Konrad’s considerations

As reported yesterday, the German province Bavaria officially gave the police the right to use tools to scan computers of potential criminals starting from August 1st (the media call these tools “Bundestrojaner” - ferderal Trojan horse - in this case “Bayerntrojaner” - Bavarian Trojan horse). Looks really like another chapter of “We lost the war“ and there have been already too many of those in the last time. I am pretty sure the salami-slice strategy will work here very well and very soon we will have not only the Bayerntrojaner but finally the Bundestrojaner. Unfortunately most people don’t bother as they don’t see the implications and danger of the potential abuse of these tools and practices.

George Carlin, the disputed libertine comedian, died last Sunday in the age of 71. Man, we will miss your awesome humor.

The DiSo project is a promising attempt to create a distributed social network which is not following the “silo” approach as other social networks do. The blog of the project offers a short (4 min) introductionary video in which Chris Messina explains the vision and ideas behind this solution. The project will make use of open standards like OpenID, XMPP and different microformats. Code is available as open source. Really looking forward to see this stuff in action soon.

Yes, maybe I am little bit too nitpicky, but this bugs me: April 30th 1993 the World Wide Web became officially accessible for the general public and libwww became open source. Some media saw this as a reason to celebrate yesterday the 15th birthday of the WWW. Due to this “birthday” I stumbled across a common mistake more often then usually: Mixing up WWW with the Internet.

The WWW is not the Internet!

As an analogy - a car is not a highway. The WWW is one of many internet-based services like email, IRC or p2p networks. The Internet is the underlying network that is using the Internet Protocol (IP). I personally would like to see a little bit more awareness of this issue.

After 6 months of hard work the OpenBSD project released version 4.3 of the great, (non-)fishy operating system. As usually there is a collection of micro-interviews with some of the developers about new features at the O’Reilly’s BSD DevCenter.

This year the well known EMBL PhD Symposium will cover fields belonging to the topic “Decision Making in Biology - Nature at the Crossroads” and you can already register. It is still some time until October (23rd - 25th) so the program is not yet available but the list of speakers looks very promising.

Outch! Styczynski et al. [1] found an error in the BLOSSUM62 - THE substitution matrix used since 16 years in bioinformatics for protein database searches.

Lessons learned:

• Don’t stop questioning even fundamental laws/tools/assumptions/etc.
• Transparency - in bioinformatics the access to the source code and the data - is essential for proper science

[Via Suicyte Notes]

[1] BLOSUM62 miscalculations improve search performance. Styczynski MP, Jensen KL, Rigoutsos I, Stephanopoulos G Nat Biotechnol. 2008 Mar ; 26(3): 274-5

Steven M. Thompson has initiated a petition to make Accelrys‘ GCG and SeqLab available under an open source software. He wants to prevent the loss of these bioinformatics tool sets after Accelrys’ recent decision to stop the support and development of them.

Sometimes a warm hug can make a difference: The CouchSurfing community will carry out a wordwide Free Hugs campaign tomorrow, March 22nd. The the CouchSurfing wiki lists 51 cities in which people will give hugs to strangers to make the world a better place.

Join in, I am pretty sure you have some hugs to give away, too!

(Photo taken by moonwire)

Craig Venter gave a talk at the TED conference this year in which he presented a synthetic biology approach to create an organism that might solve two major problems of mankind: The increasing CO₂ concentration in the atmosphere and limited fuel resources. Venter claimed that the project will take further 18 month. The video of the talk is now available.