Saturday, July 26, 2008

The DNA Network

The DNA Network

What should an environmentalist eat? [Tomorrow's Table]

Posted: 26 Jul 2008 05:22 PM CDT

Organic farming and eating locally make intuitive sense. But does conventional wisdom about eating sustainably hold up to the science?

This is the question posed in the latest issue of Conservation magazine

The writers ask if buying local reduces your carbon footprint, if it is realistic to give up nitrogen fertilizer and if it is time to replace the plow. I especially like the article suggesting that it is time to integrate genetic engineering with organic farming.

Theses topic deserves wider discussion. If you're interested, please check it out.

Recent selection among non-Africans at gene related to circadian rhythms [Yann Klimentidis' Weblog]

Posted: 26 Jul 2008 04:27 PM CDT

The gene PER2 is involved in the regulation of the circadian clock.
What are the patterns of variation in this gene across worldwide human populations?
They examine this question by sequencing 20 people, then genotyping 499 people from around the world for five polymorphic sites. They then looked at haplotype diversity, linkage disequilibrium, Fst and other measures of diversity.
They look for signs of correlation between latitude and measures of genetic distance, and at differences genetic diversity between groups with similar latitude...and find no evidence of a relationship between genetic variation and latitute.
They do find high levels of differentiation between populations and they find a low degree of sequence variation in the associated haplotypes, suggesting recent selection. For the haplogroup with the lowest sequence diversity they fnd a TMRCA of 8.7 +- 8.7 kya.
There's some discussion at the end regarding variation in this gene being associated with a person's preference for morningtime or eveningtime... they didn't look at this variant. It remains to be seen what explains the patterns of variation and recent selection that they find.

Genetic diversity patterns at the human clock gene period 2 are suggestive of population-specific positive selection
Fulvio Cruciani, Beniamino Trombetta, Damian Labuda, David Modiano, Antonio Torroni, Rodolfo Costa and Rosaria Scozzari
European Journal of Human Genetics Advance online pub. 25 June 2008
Abstract: Period 2 (PER2) is a key component of the mammalian circadian clock machinery. In humans, genetic variation of clock genes or chronic disturbance of circadian rhythmicity has been implied in the onset of several phenotypes, ranging from periodic insomnias to advanced or delayed sleep phases, to more severe disorders. Peculiar geographic diversity patterns in circadian genes might represent an adaptive response to different light/dark cycles or environmental changes to which different human populations are exposed. To investigate the degree and nature of PER2 gene variation in human populations of different geographic origin, and its possible correlation with different latitudes, we sequenced a 7.7 kb portion of the gene in 20 individuals worldwide. In total, 25 variable sites were identified. The geographic distribution of haplotypes defined by five polymorphic sites was analyzed in 499 individuals from 11 populations from four continents. No evidence for latitude-driven selective effects on PER2 genetic variability was found. However, a high and significant difference in the geographic distribution of PER2 polymorphisms was observed between Africans and non-Africans, suggesting a history of geographically restricted natural selection at this locus. In support of this notion, we found several signals for selection in the sequences. The putative selected haplotype showed a recent coalescent age (8.7 Kyr), and an unusually high frequency in non-African populations. Overall, these findings indicate that a human clock-relevant gene, PER2, might have been influenced by positive selection, and offer preliminary insights into the evolution of this functional class of genes.

Web vs real life: Advice for medical students [ScienceRoll]

Posted: 26 Jul 2008 03:02 PM CDT

There is an interesting article at about the web usage of medical students. This generation of medstudents is already on the web (Facebook, blogs, community sites, Twitter, etc.). If they think their web life doesn’t represent their real identity, they are absolutely wrong. An excerpt from a recent study:

Thompson and several researchers from the UF's colleges of Education and Medicine did a review of the Facebook sites of 362 UF medical students and residents and found that a significant portion of them were publicizing personal information most physicians would never share with their patients.

The researchers randomly selected 10 Facebook profiles for a more in-depth analysis, looking for hard-to-quantify items that patients or colleagues might find objectionable. Seven of the 10 included photographs in which the subject was drinking alcohol, and some form of excessive or hazardous drinking was implied in as many as half of those photos.

Image source

My dear fellow medical student friends! If you accept my pieces of advice:

Don’t forget, patients and your future employers will find what you publish about you and your life on the web. So use it wisely…

Crocodile Fishing [evolgen]

Posted: 26 Jul 2008 01:30 PM CDT

So, I'm just hanging out here by the side of the water waiting for my lunch. Sure, I could go in the water and get my lunch. But that's not how I roll. I wait patiently for my prey to get within striking distance, and then I attack. So, here I am just hanging out by the side of the water.

Click to enlarge.

There they are. Just a bunch of cichlids waiting to be eaten. By me. Lunch would be good right now. But they won't get close enough. So I'll just hang out here with my jaw agape.

Read the rest of this post... | Read the comments on this post...

Medicine 2.0 Carnival at Monash Medical Student [ScienceRoll]

Posted: 26 Jul 2008 01:12 PM CDT

Post-OSCON thoughts: Platforms, machine learning & Freebase [business|bytes|genes|molecules]

Posted: 26 Jul 2008 12:42 PM CDT

Freebase is a service (I use that word very deliberately) that I have talked about before. I have long had plans for Freebase, but never quite gotten around to doing more than some minor type creation and edits (as opposed to Pierre, who is quite well known with the Freebase crowd). I have also been somewhat annoyed at Freebase’s not quite Semantic Web status and requirement to reside within their environment.

Yesterday, at OSCON, I had the chance to listen to a talk by Jamie, Colin and Toby from Metaweb/Freebase. It was a great, enlightening talk, very much a computer science/technology talk, helped by interesting garb (pirate eye patches anyone). I left wanting to go back and play with the system. I really liked the examples that they showed, which really demonstrated the power of the system and highlighted the fact that a lot of smart people work there.

jamie, colin and toby from Freebase

The other aspect of this comes from hallway discussions. I have always viewed the ultimate power of Freebase to be as a service, rather than a destination. Given the API, given the ability to get data dumps in multiple formats (including RDF), I have come to the conclusion that Freebase should not necessarily be thought of as a Semantic Web offering, but rather a repository that allows you to add structure to weakly-structured data and make it amenable for additional downstream analysis and mashups. In such a scenario, I could imagine uploading data into Freebase, doing the cool structure stuff, pulling out the data as RDF and uploading that into Talis and then building a web app on top of the Talis Platform. Or one could just keep the data in Freebase and essentially use Freebase as a backend for various mashups or for advanced machine learning/NLP exercises. IMO, at least in principle, you could replicate Powerset (or perhaps do better) on the Freebase backend.

I still think we are in the infancy of working with large datasets online. For this to work, obviously we need open data. The ability to share, slice and dice and re-purpose datasets is necessary and essential. Once we have such datasets, or access to those datasets, then what we do with them becomes a function of the abilities and ingenuity of the person using the datasets. That’s why the platforms available for us to do so are important. There are some tremendous data sources for the life sciences. With few exceptions most don’t really enable smart people to do crazy good stuff. I am sure that will change. It must.

Zemanta Pixie


Personalized Medical Search Engine: Sort by Date [ScienceRoll]

Posted: 26 Jul 2008 12:16 PM CDT

Scienceroll Search is a personalized medical search engine powered by You can choose which databases to search in and which one to exclude from your list. It works with well-known medical search engines and databases and we're totally open to add new ones or remove those you don't really like.

After we updated the list of databases you can search in, now you can sort the results by date as well. We hope you will like this feature and let us know if you have a suggestion.

More information:

Please don’t let me be misunderstood []

Posted: 26 Jul 2008 10:09 AM CDT

On the Media, arguably my favorite show on NPR, tackles direct-to-consumer personal genomics:

DAVID MAGNUS: Well, they have a right to that information, but that's not the same as saying they have a right to get it in an unencumbered fashion.

BROOKE GLADSTONE: It is the same as saying that. Why should the medical establishment stop me from [getting] information about me?

DAVID MAGNUS: It's about making sure that you understand and that there's adequate informed consent for what you're getting, so that we can avoid harm. In the story that the reporter wrote about cardiovascular disease, if because of his misunderstanding he starts thinking he doesn’t have to worry about his diet and his exercise and has a heart attack at a much younger age because he misunderstood that information - that is very clearly a direct harm that's a function of the genetic testing.

BROOKE GLADSTONE: I understand the risk. I do. But the harm comes from the action he takes based on that information. The government, and companies, and all sorts of interests around the world frequently say that certain kinds of information could harm us because of the actions we could take, regardless of whether the information is true or false.

I’m afraid that, in the case of my own medical information, in which the only real victim is likely to be me, if I take ill-advised action, that if a physician says that he or she deems it unnecessary for me to take such a test, then I don’t get access to it.

DAVID MAGNUS: What we’re saying is not that you can’t get access to it but that you need to have a physician involved. If you get to the point where there's generally understood standards and people start to understand the information pretty well, you start to have a clear understanding of what the harms are, you have a clear understanding of the efficacy of the tests for different traits, when you get to that point, that's when you tend to allow things to go over the counter or direct to consumer. But you don’t start that way.

But who will decide exactly when “people start to understand the information pretty well?” Will it be doctors, most of whom probably think “SNP” is slang for a vasectomy? Or should it be bioethicists?

Living Life to its Fullest: The Song of Randy Pausch [Highlight HEALTH]

Posted: 25 Jul 2008 10:15 PM CDT

Randy Pausch.jpgRandy Pausch lost his battle with pancreatic cancer today. In September 2007, the Carnegie Mellon Computer Science Professor was asked to give a Journeys Lecture, in which faculty speak to their students as if it were their last lecture. In Pausch’s case, it was indeed. He had been diagnosed with pancreatic cancer in 2006; by August 2007, the cancer had metastasized to his liver and spleen and he was given just six months to live.

Pausch lived longer than his doctors said he would. He used his illness to deliver an important lesson about living. Pausch’s Last Lecture has been watched online by millions of people worldwide.

Randy Pausch’s book, The Last Lecture, has become a best-seller. In it, he writes about living; the importance of overcoming obstacles, of enabling the dreams of others and of seizing every moment in life.

In his Spring 2008 Carnegie Mellon commencement speech, Pausch said [1]:

We don’t beat the [grim] reaper by living longer, we beat the reaper by living well and living fully. For the reaper will come for all of us, the question is ‘what do we do between the time we’re born and the time he shows up?’. Because when he shows up, it’s too late to do all the things that you’re always going to get around to.

A tribute to Randy Pausch can be found on the Carnegie Mellon University website.

On Death

From The Prophet by Kahlil Gibran
You would know the secret of death.
But how shall you find it unless you seek it in the heart of life?
The owl whose night-bound eyes are blind unto the day cannot unveil the mystery of light.
If you would indeed behold the spirit of death, open your heart wide unto the body of life.
For life and death are one, even as the river and the sea are one.

In the depth of your hopes and desires lies your silent knowledge of the beyond;
And like seeds dreaming beneath the snow your heart dreams of spring.
Trust the dreams, for in them is hidden the gate to eternity.
Your fear of death is but the trembling of the shepherd when he stands before the king whose hand is to be laid upon him in honour.
Is the shepherd not joyful beneath his trembling, that he shall wear the mark of the king?
Yet is he not more mindful of his trembling?

For what is it to die but to stand naked in the wind and to melt into the sun?
And what is it to cease breathing, but to free the breath from its restless tides, that it may rise and expand and seek God unencumbered?

Only when you drink from the river of silence shall you indeed sing.
And when you have reached the mountain top, then you shall begin to climb.
And when the earth shall claim your limbs, then shall you truly dance.


  1. Randy Pausch 2008 Carnegie-Mellon Commencement Speech. 2008 May 19.
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