For the past few days I've been fiddling with a set of data that measure the effects of single nucleotide changes on an organism's phenotype across a variety of environments and genetic backgrounds. Any good statistics manual will tell you the best way to analyze the type of data I have is through logistic regression with a generalized linear model.  So, I tried that.  Here are the results: 

> logistic <- glm(y~full_model, family=binomial(link="logit"))
> summary(logistical)
Null deviance: 20650253  on 860  degrees of freedom
Residual deviance:   118972  on 573  degrees of freedom
AIC: 128316

All the cells in our body have the same set of genes.  The reason that we have arms, legs, heads, etc. is because transcription factors turn genes on and off in the right places at the right time.  This report out of Colorado Springs shows what happens when genes get turned on in the wrong place.  It appears that the poor child in this report was suffering from a teratoma:  an inappropriately placed but otherwise normal-looking  growth of a body structure in the form of a tumor.  Fortunately, the child is alive and hopefully will recover fully.

The astronomy/physics sector of the internets is all abuzz about Dark Energy.

It was originally thought that gravity would slow the expansion of the universe as huge astronomical bodies become attracted to each other and pull together like Sumo wrestlers trying to share a waterbed.  That has not happened.  Instead, the universe is expanding, and doing so at an increasing rate.  Dark Energy is the general repulsive force that is kicking gravity's butt and driving the expansion of the universe.

Last weekend I visited the St. Louis Zoo to witness their first ever Penguin Walk.

A cyber-war has broken out between creationists and evolutionary biologists.  PZ Myers is calling upon those who are critical of creationism/intelligent design to crash an online poll about a zoo partnership.  In the few hours after his first call to arms, the YES votes (those critical of creationism) mushroomed from around 200 (20% of the vote) to 18,000 (95% of the vote).  Go vote in the poll to take part in this Stephen Colbert-esque demonstration of grass roots power.

Squirrels are also facing an economic crisis.  Apparently, acorns are disappearing all over the country...or at least on the East Coast.  I know some fellow turkey hunters on the East Coast have reported a very spotty acorn crop.  Supposedly it's not just acorns, but hickory nuts as well.  This is very bad news for woodland creatures.  Acorns are a mainstay of their winter diet and are a valuable source of protein after the grasshoppers die in first fall frosts.  No acorns or hickories means less food for squirrels, turkeys, etc.  That in turn means less food for owls, coyotes, and so on.  If this year really is worse than most in terms of acorns, it will be interesting to see how wildlife nu

During the 2000 presidential election I was living in a fraternity house with a roommate serving in the Air Force.  When Bush was projected to be the winner, he jumped up and yelled,

"We're gonna have toys!  We're gonna have more toys!"

As he predicted, the next 8 years resulted in plenty of work and funding for the flyboys.  With the election of Barack Obama, perhaps us geneticists can start doing the same kind of dance.

As Adaptive Complexity writes, last week's issue of Nature  included the publication of  West-African and Han Chinese individual genomes.  The ability to sequence and analyze individual genomes for a reasonable price is a major technological advance of the past few years.  But, you can't learn a whole lot about populations from the study of individual genomes.  For that reason, I'm not sure you will ever see another individual genome published in a high-profile journal (unless it's a cancer genome).

I had lunch today with Jim Anderson, a Professor in the Department of Cell and Systems Biology at the University of Toronto.  Jim asks questions about how genetic changes over time (evolution) leads to the generation of new species (speciation).  Jim's way of asking questions is by watching the generation of new species in the lab.

A little background:

Transcription factors do a lot of things for us, like make arms and legs in the right places.  It turns out they may also make us go bald.