomass" is my scrap book to keep, share and discuss trends in the life sciences. I work as bioinformatician at the Max-Planck-Institute for Infection Biology and the Max-Planck-Institute for Molecular Genetics in Berlin, Germany. This blog is a private activity and not reviewed or actively supported by any of the institutes.

Read more about my affiliations and research interests on my home page. For questions and comments please send an email to

Mandantory post

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]

The internet is changing everything but scientific communication

With all the changes of the way people using the internet for commerce, such as they are discussed by Steve Rubel here - what happens to the sciences and the way we communicate it?
Initial, scientists such as Newton and Leibniz exchanged letters directly; later, periodic journals published those letters. These publications turned out to be a profitable business and finally the publications and their citations have become the prime the source for the evaluation of scientists.
Recently, initiatives such as the Public Library of Science, backed by established scientists and funding changed the way we think how these publications should be payed for.
What's missing to me is the exchange of ideas and communication using the internet. Of course, there are chat rooms, most scientific programs from academia are released under one open source licence or the other and available quickly (not that they are usually maintained but that's a different story).

However, the way science is performed has not changed much: Work is usually not communicated to the outside, unless publishable in a journal with appropiate impact factor. Yes, there is email communication but that's only within a closed circle.
Good ideas and important results are not placed on a scientists website but get under a blanket until the PR and the law department of the research departement agreed to - and publishing on ones web site usually prohibits publication.

In mathematics and physics, preprint server have taken a role that might be closer to what I think how scientific communication would occur if we would not have the publishing legacy and would communicate more freely. Biological sciences on the other side have not ever come close to such an open way of publishing.

The internet has changed scientific discovery completely - but the way we communicate the results feels ancient. Even the little things, such as the one-dimensional author list, which does not recognize inidividual contributions in any way, appears to be carved in stone. As science is funded top down and there is little possibility to be successful with a handful of smart ideas and fund your own research, will there be change? Or is the change already there and I am just a little annoyed about some decorating relict?

Academic bloggers and the job hunt

The Chronicle of Higher Education features an article, titled Bloggers Need Not Apply, which is an interesting - and scary - read for the academic job seekers. I wonder whether the board, who was disappointed by the content of the blogs for one or the other reason would actually think that the applicants that did not blog were more capable and did not possess such flaws. Better the devil you know...

I've read a number of silly rants where young scientists commented on their PIs - doing that is stupid to begin with. Most science blogs that I read do not talk about much about the daily grind but reflect on the field in general, which I miss with many scientists that focus on the few angular seconds of their day sky.

A well kept blog will add to ones professional standing - certainly, there are a number of pitfalls one has to watch out for. Well, if I didn't, I should stop immediatly. Anyway, I might want to print the article and put it under my pillow.

[Via malorama]

Petition for increased EC funding

The following call from Frank Gannon deserves support. So I can sign the petition - and post it here.

Scientists petition for increased EC funding for research

Dear Colleague,

The collapse of the discussions on the EU budget has been highlighted in media. What receives less attention is the fact that preparatory discussions on a new budget were pointing towards a very major reduction on the doubling of funds for Framework 7 that had been requested by the Commission. Included in this funding were increases for the Marie Curie programme, expansion of the standard Framework activities and, significantly, the funding of the European Research Council (ERC).
All of this is now at risk and the voices of scientists need to be heard. As one effort to ensure that the politicians get a message from the scientific community, we, supported by ELSF, (European Life Sciences Forum) ( and ISE, (Initiative for Science in Europe) ( have opened an online petition on the EMBO website.

If you are in agreement with the petition, sign it at

Please ensure that all of the scientists in your institute are aware of it and encourage them also to sign. This is a case where numbers and a rapid reaction are very important!
Please note also that ELSO, (European Life Scientists Organization) have prepared a letter to be sent to Ministers of Research to underline the importance of the ERC.

This is your opportunity to influence the future of research so I suggest that you act on these initiatives now.

Prof. Frank Gannon
Executive Director, EMBO

Evolution of norms

An essay in the recent issue of PLoS Biology explores the how norms or memes evolve and strikes chord here.

Food for thought for tonight for me...

If Bioinformatics isn't science, it can't be bogus science at last

Coming back from a retreat in Oberbayern where we discussed the validity of bioinformatics as an independent science and its apparent lack of reproducability I stumble across this article. It is a little dated but certainly worth the read.

[Via Spreeblick/ Hudsonblick]

Name this blog...

Well, how creative is "A Bioinformatics Blog"?

The occasional passer by might want to leave a suggestions. Yes, that includes me.


This is my 'professional' web log, containing information that I would like to share with others interested in 'professional' bioinformatics.
There are other interesting web logs dealing with bioinformatics out there - this one will serve as my notepad, link list and as general margins on where to scribble my thoughts.

My research focus is comparative genomics, host-pathogen interaction and a good deal of classical sequence bioinformatics.



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Last update: 2006-07-16 13:11

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