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Biology

The Evolution of Music

A collaboration between a group in  Imperial College and Media Interaction group in Japan yielded a really cool website: darwintunes.org. The idea is to  apply Darwinian-like selection to music. Starting form a garble, after several generations producing  something that is actually melodic and listen-able. Or a Katy Perry tune. Whatever.  The selective force being the appeal of […]

Annotating Proteins in the Uncanny Valley

The Uncanny Valley Every day, software appears to do more things that we thought were exclusively in the human realm. Like beating a grandmaster in chess,  or carrying out a conversation. I say “appears” because there is obviously no self-aware intelligence involved, as this rather bizarre conversation between  Cleverbots demonstrates. For humans, playing chess  and carrying […]

Phound phage phootage

I am finishing up a great weekend at HHMI Janelia Farm Research Campus. The occasion is an annual symposium celebrating the Phage genomics Course taking place in dozens of universities in the USA. Here are two of our students, Erich Goebel and Morgan Light, next to the poster they presented at the meeting: This post […]

Repost: Shavuot is a Microbial Holiday

Yesterday was Shavuot. That wonderful holiday which includes midnight studies, water-bombing and dairy products. Mmmmm…. cheese. A food product heavily embedded in the science of microbiology. Cheese is the founding product of the biotech industry (along with beer and bread). So here’s to Lactobacilli and Lactococci which are at the center of the production of […]

Job opening: Scientific Curator at the Jackson Laboratory

Scientific Curator – Bioinformatics Interested individuals should apply on-line at www.jax.org/careers, referring to job posting #3256.  Contact Jeannine Ross at ext. 6045 with questions. The incumbent in this position plays a critical role in data annotation and curation for the Gene Ontology (GO) and Protein Ontology (PRO) programs at The Jackson Laboratory in Bar Harbor […]

Crowdsourcing Genomics II: Unveiling HINdeR and Phrux

About this time last year, I posted about a new course I was going to teach, Phage Genomics. Briefly: Phage isolation, electron microscopy, DNA sequencing in the first semester, annotation and comparative genomics in the second. And I get to teach the bioinformatics bit: annotation and comparative genomics. Woo-hoo! The great thing about this course, […]

Repost: the Scope(s) of Substance

This tweet from Neil Degrasse Tyson jolted me from a pleasant rest before tomorrow’s race:   …which led to the (in)famous Scopes Trial. On May 5, 1925 John Scopes was charged and subsequently tried, found guilty, and fined $100 for teaching Evolution, a violation of Tennessee’s Butler Act. The trial became a battleground for science […]

The Inside Poop

It’s pretty much common knowledge that mother’s milk is the healthiest food for infants, and that it bestows health benefits upon mother and baby that formula feeding cannot match. The unique combination of lipids, sugars, proteins and antibodies is not even close to being rivaled by baby formula manufacturers. With few exceptions, such as when […]

It’s a smORF world, after all?

Here is a study that looked for a type of genes that the authors felt was neglected by classic genomic annotation. The research shows how to employed concepts in molecular evolution to validate the existence of these genes. Some background: the first question we ask after assembling a genome is: “where are the genes”? Not […]

Biocuration 2012

  Great meeting:  Biocuration 2012, Georgetown University, DC.  When I leave a meeting with my head exploding with new ideas and a need to try them all out at once, I know I got my money’s worth, and then some. Even a three hour flight delay followed by discovering my car with a dead battery […]

You. Want. This. Job.

NSF grant funded, woohoo! Now I am hiring a programmer. So if you want to be part of a dynamic, growing lab, do lots of interesting stuff and upgrade yourself from just a great bioinformatician to a super-bioinformatician, this job’s for you.  You’ll be working primarily on microbial genome evolution, including setting up a kick-butt […]

Dirty Genomics

Repost: a very loose and circular association to Pi Day

(Originally published March 14, 2009) Happy Pi (π) Day! Americans write dates in the MM/DD/YYYY format instead of the DD/MM/YYYY format used by the rest of the world.  Usually a rather painful and confusing format if you did not grow up with it, causing checks to bounce and leases to expire for those who recently […]

The Origin of Gender Symbols in Biology

A quick post for International Women’s Day: how did the gender symbols originate in biology? What do ♀ and ♂ actually stand for? The answer starts in antiquity, when planets and gods were almost synonymous. Religious rites (at least in Europe) were also associated with the working of metals. Thus, each heavenly body was associated with a […]

Microbial Art

  We have some really talented students in our department. And I don’t just mean the science. I am honored to present the colorful and hilarious microbial artwork of Amber Beckett. Created between gel runs at Natosha Finley’s lab: