Saturday, November 15, 2008

The DNA Network

The DNA Network

Sharing documents with others via the web using Google Docs [Discovering Biology in a Digital World]

Posted: 15 Nov 2008 05:48 PM CST

Poor PZ! Stranded without a working laptop in a strange town! This is the kind of situation that gives me nightmares, so I like to upload presentation materials to the web just in case.

Lately, I've been looking at different methods for doing this to see which ones l like the best.

A few days ago, I tested this with Scribd.

Today, I'm going to see what we can do with Google Docs.

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today it's Join The Impact day! [the skeptical alchemist]

Posted: 15 Nov 2008 04:27 PM CST

That's right, it is time to get out on the street with your local LGBT association and protest against the passing of Prop 8.

If you want to get involved and get more information, you can visit these pages:
I am also following the protest on Twitter, so you can get fast updates by becoming one of my followers, or simply by refreshing this blog -- new tweets appear in the right column.

View blog reactions

Blogging from Bangladesh, Part 5 [Tomorrow's Table]

Posted: 15 Nov 2008 02:06 PM CST

November 6th Thursday

Today was filled with sorrow and joy.

We left our hotel in Kolkata in West Bengal at 5 am so that we could catch an early plane to Bhubaneswar in the state of Orissa. The bus took us one last time through the town of vendors, beggars and people sleeping on the streets. On one corner of the pavement on a singly dirty blanket slept 2 young women with their children of 5 months and 5 years, snuggled into their arms. Next to them was the form of a man covered head-to-toe by his blanket. The only thing I could see were his bare feet and his crutch.

From the airport, we drove directly to the Central Rice Research Institute in Cuttack. After lunch of paneer (Indian cheese) with curry, chapati, rice, spicy mango chutney, and fish we piled once again into the vehicles and drove to visit farmers in the village of Nuagawn, east of Cuttack.

Soon we arrive in the village of Nuagawn. We see vast fields of rice bordered by palm, mango and banana trees. A young girl in a bright yellow sari peddles here bicycle along the levees. A shirtless older man herds 5 cows in the distance. Music is playing in the village nearby.

Nuagawn is bordered by two large rivers, which often overflow during the wet season (June-November), making the rice fields vulnerable to flash flooding. If the flood comes early in the season, the farmers can replant. If the flood comes late, the entire crop can be lost. For this reason, 15 farmers here were willing to experiment with the new Sub1 varieties provided by CRRI. These farmers are part of a larger participatory varietal selection trial (55 farmers in 9 villages) that has been carried out over the last 3 years.

About 1/3 or the rice grown in the state of Orissa is Swarna. Another favorite here is the locally improved variety Gayatry. Both these varieties are intolerant of flooding. Thus even incremental increases in submergence tolerance would greatly benefit farmers here.

As we descend from our vehicles we see that many of these famers are here to greet us. The people here speak Oriya, a dialect closely related to Bengali, reflecting the fact that Orissa, West Bengal and Bangaldesh were part of the same state before colonial times.

We walk towards a thick stand of Swarna Sub1 rice to speak with Basanta Kumar Raut, the first farmer to participate in the trials in 2006. Barefooted and dressed in a white shirt, he looked to be about 50, with teeth darkened by chewing on beetlenet a slightly intoxicating fruit, the Orissan's chewing tobacco. CRRI scientist SSC Patnaik translates into English for us. With a large grin and clear pride Raut tells us that this year his farm was flooded for 12 days. His entire crop of Gayatry, which is tolerant of stagnant flooding but not complete submergence, died. Some of the Swarna plants survived but were so damaged they did not produce grain. His entire field of Swarna-sub1 survived.

After meeting with a few more farmers and looking at some more varieties, my mother and I decide to walk towards the village rather than get in the bus again. The sun is going down and there is a pleasant breeze. There is music in the village and we can see people milling about in the distance near some banana trees. Farmer Raut walks with us. We pass two young girls dressed in blue. Their solemn faces break into a grin when I put my hands together in the traditional Indian greeting and say "Namaste", a common spoken greeting or salutation in the Indian subcontinent. Shy no more, they come to us and touch our feet, a sign of respect for elders.

Suddenly we arrive in the village. For the village meeting, a large tent has been set up on poles, with cloth that is printed with yellow Bengali tigers. There are about 30 chairs. The first row is filled with about 10 village women dressed in their finest saris, some have children sitting in their laps. Raut motions to the chairs in front that have been set up on the stage.

Once the rest of the group joins us, the meeting gets started. The meeting is led by CRRI scientist SSC Patnaik. He explains to the assembled villagers that that this was their chance to ask us questions about the new variety and an opportunity for us to learn from them how the varieties performed in their hands.

One farmer tells us that the Swarna-Sub1 variety produced twice as much rice this year compared to his previous variety. He asks us if their might be problems that will come later. Will Swarna-Sub1 be more susceptible to insects? Dave Mcakill explains that because Swarna and Swarna-Sub1 differ by only a few genes, that it is unlikely that such a problem will occur. After 5 years of on-station and farm trials, there have not been new pest problems.

Another farmer asks if the flowering time will differ. Dave answers that so far, Swarna and Swarna-Sub1 flower at the same time.

A young woman in the front row, dressed in a pink sari, stands up and tells us that the new variety has provided more food for her family and even extra rice so that they can sell some on the market. She is glad to have some money for her family she says.

"When will we put Sub1 into Gayatry?" the next farmer asked. A breeder at CRRI tells him that the Sub1 Gaytry is now being developed.

Several more farmers stand to tell us how well the Sub1 variety is doing. "It is magic", one says. Several woman tell us how pleased they are that we came to visit and that we have worked for them from so far away.

After about 30 minutes, the villagers pass us small boxes filled with homemade somosas (spiced potatoes wrapped in pastry) and sugar sweetened panner (Indian cottage cheese). We give them 2 soccer balls and pumps.

As the meeting breaks up, one woman comes to me, her hands sliding comfortably into mine. Patanaik translates.

"Thank you for coming to our village. Thank you for working for us. Thank you for the rice. We have more food and more money for our families."

And to her I say, "Thank you for welcoming us, thank you for testing the rice, thank you for growing it and feeding your families. We are honored to be useful. It is a joy to be here."

This is the 5th in a series of posts describing our trip to Bangladesh and India. For part 4, see this post.

Graph. [Genomicron]

Posted: 15 Nov 2008 11:38 AM CST

True, that.

Weekend fun: Build your own virus! [Discovering Biology in a Digital World]

Posted: 15 Nov 2008 10:17 AM CST

If you're going to create a new life form (even if it's only digital), Sunday Saturday seems like the best day to give it a try.

influenza A virus

Reposted from an earlier year.

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Genetic Genealogist deconstructs ASHG criticisms of ancestry testing [Genetic Future]

Posted: 15 Nov 2008 08:41 AM CST

Blaine Bettinger at the Genetic Genealogist has an extensive and thoughtful critique of the American Society of Human Genetics' recently released statement on genetic ancestry testing (pdf). (You can read about the Society's statement at GenomeWeb News and Science Now; 23andMe also comments from the point of view of a company engaged in ancestry testing.)

If you have comments on the issues surrounding genetic ancestry testing I'd encourage you to add them to Blaine's post.

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Why do we blog and other important questions. [Genomicron]

Posted: 15 Nov 2008 07:42 AM CST

I am a member of the Nature Network, though my blog there, Pyrenaemata, has been dormant for some time. That's largely because I have enough trouble posting (semi-)regularly on this blog and its counterpart at Scientific Blogging (Genomicron 2.0). In any case, there is a forum message at the Nature Network (though I saw it on Sandwalk) that asks a set of questions about blogging that I thought I would answer.
  1. What is your blog about?
    My blog is about science, in particular evolution and genomes. Much of the content of my blog has been about non-coding DNA, and the various myths and misconceptions that this topic entails. I veer into politics infrequently, and I also post some attempts at humour now and then. Unlike several of my favourite blogs (and no doubt to the detriment of my visit count), I do not talk about religion although I do discuss anti-evolutionism.

  2. What will you never write about?
    Never say never -- but I made a conscious choice early on to focus on science.

  3. Have you ever considered leaving science?
    Not seriously.

  4. What would you do instead?
    I would probably write. About science.

  5. What do you think science blogging will be like in 5 years?
    I think more professional researchers will join the blogosphere as this becomes socially acceptable. The stigma that poking one's head out of the ivory tower is not what real scientists do is quickly being replaced by an acceptance that the medium can be useful. I think (ok, hope) that blogs will become a more common source of science news than press releases. That said, I hope there is never any move toward making blogs a venue for actual science, as I believe the peer review system (flawed though it is) is essential.

  6. What is the most extraordinary thing that happened to you because of blogging?
    Nothing extraordinary per se, though more than one interview I have conducted involved the reporter indicating that he/she had found my blog.

  7. Did you write a blog post or comment you later regretted?
    Somewhat. Early on I had an argument with Nick Matzke in which I was a little more adamant than was called for. However, in the end it worked out and we stay in touch. I have also written some posts that I am proud of -- the one on Remembrance Day, I have been told, was very moving.

  8. When did you first learn about science blogging?
    My graduate student introduced me to blogs about two years ago. It took a while for me to be convinced to read them ("I'm too busy for that" was probably my mindset), but then I began to see the value for finding information in fields outside my own. Plus, some of them are rather fun. Later, I decided I would try setting up a blog to talk about my research and related work. Voila.

  9. What do your colleagues at work say about your blogging?
    I list my blog in my "service" contributions as I consider this an exercise in public outreach, and that seems to go over ok.

Second Life 2.0? [ScienceRoll]

Posted: 15 Nov 2008 05:57 AM CST

Personalized medicine: report of US President’s Advisory Committee [ScienceRoll]

Posted: 15 Nov 2008 05:29 AM CST

I’ve recently come across the newest US report on personalized medicine on the site of PHG Foundation. It’s definitely worth reading it.

The report explains some of the barriers preventing widespread adoption of personalised medicine such as ambiguous regulation, lack of translational research and limited coverage by health insurers, as well as potential mechanisms to overcome them.

Much of the report echoes and re-iterates the PHG Foundation's findings in relation to the evaluation of genetic tests and molecular biomarkers, which is an area of ongoing focus at national and international levels. With more diagnostic tests becoming available all the time, it is becoming increasingly important to produce appropriate mechanisms to assess and evaluate them, to distinguish between clinically useful and redundant tools, and to understand their possible impact on clinical practice.



What’s on the web? (15 November 2008): National Dialogue [ScienceRoll]

Posted: 15 Nov 2008 05:16 AM CST


The goal of the week-long Web-based dialogue is to solicit input from health care stakeholders and the American public on health IT, which is a top priority of the federal government. The forum seeks to answer the question: How can the country best use health IT to improve patient interaction with the health care system while sufficiently safeguarding patients’ privacy? (Source)

  • My Health: A new personal health records system.



Why Journalists Don’t Ask Questions That Matter in Technology [Think Gene]

Posted: 15 Nov 2008 02:35 AM CST

Gene Screen: Will We Vote Against a Candidate’s DNA?

While still high, the cost of high-speed genetic analysis is falling fast. It took 13 years and $2.7 billion to determine all the DNA in the first complete human genome, finished in 2006. Earlier this month, a Mountain View, Calif., company called Complete Genomics announced that by next year it will be able to read out an entire personal genome for $5,000.

What an effective piece of technology journalism. You see, some people think that technology journalism reports important topics in science. This is ridiculous. Technology journalism reports fancy theme parties.

I’m not going to discuss “voting against a candidate’s DNA” for the same reasons why I not going to discuss if the modern luxury automobile really can be “Pure. Performance.” today in the 21st century. Instead, I have destructed Robert Hotz’s work and offer my own modern adaptation. I hope this will help contemporary generations better appreciate the work as it was understood by its author.

A W! Exclusive: Genomes, Revealed!

“Wazzup! I’m your host, Robby H, and I’m broadcasting la-la-live here at the fabulous Wall Street Club for the exclusive Genomes for Democratic Awareness Drive —brought to you by Complete Genomics of Mountain View, Calif. Yes yes yes this part-ay is hot hot hot, and for such a good cause, too. Let’s meet some of the guests before, you know, the coming era of personal genomics leaves us behind!

“Omigawd, that hunk in the foyer is George Annas, the hottest name in bioethics and human rights hailing from Boston University. Let’s go check him out. George! How have you been? I love your hair. Where did you get that coffee? Tell us about tonight’s cause!”

“Rob, let me tell you, this sh*beep*t is so hot. DNA is not an issue in this campaign, but next campaign —it will be bigger. Dude, it’s coming.”

“And hey, what about Complete Genomics, huh? They sure know how to throw a party? Remember the first human genome back in 06? Complete Genomics is all about releasing the remake next year. This is going to be huge… and you know, it’s all for democracy, too. Oh! oh! look! through this crowd of VIPs, by the spit kit table, it’s George Church! George!!!” Rob waves frantically, pushing through the crowd of international dignitaries towards a beaded man encircled by an overly attentive audience sipping oragenes. “George, George Church. People: this is The George Church, director and producer of the Harvard’s Personal Genome Project.”

Flashing a contemptuous glace, George willfully ignores Rob and continues to address his admiring crowd. “…I would be shocked if Americans and people in other countries don’t want this type of data. It is not like we are collecting horoscope data or tea-leaf data. These are real facts!” his face reddens, the spit-kitting must be catching up to him, “…just as real as bank accounts and the influence of political action committees or family members.” Rob is subtly jostled back as well-dressed security notice the situation and discretely places themselves between Rob and George’s circle.

“Oh. My. Gawd. That was Harvard neuroscientist Steven Pinker, Internet visionary Esther Dyson, Rosalynn Gill, chief scientific officer of Sciona. The technocrat crowd is hot hot hot tonight! I just know the PGP will be a volunteering smash. I mean, with a budget of 100,000 personal genomes, how could it not? Speaking of the Harvard crowd, here’s Aaron Kesselheim. Aaron, what can you say about tonight’s cause?”

Aaron launches into monotone recollection of tangentially related historic facts as Ron begins to slump, making little effort to conceal the misfortune of engaging the party bore as the camera pans over Aaron’s shoulder to the tacky multimedia display on the wall.

“Mildred!” Rob grabs the arm of a woman walking by. “People, this is, um, Mildred Cho of Stanford. Mildred, would you comment on Aaron’s, um, Aaron’s viewpoints?”

Mildred notices the camera and hesitates, then smiles disingenuously before pulling away. “Sometimes, there’s less to it than meets the eye.” By this time, Rob and his camera crew have drifted back to the outside of George Church’s circle. In the background, his back to the camera as it pans away from the retreating Mildred, Steven Prinker exclaims a too loudly, “But you know, George, I do have some susceptibility to having irregular menstrual periods! Uh ha!” Rob theatrically rolls his eyes.

“T.M.I. Let’s um, let’s go over here… ooo, look at this fine group of love-ly ladies!”

The women in the circle break their conversation and flirt with the camera. “Hiiii Ronny!” *giggle*

“Ok, let’s break this down: people, this is Anita Allen of University of Pennsylvania, Lori Andrews of Chicago-Kent, and Tenielle Brown of Stanford. And how fine they look! Anita, darling, you look so hot in that slinky dress, and we’ve got it all on film here at W!”

Anita poses seductively, “Oh Robby, you know it would end up on sleazy blogs and in attack ads.”

“Oh, you know it girl. Oh, here’s Henry Greely, director of Stanford’s Center for Law and the Biosciences. Henry, weigh in for the ladies.”

Henry leers, obviously drunk. “They are not… private people, Ron. You know, so far, no one has tested the legal limits of a candidate’s genetic privacy. Candidates may have the right to refuse to disclose genetic data, but their refusal is something that voters could and probably should… hold against them. Mmm.”

“Haha, ooo-kay, tiger, calm down. Gr-owl! Well, I think this wraps up W! exclusive coverage of the Genomes for Democratic Awareness Drive by Complete Genomics. OOOoo yah! We really know now who’s who in genomics tonight! Be sure to come back next week for some more big “Sergey-Shakeups” and remember, I love you all! Muah! Don’t forget, I love your emails! Txt me! This is Robert Lee Hotz of the Wall Street Journal —peace out.”

Harvard Harvard Stanford George Church Complete Genomics Harvard buy something I’m famous

World Diabetes Day: A day of a diabetic vlogger [ScienceRoll]

Posted: 15 Nov 2008 02:18 AM CST

Kerri Morrone is a world-famous diabetic blogger who is a great encouragement to diabetic patients all over the world. Recently, she has made a video for my Medicine 2.0 credit course and now she posted a video for the World Diabetes Day.

Don’t miss her interview with Dr. Val.


Demonstration of epigenetic changes due to early stress, and how do you measure methylation? [Yann Klimentidis' Weblog]

Posted: 14 Nov 2008 01:53 PM CST

An interesting paper showing epigenetic changes caused by early stress has recently come out in PNAS (see below). Siblings who were in utero during the Dutch Famine in the winter of '44 - '45 had less methylation on the IGF2 gene compared to their same-sex siblings who were not in utero during the famine.

So, how exactly does one measure methylation?
According to the paper, and a Wikipedia entry:
First, methylation usually occurs on CpG cytosines, and when you treat your piece of DNA with bisulfite, the methylated cytosines becomes reduced to uracil. Then a variety of PCR methods and/or sequencing methods can be applied. In this paper they use a mass-spectroscopy based method called Epityper.

Persistent epigenetic differences associated with prenatal exposure to famine in humans
Bastiaan T. Heijmansa, Elmar W. Tobia, Aryeh D. Stein, Hein Putter, Gerard J. Blauw, Ezra S. Susser, P. Eline Slagboom, and L. H. Lumeye
PNAS 2008 105:17046-17049
Abstract: Extensive epidemiologic studies have suggested that adult disease risk is associated with adverse environmental conditions early in development. Although the mechanisms behind these relationships are unclear, an involvement of epigenetic dysregulation has been hypothesized. Here we show that individuals who were prenatally exposed to famine during the Dutch Hunger Winter in 1944–45 had, 6 decades later, less DNA methylation of the imprinted IGF2 gene compared with their unexposed, same-sex siblings. The association was specific for periconceptional exposure, reinforcing that very early mammalian development is a crucial period for establishing and maintaining epigenetic marks. These data are the first to contribute empirical support for the hypothesis that early-life environmental conditions can cause epigenetic changes in humans that persist throughout life.

Updated refresher course on genes [Yann Klimentidis' Weblog]

Posted: 14 Nov 2008 11:06 AM CST

There's an article in the NYT by Carl Zimmer called "Now: The Rest of the Genome" that discusses some of the new findings about how genes work:
Here are some of the more interesting nuggets:
  • "the average protein-coding region produces 5.7 different transcripts"
  • "cells often toss exons into transcripts from other genes. Those exons may come from distant locations, even from different chromosomes."
  • "When an embryo begins to develop, the epigenetic marks that have accumulated on both parents' DNA are stripped away. The cells add a fresh set of epigenetic marks in the same pattern that its parents had when they were embryos."
  • "As an embryo matures, epigenetic marks in different cells are altered, and as a result they develop into different tissues. Once the final pattern of epigenetic marks is laid down, it clings stubbornly to cells. When cells divide, their descendants carry the same set of marks."
  • "Although only 1.2 percent of the human genome encodes proteins, the Encode scientists estimate that a staggering 93 percent of the genome produces RNA transcripts."
  • "Dr. Prohaska argues that a gene should be the smallest unit underlying inherited traits. It may include not just a collection of exons, but the epigenetic marks on them that are inherited as well."

When family history falls short v.1 and the Wall Street Journal [The Gene Sherpa: Personalized Medicine and You]

Posted: 14 Nov 2008 08:05 AM CST

Andrew Yates at ThinkGene asks a very valid question..... When does family history fall short? I outlined it in my last post but I figure now might be a good time to review one of the instances...

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Sleep on it.......Nawhhh [The Gene Sherpa: Personalized Medicine and You]

Posted: 14 Nov 2008 05:45 AM CST

That's the advice I get......often.....Sometimes I take it, sometimes I don't........ My friend has pointed this out several times.......In fact in my last post, my generalizations lead some people...

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1 comment:

Imgenex said...

I read your blog and really it so impressed me. Your style of presentation regading DNA Methylation is very interesting.Thanks for giving more ideas about cell.