1. What made you want to be a chemist?

I took high school biology from a person who spent the first third of a semester teaching us about atoms and molecules, because he saw life as a chemical phenomenon. I’ve been entranced with the edge of life ever since, and have spent my entire career on that cusp, sometimes venturing into biology, and sometimes into chemistry. The structural beauty of crystallography and informational nature of nucleic acids seduced me into working at their interface. Being able to make things, rather than just analyze them, vectored me into structural DNA nanotechnology.

2. If you weren’t a chemist and could do any other job, what would it be – and why?

Chemistry gives me an outlet for my creative urges. If I couldn’t do that, I’d probably try to be an artist (though I lack talent in that direction). I’m a totally visual person, with not a lot of response to acoustic phenomena.

3. How can chemists best contribute to the world at large?

By doing what they do – creating and analyzing new forms of matter, and gaining control over the structure of matter on the finest possible scale. Saying that, one cannot forget that chemists are subject to the same social responsibilities as other citizens of the world, and they must recognize them.

4. Which historical figure would you most like to have dinner with – and why?

Probably one of the early empiricists, such as Bacon. It was a huge conceptual leap to go from arguing about what might happen in some circumstances, to actually looking to find out. I would hope my dinner companion had eclectic culinary tastes.

5. When was the last time you did an experiment in the lab – and what was it?

I’ve never done much in the wet lab. Mostly, I’ve programmed and modeled. I continue to model.

6. If exiled on a desert island, what one book and one CD would you take with you?

My favorite author is Thomas Pynchon, but if exiled alone on a desert island, his paranoiac tilt would not resonate with the isolated circumstances. I’d probably try to take a book on how to build boats from earth, air, fire and water, or more conducive materials if they were present. I don’t listen to music, so I would trade in the CD for a DVD, probably of ‘Casablanca’.

Ned Seeman is in the Department of Chemistry at New York University and works on structural DNA nanotechnology. He builds objects, lattices, and nanomechanical devices from DNA.

IMHO the way we present genomic and proteomic data on the web sucks.

Part of this is down to the fact that our basic visualizations are a bit lame. Not the one-offs you see rendered for the front of magazine covers or science documentaries on TV, the everyday ones you get in journal articles and the big genome browsers. The ones scientists actually use. Pages like this. Seriously, how much of that page is actually useful to any one researcher? Does anybody wonder why people need training courses to use genome browsers? Does it really make full use of the web as an interactive medium?

This isn’t a dig at Ensembl, incidentally. Ensembl is an excellent, progressive resource and their last application note hinted at cool things to come. It’s more of a general complaint: why are we stuck representing genomic regions with flat images of lines and boxes (with the occasional flag or lollipop)? Can’t anybody think of a better metaphor? Try zooming out on the Ensembl page above. The features that make sense as individual elements when you’re looking at a single gene don’t scale as lines and boxes and the page becomes a mess.

Speaking of zooming out, why is everything static? Ensembl have already brought in dynamic image loading to some extent and the GBrowse prototype from Ian Holmes’ lab shows a lot of promise, but we’re still a long way away from any Google Maps style scrollable, zoomable genomes. It should be painless to jump a megabase to the right or left of wherever you’re currently looking in a genome browser, but that’s not currently the case.

When was the last shift in the way that we represented sequence alignments? NCBI’s BLAST just relaunched with a spiffy new interface, but the results still look like they’d be at home in a web browser circa 1990, which coincidentally was when sequence logos were first introduced.

Progress in visualizing biological networks is just as poor: is there ever a good reason to produce static images of large scale protein-protein interaction networks (where the text is too small, everything is a mess of connecting lines, attempts at grouping proteins together are – by necessity – one dimensional, etc. etc.)? Some authors think so. Network visualization software is already out there, somebody just needs to spend some time adapting it.

Ben Fry at MIT’s Media Lab – now well known for Processing – produced some great stuff while a grad student, but that was back in 2004. Does anybody know of any other groups or individuals who are currently exploring better ways of looking at life science data?

Perhaps issues of aesthetics and design are a low priority for the scientific community online and it’s more important to just get the data out there for people to use? As time goes on and we accumulate more and more data – while stuck with systems not designed to handle it – that could prove to be a problem.