Tuesday, February 09, 2010

Disclaimer: I am not a poet

I had to write a short explanation of my research (to be put on the lab's website), and in the process of figuring out how to explain it concisely, I, in a fit of conceit, proclaimed that it would be just as easy to write it as a sonnet. My father suggested a Haiku. So here is the published (drabble: 100 words) version, a haiku veresion, and a sonnet version. I know the Haiku doesn't get into specifics, and the sonnet has some dodgy rhymes and phrasing, but they were written rather quickly.


I am interested in the epigenetic regulation of placental development, in particular the role of DNA methylation. The epigenetic profile of the placenta appears to be more flexible and dynamic than the embryo proper, as evidenced by significantly lower levels of total DNA methylation and striking loss of imprinting at many loci in extraembryonic tissues. However, knockouts or inhibition of the DNA-methylating enzymes (DNMTs) result in malformation of the placenta. I am examining the role of DNMTs in the placenta with tissue-specific knockdowns, and using high throughput sequencing techniques to clarify the extent of loss of imprinting in the placenta.
How cells interpret genomes
And environment
Though strictly controll'ed in embryo
The genome seems more flexible outside
And where development will progress slow
Environment must always be denied

Those marks which seem to regulation tied
Are rarer far in afterbirth than son;
And in placenta both alleles transcribed
Which fetus sees the choice of only one.

And yet those tissues with controls undone
In both the embryo and extra part
Are compromised and stunted every one
So necessary the controlling mark

I study why this freed placenta fails
And what its flexibility entails.

Friday, February 05, 2010

The first Friday of the Month...

Is, generally speaking, the worst day of the month in terms of getting anything done for me. Reason being, the first Thursday of every month is a fellowship meeting during which people present their progress over the course of the past year, and these presentations have almost always shaken my dedication to the scientific enterprise as a whole. They're poorly done, inconclusive, misrepresented, and it seems like almost everyone is just doing random, unconnected experiments, most of which do not work, in the hopes that someday they'll be able to find a thread that ties their experiments together and publish.

Seriously? This is science?

Yesterday's talks were made worse by one person who actually said that, as he was writing a manuscript at the time, he intentionally removed all identifying information from his single data slide. That, more than anything, struck me as very strange. I'm used to talking about everything to everyone. Talking through a problem is often my most effective way of figuring out how to solve it, and explaining a success is often my most effective way of figuring out where to go next, where the holes remain in hypothesis and theory that need to be shored up. What was he afraid of; that we would rush off and tell a competing lab, who would scoop him? Were he working with a company, and dealing with the nondisclosure and confidentiality clauses that allow for competition between biotech firms, I could understand his reticence, perhaps. On the other hand, in my idealized version of academia it is progress and the spread of ideas that is important, and not who thought of it first: Newton or Leibniz, the Calculus is the same.

Conferences and seminars can be full of unpublished or soon-to-be-published results; which is one reason why conference abstracts are largely misleading and often disproved later. And grants, of course, must be based on preliminary data; some comes from previous papers and my sense is that in the best grants, some comes from unpublished results. So in a way, it is true that communicating one's research even before it is ready to be published in a journal is an important part of science. What's more, this was a fellowship meeting -- a group which was designed and existed largely to support the research of the students who were presenting; it was not a thesis committee meeting, certainly, and it wasn't a lab meeting, but it was the next closest thing. What did this student have to fear, or think he had to fear, that caused him to remove all trace of data? On the other hand, I have several times balked from posting any specifics of my research here, in part because I don't think it would hold many people's interest, but mostly because it seems terribly unprofessional to post unpublished information on a private blog. That justification falls apart as well, I find, in an internal scientific meeting designed to be an annual litmus test of progress and provide support and ideas for those in need.

I'm not certain I remember this correctly, but I think when I went to hear James Watson speak, he said that the biggest difference between successful scientists and unsuccessful scientists was that successful scientists talked to everyone, absolutely everyone, about what they were doing. At the same time, fear of being scooped plays a huge role in The Double Helix. Maybe it would have been safer for them to say nothing, but to worry that every single thing they said would make it back to Linus Pauling, and provide for him the key to the riddle they were trying to solve, was not constructive. And in the end, it's hard to say whether the final breakthrough in that particular story was the result of any particular conversation, but it's likely that without as many conversations with as many different people as they did have, they would not have been able to make the discovery.

I'd like to think I live in a society (academia) where openness and collaboration is paired with success and progress more often than not. I think that the scientific enterprise requires communication, and not just because we see farther standing on the shoulders of giants. And when I feel like the status-quo, on the other hand, is secretive and reclusive and more focused on order of publications that spread of knowledge, it is yet another thing that disillusions me. On the up side, there was free food, and leftovers for today. It seems like a strange trade: we'll feed you, if you give us your hopes and dreams and idealism. But in a depressing sort of way, perhaps that's the trade that most people make every day of their lives. At least I only have to be reminded of it once a month before retreating back to my ivory tower.