Grab that glutamate

This month's Nature Genetics (subscription required) has a cool short communication by Fabien Burki and Henrik Kaessmann about a gene that is most likely only expressed in the brain, and is only found in humans and apes. This gene, GLUD2, and its more widespread relative, GLUD1, encode proteins which help break down glutamate. Glutamate is an important neurotransmitter in the brain, and can be released in large amounts during intense neural activity. However too much released glutamate can be toxic, and these two genes are important for control of glutamate levels.
The gene GLUD2 has a fascinating natural history. It originated relatively recently in the hominid lineage as a retro-duplication, an event in which retroviral proteins grab host gene products known as mRNA, transcribe them back into DNA, and tuck them back into to the genome in a new location. These retro-duplications create a partial copy of the original host gene, lacking the "control panel" of DNA sequences which are responsible for gene activity and other features of most genes. These copies are called pseudogenes, because most often they are never made into mRNA.
The insertion site of GLUD2 somehow came under the control of elements that allow it to be expressed only in the brain. In addition, selective evolutionary pressure allowed the protein encoded by GLUD2 to accumulate mutations improving functioning in the brain environment relative to the parent gene, for example functioning well at low pH and in the presence of high GTP. The result is that humans and apes have an evolutionarily new enzyme to metabolize glutamate in the brain.
Pseudogenes are very numerous in the human genome, and can be analysed in great detail now that the human genome has been sequenced. All of this copying, shuffling, and refurbishing can give natural selection plenty of differences to act upon, meaning that little stories like that of GLUD2 can be a big part of the evolutionary process.

Old oaks

Oktoberfest and fall have arrived in Munich. The days are cool and frequently rainy; lederhosen and dirndls are seen everywhere; and leaves are covering the bike trails. It's this time of year that I start to notice the really big trees, whose trunks are usually hidden in greenery in the spring and summer.

The Fuerst, or prince (brother of King Ludwig), must have really loved oak trees, because he lined his forest avenues with them, and even spellt out his initials with a planting of oaks. In most of the Forstenrieder Wald, the oaks are continually replaced and rather young looking. But here and there, on the back paths, you can spot what look like ancient individual trees. With the exception of the main botanical specimens in the Eichlgarten, these trees are pretty gnarled, with maybe one or two massive branches still alive. But the foresters seem to treat them like honored grandparents. They are mulched, and the underbrush is cleared away, so they still hold the space that they once must have dominated.

I am always a bit touched by the sight of these old oaks, even just glimpsed as I'm whipping past on my bike. They remind me of a different scale of time and living; a notion of patience, maybe, or "wohlgefuel," that has been hard to come by in my stay abroad.

Tangled Bank carnival is coming

To all science bloggers: the Tangled Bank carnival of science weblog entries is coming up soon, and will appear in Preposterous Universe . So get a good blog entry together and email the link to hhim!

Feeeeed me

I was away for a few days and watched my traffic go from a pittance to nothing at all. No new posts, and it just wilts. Just like the plant in the little shop of horrors.

The coolest web page

Thursdays are big in the molecular biology world, because the major journals- Science, Nature, Cell- all come out on the web. These journals are hidden behind subscription walls, although Science and Nature send out email alerts which I believe are open to everyone.
(I should say that most journals allow access to older content without subscription).

Today I clicked over instead to the Public Library of Science, a journal in which scientists pay the cost of publication, so that published articles are availble to everyone. Today's link of choice is a cool article about the search for life outside earth. This search has really gained momentum with the discovery on earth of microbial life in what seem to be extremely inhospitable niches-- oil deposits, hot vents, antarctic permafrost. I think the state of the search is that "we'll know it when we see it," meaning knowing how to look is crucial. As a recovering Trekkie (actually, Star Wars- great hair, better explosions) with a philosophical bent, I feel like these searches could yield the ultimate Keats' telescope moment.

In any case, click on, link to, and promote the Public Library of Science!

Laws of Nature

1. Why is it, that given a teddy bear and an old shoe both lying on the ground, a crawling infant goes straight for the shoe?
1a. Is this why dogs always get the teddy bear first?

Re-genesis

It looks like the solar wind samples in the Genesis capsule can be recovered after all. Click on the title bar for the link!

Three grand old oaks

I was reminded yesterday by a newspaper clipping that three people I have admired from afar- Julia Childs, Elizabeth Kuebler Ross, and Czeslaw Milosz- all passed away this summer after very long and productive lives. I couldn't possibly do justice to the lives of these three, and actually have read only smatterings of their works. But what I got was enough to help me along with my personal journey. For me they each were like distant pole-stars, representatives of a philosophy which accepts and then celebrates the cold clay of life. I was brought up on St. Augustine's manic Manicheism, in which the daily world was at best a distraction to higher aspirations. It took a long time for me after college, starting with Karl Rogers but with Kuebler-Ross not far behind, to realize that for me life has got to be about living. Cooking, loving, dying, it all *is*, and it makes me happier to try to think it's all good.

I wrestled with that last line; the kids at Beslan came back to me.


Good bye, you three. May other oaks grow in the places you left.

Still waiting

I've already managed to link to 3 or 4 of my blogroll, which means either I'm living in a very small world, or I'm not picking up my HTML skills fast enough to build up the list. I have wanted to link to Andrew Sullivan for all of three days, but it won't be today either. Even though his politics are well to my right, I really appreciate the way his blog shows his struggle to find a way forward for his adopted country.
There are some crazy things happening in the world, some nasty people afoot, and the combination of the September 11 attacks and the bald assertion of US unilateral capability (which has been latent for 2 decades) has created foreign policy challenges-- right here, right now-- that are going to need a magical level of creativity for the next administration to turn to advantage. I mean that John Kerry's people, should they win have their work cut out for them. They cannot go backwards and should not try.
People, like Andrew, who are ready to admit that their views are a work in progress are in desparately short supply. It doesn't hurt that he's drifting leftward..

UPDATE: Apologies, Andrew ! In fact his paragraph on Fareed Zakaria is completely linkable. Am I drifting rightward?

Genesis crash

The Genesis probe has crashed to earth instead of being caught in midair. This spacecraft was holding miniscule samples of solar wind matter, which may well be lost for analysis if they were contaminated with even a few milligrams of earth dust upon impact.
What a bummer! I can't help thinking about the Ph.D. students and others who really wanted to see these samples. Keat's telescope-- astronomy really has that potential for just thrilling new possibilities. And, being in the career grind myself, I can just picture the professional delays for everyone who wanted this project to be the basis for their next career step. I have the luxury of clicking onto the Mars probes or the Cassini mission, but the career people do not. Please don't worry, people, it's all good.

Chapman's Homer

Here is the link to the poem I mentioned in the first post.

Up and running

Hello world,
This is my absolutely first weblog post of any kind. My biggest motivation for this blog is the upcoming election, and especially this week the anniversary of the September 11 attacks. I'm pretty excited to start the linking game etc. and even to get some control over this blog's behavior!
The title of this blog refers to a phrase in Keats' poem On first looking into Chapman's Homer in which Keats alludes to the huge thrill a scientist feels when seeing something completely unexpected. These moments (they have been few for me, but vivid!) shape a lot of my take on the world and my fundamental optimism about people, which in turn becomes a political stance.
My next effort in this blog will be to add the crucial links, the bloggers I'm reading and mentally engaging all of the time.