The DNA Network

Will data-euphoria kill scientific theory? [The Daily Transcript]

Posted: 27 Jul 2008 04:19 PM CDT

Now that I have a good chunk of time where I'm not scheduled to run off to some distant land for vacation or to give some talk, I have decided to work extra hard. Right now I'm incubating my samples. This post is the result of me killing that time.

I want to bring up an article that appeared n WIRED over a month ago. I know, that's ancient history in the world of blogs, but it's an idea that pops up once in a while and it is common in certain young naive scientists. Let me just quote a passage from the article:

This is a world where massive amounts of data and applied mathematics replace every other tool that might be brought to bear. Out with every theory of human behavior, from linguistics to sociology. Forget taxonomy, ontology, and psychology. Who knows why people do what they do? The point is they do it, and we can track and measure it with unprecedented fidelity. With enough data, the numbers speak for themselves.
The big target here isn't advertising, though. It's science.

....

But faced with massive data, this approach to science -- hypothesize, model, test -- is becoming obsolete.

And here is the part that I want to focus on:

In short, the more we learn about biology, the further we find ourselves from a model that can explain it.
There is now a better way. Petabytes allow us to say: "Correlation is enough." We can stop looking for models. We can analyze the data without hypotheses about what it might show. We can throw the numbers into the biggest computing clusters the world has ever seen and let statistical algorithms find patterns where science cannot.

OK this is just plain naive. Collects tons of random data and out pops ... what? Correlations? A Google search? Is this the advent of Deep Thought? If so, I'm afraid that the answer will be as meaningful as 42.

I think that the underlying problem with the whole concept of replacing the scientific establishment with a Google like data cruncher is that it misunderstand how scientific insight is achieved. I would like to point out two trends in the biological sciences that have produced this Google-induced data-euphoria.

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Do I have the right to know my own genetic makeup? [On Genetics]

Posted: 27 Jul 2008 02:17 PM CDT

I took a little time yesterday (July 12) to attend a panel discussion on direct to consumer genetic testing at the Genetic Alliance annual conference. Panelists were Sue Friedman, from FORCE; Trish Brown, from DNA Direct; Joanna Mountain, from 23andMe and Sean George, from Navigenics. Francis Collins, Director of the National Human Genome Research Institute, moderated. Once each of the panelists had made their opening remarks, Collins started the discussion by asking why, if personalized genetics is so wonderful, the states of California and New York have issued cease and desist orders to several personalized genetics companies (story). The response was conciliatory, echoing statements on the 23andMe blog (the spittoon):

We agree that this evolving field of personal genomics is in need of proper regulatory oversight. While our mission to provide accurate and contextual information to our customers about their genetic information is aligned with the regulatory mandate to protect the public health, we also want to ensure that efforts to rein in our industry do not hamper the potential benefit of genetic knowledge to our health.

Many relevant issues were brought up, by panel members, or by those in the audience. Can people deal appropriately with uncertainty? Do they understand the relationship between genotype, the environment and phenotype? What about genetic information with predictive value, but about which the consumer can do nothing? The case of APOE was discussed at length.

I do feel that we have a right to obtain information about our own genetic makeup without having to justify ourselves, to a physician, to an insurance company, or to the state of California. I am also skeptical of the perception that "most people are incapable of grasping the relevance of provisional, statistical information." In any case, an enterprise that feeds users with 500,000 bits of information, most of which have no significance, seems more likely to help people understand that genotype is not fate than to have the opposite effect.

Giving people genetic information can be separated from giving them advice, and it seems to me that providing information about genotype should be regulated only to the extent that technical standards are met. This is analogous to surveyors giving me information about the elevation of my house. That information, by itself, is not advice about flood risk, and I would be surprised if surveyors were required to provide accurate assessments of that risk in order to operate, or forbidden from providing consumers with data that a third party judged to be of little value.

The panel helped me to understand the risk of consumer fraud, but, ultimately, I feel, strongly, that I have a right to know my own genetic makeup. Furthermore, I find it insulting to say that consumers are incapable of understanding uncertainty. There is certainly room for regulation, but I hope that my right to pay someone to tell me about my own genes is not infringed. Perhaps it is most important to prevent companies from taking money for tests without providing portable genotype data whose implications can be evaluated by a third party in the light of new information, which could be information about the implications of that specific information, other genetic information that might influence how it is interpreted, or information about the interactions between that bit of genotype and other factors such as one's diet or medical history.

Links for this article:

NHGRI (National Human Genome Research Institute), with news, links to research, funding opportunities, fact sheets, and career opportunities, including such tidbits as a Catalog of genome-wide association studies.

"Should Personal Genomics Be Regulated" Tim O'Reilley's blog on the subject (with interesting comments and discussion).

DNA Direct. DNA Direct's services focus on personalized test result interpretation and supportive materials and services.

Genetic Alliance. The Genetic Alliance works to eliminate obstacles and limitations within the genetics community through novel partnerships among stakeholders and integration of individual, family, and community perspectives to improve health systems and inform decisions.

The Spittoon (23andMe's forum): "... in step with regulatory oversight."

Getting geeky with Ruby and Python on Friendfeed [business|bytes|genes|molecules]

Posted: 27 Jul 2008 12:24 PM CDT

Image via WikipediaFriendFeed might be a subject of silly Silicon Valley blogger debates, but for the life science community it’s a lot more. The Life Scientists is a poster child for microcommunity, the ISMB2008 room was a wonderful example of a group of people coming together to make a conference come to life, and there are other rooms as well, e.g. for BioBarCamp

Now, something a little different, with the launch of two new rooms, Ruby for Bioinformatics and Python for Bioinformatics. More and more Bioinformatics/molecular modeling types are using those two languages. I am busy trying to recast myself as a wannabe Ruby hacker, so the opportunity to learn from people like Matt Wood is something I am looking forward to.

I quite like Ruby. It’s got some great functionality, a number of web frameworks and other associated utilities, and a wonderful community. While in the end, I don’t really think languages are religion, it would be nice to see more Ruby and associated frameworks in the life sciences. Perhaps a room like this will expose more people to the language.

Someone just pointed out that there is a room for R for Bioinformatics as well, so all you stats types, head there.

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Everybody is into bio these days… [My Biotech Life]

Posted: 26 Jul 2008 09:50 PM CDT

I was returning home on the MIT shuttle yesterday, when these two guys got on and sat on the bench behind me. They were talking rather loudly because the shuttle was full and noisy.
From what I could understand they were high school buddies. The conversation was about how they just graduated, one from MIT and the other from BU.

The MIT kid, possibly a computer science graduate, was going on about how all his friends were coders working at Cisco earning 33 bucks an hour. Some where at Google, got paid less but had better perks.

The BU guy followed by saying something along the lines: “Wow, 33 an hour! I should have gone into computer sciences…”. To what the MIT kid replied “Nah, everybody is into bio these days… That’s where the money is!”.

Shortly after, the MIT kid said “Anyways, I hate bio!”. The BU guy concurred with a simple “Me too”.

Everybody is into bio these days…