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| Gossip Friday [the skeptical alchemist] Posted: 14 Nov 2008 05:55 PM CST Friday afternoon, time to ramble... here are a few interesting things for you to read:
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| Blogging from Bangladesh, Part 1 [Tomorrow's Table] Posted: 14 Nov 2008 04:24 PM CST  This is the first in a series of 7 posts from Bangladesh and India. Saturday, 01 November 2008 Bangladesh is a land of rivers. I can see that from my airplane window as we flying into Dhaka. The waters flow into the Bay of Bengal, along seemingly orderly channels. The riverbanks and small low-lying islands are planted to rice. Upon landing our group (scientists, breeders, writers and photographers) make our way through the crowded parking lot to find our limousine. The cars line up bumper to bumper; the drivers blowing their horns every few seconds to encourage the beggars, mostly young barefooted boys, to move aside. One boy sleeps soundly on the pavement. One hundred and fifty million people live in Bangladesh, in a geographic area the size of Wisconsin. After checking into hotel Laurel (certainly nothing like the Mayflower hotel in Washington DC where my husband I stayed last week), we squeeze back into the vehicles and drive to our first meeting at Dhaka University. Built in 1921 by the British, Dhaka University is the main research and teaching center in the country. The edges of the dirty, worn stairs are hand painted with colorful flowers. I wonder if enthusiastic students did the work on a day where they had some spare time, perhaps during a power outage that are frequent here. Our host, and the leader of the laboratory, Zeba I. Seraj, introduces us to her 10 students who have waited until late in the day (our plane was delayed for 2 hours) to meet us. We walk through the hallways where the AC whirrs loudly in an attempt to cool the building. Because the outside air moves in through gaps in the wall, it is still hot.  The room where we meet the students is beautiful; every foot of wall is covered with 100-year old wooden cabinets filled with biology books and journals. I imagine that this room is filled with young hardworking students during the day anxious to learn what is before them and perhaps relieved to escape the hot ill-equipped labs for a short while. Zeba tells us that salinity is a problem for rice farmers here. Not only is the sea water rising, but fresh water supplies are under pressure partly because farmers are pumping more every year and also because Bangladesh is downstream from India, who gets first dibs on the fresh water through a network of dams. The result is that every year the saline lands encroach north, hurting rice yields, a serious problem here where the average Bengali receives 2/3 of their diet from rice. And then there are floods that arrive unpredictably, sometimes wiping out the entire crop.  Zeba and her students are working to develop salt tolerant rice. They have had success in identifying a chromosomal regions from local landraces that confer salt tolerance to the rice. They are now trying to introduce those regions into higher-yielding varieties. They have also had some success with a genetic engineering approach. She shows us a dramatic picture of their newly developed transgenic lines thriving under high salt concentrations that kill the conventional variety. Zeba's group is now testing to see how the transgenic lines yield under normal growing conditions. |
| Blogging from Bangladesh, Part 2 [Tomorrow's Table] Posted: 14 Nov 2008 04:22 PM CST  Sunday, November 2 This is the second post in a series describing my trip to Bangladesh and India. For part 1 please see this post. Our first morning in Bangladesh, we wake to the morning prayer (Bangladesh is largely a Muslim country) and the sound of birds. After breakfast, we drive 7 hours to visit the Bangladesh Rice Research Institute in Rangpur where breeders are field testing four newly developed rice varieties carrying the Submergence tolerance 1 chromosomal region. Before I get to the results of the field trials, let me first explain why we are here and who we are. I am part of a collaborative group of scientists who developed new rice varieties for Bangladesh and India that can survive flash floods My contribution to this work began 13 years ago when my colleague and friend Dave Mackill a breeder at IRRI (International Rice Research Institute (IRRI, Philippines) asked if I would clone a gene from a traditional variety found in the Eastern Indian state of Orissa that can survive 2 weeks of submergence. Although rice is typically cultivated in a paddy with the root system flooded, complete submergence of the plant is lethal to most varieties within a matter of days.  Using the rice populations that Dave and his group developed from the submergence tolerant variety, Postdoc Kenong Xu in my lab isolated the submergence tolerance (Sub1) locus, cloned it, sequenced it and identified an ethylene responsive transcription factor called Sub1a that is induced in response to flooding. My laboratory genetically engineering a rice variety with Sub1a and found that the transgenic plants survive 2 weeks underwater. Normally, 3 days of submergence is enough kill any rice variety. Julia Bailey Serres (Professor, UC Riverside) joined our project in 2001 and has begun to elucidate the molecular mechanisms of action of this gene. Using the sequences we identified, Dave's group used marker assisted breeding (a hybrid of genetic engineering and conventional breeding) to introduce Sub1 into rice varieties that are adapted to the local growing conditions in India and Bangladesh.   This work was initially supported by s NRI Plant Genome Program (1996-1999; Grant 96-35300-3723) to Mackill (PI) and Ronald (coPI) and then by a second NRI Plant Genome Program (2000-2003; Grant 00-35300-3723) to Ronald (PI) and Mackill (coPI). The recent grants from the USDA environmental stress group were awarded to Julia Bailey Serres (PI) and Pam Ronald (collaborator) from 2004-2008. We are also joined on this trip by scientists, breeders and communication staff from the IRRI, The Bangladesh Rice Research Institute (BRRI) and the Central Rice Research Institute (India). Our traveling team numbers nearly 30 people. This visit wraps up an IRRI project, funded by the German government (BMZ) "From genes to Farmers fields: enhancing and stabilizing productivity of rice in submergence-prone environments". As biologists who research the nitty gritty of how plants endure the stress of attack from pathogens and sub-optimal growth conditions, Julia and I look forward to seeing firsthand the needs of the people of Bangladesh and hearing how the efforts of researchers at BRRI and IRRI have dramatically increased the amount of rice produced per acre each year.  In the picture to the left, Dr. Mazid (BRRI) shows the Sub1-Swarna variety on the left and the Swarna variety to the right. The results are dramatic - the Sub1 variety yielded 2-3 fold more when the field is flooded. Increased yields were observed for every Sub1-variety tested, no matter what genetic background was used (IR64, Swarna, BR11 and Samba Mashuri). In each case in the BRRI fields, the yields were similar in non-flooded conditions. Tomorrow we will visit farmers fields to see how the rice plants behave in the farmers hands. |
| Making Sense of Biological Networks [adaptivecomplexity's blog] Posted: 14 Nov 2008 01:55 PM CST Molecular biologists have long operated on the principle that knowing the structure of a biological entity is critical for understanding how it works. Most famously, this was the premise behind one of biology's most iconic discoveries, Watson and Crick's model of the structure of DNA. Structure-function studies have been the foundation of much of molecular biology ever since. Although the structure of DNA yielded almost immediate insight into an important biological problem, solving structures hasn't always resulted in a eureka moment. The same year Watson and Crick received their Nobel Prize, two other scientists, John Kendrew and Max Perutz, were also awarded the Nobel for determining the structure of a biological molecule. Unfortunatly for Kendrew and Perutz, instead of a flash of insight the result was incomprehension. They had determined the structure of two related proteins, myoglobin and hemoglobin, and these structures at first glance looked like just an irregular mass of thousands of atoms. Happily, the befuddlement didn't last long. Scientists quickly learned how protein structures explain their function, and today we have amazing structural snapshots of proteins in action. These studies of structure have helped biologists understand the gritty details of key biological processes, such as how membrane-embedded ion pumps enable our nerves to conduct electrical signals. Using a protein's structure to understand its function has now become routine. But today biologists are facing another moment of incomprehension. We're staring at structures of a different type of biological entity: a network, not an irregular mass of atoms, but one of connections. We know that biological networks give cells their ability to make sense of the world, to process information, to sense the environment or the cells' own internal state, and to take appropriate action. Scientists have been mapping these networks in great detail for years now, but the result is frequently just a giant, molecular hairball (or 'ridiculogram', as a friend calls it). In other words, scientists are facing yet another giant structure-function problem. How do the strucures of biological networks result in something functional?  |
| Lab Atmosphere: Good, Bad, or Indifferent? [Epigenetics News] Posted: 14 Nov 2008 01:29 PM CST One of the labs that I visited during my job interviews had the most amazing atmosphere of any lab that I have been in during my work thus far. Undeniably, it didn’t hurt that everything was clean and equipment was mostly boxed up, which meant there was no clutter to make the space less appealing. But the open sky windows and big glass windows didn’t hurt either, as well as the high, raised ceilings and plenty of space in between benchtops. Also, the adjacent lab was separated by an unclosed wall, which had the effect of making the space seem even larger. I was really looking forward to the chance to work there, knowing how much a working environment can affect your mood and, ultimately, productivity. The lab that I’m in now has no windows, although I have plenty of benchtop and desk areas, and there’s very few people around to make noise or provide distraction, which can be a good or bad thing depending on how you want to to look at it. My question is: what is your lab environment like? Do you feel like it helps you be more productive, or could there definitely be some improvments that would make it much better?         |
| Sequencing one genome at a time is so last week [Genetic Future] Posted: 14 Nov 2008 01:18 PM CST Last week I posted on the publication of three papers in Nature describing whole-genome sequencing using next-generation technology: one African genome, one Asian genome, and two genomes from a female cancer patient (one from her cancer cells and one from healthy skin tissue). At the end of that post I noted that the era of the single-genome publication is drawing to a close as the age of population genomics commences. Today GenomeWeb News reports from the American Society of Human Genetics meeting on the biggest current foray into the field of population genomics: the 1000 Genomes Project. The project aims to sequence somewhere between 1,200 and 1,500 whole genomes at low coverage (sequencing each base an average of 2 to 4 times), providing a powerful catalogue of human genetic variation extending down into the variants below 1% in frequency. At ASHG, David Altshuler announced the near-completion of three pilot projects for the 1KG project and the generation thus far of 3.8 terabases (that's 3.8 million million bases) of sequence data. Over the last two months, according to GenomeWeb News, "the team deposited as much data each week as was present in GenBank when the effort began". That's a mind-boggling amount of data, and an indicator of the staggering volumes of data still to come: in 2009 the project is expected to generate about 250 times that volume of sequence. The hard part of human genomics - linking sequence variation to disease risk and other traits - is still to come, but the 1KG project (as Brendan Maher calls it) will pave the way for these difficult experiments, both by creating a map of human genetic variation and by driving the development of the tools required for large-scale human genome sequencing. Exciting times... Read the comments on this post...      |
| Posted: 14 Nov 2008 01:00 PM CST Masha Gessen was faced with a terrifying choice: cut off her breasts, and possibly save herself from cancer, or use them to feed her child. Read the rest of this post... | Read the comments on this post... |
| ERIC, E. coli, and you [The Tree of Life] Posted: 14 Nov 2008 12:32 PM CST Just a little posting here. I have been playing around with a website called ERIC and thought I would post about it since it seems pretty useful. ERIC - Enteropathogen Resource Integration Center is one of eight Bioinformatics Resource Centers (BRC) for Biodefense and Emerging/Re-Emerging Infectious Diseases. Funded by the National Institute of Allergy and Infectious Diseases (NIAID), ERIC serves as an information resource for five members of the bacterial family Enterobacteriaceae.So if you want to learn more about E. coli and its relatives and their genomes, this is a good place to start         |
| Elementary science experiment [Bayblab] Posted: 14 Nov 2008 11:59 AM CST A total FOB (friend of the bayblab), who's all talk no post, recently sent me this email about an interesting science story she heard on CBC. Pretty impressive for an elementary student. thought this is a cool story... dad (geologist) studies paleoclimatology    |
| Shameless Self Promotion [The Daily Transcript] Posted: 14 Nov 2008 10:35 AM CST If you were flipping through the latest issue of Cell, you may have noticed an article entitled Tough Challenges for the Next NIH Director. Yes, way at the bottom that's yours truly making some remarks about the problems of postdoc-hood and how the next NIH director may have to rethink the academic pipeline. Feel free to leave your thoughts in the comment section. Read the comments on this post... |
| Blogs and teaching. [Genomicron] Posted: 14 Nov 2008 08:16 AM CST There are many beneficial aspects to reading and writing blogs about science. I have found that they are often much better than news feeds (which generally are uncritical repetitions of press releases) for learning about research in areas other than my own specialization. This also makes them very useful for teaching, as new examples that otherwise might be overlooked can be found and added to the course material. Case in point, Not Exactly Rocket Science (a blog you should be reading, btw) has a post about a new paper in today's Cell in which yeast behave in a cooperative way if they possess a certain "green beard" gene (Smukalla et al. 2008; see also Brown and Buckling 2008). I introduced green beard genes to my upper year evolution course back when I discussed altruism, but it so happens that this afternoon I will be covering major transitions, including the evolution of multicellularity. This paper provides a great way to tie the earlier discussion about altruism to the concept of very basic cooperative cell behaviour, cell adhesion, etc. Plus, I enjoy telling the class "Here is a paper that came out this morning...".   |
| Vitamin D Dilemma - To D or Not To D [Sciencebase Science Blog] Posted: 14 Nov 2008 07:00 AM CST
Hayes explains that calcitriol, the active form of vitamin D, could be the oral agent, that medics have been searching for to provide a quick, simple, and inexpensive way to protect us when the warning sirens sound. Having spoken to various researchers with markedly different views on vitamin D, its benefits and its its potentially detrimental effects on health, I wasn’t too sure about how adding yet another dietary supplement to our daily intake would be beneficial. I asked Hayes to expand. “One should get vitamin D3 either from solar irradiation of the skin or from dietary supplementation,” he told me, “I personally take 2000 IU daily which is obtained without a physician’s prescription…2000 IU is definitely safe, I can dig up the documentation.” There are claims from some quarters that getting plenty of sun is a good thing, and they’ve published a guide, which I mentioned in a post on how to sunbathe safely, but the cancer research charities suggest that really there is no safe way to get a sun tan and that a dietary supplement of vitamin D would be a much safer alternative to increasing one’s exposure to the sun. However, the only prescription vitamin D preparation available in the US and the US is vitamin D2 (ergocalciferol). “Vitamin D2 should not be regarded as a nutrient suitable for supplementation or fortification,” Hayes says, “physicians resorting to the use of vitamin D2 should be aware of its markedly lower potency and shorter duration of action relative to vitamin D3.” As such, he asserts that you should get vitamin D3 either from the sun or through dietary supplementation. Unfortunately, vitamin D, being several different compounds with different physiological activities, is not a clearcut medical case. There are some who see it as a “clap-hands-hosanna”, but there are others, particularly scientists associated with the Marshall Protocol, and in the California non-profit association Autoimmunity Research Foundation, who see it as something to be avoided. Biomedical researcher Trevor Marshall, who runs the ARF, has produced what has been described as the first working model of vitamin D metabolism. Proal explains that the model, which demonstrates the complexity of vitamin D metabolism, emphasizes the importance of distinguishing between the different forms of vitamin D. According to ARF scientists, the form of vitamin D that Hayes recommends and takes himself - that derived from supplements and excessive sun exposure - is apparently converted into 25-hydroxyvitamin-D or calcidiol. “Unfortunately,” says Proal, “molecular biologists have long realized that 25-hydroxyvitamin-D3 is actually a potent secosteroid. Marshall’s research indicates that, like corticosteroid medications, it actually slows the immune response, and this ultimately allows chronic bacterial infection to exist uninhibited, which could be the ultimate cause of such inflammation. “Under such circumstances,” says Proal, “25-hydroxyvitamin D’s ability to slow the immune response allows for short-term relief, but aggravates the disease over the long-term by allowing chronic pathogens to proliferate with much greater ease.” The difference Reporting for CBCnews.ca, Stephen Strauss explains how Marshall researchers looked at more than 1000 people with a host of autoimmune and related diseases. “When combined with a particular drug treatment program, people who consciously tried not to take vitamin D and stayed out of the sun showed an often-dramatic reduction in symptoms. Dramatic means a reduction of 81 per cent in symptoms for people suffering from conditions ranging from Type 2 diabetes, to rheumatoid arthritis, to multiple sclerosis, Lyme disease and Crohn’s disease.” It seems that some forms of vitamin D have steroidal activity and rather than helping fight disease it modulates the immune system and potentially increases inflammation. Marshall explained the apparent paradox in the journal BioEssays: “For half a century, medical science has been noting the association between vitamin D serum levels and disease. What developed has been a concept of ‘vitamin D deficiency’ based solely on the notion that ‘low’ vitamin D serum levels somehow cause disease processes. But this ignores the alternative hypothesis — that the disease processes themselves regulate the vitamin D metabolism —that the observed ‘low’ values of vitamin D in disease are a result of the disease process, not the cause.” I asked Amy Proal, a medical researcher and an advocate of the Marshall Protocol, for her thoughts on vitamin D. “Who is getting better as the medical community dishes out more and more vitamin D,” she asked in response. She points to a report in The New York Times that says children as young as five years are developing kidney stones and that infant eczema is rising at an alarming rate, these trends and the trend towards obesity, she says are not what one would se with genetic or autoimmune diseases. “They are trends that indicate chronic infection egged on by the use of immmunosuppressive steroids, and vitamin D fortification, among other trends of modern medicine,” she says. The NYT article alludes to the recent melamine in milk scandal in China, but stakes its claim on common salt (sodium chloride) being to blame for the rise in kidney stone incidence in the US. So, is vitamin D good or bad? Either way, which forms should we allow ourselves to be exposed to and which forms should we really avoid? And, if there’s a radiation incident… Daniel P. Hayes (2008). The protection afforded by vitamin D against low radiation damage International Journal of Low Radiation, 5 (4) DOI: 10.1504/IJLR.2008.020980 Vitamin D Dilemma - To D or Not To D      |
| Oh Dr. Gene Sherpa… [Think Gene] Posted: 14 Nov 2008 05:28 AM CST
But seriously, every time the children aren’t exactly like how they remember their families. Well, that was easy. Let’s celebrate by taking a break from Serious Business with a rerun of my favorite funny picture.    |
| Navigenics’ Medical Advice [Think Gene] Posted: 13 Nov 2008 11:07 PM CST As mentioned in The Unusually High Standards of Genomics, here is a screenshot of Navigenics’ “[medical advice] that is not [medical advice]” highlighted and captured directly from Navigenics’ own website. [pdf local copy of press release]  Navigenics Medical Advice Frankly, I don’t have a problem with Navigenics so much as I do with the pathetic legal culture in America that tolerates the sale of “[blank] that is not [blank].” Why can’t Navigenics simply make no statement regarding its status as “medical advice” and Navigenics can be judged as it is —as medical advice? Since when was truth contingent on some disclaimer? Oh right, since America became a marketing economy, and anybody can say anything as long as it’s “not willfully false.” But “not willfully false” is not “demonstrably true,” and while that might be good enough to sell cars, soda, and tampons, it’s not good enough for medicine. America has staked a precious few critical domains, like medicine, in which statements must be demonstrably true. Navigenics is trying to circumvent that standard by trying to claim its service should only be held to the same standard of truth we demand from everything else: none. And they’re succeeding! This is a press release. It was sent to every news agency. It has been live on the web for months. And who asked:
Instead, I read a bunch of limp-wristed bleating about unspecified calls for “more regulation.” What regulation? You mean more regulation like the kind that regulated finance? The kind where I can sell “[blank] that is not [blank]” and everybody sort of hopes that everything is OK because they have no idea what is going on but somebody once sort of alluded that there is an Authoritative Corpus of Abstruse Law that somebody probably knows about somewhere and everything is probably “being taken care of” and besides you have work in the morning and you have your own problems and that’s how democracy works anyways? Do you mean that there should be “regulation” that specifies that words have meanings? Good luck. I know, how about we cut the double-speak and demand as free-thinking, self-organizing, intelligent individuals that truth is truth. If you see something wrong, then say so specifically and clearly instead of vapidly announcing that somebody else should do so for you through “regulation.” Truth is not what some guy probably wrote in some document that one time but somebody will probably let us know if there’s a problem and anyways they probably couldn’t have done that if it was wrong because somebody would have sued them or something. The law is only as good as the people it governs. Do not let Navigenics get away with selling the credit swaps of medicine!    |
| Posted: 13 Nov 2008 10:40 PM CST Oh, I simply cannot resist posting this lovely review of our book "Tomorrow's Table" that I just saw on Amazon. Thanks Phil, whoever you are! A pleasant surprise, August 30, 2008 By Phil Stewart "Real Name gets a ™?" (Gainesville, FL USA) - I was given this book by a friend who is an organic "true believer" and when he handed me a book I sort of expect a re-hashing of the usual pro-organics arguments I've heard many times over the years. Instead I was pleasantly surprised. The book is straight forward, well-reasoned, and accessible. I have a background in agriculture and molecular biology, and so at times I found the science a tad too simplistic to strongly hold my interest, but I suspect that for the average reader, it strikes a nice balance between addressing the subject fully and excessive complexity and jargon. The case they build is in my view quite compelling, and I hope this book serves to open many minds. When I was starting out in plant science, I remember a professor telling me that when the first transgenics were being developed, he really thought the organics crowd would be the biggest supporters. "We'd just come up with a solution to their biggest problems, but instead they decided we were the enemy". Although I think that organics are, ultimately, a positive development in agriculture, they are like most "movements" a mixture of real reasons and irrational, emotional impulses. Although organic agriculture has been an important step towards a sustainable future, it has brought with it a fair amount of baggage, based on not on science or reason, but on a nostalgic idealization of traditional agriculture--even though such agriculture was often neither natural nor sustainable nor especially desirable, even then. The fear of genetic engineering seems to me to come from that deeply conservative undercurrent in an otherwise progressive movement. By making the facts behind genetic engineering and its impacts on agriculture and environment accessible to a general audience, this book can hopefully be a step towards calming that reactionary impulse. It helps too that it is also an easy and enjoyable read. By the end I felt as though I'd kind of gotten to know the authors (in fact since we don't live all that far apart and work in vaguely the same field, it crossed my mind that I might someday bump into them). The style is casual without being superfluous, making it easy to lose yourself in the book. I started this book as I tended the grill before dinner, and finished it as I went to bed the same night. Putting aside the genetic engineering part, even, this book is also simply one of the best scientific presentations of organic agriculture I have read, in that it is soundly grounded in the literature and does not over-reach, while remaining staunchly and reasonably pro-organic. There are few other books on the topic I can say the same for. All in all a good read about an important topic. |
| Posted: 13 Nov 2008 10:34 PM CST Well, I had to test Scribd with something. Why not use a document on the Massachusetts Life Sciences Industry? Scribd is sort of like the YouTube of electronic paper. I found Scribd from TomJoe's post about Life on Mars. His PowerPoint talk is really much more interesting than the life science document that I uploaded as a test, but since you're here anyway, you might as well take a look. Read the rest of this post... | Read the comments on this post... |
| Suggestions for Obama's CTO [The Tree of Life] Posted: 13 Nov 2008 09:23 PM CST |
Radiological health expert Daniel Hayes who works at the New York City Department of Health and Mental Hygiene recent published on the subject of low dose radiation and the possibility that a form of vitamin D could be the key to protecting us from background radiation and perhaps save lives following a nuclear incident or terrorist attack involving a so-called dirty bomb.
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