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Biology

Baby it’s cold outside

Most of the Earth’s surface is colder than the inside of your refrigerator. Deep sea temperatures are almost universally 2-4C. That’s already 73%  of the Earth’s surface. Then add to that the  polar regions, mountain ranges and permafrost and you have about 85% of the Earth’s surface constantly at refrigerator or freezer temperatures. While there […]

Mad Scientist

From Abstruse Goose

Not dead, overloaded

When the Moon is in the Seventh House, and Jupiter aligns with Mars, a bunch of people gather for their “Bioinformaticians anonymous” group therapy. There they metaphorically gather, commiserating about how bioinformatics is dead (or was it bioinformaticians?), just smells funny or suffers from identity theft, probably because it got drunk at the last ISMB, […]

Searching for Life on Earth

But if you know what life is worth, You will look for yours on Earth — Bob Marley – “Is there life on Earth?” – “Well, duh.” – “I mean, is there another kind of life on Earth?” – “WTF?” – “You know… there could be these bugs that, like, they’re all around us and […]

Ten years of coding with the snake

Biopython is entering its 10th year; the unofficial birthday is on September, since that is when the mailing list started: September 1999. I stumbled onto that list mid-September, 1999. I believe the Python version was 1.5, I was still working on SGI Irix, and I was an 0.3 PhD candidate. Today I am coding with […]

Metagenomes as a diagnostic tool?

Can we learn about an environment by looking at the bacteria living in it? Can we sequence a metagenome, and then say: ”according to the active genes in this water sample it appears to be too rich in metal ions / sewage products / other pollutants” ? In the foreseeable future could we sequence a […]

Blog for Darwin: on Mass Extinctions

Happy Darwin Day! If you are reading this then you probably do not need an introduction to Charles Darwin, the importance of his work, how his theory of evolution by natural selection shaped modern Biology. Or if you do, I bet there are plenty of posts in today’s blogswarm that will address this. There is […]

Metagenomics Metadata and Metaanalysis

I am a co-organizer of this… see for yourself. Cutting edge metagenomics research, discussion of standards applications to genomics and metagenomics, all in beautiful Stockholm this summer. If you are coming to ISMB/ECCB 2009, consider coming to the M3 SIG. Link to announcement 1-page poster, because you really want to tack this to your departmental […]

Naturally Obsessed

A new documentary film follows life in a molecular biology lab in Columbia University over the course of three years. It looks very promising: the title is certainly something many of us identify with.

Now this looks a lot better!

In any data-rich science, data visualization is of prime importance.  Finding ways to visually depict data is challenging, as we have opposing demands: we would like to see the data in the whole, but also be able to zoom in and analyze the details; we would like to know how the many details add up […]

Enzyme Promiscuity

Gradualism is a cornerstone principle in evolution.  Things happen in small increments;  all the time that changes happen, overall organism fitness cannot be compromised.  So how then do full-featured complex functions appear? One way is by functional re-purposing of an existing organ: …an organ may become rudimentary for its proper purpose, and be used for […]

My own post genomic moment

Maybe I am slow on the uptake, but I never quite liked the term “post genomic”, and I used it very sparingly. (Yes, I do have that term in one of my better cited papers, smack in the first sentence of the abstract, but I never liked that).  Perhaps because of all the associated abuse […]

Peace on Earth

Here is a little trick I performed as a first year grad student a while ago and which I would like to share. My PhD adviser, Hanah Margalit was supposed to give a talk at a  joint Israeli-Palestinian meeting. (Hopefully, such days will be back soon and permanently!) The audience was rather broad, and included […]

Every Man an Island, Pt. 2

(Continued from  part 1) Why we are islands In the previous post we have seen how  our bacterial population affects  our weight  and that by changing our dietary habits we can change the species composition in our guts. Also, we saw how a metagenomic analysis can lead to verifiable hypotheses: using a metagenomic analysis, Gordon’s […]

Every Man an Island, Pt. 1

No man is an island, entire of itself — John Donne, Meditation XVII Scanning electron microscope images of B. thetaiotaomicron, a prominent human gut bacterium, and the intestine. From: Human Gut Hosts a Dynamically Evolving Microbial Ecosystem Gross L PLoS Biology Vol. 5, No. 7, e199 doi:10.1371/journal.pbio.0050199 Only one out of ten cells in our […]