Novel Findings in Publicly Available Data Sets

A group of researchers from the University of Sydney in Australia presented findings they obtained from a publicly available astronomy data set at the 211th meeting of the American Astronomical Society in Austin, Texas. What made it super interesting is that they concluded the Milky Way galaxy is twice as thick as originally thought!!

While I don’t understand the physics behind this, the point is that making data sets available publicly has great value because it expands the pool of researchers who can investigate a particular data set. This helps in validating findings but also in allowing researchers to test new ways of looking at data. Had the data been locked in someone’s closet, the original, presumably incorrect results would have been assumed for a longer period of time. In this case, the implications of the subsequent analysis were huge…a 6,000 light-year difference from the original results.

And it’s fortunate for the PhD student on the project who had the opportunity to work with a data set for her dissertation without having to collect it first. This allowed her to focus on her analysis methods rather than data collection.

See http://www.usyd.edu.au/news/84.html?newsstoryid=2163.

Biomedical Research and Innovation

Andy Grove, former CEO of Intel and fabled leader, trashed the biomedical research community in the US, stating that the current system discourages innovation. He has some interesting points.

It seems he’s simplifying quite a bit. I’m sure there are problems in the system and that innovation is reduced by near-sighted focusing on smaller ideas that can get funded rather than bigger questions that can win Nobel Prizes. However, I think those smaller pieces will continue coming together to address big problems over the coming years, despite some inefficiencies in the system (which should be addressed).

In a way, this reminds me of the Bill and Melinda Gates Foundation that aims to run their non-profit like a business to maintain high efficiency and wise use of resources. Maybe Grove can use his assets and leadership to show that something similar can be accomplished in biomedical research.

http://www.newsweek.com/id/68221/page/2

Designer Genomes?

Craig Venter’s latest pursuit is to artificially construct a chromosome of a simple bacterium and then insert it into an existing bacterium of another species with the goal of converting that organism to that specified in the artificial DNA. Lots of interesting ethical questions if you think about the long-term implications of this kind of capability.

http://www.guardian.co.uk/science/2007/oct/06/genetics.climatechange 

Sequencing Entire Genomes

In 2001, two groups published a version of the human genome. Each was a conglomeration of the DNA of multiple people. Recently, the entire genome of both Craig Venter and James Watson have been recorded. Venter’s genome has now been published.

This is significant because it means we are getting closer to having the entire genome for groups of people, which can help research efforts. Currently researchers and clinicians can only work with a snapshot of a person’s DNA. The intermediate goal, which is motivated financially by a a $10,000,000 reward by the X-Prize Foundation, is for a person’s genome to be sequenced for $10,000 or less in a reasonable amount of time. The ultimate goal is for clinicians to use a patient’s genome as a personalized guide in treating disease. (There are legal and ethical considerations with this, but it’s the ideal.)

What Is Needed for Biomedical Researchers to Collaborate?

A recent article on CNN states that big drug companies are starting to collaborate more in an effort to combine resources and mitigate risks. It sounds like these collaborations are for very specific purposes rather than wholesale sharing of resources (including data and tools).

One of the goals of translational informatics is to help disparate groups come together and share resources for a greater benefit. This article doesn’t mention any informatics methods drug makers are using. If they are not already using them, they could likely benefit from such methods.

Sharing resources between institutions is a big focus lately in academic research where competition is also fierce. The National Cancer Institute is sponsoring the caBIG(TM) project, which is one example of funders encouraging groups to collaborate and providing a framework that makes it easier. i2b2 is another data sharing initiative.

An ideal goal would be for public and private institutions to work together rather than in their own silos. However, this will only be possible as the rewards of success and the penalties of failure are shared (at least somewhat fairly) between participants. As the article suggests, this type of arrangement can open the door for fierce competitors to cooperate in ways that benefit both parties–and hopefully also consumers.