The DNA Network |
| Lunch with Dr. O [genomeboy.com] Posted: 05 May 2008 08:12 PM CDT
Can you spot the real scientist? (photo by Bob Cook-Deegan) I was walking through Tower City, the teeming mall in downtown Cleveland, regretting not calling friends I used to know when I lived there, when I spied, sitting alone at the food court with a New York Times, one of the giants of genome history, Maynard Freaking Olson, in town to give a brilliant plenary address. As is my wont, I shamelessly pulled up a chair and started interviewing him. I mentioned the PGP and his eyes lit up. We talked about personal genomics, why he thinks it’s all so much “Freudian genetics,” ELSI, race, changing fields, George Church, health care, liberal politics, the disappointments of GWAS, Jim Watson, and on and on. I was wrong: George Church is unique in many ways, but he is not the only hardcore genome sequencer who actually takes a real interest in the societal implications of his work. Thank you, Maynard! |
| Genes and the environment contribute differently to drinking among young adolescents [Think Gene] Posted: 05 May 2008 07:53 PM CDT A 2001/2002 report by the World Health Organization found that, among young people in western countries who began drinking before 16 years of age, the average age of initiation was 12 years of age. A new twins study from the Netherlands has found that genetic factors appear to be involved in the early initiation [...] |
| 65-million-year-old asteroid impact triggered a global hail of carbon beads [Think Gene] Posted: 05 May 2008 07:49 PM CDT The asteroid presumed to have wiped out the dinosaurs struck the Earth with such force that carbon deep in the Earth’s crust liquefied, rocketed skyward, and formed tiny airborne beads that blanketed the planet, say scientists from the U.S., U.K., Italy, and New Zealand in this month’s Geology. The beads, known to geologists as carbon cenospheres, [...] |
| Cells lining milk ducts hold key to spread of common form of breast cancer [Think Gene] Posted: 05 May 2008 07:48 PM CDT When a form of cancer that begins in the milk ducts of the breast invades neighboring tissue to spread to other parts of the body, the cause lies not in the tumor cells themselves but in a group of abnormal surrounding cells that cause the walls of the duct to deteriorate like a rusty pipe, [...] |
| A study reveals how cells communicate to activate the cell division machinery [Think Gene] Posted: 05 May 2008 07:46 PM CDT A study performed by researchers at the Institute for Research in Biomedicine (IRB Barcelona) on the fruit fly, Drosophila melanogaster, unveils how distinct signaling pathways operate between neighboring cells in order to activate the cell proliferation machinery that results in the organized growth of the fly wing. The signaling pathways involved in this process [...] |
| The secret to long life may not be in the genes [Think Gene] Posted: 05 May 2008 07:36 PM CDT A research on the bone health of one of the oldest persons in the world, who recently died at the age of 114, reveals that there were no genetic modifications which could have contributed to this longevity. The research team, directed by Universitat Autònoma de Barcelona professor Adolfo Díez Pérez, pointed out a healthy lifestyle, [...] |
| The tachykinin receptor 3 gene has been linked to alcohol and cocaine dependence [Think Gene] Posted: 05 May 2008 06:26 PM CDT The tachykinin receptor 3 gene has been linked to alcohol and cocaine dependence The search for genes associated with alcohol dependence (AD) has recently been extended to the tachykinin receptor 3 gene (TACR3), located within a broad region on chromosome 4q. Researchers have found that seven of the nine single nucleotide polymorphisms – DNA sequence variations – [...] |
| Genetic Testing on The John and Ken Show [BUZZYEAH » My Genome] Posted: 05 May 2008 04:38 PM CDT
Note: I tried to figure out a way to incorporate "100,000 watt blowtorch lighting the LA afternoon skies" into the above paragraph but gave up. They invited Trish Brown, a VP at DNA Direct, and myself to talk during the segment. I guess someone over at The John and Ken Show found my blog while doing some random Googling. During the interview, John & Ken were surprisingly quieter and less angry than I thought they were going to be. They asked me basic questions regarding the DNA test I chose, my test results and raising donations on my blog for the DNA test. You can listen to the genetic testing segment on the podcast below. The genetic testing segment starts at 33:40min and goes to 59:40min (They talk to me at the 45:30min mark):
This posting includes an audio/video/photo media file: Download Now |
| Goodbye to all that? [genomeboy.com] Posted: 05 May 2008 04:02 PM CDT At last week’s Translating ELSI meeting, I was amazed at how large the topic of race and genetics loomed. Perhaps I shouldn’t have been: Race is our deep and abiding national wound — it never seems to heal. In Slate, Will Saletan rethinks his earlier defense of James Watson’s unfortunate remarks:
Might personal genomics and widespread sequencing help to change this? |
| Sun and Amazon jump into the pool together [business|bytes|genes|molecules] Posted: 05 May 2008 02:23 PM CDT At JavaOne, one of the big announcements was a hookup between Amazon, specifically EC2, and OpenSolaris (finally generally released as a full open source OS). The collaboration between Amazon and OpenSolaris will give customers access to OpenSolaris (for feree) and MySQL premium technical support, and more. The key selling points are ZFS and D-Trace. Now, I am a big Linux guy, but options are always good and enterprise relationships/partnerships are just a sign of the maturing and relevance of cloud computing. Aside. It’s interesting that Sun talks about OpenSolaris as the OpenSolaris community  |
| A Big Day For Genetic Genealogists - A New Y-DNA Tree And The New SNP Test [The Genetic Genealogist] Posted: 05 May 2008 12:49 PM CDT An Updated Y-DNA Tree at ISOGG The International Society of Genetic Genealogy (ISOGG) announced today that their Tree Team has completed the 2008 version of the Y-DNA Haplogroup Tree. This revision was a major undertaking, because, as ISOGG states in the version history, “[t]he Karafet et al paper (2008) required a significant revision to the tree and affected all haplogroups.” The reference for this paper is (Karafet T M, Mendez F L, Meilerman M B, Underhill P A, Zegura S L, Hammer M F, (2008).
The site also has a Haplogroup Conversion Table (MS Word) to convert a 2007 haplogroup to an updated 2008 haplogroup. Updates at FTDNA and ySearch The Karafet et al paper also resulted in updates to haplogroup designations at Family Tree DNA and ySearch. Users who have tested their Y-DNA through FTDNA or have created a profile at ySearch automatically had their haplogroup designation updated this morning (May 5th, 2008). For instance, before the update my haplogroup was R1b1c9a. After the update, the haplogroup is called R1b12a1c. New Deep Clade Tests Reflects Changes As a result of the SNPs analyzed in the Karafet et al paper, Family Tree DNA has updated their “Deep Clade” SNP tests. From the official announcement this morning:
To order the test, FTDNA users should check under the “Haplogroup” page on the left side of their personal page. Note that the FTDNA tests do not incorporate all the SNPs used by the ISOGG Tree Team to create the updated 2008 Y-DNA Tree. The ISOGG tree uses some SNPs that are new, provisional, or private and are not yet used by testing companies. |
| Hillary Clinton: 'Elite' Experts are Bad for America [adaptivecomplexity's column] Posted: 05 May 2008 11:14 AM CDT Hillary Clinton has gone off the deep end:
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| Defining Life Itself [Bitesize Bio] Posted: 05 May 2008 10:29 AM CDT
In What is Life?, Schrödinger introduced the idea of an “aperiodic crystal” that contained genetic information in its configuration of covalent chemical bonds. In the 1950’s this idea both stimulated enthusiasm for discovering the genetic molecule and could be seen (in retrospect) as having been a well-reasoned theoretical prediction of what biologists should have been looking for during their search for the genetic material. Francis Crick attributed his interest in DNA to having read this book. What is necessary for a reading of What is Life?, and indeed any understanding of molecular biology, is recognition of how biology transcends the physical realm. Yes, biology operates according to the laws of physics, but physics alone cannot recapitulate life. Ernst Mayr, in What Makes Biology Unique describes the autonomy of biology in much the same sense. That is, new phenomenon emerge in living organisms that could never be anticipated by physics alone. Or at least not until we understand life and its emergent properties better. And no one has better described these aspects of life than Schrödinger, to my knowledge, in the sixty-four years since the book was published. |
| Posted: 05 May 2008 09:40 AM CDT  I watched the newest vidcast of diggnation over the weekend, as I usually do. It is a reasonably good show about the most popular stories covered on digg.com. Alex Albrecht is too cool, mostly because he drinks beer, plays pencil and paper D&D, is on the totallyradshow, and kicks Kevin Roses arse at Call of Duty 4. That is some serious geek street cred. This past eppisode though, they revealed some ignorance about the mechanism of Viagra. Kevin Rose (seriously check out how badly he is pwned by Albrecht on CoD4) thought that you could take Viagra and have a voluntary errection where you would have to 'be in the mood'. Someone from the audience who identified themselves as a 'life scientist' said that it was not voluntary. Well, Kevin Rose was right and the 'life scientist' was wrong. Strange since I find Kevin Rose usually talks out his ass. As I understand it viagra mearly inhibits the degradation of cGMP, which directly initiates and maintains an errection. However it is produced in response to nitric oxide. The nitric oxide is produced upon sexual stimulation, therefore even with viagra it should still be a voluntary thing. That's got to be a relief for those who take the drug since you are supposed to take it 4 hours before you think you will need it. That would be a long 4 hours if it was involuntary. |
| NextBio: Life Sciences Data Search Engine [ScienceRoll] Posted: 05 May 2008 08:55 AM CDT
Almost a year ago, I wrote NextBio was just like using Pubmed but in a more dynamic way. Now the public version was launched so it’s free for everyone.
I gave it a try by searching for psoriasis and it looked impressive as it offered me the subtypes of psoriasis to search for (auto-complete list).
There were some genes that can play a role in the pathogenesis of the disease and some groups as well. It would be interesting to see how and why it shows only these genes (take a look at Gene2Mesh for a clearer example).
And one more thing:
I still need time to get used to this system but looks quite useful and can really ease the job of a scientist. Give it a try!
Further reading:
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| Kudos to New Scientist's "24 myths and misconceptions" about evolution [The Tree of Life] Posted: 05 May 2008 08:53 AM CDT New Scientist has a pretty good article on myths and misconceptions about evolution (see Evolution: 24 myths and misconceptions). They really hit on many of my pet peeves on evolution. Among my favorites:
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| Back in Boston [The Daily Transcript] Posted: 05 May 2008 08:13 AM CDT What a week. I spent half of it at University of Montreal's IRIC, or Institut de recherche en immunologie et en cancerologie. I was truly impressed. |
| 4 in 1: Video, podcast, photo and Pubmed [ScienceRoll] Posted: 05 May 2008 07:50 AM CDT There are nearly 25 sites and services focusing on medical videos and animations on my list I’ve been working on for months. Here is the newest addition, The DAVE Project - Gastroenterology:
We can watch the videos or download them; listen to the podcast; see some related photos or do a Pubmed search in that specific field of interest. DAVE stands for Digital Atlas of Video Education Gastroenterology…         |
| A Wrench for Social Engineering [Sciencebase Science Blog] Posted: 05 May 2008 07:00 AM CDT
Social engineering attacks, what used to be known as a confidence, or con, tricks, can only be defeated by potential victims taking a sceptical attitude to unsolicited approaches and requests for privileged information and resources. That is the message that arrives from European researchers. Most of us have received probably dozens of phishing messages and emails from scammers on the African continent seeking to relieve us of our hard-earned cash. Apparently, these confidence tricksters are so persuasive that they succeed repeatedly in hustling funds even from those among us with a normally cynical outlook and awareness of the ways of the world. On the increase too are cowboy construction outfits and hoax double-glazing sales staff who wrest the life savings from senior citizens and so-called boiler room fraudsters who present get-rich-quick schemes so persuasively that thousands of unwitting individuals lose money totalling millions of dollars each year. Con artists and hustlers have Now, Jose Sarriegi of the Tecnun (University of Navarra), in San Sebastian, Spain, and Jose Gonzalez, currently in the department of Security and Quality and Organizations, at the University of Agder, Norway, have taken a look at the concept of social engineering, and stripped it down to the most abstract level (International Journal of System of Systems Engineering (2008, 1, 111-127)). Their research could lead to a shift in attitude that will arm even the least sceptical person with the necessary social tools to spot an attempt at social engineering and stave off the attack with diligence. Fundamentally, the researchers explain, social engineering is an attempt to exploit a victimsocial engineering is an attempt to exploit a victim, whether an individual or organization, in order to steal an asset, money, data, or another resource or else to make some resource unavailable to legitimate users in a denial of service attack or in the extreme instigate some terrorist, or equally destructive, activity. Of course, a social engineering attack may not amount to a single intrusion, it could involve layer upon layer of deceptions at different places and on different people and resources. The creation of a sophisticated back-story, access to less sensitive resources, and targeting of the ultimate goal is more likely to be a dynamic process. This, the researchers suggest, means that looking for “heaps of symptoms”, as might occur in attempting to detect someone breaking into a computer system, is no longer appropriate and a dynamic response to a dynamic attack is more necessary now than ever before. Recognising the shifting patterns of an ongoing and ever-changing social engineering attack means better detection of problems low in the metaphorical radar, the team suggests. Better detection means improved efficacy of security controls. The best defence is then to build, layer-by-layer, feedback loops that can catch an intruder at any of many different stages rather than relying on a single front-line defence that might be defeated with a single blow. A post from David Bradley Science Writer A Wrench for Social Engineering |
| Scientists discover why plague is so lethal [Think Gene] Posted: 05 May 2008 04:05 AM CDT Bacteria that cause the bubonic plague may be more virulent than their close relatives because of a single genetic mutation, according to research published in the May issue of the journal Microbiology. "The plague bacterium Yersinia pestis needs calcium in order to grow at body temperature. When there is no calcium available, it produces a large [...] |
| Bacterial slime helps cause serious disease [Think Gene] Posted: 05 May 2008 04:05 AM CDT Leptospirosis is a serious but neglected emerging disease that infects humans through contaminated water. Now research published in the May issue of the journal Microbiology shows for the first time how bacteria that cause the disease survive in the environment. Leptospirosis is a major public health problem in South East Asia and South America, with over [...] |
| Scientists identify genomic ‘fingerprint’ for alcohol-induced heart failure [Think Gene] Posted: 05 May 2008 03:49 AM CDT A person with dilated cardiomyopathy has an enlarged and stretched heart cavity, usually too weak to pump normally; most people will go on to develop heart failure. While clinicians know that up to 36 percent of all cases of dilated cardiomyopathy may be due to excessive drinking, it has been difficult to differentiate between alcohol-induced [...] |
| Posted: 05 May 2008 03:48 AM CDT Finding also raises questions about the use of sentinel node biopsy with prophylactic mastectomies in high-risk women A preliminary analysis of ongoing research suggests that high-risk women with breast cancer who do not have a BRCA1/2 mutation may face a greater chance for developing a second breast cancer than previously thought. With the increased risk of [...] |
| Second genetic link to weight and obesity [Think Gene] Posted: 05 May 2008 03:47 AM CDT New DNA variants found that can help to pile on the pounds A study of 90,000 people has uncovered new genetic variants that influence fat mass, weight and risk of obesity. The variants act in addition to the recently described variants of the FTO gene: adults carrying variants in both genes are, on average, 3.8 kg [...] |
| Around the web - May 4, 2008 [business|bytes|genes|molecules] Posted: 04 May 2008 04:23 PM CDT It’s been a while, so will jump right into it. Linkfest
Multimedia & Presentations
Blogspotting
Events
Self AssemblyNot much really. Had fun at Bio-IT World, which is the perfect conference for me, a place where I can combine work with subjects (and hardware) that really get me excited. Someday, Bio-IT World will be a mix of the current Bio-IT, Web 2.0 Expo and Gnomedex; a gathering of minds and industry folk. I do have my macbook pro now and wishing I hadn’t taken the bad Windows/Dell detour late last year.  |
The 
What is this thing called ‘Life?’ One popular game in the relevant area of philosophy is to provide robust counter examples, which reveal failures in operational definitions of life. Failed attempts include physiological, metabolic, biochemical, genetic and thermodynamic definitions of life, all of which face problems. For example, a metabolic definition finds it hard to exclude fire (which grows and reproduces via chemical reactions), a biochemical definition does not exclude enzymes (which are biologically functional but not living systems), while a thermodynamic definition does not exclude mineral crystals (which create and sustain local order and may reproduce).
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