Posted: 09 Oct 2008 05:33 PM CDT
A review of Tomorrow's Table has just come out in Nature Biotechnolgy. Check it out here.
A timely marriage
Having spent most of the past 25 years working in agricultural biotechnology, I cringe each time I find myself trapped in some inextricable situation where a complete stranger asks me what I do for a living. I know that an honest answer to a seemingly innocent question inevitably brings forth an uninvited litany of urban myths, unsubstantiated opinions, technological misconceptions and other half-baked nonsense best left to the pages of The National Enquirer. What's worse, the inquisitive stranger will usually expect me to defend my career choice. I can tell you from painful experience that "It pays well," is never a well-received justification.
Once, while having breakfast in Des Moines, Iowa, in the mid-1990s, I tried to head off the issue by telling my waitress that I was a plant breeder—assuming that someone from the Midwest would know what a plant breeder does, and that my answer would discourage further comment. No such luck: the waitress put down her pot of coffee, set down the Marlboro that until then I assumed was superglued to the lower left corner of her mouth, looked me straight in the eye and informed me that if I asked for her opinion plant breeding was simply, "Half genetics...and half heredity!" She then menacingly challenged me to tell her something different. But now comes a book that sets out to provide the general reader with a fair and balanced account of what folks in my line of business actually do, set within the intriguing framework of a discussion between married practitioners around the benefits and issues associated with two supposedly antagonistic trends in modern farming: transgenics and organics.
The authors of Tomorrow's Table: Organic Farming, Genetics, and the Future of Food are Pam Ronald, a University of California, Davis, geneticist, who has spent her professional career dissecting disease resistance and flooding tolerance in rice (disclaimer: I've known Ronald for over 20 years including, while at a previous employer, helping to spin out her venture from UC-Davis back when she was a budding tenurepreneur—an academic who mitigates the employment risk of starting a new company by not giving up their tenured faculty position—and more recently as a scientific advisory board member at Targeted Growth); and Raoul Adamchak, an organic farmer for over 25 years, manager of the certified organic farm on the UC-Davis campus and an inspector and past president of California Certified Organic Farmers, and Ronald's husband. The book successfully integrates the knowledge and insights of a practicing plant geneticist and the practical training of a long-time organic farmer to consider a range of arguments both for and against organic farming and genetic engineering in a manner that is conversational and informative, rather than confrontational or overly biased. Ronald and Adamchak suggest that both approaches to modern farming will contribute significantly towards the sustainable production of food in the future, and argue that the continuing sustainability and productivity in agriculture will benefit from the integration of the most useful aspects of transgenic crops, such as the reduction in the need for crop protection chemicals, the potential reduced water and nitrogen fertilizer requirements of next-generation agronomic trait products, with the more productive of organic farming practices, including a heightened awareness of environmental stewardship issues and a focus, whether real or perceived, on food quality.
Who could argue with this well-reasoned position? Well, as most readers of this publication are aware, some consumers, especially those living in Europe, take exception to transgenic agriculture, viewing genetically modified (GM) crops as unnatural, potentially unsafe to eat, environmentally disruptive or aiding the corporatization of global agriculture. However, I have not had one single European visitor show up at my home with their luggage packed full of enough non-GM foods to support them through their lengthy stay in the United States. On the contrary, they consistently display no hesitation about benefiting from the ample supply of GM-derived foods in my kitchen, all prepared with lavish helpings of GM canola oil, presumably so they can generate the energy needed to stuff their bulging suitcases full of affordable GM cotton goods for the trip back home.
Tomorrow's Table is not just another biology textbook posing as a general reader in a shallow attempt to garner extravagant royalty payments for their academic authors, but one of the best, most balanced accounts of transgenic agriculture that I have read. It will appeal to laypeople, seasoned practitioners and anyone who cares about the future of sustainable farming. It also includes an intimate look into the private lives of the authors, their family and friends—and furthermore, it's also a cookbook! Chapters are generously peppered with details of the elaborate meals the couple assemble on a nightly basis. All of this makes for an even more interesting read. My only regret is that this kind of book wasn't available when I was having breakfast back at Denny's in Des Moines, but the good news is that going forward I'll be providing my European visitors with a copy of Tomorrow's Table for their flights home.
Posted: 09 Oct 2008 03:16 PM CDT
Another third-gen sequencing company has posted some info. Thanks to genseq for reposting it here! See below for the announcement. -=ECO **************** " Mobious Biosystems is proud to introduce the Nexus I, the worlds first and only 24hr Genome Sequencer. Drawing from over ten years experience in the field of next generation sequencing and employing unique biophysical & biochemical techniques the Nexus I offers unparalleled throughput and accuracy. System Benefits: Over 6...
Read more and join the community...
Posted: 09 Oct 2008 12:45 PM CDT
You've probably read an article or two that reports the results of a race-based investigation. Perhaps it was a study of health disparities, a survey of patient attitudes, an examination of a race-based intervention or new medication to be marketed to a specific race-based demographic. If you wanted to do a systematic review of these papers, you might be vexed by the difficulty of finding a common, valid definition of "race". As a socially-constructed category, defining the limits of race and ethnicity is a slippery business and one that has a problematic past in the history of science and medicine. With this in mind, Vural Ozdemir, Janice E. Graham and Beatrice Godard make a call for clarity in "Race as a variable in pharmacogenomics science: from empirical ethics to publication standards" (Pharmacogenet Genomics. 2008 Oct;18(10):837-41. - PubMed CiteULike). The authors argue for the use of empirical ethics research to inform the development of new publication standards to "minimize the drift from descriptive to attributive use of race in publications". In this context, empirical ethics, or "applied social science methodologies … to better understand, for example, the 'lived' experiences of user groups", would identify blind-spots in predictive health research and would help researchers, regulators, policy-makers, and editors "differentiate between an imprecise (yet measurable) predictive biomarker, from a construct such as race".
Given the uproar around BiDiL and other race-based pharmacogenomic ventures, the authors have made a timely, if not over-due, call for publishers and ethics researchers to collaborate in developing standards for the use of the controversial category in published research. - J.O.
Posted: 09 Oct 2008 12:30 PM CDT
The Penn State Alumni Association has produced trading cards featuring the best and the brightest of the university's faculty (Pa. trading cards highlight brains, not brawn). The cards are only available at University President Graham Spanier's tailgate parties on home football weekends. The biologists featured include entomologist Jim Tumlinson and molecular evolution pioneer Masatoshi Nei.
I haven't been able to find a complete list of all ten faculty members featured, and I don't think that individual images of the ten cards are available online. If anyone can track them down, post a link in the comments.
Update: Nina Fedoroff has a card as well.Read the comments on this post...
Posted: 09 Oct 2008 11:21 AM CDT
This paper has been discussed by Razib at GNXP, and probably others. I thought I would take a closer look at it myself.
One of the main findings here is the north-south gradient within England in the frequency of the lactase persistence allele.
But they also examine relationships between this genotype and health measures in order to uncover the mechanism by which lactase persistence may have been selected for.
For example, did lactase persistence arise due to the benefits (sugar, protein, fat) or because it enabled one to avoid the ill effects of lactose non-persitence (adverse health reactions)? In this paper, they test for associations between the LCT genotype and various health-related measures.
They also have a good discussion about the selection pressures that may have led to the lactase persistence trait being favored. Among the hypotheses, many of which I had never heard of, as outlined in the paper:
1) "nutritional (and survival) advantage of milk consumption in populations that have milk availability"
2) "the calcium absorption hypothesis which considers the ability to use milk as of particular importance for high latitude
populations with low ultraviolet light exposure who are thus subject to potential vitamin D deficiency and poor calcium absorption and for whom the calcium absorption-stimulating effect of lactose would increase fitness."
3) "a reduced diarrhoeal disease mortality hypothesis that considers that, in populations that have become high consumers of milk, this consumption will increase risk of diarrhoeal disease in individuals who are not lactase persistent and thus select for lactase persistence"
4) specifically for African populations: "in arid regions with animal husbandry practices allowing access to milk, the ability to use milk has a selective advantage through the provision of water and electrolytes"
5) "the enhanced fertility by early weaning hypothesis that postulates that lactase persistence leads to earlier weaning and that earlier cessation of breastfeeding reduces the infertile period following each birth"
It doesn't seem like this study provides any conclusive or even suggestive evidence in favor or against any of these hypotheses, although there is some data that does goes against the diarrhea hypothesis:
"the consequences of prolonged childhood diarrhoeal disease that might be expected in survivors – shorter body height, leg length and perhaps higher blood pressure – were not seen in our data"Lactase persistence-related genetic variant: population substructure and health outcomes
George Davey Smith, Debbie A Lawlor, Nic J Timpson, Jamil Baban, Matt Kiessling, Ian N M Day and Shah Ebrahim
European Journal of Human Genetics advance online
Abstract: Lactase persistence is an autosomal-dominant trait that is common in European-derived populations. A basic tendency for lactase persistence to increase from the southeast to the northwest across European populations has been noted, but such trends within countries have not been extensively studied. We genotyped the C/T-13910 variant (rs4988235) that constitutes the putatively causal allele for lactase persistence (T allele representing persistence) in a general population sample of 3344 women aged 60–79 years from 23 towns across Britain. We found an overall frequency of 0.253 for the C (lactase non-persistence) allele, but with considerable gradients of decreasing frequency from the south to the north and from the east to the west of Britain for this allele. Daily sunlight was positively related to C (non-persistence) allele prevalence. However, sunlight exposure and latitude are strongly correlated, and it was not possible to identify which is the primary factor statistically underlying the distribution of lactase persistence. The C/T-13910 variant (rs4988235) was not related to drinking milk or bone health (although drinking milk itself was protective of bone health), and was essentially unrelated to a wide range of other lifestyle, health and demographic characteristics. One exception was general health being rated as being poor or fair, for which there was an odds ratio of 1.38 (1.04, 1.84) for women homozygous for the C allele; on adjustment for latitude and longitude of place of birth, this attenuated to 1.19 (0.87, 1.64). The lactase persistence variant could contribute to the examination of data for the existence of, and then statistical control for, population substructure in genetic association studies.
Posted: 09 Oct 2008 10:56 AM CDT
Two gold medals for reportergenomics! Last year was the gene targeting in mouse (knock-in, knock-out). This year is the GFP reporter protein. By combining animal engineering with molecular imaging techniques it has become possible to conduct dynamic studies on specific molecular processes in living animals. Synergism is more than two Nobels. Great!
Posted: 09 Oct 2008 08:07 AM CDT
This year, the topic of direct-to-consumer genetic testing has been highly discussed and debated in the media. A previous post discusses the different types of genetic testing available to consumers today. At particular issue is the actions or behavioral changes someone might make after learning about his or her health risks and predispositions via a [...]
Posted: 09 Oct 2008 08:00 AM CDT
Those words come from Eric Schmidt, talking about the Internet. The context of the statement was magazines and publishing. Got me thinking how in this day and age do we measure brands, especially in the context of science. This fits in well with the discussion we are having about scientific publishing, science 2.0, etc etc.
What is a brand? In today’s world, you cannot limit brands to macro-brands, a brand like Nature or PLoS. You have to take into account the personal brand, something we build via our actions and statements online. Take someone like Russ Altman or Jonathan Eisen. They have brands independent of their online presence. That they are online adds to their brand, but due to who they are we lap on to their words. But they do so at some risk to their existing brands. What if the quality of their writing was inferior? What if it turns out they really didn’t have anything interesting to say? Personally, I feel this is a big part what keeps many PIs and faculty away from penning their thoughts in a public forum like a blog.
Then there are young scientists; graduate students, postdocs, young faculty, people early in their careers. Their personal brand is a very different entity. It too comes with some risk, but in general, and perhaps not surprisingly, you will find that many find it easier to pen their thoughts in public. Part of it is the world they live in, a world of social networks and Twitter, and part is the desire to express their thoughts and impressions. Whether they know it or not, whether they like it or not, that side is as much part of their brand as their publications and work, perhaps even more so.
But that’s not all. Clay Shirky talks about filter failure. That is not just about tools. It’s about our inability to channel trust and identify those brands to scale. We can do it on a small scale, but how do we scale it to the web? How do we scale it beyond our first or second line of trust? Jon Udell likes to talk about the circle of trust. The question is how do we scale that. Personally, that’s how I use something like Lijit or the Life Scientists, but even that does not do much in the way of autodiscovery. How do you trust content delivered to you based on your interests? How do you measure reputation on the web to scale? What should the reputation be measured against? All questions we will need to answer over the next few years. Personally I feel that any such filter will have to combing an individuals circle of trust and a broader online reputation.
Posted: 09 Oct 2008 06:54 AM CDT
I just finished reading an article by Alondra Nelson in the journal Social Studies of Science entitled "Bio Science: Genetic Genealogy Testing and the Pursuit of African Ancestry" (Social Studies of Science 2008 38: 759-783). Dr. Nelson is Assistant Professor of Sociology, African American Studies and American Studies at Yale University.
This very interesting and insightful article aligns with my own premise, which I’ve stated previously, that receiving the results of a genetic genealogy test is only the beginning of the journey for any individual interested in their own identity or genealogy.
Based on her research in this area, Dr. Nelson writes about the complex interpretation of the results of genetic genealogy testing by African-Americans and black British. Rather than completely altering their preconceived biographical narratives based on the results of testing, many people struggle to mesh genetic results with these narratives. From the abstract:
Nelson goes on to provide a deeper view into how some consumers of genetic genealogy “exercise some control over the interpretation of their test results” to formulate their own narrative “despite the presumption of [the tests’] conclusiveness”:
I agree with Dr. Nelson’s assessment because I’ve seen it happen numerous times myself. And, for at least two reasons, even the scientist in me finds support for why people might interpret their results personally: first, the results of a genetic genealogy test do not define me, since I am more than my DNA. Second, genetic genealogy is still a young and rapidly developing field of science.
What do you think? Should genetic genealogy consumers accept the results as definitive, or are they subject to personal interpretation?
As part of the analysis, Dr. Nelson describes the effect testing can have on some individuals, in which “the receipt of genetic facts about ancestry open up new questions about identity and belonging, rather than settling them absolutely,” and can create a “lack of orientation.” She terms this effect “genealogical disorientation.” I think this is a terrific term, and is undoubtedly one of the possible side-effects of genetic genealogy.
In fact, I have personally experienced my own genealogical disorientation, although it was minor compared to others. My Y-DNA test revealed an anomaly found in only a tiny fraction of males - all of whom from England - and which had never been identified in Germany (where my ancestor was supposed to have originated). This led me to wonder if there had been an NPE (non-paternal event) in my line and thus that my surname was possibly incorrect. However, since I received my results others with nearby German origins have been shown to possess this particular anomaly, and thus my genealogical disorientation has subsided.
Where you disoriented when you first discovered your results?
So does the possibility of personal interpretation or genealogical disorientation mean that genetic genealogy is dangerous or unwarranted? My answer to that question, perhaps unsurprisingly, is a resounding no. It means that scientists, genetic genealogists, and testing companies must be aware of these possibilities and must continue to educate and support individuals who are interested in genetic genealogy testing.
Posted: 09 Oct 2008 06:44 AM CDT
After the initial hullaballoo with the Large Hadron Collider going online, it quickly - in a move that wasn't reported with nearly the enthusiasm - was taken offline for repairs before it even had a chance to destroy the world in a black hole.
While the team is tinkering around inside the LHC, it gives us an opportunity to follow up on AC's recent "what would happen if..." post. In this case, what would happen if you were hit by the beam of a particle accelerator?
Believe it or not, it's happened before. Thirty years ago, Anatoli Bugorski was working on the Soviet U-70 synchotron repairing malfunctioning equipment. He stuck his head into the area where the beam was running, but apparantly the safety mechanisms were not. He saw a flash of light "brighter than a thousand suns" but the initial encounter with the beam was otherwise painless. WIRED magazine has more on the outcome:
The left side of his face swollen beyond recognition, Bugorski was taken to a clinic in Moscow so that doctors could observe his death over the following two to three weeks.According to his wikipdia entry, Bugorski lost the hearing of his left ear and the fatigue of mental work increased, but despite the accident he was still able to finish his Ph.D. Still, I hope the scientists at the LHC really have it turned off before stepping in there.
Posted: 09 Oct 2008 05:55 AM CDT
I just came across a very interesting book relating to biotechnology, but sadly it’s not due out until next year. By Janine Benyus and Gunter Pauli, Nature’s 100 Best: World-Changing Innovations Inspired By Nature, this book promises to tell of stories of past innovations coming from biology.
There is no landfill in nature, only a ready market for everything that is produced. Entrepreneurs and readers of all stripes will learn that our biological elders have already developed the technologies needed to: Keep the Earth's climate tuned for the needs of all life-forms; Harvest, store, and distribute energy locally, cheaply, and in a variety of ways; Separate salt from water with sun power; Sequester carbon while increasing the fertility of soils and sea; Spin CO2 into durable plastics that biodegrade on cue; Produce fiber, food, and fuel without erosion or pesticides; Manufacture without fossil-fuel driven heat, pressures, and toxins; Stay germ-free without developing antibiotic resistance; Bounce back from floods, hurricanes, earthquakes, wind, disease, and fire; Keep an incredibly complex economy productive for all; Innovate as changes in the environment require while always reducing their footprint to zero; And much more.
Nice description. Now it makes me want to hear about the 100 Best of Nature themselves.
Posted: 09 Oct 2008 05:39 AM CDT
I feel rationally obligated to distrust anything self-promoted as “Web 2.0″ in the same way I distrust statistics tacked with some vague quality like “40% more kick!” It’s as if those tacks are nailed right in to the body of Science itself, and I feel its pain. I feel it. Nonetheless, as I can be trusted to regularly grease the world economy $3.29 USD every late night caffeine sortie at the 7/11 across the street, there’s nothing physically impairing me from both believing that savant-like super powers wrought at the heights of all human achievement will give me more energy and help my money work for me while simultaneously loathing the idiocy that same electric blue sans-serif salespitch will sap my attention and wallet if only they could brand their goods with some impressive looking number. You know, like science and stuff. It’s as if behind the decimal point lies a secret realm where mere digits morph into runes of ancient magic, drawing the true, terrible power of tenth decimal place into a furious ball of psychogenic witchcraft burned by marketers into every web service and sugary softdrink for their duplicitous intent of short-circuiting my brain —not impairing rational thought itself, merely its ability to keep my money in my pocket and my faith to myself. It’s a near optimal function to illicit self-disgust.
Hey, I have an idea for a radical new financial instrument, it’s called: the hundredth decimal place. With marketing that tight, I may as well be selling soma to cashiers, right? It’s a brave new world out here on the interwebs, and I’ve got the confidence interval for you right anterior to my magic symbol “%.”
What was I talking about? Oh right.
Bertalan Meskó of Science Roll has officially launched Webicina, a service that sells education material and consulting to doctors about using the Internet and helps them launch a website. Regarding doctor blogs: Dr. Steven Murphy said today about his doctor blog, Gene Sherpas: “all they good things that happened to me this year have come from my blog.” Webicina is a valuable service that I endorse that will help your professional career as a medical professional —and it’s fun, too.
Here’s a funny picture of a dancing little boy wearing decimal point on his shirt. I want you think of it every time somebody uses a decimal point or any other statistic without justifying their significant digits or measurement confidence.
PS: I never want to see the expression “Web 2.0″ ever again, and God help you if I see anybody try to peddle *shutter* “Web 3.0.” To a lesser extent, that goes for that “59.5%” penetrance estimate for g2019s LRRK2 report at 23andMe, too.
Posted: 09 Oct 2008 04:17 AM CDT
CLC bio announced today an agreement with the J. Craig Venter Institute, a not-for profit genomic-focused research institute. The accord consists of a multi-year site license for the entire CLC bio bioinformatics suite of products. The goal is to implement CLC bio's enterprise solution as a scientific platform across all JCVI sites. This enterprise solution [...]
Posted: 09 Oct 2008 02:48 AM CDT
A new paper that just came out by friends and colleeagues of mine from my days at TIGR (Comparative genomics of the neglected human malaria parasite : Plasmodium vivax) reminded me I wanted to blog about how it is a good thing that Nature is using a Creative Commons License for some (maybe all) genome sequencing papers they publish (at least in the main Nature journal). They do not use the fully open CC license that PLoS/BMC use but hey, it is better than many other journals who claim they are making this "Open."
The license they use is
"This article is distributed under the terms of the Creative Commons Attribution-Non-Commercial-Share Alike licence (http://creativecommons.org/licenses/by-nc-sa/3.0/), which permits distribution, and reproduction in any medium, provided the original author and source are credited. This licence does not permit commercial exploitation, and derivative works must be licensed under the same or similar licence."Too bad they do not do this for all the papers they publish. Maybe Chris Gunter can convince them to do that even though she is now at Hudson Alpha. I think when she was at Nature she helped convince them to do this for genome papers.
Posted: 08 Oct 2008 09:43 PM CDT
The idea of writing this particular grant proposal at this specific time clearly makes no sense in the framework of my life, with teaching and traveling and kids and a million other things to do. It would border on the insane to try to do this now and to do it well. Yet the intrinsic impossibility of writing this proposal stays with me. It was with me in the pool this morning, where all was quiet except for the sound of strokes and flip turns in the water. It is with me now. I cannot resist thinking through some of our latest results.
And so it begins. Before I fully realize it, I am sucked into a whirlpool of ideas. I float on them, soon lost in the absolute freedom of thinking. I am absolutely engaged.
I am fascinated with something no one understands and only a few of us would care to. I am consumed with the desire to think through this mystery, to know it. As Thoreau said, "to gnaw at it, bury it, unearth it and gnaw at it still". It is exhilarating to be drawn into the deep realm of the undiscovered and it is a challenge to harness the wild power of scientific ideas by writing about them. I want to explain our research results clearly to my colleagues, propose a model and ask them "don't you see it too?" My intellect is engaged and my heart too, because I love this work.
I am oblivious to the looming demands of the 100 students that I will begin teaching tomorrow, deaf to the requests of colleagues to help out on this or that, rushed with my graduate students that need my advice, and indifferent to the calls of my husband for my attention. Yes, tonight, I will surely even be slow to respond to the hunger of my children.
"What?" I will say, looking up in a daze from the computer, "Dinnertime already?"
The scaffold of my day, the family schedule that brings a peaceful haven to our lives will be submerged in the pursuit of hypotheses and the design of experiments to test them.
So I adapt myself to the need to write. Oblivious to everything, as if time was ample, except for the pressing and peculiar desire to post this blog before I dive back in.
This post greatly benefited from Annie Dillard's wonderful book "The Writing Life"
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