Sunday, October 19, 2008

The DNA Network

The DNA Network

Selection may not be responsible for worldwide variation in circadian clock genes [Yann Klimentidis' Weblog]

Posted: 19 Oct 2008 08:16 PM CDT

some suggestive evidence, at most (look here for related post about PER2 gene variation):

Genetic differences in human circadian clock genes among worldwide populations.
Ciarleglio CM, Ryckman KK, Servick SV, Hida A, Robbins S, Wells N, Hicks J, Larson SA, Wiedermann JP, Carver K, Hamilton N, Kidd KK, Kidd JR, Smith JR, Friedlaender J, McMahon DG, Williams SM, Summar ML, Johnson CH.
J Biol Rhythms. 2008 Aug;23(4):330-40.
Abstract: The daily biological clock regulates the timing of sleep and physiological processes that are of fundamental importance to human health, performance, and well-being. Environmental parameters of relevance to biological clocks include (1) daily fluctuations in light intensity and temperature, and (2) seasonal changes in photoperiod (day length) and temperature; these parameters vary dramatically as a function of latitude and locale. In wide-ranging species other than humans, natural selection has genetically optimized adaptiveness along latitudinal clines. Is there evidence for selection of clock gene alleles along latitudinal/photoperiod clines in humans? A number of polymorphisms in the human clock genes Per2, Per3, Clock, and AANAT have been reported as alleles that could be subject to selection. In addition, this investigation discovered several novel polymorphisms in the human Arntl and Arntl2 genes that may have functional impact upon the expression of these clock transcriptional factors. The frequency distribution of these clock gene polymorphisms is reported for diverse populations of African Americans, European Americans, Ghanaians, Han Chinese, and Papua New Guineans (including 5 subpopulations within Papua New Guinea). There are significant differences in the frequency distribution of clock gene alleles among these populations. Population genetic analyses indicate that these differences are likely to arise from genetic drift rather than from natural selection.

Politics and US Innovation: It Has To Be About The Future, Not Just The Present [adaptivecomplexity's blog]

Posted: 19 Oct 2008 04:24 PM CDT

Have a problem: Build a web resource [business|bytes|genes|molecules]

Posted: 19 Oct 2008 03:25 PM CDT

Via a post on Hacker News I ran into the Tulane School of Medicine Student Portal.

As one of the developers writes on Hacker News

Our goal is ‘making med school easier, one less click at a time’. We have no business model, just trying to make our own lives easier.

There is further description on the site

Hello, and welcome to the Tulane University School of Medicine's Student Portal! This website came into existence over the course of the latter part of the 2007-2008 school year through the hard and volunteered work of a group of students concerned with making the lives of TUSOM medical students a bit easier. Our university community is a dynamic place with much do, and many resources to use on a daily basis. In an effort to reduce the amount of time and energy required to accomplish these activities, we developed this site. Our work has been led, and graciously supported by the Medical Student Government, the Office of Medical education, and the Deans.

This site was developed by students, and for students. As such, if there is a feature that you feel would benefit the community as a whole, please feel free to drop us a line at We'll take your suggestion into serious consideration, and see if it within our abilities to accomplish.

That’s the kind of initiative that one loves to see. With hosting cheap, good web frameworks and people increasingly looking to the web for information, not the last time you’ll see something like this either. The key is realizing that often, if you have a problem, you can solve it yourself, and relatively inexpensively. Sometimes you can build a business out of it, a la 37signals

They (or at least Niels Olson) have some pretty ambitious future plans as well

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Medicine 2.0 Blog Carnival #33 [ScienceRoll]

Posted: 19 Oct 2008 12:16 PM CDT

The 33rd edition is up at the Ivor Kovic, MD blog! Check out all the posts and news about the world of medicine 2.0 and health 2.0. Thank you, Ivor Kovic, for hosting Medicine 2.0!

Medicine 2.0 is a blog carnival about the impact of web 2.0 on medicine and healthcare.


Extracting .lit files [Mailund on the Internet]

Posted: 19 Oct 2008 10:15 AM CDT

I have a bunch of ebooks in Microsoft’s .lit format, but I want to read them on my Linux box.  I tried installing Microsoft Reader through wine, but that doesn’t work for me.  It will pop up and crash down again just as fast.

I used to use the Openberg Firefox addon, but it has not been updated to Firefox 3 so that is not an option any more.

So now I just need to extract the files and then I can read the damn books as html.

There’s a program for doing this called clit (really it is, I am not making it up).  You can get it here.

To make it sligthly easier for me to extract the files I wrote a small script:

!/bin/bash  for litfile in "$@"; do     dir=`dirname "$litfile"`     outdir=$dir/`basename "$litfile" .lit`/     clit "$litfile" "$outdir" done

and added it to my nautilus-actions.

Excellent, now I can just right-click on the files I want to extract, and viola I have the html hidden under the .lit file.

Medicine at the Cutting Edge [Discovering Biology in a Digital World]

Posted: 19 Oct 2008 12:37 AM CDT

Yes, that's right, another Medicine 2.0 blog carnival has been posted for your enjoyment.

And the host, Ivor Kovic, has done an amazingly creative and interesting thing with images from all the past hosting places..., and well, you just need to go see it yourself.

Read the comments on this post...

An enjoyable book, amazing story, and a view into Aspergers' [Discovering Biology in a Digital World]

Posted: 18 Oct 2008 11:24 PM CDT

Sometimes I'm thankful for all extra restrictions on air travel that got imposed after 9/11. Not the ones involving personal searches, taking your shoes off, or putting all your liquids in plastic bags, but I do like having to arrive at the airport 2 hours ahead of any scheduled trip.

The reason is that I'm a sucker for airport book stores. Almost every time I go on a trip, I bring home more books than I packed. Sometimes surprisingly, as in the case of "Look Me in the Eye: My Life with Asperger's" by John Elder Robison, I even have to fight with my children to get the book back.

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Cilantronomics [Omics! Omics!]

Posted: 18 Oct 2008 10:12 PM CDT

We had dinner last night in one of favorite local eateries, a wonderful little Mexican place in a neighboring town. When I sat down, my eye was drawn immediately to my sort of dish -- one with a rich sauce combining the tang of tomatillos with the zing of cilantro. I picked well.

I really do love cilantro. Despite an extensive garden growing up, it was only in my adult life that I encountered this herb. I've been making up ever since. It works well in so many situations, not only in Mexican but also a lot of Asian cooking. The excellent Tibetan buffet in Central Square uses it extensively, particularly in a salad that works equally well before the meal as after, with the bite of cilantro contrasting with sweet cherry tomatoes and mango chunks. I even have a pot of it on my desk, which I share with my neighboring cilantrophiles.

However, not everyone loves cilantro. And it isn't just some folks might not like that little edge -- no, for some it tastes awful. Rather than some herbal bite, they taste soap. Or weirder. What other herb has its own

Is it genetic? Alas, there has been a dearth of research on cilantro tasting -- indeed, it doesn't seem to rate an OMIM entry. There is a compound called PTC which is known to untastable by some, including this correspondent, and is genetically linked (my father can taste it; haven't surveyed the rest of the clan). With the help of some research by one of my office neighbors (and fellow cilantro fan), I did learn that 23andMe includes cilantro taste in their questionnaire. It isn't clear whether the other public and private genome projects are tracking this key phenotype.

Okay, I jest a bit. But while the ability to taste cilantro, or PTC, or the host of other innocuous traits which are staples of grade school genetics labs (e.g. widow's peak, hitchhiker's thumb, attached earlobes, etc) aren't exactly critical to understand, they will be interesting to understand. Widow's peak doesn't change someone's life, but to understand it is to understand a bit more about how patterns are laid out. The sciences of smell and taste have advanced tremendously over my lifetime; a whole new taste was found! Identification of smell receptors (recognized by a Nobel) and taste receptors have given great insights -- but we still understand very little.

Are there practical applications for smell & taste research? Of course. But to me the most interesting part is to figure out how it works. PTC doesn't seem so complicated, as the test paper doesn't have any flavor other than paper. But cilantro seems like a much more complicated, and interesting, question. Why does it taste bad rather than just not taste?

Is there an underlying soapiness which I just don't taste? In this case, tasters have a receptor for the magic compound (which is what?) and non-tasters simply lack it. Or does a different receptor bind the compound in tasters, in which case they have a gain-of-function mutation? Or, perhaps they have a partial loss of function -- there are a number of known compounds with concentration-dependent odor, probably due to differential binding to different receptors. In other words, at low concentrations these compounds bind to high-affinity receptors (yielding one perception) and at high concentrations some additional one Or, perhaps a partial gain of function in the non-tasters -- the same model could apply.

No, I wouldn't recommend basing an R01 application on the science of cilantro taste. Nor is it likely to tease a few million from some VCs as the core of a business plan. Cilantro haters will probably never have the option of genetic therapy to alter their perception. But it is still an interesting scientific question, and I look forward to personal genomics shedding some light on it.

OMG! Baby animal pictures! [Discovering Biology in a Digital World]

Posted: 17 Oct 2008 06:28 PM CDT

I used to get e-mails from relatives that were filled with cute pictures of kittens and puppies. It's luck they didn't know about this site:

These are the some of the absolutely cutest baby pictures I have ever seen!

I hear Raffi songs in my head when I look at these (can you sing Baby Beluga?)

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Blocked Access Bummer #1 [The Tree of Life]

Posted: 17 Oct 2008 09:37 AM CDT

I have decided to start posting when I want to read an article at home but cannot due to lack of access (even though I might have it at work).  Today's bummer is I wanted to read an article by Joel Sachs on "Resolving the first steps to multicellularity" but I could not get it because I do not have access to Trends in Ecology and Evolution at home.  Bummer.  Looks like it could be good. 

Larry Moran on Phylogenomics, my new paper, and species [The Tree of Life]

Posted: 16 Oct 2008 09:50 PM CDT

Just a quick note to encourage people to check out Larry Moran at The Sandwalk blogging about my new phylogenomics paper (with Martin Wu) and talking about whether one can use species as a term for bacteria.

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