The Scientist contemplates things needed to be re-engineered/designed in humans if we were allowed to do so. It is a roller coaster ride of thoughts with the goal of making humans immortal. I know I am sounding a bit odd, but the article is the way it is. Check the article out.

Today, Microsoft awarded more than $500,000 (US$) in grants to six outstanding projects in the area of synthetic biology. Microsoft identified the proposals best positioned to tackle the computational challenges in two areas of synthetic biology:

1. Examining the re-engineering of natural biological pathways to produce interoperable, composed, biological parts

2. Building tools and information repositories relating to the use of DNA in the fabrication of nanostructures and nanodevices

A total of 49 proposals were received from eleven countries, truly outstanding for our first RFP in this field. Proposals were received from many of the most prominent researchers and labs in the field. Following an external peer-review process, six outstanding proposals were selected and are listed below; for biographies of the recipients and additional information, please refer to: http://research.microsoft.com/ur/us/fundingopps/RFPs/Synthetic_Biology_Awards_2006.aspx

- Computational Interchange Standards for Synthetic Biology. Herbert Sauro, University of Washington

- Design and Synthesis of Minimal and Persistent Protein Complexes. David Green and Steven Skiena, Stony Brook University

- BioStudio: A Collaborative Editing and Revision Control Environment for Synthetic Genomes. Joel Bader and Jef Boeke, Johns Hopkins University School of Medicine

- Identification of Standard Gene Regulatory Sequences for Synthetic Biology. Robert Holt, University of British Columbia

- Using programmable stacking bonds to combine DNA origami into larger, more complex, reconfigurable structures. Paul W.K. Rothemund and Erik Winfree, California Institute of Technology

- Noise Suppression and Next-Generation Cloning Vectors. Johan Paulsson, Harvard University

Surprisingly, all the projects are from Americas.

Bacillius subtilis has been hacked to store “e= mc2 1905!” in its DNA. Check this out.

Even tiny pests do it. Check this news story.

Researchers have successfully hacked the puny bacteria into propelling a bead. Unlike previous research, they have used the whole bacteria for propulsion instead of the flagella only. Read the research here.

A Happy New Year to you all!

This time I have got the privilege of hosting an edition of Bio::Blogs on my blog Biohacking. Well, I start with a little disappointing news (at least for me) that Wikipedia has deleted the article on Biohacking. They claim that it is a pseudo-scientific term and it’s not acceptable to the scientific community. To add credibility to their claim, they say that since there is no journal named Biohacking, so the article should not persist in Wikipedia. “What the heck”, I say. I never claimed that Biohacking is a scientific term and, moreover, Wikipedia is not just for science. Nevertheless, Biohacking (as a term) will persist. Neologism is not that bad.

Biomathematics

Suddenly my interest in biomathematics has peaked up due to my research internship at National Center for Biological Sciences, Bangalore under Dr. Mukund Thattai during December 2006. As we were brainstorming for a particular project, I was mesmerized by his approach to science. He was using mathematical concepts to describe real biological entities and manipulating those entities in his head. The biological entities are just an instance, the real power of mathematics lies in ability to describe any arbitrary concept. Also, even though we were able to describe equations for our system easily, so, we could have easily simulated the system, but he insisted on cracking the system analytically as it yields exact answers and is much faster than simulating the system. I believe that biomathematics (or mathematical biology) has traditionally been ignored by the computational biology community. For them, insistence is usually on simulations, which of course look cool but are not the only way towards the solutions. Now for the starter links on biomathematics, see this excellent set of lectures. And this is the web page of the Society for Mathematical Biology. Although I haven’t read it for myself, I would recommend this textbook for an introduction. Of course there is the bible for mathematical biology by J.D. Murray.

Entrepreneurship
How about using your expertise in bioinformatics to earn easy money by taking a plunge into risk ladden world of entrepreneurship? Jokes apart, I, myself, am little ambivalent on this whole issue of entrepreneurship in bioinformatics. With the extent of hype around this field (in India) one would almost want to jump into it immediately. But, a little research will show that most bioinformatics companies are perishing. So, unless you have a really good business model, don’t think about starting your venture in bioinformatics for its own sake. A company can’t really survive on breakthrough research unless it makes it marketable.

Conferences
Regarding conferences, there was one which I attended in Bangalore called Computational Insights into Biological Systems. It was actually a satellite meeting of the International Conference in Bioinformatics 2006. The CIBS06 had great talks from well known people in this field such as Sarah Teichmann, Ravi Iyengar and Rama Ranganathan. Apart from the talks, the free lunch there was nice too..

Synthetic Biology
Here are some links (chosen randomly) for the blogs (on synthetic biology) which I like to read. Biohackery discusses some cool topics on biology. The Greythumb blog takes a very unconventional approach to the “intersection between biology and technology”. Omics Omics is also an informative blog. The Synthesis Blog discusses topics mainly related to Synthetic Biology. Also see DigitalBio @ http://digitalbio.blogspot.com/. Biomedical Computation Review is not a blog but an excellent magazine; make sure you don’t miss checking it out.

Links from the fellow bloggers
Pierre discusses about the features of Java 1.6 from a bioinformatics point of view. He thinks that the new integrated db engine is cool enough and he also uses the new scripting engine for making a little awk-like tool.

Pedro Beltrao discusses the exciting possibility of extracting (or mining, i must say) useful biological information from social bookmarking sites such as Connotea.

Sandra Porter has been writing a series on DNA sequencing on her blog. First she discusses the basics. Then she moves on to explain Sequencing strategies, Reads and chromats and How many reads does it take?. At the time of writing this post, the fifth part of the series has also been released – and the sixth one also coming out soon.

Finally, Neil has interesting posts on “computing tips and tricks”. Check out his posts on Automated SRS using Perl and LWP and Running a background process in PHP.

The End
That was all from the (first ever, i hope) Indian edition of Bio::Blogs. The bioinformatics field is very hot in my country as large number of so-called students are getting trained in it. But they don’t really have the real sense of doing bioinformatics. From what I have observed, the majority of them just know Perl & Blast and have programmed a DNA to Protein sequence translator once in their life. And they claim to be bioinformaticians. Bioinformatics is much more than mere programming. Enjoy.

I will be publishing the 7th edition of Bio::Blogs by tomorrow. Till now, I have got links only from one person. This is the final call for links. Please submit your favorite links to me from the world of bioinformatics as soon as possible.

Email them to me at paras1987 “at” gmail “dot” com or post them as the comments to this post.

Wouldn’t it have been really nice if there were an exclusive Digg.com for scientific literature or if Faculty of 1000 were free to access and open to all?

Well, the much needed service of the kind just described above has been launched in the avatar of Scientific Debate. It is a platform for post-publication discussing and rating of scientific papers. Anyone can post, rate and discuss about the scientific papers which have been published. This service is an important prototypic (or revolutionary, only time will tell) step towards a platform in science in which the importance of a work is not judged just by a handful of scientists on an editorial board of a conventional journal (or a citation service), but by many people across the world. I was waiting for such kind of service and now it has finally arrived. I thank the creators of ScientificDebate.com for bringing it on.

My best wishes for the ScientificDebate.com. I really hope the concept proves to be successful. Good Luck!

This article argues that the terms species, organism or the evolution itself might not be valid in the world of microbes.

Check out this interesting article. I wonder how much more is left in Nature’s kitty to discover. Now, they have discovered a bacterium living inside a mitochondria. Its wonderful to see that basic discovery has not been stopped yet.