The DNA Network |
| At least she’s got half her Mom’s DNA to fall back on [genomeboy.com] Posted: 21 Jul 2008 08:32 PM CDT The author and his daughter, Lena, who has half his DNA.
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| More Genetically engineered toys are what the public needs [Tomorrow's Table] Posted: 21 Jul 2008 08:15 PM CDT If your son asks for a genetically engineered glow-in-the dark zebra fish for his next birthday, don't be startled. It simply means that the public has begun to accept biotechnology. Or so suggests Freeman Dyson in a provocative lecture this week on TED.com. According to Dyson, a proliferation of glow-in-the-dark zebra fish, fruit cocktail trees (7 species on one tree -already very popular with backyard gardeners) or even a grow your own dog kit is exactly what it will take before biotechnology becomes an accepted part of the human condition. "We should follow the model that has been so successful with the electronic industry." Dyson said. "What really turned computers into a great success in the world as a whole was toys. As soon as computers became toys, when the kids could come home and play with them, then the industry took off. That has to happen with biotech." We may believe this or even recognize that it is true, but if so, doesn't this vision condemn us to a kind of self-centeredness? Isn't it a kind of declaration that most human behavior is governed primarily by an emotional response to pleasure and an acknowledgement that the entertainment and consumer industries are what truly drive us to action? I would like to believe that most wealthy world citizens have more compassion, more imagination and more humanity than that. That we will soon wake up and applaud applications of biotechnology that have reduced the amount of pesticides in the environment, aided poor farmers and have the potential to save the lives of thousands of malnourished children. What do you think? Will such humanistic inventive applications of biotechnology ever appear as essential as a lego set that self-assembles into a live cat? Are more glofish needed to pave the way for public acceptance of biotech? Must we wait for more toys in every home before we accept biotechnological advance in agriculture and medicine? This posting includes an audio/video/photo media file: Download Now |
| Genetic Technologies takes back its "gift to the people of Australia" [Genetic Future] Posted: 21 Jul 2008 06:23 PM CDT A quick bit of news from my side of the world. An Australian company, Genetic Technologies, obtained exclusive Australian and New Zealand testing rights for the breast cancer genes BRCA1 and BRCA2 from Myriad Genetics back in 2003; amidst public furore about the prospect of increased costs to women of having these tests done, the company announced that it would refrain from enforcing the patent as a "gift to the people of Australia and New Zealand". Now it's taking that gift back. On July 7, familial cancer screening laboratories around Australia and New Zealand received letters from the company ordering that they cease offering the tests within seven days. The people I've spoken to in these labs were shocked by the letter - there was no prior warning, and there's now considerable uncertainty about what will happen next. The concern, of course, is that this move will grant a complete monopoly to Genetic Technologies as the sole testing facility in the region, driving prices up. It's likely that there will be legal challenges to the decision over the next few months, which I will follow with interest. So why did Genetic Technologies make this move now, after five years of inaction? I'm not sure, but this graph from the Australian Stock Exchange sheds some light on the issue:
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| New Gene Makes Flies Less Gay [evolgen] Posted: 21 Jul 2008 10:00 AM CDT We all know that Drosophila are the gayest bunch of gays that ever gayed up genetics. This is especially true when you create mutations in fruitless (nee fruity), "the gay gene". Male flies with mutations in fruitless will try to get it on with other males (e.g., doi:10.1016/S0092-8674(00)81802-4). That's gay!
But fruitless is an old school gene that needs to be fucked up to turn the flies gay (doi:10.1093/molbev/msj070; the first author on that paper is, I shit you not, named Gailey). Drosophila really aren't as gay as they are made to appear in the articles describing fruitless mutants. But the males are still kind of in to dudes, as is shown by a new paper from Manyuan Long's group (doi:10.1073/pnas.0800693105). Read the rest of this post... | Read the comments on this post... |
| Merging Blogging with the Pursuit of Academic Tenure [Epigenetics News] Posted: 21 Jul 2008 09:30 AM CDT John Hawks, who has maintained a popular blog focused on his field of expertise in paleoanthropology, has begun a series of posts discussing some of the pros and cons of blogging during the early years of a tenure-track position, and how he was able to successfully integrate his blogging activity into his tenure application (Hawks was granted tenure last month). The first segment (How to blog, get tenure and prosper: Starting the blog) is both insightful and honest, which is just the sort of writing I’ve come to expect from John Hawks. |
| Statistical alignment and virus selection paper now online [Mailund on the Internet] Posted: 21 Jul 2008 09:21 AM CDT The paper I described in a previous post: Investigating selection on viruses: a statistical alignment approach, just got published online today. Yeah us! |
| Using People Skills to Get that Job [Bitesize Bio] Posted: 21 Jul 2008 09:13 AM CDT So, you see an ad for your dream job and, of course, decide to apply. But how do you make sure you get it? Your chances of getting any given job are mainly influenced by two things; your technical abilities and how you come across in the job interview. At short notice, you can’t do too much about your technical skills, apart from making sure you present them optimally in your CV/resume but you can do something about how you come across, and that can set you above the competition in the eyes of the interviewer. One approach, according “job interview master” Vj Vijai is to use his tried and tested formula, which he describes briefly in the following short, entertaining video. Let us know what you think of his ideas in the comments.
Photo: language translation |
| Atmospheric, Spectroscopic, Arsenic [Sciencebase Science Blog] Posted: 21 Jul 2008 07:00 AM CDT
Listening to tomographic tales - Researchers in the USA and The Netherlands have pieced together a picture of the most exquisite of molecular machines using electron-microscopic tomography. The team has for the first time obtained a three-dimensional structure of the gossamer-like filament of proteins found within the inner ear that gives us our sense of hearing and balance. More… Atmospheric NMR - Nuclear magnetic resonance spectroscopy has been used to study the kinetics of atmospheric pollutants in the gas phase for the first time. The method provides an empirical correlation between the atmospheric lifetimes of atmospheric pollutants and their relative reaction rates with chloro radicals at ambient temperatures. Read on… Ebola spiked - An X-ray structure of the surface spike of the Ebola virus could explain how this lethal pathogen infects human cells and may help researchers devise preventative measures to stop the virus spreading during an outbreak. Full story… a Atmospheric, Spectroscopic, Arsenic |
| Brave New Epigenome [The Gene Sherpa: Personalized Medicine and You] Posted: 21 Jul 2008 06:52 AM CDT Daniel at Genetic-Future asks "Which baby do you want? A dilemma for the 21st century parent-to-be" There is a lovely recap of an article from Nature News.....from Daniel's blog, Nature News has an... [[ This is a content summary only. Visit my website for full links, other content, and more! ]] |
| Blogging and tenure [Mailund on the Internet] Posted: 21 Jul 2008 02:41 AM CDT John Hawks tells us how to combine blogging with getting tenure. It is something that, obviously, is of great interest to me. Blogging takes up a lot of time. It doesn’t have to, of course, but it tends to fill the time available. The same does research. If you try to do both, chances are that research will suffer. Since you are not likely to get much credit for blogging when you struggle to get tenure, this could be a problem. On the other hand, I find that blogging about the papers I read and the research I do helps me to better understand what I’m reading or doing. Writing down a summary of a paper I’ve read requires that I understand the paper at least in some detail. You cannot really kid yourself into believing that you understood the paper. Believing I understood a paper while not really getting it happened a lot to me. Discussing papers in a journal clubs opened my eyes for this, and now I read papers more carefully. At least when I am going to discuss them later on. Reviewing papers on my blog works in a similar way. I have to be careful if I am presenting a paper where everyone can read the review. So in a way, blogging doesn’t really subtract time from my research as much as it supplements my research work. Putting my thoughts on a public web page forces me to be more careful in what I write, which is the main benefit of using a blog rather than a notebook. It is not without problems, though. Quoting the post I linked to above:
You are risking your reputation. You always are when you do something public, so I guess you always have to choose between risk or obscurity. With a blog you are less careful and certainly more informal in what you write than in a research paper, so perhaps there is a greater risk, but on the other hand people do not expect as much from a blog post as a paper, so perhaps not… There is another risk, though, and that is leaking some secret. I’m not good with secrets and keeping research projects secret until paper submission is a bit strange to me. There are a lot of ideas out there and most of them are crap, so why protect them? Anyway, not all see it that way, especially the biologists I work with — I’ve learned that the hard way — so I’m trying to keep my current projects out of my blogging until papers are submitted. At least the projects where there could be problems with leaking secrets. I would love to write about my current projects and get feedback on it, but I guess I will have to make due with published results. At least I get a lot of practice writing in English by blogging. My writing is not appreciated by reviewers on my papers, so I need the practice. This is also something John Hawks mentions:
I’ll read John’s post carefully and hope that I can get to tenure as well ;-) |
| TGG Interview Series VII - Katherine Hope Borges [The Genetic Genealogist] Posted: 21 Jul 2008 02:00 AM CDT In addition to the her work with the ISOGG, Katherine recently launched DNA Fund to provide scholarships and funding for DNA testing, which can often be expensive. In the following interview, Katherine talks about her introduction to genetic genealogy as well as the launch of DNA Fund. TGG: How long have you been actively involved in genetic genealogy, and how did you become interested in the field?
Katherine Hope Borges: I learned about genetic genealogy in 2003 from a speaker at a Daughters of the American Revolution (DAR) meeting. The speaker, a DNA Project Administrator, shared her success in using DNA for genealogy so I decided to try it. My father tested in May 2003 and I established a DNA project in October of the same year. TGG: You are one of the founders of the International Society of Genetic Genealogy. How did the group come about, and what are the goals of the organization? ISOGG is a dues free society with no revenue sources. It probably sounds a little crazy to run an organization with no funding, but as a dues paying member of several lineage and genealogical societies, if I have extra spending money, I want it to go to DNA testing! Since ISOGG is primarily an internet-based society, the costs are relatively low. Those who share the mission of ISOGG, to promote and educate about genetic genealogy support it by answering questions on the mailing lists, compiling information on web pages, giving a speech to a local society, etc. TGG: Has genetic genealogy helped you break through any of your brick walls or solve a family mystery?
KHB: Many times now, but what is funny is that when my father tested and compared against two others of the same surname, no one matched! Good thing a close match came in later that year or otherwise, I might have thrown in the towel on the whole business. The brick wall that was broken by my father’s match was whether two men with the same surname in the same county listed in the 1790 South Carolina U.S. Census were related or not. Indeed they were and a bible record was later discovered showing the two men were brothers. TGG: What do you think the future holds for genetic genealogy? KHB: Currently, genetic genealogy still seems to be used as a “last resort” to get through a brick wall; but I think that as it grows in popularity and use, that people just beginning genealogy may start by doing a DNA test. Additionally, I think that advances in genetics research hold many amazing discoveries to come on what can be learned about our ancestral origins. TGG: Aside from the ISOGG, what other genealogy-related projects are you involved with?
KHB: I recently launched The DNA Fund www.dnafund.org - an organization to provide scholarships and grants for DNA testing. There is a real need for this as it can be a rather costly aspect of genealogy, but I also want it to benefit the scientific genetics community as the two are symbiotic. TGG: Thank you for a great interview Katherine!
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| I’m back! [Mailund on the Internet] Posted: 21 Jul 2008 01:49 AM CDT As you might have noticed I haven’t blogged for ages. I was busy for a few weeks with projects and the last week and a half I’ve been out of the office taking a little holiday. Not travelling anywhere, just not working, and not blogging either. Well, that got boring so now I’m back again. I have a deadline for a paper submission at the end of the week, so I guess I’ll be working on that. Otherwise it is still a bit slow around here which is both good and bad. It means I have time to focus on research rather than teaching or writing, but it also means that I am likely to slack it a bit. Oh well, back to work :) |
| Trendspotting: Molecular profiling data resources [business|bytes|genes|molecules] Posted: 21 Jul 2008 12:35 AM CDT
Fast forward a few years. I am convinced that a lot of such data will be available via search engines or data portals. Already you are beginning to see a number of commercial and public engines come to life (NextBio, Oncomine, etc). Earlier this week I read an announcement (sub reqd) by the NCI to create a Cancer Molecular Analysis Portal, which will integrate data sets from the Cancer Genome Atlas project and other cancer genomics studies. The key here is that we already have a body of work using microarrays and other molecular profiling systems, and in many cases, people are just repeating experiments which someone, somewhere has already carried out. Unless there is something inherently proprietary in those studies (e.g specific dose-response studies), there is no reason to repeat that experiment, especially for technologies that are relatively stable and don’t have too much cross-platform/cross-lab variation (one of the goals of the MAQC projects has been to understand these variations). The second key, and to an extent perhaps even more important, is how these data are made available. Personally, I really like the NextBio interface. Will the business model work? I am not sure, but definitely the idea and concept make a lot of sense. It’s a sign of maturity in many ways, accelerated by the way the web has advanced in the past few years. If we trust data not generated internally, enough to make key decisions, then a scenario where data and analysis results are served up via web services, allowing users to mash up different sources, including internal sources, and develop a relevant scientific intelligence is a distinct possibility. Personally, I would like to think that the value and the users expertise comes from how they integrate all these resources in a manner that makes it a unique asset to the user, i.e. the value of the results come from the way the data are brought together and not any individual data sources Related articles by Zemanta |
| A Professor and a Graduate Student Mull Over Epigenetics [Epigenetics News] Posted: 20 Jul 2008 10:42 PM CDT PZ Myers (Pharyngula), an associate professor in developmental biology, and Abigail Smith (erv), a graduate student studying retoroviral evolution, talk about a number of topics in a bloggingheads.tv exchange, including epigenetics. The segment of the video discussing epigenetics is embedded below. |
| You can blog and still get tenure [adaptivecomplexity's column] Posted: 20 Jul 2008 10:02 PM CDT Yes, it's possible, according to John Hawks (who writes an excellent blog): |
| Posted: 20 Jul 2008 09:12 PM CDT Tony Snow, the conservative writer, commentator, and former Bush administration Press Secretary, died on the morning of July 12 at the age of 53 of colorectal cancer. It's worth mentioning that Mr. Snow had a family history of colon cancer, as his mother apparently died of the disease when he was 17 years old. As Mr. Snow has publicly acknowledged a diagnosis of ulcerative colitis (UC), it seems most likely that the cancer in his family is related to UC, rather than to what are arguably the two most important hereditary cancer predisposition syndromes for colon cancer, Lynch syndrome (aka hereditary non-polyposis colorectal cancer or HNPCC) and familial adenomatous polyposis (FAP). The lifetime risk for colon cancer in individuals at average risk in the United States is about 5 percent. Nine out of ten cases occur after the age of 50. Individuals with ulcerative colitis have a ~3- to 12-fold elevated risk of developing colon cancer depending on the extent of colon involvement and the length of time the disease has been present. Ulcerative colitis risk is influenced by genetics, but the inheritance is complex, without major deterministic susceptibility genes like those for FAP (APC) and Lynch syndrome (MLH1, MSH2, MSH6, PMS2). Mr. Snow's death is an opportunity to remind folks that colon cancer, in general, is a highly preventable disease. Stay tuned to future posts for more details. |
| Gender and Science in the News: Should We Have Grant Quotas For Women? [adaptivecomplexity's column] Posted: 20 Jul 2008 09:11 PM CDT OK, I'm about to dive into an issue I probably shouldn't be talking about on a blog, at least if I have any hope of convincing a hiring committee to consider me, but I'm going to dumbly rush ahead. John Tierney at the NY Times has been looking into the issue of whether Congress is considering "Title IX'ing" science, by requiring some sort of gender quota in funding decisions by federal science agencies. Tierney argues that in this day and age, it is less a matter of discrimination and more a matter of which subjects women choose to pursue: "The members of Congress and women's groups who have pushed for science to be "Title Nined" say there is evidence that women face discrimination in certain sciences, but the quality of that evidence is disputed. Critics say there is far better research showing that on average, women's interest in some fields isn't the same as men's." |
Remote arsenic assessment - A topic I’ve come back to again and again since I first covered for The Guardian the breaking news of arsenic contaminated tubewells on the Indian sub-continent in 1995. Now, an informatics approach to surface data could allow geologists and environmental scientists to identify regions of the world where people are at risk of exposure to arsenic in their drinking water without the need for widespread sampling to be undertaken. 
The next interview in the TGG Interview Series with members of the Genetic Genealogy field is with Katherine Hope Borges. Katherine is the Director of the 
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