Friday, October 24, 2008

The DNA Network

The DNA Network

Turning Oil Into Neuroscience [Bayblab]

Posted: 24 Oct 2008 06:46 PM CDT

This report just in - neuroscientist and Ottawa native Bruce McNaughton was lured back across the border from Arizona to the academic powerhouse that is the University of Lethbridge. The bait? A cool $20 mill from the province of Alberta - the Polaris award. A lot of people are saying "HOLY SHITBALLS!!!!! THAT'S A LOT OF $$$$$$$!!!" And right they are. That's almost as many hits as we get by the minute here at the BayBlab (although we certainly aren't getting paid any coin for it). But let's not get too worked up about the whole thing. After all, the guy had a paper in SCIENCE (tm) just last year. He's a SCIENCE (tm) SuperStar! SuperStars are SuperStars and so we shouldn't be surprised to see that it takes SuperStar cash to reel them in. This deal seems pretty reasonable to me when you line it up with some other Alberta blockbusters:

Bruce McNaughton (Neuroscientist): $20,000,000 over 20 years.
Jarome Iginla (Hockey Player): $21,000,000 over 3 years.
Stephen Harper (Politician): $840,000 over 3 years.
Boone Pickens (Oil Tycoon): $1,000,000,000 + per year.

So be warned world - Alberta oil is waving a big fat wad of cash and they're coming after your scientists! And by the looks of it, some of them might even be crazy enough to go live there...

Glow-Kitty []

Posted: 24 Oct 2008 04:08 PM CDT


We have just got to get ourselves one of these. We’re waiting for Mr. Greengenes to become the next Lolcat superstar.

Transgenic Turbo-Strawberries []

Posted: 24 Oct 2008 03:38 PM CDT


Strawberries just got a little sweeter.

Honey Bee Genomics Revisited [Genome Blog]

Posted: 24 Oct 2008 02:45 PM CDT

A couple of years ago I posted a blog about honey bee genetics after some of the wild speculation about GMO crops and cell phones being involved in the demise of the honey bee. This proved to be one of my most read blog postings. Today (October 24,2008), a headline in the Vancouver Sun announces that Genome B.C. is launching a $2.8-million research project that will investigate ways to halt the worldwide decline in bees. The three year study will be looking at bee genomics with regard to predicting and selecting bees that are more resistant to the mites and associated virus that seems to be involved with the decline of the bees. UBC biochemistry professor Leonard Foster will be leading the project. Certainly as more information is revealed, I will post more on this very popular topic.

Another study on European genetic structure [Yann Klimentidis' Weblog]

Posted: 24 Oct 2008 01:43 PM CDT

...this time focused on Northern Europe, and especially Finland, using 250,000 SNPs, STRUCTURE, MDS plots and other measures of population differentiation.
see Dienekes' post for STRUCTURE output, and other comments.

Health 2.0 Unconference [ScienceRoll]

Posted: 24 Oct 2008 01:02 PM CDT

Carlos Rizo (LinkedIn and Friendfeed profiles) and Francisco J Grajales III (LinkedIn and Friendfeed profiles) sent me some material about the ongoing Health 2.0 Unconference:

Live here from San Francisco these are the topics for today.

  1. Transparency, the role of healthcare quality in health 2.0.
  2. Stress solutions  of current times.
  3. What would you do with $30 Billion for healthcare?
  4. The doctor/patient appointment in the health 2.0 world.
  5. Is a direct (Active) human interface better than passive interface for Health 2.0 social networking.
  6. The place for professionally development + vetted control in the user generated eco-system.
  7. Health 2.0 Accelerator.
  8. Inspiring fitness lifestyle using carrots rather than sticks.
  9. Data reliability and interoperability in the patient social networks Connecting health 2.0 platforms and traditional healthcare providers.
  10. Wireless health, Cellular Technologies in healthcare.
  11. Challenges of engaging different demographics in health.
  12. Genetic privacy.
  13. Can clinical training measurably impact quality?
  14. Health 2.0 and health travel and medical tourism.
  15. Linking emergency medicine with people and PHI.
  16. Scoping business systems integration Modeling and Health care 2.0?
  17. Video Games for Health.
  18. Online Patient Self management interventions.
  19. Advise to the established providers, responses to change.
  20. Health 2.0 tools for independent living for people living with disabilities.
  21. Navigating healthcare tangled financial times.
  22. Physician engagement.
  23. User moderated content vs user generated content.
  24. Social network and the pharmaceutical industry
  25. Rules of engagement between patient record and online media.
  26. Clinical Decision support.
  27. Do you want to buy healthcare online?
  28. The national dialogue (telling the candidates what needs to happen in IT).

I cannot be there because of my bloody neurology exam on Monday, but I highlighted the topics I’m really interested in. I’m wondering when I can present Webicina to the innovative people of the Health 2.0 conference.

An image taken by Cisco


Repair Stem Cell Institute Clarification and ESC hurting ASC research [Mary Meets Dolly]

Posted: 24 Oct 2008 12:19 PM CDT

A few days I blogged about the Repair Stem Cell Institute which has a large list of diseases being treated with adult stem cells in other countries. Don Margolis, the man behind the RSCI, e-mailed me with a clarification. Here is what Mr. Margolis had to say:

Thank you very much for your mention of us in your post. What you stated in your post is the same reason I formed the Repair Stem Cell Institute in the first place. I was (and still am) angry that we in the USA have the greatest medicine ever discovered- adult stem cells and are unable to use it or have access to it unless a patient goes to China, Argentina, etc.

Just to be 100% clear (if my comment on your post was not), we are a public service company (not a stem cell treatment company) and we just want to promote the benefits of adult stem cells (or as I like to call them, Repair Stem Cells) and give sick patients the help and hope that they need. The list of diseases is one that we have compiled from the 7 stem cell treatment center companies who meet our standards and we don't receive any money from these centers. It is just for the patient's info if they decide to seek out treatment.

Since we are trying to spread the word, I humbly ask if you could add our websites to your links and blog roll respectively as well as my blog - focusing on adult stem cell success stories.

Thank you so much Don Margolis and up the good work!

As Don Margolis pointed out adult stem cell research is not getting the attention it deserves in the United States.  It seems England has the same problem.  A major adult stem cell researcher is leaving England to work in France because England over-focuses on embryonic stem cell research and cloning.  From Times Higher Education:

Colin McGuckin, professor of regenerative medicine at Newcastle University and an expert in adult stem cells, this week hit out at both his university and UK funding agencies. He said that they were prioritising embryonic stem-cell research above work with adult stem cells, despite the more immediate clinical benefits offered by his work.

Professor McGuckin plans to leave for the University of Lyon in January, taking a research team of about ten from Newcastle, including his research partner Nico Forraz. He will open the world's biggest institute devoted to cord blood and adult stem-cell research at Lyon.

He said that France had kept a "much more reasoned balance" between supporting adult and embryonic stem-cell research, unlike the UK, which had focused on embryonic research to the detriment of adult stem-cell research.

"(France) is very supportive of adult stem cells because they know that these are the things that are in the clinic right now and will be more likely in the clinic," he said. "A vast amount of money in the UK from the Government has gone into embryonic stem-cell research with not one patient having being treated, to the detriment of (research into) adult stem cells, which has been severely underfunded."

"We desperately need more funding for adult stem-cell research because with these cells we really can make a difference to patients' lives, and we can do it now, not in ten years' time as is promised for embryonic stem cells," said Anthony Hollander, a professor of rheumatology and tissue engineering at the University of Bristol.

Using spam to break bad news [Discovering Biology in a Digital World]

Posted: 24 Oct 2008 11:15 AM CDT

10.1371_journal.pmed.0050213.g001-M.jpgI probably shouldn't find this amusing, but...

Back a few years ago, a friend of mine worked at a biotech company in Seattle that had large windows looking out onto Puget Sound. They always cheered when the Navy ships came in, 'cause they knew it meant they'd have more work.

Tom Joe has a funny post about the same topic, with a different twist. He's not talking about learning your status through any sort of laboratory test. He suggests using e-mail.

UPDATE: Since Bora pointed out the PLoS article in the comments, I thought I should add some of the pictures from the article. I love the quote on one of them, "its' not what you brought to the party, it's what you left with."

Oh yeah, and if you should need a postcard, you can get one at

Read the comments on this post...

The Genetic Tests Results are in ... Now What [Genome Blog]

Posted: 24 Oct 2008 11:15 AM CDT

That was the topic of a Forum I spoke at this week and it was one of the more interesting ones  I've been part of since I had my 23andMe and deCODE tests done and posted on the 'net. For a start the rest of the panel had me experiencing some trepediation going into the evening and once they started to talk I may have actually felt a bit more nervous. Dr. Elaine Mardis, Washington University at St. Louis;Dr. Wylie Burke, University of Washington; Dr. Darren Platt, human genomics scientist and former Senior Director of Research at 23 & Me and the moderator was Dr. Michael Morgan CSO for Genome Canada. And me - a former journalist turned Communications Director with a ranch and a past that never really touched the world of science.
In the end though I didn't have to worry because my views and experience with scientists proved  to be in fact real and useful. Scientists have to discover how things work, collect the data, translate it and maybe even commericalize it. Communications staff have to take all the
information and make it real.

Number Crunching and Evidence-Based Medicine [adaptivecomplexity's blog]

Posted: 24 Oct 2008 10:32 AM CDT

Newt Gingrich, John Kerry, and someone named Billy Beane (I have no clue who he is) argue that medicine is not yet sufficiently data driven.:

In the past decade, baseball has experienced a data-driven information revolution. Numbers-crunchers now routinely use statistics to put better teams on the field for less money. Our overpriced, underperforming health care system needs a similar revolution...

Remarkably, a doctor today can get more data on the starting third baseman on his fantasy baseball team than on the effectiveness of life-and-death medical procedures. Studies have shown that most health care is not based on clinical studies of what works best and what does not — be it a test, treatment, drug or technology. Instead, most care is based on informed opinion, personal observation or tradition.

read more

Tid Bits - Financial Crisis Edition [The Daily Transcript]

Posted: 24 Oct 2008 09:09 AM CDT

The New York Times Editorial Board on Proposition 1: Courting Chaos in Massachusetts

From NPR, Brian Lehrer interviews Naomi Klein. Also check out her latest book, The Shock Doctrine.

And if you missed it here's Klein on the Colbert Report:

Note trhat even Colbert is shocked by Klein's last line on the prison industrial complex.

Thomas Frank, Columnist for the Wall Street Journal and author of What's the Matter with Kansas?, wrote an excellent expose on how right wing ideology drove the current wave of corruption in Washington. This new book is called The Wrecking Crew and I highly recommend it.

Alan Greenspan on the unfettered free market:

Those of us who have looked to the self-interest of lending institutions to protect shareholders' equity, myself included, are in a state of shocked disbelief


This modern risk-management paradigm held sway for decades.The whole intellectual edifice, however, collapsed in the summer of last year.

And lastly, if you haven't done this already, subscribe to NPR's Planet Money Podcast - one of the best sources of information out there on the financial crisis.

Read the comments on this post...

Sequencing cancer genomes: the inside story [Genetic Future]

Posted: 24 Oct 2008 09:05 AM CDT

Over at PolITiGenomics, Washington University's David Dooling discusses his work as part of the Tumor Sequencing Project. The TSP and a variety of other groups (like The Cancer Genome Atlas) are using large-scale sequencing to create comprehensive maps of the genetic changes that underlie cancer formation.

The cancer genome sequencing community have already made impressive headway - Dooling notes two papers in this week's edition of Nature, one from the TSP on lung adenocarcinoma, and another from The Cancer Genome Atlas on glioblastoma (which received extensive media attention when it was published online back in early September).

It's worth noting that both studies relied heavily on old-school sequencing technology to generate their data, and focused their attention on sets of candidate genes with an a priori probability of being involved in cancer formation. This really emphasises the long time delay between data generation and publication: as Dooling notes, the TSP has been applying next-generation sequencing methods to generate whole-genome data for the last year and a half, while TCGA is doing the same thing on an even larger scale. In other words, many of the methods described in these two papers have been largely obsolete for over a year - but such is life in the fast-moving field of genomics.

Dooling rather sensationalistically titles his post "Towards a cure for cancer" - I suppose this is fair enough, since the novel molecular pathways of cancer formation uncovered by these analyses will almost certainly eventually provide new drug targets for chemotherapy. However, it's worth bearing in mind the incredibly long and tortuous road between target identification and successful drug launch: genomics will provide a powerful starting point, but by itself it won't cure cancer.

Read the comments on this post...

Sound advice on applying to grad school [adaptivecomplexity's blog]

Posted: 24 Oct 2008 08:38 AM CDT

From Cosmic Variance:

It's usually not a good idea to have one of your parents call the department on your behalf.

I'm surprised this even needs to be said.

read more

A bizarre comment from John Hawks [Genomicron]

Posted: 24 Oct 2008 08:26 AM CDT

If you don't read John Hawks's blog, you probably should. He regularly has interesting posts about human evolution, and he appears to be someone who is sincerely interested in research and education. You can imagine, therefore, that it would be puzzling to me that he so badly missed the point about a recent review of the video game Spore in Science magazine.

John's basic points in the post appear to be:

1) The scientists who critiqued the scientific basis of the game are "whiners".

2) Dude, it's only a game.

3) He hasn't played the game, but there is no reason to criticize it from a scientific viewpoint.

4) Science shmience, the review should have told us how fun it is instead.

Some context is perhaps necessary here. The game has been promoted as being about science, in particular evolutionary processes. You can check out part of the documentary that was produced by National Geographic here. SETI has endorsed it on their webpage. A representative from the developer was quoted in the article as noting "Since the game's release we've received a lot of interest from various schools and universities around the world, so that's a good sign that there's a lot of interest in [the] academic/education community." Dude, it's not just a game.

Within this context, a scientific journal contacted several researchers to provide comments on the game from the perspective of the science. It would seem reasonable, therefore, that the comments we gave were about science. If you want to see a review of how entertaining or interesting from a gaming perspective it may be, Science is not the right publication.

John also dislikes some of our ideas about how the game could be made more realistic, if indeed the goal was to simulate biology. We suggested some things like having consequences for design choices, a cost for major physical updates (e.g., less than 100% refund for exchanging parts), and some limitation on how much you can change in any single upgrade. All of these features can be found in other games.

Cancer Carnival Call for Submissions [Bayblab]

Posted: 24 Oct 2008 07:45 AM CDT

The 15th edition of the Cancer Research Blog Carnival is coming up, but we've only had a trickle of submissions. It's not too late! Either start typing or dig up your best cancer blogging from the past month and submit it here. The carnival will appear Friday, Nov. 7.

As always, we're looking for future hosts so drop us a line if you're interested and head to the carnival homepage for submission and hosting guidelines and past editions.

Open Access in Africa [Sciencebase Science Blog]

Posted: 24 Oct 2008 07:00 AM CDT

development-heatmap-africaThere is much talk about Open Access. There are those in academia who argue the pros extensively in all fields, biology, chemistry, computing. Protagonists are making massive efforts to convert users to this essentially non-commercial form of information and knowledge.

Conversely, there are those in the commercial world who ask, who will pay for OA endeavours and how can growth (current recession and credit crunch aside) continue in a capitalist, democratic society, without the opportunity to profit from one’s intellectual property.

Those for and against weigh up both sides of the argument repeatedly. However, they often neglect one aspect of the concept of Open Access: how they might extend it to the developing nations, to what ends, and with what benefits.

Writing in a forthcoming paper in the International Journal of Technology Management, Williams Nwagwu of the Africa Regional Center for Information Science (ARCIS) at the University of Ibadan, Nigeria and Allam Ahmed of the Science and Technology Policy Research (SPRU) at the University of Sussex, UK, suggest that developing countries, particularly those in Sub-Saharan Africa (SSA), are suffering from a scientific information famine. They say that beginning at the local level and networking nationally could help us realise the potential for two-way information traffic.

The expectation that the internet would facilitate scientific information flow does not seem to be realisable, owing to the restrictive subscription fees of the high quality sources and the beleaguering inequity in the access and use of the internet and other Information and Communication Technology (ICT) resources.

Nwagwu and Ahmed have assessed the possible impact the Open Access movement may have on addressing this inequity in SSA by removing the restrictions on accessing scientific knowledge. They highlight the opportunities and challenges but also demonstrate that there are often mismatches between what the “donor” countries and organisations might reasonably offer and what the SSA countries can actually implement. Moreover, they explain the slow uptake of Open Access in SSA as being related to the perception of the African scientists towards the movement and a lack of concern by policymakers.

The researchers suggest that the creation of a digital democracy could prevent the widening information gap between the developed and the developing world. Without the free flow of information between nations, particularly in and out of Africa and other developing regions, there may be no true global economy.

“Whatever might emerge as a global economy will be skewed in favour of the information-haves, leaving behind the rich resources of Africa and other regions, which are often regarded as information have-nots,” the researchers say. It is this notion that means that it is not only SSA that will lose out on the lack of information channels between the SSA and the developed world, but also those in the developed world.

The current
of the
globalisation process is
leaving something
very crucial behind
The current pattern of the globalisation process is leaving something very crucial behind, namely the multifaceted intellectual ‘wealth’ and ‘natural resources’ of Africa,” they add. “The beauty of a truly globalised world would lie in the diversity of the content contributed by all countries.

From this perspective, they say, the free flow of scientific articles must be pursued by developing countries, particularly SSA, with vigour. “African countries should as a matter of priority adopt collaborative strategies with agencies and institutions in the developed countries where research infrastructures are better developed, and where the quest for access to scientific publication is on the increase.”

They suggest that efforts could begin locally having found that even within single institutions in most African countries, access to scientific articles is very scant. “Local institutions should initiate local literature control services with the sole aim of making the content available to scientists,” they suggest.

Proper networking of institutions across a country could then ease access to scientific publications. One such initiative in Nigeria has started under the National University Commission’s NUNet Project but wider support from governments is necessary to build the infrastructure. Research oriented institutions could use their funds to grant free access to their readers, especially given that many already pay subscription fees for their readers in large amounts.

Williams E. Nwagwu, Allam Ahmed (2009). Building open access in Africa International Journal of Technology Management, 45 (1/2), 82-101

Open Access in Africa


joyce said...

The Agribusiness Sector
Long development times of up to 15 years means that the sector is dominated by six multinationals BASF,Bayer CropScience,Dow Agrosciences, Dupont,Monsanto and Syngenta.The Agricultural Biotechnology Council (ABC) is the intermediary for the multinationals.The UK has world-class plant and crop science, particularly in the BBSRC institutes.The UK also has world-class animal science at the Roslin Institute, Babraham and the Institute of Animal Health.The Genesis Faraday Partnership in farm animal genetics and genomics based at Roslin has received BERR Bioscience Unit funding.Key issues for the sector include regulation and public perception (eg Genetically Modified crops).BERR is focusing on:

* improving the exploitation of the science base
* attracting inward investment
* fostering a societal climate in which innovation in agricultural bioscience is supported and welcomed


gillberk said...

The DNA Network is a Feedburner Network that is an aggregation of the latest headlines from blogs documenting the genome revolution.The DNA Network is not a money-making venture. We exist to make it easier for readers to learn more about current opinions on genetics, genomics, and health from a group of qualified experts.The DNA Network is growing not only in quantity but in quality.