Thyago Duque

Yesterday several sources published news about the discovery that two mutations (out of 740 units) in the gene FOXP2 may be responsible for our ability to speak.
FOXP2 association with speech was reported in 2001, after a study in a British family with speech problems on more than half of it’s members. However, the gene has analogous in several other species including chimps and mice.
From the chimp version two the human version only two mutations have occurred, however, these mutations have significant impact in the function since FOXP2 regulates the expression of hundreds of other genes.
The experiment that confirmed the importance of this gene consisted in replacing the human version by the chimp version in a human neuron culture. The replacement generated large changes in gene regulation.

The original work was published in nature: Konopka, G. et al. Nature 462, 213-217 (2009). (here)
The new was published in several websites including:
http://www.nytimes.com/2009/11/12/science/12gene.html?partner=rss&emc=rss
http://www.nature.com/news/2009/091111/full/news.2009.1079.html?s=news_rss
http://news.discovery.com/animals/chimpanzee-speech-language-gene.html

I am on the wave.

I did not start waving about anything useful yet and therefore, google wave still just an useless toy for me, but I can see that it has potential to be useful and chaotic. A lot more potential to be chaotic than useful, but it is still evolving.

I will come back and post my impressions once I use it for something useful, but for now, all I can say is that I feel that superiority feeling that people that are member of an exclusive group feel, even if there is absolutely nothing special about this group.

BTW: Do people use waving for that? Well, I am guessing they will, so I am trying to be one of the early adopters =D

If you are interested in neuroscience but do not have too much time to dedicate to the subject I highly recommend the Howard Hughes Medical Institute’s 2008 Holiday Lectures in Science.

The holiday lectures in science are usually composed of four lectures on a specific topic presented by HHMI investigators from universities in US. The lectures (at least the ones from 2008) are very well produced both in a scientific aspect as in the technical/cinematographic aspect and they condense an impressive amount of information in little less than 4 hours. I was impressed with how much I learned very little time.

You can watch the lectures in HMMI’s website :
http://www.hhmi.org/biointeractive/lectures/

or download then for your ipod:

http://deimos3.apple.com/WebObjects/Core.woa/Browse/researchchannel.org.1420284301.01420284308.2149823379?i=1754545314

http://deimos3.apple.com/WebObjects/Core.woa/Feed/researchchannel.org.1420284301.01420284308

http://deimos3.apple.com/WebObjects/Core.woa/Feed/researchchannel.org.1420284301.01420284308

http://deimos3.apple.com/WebObjects/Core.woa/Feed/researchchannel.org.1420284301.01420284308

Enjoy

I just finished the following iTunes U course: http://deimos3.apple.com/WebObjects/Core.woa/Browse/yale.edu.1900004221

It is very good. Very interesting both in the biological stand point and in the engineering point. It also reminded me of my advisor David Goldberg several times, and of his view of what it means to be an engineer.
The only problem is that the slides are copyrighted and therefore not presented, so you loose the animations and other important visual material. Therefore I recommend using downloading this lecture in MP3 instead of videos, and watching it in times you wouldn’t be able to see a video (for example while you work out, in the bus, while you make your breakfast).

It is pretty short course and covers a large spectrum of bioengineering. Really interesting.
Enjoy =D.

Just finished watching Intro to Biology From MIT http://bit.ly/1Vvji1 (iTunesU). Highly recommended (and free).

Pier Luca Lanzi, from the Politecnico di Milano university made his lectures on data mining available on the web trough Vimeo. It is a good resource if you whant to learn some principles of data mining. The lectures can be found here. You can also visit Pier Luca’s website here.

In the past weeks, we talked about the question of Why Semantics (here) and how to build scientific ontologies (here). Now it is time to start building our own ontologies using Protégé.

Protégé is an open source tool to build OWL ontologies and it can be found here, under downloads (here) . The version 3.4 is the last stable version, and it recomended by several specialists. Version 4.0 is a release candidate and is quite stable.

Finally,  a tutorial that teaches how to use Protégé and introduces some concepts of OWL can be found here.

Genetic Algorithms are actually my primary research interest (not semantic web) but I have been in the field for quite long time and I haven’t looked on basic/interesting stuff for a while. My plan is to start blogging more about GAs in the near future but for now I have a bunch of semantic web topics in my queue.

However, today I came across this video that performs the strange crossover between GAs and Semantic Web and, although the results are bad, I think it is strange enough to deserve a post.

This video (here) is a presentation on the IWSC08 of the paper Anytime Query Answering in RDF through Evolutionary Algorithms, by Eyal Oren and colleagues, which can be found here.

Note that I do not recommend using this method for your RDF queries, but still found the paper strange, if not interesting.

Continuing the series of videos about semantic technologies, a good suggestion is this video (here) . In this video Barry Smith walks through some basic concepts of ontology engineering and scientific ontology. The Basic Formal Ontology and the RCT Trial bank are used as a base for a Clinical Trial ontology.

Message in a Bottle or: How can the Semantic Web Community be more convincing?
http://videolectures.net/iswc08_decker_mib/
Stefan Decker, DERI Galway

Description

Enormous resources are poured into projects like the Large Hadron Collider, the Hubble space telescope, or the Iter fusion reactor. Computer science resources pale in comparison – the European Semantic Web effort is tiny compared to those projects. Why is this the case? In this talk Stefan Decker will argue that the Physicists are much better in formulating an engaging mission and message. Especially the Semantic Web community has not been very good in coming up with a convincing mission directed to the public. We need to and we can do better.