The DNA Network

Pubget - The next step in the evolution of academic search engines [The Daily Transcript]

Posted: 12 Sep 2008 04:58 PM CDT

WOW! This website is order of magnitude better then Pubmed. I am totally converted!

And check this out, on the top right hand corner of Pubget are direct links to all the top journals:

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Cytogenetic arrays to the clinic - stat ! [biomarker-driven mental health 2.0]

Posted: 12 Sep 2008 02:29 PM CDT

Image via Wikipedia Doctor David Ledbetter gives an eloquent editorial overview in his piece, "Cytogenetic Technology: Genotype and Phenotype" [doi: 10.1056/NEJMe0806570] on the renaissance underway in the field of medical cytogenetics. The use of high density arrays for genome-wide copy number variation has identified a slew of new sites showing recurrent microdeletion that are reliably found in patients with mental developmental disabilities (autism, mental retardation, schizophrenia to name a few). Ledbetter suggests that the 'genotype first' process of diagnosis is now much more effective with the help of the new arrays. He notes, "a pediatrician has the option of ordering this test as an adjunct to or replacement of a standard karyotype and can expect a much higher yield of clinically significant results". This is an exciting realization of the long-awaited promise of genetics in medicine.

10 argumenter for, ja du leste riktig, -for- genmodifisert mat [Tomorrow's Table]

Posted: 12 Sep 2008 01:27 PM CDT

No I dont yet speak Norwegian but Nils Reinton does.

He just translated the post "10 Things about GE crops to Scratch From Your Worry List"

Check it out here

Thanks SciPhu

Why the “Database Sale Story” is Silly [Think Gene]

Posted: 12 Sep 2008 01:20 PM CDT

It’s not a sale if your left hand pays your right.

Left… 23andMe: Right! Google (the world’s most successful mass computation company… and the most profitable)

Left… deCODEme: Right! deCODE (a genomics research company)

Left… Navigenics: uhhhhhh…. You don’t sell your test at a 250% mark-up from your competitors if your plan is to build the biggest genomic database first. However, you might lie about how the real market is “for the database” later when nobody buys your product… and hope that nobody remembers that the “customer” for that database is already supposed to be fronting the losses of your business.

I’ve heard chatter that some people are upset because 23andMe is likely getting special pricing from Illumina and that they are selling their tests ludicrously below cost.

23andMe isn’t operating by the meritocratic rules of business of profitability because of their private connections?

Gosh gee golly! That just ain’t how alls I remember learning the American Dream back at the ol’ high school like.

Well, don’t worry. Good ol’ Midwestern morals always win in the end, and attempts to nuke the market by artificially lowering the price are never rewarded.

I promise.

DNA News: Paternity Test Reveals Answers in Vasectomy Dispute [DNA Testing Blog]

Posted: 12 Sep 2008 12:46 PM CDT

Fox News reported that Brady and Mindy Hill of Arkansas is suing a medical facility after a failed vasectomy and miscarriage. The medical staff allegedly suggested that infidelity was the reason for the pregnancy, but paternity testing confirmed that Brady was the father. The Hills sued the staff for negligence and defamation, arguing that they [...]

Evolution vs. creationism in the classroom: evolving student attitudes. [Genomicron]

Posted: 12 Sep 2008 10:10 AM CDT

The August 2008 issue of Integrative and Comparative Biology has the following papers in a special section entitled Evolution vs. creationism in the classroom: evolving student attitudes.

Teaching evolution: challenging religious preconceptions
by Eric C. Lovely and Linda C. Kondrick

Trickle-down evolution: an approach to getting major evolutionary adaptive changes into textbooks and curricula
by Kevin Padian

Still creationism after all these years: understanding and counteracting intelligent design
by Barbara Forrest

Thomism and science education: history informs a modern debate
by Linda C. Kondrick

Teaching evolution (and all of biology) more effectively: strategies for engagement, critical reasoning, and confronting misconceptions
by Craig E. Nelson

Curricular reform and inquiry teaching in biology: where are our efforts most fruitfully invested?
by Brianna E. Timmerman, Denise C. Strickland, and Susan M. Cartsensen

Not all genetic tests are created equal [deCODE You]

Posted: 12 Sep 2008 09:33 AM CDT

Here are a few thoughts on Nic Fleming’s piece on personal genome scans, of which one was our own, deCODEme: Our genomes are all remarkably similar. And so it is the differences that are most interesting and important, and that make us who we are. The same can be said of genetic testing services. We at deCODE [...]

Let's talk about facts this election - Part VIII - John McCain DOES NOT support the troops [The Daily Transcript]

Posted: 12 Sep 2008 08:49 AM CDT

We ask our volunteer army to go out and fight for our country, the least we could do in return is to treat them well, regardless of whether any one of us supported the decision to send the army in the first place. One of the best pieces of legislation ever to be passed was the GI bill - it send many WWII vets off to college and helped build the large middle class. In contrast, the Bush administration has treated its soldiers and vet like crap. But let's focus on John McCain, of all politicians we should have expected that HE would have supported legislation that would have improved the lives of our current and ex-soldiers.

Let's look at his voting record:

McCain voted against the Webb amendment calling for adequate troop rest between deployments.
McCain voted against an amendment that would provide $20 million to the Department of Veterans Affairs (VA) for health care facilities.

McCain voted against increasing Veterans medical services funding by $1.5 billion in FY 2007 to be paid for by closing corporate tax loopholes.

McCain voted to table an amendment by Senator Dodd that called for an additional $322,000,000 for safety equipment for United States forces in Iraq.

McCain urged other Senate members to table a vote (which never passed) to provide more than $1 billion for National Guard and Reserve equipment in Iraq related to a shortage of helmets, tents, bullet-proof inserts, and tactical vests.

McCain voted against increasing the amount available for medical care for veterans by $650,000,000.

(All this info is from Booman Tribune, HT, Crooks and Liars)

Like the rest of the GOP, John McCain wants to cut taxes and spending, even if means screwing our soldiers and vets.

Again, it looks like John McCain fights for the upper crust, but not hard working Americans. Why? Could it be because after VietNam, John Sidney McCain III had his well-to-do family to support him? I'm not sure. All I know is that his record on this topic is indefensible.

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R&D efficacy revision? [Reportergene]

Posted: 12 Sep 2008 08:27 AM CDT

An ongoing LinkedIN conversation is wondering about the steady decrease in the discovery of drugs that would eventually reach the marketplace worldwide per year per billion dollars R&D investment. What does it mean? Basically, even if we daily develop new techniques, we are not discovering new drugs (Note, we are talking about Discovery, not Market).

Michael Gold, VP at GlaxoSmithKline spotlights:

Advances in molecular biology and molecular genetics made it pretty simple to isolate and characterize novel receptors, peptides etc. These technical advances were coupled with a belief that if you dissected a disease deep enough, we'd find a single root cause..some defective receptor or mis-folded protein. This led us to neglect cell physiology or as some call it now "systems biology" and become almost unable to deal with disorders that involve physiological systems and cascades.

Really, we don't need more cell lines.

Industry watching: Next generation biopharma [business|bytes|genes|molecules]

Posted: 12 Sep 2008 08:00 AM CDT

We wonder whether the traditionally do-it-all, own-it-all from every part of the value chain is sustainable. It's certainly a risky and costly model

That quote comes from Elliot Sigal, the CSO at Bristol Myers-Squibb. Bio-IT World has an article where it talks about Sigal’s proposal to make BMS a next generation biopharma company. Hmmm, wonder what that means.

As far as I can tell it means taking some of the blue sky research ethos of biotech and marrying it to the scale and commercial expertise of pharma and the ability to work in multiple therapeutic areas. Somehow I find that underwhelming, even distressing. Both are cliches to the core, and just words to a degree. What the industry needs is for people to think differently, not just talk about stuff that people talk about all the time.

It is somewhat obvious that the industry needs to marry agility and innovation with the ability to bring products to market, but the models chosen are wrong. I don’t know for sure what the right answers are, but people need to look at where the innovation is happening, what the key needs are, and how they can be leveraged into successful therapeutics and sustainable pipelines. It must come through new models of collaboration and IP sharing between academia/non-profit and companies big and small. People should focus on their strengths and core competencies and not do too much. Where I agree with him is on focus and the following

We actually set our discovery engine to less capacity than what we thought the whole organization needed so that we would force our portfolio strategy to go outside, level attrition, and to access innovation.

What they also should force themselves to do is rethink that access layer.

Sex and Social Networking [Sciencebase Science Blog]

Posted: 12 Sep 2008 07:00 AM CDT

Ultimately, the only truly safe sex is that practised alone or not practiced at all, oh, and perhaps cybersex. However, that said, even these have issues associated with eyesight compromise (allegedly), repetitive strain injury (RSI) and even electrocution in extreme cases of online interactions (you could spill your Mountain Dew on your laptop, after all). And, of course, there are popups, Trojans, packet sniffers and viruses and worms to consider…

No matter how realistic the graphics become in Second Life or how good the 3rd party applications in Facebook, however, unless you indulge in direct human to human contact in the offline world, you are not going to catch a sexually transmitted disease, STD. Real-world social networking is, of course, a very real risk factor for STD transmission, according to a new research report in the International Journal of Functional Informatics and Personalised Medicine. This could be especially so given the concept of ~~six~~ five-degrees of separation through which links between individuals are networked by ever short person-to-person-to-person bonds.

According to Courtney Corley and Armin Mikler of the Computational Epidemiology Research Laboratory, at the University of North Texas, computer scientist Diane Cook of Washington State University, in Pullman, and biostatistician Karan Singh of the University of North Texas Health Science Center, in Fort Worth, sexually transmitted diseases and infections are, by definition, transferred among intimate social networks.

They point out that although the way in which various social settings are formed varies considerably between different groups in different places, crucial to the emergence of sexual relationships is obviously a high level of intimacy. They explain that for this reason, modelling the spread of STDs so that medical workers and researchers can better understand, treat and prevent them must be underpinned by social network simulation.

Sexually transmitted diseases and infections are a significant and increasing threat among both developed and developing countries around the world, causing varying degrees of mortality and morbidity in all populations.

Other research has revealed that approximately one in four teens in the United States will contract a sexually transmitted disease (STD) because they fail to use condoms consistently and routinely. The reasons why are well known it seems - partner disapproval and concerns of reduced sexual pleasure.

As such, professionals within the public health industry must be responsible for properly and effectively funding resources, based on predictive models so that STDs can be tamed. If they are not, Corley and colleagues suggest, preventable and curable STDs will ultimately become endemic within the general population.

The team has now developed the Dynamic Social Network of Intimate Contacts (DynSNIC). This program is a simulator
that
embodies the
intimate dynamic and
evolving social
networks related to
the transmission of STDsa simulator that embodies the intimate dynamic and evolving social networks related to the transmission of STDs. They suggest that health professionals will be able to use DynSNIC to develop public health policies and strategies for limiting the spread of STDs, through educational and awareness campaigns.

As a footnote to this research, it occurred to me that researchers must spend an awful lot of time contriving acronyms and abbreviations for their research projects. Take Atlas, one of the experimental setups at the Large Hadron Collider at CERN in Geneva Switzerland. Atlas stands for - “A Toroidal LHC ApparatuS”. So they used an abbreviation within their acronym as well as a noise word - “A” and the last letter of one of the terms. Ludicrous.

But, Atlas is not nearly as silly as the DynSNIC acronym used in Corley’s paper, I’m afraid. Dynamic Social Network of Intimate Contacts, indeed! I thought the whole idea of abbreviating a long research project title was to make it easier to remember and say out lead. DynSNIC, hardly memorable (I is it a y or an I, snic or snick or sink or what. Students will forever struggle with such contrivances. They could’ve just as easily used something like Sexually Transmitted Infections Contact Social Intimate Networks - STICSIN. This would be a double-edged sword that would appeal to both to the religious right and to the scabrous-minded, depending where you put the break (after the Contact or after Social.

Courtney D. Corley, Armin R. Mikler, Diane J. Cook, Karan P. Singh (2008). Dynamic intimate contact social networks and epidemic interventions International Journal of Functional Informatics and Personalised Medicine, 1 (2), 171-188

Sex and Social Networking

surprise in my shared readings [Reportergene]

Posted: 12 Sep 2008 06:25 AM CDT

Some months ago, I've started to share my google reader readings. Because there is a feed of it, I put it in the wordle claws. It seems that I'm a very interested person in fluorescence and microscopy.

I can not recognize myself, I was quite sure to be a supporter of luciferase and in vivo imaging.

Around The Blogs [Bitesize Bio]

Posted: 12 Sep 2008 05:16 AM CDT

Highlights from the blogsphere this week include 25 million year beer, googlising your lab culture and, of course, the LHC rap.

Careers talk with Mr Big. Jonathan at Working the Bench shares some enlightening, and somewhat sobering, excerpts from a recent conversation he had with an industry leader on science careers.

Old beer. Aminopop covered recent work in which a 25 million year old yeast was revived, and then used to make beer. Yum!

Research Posters 2.0. Berci at ScienceRoll picked up on a new addition to SciVee, the science video sharing site. Now you can upload your research poster and make a postercast video to talk people through it.

Googling your lab. At Mario’s Entangled Bank, Mario outlines the lessons he thinks academic labs could take from Google’s famously generous work culture.

…and finally…

We couldn’t go through this week without at least mentioning the LHC project. Nobel Intent highlighted the excellent LHC rap, that explains what the project it all about.