The DNA Network

It was 150 years ago today... [T Ryan Gregory's column] Posted: 01 Jul 2008 04:35 PM CDT My Dear Sir,-- The accompanying papers, which we have the honour of communicating to the Linnean Society, and which all relate to the same subject, viz Read More...

Big Think: The Future of Genomics [ScienceRoll] Posted: 01 Jul 2008 03:27 PM CDT Big Think is a new service featuring interviews with famous experts about important topics. Here is a recent interview with Dr. Pardis Sabeti, Assistant Professor at Harvard University who focuses on the future of genomics: Some other interesting talks: The Dilemma of Organ Donation The Human Genome an Imperative Discovery Tool What is the state of global medicine today? Jimmy Wales: What are you thinking about?

Is Organic Farming simply an ideology or is it better than conventional farming? [Tomorrow's Table] Posted: 01 Jul 2008 01:19 PM CDT Please see a discussion on these questions and more on the Nature Network. Read the 27 comments on this blog to hear what some science bloggers have to say.

Cloning Trakr [Mary Meets Dolly] Posted: 01 Jul 2008 01:13 PM CDT From BusinessWire: CANINE HERO OF 9/11 TO BE CLONED BY BIOARTS INTERNATIONAL "Trakr", now Disabled, wins Golden Clone Giveaway "Once in a lifetime, a dog comes along that not only captures the hearts of all he touches but also plays a pivotal role in history." So begins the winning essay submitted by James Symington to the BioArts Golden Clone Giveaway contest. Symington, a former police officer who now lives in Los Angeles, and his German Shepherd, Trakr, were among the first search & rescue teams to arrive at Ground Zero following 9/11. Together they braved horrific conditions while searching for both living and dead, ultimately locating the last human survivor under approximately 30 feet of unstable debris. Trakr's story was selected from a large pool of submissions from around the world. BioArts International, which is also holding an auction of 5 dog cloning slots from July 5th-9th, sponsored the Golden Clone Giveaway with the goal of identifying the world's most "clone-worthy" dog and replicating it at no cost to its owner. Both the Giveaway and upcoming auction are part of the Best Friends Again program, described on the web at www.bestfriendsagain.com. "We received many very touching submissions to our contest," said Lou Hawthorne, CEO of BioArts, "describing some truly amazing dogs. But Trakr's story blew us away. His many remarkable capabilities were proven beyond all doubt in our nation's darkest hour – and we view the work of cloning him as a great honor."

Nature rejects idea of "human dignity" [Mary Meets Dolly] Posted: 01 Jul 2008 12:52 PM CDT Scientists used to know that answers to questions of morality were outside the scope of science. Collect data, make discoveries about our world and leave the ethics to philosophers, historians, theologians and lawmakers. Of course scientists can have an opinion on such things. We all should. But their scientific knowledge does not make them experts on issues of morality. So when I read this in a Nature editorial, it left me scratching my head: Dignity as a concept cannot be a director of moral judgement. Micahel Cook has a great commentary on this editorial. It is FULL of great stuff, I recommend reading the whole thing. I will leave you with a couple of great quotes: So it was dismaying to discover that Nature has discarded the concept of "human dignity" as unworthy of mature, intelligent argument. According to an editorial published earlier this month, it is a contradictory, "notoriously subjective" and "slippery" concept. In four glib paragraphs, it jettisons 2,500 years of Western civilisation, the UN Declaration of Human Rights, and the constitutions of numerous countries.... However, underlying Nature's rejection of human dignity is something else. Human dignity is a mainstay of arguments against research on embryos. As it is commonly understood, human dignity is indivisible. You cannot affirm that a black African is a human being and then pass laws to make him a slave. You cannot affirm that the elderly are fully human and pass laws to euthanase everyone over 85. The problem for stem cell scientists and their boosters, is that the embryo is clearly human. It has the full human genome and barring any mishaps, it will someday become successively a foetus, a baby, a child, and an adult. It is a human being in an embryonic stage of development.... The consequences of rejecting centuries of human dignity and replacing it with a self-serving, gimcrack theory are momentous. Embryos may be small but upon them rests our dignity, too.

Quotes about non-coding DNA. [T Ryan Gregory's column] Posted: 01 Jul 2008 11:50 AM CDT I had a series of posts on Ye Olde Genomicron about what people actually said regarding "junk DNA& Read More...

The Loom has left the Sciblings. [T Ryan Gregory's column] Posted: 01 Jul 2008 09:50 AM CDT Scientific wordsmith Carl Zimmer, most recently the author of the widely touted book Microcosm, has left Scienceblogs (the bl Read More...

TiddlyWiki: A 21st Century Roladex [Bitesize Bio] Posted: 01 Jul 2008 09:24 AM CDT A good way to streamline the way you work is to keep a Roladex on your bench or desk containing all of the little bits and pieces that you need to do your job - things like stock solution recipes, abbreviated protocols for example. (for 19 more ways to streamline your work, click here) Having these notes at your fingertips allows to you work faster because you don’t have to find the original information from the original source; a text book, your lab book or a colleague. TiddlyWiki is a great piece of open source software that can be used as a 21st century version of a Roladex. It’s creators call it “A non-linear, re-usable notebook”, which is a pretty good description. Basically it is a souped-up HTML file that you can use to create a searchable archive of notes (a.k.a. a Wiki), that can be opened in any web browser. The amazing thing about TiddlyWiki is that there is no server involved, so you can put your TiddlyWiki file containing your personal notebook of time saving notes and protocols (or whatever you like really) onto a USB stick and carry it around with you wherever you go. TiddlyWiki is very versatile and easy to customise… to get started, check out this guide. And, being open source, it has a community of developers who have created some very nice variations on the original theme. Two of my favorites are GTD TiddlyWiki, a modified TiddlyWiki that you can use to organise your tasks, and TiddlyWiki-SE (Student edition), a TiddlyWiki version that is designed to be used for or note-taking. Photo: Phillie Casablanca

IndyStar - Do you want to know? Direct-to- consumer DNA tests ... [PredictER Blog] Posted: 01 Jul 2008 09:19 AM CDT PredictER's Kimberly Quaid and Indiana University Department of Medical and Molecular Genetics' Dr. Gail Vance comment on direct-to-consumer genetic testing in today's issue of The Indianapolis Star. Quaid notes: "For a lot of genetic conditions, there is not much we can actually do to change them. So, what are people getting out of the tests?" … While legitimate genetic tests exist, such as one to detect the BRAC mutations for breast cancer, Quaid said, she doesn't see the sense in identifying risks for every disease. She also doubts the validity of tests used by some firms. … Traditionally, health-related genetic tests have been available only through health-care providers, who decide whether they are based on family history and symptoms, and who interpret results for patients. Quaid said that method better safeguards consumers.

The End of Theory? [evolgen] Posted: 01 Jul 2008 08:00 AM CDT Wired Magazine has published an article by Chris Anderson arguing that theory is dead (The End of Theory: The Data Deluge Makes the Scientific Method Obsolete). The argument: with our ability to generate vast amounts of data, there is no need for theory. Now, it's hard to parse what Anderson means by "theory" from the article. But he seems to be arguing that scientists are merely looking for correlations between various parameters, and claiming that's a sufficient analysis. Is it? Well, sometimes, yes, if it's based on a sound theoretical framework. Deepak Singh has already called out Anderson (Chris Anderson, you are wrong), and Andrew at the Social Statistics blog has commented (The End of Theory: The Data Deluge Makes the Scientific Method Obsolete). I would like to weigh in with my perspective as an evolutionary biologist. Is theory dead in this subfield of biology? Read the rest of this post... | Read the comments on this post...

Science Tuesday: The MMR vaccine and autism - truth, lies and the media [chrisdellavedova.com » Science] Posted: 01 Jul 2008 07:06 AM CDT Zach’s coming up on the time for his MMR vaccine. As with most of the jabs he’s gotten to date, it’s just a thing that we do, a right of passage designed to keep my child healthy. Not something I would have thought about much at all, except that I’ve had a little bird (who shall remain nameless) chirping in my hear about the MMR vaccine and autism. It’s a link that I’d heard about once or twice, generally as being absolutely mythical based on apocryphal stories by grieving parents. But, when it’s your own child you think twice and just to quiet that little quiver of doubt in the tin-foil hat part of my brain, I decided to take a look at the science behind autism and MMR. It turned out to be quite a story. It all stems from a single scientific publication. In 1998 a paper by Andrew Wakefield of the Royal Free Hospital in London and twelve colleagues was published in the British medical journal The Lancet purporting a link between the MMR vaccine and childhood autism. Wakefield and his colleagues hypothesized that the vaccine caused an irritation to the bowel, making it more permeable to the proteins delivered by the vaccine allowing them to leak into the bloodstream. The researchers claimed that these proteins acted as toxins and caused serious developmental brain damage, particularly autism. Wakefield’s paper was riddled with problems and the scientific community was almost immediately skeptical. It was based on an extremely small sample, only twelve patients. While Wakefield did find histological evidence to support intestinal damage in the autistic children, there was no control group to compare against. The study noted that “onset of behavioural symptoms was associated, by the parents, with the (MMR vaccine) in eight of the 12 children.” In other words, the researchers relied on parents of autistic children’s memories of events rather than health care professionals. Parents that were understandably upset and far from objective observers. Finally, thepublished article stopped well short of concluding that there was a causal link between the MMR vaccine and autism. However, when Wakefield spoke to the press he made no such disclaimer. Predictably, the Lancet paper set off a firestorm in the British and world media. For example, in just six months in 2002 in Britain there were over 500 stories about MMR and autism. The MMR vaccine and any other vaccines containing a mercury based compound known as thimerosol (TCV) came under scrutiny by the press. Unfortunately, these stories rarely featured a rigorous examination of the facts on the ground. Every time that one of these stories hits the press more parents opt out of vaccination. Since 1999, the number of parents in the U.S. opting out of the MMR vaccination has nearly tripled. Cases of measles, which had been eliminated in the U.S., are on the rise. There were 72 cases reported in ten states in the first half of 2008. This can be causally linked to people opting out of the vaccine. More striking however, is that nearly 900,000 people worldwide, many of them children, died from measles in 1999. That figure was down to 345,000 in 2005 due largely to an initiative by the Measles Initiative to make the MMR vaccine more available in the third world. The resurgence of measles in North America should be a cold hard reality check - this is what happens when you do not get your children vaccinated. What makes things worse is that Wakefield lied. Since the publication of the original Lancet paper, ten of the twelve authors have retracted the conclusions claiming that Wakefield went too far in claming a causal relationship between the vaccine and autism. Wakefield, who was sacked from his post at the Royal Free Hospital in 2001, has since been charged with professional misconduct. This is based in part on the 2004 revelation by The Times (London) that some of the parents who took part in the original study had been recruited by a UK attorney planning to file suit against MMR manufacturers. Four or five of the children were covered by the legal aid study and Wakefield had been awarded £55,000 to assist their case by finding scientific evidence of the link. Wakefield did not tell his colleagues or medical authorities about this case and personally received £400,000 for his troubles. The effort to sort out the science that Wakefield corrupted has been intensive. Scores of papers have been published refuting Wakefield and his colleagues’ results. There have been large, well controlled epidemiologic studies in North America, Europe, Asia all of which conclude the same thing. For example, one of these studies looked at over half a million Danish children, 20% of whom were not vaccinated. Compare this to Wakefield’s study that looked at 12 children, all of whom were autistic and had been vaccinated. All of these studies come to the same conclusion - there is no significant causal link between the MMR vaccine (or and thimeresol containing vaccines) and childhood autism. There have been no studies published in reputable scientific journals that claim such a link since Wakefield’s paper. The truth is that incidents of autism are increasing and have been for the last half century or so. Autism has a genetic component, but the marked recent rise suggests that there is some environmental factor involved. The first signs of autism in children are generally detected between one and two years of age, the same time period in which most children receive their MMR vaccinations - this is one of the problems in dispelling the myth of a link. But, except for Wakefield’s compromised work all studies undertaken have concluded that the rise in cases of autism is independent of the increased use of the MMR vaccine. Yet the fear surrounding the vaccine remains. Which brings us around to two common themes here on chrisdellavedova.com - crappy journalism and scientists inability to communicate. The fear surrounding MMR is largely being propagated by the media, whose obsession with “balance” insures that in every story about MMR and autism both sides of the issue will be presented. In this case one side is the truth - that there is absolutely no link between autism and the MMR vaccine - and the other side is the lie fabricated by one greedy and corrupt scientist and his gullible colleagues. A lie that is, presumably unknowingly, being propagated by a press obsessed with sensationalism. Thus, having made its way into our cultural consciousness (it’s been on the TV, so it must be true) it is nearly impossible to rid ourselves of the misinformation. And well meaning people suffer. This happens, as it did for me, when little birds have friends who have friends who blame the vaccine for their child’s autism. It also happens when public figures, like presidential candidate John McCain, recite as truth something they read somewhere. The media is not completely at fault, however. They are simply doing their job to inform and entertain the public, with the latter becoming increasingly important. Most scientists fail miserably to effectively communicate the realities of their research. Take for example, this reply to a Horizon program on the MMR/autism drama. Dr. Neville Goodman, writing in the British Medical Journal, responds to this program with the frustration that a lot of scientists feel with the media still spewing this swill. He writes: “In 2002, according to the Child Accident Prevention Trust, more than 36 000 children were hurt in road accidents and around 200 were killed… five cases annually of childhood leukaemia may be associated with power lines. But perspective is precisely what is rejected by personal experience: so we have illogical campaigns to uproot speed cameras, to move pylons, and to give single vaccines.” Goodman’s mistake is that he callously dismissed the “five cases of leukemia associated with power lines”. A mistake that many scientists make, we are so obsessed with statistics and data that we tend to forget the individual subjects of our research, we neglect to treat them not as numbers but as human beings. The families of those five children who developed leukemia by living under power lines probably do not feel that their campaigns are illogical. Nor would parents of autistic children consider their belief that the MMR vaccine destroyed their children illogical. There is no link, but we as scientists need to endeavour to educate - loaded with the facts, but deployed with compassion - rather than mock, deride or scorn. ——- As you may have guessed, Zach will be getting his MMR vaccine next month. I feel good that I’ve done the research, that I’ve looked at the primary literature and the “other side”. (Guess that Ph.D. was good for something).

Innovation Integration Timeline: Where is Medicine 2.0? [ScienceRoll] Posted: 01 Jul 2008 05:17 AM CDT I found this great timeline on the blog of Jay Parkinson (original: juliaallison). This is the Innovation Integration Timeline: they are invented they are adopted by a few they are ridiculed they are adopted by a few more they are feared they are adopted by a few more they are discussed they are adopted by many they are praised they are absorbed into everyday life they are seen as so obvious it's hard to imagine the world any other way they are written about in mainstream media Medicine 2.0 is currently somewhere between number 2 and 6. We need much more participants and innovators (like Jay, like Jen or like Alex). I believe in 5 years we might get to number 12… The Myths of Innovation

Medical Education Evolution: Time for a change [ScienceRoll] Posted: 01 Jul 2008 04:56 AM CDT I just finished my last exams so now I’m officially in the last year of medical school. I believe I know exactly the problems of medical education as there are some of them even at the best universities. I believe medical education is still traditional while medicine is not traditional any more. Do you think today’s residents and physicians can answer the questions of e-patients? I know, medicine will never be an online service but there will be more and more e-patients who would like to contact their doctors through e-mail or Skype and would like to get some relevant/useful resources where they can find more information about their medical condition. Do you think today’s physicians can help these patients? If we do not change medical education, there will be a strange situation: e-patients will know more about e-health than medical professionals. How could they help them that way? I believe medical education is not ready for the 21st century and there are just a few good initiatives (one example). It’s not about changing the whole concept of medical education, but we have to implement the tools of medicine 2.0 into all the medical curriculums. We came up with an idea regarding how to achieve this: Jen McCabe Gorman, Ted Eytan, and me created a Ning community for those who are interested in changing medical education. We’re working on a new concept and plan to find a medical school that would use it. Feel free to join us and let us know your thoughts. Don’t forget to check Jen’s wonderful post about it.

Finally, High Througput Sequencing put to good use [Next Generation Sequencing] Posted: 01 Jul 2008 02:50 AM CDT Today, a U.S. Department of Agriculture team, funded with more than $10 million from Mars Inc., announced that they will start sequencing the cocoa genome. The results are likely to help in the battle against cocoa plant diseases and, much more importantly, they could also lead to better-tasting chocolate. A lot of people would probably also [...]

Your Monday evening simulations [business|bytes|genes|molecules] Posted: 01 Jul 2008 12:14 AM CDT Image via WikipediaHot, long day, so just wanted to point folks to a couple of interesting papers that crossed my feed reader. Alexey Onufriev and colleagues at Virginia Tech have carried out the kinds of simulations that get me all excited. An atomistic-level study of dynamic pathways of ligand binding in myoglobin. The paper will be published in PNAS (I can’t find it on the PNAS site yet). Strategies to study molecular motions at this level of detail and longer timescales are going to be the driver of MD over the next few years and I suspect you’ll see more such studies. Another paper in PNAS is a simulation of the binding of ADP to a carrier protein (although I don’t get the part about the first simulation of binding. I am sure I’ve done some of my own beforeUpdate: Clarified in the comments). Some pretty impressive stuff from Emad Tajkhorshid whose work I’ve long followed. ShareThis

Mendeley = paper management + collaboration goodness [My Biotech Life] Posted: 30 Jun 2008 10:35 PM CDT Some months ago, I was looking for software to manage the papers I had been consulting for a large group project I had been working on. At the time, the best (aka cheap or free!) available options where either for Mac or Linux, nothing for Windows. Mac users have an award winning software application called Papers (not free) that is all the rage or even Yep (free?), the Linux gang have some options like Referencer that did a decent job of organizing and downloading metadata for the files. But Windows users were stuck with… well, expensive software packs like Endnote. Oh, and maybe Zotero that is a Firefox addon. Well, it seems that this is not an issue anymore, someone has been hard at work and there is now a real option for Windows users (Mac & Linux too (sort of…)), it is called Mendeley. Mendeley is still in closed beta but it is already packing a punch with some features that make it much more than just a paper manager. In their words: Mendeley Desktop helps you to manage your research papers as easily as MP3s. When you import your research papers (in text PDF format), Mendeley Desktop will try to automatically extract the metadata (authors, title, journal, etc.), thus giving you a hand in setting up your digital library. In the next versions, we will also introduce Microsoft Word integration, OCR for converting your image PDFs, sharing and collaboration features, and exciting 3D visualizations of your library. But Mendeley Desktop is just the starting point to get more out of your research papers. In the coming weeks and months, Mendeley Web will begin to provide you with personalized reading recommendations, statistics about your own publications, up-and-coming topics in your academic discipline, a network of fellow researchers, and much more One of the cool features here is that there is a Desktop and a Web component that leverage the strengths of each platform. It will be interesting to see how the collaborative features in Mendeley Web work. I’ve just began to use the software today so I can’t really get into any technical issues I may have noticed, but from what I’ve seen so far, it looks great. The user interface is functional and the overall design is also quite pleasant, on both Mendeley Desktop and Web. The friendly folks at Mendeley have given me access to beta test the application along with 20 14 4 invites for my readers. If you are interested in being a beta tester, feel free to comment below and I’ll send out invites first come, first served. I’m sure we’ll be hearing much more about Mendeley in the near future as the features start rolling out. Meanwhile, take a look at this demo (youtube) and let me know what you think about this app. Post from: My Biotech Life

Laying the groundwork for the one ton tomato [Omics! Omics!] Posted: 30 Jun 2008 09:25 PM CDT Somewhere in life I've heard a children's/novelty song about a one ton tomato; eventually (if I remember correctly) it ends up as a similar quantity of ketchup. Nearly half-ton pumpkins show up pretty regularly at the big agricultural fairs every fall, but tomatoes aren't in that league. But, the difference between an ancestral tomato (small berries) and a multi-pound beefsteak is nothing to sneeze at. Domestication has made great strides. A paper last month in Nature Genetics laid out part of this process. Interestingly, there are two different developmental processes that have been utilized to enlarge tomatoes. A tomato fruit is composed of multiple subunits, the carpels. One change has increased the number of cells per carpel by tinkering with the cell cycle -- a much more delicious change than what a similar process will yield in a person. The new work details the genetic change which increased the number of carpels. Of course, of interest is how universal these mechanisms are. Most domestic fruits are greatly enlarged over their wild counterparts -- though perhaps raspberries show very little enlargement & blueberries it is a small multiple. On the other end are those monster curcurbits at the fair and their watermelon cousins. But getting back to the title. Now the question is whether these mechanisms have reached their biological maximum or simply what a few mutations can do (there are also practical considerations, such as the stem strength required to support larger tomatoes). Or, can we use this new knowledge to bring up the laggards -- or figure out why there are no fist-sized raspberries or basketball-like blueberries? A strawberry the size of my dog? Of course, purely economic forces might lead to the fruits commanding the most money per unit weight -- perhaps pomegranates will have an order of magnitude more seeds! Healthy for you -- so long as you watch where you eat them.

You are subscribed to email updates from The DNA Network To stop receiving these emails, you may unsubscribe now.	Email Delivery powered by FeedBurner
Inbox too full? Subscribe to the feed version of The DNA Network in a feed reader.
If you prefer to unsubscribe via postal mail, write to: The DNA Network, c/o FeedBurner, 20 W Kinzie, 9th Floor, Chicago IL USA 60610