Posted: 16 Nov 2008 07:00 PM CST
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.
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
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.
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.
Posted: 16 Nov 2008 01:25 PM CST
Hospital 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.Read the rest of this post... | Read the comments on this post...
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:
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?).Read the rest of this post... | Read the comments on this post...
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- msnbc.com) 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
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.
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.Read the rest of this post... | Read the comments on this post...
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
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.Read the rest of this post... | Read the comments on this post...
Posted: 16 Nov 2008 06:59 AM CST
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:
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.
|You are subscribed to email updates from The DNA Network |
To stop receiving these emails, you may unsubscribe now.
|Email Delivery powered by FeedBurner|
|Inbox too full? Subscribe to the feed version of The DNA Network in a feed reader.|
|If you prefer to unsubscribe via postal mail, write to: The DNA Network, c/o FeedBurner, 20 W Kinzie, 9th Floor, Chicago IL USA 60610|