My parents and I moved to the US from Russia when I was ten. I started learning English when I was six and now don’t really have an accent. This is why most people who meet me can’t tell that I wasn’t born in the States. I delude myself into thinking I don’t look all that Russian/Jewish, but obviously I do since my appearance is what most often gives me away (that, and the fact that I cross my sevens).

The immigration process wasn’t nearly as tough on me as it was on my parents. At 10 years old, I was just self centered enough to be insensitive the pain and separation that my parents were going through, having left everything they knew behind in Moscow. All the irritations, struggles, and stumbles were worth it. As far as I am aware, my parents never regretted leaving nor considered moving back (not that we had that option anyway).

Almost twenty years later, we are fully integrated into American society. My family and I have adopted all of its quirks, positives, and some of the negatives (lord, how I do love Cheetos). We are naturalized citizens, registered voters, and proud contributors to the economy (no, I don’t make much money, but I do spend a lot of it). I have never once felt sad for having left Moscow, never experienced regret. Not until yesterday, that is, when I received a notice for jury duty. For June 5. For the same day as the commencement and hooding ceremony that will harness all the pomp and circumstance that Harvard is capable of in order to put an official and florid end to my seven years in grad school. I was not a happy camper. All of a sudden, having registered to vote seemed kinda dim of me in hindsight.

So I exaggerate.

I didn’t regret anything, but I was plenty frustrated. I spent a day gearing up for a fight with the Massachusetts jury service. I was going to go in guns blazing into the phone call, trying to weasel my way into a different day to serve. The fight was going to go a little something like this: “Do what you will to me, arrest me if you have to (ok, maybe don’t arrest me) but I am not going to sit in a stuffy courtroom all day instead of walking in my own graduation. It is going to take an awful lot more than an arrest warrant to keep me away from JK Rowling. Please don’t tell her that though. That would be bad.”

But you know what? It wasn’t that bad. I explained that I had already postponed jury duty once (I think last time the date was right close to a committee meeting), that I was being awarded a PhD on June 5 and that, and that pleeeeeaaase help me, what do I doooooo? And you know, the man was supremely nice, congratulatory, and wonderfully calming. We happily negotiated another date for me to show up for jury duty. He did assure me that all kinds of doctors are accepted to serve on juries. Oh good. I was worried there for a second.

Although the online manuals are still are an important source of program information, a cool new development in the online crystallography world are the many new wikis that were started in the last year.

Mostly based on the mediawiki platform, these wikis are constantly updated with crystallographic tips and tricks and plain old documentation by everyone from the creators of these powerful packages to seasoned users and even beginners.

Like many micro-communities on the web, crystallographers have long gathered around the many email-centric news groups. The membership for some of these groups probably numbers in the thousands . Interestingly, some of these wikis were seeded after discussions on these newsgroups. And its quite often that one sees a email discussion summarized as a wiki article. Having just spent three hours to debug the installation of a new crystallographic package, I couldnt be happier.

For a summary of these crystallographic wikis check out this link

Cameron Neylon has a must-read post on the this aspect of the data commons :

So I started with the notion of paying researchers to make data available, originally phrased as ‘pay the journals to buy papers’. What I really meant was paying people to put research results somewhere useful. So let us imagine we can pay people to deposit data (we’ll figure out how later). We don’t want to be swamped with rubbish so the data has to be well structured, tagged up and machine readable. If we’re paying for it, we set the standards. We also want to encourage re-use of data, perhaps by paying a premium for the deposition of data that re-uses other data. And in turn, perhaps pay a premium to those whose data is re-used.

Funders are putting hundreds of millions into data centres that no-one is too sure what to do with. Maybe that money could be used more effectively to drive data deposition quality. Some funders may also see this as a good model for direct funding. Putting money in to drive the generation of specific data set. Channel funding through the foundation to pay groups to deposit the results rather than pay them to do the research. For small foundations or charitable concerns this may be a much more effective means of driving the outcomes they want.

• Boost the NIH budget by $10 billion
• Declaring a “second war on cancer”
• Apologizing for vetoing stem cell bills
• Appointing Al Gore as head of his new conservation initiative

favorite quotes:

“Let’s get these embryos into the hands of scientists who can use them for good.”

“In retrospect, having oil industry lobbyists edit our climate reports was probably a bad idea.”

About cancer – “Let’s finally rid our bodies of this weapon of mass destruction.”

Does anyone else think this is a legitimate change of heart? I feel like it is a political stunt aimed at winning votes for his party in the upcoming election.

I keep expecting to hear him come back today with “april fools”... Or, maybe I am still asleep and this is just one of those crazy dreams that feels all too real.

I thought I would make the first posting on an area of technology development that has been capturing my attention/imagination along with a lot of press lately – next-gen sequencing. The advances in this area have been nothing short of amazing. When I started graduate school in 1997, all the sequencing I did used either S-35 or P-32 and the enzyme Sequenase. I was thrilled when I could read 400 bases for a reaction. And even with automated sequencers available at this time, it still took warehouse-sized rooms filled with hundreds of these machines to decode a single human genome.

Flash forward ten years and I write a tech feature for Nature on genomics focusing on next-gen sequencing technology. These new systems are capable of producing the equivalent of a third of the human genome in a single run (1 to 4 Gigabases in most cases) from one machine. Although issues like read length are still being solved for applications such as de novo sequencing, the data is here now and the short read-lengths seem to be working.

But now developers are trying to move beyond even this tremendous output. Several weeks ago a company called Pacific Biosciences made a huge splash at the Advances in Genome Biology and Technology meeting when they announced the development of a system they claim will be able to deliver 100 Gigabases/hour by 2013. I did not miss type….100GB/hour is the prediction. Other developers are working on different technologies for a genome in less than an hour, but they all have the same goal—a fast, ‘$1000-genome’. And most developers think this is a very realistic. If you are interested in the technology behind Pacific Biosciences system—it is a very interesting approach to single molecule sequencing—check out Methagora, the Nature Methods blog, for technical details.

Some of you out there may have had the chance to use these new systems (Illumina, ABI, 454….anyone?), while many of you probably have not. But I am very curious to find out what everyone thinks about these developments and their potential to advance personal genomics and medicine. Is too much effort going into developing faster sequencing methods right now? Will you want your genome sequenced in the future, along with all the insights that could bring?

One of my favorite strangers in the whole wide world died this summer, but I just found out about it today. Grace Paley was a friend of mine, a person I loved, who could make me laugh and cry, mad as hell or happy like a little kid. What a way she had with describing everyday life. E. Annie Proulx’s writing reminds me a lot of Paley’s even though Proulx’s characters are full of rural twang these days (it makes me homesick to read Proulx’s stories anymore). Paley wrote of everyday people doing everyday things. She captured the majesty of mundane existence and the complexity of people’s inward selves, their simple joys and the tragedy of what comes to us all, in one way or another, if we live long enough. She taught us to smile anyway.

Grace Paley was a hero of mine. It’s a hard thing when your hero dies. It doesn’t make me feel older, just a bit more alone. I never got to meet Grace. That said, it sure seems like we knew the same people.

Aside from another name for the Roman god Jupiter, I found out yesterday that JoVE (Journal of Visualized Experiments) is an online, freely available, video database of experimental techniques. Now in its 4th issue, JoVE aims to address poor reproducibility of biological studies by bridging the gap between the methods sections of scientific papers and physical demonstrations of how to perform a technique. Currently arranged in five sub-sections, the site contains video footage of researchers performing advanced experimental techniques in Neuroscience, Developmental Biology, Cellular Biology, Microbiology and Plant Biology.

I thought it odd to call the site a ‘journal’ (opposed to ‘archive’ or ‘database’); especially because, at the moment, submissions are not peer-reviewed. Instead, ideas for submissions go through an associate editor with expertise in the field (there are some well-known names on the editorial board). According to the Editor-in-Chief Moshe Pritsker (speaking yesterday at a HMS postdoctoral association event) the journal format is to encourage submission of ideas and participation in the process by current researchers (its worth noting that JoVE will videotape and edit the final piece and so the researcher is not required to have skills in this area). There are certainly benefits to submitting videotaped experiments to the site, if the take-up rate is good then your expertise in a particular technique will be widely disseminated. Also, having a visual recording of a procedure may help to establish a standard operating procedure and contribute to more effective comparison of experiments between labs separated by distance.

Will people submit details of novel procedures to JoVE? Progress in biology is founded on the dissemination of ideas and techniques, and in theory, once a technique is published it is in the public domain unless patented. However, brief methods sections in written journals can potentially ‘buy time’ so that a lab pioneering the new technique does not lose its leading edge. In addition, publishing a less detailed methods section in the context of a full scientific paper can encourage interested parties to contact the lab that has published the technique and this may potentially lead to useful collaborations. It is likely to be difficult for JoVE to establish the kind of reputation that will encourage scientists to submit reports of novel techniques, and it may be that this idea of a visual record of experiments will be appropriated by the more established journals. How long before ‘print’ journals go multimedia and each technical article contains a weblink to the video record of the experiment?

All random speculations and theoretical considerations aside, I think that JoVE will become a useful resource because, as far as I can tell, the detailed demonstrations are of a good standard. Whilst video will not replace quality one-to-one tuition it’s still really useful for anyone who wants to check out a technique, in detail, before getting hands-on. Most people that I’ve showed it to far seem pretty impressed too. Check it out at: www.jove.com

NOVA/WGBH producer Larry Klein, a panelist on a Science in the Media session, argued that the gap between science and society that was the focus of the conference is not a gap unique to science. He noted that a similar gap exists between society and other areas of knowledge (including knowledge of the political process and world affairs) and that perhaps it is best to frame the issue as an education gap: educated elites version non-elites.

So it all comes down to education. Not a surprise, but a good point to make nonetheless. Al Gore, in his keynote talk, noted that “retrofitting new technologies [such as the Internet] into old educational setting[s]” is unlikely to accomplish much; he argues that “we need to re-think education.”

A vote in favor of teaching science was not an obvious bet in either case, though. Both Dover County and the Kansas Republican primary (all of the Kansas Democratic primary candidates were pro-science) had lots of voters who consider themselves very religious and very aligned with religious teachings on many political and moral issues.

So how did science win these votes? Did voters accept that science won’t threaten religion and that religion can’t be taught in public schools? Were voters wary of the cost and consequences of lawsuits challenging the teaching of intelligent design? Or was the electorate just tired of being ridiculed by every late night show on television?

I don’t know. You tell me.