The DNA Network |
| What would Rachel Carson think about genetically engineered crops? [Tomorrow's Table] Posted: 26 May 2008 07:25 PM CDT In our book, "Tomorrow's Table: Organic Farming, Genetics and the Future of Food", Raoul and I discuss whether or not GE varieties can help forge a future sustainable agriculture. Both conventional and organic farmers rely on genetically diverse and improved plant varieties to increase their yields, and I see no reason why GE seed should be viewed differently. I like to think Rachel Carson would also agree. After all, in 1962 she said: "A truly extraordinary variety of alternatives to the chemical control of insects is available. Some are already in use and have achieved brilliant success. Others are in the stage of laboratory testing. Still others are little more than ideas in the minds of imaginative scientists, waiting for the opportunity to put them to the test. All have this in common: they are biological solutions, based on understanding of the living organisms they seek to control, and of the whole fabric of life to which these organisms belong. Specialists representing various areas of the vast field of biology are contributing—entomologists, pathologists, geneticists, physiologists, biochemists, ecologists—all pouring their knowledge and their creative inspirations into the formation of a new science of biotic controls." Isn't GE as exactly the kind of biological approach that Rachel Carson was hoping for? |
| Finch 3: Managing Workflows [FinchTalk] Posted: 26 May 2008 07:00 PM CDT Genetic analysis workflows begin with RNA or DNA samples and end with results. In between, multiple lab procedures and steps are used to transform materials, move samples between containers, and... |
| Equal opportunity genomics [Genetic Future] Posted: 26 May 2008 06:42 PM CDT ScienceDaily reports a bold strike against the human genomics patriarchy:
Well, there are other female genomes out there - the 1000 Genomes Project has already generated moderate-coverage sequence for at least one female (an anonymous woman of European ancestry, collected in Utah) and low-coverage sequences of perhaps half a dozen more, and I think the Cancer Genome Project has sequenced at least one tumour sample from a female patient - but perhaps Leiden beat them to it, and at the very least they can legitimately claim to be the first to realise that the gender of a genome donor by itself was enough to warrant publicity.
That's right - they sequenced an entire human genome using just the left-over capacity of their sequencing machines, in six months. This sort of capacity certainly isn't limited to Leiden: sequencing facilities around the world are all churning out human genome equivalents every few days. Now, consider that the first human genome took the combined work of hundreds of scientists from over 18 countries for thirteen years, and you have you a taste of how rapidly sequencing technology is moving.  Subscribe to Genetic Future. |
| New Developments in the War on Science: Policing Your Hard Drives and the Internetz [Bayblab] Posted: 26 May 2008 06:34 PM CDT Although he can't be bothered to discuss the issue with voting taxpayers in his own country, Canadian Industry Minister Jim Prentice has apparently joined up with an international task force (under the guise of an Anti-Counterfeiting Trade Agreement) that aims to restrict the movement of digital information between countries. We're talking potential hard drive searches at airports and wide latitude to seize information. Who knows, maybe our brains will even be scanned for copyrighted information? Better get those Metallica tunes out of your head before travelling! Such measures are totally uncalled for and if enacted, would represent a serious impediment to the daily activities of the thousands of scientists who rely on communicating and exchanging ideas around the globe in order to do their work. Read about this nonsense here. Michael Geist provides more in depth coverage. |
| Handbook of Genetic Counseling [ScienceRoll] Posted: 26 May 2008 04:11 PM CDT I’ve already come up with some posts about how to keep yourself up-to-date in the field of genetics and which resources to choose:
But far the best resource I regularly use is in WikiBooks: Handbook of Genetic Counseling
It’s really comprehensive, but lacks of images and longer descriptions. Let us know which genetic resources you prefer!         |
| Semantic search vs Google: In Medicine [ScienceRoll] Posted: 26 May 2008 03:23 PM CDT I’ve been playing with Powerset for a while. It seems to be a service that can take us to the world of semantic web or web 3.0. It uses Wikipedia and Freebase as resources. The main idea is to ask questions instead of search for terms. Let’s give it a try.
If you make a search for “Who discovered penicillin” in Google, you will see this (Alexander Fleming Discovers Penicillin) and many more similar articles. Even if we know the truth is different. If you ask the same question in Powerset, you get this:
It’s a bit more accurate, isn’t it? Try it and let me know if you find something interesting. And don’t forget to check out my Personalized Medical Search! Further reading:
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| SNPedia Releases a Mac Version of Their Promethease Tool. Hurray! [BUZZYEAH » My Genome] Posted: 26 May 2008 02:25 PM CDT
Well, last night Mike emailed me and told me they now have a Mac version. I immediately ran my raw genome data (a file downloaded from my 23andMe account) through the tool, which took about 2 hours.
The tool compares your raw genome data against SNPedia's impressive collection of DNA information and creates a report that you can browse. Here's a screen grab of my Promethease report:
SNPedia explains how to read the Promethease results here. This is the general format for the results:
As you can see above, the presentation of the report's results is very basic. They plan on improving the report in future iterations. Stay tuned here and over at SNPedia's blog. You can subscribe to my 'My Genome' posts only by |
| How Good Scientists Go Bad [Bayblab] Posted: 26 May 2008 09:37 AM CDT The armies of unreason, whether they be deniers, cranks or quacks, often trot out MDs and PhDs to bolster their arguments. Some of them are doctors or scientists with dubious credentials, but sometimes these are competent (or better!) scientists who have made real contributions to their field. We've covered a few of these examples before. ERV has an explanation of how the transition is made from scientist to crackpot in a post entitled When Good Scientists Go Bad: How Kooks are Made. |
| Words to live by [genomeboy.com] Posted: 26 May 2008 08:05 AM CDT Well, I'm an oversharer — it's not like I'm entirely reformed. But lately, online, I've found myself doing something unexpected: keeping the personal details of my current life to myself. This doesn't make me feel stifled so much as it makes me feel protected, as if my thoughts might actually be worth honing rather than spewing. |
| Free personal genomics! [Genetic Future] Posted: 26 May 2008 07:04 AM CDT Over at Eye on DNA, Hsien wonders about the effects of a slowing economy on the personal genomics market. Well, no matter how hard it's getting to make your mortgage repayments, you can probably still afford personal genomics if it doesn't cost you anything:
(From a recent piece in Wired). You can sign up here; there is a pretty extensive FAQ here. Note that you will need to physically attend an enrollment session at the Coriell Institute in New Jersey. Also, I see that Coriell is adopting the paternalistic "need to know" approach pioneered by Navigenics, and won't provide participants with any information about genetic variants that aren't "medically actionable" (e.g. incurable disease risk variants), although they will hand out information on non-disease traits like eye colour. Still, if I lived anywhere near New Jersey I'd be signing up right now rather than wasting time writing this post. (As an aside, I wonder why Coriell is using a saliva-based method when it could be using its considerable expertise to create and store cell lines from blood - essentially generating an endless source of DNA for researchers to analyse. That seems like a missed opportunity that someone will be seriously regretting in a few years when there's no DNA left for whole-genome sequencing, or epigenome analysis, or whatever.) If you're more ambitious, you could also sign up for (eventual) free genome sequencing via the Personal Genome Project. Subscribe to Genetic Future. |
| Catching the Travel Bug [Sciencebase Science Blog] Posted: 26 May 2008 07:00 AM CDT
Our first line of defence against many of these diseases is our immune system. Unfortunately the immune system is not perfect and cannot always mount an effective attack against invading viruses, bacteria, and parasites. This is where vaccination often comes into play. Vaccines were essentially discovered by Edward Jenner in the late 18th century. They are based on the idea that the immune system can be stimulated by components of a pathogen – i.e. the virus or bacterium. Proteins or protein fragments (antigens) produced by pathogens alert white blood cells to their presence, which then engulf the pathogen and destroy it. The cells also start to produce Y-shaped protein molecules (antibodies). The tips of the Y match the antigens produced by invaders like a lock to a key. The antibodies travel through the blood stream and every time they bump into an antigen that they recognise, they lock on to it. This labels other pathogen particles for attack by yet more white blood cells which see the antibody signal and digest the invaders or infected body cells. The immune system retains the chemical blueprints for making the same antibodies again for the next encounter. This is why if you survive childhood diseases such as chicken pox you are unlikely to catch it again in adulthood, although this example belies the fact that chicken pox apparently lies dormant and can re-emerge later in life as shingles. Vaccination tricks the immune system into thinking a pathogen is attacking by using dead or a deactivated version of the virus or bacterium. The white blood cells respond, creating antibodies against the antigens but without you having to catch the disease first. The blueprints for the antibodies are stored chemically ready for a real invasion of the disease. You need Diphtheria Among the diseases for which a vaccine is available is diphtheria. This highly infectious disease is caused by the bacterium Corynebacterium diphtheriae, which affects the upper respiratory tract. Symptoms include a severe sore throat and fever which is followed by the formation of a lethal sticky coating in the nose and throat. The bacteria also release a toxic molecule into the blood – a chain of 535 amino acids, which penetrates cells and kills them. In the 19th century, scientists discovered a serum that neutralises the diphtheria toxin. This 'antitoxin' is made by extracting antibodies and other molecules from the blood of horses that have been vaccinated against diphtheria. To work, the potion has to be administered as soon as symptoms appear because it cannot undo the damage caused by toxin that has already entered body tissues. During the past 10 years, researchers have been trying to find drugs that can kill the diphtheria bacterium. Researchers at Brandeis University in the USA discovered the switch that starts production of diphtheria toxin, a protein called DtxR. They have determined the exact atom-by-atom structure of this protein and drug designers are now looking for compounds that can deactivate the switch before the toxin is released and so save the lives of diphtheria victims that would otherwise die. Hepatitis B Another serious illness you may encounter when travelling the globe is hepatitis B. It is caused by the hepadnavirus but the source in half of all cases is not known. However, sexual transmission, needle sharing among drug users, tattoos and transmission from mother to unborn child cause the other half of cases. The virus incorporates itself into the DNA of liver cells, leading to chronic liver damage and potentially liver cancer. Fortunately, vaccination before exposure provides lifelong protection. Researchers have also discovered antiviral drugs to treat hepatitis B. These drugs resemble the nucleotide molecules that act as the natural building blocks of viral DNA (the virus’ genetic code). The fake building blocks have unreactive fluoro groups instead of hydrogen atoms at strategic positions. So, once the virus starts to use these fake molecules the duplication mechanism is jammed because unreactive fluoro groups cannot be removed to attach the next nucleotide in the chain. Viral replication is significantly slowed down, giving the immune system a chance to overwhelm the disease. Unfortunately, the viral DNA is prone to damage, or mutations, which lead to changes in its genetics. Most mutations stop the virus working but occasionally one will benefit the virus. If, for instance, the mutation changes the virus so that it ignores the fake building block, then the antiviral drug will fail and the virus continues to replicate, passing on the mutant genes (DNA fragments) to its offspring. Some strains of hepatitis have already evolved resistance to Rabies If you are bitten by a dog or other mammal – notably a bat – when travelling, the wound itself is the least of your worries. Rabies is yet another viral disease best avoided. Its name derives from the Latin word for madness or rage, and it leads to a fear of water (hyrophobia), foaming at the mouth, a swelling of the victim’s brain, and ultimately death. Louis Pasteur and Emile Roux developed a vaccine in 1885, but it only works if administered before symptoms appear. In 2006, scientists in Brazil investigated the potential of a group of natural plant compounds, phenolic compounds, as antiviral drugs to treat rabies. They discovered that just three of a whole range of compounds tested had some antiviral activity. The structures of these three compounds – 3,4,5-trimethoxybenzoic acid, 3,4,5-trimethoxyacetophenone, and 3,4,5- trimethoxybenzoic acid ethyl ester – could provide a starting point for designing more effective compounds. There is no way of predicting how long that might take and any potential drug would have to go through safety tests and clinical trials before it could be used in medicine, which might take up to 10 years. In the meantime, vaccination remains the only defence, that and avoiding rabid animals. Typhoid The disease that killed Alexander the Great, typhoid fever is alive and well across the globe. The Salmonella typhi bacterium multiplies in the blood and spreads by ingestion of food or water contaminated with infected faeces. The bacterium causes a high fever, headache, aching muscles, and death in severe cases. Previously, antibiotics, such as ampicillin and chloramphenicol, were the standard treatment and saved many lives. However, like so many other diseases, typhoid has evolved resistancetyphoid has evolved resistance, particularly in India and South East Asia. Vaccination, if you’re travelling in affected areas, is therefore essential. Tuberculosis Tuberculosis, or TB, a disease once consigned to the history books is now carried by a third of the world’s population. TB is a bacterial infection and as with viruses the bacterial DNA, its genetic code is susceptible to mutations that can help it evolve resistance to antibiotics. This has already happened in many parts of the developing world and among certain sections of society such as the homeless, drug users, and HIV sufferers. However, the issue of resistance is more complicated than it at first appears. A study published in March 2007 in the Journal of Infectious Diseases suggests that most cases of drug-resistant TB may be due to new infections rather than acquired resistance to the antibiotics. If this research is confirmed it might help scientists devise a new strategy for stopping the spread of this disease. Malaria Malaria kills up to three million people each year. Malaria is caused by the Plasmodium parasite carried by infected mosquitoes. The parasites are carried into a person's bloodstream by a bite from an infected mosquito, they then multiply in the liver and the blood causing a lethal fever. There is no vaccine against malariaThere is no vaccine against malaria, but there are drugs that protect you from infection. Plasmodium, like many viruses and bacteria, has also evolved resistance to some of these drugs. However, a novel drug derived from Chinese medicine, known as qinghaosu, works well in treating the disease and so far has staved of resistance. There is a great deal of research underway to find novel drugs to defeat malaria. Scientists at the Toronto General Research Institute and Ontario Cancer Institute recently, for instance, discovered a synthetic compound that targets and kills malaria parasites, including one drug- resistant strain. In January 2007, researchers at Northwestern University in the US worked out how the parasite tricks red blood cells into engulfing it and so perpetuating its lifecycle. New drugs aimed at blocking this process might beat malaria. Today, most of the diseases we have discussed are confined to the developing world where they pose an enormous public health problem and one that usually affects privileged Westerners only when they travel to such places. However, if climate change occurs some of these could spread to the developed world. Unless we can halt global warming, the time may come when you could catch some of these diseases just by staying at home. Stepping in donkey droppings will then be the least of your worries. Where in the world? A selection of souvenirs you might pick up on your travels Diphtheria - bacterium: former USSR, South America, Northern Africa You can obtain specific advice on diseases via the WHO and CDC sites. Your doctor or national health organisation may also produce online information. For those in the UK that can be found here. A post from David Bradley Science Writer |
| Pad your resume and hide your risks, little meaty cogs [Think Gene] Posted: 26 May 2008 05:37 AM CDT Misha Angrist of Genome Boy writes in response to a comment I made about a challenge to produce an explanation why it is theoretically wrong if genetics is used as an objective standard to select people for services, employment, and admission.
Listen, I’m sure Misha is a great guy and science editor. I wish I could express my (strong) opinions on this topic without seeming like I’m attacking the author or being disrespectful. I wish that I could be passionate and express my appreciation for the sites, writers, and commenter who make these discussions (it doesn’t help that it’s 3am and the moonlight puts my PC-filter on the frizz) Yet, I stand by my opinion that the problem is that society doesn't value people beyond than any potential liabilities. Genetics is merely the latest means by which to disqualify yourself or mark yourself replacement. It's not special or problematic this way itself. Genetic testing ist’t the problem. We are. There isn’t a simple law to fix a vestige social injustice since probably civilization and certainly industrialism. Stop pretending that whatever latest science/social/political doo-dad X is the reason why people treat people like meaty cogs with resumes just because X is strange enough to outshine the cultural noise. And the greatest irony is that as genomics matures, we’ll increasingly have the ability to address risks before they’re realized. Yet, in our culture, that information is taboo because we expect to be treated as liabilities by our employers, schools, health care providers, and governments. So, again we lose the opportunity to act intelligently, and we continue to blunder about in a haze of ignorance until some emergency compels some myopic intervention. It’s like we’ll binge weekends on oreos and CNN, but we’re embarrassed to weigh ourselves. We act as if “maybe people didn’t know,” that risks will go away. That’s GINA in a nutshell, and while I support the legislation, it’s just caulking to keep back the freak opportunists like Burlington Northern Railway, not landmark legislation. That said, don’t gimp genomics because genetic testing reminds you that this fact is depressing. It’s my generation’s turn to be garage engineers, and I’ve me a hankering for the genomic Apple I. |
| How I Chose a Grad School [Bitesize Bio] Posted: 26 May 2008 05:24 AM CDT
For starters, I didn’t know precisely what I wanted to do. I had been told that a higher degree would help a lot for any job in biology, and I had a very rudimentary idea of what I wanted to do after grad school (i.e., what my degree would accomplish for me). It is probably very common to be so naive going into grad school, so it’s understandable that I was like this, but they were important issues that I should have addressed and did not. I had it in my head that being a researcher would be intellectually stimulating, and well-paying. I was particularly interested in one day working in a pharmaceutical company such as Merck - as I grew up near Merck’s research campus in Pennsylvania, and several of my close friends were children of Merck employees. I saw them happy with their jobs, and was interested in chemistry and biology in school, so I thought it would be the ticket to that stimulating and well-paid job in science that I dreamed of. For those who’ve already made it to grad school, and particularly for those who’ve finished and moved on after grad school, you’re probably chuckling now about how I really was that naive. Often, being a researcher is intellectually stimulating, but in a way that takes all the fun out of it, with lots of stress. That’s why I suspect that many such individuals secretly seeing a psychologist to help deal with stress and anxiety. (I’m sure this is a good topic for future blog posts). But being a researcher is not frequently well-paid. If you’re at a top-tier company such as Merck, then maybe; but generally, the research establishment is spread too thin, with too little funding. I digress… As I said, I was interested at the time in pharmaceutical research, so I went looking for some of the top PhD programs in pharmacology and molecular medicine in my region. That narrow focus of research and region limited me to UPENN (one of the top 3 in the country in pharmacology), Georgetown, Cornell, and I applied to a related field at Penn State also. Georgetown lost my application, found it after they’d finished their recruiting weekends, and invited me for a late interview anyway. By that time, I had already committed to Cornell, so I turned them down - and two weeks later I received a rejection letter from them. *shrug* Whatever. I don’t remember what happened with Penn State, but UPENN and Cornell invited me for their recruitment weekends. UPENN was quite impressive, but they clearly thought my CV and transcript suggested that I intern for a year somewhere and reapply the following year. They told me so - I needed more experience. Two faculty from Cornell sponsored me to join their program, and I was sufficiently interested that I took their offer. Thus began my planning for what rotations to pursue in my grad school program. Some thoughts though on the process: 1 - UPENN had a very good point… looking back, I would have been far more prepared by a year or so of experience between undergrad and grad school. 2 - I should have known better more about my field before embarking on a graduate program in it. Vague ideas of what field seems cool does not cut it. And about what to look for in graduate programs: 3 - Of course, check out the blog posts we have relating to the subject on choosing a mentor and a postdoc position. Many of the same issues apply, since grad school (and postdoc) positions are basically apprenticeships. 4 - Think about what you’re good at (lab course grades in undergrad are a good indicator) to steer what field to go into. Some other issues: Taking the GREs - Plainly put, choose what GRE subject tests to sit for based on the field that you want to go into. The GRE subject tests are a great way to boost your claims of aptitude in a field. Visiting campuses - As mentioned, you’re basically looking for a mentor to do an apprenticeship with. Keep that mindset, and know everything that you can about each professor that you’ll be meeting with. Think about what you’d like to do in his/her laboratory, and why you’re suited for it. |
| The Phoenix has landed [Mailund on the Internet] Posted: 26 May 2008 01:47 AM CDT The Phoenix Mars probe landed this night. The mission is to learn about the history of water on Mars and to learn if arctic Mars can support life. There’s a few Danish components on this probe — which makes me a bit proud — including a wind telltale from my own university. |
| GINA Series: Genetic Tests Unfairly Favor the Employer [Page 2] [Think Gene] Posted: 25 May 2008 11:00 PM CDT Recently, President Bush signed GINA, the Genetic Information Nondiscrimination Act, into law. GINA makes it illegal for employers or health insurers to discriminate based on genetics. Virtually the entire genetics community has lauds this legislation, yet few have written why its wrong that employers and services review objective facts to make decisions. “It’s not fair…” but why? Genetic Tests Unfairly Favor the Employer Scenario: many of my employees complain of condition X. I test their genes. The tests claim that the majority of the employees are:
Seem too slimy to be possible?
Seem even more outrageous? Yet, this is the exact scenario of Gary Avary of Nebraska, an employee of Burlington Northern Railway (BNSF). A doctor diagnosed Gary with work-aggravated Carpal Tunnel Syndrome and recommend surgery, which Gary’s employer approved. Gary received the surgery and returned to work after a three week medical leave. Two months later, BNSF subjected Gary to a genetic test regarding his predisposition to Carpal Tunnel without his permission.
Quick Quiz: Gary has Carpal Tunnel Syndrome. Gary tests negatively for a mutation associated with Carpal Tunnel Syndrome. Does Gary have Carpal Tunnel Syndrome? Without GINA, BNSF says: no. GINA “helps” employers like BNSF score higher on my quizzes. |
| Bio International Convention Fringe Festival. Get Your Tickets Now. [] Posted: 25 May 2008 09:07 PM CDT
Looks like there’s some planned disruption of the upcoming Bio International Convention in San Diego. Watch as kids who didn’t pay attention in Biology class bludgeon attendees with paranoia and conspiracy theories. (Like, biotech companies “create weapons and the wars to sell their products”? WTF, Dude?) |
| Where are the Einsteins Today? [adaptivecomplexity's column] Posted: 25 May 2008 03:00 PM CDT No, I don't mean the bagel shops. Why do towering scientific geniuses seem to be a thing of the past? |
I've been waiting for Mike Cariaso over at 
Long gone are the days of a summer break where the biggest health risks were stepping in donkey droppings on the beach or being sick on a fairground ride. These days, trips abroad provide the traveller with a whole range of diseases, so what’s our defence?
A reader recently asked for an explanation “about choosing grad schools, taking the GREs, visiting campuses, speaking to potential advisors, and how you guys decided on where to go.” For me, to be honest, I think that I was astoundingly naive in my decision-making for where to go for graduate school.
Ok, pick a common work-related condition: Carpal Tunnel Syndrome. Now pick a job where Carpal Tunnel is an obvious environmental hazard: Railroad Bolt Pounder. Say an employee is diagnosed with Carpal Tunnel, has surgery, and returns to work in three weeks. Say I’m the employer, and after the surgery which I had already approved, I mandate that my employee must undergo a genetic test to provide “additional, objective medical information to determine whether or not your condition is work-related.” The results of that genetic test aren’t interpreted as percentage-risks for a specific disease, but look like this:
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