Sunday, November 16, 2008

The DNA Network

The DNA Network

Blogging from Bangladesh, Part 7. Last post in the series [Tomorrow's Table]

Posted: 16 Nov 2008 07:00 PM CST

November 8th

This is the last post in the series "Blogging from Bangaldesh". For #6, see this post.

Bells ringing and birds singing at 5 am. Yoga and meditation on the balcony overlooking the temple. A walk through the rice fields with my mother where we see two green parrots, a brilliantly-colored blue and red kingfisher and a black and white bird with a fish in its long beak. The birds darts among the 80 rice varieties being tested here.

One variety has been bred for erect flag leaves that extend above the ripening grain to protect it from the birds. Another has been genetically improved for dwarfism so that it will not fall over and spill its grain into the paddy when mature. And then there are the thick stands of the three new Sub1 varieties, each plant heavy with full panicles of rice. Their parents (Samba, IR64 and Swarna) that lack the Sub1 locus have not faired so well. Only 3-4 plants survived the 15 day flood.

In India, 70% of the farmers cultivate 1 hectare or less. These small and marginal farmers are benefitting from the work here at the Cuttack Rice Research Institute and the international collaboration that has brought our team together. They are also benefiting from innovative approaches being developed here that integrate the most modern varieties into diverse cropping systems.

In one trial, an acre is planted to a creative mixture of food crops. A pond was dug to grow low-yielding deep-water rice and fish during the wet season. Once harvested, the fish is eaten and two more crops of a genetically improved high yielding irrigated rice are grown. On the banks of this small farm grow, pineapples, coriander, peppers, cowpea, bananas, mango, and papaya. They also grow bamboo that can be sold for a good price. The soil is fertilized with less synthetic fertilizer than many of the rice farms in Asia because the a cow and some chickens provide compost for fertilizer. The organic fertilizer is supplemented with a small amount of synthetic fertilizers toenhance the productivity of the farm. A husband and wife work the land and sell the produce- a real life test of the sustainability of the system.

This small model farm may be the future of agriculture- by integrating a diverse array of crops and the most modern seed with the best organic methods daily food security can be enhanced. If this mixture of crops produces well throughout the year the farmers and their families will thrive.

In 1996 when my laboratory first began this work with Dave Mackill, I could not have known that the project would take me to these fields in Cuttack. We finally isolated the Sub1 gene that we had sought for so many years in 2004. Now, thanks to an international team of breeders, it has been introduced into 6 varieties popular with farmers in India, Indonesia, and Bangladesh. The gene is now on its own journey in the hands of breeders and farmers. I feel as if my child has grown up and developed his own, successful life.

Later today we will fly to Dehli where I will give a lecture at the University of Dehli. Our host Anil Grover, Department of Plant Molecular Biology, University of Delhi, later tells me "It is mind-blowing how one gene is doing so many wonders, particularly when everybody says abiotic stresses can not be handled with genetic engineering, it is just a matter of getting the right gene, following the right approach." After dinner with our Indian colleagues we will begin the long journey home.

Goodbye gentle India. Namaste.

Blogging from Bangladesh, Part 6 [Tomorrow's Table]

Posted: 16 Nov 2008 05:01 PM CST

November 7th Friday

Today we woke to Indian chants and drumming. Curious, I stepped out onto the balcony of the Cuttack Rice Research Institute guest house where we are staying. Across the street is a white temple big enough for 2-3 people to pray inside. It is adorned with golden turrets and decorated with images of the God Vishnu. I watch a young girl, her orange sari bright against the green of the rice fields beyond, sweep the grounds of a small temple with a grass broom. After yoga and meditation on the balcony, I reflect on the surprises of yesterday.

Then it is back to work. I attend an all-day workshop of scientists and breeders at the Cuttack Rce Research Institute. We tell each other about our Sub1 research and make plans for more collaborations.

This is the 6th in a series of posts describing my trip to Bangladesh and India. For part 5, see this post

Sunday Science Book Club [adaptivecomplexity's blog]

Posted: 16 Nov 2008 02:59 PM CST

Oppenheimer: The Tragic Intellect

Charles Thorpe, University of Chicago 2006

For decades, there was a dearth of comprehensive Oppenheimer biographies. As Thomas Powers noted in the New York Review of Books, biographies of other major Manhattan Project figures came out long before truly adequate Oppenheimer biographies: "Oppenheimer, the truly central figure, seemed to resist the attempt to write his life on the grand scale." That is no longer the case, and a shelf of very good biographies makes it difficult to know where to start reading.

read more

The ASHG Ancestry Testing Task Force [The Genetic Genealogist]

Posted: 16 Nov 2008 01:41 PM CST

Charmaine Royal, Ph.D., discusses “The pitfalls of tracing your ancestry” at NatureNews.  Dr. Royal, an associate professor at the Duke Institute for Genome Sciences and Policy, co-chairs the ASHG Ancestry Testing Task Force.

Brendan Maher of Nature’s In the Field blog has more at “ASHG 2008: A stance, more or less, on genetic ancestry testing.”  Not much more covered here that was already written at The Spittoon - see “ASHG Releases Ancestry Testing Statement Emphasizing Interpretation.”

If you’re interested in seeing the Task Force’s webcast, it’s available here.

The Seattle Times takes on hospital-acquired MRSA [Discovering Biology in a Digital World]

Posted: 16 Nov 2008 01:25 PM CST

mrsa_bacteria.gifHospital cases of methicillin resistant Staphylococcus aureus (MRSA) have risen 33-fold during the past ten years in Washington state, yet our hospitals fail to identify or track cases in a systemic fashion (Seattle Times).

The Seattle Times began a three-part investigative report today describing the rise in MRSA incidence, the consequences for patients, and the failure on the part of our hospitals to take measures to address the problem.

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The Science Blog meme [My Biotech Life]

Posted: 16 Nov 2008 12:45 PM CST

And yes… another meme. But this one is a bit more substantial. It’s a series of questions regarding science blogging and started off over at Nature Network via Martin Fenner.

So off to the questions:

  1. What is your blog about?
    My blog is mostly biotech related, with special focus on topics that I’m interested in and feel the need to write about. Either to spread the news or to put my own spin on a topic.Oh, and a personal rant here and there to spice things up.
  2. What will you never write about?
    Topics I know absolutely nothing about, namely telenovela reviews, eastern European gastronomy, seashell collecting, among others.
  3. Have you ever considered leaving science?
    I’m still working my way into science per se. So no, I’ve never considered it.
  4. What would you do instead?
    I’d most probably enjoy being a graphic designer. I’ve tried it at an amateur level and have enjoyed it quite a bit.
  5. What do you think will science blogging be like in 5 years?
    Blogging has evolved so quickly over the last couple years and has been used for so many different goals that it’s quite hard to say what it will be like in 5 years. However, I hope that blogs and other online mediums are used to share scientific knowledge, making it available to more and allowing fellow scientists to communicate with ease.
  6. What is the most extraordinary thing that happened to you because of blogging?
    I can say that the decision to start blogging, after years of lurking on other blogs and only participating via comments, was the best thing I could have done. I’ve connected with people from all over the planet, co-founded a network of science bloggers (The DNA Network) and been invited (and accepted!) to work at MIT.
  7. Did you write a blog post or comment you later regretted?
    Aside from my whining and rants, I’m yet to really regret posting something. *crosses fingers*
  8. When did you first learn about science blogging?
    I just happened to read blogs that I thought were interesting. I guess I noticed a stronger flux of science related blogs pop up around 2 years ago. And therefore the DNA Network came about as a form to connect bloggers of topics that I find interesting. There are now many science blogging networks.
  9. What do your colleagues at work say about your blogging?
    Blogging took a bit longer to hit mainstream here in Portugal and is usually not taken too seriously. However, my blogging was well accepted while in the US and has been a point of connection with folks from all over the globe.

(HT: Bora)

The Science Blog meme

Is Nested Clade Analysis Worthwhile? [evolgen]

Posted: 16 Nov 2008 11:30 AM CST


Population biologists often want to infer the demographic history of the species they study. This includes identifying population subdivision, expansion, and bottlenecks. Genetic data sampled from multiple individuals can often be applied to study population structure. When phylogenetic methods are used to link evolutionary relationships to geography, the approaches fall under the guise of phylogeography.

The past decade has seen the rise in popularity of a particular phylogeographical approach for intra-specific data: nested clade analysis (Templeton et al. 1995; Templeton 2004). Many of the methods used in intra-specific phylogeography have been called into question because of their lack of statistical rigor, as I have described previously (How do you really feel, Dr. Wakely?). Nested clade phylogeographical analysis (NCPA) is no exception. Lacey Knowles summarizes the criticisms of NCPA in the most recent issue of Evolution (Why does a method that fails continue to be used?).

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Microbiology in the news: How bleach kills germs [The Tree of Life]

Posted: 16 Nov 2008 10:29 AM CST

I am starting a new thread here - microbiology in the news. And my first posting is about bleach. Everyone probably has used it at one time or another to clean something. And some people use it to kill "germs" (aka microbes) too. Well, MSNBC is reporting (Mystery solved: How bleach kills germs - Science- on a Cell article that presents evidence regarding how the active ingredient in bleach (hypochlorous acid) kills bacteria. Apparently, it works in a similar way to heat in destabilizing protein structures. Anyway, the researchers claim that this is relevant to killing of microbes inside of people because
"Hypochlorous acid is an important part of host defense," Jakob said. "It's not just something we use on our countertops."
Whether this is true or not, I do not know. But what I do know is that microbes are in the news. And that is good.

For more on the bleach story see

Corn - it's not just in your food, it's in your packaging [Discovering Biology in a Digital World]

Posted: 16 Nov 2008 10:14 AM CST

Last spring, in a coffee shop in Berkeley, I saw an amazing thing. It was a cup made from corn. The information on the cup says that it is made from corn, is environmentally sustainable, and 100% compostable.corn_cup.jpg

My fellow ScienceBloggers have written several articles lately about corn in fast food (here, here, and here), but I'm not sure they realized that corn is used for more than fast food.  Corn is also used to make the packaging.

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Distinct RNA Binding Proteins for Distinct Classes of mRNAs [The Daily Transcript]

Posted: 16 Nov 2008 09:00 AM CST

Over the last few years it has become increasing clear that gene expression is partially regulated at the mRNA level.

What do I mean by that?

In eukaryotic cells, the first step of gene expression occurs in the nucleus when regions of DNA are transcribed into RNA. These "transcripts" then encounter RNA binding proteins (RBPs), some which act to process the RNA into a mature message, others that simply bind the mRNA. The whole collection of RNA and its associated proteins is often referred to as the Ribonuclear Particle (RNP). The protein content will dictate whether the RNA is spliced, exported from the nucleus to the cytoplasm, transported to various cytoplasmic sites, translated by the ribosome into protein, or degraded. You can then imagine that in any given cell, gene expression relies on the levels of various

1) transcription factors, which dictate which mRNAs are going to be synthesized
2) RBPs, which dictate how these mRNAs are going to be treated

In addition the types of RBPs bound to any one transcript may vary over its life time. Some may accompany the mRNA from the nucleus to the cytoplasm then fall off, some may bind when the transcript has reached its cytoplasmic destination, some may bind during translation, and others may only recognize the RNA at the very end of its life.

So how many of these RBPs are there? In yeast there are over 500. If you take into account the size of the yeast genome (4,300 genes) that means that over 10% of the protein-coding genes of this organism encode RBPs!

So now that we have some context, I would like to describe some results from a recent PLoS Biology paper where scientists examined the types of mRNAs bound to 40 different RNA binding proteins in budding yeast, S cerevisiae.

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My dog would like his sequence, too…assuming it’s edible []

Posted: 16 Nov 2008 06:59 AM CST


James P. Evans, a genetics professor at UNC-Chapel Hill, cautions against making too much of genetic information.

Even if Angrist or one of his fellow participants learns he has the gene for a horrible disease. that is far from a guarantee that the disease will ever occur, Evans said. Even in a larger group of donors, Evans said, it would be difficult to make solid medical decisions based on what DNA shows. A woman whose DNA suggests future breast cancer, for example, shouldn’t necessarily run out and get a mastectomy.

“The information one gets is virtually all probabilistic; it’s not actionable information, medically,” he said. “To me, the biggest danger is that its utility will be exaggerated because people put this mystical value on DNA.”

As usual, Dr. Evans is absolutely right.

I appreciate the reporter’s hard work and I like the story, but I would offer a few corrections/clarifications:

  • “Americans are notoriously hung up on privacy, and I get that,” he said. “[But] I don’t think that information is toxic.” That is an accurate quote, but that doesn’t mean I think we should all walk around naked or read each other’s mail.
  • “When you make everyone anonymous, you impoverish the data,” he said. “You may have that person’s DNA, but you don’t have a name or a lot of the details that you may want someday.” Again, accurate, but I shouldn’t have emphasized names. I should have said that re-contacting research participants is important and you can’t do that when you sever the link.
  • Since then, two pioneers in the field, James Watson and J. Craig Venter, allowed their DNA to be totally decoded and made public.  At the risk of nitpicking, Watson wanted his genotype at the Alzheimer’s risk gene APOE redacted. Alas, it couldn’t be done.
  • In Angrist’s case, DNA was taken from a graft of his skin and mechanically sheared into smaller pieces; it will be put through a complicated, multistep process until the sequence is determined. Angrist’s DNA sample was taken in late October, and he hopes to have his genome sequence information within weeks. Actually, my genome sequence will be determined from white blood cells I donated in 2007. My skin cells will be used to create a cell line that is stem-cell-like.
  • A native of Pittsburgh, he came to Duke in 2003 and works primarily in the areas of intellectual property and gene patenting. While it certainly feels that way at the moment, I’d like to think my work encompasses a lot of other stuff too: personal genomics, teaching, science writing, etc.
  • [”Alzheimer’s is] in your 70s,” Angrist said. “Something that’s going to happen to me 30 years from now is not going to keep me up at night.” Of course I realize that many people develop AD much earlier. I did not mean for this to sound as blase and callous as it might. My point was, I have plenty of other stuff to worry about for the next couple of decades.

Is science boring? [Mailund on the Internet]

Posted: 15 Nov 2008 11:46 AM CST

Hi there, dear reader. Sorry I haven’t updated the blog lately, but I’ve been lazy and haven’t really had anything to say.

However, I’ve just had a chat with some guys about this and, slightly drunk as I am on a Saturday evening, I feel like venting some steam.

I’ve attended some talks this week that I found extremely boring.

Why? Does science have to be boring?

Fuck no! It is very exciting, but lately I find that reading papers is a lot more interesting than attending talks.  Talks are a complete waste of time.

Why is that? I really don’t undestand it.

If you have something exciting to say, why turn it into an academic boring lecture where all the emotions have been completly removed? Are you afraid of offending anyone? Why? If your science is good, then why be afraid?

Talks are supposed to get me interested in the topic. The effect they have is getting me to sleep.

I would love to start a movement against this.  If you don’t like the talk, then leave, noisily.  Teach those fuckers that you they should prepare a talk, before they open their mouth.

Damn it!

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