MedWorm: Geneticists and Genetics Commentators

Life hacks for doctors: slideshow

ScienceRoll — Sat, 17 May 2008 10:03:31 +0100

Joshua Schwimmer, the author of the Efficient MD Blog and the Efficient MD wiki, came up with a fantastic slideshow about life hacks for physicians. According to Wikipedia: The term life hack refers to productivity tricks that programmers devise and employ to cut through information overload and organize their data. (Source: ScienceRoll)

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Hair color and skin pigmentation in europeans

Gene Expression — Sat, 17 May 2008 09:48:00 +0100

A Genome-Wide Association Study Identifies Novel Alleles Associated with Hair Color and Skin Pigmentation:It has been a longstanding hypothesis that human pigmentation is tightly regulated by genetic variation. However, very few genes have been identified that contain common genetic variants associated with human pigmentation. We scanned the genome for genetic variants associated with natural hair color and other pigmentary characteristics in a multi-stage study of more than 10,000 men and women of European ancestry from the United States and Australia. We identified IRF4 and SLC24A4 as loci highly associated with hair color, along with three other regions encompassing known pigmentation genes. Further work is needed to identify the causal variants at these loci. Improved understanding of the genetic determinants of human pigmentation may help identify the molecular mechanisms of pigmentation-associated conditions such as the tanning response and skin cancers.....Taken together, these four regions explain approximately 21.9% of the residual variation in hair color (black-blond) after adjusting for the top four principal components of genetic variation. (Conversely, after adjusting for these four regions, the top four principal components of genetic variation explain 2.6% of the residual variation in hair color.)....There are four regions because areas around HERC2/OCA2 and MAPT showed signals. MAPT is also known as AIM1 and SLC45A2, so this makes 3 genes of the potassium-dependent sodium/calcium exchangers implicated in pigmentation (the other is SLC24A5 obviously). They adjusted for the components of genetic variation so as not to be confounded by population stratification (i.e., there was some ethnic variation among their whites and so you don't have a random mating population).It's in PLOS; you can read the whole thing, etc.Related: Why white people are so colorful!. (Source: Gene Expression)

What is conservatism?

Gene Expression — Sat, 17 May 2008 05:32:00 +0100

Austin Bramwell, Who Are We?:Whatever the difficulties of conservatism, surely one can improve upon the typical performance of those who take it upon themselves to explain it. In place of the conventional accounts, try this one: Conservatism is the defense of legitimacy wherever it happens to exist. "Legitimacy" here is defined in the empirical, Weberian sense: that is, an institution is legitimate if and only if the opinion has become widespread that it is right (for whatever reason or lack thereof) to obey it. The conservative, in short, cultivates obedience to existing institutions. This definition, I submit, has all the advantages of the conventional definitions, none of their defects, and some important advantages of its own. To some extent I think one might make the case that Liberalism is the inverse of Bramwell's definition of Conservatism; what was Liberal in 1920 might be viewed as quite Illiberal today, and what is Liberal in 2008 may seem rather Illiberal in 2028. In any case, I would add that though I don't agree with Bramwell much of the time I'm always impressed with the breadth of his erudition and his good faith attempt to argue rather than scream. Unfortunately most political and social commentary is much closer to the level of morons like Kevin James. Even when one dodges the rank stupidity of someone like James the "punditry" on offer is generally grounded in the incestuous circle-jerk of CW as opposed to facts.Back to Bramwell's point, if you read this blog regularly you know that I have an amateur interest in antiquity, particularly the period of the Roman Empire. Today we assume that Christianity and the Christian clergy are the Conservative party at prayer.1 But if you focus on the 4th and 5th centuries, when Christianity went from being a marginalized sect to the established Church of the Empire, you encounter the fact that the Christian religion was fundamentally one perceived as radical and deeply undermining the legitimacy of the ancients (who were pagans after all).2 In the late 4th century you have powerful pagans such as Symmachus making arguments defending tolerance and subsidy for the ancient faith based on reverence for the institutions and precedents of the past and the ancestors. Fundamentally deeply Conservative reasoning arguing for the legitimacy of what has become before. By the late 5th century the pagan historian Zosimus had become quite dyspeptic toward the new dispensation, bemoaning the fall of the older order and observing the decline of his civilization all around him due to the abandonment of the old gods (Zosimus flourished in the years following the Western Empire's fall). To a great extent Zosimus reminds me of modern Conservatives of a Christian bent, who seem pessimistic by constitution when observing the decline of Christendom and the repudiation of its truths.Today I would suspect that post-Christian Liberals would not necessarily align themselves with radicals for change such as St. Ambrose or rationalist refuters of the relevance of the pagan past such as St. Jerome; rather, their sentiments might be with the pagans who were on the losing end of the march of history because of their current quarrels with Christianity. Similarly, of course Conservatives in the West who are Christian or Christian sympathetic would admire the pugnacity of St. Ambrose and other Church Fathers in overturning thousand year old traditions & customs. The axioms of Christianity made such a rejection of the past eminently rational. And yet if temperament was the guide toward affinity I do not think that this would hold. Church Fathers who admitted pagan learning into the canon offered reasons of utility, as such wisdom might be useful toward Christian ends. A convinced pagan would not have to make such an argument because the classical canon was simply part of the customary education of the non-Christian elite; it was received tradition which needed no reflective analysis and justification. In the 4th century Christian intellectuals dreamed of a new world transformed and shorn of the dead weight of the past with its irrational and unnecessary traditions. Nearly two thousand years later the shoe is on the other foot....1 - Despite the emergence of Leftish Christian movements such as Christian Socialism or the Social Gospel, I think one can make a strong case that on the balance Christianity has been more associated with Conservatism than Liberalism since the French Revolution and the emergence of a modern politics.2 - Obviously the influx of classically educated men such as St. Augustine and the Hellenic patina which accrued to the religion moderates this judgement. (Source: Gene Expression)

Bonus katz

Gene Expression — Sat, 17 May 2008 04:10:00 +0100

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Synthesis

Gene Expression — Sat, 17 May 2008 03:47:00 +0100

About 5 years ago William Gunn was about to start blogging at Gene Expression; but life intervened and it never happened. Well, he's started posting at his own blog regularly, Synthesis, and I recommend it for anyone's RSS feed (you already have it if you are subscribed to The DNA Network, a really great way to introduce yourself to the "genetic blogosphere"; boy have things changed since 2002!). (Source: Gene Expression)

Katz

Gene Expression — Sat, 17 May 2008 03:12:04 +0100

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Invasion of not so tasty truffles.

Fungal Genomes and Comparative Genomics — Fri, 16 May 2008 20:15:14 +0100

(Truffle picture from BBC.com) The BBC (link) has an interesting article about a Chinese Black truffle being found as an invasive species in Italy. The Italian's and European truffle aficionados are worried that the Chinese Black Truffle will outcompete the Perigord Black truffle, which is supposed to be very tasty and the second most expensive truffle by weight, behind only the Piedmont White Truffle. The scientific journal article (link) the BBC cites is present in the new phytologist and was authored by a lab from the "Dipartimento di Biologia Vegetale dell’Università di Torino. Looks like the Chinese truffle species could be a good invasive species model and also economically important. Truffles are interesting its amazing people would pay so much for a mushroom, sadly I can't say if one tastes better than the other since I have not had the chance to try of the truffles mentioned above. © Chris Villalta for Fungal Genomes and Comparative Genomics, 2008. | Permalink | No comment Add to del.icio.us Search blogs linking this post with Technorati Want more on these topics ? Browse the archive of posts filed under adaptation, ascomycota, evolution, fungi, pezizomycota. (Source: Fungal Genomes and Comparative Genomics)

Wubi

Gene Expression — Fri, 16 May 2008 20:04:30 +0100

If you don't have a spare computer, want to try out a Linux distribution, and are a little intimidated by the details of setting up a dual-boot, check out Wubi. It makes a dual-boot pretty much a "one-click" affair, loading up the Ubuntu distribution via a Windows installer. Read the comments on this post... (Source: Gene Expression)

Heavy heart

Gene Sherpas: Personalized Medicine and You — Fri, 16 May 2008 17:43:00 +0100

I vowed I would never post when family took precedence. I have to break that vow today. I wish I didn't but there is something so vitally important that I must share with you. Why is this important? Because it might save more lives than have been previously lost.The scourge of Ovarian and Breast cancer has ravaged several populations. With very few cases of early detection in Ovarian cancer, many women present with spread of the cancer and very poor prognosis. Even more importantly, women who have ovarian cancer and BRCA mutations still are at risk for other cancers including breast cancer.Despite this I have heard comments from Oncologists like "Why do we need testing?" This is why I have pulled myself away from my grief stricken family. To fight this lack of knowledge I have dedicated and arm of Helix Health to educate and promote genomic medicine. This arm will host at minimum monthly podcasts on very important topics. The first of these is Hereditary Breast and Ovarian Cancers and the BRCA genes. The panel will include a patient with BRCA1. She not only happens to be afflicted, she has written about her experiences. Jessica is gifted with the pen and is a very successful writer. Her book "Pretty is What Changes" raises significant issues and serves as a wake up call to clinicians and patients. It serves to empower us all. Jessica will join David Ewing Duncan, bestselling author of Masterminds: Genius, DNA and the Quest to Rewrite Life, and a panel of distinguished medical and legal professionals to discuss how the doctor-patient relationship is changing and what the potential liability is for physicians in this new era of breast & ovarian cancer and genomic medicine.The Sherpa Says:The Helix Health webcast series is dedicated to my grandmother who died at 35 years of age from metastatic breast cancer. Too young for me to ever know. Please sign up for this conference. The information may just save a life......If Helix Health can save just one life then all the hard work is worth it. Please sign up now. Seats are limited, but you can also sign up for the podcast. (Source: Gene Sherpas: Personalized Medicine and You)

What’s on the web (2008 may 15)

ScienceRoll — Thu, 15 May 2008 20:26:36 +0100

Hackers’ posts on epilepsy forum cause migraines, seizures (AP) Greetings from Games for Health 2008 (Resilient Ambassadors of Change) Defining Health 2.0 - Debate Rages On (Health Management Rx) Web 2.0 Business Trends (Health2Zero (Health 2.0)) Introducing The Efficient MD Wiki (The Efficient MD): Visit the Efficient MD Wiki at http://wiki.efficientmd.com. Wikiversity interview: Do you know what Wikiversity is? (Source: ScienceRoll)

Polar bears: a species?

Gene Expression — Thu, 15 May 2008 20:22:07 +0100

Since everyone is talking about the fact that the Polar Bear how become a protected species, I thought I'd point to this cool study, Mitochondrial DNA Phylogeography of the North American Brown Bear and Implications for Conservation. Additionally, check out the figure below.... Read the rest of this post... | Read the comments on this post... (Source: Gene Expression)

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When genetic drift = more adaptation?

Gene Expression — Thu, 15 May 2008 14:58:34 +0100

I know I've posted on this topic before, but I thought I'd revisit it again. You do know that sometimes population bottlenecks can actually result in more variation being freed up for selection? This may strike you as a bit strange; after all, the power of selection to effect phenotypic change is proportional to genetic variance, specifically, additive genetic variance. Population bottlenecks imply a reduction in effective population size, the increase of sample variance across generations, that is, random genetic drift. As population size drops the stochastic change in gene frequencies becames proportionately much greater and alleles rapidly go extinct, or fix, within populations (average time until fixations in generations is proportional to 4Ne, where Ne is effective population size). The homogenizing effect of this dynamic is similar to what might occur with inbreeding, where effective population size is reduced through population substructure, and individuals within the demes quickly become closely related over a few generations. Obviously you know that inbreeding leads to a loss of variation. So how exactly can we extract more additive genetic variance from this? In short, but converting other types of variance.... Read the rest of this post... | Read the comments on this post... (Source: Gene Expression)

One child future?

Gene Expression — Thu, 15 May 2008 06:40:00 +0100

Over the past few days I've heard some coverage of the horrible earthquake in China, and the anguish of the parents whose children were lost as schools collapsed. I was struck when one reporter noted that for many of the parents this was their only child.... That got me thinking about the implications of the one child policy, which is now approaching its 30th year. Most of you who read this weblog know that I think that the Bare Branches argument is a serious one; in short, that the sex imbalance within China due to son-preference will result in social instability. But what about the fact that for so many older Chinese they have only one child to support them in the future? Obviously the greying of the Chinese population is something to keep in mind when we postulate the path of the power of the People's Republic; China's active workforce will start to shrink in the near future, while its dependent class will increase in proportion. But in terms of the irratonal bellicosity which is par for the course for ascendent powers attempting to stake out a place in the sun...I wonder how eager the Chinese will be to send their sons abroad if so many of them are their only sons? Does anyone know of any social science correlating levels of international conflict with TFR? There are obviously angles to analyze this problem theoretically via social evolution, assuming that each offspring is one iteration in a "game".... (Source: Gene Expression)

Glut2 (slc2a2) & sugar intake

Gene Expression — Thu, 15 May 2008 05:21:00 +0100

Via Luis, Genetic variant in the glucose transporter type 2 is associated with higher intakes of sugars in two distinct populations:Glucose sensing in the brain has been proposed to be involved in regulating food intake, but the mechanism is not known. Glucose transporter type 2 (GLUT2)-null mice fail to control their food intake in response to glucose, suggesting a potential role for this transporter as a glucose sensor in the brain. Here we show that individuals with a genetic variation in GLUT2 (Thr110Ile) have a higher daily intake of sugars in two distinct populations. In the first population, compared with individuals with the Thr/Thr genotype, carriers of the Ile allele had a significantly higher intake of sugars as assessed from 3-day food records administered on two separate visits...demonstrating within-population reproducibility. In a second population, carriers of the Ile allele also reported consuming a significantly greater intake of sugars...over a 1-mo period as measured from a food frequency questionnaire. GLUT2 genotypes were not associated with fat, protein, or alcohol intake in either population. These observations were consistent across older and younger adults as well as among subjects with early Type 2 diabetes and healthy individuals. Taken together, our findings show that a genetic variation in GLUT2 is associated with habitual consumption of sugars, suggesting an underlying glucose-sensing mechanism that regulates food intake.Seems like nutrient metabolism & taste preferences are some really important angles for personal genomics; people spend so much time trying to decide what to eat, and arguing about what and how to eat amongst each other. Looks like there's a fair amount of between population difference on this SNP.Related: Posts on taste and genetics. (Source: Gene Expression)

Il1rapl1 and human cognitive ability

Gene Expression — Thu, 15 May 2008 05:06:00 +0100

A study on the correlation between IL1RAPL1 and human cognitive ability:This study aimed to investigate the effects of IL1RAPL1 on the human cognitive ability...Results indicated that genotypes of DXS1218, DXS9896 and rs12847959 were associated with memory/concentration factor intelligence quotient (IQ)...DXS1218 also associated with full IQ, verbal IQ, and performance IQ...rs12847959 were related to verbal comprehension factor and perceptual organization factor IQ...Further study on rat brain revealed that Il1rapl was mainly expressed in memory/concentration-associated encephalic regions, such as hippocampus, dentate fascia, osmesis perithelium, and piriform cortex. mRNA expression levels of Il1rapl in brains of rats with different learning and memory abilities showed significant difference. Combined data suggested that IL1RAPL1 affected human cognitive ability to some extent, especially the memory and concentration capability.Check out the HapMap on that SNP. Remember to wait up on reproducibility here. Sandy has a longer post addressing the radioactivity of such research (obviously he is lying when he says he's an anthropologist; doesn't pass the smell test). (Source: Gene Expression)

Neural buddhism & the psychology of religion

Gene Expression — Thu, 15 May 2008 03:35:08 +0100

Many people are talking about David Brooks' new column, The Neural Buddhists. First, I think much respect should be given to Brooks for introducing science into his column; too much punditry today is informed by seat of the pants introspection & anecdote, as opposed to what scholars have uncovered thanks to the funding of the taxpayer. That being said, I think on the specifics there are problems with his interpretation of the literature in the area of neuroscience. Frontal Cortex, Island of Doubt and Evolution Blog have all hit the main points (though I tend to think that Jonah's reaction most closely reflects my own). I think the idea that neuroscience lends some weight to the validity of mysticism as such is about as plausible as the contention that cosmology buttresses the case for a Creator. These results are interpreted through a filter contingent upon your prior beliefs; for those looking for confirmation of their spirtual or metaphysical beliefs science will no doubt offer it because of the vast sample space of findings and the imperfect mapping of words to the phenomena being described. Read the rest of this post... | Read the comments on this post... (Source: Gene Expression)

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Well, i'm a doctor

evolgen — Wed, 14 May 2008 19:00:00 +0100

I can officially claim myself as a member of the ivory tower elite. At least, that's what they tell me. Read the comments on this post... (Source: evolgen)

X-prizes for health and medicine?

ScienceRoll — Wed, 14 May 2008 17:21:44 +0100

Have you ever heard about the Ansari X Prize that resulted in constructing the world’s first privately developed spacecraft? Source Have you ever heard about the Archon X-Prize for Genomics? It will lead us to a new generation of genome sequencing methods. What about an X Prize for Health and Medicine? Students at the Massachusetts Institute of Technology came up with some interesting ideas. Of the specific proposals, one team suggested a prize for a major milestone in dealing with the problem of TB, which remains endemic in 22 nations and costs 1.7 million lives every year. Effective treatments exist, but the testing is relatively expensive and often misses active cases. So they proposed a $10 million prize for a new cheap, fast and accurate diagnostic system that could reach most of the 50 percent of cases that now go undiagnosed. Winning the prize would require not just laboratory demonstrations but field tests on 1,000 patients to show that it really works under difficult conditions. The second proposal was for a simple, portable system that could be used by community health workers to carry out initial diagnostic evaluations for the 10 most widespread fatal, transmissible diseases. Such screening could lead to prescriptions of drugs or treatment for some conditions or referral to a doctor or nurse for conditions that require skilled care or more difficult diagnosis. What do you think? An X Prize for Health and Medicine would be a good idea? Which medical specialty would be your choice? (Source: ScienceRoll)

Banana: the fate of the fruit that changed the world

Gene Expression — Wed, 14 May 2008 08:48:00 +0100

When I was a child in Bangladesh one of my "charming" activities would be to give the local banana seller some unsolicited advice. As he walked down the street carrying his banana-bunch I would shout down from the balcony and tell him which cultivars my family preferred, and that he better get with the program if he wanted our business. What he had on offer was similar to the Cavendish which you encounter in American supermarkets; my family tended to prefer a smaller, sweeter, variety which was often seeded. Despite all the problems (e.g., pathogen load) associated with living in an underdeveloped tropical country, if you had some marginal income the diversity of fruit accessible because of local abundance is something that American supply chains can never recreate.1 In Banana: The Fate of the Fruit That Changed the World Dan Koeppel uses the story of this fruit as the window through which one might examine the intersection of biology, economics, politics and ethics; in other words, modernity. Though the book's title is obviously a bit hyperbolic, I was surprised to find out that the banana is currently America's #1 fruit in terms of consumption, not the apple! And of course it is important to note that the plantain is much more than a snack for millions across the world. This reality frames the overarching plot point in Koeppel's narrative: the fact that a disease is sweeping across banana plantations and the ubiquity of this fruit might be under threat. Read the rest of this post... | Read the comments on this post... (Source: Gene Expression)

Soul gene?

Gene Expression — Wed, 14 May 2008 07:56:32 +0100

Ron Bailey in Reason, The Genetics of Ensoulment: Advances in stem cell research may be provoking a kind of "God of the Gaps" retreat on the moral status of embryos. People who subscribe to God of the Gaps thinking believe that the hand of God can be seen in those things which science cannot explain. In this case, the closing gaps in the details of molecular biology are forcing pro-lifers into an uncomfortable corner where they have to decide whether or not a cell can be imbued with a soul by turning a single gene on or off. Read the comments on this post... (Source: Gene Expression)

Scientific research and medicine in second life

ScienceRoll — Tue, 13 May 2008 21:35:46 +0100

David Pescovitz at BoingBoing had an interesting post about scientific research in Second Life, the virtual world: This week’s Science News discusses several real scientific research projects inside Second Life. For example, Drexel University neurobiologist Corey Hart is building a virtual frog to study the neural pathways involved in hopping. Meanwhile, Robert Amme, a physicist at the University of Denver, is modeling a nuclear reactor as a training tool. Indeed, many research institutions are leveraging the simple sim tools of SL to create immersive science learning experiences. This is a great example about how to close the gap between real science and the virtual world. You may also know about our medical exercises at the Ann Myers Medical Center where they train medical students (just like me) with case presentations. Now here is a tool with serious potential that could help us do it even better: Text files, images and videos in one place. The aim is to create virtual patients with virtual medical conditions. Why is it beneficial for medical students? The entire medical education is about case presentations. We move forward clinic by clinic during our studies and listen to case presentations all the time. That’s what we can do in Second Life but with even more educational material and without time or geographical restrictions. According to DusanWriter, there are pharmacy patient case studies as well in Second Life. The school has started to use SL as a training module, and has created a virtual version of Greensboro’s Moses Cone Family Practice Center, a local medical center. Students create an avatar and move through the center either as a student interviewing a patient, or as a patient. At the end of the simulation, the student takes a quiz to test his knowledge of the case history and of the practice center. If you want to know everything about Second Life & Virtual Worlds for Academic Healthcare & Education, check out the slideshow of Patricia F. Anderson. And if you don’t have a computer at home, let’s use a mobile to enter Second Life: Further reading: Top 10: Virtual Medical Sites in Second Life! How and Why to use Second Life for Education? Nature’s role in e-Science: Second Life conference LIVE Famous Scientific Bloggers in Second Life: LIVE Live Coverage: SciFoo lives on session about videos in science Live Coverage Now: SciFoo lives on session about the definition of Open Science SciFoo lives on in Second Life: Web 2.0 and Medicine SciFoo lives on: in Second Life Live Blogging Today: First Medical Simulation in Second Life! Everything about Second Life and Medical Education Genetics in Second Life Medical Training in Second Life Medicine in Second Life: virtual doctors, hospitals, and of course, sperm donation Virtual Medical Center: the Future of Medical Education Take Part in Constructing the Future of Medical Education: Join the Virtual Medical Center NHS London in Second Life Interview about the genetic revolution of Second Life Electronic Medical Records in a Virtual Hospital: Interview! (Source: ScienceRoll)

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Executive functions mostly heritable?

Gene Expression — Tue, 13 May 2008 16:37:00 +0100

99% Genetic? Individual Differences in Executive Function Are Almost Perfectly Heritable:The results from this approach are jaw-dropping: variance shared among each variety of executive function (inhibition, updating, and shifting) is nearly perfectly heritable: the contribution of the "A" component to those correlations is 99%. This heritable variance in the common executive function predicts nearly all of the genetic variance in the inhibition factor, consistent with the idea that those constructs are isomorphic from a heritability standpoint. Second, genetic influences on updating and shifting were roughly half due to the common executive function (43% and 44%, respectively) and half due to unique genetic influences (56% and 42%, respectively). Thus, the overall picture is that executive functions, in both their unity and diversity, are somewhere between 86 to 100% heritable.I wonder if such high heritabilities imply many adaptive equilibria in terms of personality phenotype with all populations? (remember the rule of thumb that the more heritable a trait is the less fitness implication it has) (Source: Gene Expression)

The epi-genomic canary

Gene Sherpas: Personalized Medicine and You — Tue, 13 May 2008 13:51:00 +0100

So many people talk about guniea pigs as the research subject. I think this is a disservice for the pigs. Personally I think the Shaft Canary is a much better analogy. You see, the subtle changes from the human guinea pigs may not make big headlines or get the public to listen....But, the canary in the shaft always makes big press.If you don't know what I am talking about, let me explain. One of coal miners earliest and continuous problems was carbon monoxide. It can kill fairly quickly. But way back when, there were no gas detectors.....we had a vey limited ability to identify the dangerous gas. So what did they do? They carried a surrogate into the mine...The canary was a pretty easy to read detector. If the bird died, then you should leave the mine shaft. With our ever expanding set of genetic risk profiling we need an easy way to read and interpret it. The problem is not that there exists a risk profile. The problem lies in what we can avoid to decrease that risk. Thus the new canary......I spent the afternoon speaking with David Duncan, if you don't know about David, let me fill you in. David is a writer/editor and I covered him and KK of Quantified Self briefly the other day. David is the bestselling author of Calendar (published in 19 languages) – Chief Correspondent of National Public Radio’s “Biotech Nation”; Contributing Editor and Columnist, Portfolio; Director, Center for Life Sciences Policy, UC Berkeley. He is author to articles and short stories, and a television, radio and film producer and correspondent. He is the co-host of NPR’s Biotech Nation.David has been working on himself for the last few years. He has done things like expose himself to environmental toxins like mercury to see if he can detoxify the load, 321 toxins to be precise. He also has been getting genomic screening and recently joined our project at The Delaware Valley Personalized Medicine Project. David is poised to really bring attention to the utility and limitations of modern Genomic Medicine. He also is going to show us how Enviro-Genetic interactions affect the Everyman. In addition to this testing, he also examined the Mind and body through things like functional MRI, systems biology analysis. If you ask me David, your genotype OddsRatio of 1.6 for MI is only useful when you mention your family history. I would like to see your 3 generation pedigree. We talked about many things including the erosion of med students' genetic knowledge, Helix Health (The Early Years), 50 year old white men, Navigenics, 23andMe, Josh Adler, and the future of medicine. The Sherpa Says:David is the Canary, not the Guinea Pig. I admire him and look forward to his future experiments. I hope he didn't take offense to my "50 year old white man" comments! Thanks for coming into the mine with us David.....Your work is a necessity that will save countless lives. (Source: Gene Sherpas: Personalized Medicine and You)

Richard dawkins interviewed by 3 quarks daily

Gene Expression — Tue, 13 May 2008 03:25:14 +0100

Here. The embed is the best bet if you can view it; the download often fails (server has been slammed?). Only a moderate amount of discussion about religion; Dawkins talks a fair bit about an obscure field, evolutionary biology. Well done. Via Accidental Blogger. Read the comments on this post... (Source: Gene Expression)

Richard dawkins interviewed by 3 quarks daily

Gene Expression — Tue, 13 May 2008 02:25:00 +0100

Jessica queller and the sherpa

Gene Sherpas: Personalized Medicine and You — Tue, 13 May 2008 01:29:00 +0100

So I can finally announce my big news. Helix Health will be hosting a webinar with the Author of Pretty is What Changes: Jessica Queller. I am excited to let everyone in on the big news. I will be letting you all know where to register shortly. With the recent introduction of books like Jessica's in the market it is becoming obvious that there is a significant population of women who are sharing their tales.The reason I love Jessica's book is because it is written in a such a readable fashion. You can tell that Jessica is a storyteller even without knowing she writes for Gossip Girl!So before you attend the next Helix Health webinar you can read her book! More Info to follow!!! (Source: Gene Sherpas: Personalized Medicine and You)

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Ways to skin the cousin marriage issue

Gene Expression — Tue, 13 May 2008 00:12:47 +0100

Another article about cousin marriage in the UK. The issue here is simple; you have a National Health Service which covers everyone, and doctors are noticing that Pakistanis are overrepresented in many cases of recessive diseases. The culprit is probably cousin marriage. Here are two points which are both valid: 'In our local school for deaf children, half the pupils are of Asian origin though Asians only form about 20 per cent of the population,' said Ann Cryer, MP for Keighley. 'I also know of several sets of parents in my constituency who are cousins and whose children are severely disabled. I have no doubt that the mothers and fathers being closely related to each is a key factor. ... This last claim is hotly disputed by genetic counsellors and Muslim doctors. They point out that the danger of a child having birth defects if the parents are cousins is double that of other children, which means the risk rises from about 2 per cent in the general population to about 4 per cent when the parents are closely related. A risk of 4 per cent therefore does not make it 'likely' there will a genetic problem, as Woolas claimed, say genetic counsellors. Read the rest of this post... | Read the comments on this post... (Source: Gene Expression)

President apostate?

Gene Expression — Mon, 12 May 2008 19:50:00 +0100

Edward Luttwak has a column (via The Corner) up pointing out that by Muslim measures Barack Obama is an apostate; so it is permissible that he should be killed. This is true, and I think if you asked most Muslims they would accede to the principle here. But as a matter of practicality these sorts of laws aren't enacted or enforced in all circumstances without sensitivity to other parameters; unlike Barack Obama the former president of Argentina, Carlos Menem, converted to Roman Catholicism from Islam as an adult (there have also been African leaders who converted from Islam to Christianity, but I don't believe they visited the Arab world), and he remained on good terms with the Arab nations. If you look at the cases where apostasy is an issue, they seem to fall into two broad categories. The first is one of crass material interest on the part of Muslims and marginality in the case of non-Muslims; in other words, there is a rational reason for a Muslim to use the letter of the law against the apostate or non-Muslim, and that individual who is being persecuted has very little recourse because of their lack of power. Second, there is the perception that the individual is being too vocal and so disrupting social norms and public disorder. It seems from all that I have heard atheism is known and tolerated in the Muslim world so long as atheists remain silent; the problem is public profession of views which go against majority norms. I strongly suspect in the case of the president of the United States most Islamic powers that be would simply ignore the letter of the law (that is, the consensus of Muslim scholars over the ages).This does not imply that I think the attitudes of Muslims are appropriate to the modern world. Nor do I think it implies that the probability of Obama being assassinated due to his religious history is the same, all things controlled, as someone who had a less complicated past. I'm arguing simply that his "apostasy" really shouldn't be the primary predictor when we consider this issue; powerful men are simply held to different standards in our species, that's culturally invariant and the biggest issue of context in this case.Addendum: I'm going to take a moment here to make a political comment which I hope won't spawn a thread-closing tirade from readers; but conservatives often complain that liberals don't take cultural complexity into account when they're making models of societies. Additionally, they often accuse liberals of adhering to an idealized noble savage conception of non-Western peoples (e.g., I have heard some liberals argue that Obama's Muslim background will even encourage good feelings from the Islamic world!). Unfortunately, many conservatives are guilty of the same; simple models make good rhetoric and ignorance breeds supreme confidence (I've been guilty of this, you've been guilty of this). But if any individual looks to their own life, their social circle and their culture, they will see a great deal of texture, subtly and nuance which can't be shoehorned into the avowed heuristics. (Source: Gene Expression)

Trichoderma reesei genome paper published

Fungal Genomes and Comparative Genomics — Mon, 12 May 2008 19:27:46 +0100

The Trichoderma reesei genome paper was recently published in Nature Biotechnology from Diego Martinez at LANL with collaborators at JGI, LBNL, and others. This fungus was chosen for sequencing because it was found on canvas tents eating the cotton material suggesting it may be a good candidate for degrading cellulose plant material as part of cellulosic ethanol or other biofuels production. The fungus also has starring roles in industrial processes like making stonewashed jeans due to its prodigious cellulase production. The most surprising findings from the paper include the fact that there are so few members of some of the enzyme families even though this fungus is able to generate enzymes with so much cellulase activity. The authors found that there is not a significantly larger number of glucoside hydrolases which is a collection of carbohydrate degrading enzymes great for making simple sugars out of complex ones. In fact, several plant pathogens compared (Fusarium graminearum and Magnaporthe grisea) and the sake fermenting Aspergillus oryzae all have more members of this family than does. T. reesei has almost the least (36) copies of a cellulose binding domain (CBM) of any of the filamentous ascomycete fungi. They used the CAZyme database (carbohydrate active enzymes) database which has done a fantastic job building up profiles of different enzymes involved in carhohydrate degradation binding, and modifications. Whether T. reesei is really the best cellulose degrading fungus is definitely an open question. That it works well in the industrial culture that it has been utilized in is important, but there may be other species of fungi with improved cellulase activity and who may in fact have many more copies of cellulases. So it will be good to add other fungi to the mix with quantitative information about degradation to try and glean what are the most important combination of enzymes and activities. One technical note. The comparison of copy number differences employed in the paper is a simple enough Chi-Squared, work that I've done with Matt Hahn and others include a gene family size comparison approach that also taked into account phylogenetic distances and assumes a birth-death process of gene family size change. It would be great to apply the copy number differences through this or other approaches that just evaluate gene trees for these domains to see where the differences are significant and if they can be polarized to a particular branch of the tree. So will this genome sequence lead to cheaper, better biofuel production? Certainly it provides an important toolkit to start systematically testing individual cellulase enzymes. It's hard to say how fast this will make an impact, but the work of JBEI and a host of other research groups and biotech companies are going to be able to systematically test out the utility of these individual enzymes. There is also evolutionary work by other groups on the evolution of these Hypocreales fungi trying to better define when biotrophic and heterotrophic transitions occurred to sample fungi with different lifestyles that might have different cellulase enyzmes that may not have been observed. Defining the relationships of these fungi and when and how many times transitions to lifestyles occurred to choose the most diverse fungi may be an important part of discovering novel enzymes. Also see Discovery Channel Blog JGI press release Martinez, D., Berka, R.M., Henrissat, B., Saloheimo, M., Arvas, M., Baker, S.E., Chapman, J., Chertkov, O., Coutinho, P.M., Cullen, D., Danchin, E.G., Grigoriev, I.V., Harris, P., Jackson, M., Kubicek, C.P., Han, C.S., Ho, I., Larrondo, L.F., de Leon, A.L., Magnuson, J.K., Merino, S., Misra, M., Nelson, B., Putnam, N., Robbertse, B., Salamov, A.A., Schmoll, M., Terry, A., Thayer, N., Westerholm-Parvinen, A., Schoch, C.L., Yao, J., Barbote, R., Nelson, M.A., Detter, C., Bruce, D., Kuske, C.R., Xie, G., Richardson, P., Rokhsar, D.S., Lucas, S.M., Rubin, E.M., Dunn-Coleman, N., Ward, M., Brettin, T.S. (2008). Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nature Biotechnology DOI: 10.1038/nbt1403 © Jason Stajich for Fungal Genomes and Comparative Genomics, 2008. | Permalink | No comment Add to del.icio.us Search blogs linking this post with Technorati Want more on these topics ? Browse the archive of posts filed under filamentous, gene family, genome, genome annotation, genome sequencing, trichoderma. (Source: Fungal Genomes and Comparative Genomics)

Will mushrooms save the world?

Fungal Genomes and Comparative Genomics — Mon, 12 May 2008 16:14:16 +0100

Paul Stamets thinks so and he's done work to make this happen. The founder of FungiPerfecti and author many books on mushroom cultivation spoke at a TED talk recently that is worth taking a look. We also wrote about how Paul has contributed (and donated in some cases) Pleurotus spawn as part of Dioxin cleanup in Ft Bragg, CA and cleaning up the SF Bay with hair and mushrooms. See Paul Stamets' TED talk. © Jason Stajich for Fungal Genomes and Comparative Genomics, 2008. | Permalink | No comment Add to del.icio.us Search blogs linking this post with Technorati Want more on these topics ? Browse the archive of posts filed under bioremediation, fungi, news. (Source: Fungal Genomes and Comparative Genomics)

Browsing biology on the web: nextbio

Gene Expression — Mon, 12 May 2008 15:14:15 +0100

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Stuck at the ritz

Gene Sherpas: Personalized Medicine and You — Mon, 12 May 2008 14:43:00 +0100

I just received my itinerary for the Beyond Genome Conference in San Francisco? What's this conference? Well, in case you missed it.... The conference is the biggest organization of stakeholders and speakers of Genomic Technologies, Genomic Medicine and Policy Wonks. There are 4 themes which the conference is organized around. 1) Applying Sustems Biology 2)RNA Interference 3) Personal Medicine 4) Targeted Gene Therapy. It is a must attend conference. I will be speaking for approximately 20 minutes on Patient Centered Genomic Care. I will be bookended by Kari Steffanson and 23andMe.... The lead off is Misha Angrist of PGP fame and GenomeBoy distinction.That's not why I am writing. I am writing to tell you that if you want a room in San Fran from the 9th to the 12th you can forget about it. Unless that is you are willing to be stuck at The Ritz Carlton......If you are, come and chat with the Sherpa.The Sherpa Says:Hopefully Kari won't punch me ;) nor will Ryan kick me.....I hope. (Source: Gene Sherpas: Personalized Medicine and You)

Powerset

Gene Expression — Mon, 12 May 2008 10:04:53 +0100

...is live. Don't know what I'm talking about? Natural language search; people have been talking about this as the Next Big Thing for a while.... (though I will say, if people have been talking about something, it isn't likely to be the Next Big Thing) Read the comments on this post... (Source: Gene Expression)

Browsing biology on the web: nextbio

Gene Expression — Mon, 12 May 2008 08:21:00 +0100

Last year p-ter put up a post pointing to useful online tools such as Haplotter. One of the great things about biology today is that so much of the data from genomics is being thrown out there within reach of the plebs. And a lot of value is being added through user interfaces which smooth the connection between you and these databases. So check out NextBio; from the FAQ:NextBio is a life science search engine that enables researchers and clinicians to access and understand the world's life sciences information. With NextBio, in just one click you can search through tens of thousands of study results with billions of data points spanning across different experimental platforms, organisms and data types. NextBio also searches across millions of publications to help you find new articles pertaining to your query. NextBio's search engine makes massive amounts of disparate biological, clinical and chemical data from public and proprietary sources searchable, regardless of data type and origin, and empowers scientists to quickly understand their own experimental results within the context of other research.I'm sure the slick AJAX-driven search tools are a nice Web 2.0+ pitch to investors; but the substantive element is the data. There are only so many researchers with eyeballs in the world; on occasion amateur astronomers can still pick out something new amongst the constellations, and I think to some extent that that sort of dynamic also holds for the amount of unprocessed data that the post-genomic era has made available to us. I really encourage readers of this weblog to poke and prod around the data piles with these new tools; Web 2.0 isn't just YouTube and Facebook....Related: VentureBeat weighted in a few weeks ago on this company.... (Source: Gene Expression)

Gender differences in the brain?

Gene Expression — Mon, 12 May 2008 06:17:00 +0100

Gender Differences in the Mu Rhythm of the Human Mirror-Neuron System:The present findings indirectly lend support to the extreme male brain theory put forward by Baron-Cohen (2005), and may cast some light on the mirror-neuron dysfunction in autism spectrum disorders. The mu rhythm in the human mirror-neuron system can be a potential biomarker of empathic mimicry.Don't know enough about this stuff to comment, but figure readers would find it of interest.... (Source: Gene Expression)

Religion in china

Gene Expression — Mon, 12 May 2008 05:45:28 +0100

Pew has an excellent survey up about the state of religion and religiosity in China. There isn't a lot of good data out of China on this topic for obvious reasons. One of the phenomenon of recent years in the West has been the perception among evangelicals that China is the scene of mass conversions to Christianity. Because of the lack of data there are speculations of hundreds of millions of crypto-Christians; and some in the media repeat these claims rather uncritically (Jesus in Beijing: How Christianity is Transforming China and Changing the Global Balance of Power is an example of the power of anecdote synthesized with the hope of evangelicals). It is almost certainly true that the "official" numbers presented by the Chinese government probably lowball the number of Christians, but this survey (skewed toward urban areas, where one assumes Christianity might be more prominent as it is in other East Asian nations) yields a number in the 2-4% range. Higher than what the Chinese government reports, but multiplicatively, not by orders of magnitude. But let's take a closer look at the data. Read the rest of this post... | Read the comments on this post... (Source: Gene Expression)

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Bonus kat

Gene Expression — Mon, 12 May 2008 04:18:07 +0100

Read the rest of this post... | Read the comments on this post... (Source: Gene Expression)

Podospora genome published

Fungal Genomes and Comparative Genomics — Mon, 12 May 2008 01:25:59 +0100

The genome of Podospora anserina S mat+ strain was sequenced by Genoscope and CNRS and published recently in Genome Biology. The genome sequence data has been available for several years, but it is great to see a publication describing the findings. The 10X genome assembly with ~10,000 genes provides an important dataset for comparisons among filamentous Sordariomycete fungi. The authors primarily focused on comparative genomics of Podospora to Neurospora crassa, the next closest model filamentous species. Within the Sordariomycetes there are now a very interesting collection of closely related species which can be useful for applying synteny and phylogenomics approaches. The analyses in the manuscript focused on these differences between Neurospora and Podospora identifying some key differences in carbon utilization contrasting the coprophillic (Podospora) and plant saprophyte (Neurospora). There are several observations of gene family expansions in the Podospora genome which could be interpreted as additional enzyme capacity to break down carbon sources that are present in dung. The genome of Neurospora has be shaped by the action of the genome defense mechanisms like RIP that has been on interpretation of the reduced number of large gene families and paucity of transposons. The authors report a surprising finding that in their analysis that despite sharing orthologs of genes that are involved in several genome defense, they in fact find fewer repetitive sequences in Podospora while it still fails to have good evidence of RIP. Overall, these data suggest that P. anserina has experienced a fairly complex history of transposition and duplications, although it has not accumulated as many repeats as N. crassa. P. anserina possesses all the orthologues of N. crassa factors necessary for gene silencing, including RIP, meiotic MSUD and also vegetative quelling, a post transcriptional gene silencing mechanism akin to RNA interference I think this data and observations interleaves nicely with the work our group is exploring on evolution of genome of several Neurospora species which have different mating systems. The fact that the gene components that play a role in MSUD and a RIP are found in Podpospora but yet the degree of RIP and the lack of any observed meiotic silencing suggests some interesting occurrences on the Neurospora branch to be explored. The potentially different degrees of RIP efficiency and types of mating systems (heterothallic and pseudohomothallic) among the Neurospora spp may also provide a link to understanding how RIP evolved and its role on N. crassa evolution. Senescence in Podospora Another aspect of Podopsora biology that isn't touched on, is the use of the fungus as a model for senescence. The fungus exhibits maternal senescence which involves targeted changes in the mitochondria that leads to cell death. The evolutionary and molecular basis for this process has been of interest to many research groups and the genome sequence can provide an additional toolkit for identifying the factors involved in the apoptosis process in this filamentous fungi. Whether it will help find a real link for aging research in other eukaryotes remains to be seen, but it is a good model system for some aspects of how aging and damage to mtDNA are linked. Dufour et al, PNAS 2001 Esser et al, Nature 1977 Turker et al, MCB 1987 Espagne, E., Lespinet, O., Malagnac, F., Da Silva, C., Jaillon, O., Porcel, B.M., Couloux, A., Aury, J., et al (2008). The genome sequence of the model ascomycete fungus Podospora anserina. Genome Biology, 9(5), R77. DOI: 10.1186/gb-2008-9-5-r77 © Jason Stajich for Fungal Genomes and Comparative Genomics, 2008. | Permalink | No comment Add to del.icio.us Search blogs linking this post with Technorati Want more on these topics ? Browse the archive of posts filed under comparative, genome, genome sequencing, neurospora, sordariomycetes. (Source: Fungal Genomes and Comparative Genomics)

Western muslims

Gene Expression — Sun, 11 May 2008 20:45:25 +0100

I have a new sublog over at Talk Islam. My first post, A wrong track for Western Islam?: Read the rest of this post... | (Source: Gene Expression)

"harun yahya" goes to jail?

Gene Expression — Sun, 11 May 2008 10:27:51 +0100

Via The Corner, Turkish Islamic author given 3-year jail sentence: Controversial Turkish Islamic author Adnan Oktar was sentenced to three years in prison on Friday for creating an illegal organization for personal gain, state-run Anatolian news agency said. ... Oktar, born in 1956, is the driving force behind a richly funded movement based in Turkey that champions creationism, the belief that God literally created the world in six days as told in the Bible and the Koran. Istanbul-based Oktar, who writes under the pen name Harun Yahya, has created waves in the past few years by sending out thousands of unsolicited texts advocating Islamic creationism to schools in several European countries. (comments closed because of the inevitable influx of Yahyaites to this post) (Source: Gene Expression)

Gene genie #31 at adaptive complexity

ScienceRoll — Sun, 11 May 2008 07:21:51 +0100

The 31st edition is up at Adaptive Complexity. A great compilation of articles and blogposts about human genetics and personalized medicine. Thank you, Michael White, for hosting Gene Genie. Gene Genie is the blog carnival of genes and gene-related diseases. Our plan is to cover the whole genome before 2082 (it means 14-15 genes every two weeks). We accept articles on the news of genomics and clinical genetics. The news and articles of personalized genetics are also included. Check out Gene Genie for more about this unique field of medicine. Many thanks to Ricardo Vidal for the logo! The next edition is due to be published on the 25th of May but has no host at this time. If you are interested in hosting Gene Genie, drop me a mail. Don’t forget to submit your articles via the official page. Here are all the issues of Gene genie: Issue #1: Scienceroll Issue #2: Sciencesque Issue #3: Genetics and Health Issue #4: Sandwalk Issue #5: Neurophilosophy Issue #6: Scienceroll Issue #7: Gene Sherpa Issue #8: Eye on DNA Issue #9: DNA Direct Talk Issue #10: Genomicron Issue #11: Med Journal Watch Issue #12: My Biotech Life Issue #13: The Genetic Genealogist Issue #14: MicrobiologyBytes Issue #15: Cancer Genetics Issue #16: Neurophilosophy Issue #17: The Gene Sherpa Issue #18: Eye on DNA Issue #19: Scienceroll Issue #20: Bitesize Bio Issue #21: BabyLab Issue #22: Sandwalk Issue #23: Scienceroll Issue #24: biomarker-driven mental health 2.0 Issue #25: The Gene Sherpa Issue #26: Sciencebase Issue #27: DNA Direct Talk Issue #28: Greg Laden’s Blog Issue #29: My Biotech Life Issue #30: Gene Expression Issue #31: Adaptive Complexity (Source: ScienceRoll)

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Workman's compensation, stereotypes and gattaca

Gene Sherpas: Personalized Medicine and You — Sun, 11 May 2008 01:01:00 +0100

Have you ever had back pain? Almost everyone has. Who has sciatica?Sciatica a very common condition accounts for a significant amount of lost work days, medical costs and psychologic stress. Treatment failures are not uncommon, are often related to posttraumatic or work-related injuries, and may result in litigation. Although most people experience back pain during their lifetime, only a fraction experience lumbar radiculopathy or sciatica as a consequence of root compression or irritation. Almost 5% of males and 2.5% of females experience sciatica at some time in their lifetime. It is so costly to society and common that in Sweden they did a cost-benefit analysis and found the surgery to be cost effective. Although studies casting doubt on its effectiveness are now in the mainstream.Because the majority of the cases are work related....I propose to you.......The following study:Let's genotype everyone who had disc herniation and see what comes up......Sounds interesting? It is. Well, it turns out in Japan that they did just that. The study entitled "A Functional Polymorphism in THBS2 that Affects Alternative Splicing and MMP Binding Is Associated with Lumbar-Disc Herniation" was just published in the American Journal of Human Genetics.What did this group find? "A splicing-affecting SNP in THBS2 and a missense SNP in MMP9 are associated with susceptibility to Lumbar Disc Herniation"Did it stand the Sherpa test?Odds Ratio? It was 3.03. You betcha. This is stronger than any of the SNP chip companies SNPs. For just about anything....Replication? Not Yet....So why do I even bring this whole thing up? Well.....First off did anyone remember Burlington Northern Santa Fe Railroad Company? It turns out this company was secretly genetic testing their employees. You don't? Let me recap. In 2001 it was reprted that this company was testing employees who developed carpal tunnel syndrome. They tested 18 people who had filed workman's compensation claims. It turns out they had developed carpal tunnel while workin' on the rail' road.....(all the live long day)They performed genetic testing to see if these workers were predisposed to carpal tunnel syndrome, another horrible but operable condition which costs tremendous money to society.Guess what? Someone(Equal Employment Opportunity Commission) sued the dickens out of them and the company ended up settling out of court. They argued that company policy requiring genetic testing for all workmen's compensation claims related to carpal tunnel syndrome was genetic discrimination. In fact, this case had been used as a example of the rare times, genetic discrimination came to pass.Here we have a very similar situation. But now that GINA is coming to pass. I would like to pose an alternative.Young person goes to 23andME/Navigenics/ETC (They just may add this immediately)....gets predictive testing indicating that he is at a 300 fold increased risk of herniating a disc in his back. Avoids manual labor (plays video games all day) never herniates the disc. Did we do society a service? Some would argue yes....I say no.Let's say, at birth we test the genome. Let's say we find the variants. Instantly this child is marked "High Risk for Work Related Disc Herniation" Based on the societal calculation, it is not justifiable to allow this person to work manual labor jobs. Now, I ask you. Who can tell someone what to do just because of his genetic predisposition? What if this kid wanted to be a firefighter? Should we not let him save lives? What if he wanted to be a Paramedic? A plumber? A carpenter? How far do we go? The Sherpa Says:We have to address this issue soon. Because more studies like this one are coming....and I am very scared with the press and marketing push going on, we may end up believing genetic predisposition is everything. The fat cats at Burlington Northern sure did... (Source: Gene Sherpas: Personalized Medicine and You)

The 21st century in medicine: what will it look like?

ScienceRoll — Sat, 10 May 2008 21:37:30 +0100

Jeffrey Dach used one of my recent posts (Personalized Medicine: Real Clinical Examples!) as a reference in his article describing the future of medicine. It’s a quite detailed and comprehensive essay about several fields of medicine and he doesn’t forget to mention personalized medicine and its impact on the future of healthcare: Personalized Medicine is the combination of these two new powerful forces, Orthomolecular Medicine and Genetic Testing. In the future, Personalized Medicine will expand and ultimately play a dominant role in medicine. Example: Warfarin Genetic Testing allows improved calibration of coumadin dosage to avoid bleeding complications. Drug metabolism testing allows for personal modification of drug dosage. Orthomolecular and personalized medicine together? We will be able to sequence the entire genome of an individual human in milliseconds. The cost will be minimal and within the means of the average person. Individuals will have ability to reprogram our own sperm and eggs. One will be able to buy new genes on the internet based on desired traits and features, and use these genes to make one’s own children as easily as buying a copy of Microsoft office. My comment: If the government gets involved, then this sounds a lot like Aldous Huxley’s, Brave New World. Example of this new biotechnology: Human genes are inserted into microbes to make insulin. We will see a dramatic increase in gene therapies and treatments. Well, I think and hope many of these will never come true, but it’s interesting to see how others predict the future. This fantastic video tries to show us some plans and projects that can really shape this century: If you would like to know more about the future, check out some of the presentations at TED or follow CNN Future Summit (Source: ScienceRoll)

My medical career: serving medical students

ScienceRoll — Sat, 10 May 2008 21:00:36 +0100

My 5th year exam period is just about to begin, and I still need one more year to graduate from medical school as medical education takes 6 years in Hungary. I’ve been studying genetics for years and I’ve been trying to find good opportunities through my blog for more than a year now so I really know how hard it is to build a medical career. A new Australian service now aims to help medical students: My Medical Career is an online career planning portal for Australian medical students and junior doctors. Our goal is to guide you through the process of selecting and achieving a career which best suits your interests, skills and lifestyle needs. You start with Self-assessment through personality tests Specialty profiles: it helps you decide which medical specialty should be your choice Options: activities that can be undertaken during your student and junior doctor years Career plan: how to write a résumé, what to expect in an interview News and conferences in your field of interest Useful resources: websites, blogs, forums, etc. And a whole community is ready to answer your questions. The idea is fantastic, I can’t wait to see something similar in Europe as well. (Source: ScienceRoll)

One explanation to rule them all

Gene Expression — Sat, 10 May 2008 18:05:50 +0100

I've commented on height genetics now & then. It seems that the quantitative genetic supposition that variation on this trait was due to the cummulative effect of numerous loci of small effect is correct. Recent research has pinpointed about ~5% of the variance. In contrast, skin color variation is mostly due to polymorphism on about 6 loci; most of the variance is due to genes of large effect. This makes specific discussion of skin color easy, but height difficult. I've been thinking about this when it comes social phenomena. Much of the verbal treatment presupposes a few large effect explanatory variables; but what if that's not correct? What if most social phenomena are contingent upon thousands of small effect predictors? How are you going to talk about this? And since we don't know the "gene" unit of social phenomena where do you even start? Of ourse quantitative social scientists focus on phenomena which do have independent variables of big effect; but most of the action might not be low hanging fruit, but rather dispersed in the canopy. Read the comments on this post... (Source: Gene Expression)

Katz

Gene Expression — Sat, 10 May 2008 04:25:22 +0100

Read the rest of this post... | Read the comments on this post... (Source: Gene Expression)

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Good looks & monte verde

Gene Expression — Sat, 10 May 2008 03:37:00 +0100

Sandy has two posts over at Anthropology.net worth checking out; The sexiness of facial symmetry across cultures and species and Earliest known archaeological evidence of Americans found in Monte Verde, Chile. (Source: Gene Expression)

The theory of evolution

Gene Expression — Fri, 09 May 2008 18:58:41 +0100

Over at The Scientist Neil S. Greenspan has an article up, Darwin and deduction: One of the most remarkable but insufficiently noted features of Charles Darwin's conception of evolution is that its logical implications are still being worked out. I am not merely claiming that experimental and observation studies continue to make use of and bear on Darwinian ideas and principles. I am calling attention to the fact that after almost a century and a half, new deductions are still being teased out of his very fertile axioms of descent with modification and natural selection. One of the primary criterion which scientists use to judge the utility of a theory is its inferential power. It is one thing to describe; but another to predict. This is one reason I recommend all my friends to read The Genetical Theory of Natural Selection; R. A. Fisher's attempt to create a mathematical framework in which to conceptualize the action of natural selection within evolutionary process. To a great extent I think Fisher fails in his grandest objectives, but fundamentally I think the exposition clarifies one's thinking fruitfully. Read the comments on this post... (Source: Gene Expression)

What’s on the web (2008 may 9)

ScienceRoll — Fri, 09 May 2008 12:25:16 +0100

Web 2.0 101 (My MD Journey): Videos about RSS, wikis, podcast or blogs: Telemedicine could eradicate many expensive ED visits (huliq.com): A community-wide study in upstate New York found that nearly 28 percent of all visits to the pediatric emergency department could have been replaced with a more cost-effective Internet doctor’s “visit,” or telemedicine, according to investigators from the University of Rochester Medical Center. The new medical bloggers’ list is up at Medblog.nl. Check it out! Talking Up A New Role For Cell Phones In Telemedicine (ScienceDaily): Two recent studies by other researchers showed that cell phones can be used to acquire and transmit images of wounds and rashes to off-site locations for diagnosis, he notes. Prescription Drugs, Health 2.0 and the eDrugSearch.com Community - Cary Byrd (The Health 2.0 Blog) Slidesonline.org is a great resource of medical slideshows. You can download the presentations as well. (Source: ScienceRoll)

Tendentious tom wolfe

Gene Expression — Fri, 09 May 2008 05:44:00 +0100

Over at The Corner they are discussing an interview series with Tom Wolfe. Wolfe claimed that Charles Darwin was a plagiarist. Derb pushed back. Since they keep talking about the interview, I decided to watch. A few notes....Wolfe says that Darwin was an obscure man who had a famous grandfather (Erasmus I'm assuming, not Josiah Wedgewood). I don't think this is really right. Unfortunately, we can't run an experiment which deletes Charles Darwin's contribution to science, but before he became the great evolutionary thinker he was a prominent travel writer. The Voyage of the Beagle went through several editions; I'm not sure we would remember Charles Darwin today (how many popular Victorian authors do we remember now?), but he was not an obscure figure in mid-19th century England.Then he notes that E. O. Wilson believes everything is genetically predetermined. That we have no free will; we can't change our decisions. Wilson, especially during the Sociobiology years offered up a few naive quotes; but as anyone who has wrestled with heritability knows a simple affirmation of genetic determinism is so banal as to be trivial. Wolfe is either overreading, or not communicating the nuance of his genuine thinking.After this Wolfe goes on to make the distinction between genetic theory and neuroscience whereby the former is literature and the latter is science. He also suggests that the three leading lights of genetic theory are totally unversed in the workings of the brain. Who are these leading lights? E. O. Wilson, Daniel Dennett and Richard Dawkins. Wolfe correctly notes that by training Dennett is a philosopher and Dawkins is an ethologist; so it is peculiar that he considers them leading lights. Wilson is more properly a field ecologist who generally leaves theoretical work to a collaborator (Robert MacArthur or Charles Lumsden for example). Since Dennett is the co-director of the Center for Cognitive Studies at Tufts I assume he stumbles onto neuropsychological material now and then. Obviously Wolfe has fallen into the all too common trap of conflating popularizers with eminent researchers; easy if you don't do your homework. John Maynard Smith, W. D. Hamilton and Richard Lewontin are evolutionary genetic scientists of note; much of Dawkins's thinking is derivative from the first two, while Wilson was influenced by Hamilton, and finally Dennett seems clearly to have had evolution predigested for him by Dawkins. An emphasis on the evolutionary part is critical; from what I know it seems that molecular genetics along the biophysical margins does bleed into neuroscience quite a bit. One of the founding fathers of modern molecular genetics, Francis Crick, spent his last years focused on neuroscience. Wolfe knows this so he really didn't mean to dismiss all genetics as literature; just evolutionary biology. I won't object too strenuously to this characterization, but I will submit that neuroscience today is too young a discipline to be taking on airs. There are many facts strewn about, but it seems that even the skeleton of a theoretical superstructure does not exist to scaffold them into a coherent whole.Finally, you can check out the second to last interview segment (the last has not been put up yet), Wolfe here is claiming that the emergence of language resulted in a post-evolutionary age for our species. This is false of course; since dismissing genetic theory as literature he hasn't been keeping up on the literature obviously! The whole line of thinking struck me as incoherent, so perhaps I'm missing something. Wolfe also makes a host of extremely disputable assertions about unique human tool use, the rationality of humans and the lack of relation of modern status games with evolutionary genetics.In any case, I only checked it out because of the gushing in The Corner. I'm a dilettante myself so I wasn't going into it looking to pick out errors, but these seemed to be worthy of correction since obviously many people look to Tom Wolfe as an Authority and keen observer of the world. I'll probably check out his novels; I'm sure he makes up for his sloppy characterization of science with a sharp eye toward fluid prose....Update: Derb weighs in again. (Source: Gene Expression)