The DNA Network

Webcast: Genomic Medicine in Breast & Ovarian Cancer [ScienceRoll]

Posted: 17 May 2008 04:17 PM CDT

My good friend, Steve Murphy, is going to come up with something interesting again. Helix Health, the first stand alone genomic medicine practice in the US, will host a free 90-minute webcast on the 21st of May, 2008 from 1:00-2:30 PM EDT on:

How Genomic Medicine Is Changing the Management of Breast & Ovarian Cancer

Click here to register.

Every hour, 150 people in the United States are diagnosed with cancer. Yet today, there are a growing number of people who are not waiting to hear that diagnosis. They are undergoing genetic testing to determine whether they have a genetic predisposition to the disease.

That's exactly what Jessica Queller, author of Pretty Is What Changes, did after her mother, a breast cancer survivor, died of ovarian cancer. Jessica tested positive for the BRCA1 gene mutation and faced a most difficult decision. Jessica will join David Ewing Duncan, bestselling author of Masterminds: Genius, DNA
and the Quest to Rewrite Life, and a panel of distinguished medical and legal professionals to discuss how the doctor-patient relationship is changing and what the potential liability is for physicians in this new era of breast & ovarian cancer and genomic medicine.

What should a doctor and patient do when a patient tests positive?
What is the risk in taking a "wait and see" approach?
Are there alternatives to radical surgery?
What are potential tort issues in predictive genetic testing and medical uses of
genetic tests?

This posting includes an audio/video/photo media file: Download Now

Medicine 2.0 carnival at My MD Journey [ScienceRoll]

Posted: 17 May 2008 03:52 PM CDT

The 24th edition is up at the My MD Journey! Check out the many posts and news about the world of medicine 2.0 and health 2.0. Thank you, Y. S., for hosting Medicine 2.0!

Medicine 2.0 editions so far:

The next edition is due to be published on the 1st of June 2008 at Discovering Biology in a Digital World.

Submit your blog article to the next edition of medicine 2.0 using our carnival submission form.

And read about this interesting and emerging field here.

Microbial Evolution and co-Adaptation: A Workshop in Honor of Joshua Lederberg - Institute of Medicine [The Tree of Life]

Posted: 17 May 2008 03:00 PM CDT

Well, in a few days I am off to a cool workshop in honor of Josh Lederberg (for more detail see this link Microbial Evolution and co-Adaptation: A Workshop in Honor of Joshua Lederberg - Institute of Medicine). The goal of the workshop is to "to inform the Forum and the general public about the many scientific and policy contributions of Dr. Joshua Lederberg to the life sciences, medicine, and public policy."

The workshop is put on by the Institute of Medicine in Washington DC and it is open to the public. You have to register in advance and I am not sure how many more slots are available but it looks to be pretty good. The sessions topics are are: "The microbiome and co-evolution" "Microbial evolution and the emergence of virulence" "Mechanisms of resistance" "Anticipation of future emerging infectious diseases" and there are some heavy hitter speakers in there including David Relman, Jo Handelsman, Jill Banfield, Margaret Mcfall-Ngai, Stanley Falkow, Bruce Levin, Julian Parkhill, Stanley Cohen, Julian Davies, Steven Morse, Ian Lipkin, and well, me.

I will be blogging from there, but if you are in the DC area or can be, it could be a good workshop.

I am also going to be writing a bit more about Lederberg and his favorite bug (E. coli) in the next few days so stay tuned ...

Open Evolution - Open Taxonomy Mailing List [The Tree of Life]

Posted: 17 May 2008 02:50 PM CDT

In my continuing series on Open Evolution I am posting an email I got regarding the creation of a new mailing list on "Open Taxonomy". For more on Open Taxonomy see "The Other 95%" which has some really good stuff on it.

Under the umbrella of the Open Biomedical Ontologies project (OBO; http://obofoundry.org/) we have created a new mailing list, called obo-taxonomy, for the discussion of ontological representation of taxonomies and phylogenies. The OBO Foundry supports the development of orthogonal, interoperable reference ontologies for biological science.

The Phenoscape project (http://phenoscape.org) develops methods and tools for using ontologies to integrate comparative morphological data with mutant phenotypes of genetic model organisms. As such we are very interested in participation from members of the evolutionary biology community to explore how best to integrate taxonomy into an ontological framework. Issues include proper semantics of the relationship between taxonomic groups, and between specimens and species.

Subscribe to the mailing list:
https://lists.sourceforge.net/lists/listinfo/obo-taxonomy

Additional info:
http://blog.phenoscape.org/2008/05/15/taxonomy-as-ontology-opening-the-debate/

Acknowledgments:
The Phenoscape project (http://phenoscape.org/) is funded by NSF-BDI and supported by the National Evolutionary Synthesis Center (NESCent; http://nescent.org).

Life Hacks for Doctors: Slideshow [ScienceRoll]

Posted: 17 May 2008 05:03 AM CDT

Joshua Schwimmer, the author of the Efficient MD Blog and the Efficient MD wiki, came up with a fantastic slideshow about life hacks for physicians. According to Wikipedia:

The term life hack refers to productivity tricks that programmers devise and employ to cut through information overload and organize their data.

I guess I’ve been lucky [Mailund on the Internet]

Posted: 17 May 2008 03:58 AM CDT

Over at adaptive complexity there was a post yesterday discussing this editorial at sciencemag. It concerns the pipeline of young researchers into scientific careers and identifies the following problems:

In the competition for grants, it is difficult to get the first grant.
It usually takes two-three postdocs before getting on a tenure track.

Competing for grants

For point 1, the editorial mentions that the average age of the first independent grant is about 6 years after getting a Ph.D. Quoting adaptive complexity:

Part of the problem, as Leshner points out, is that younger investigators with new, unstaffed labs are automatically at a disadvantage when competing for funding with senior labs that, because of their already established research programs, are able to generate a lot more preliminary data to include in a grant proposal.

To which I would probably add that experience in writing grant proposals probably benefits senior scientists a bit as well…

In any case, in the competition for grants, it is probably safe to say that senior scientists — with their proven track record and experience in the field — are at an advantage. If they have an advantage, that means that young researchers are at a disadvantage, and if that means that they are rejected more often we have a problem.

Notice that I said if above. I have seen no statistics showing that young researchers are more likely to have a grant proposal rejected. From my limited experience and from what I’ve noticed with colleagues, the older you get the more grants you apply for (I apply for one or two a year now, and I certainly didn’t five years ago), so even if senior researchers are awarded more grants, that could just be proportional to the number of applications…

Anyway, regardless of why, we do have a problem if it is too hard or takes too long to get the first independent grant. Breakthroughs are often made by young researchers. There’s a saying that you are too old to make significant contributions to math after the age of 30. That might be a bit of an exaggeration, but I don’t expect completely novel ideas to be produced by the people who produced the current state of the art.

If we want the novel ideas from young scientists, we should let them work on their own ideas. Give them their own grants.

How do we do that? Leshner suggests:

If the consensus is that young scientists really need a regular research grant to launch their careers, why not simply tilt funding decisions more toward new investigators? After all, there are many more meritorious proposals from junior investigators–which have passed muster through peer review–than can be funded. The tilt would, of course, result in fewer senior investigators getting funded or receiving multiple grants, but if we are genuinely concerned about the pipeline, we will need to make this tradeoff.

I am not sure that I agree with this. I think that a grant should be granted on the merits of the proposal and the likelihood of the outcome, not on any other considerations such as age (or race, gender, religion, whatnot).

When evaluating an application, of course, the experience of the applicant should be taken into account, but this need not benefit the senior researchers. If you have worked a decade in a field, you had better be able to show a successful track record. If you are just starting out, you only need to show potential, and that is probably a bit easier…

That is not enough to solve the problem, of course, since I would guess that this is already the way grants are granted today.

So, after complaining about another’s suggestion I should offer my own up for criticism.

Offer smaller and short term grants, but offer more if them.

You won’t be able to solve the big problems this way, but if you need your own supercollider for a project your screwed anyway. With shorter, smaller projects (say one year projects and just money for strictly necessary equipment) there are more grants possible, and although you can do less in the timeframe of one, you get more of them for the same money, which means that more researchers can get their hands at them.

Since I don’t really need much equipment in my own research, I might be naive here in how this would work — I’m not sure how expensive it would be if the same equipment needs to be acquired at different groups and such — but reuse of equipment, or more collaborations between groups, could solve this, I think.

Getting tenure

If it takes ages to get tenure, my suggestion above could be a dead end. If you need new grants every year just to get your salary, you will spend more time writing grant proposals than doing science. It just becomes too important to get those grants.

You want some kind of guarantee that you have a job six months down the line. Not having that is one of the main problems I have with my life in academia, and a problem I know has caused friends of mine to give up on the university.

Shouldn’t we be able to do better than this? Couldn’t we somehow provide universities “young researcher groups” grants — grants that allow a university to employ young researchers for say 3-5 years for working on their own problems. Just the salary. Let them compete for additional grants as I suggested above, but give them a bit of job security! A university could pick the researchers for the group based on their potentials as scientists, but with no promise of future tenure or anything.

I guess I’ve been lucky so far…

In my own experience, I haven’t had major problems with getting grants, which is why I picked this title for the post.

After finishing my Ph.D. (in computer science) I got a one year post.doc. at the Bioinformatics Research Center, Uni Aarhus. This was a very free position, not unlike what I suggested for “researcher groups” above. I could work on anything I wanted, related to bioinformatics, and I didn’t answer to anyone (except, of course, that I needed to get some publications if I wanted to continue this career).

After the first year, the position was extended for two years. This time it was focused on association mapping, but that was my own choice, so in a sense I was still free to pick my own projects.

From this point on, all my grants have been my own. I have applied for the grants myself (with helpful suggestions from colleagues, of course) and picked the projects myself. So I guess I have been independent three years after my Ph.D. and at age 30.

Not completely independent for my first grant, I guess. That was a post.doc. in Oxford, but it was a grant I was awarded to go there and work on my own ideas, but in a post doc setting where I could learn from the experts rather than figure everything out on my own. The next grants I got, including the one financing me now, were completely independent grants.

In all honesty, I haven’t been competing with senior scientists as much, yet. I have gotten some grants in competitions where there are no restrictions on who can apply, but the major grants I’ve gotten were grants only available to researchers within 5 years of their Ph.D. These are small-ish grants not unlike those I suggested above. It’s major grants to me, working alone, but would be small for a research group with several postdocs and grad students.

I still haven’t achieved a tenured position, so when my current funding runs out (January 2011) I’ll be unemployed again. This bothers me a little bit, but I am optimistic about getting tenure soon-ish…

DNA Video: Twin DNA Differences [Eye on DNA]

Posted: 17 May 2008 03:14 AM CDT