I usually don't do this but ..

This is a really good blonde joke. Got love infectious silly memes.

BioPerl has a new site

If you use BioPerl go have a look at the re-designed site. From the full announcement at OBF:

"I am pleased to announce the release of a new website for BioPerl. The site is based on the mediawiki software that was developed for the wikipedia project. We intend the site to be a place for community input on documentation and design for the BioPerl project. There is also a fair amount of documentation started surrounding bioinformatics tools and techniques applicable to using BioPerl and some of the authors who created these resources."

Meta bloguing

I changed a couple of things on the blog template. If anybody reads this with an aggregator and all previous posts appear as updated please let me know.
I added a new section on the right bar were I plan to keep some previous post that might be interesting to discuss. I had this change in mind after reading this post in Notes from the Biomass about blogging. It is true that blogging platforms don't make it easy to revisit ideas. I'll try to find other ways to do this.

I also updated the blogroll with some links. Neil's blog and Yakafokon on bioinformatics, some tech blogs I particularly like and a the blog of a portuguese friend of mine.

Our Collective Mind II

Some time ago I posted an unusual short text about collective intelligence. I think it was motivated by the web2.0 explosion, all the blogging, social websites and the layer of other services tracking these human activities in real time. The developments in the last 2-3 years were not so much a question of technical innovation since most of the tools were already developed but it was mostly a massification effect. A lot more people started to participate online instead of just browsing. This participation is very easy to track and we have automatic services that can, for example, tell us what people are currently talking about. One can think of these services as a form of self awareness. If you go to tech.memeorandum you can see a computer algorithm tracking the currently most talked about subjects in technology and organizing them into conversations. This does not mean that the web can understand what is being talked about but it is self aware.

I read today a (very long) post by Nova Spinack about this subject of self awareness and how he proposes that we should build this on a large scale. Although I agree that this type of services are very useful I am not sure that one should try to purposely build some form of collective intelligence on such abstract terms. This idea of having everything collected under the same service feels to restrictive and not very functional. I would prefer a diversity and selection approach, just let the web decide. There is a big marked for web services right now and I don't see it fading any time soon. Therefore if collective intelligence is possible and useful then rapidly services will be built on top of each other to produce it.

If you have any interest on the topic and endorse his opinion write a post and trackback to him.

Power law distributions

Almost every time a lot of hype is built around an idea there is general backlash against the very same idea. In technology this happens regularly and it is maybe due to a snowball effect that leads to abuse. Initially a new concept is proposed that leads to useful new products and this in turn increases interest and funding (venture capital, etc). In response, several people copy the concept or merely tag their work with the same buzz to attract interest. Soon enough everyone is doing the same thing and the new concept reaches world fame. At this point it is hard to find actual good products based on the initial idea among all the noise. For a recent tech example just think of the web2.0 meme. Every startup now a days releases their projects in beta with some sort of tagging/social/mash-up thing. The backlash in already happening for web2.0.

What about the title ?
I had already mentioned a review article about power-law distributions. The author voiced some concern over the exaggerated conclusions researchers are making about the observation of these distributions in complex networks. Is the backlash coming for this hype?

Recently Oliveira and Barabasi published yet another paper on the ubiquity of power laws. This time it was about the correspondence patterns Darwin and Einstein where they claim that the time delays for the replies follow a power-law. This work is similar to earlier work by Barabasi about email correspondence. Quickly after, a comment was published in Nature suggesting that the data is a better fit for the lognormal distribution and this generated some discussion on the web. There is also some claims of similar previous work using the same data not properly cited.

The best summary of the whole issue comes in my opinion from Michael Mitzenmacher:
"While the rebuttal suggests the data is a better fit for the lognormal distribution, I am not a big believer in the fit-the-data approach to distinguish these distributions. The Barabasi paper actually suggested a model, which is nice, (...) anyone can come up with a power law model. The challenge is figuring out how to show your model is actually right."

Other papers have recently put questions also on the quality of the data underlying some of these studies. Is life all log-normal after all :) ?

What I actually want to discuss is the hype. Going back to the beginning of the post, how can we keep science from generating such hype around particular memes. People like Barabasi are capable of captivating the imagination of a broad audience and help bring society closer to science but usually at some cost. I think this is tied to science funding. What gets funded is what is perceived as the cutting edge, the trendy subjects. Trendy things get a lot of funding and more visibility until the whole thing crashes down with the weight of all the noise in the field.

In a brilliant paper (the one about a radio :) Lazebnik remembers some advice from David Papermaster:
"David said that every field he witnessed during his decades in biological research developed quite similarly. At the first stage, a small number of scientists would somewhat leisurely discuss a problem that would appear esoteric to others (...) Then, an unexpected observation (...) makes many realize that the previously mysterious process can be dissected with available tools and, importantly, that this effort may result in a miracle drug. At once, the field is converted into a Klondike gold rush with all the characteristic dynamics, mentality, and morals. (...) The assumed proximity of this imaginary nugget easily attracts both financial and human resources, which results in a rapid expansion of the field. The understanding of the biological process increases accordingly and results in crystal clear models that often explain everything and point at targets for future miracle drugs.(...) At some point, David said, the field reaches a stage at which models, that seemed so complete, fall apart, predictions that were considered so obvious are found to be wrong, and attempts to develop wonder drugs largely fail. (...) In other words, the field hits the wall, even though the intensity of research remains unabated for a while, resulting in thousands of publications, many of which are contradictory or largely descriptive."

Is this necessary ? Is there something about the way science is made that leads to this ? Can we change it?

European Research Council (ERC)

For those of you who don't usually read about European research policies, the European Research Council is a projected European structure being designed to support basic research. It is now clear that the ERC will be formed but it is still unknown how much money the EU budget will reserve for it. Recently the Scientific Council of the future ERC was nominated and the chairman is none other than Fotis Kafatos, the former EMBL director. Kafatos term as EMBL director ended in May last year and his nomination as chairman of the ERC will, in my opinion, strengthen the research council and hopefully help it attract the funding required.

For further reading:
Kafatos named Chairman of ERC Council (EMBL announcement)
Chairman explains Europe's research council (interview for Nature)
Election of Chairman of Scientific Council (press release hidden among several other)