google genomics?

August 5, 2006 at 7:36 pm | Posted in research | 8 Comments

I went to a talk this week by Leroy Hood of the Institute for Systems Biology.  He talked about his group’s work on identifying genes that were involved in the pathogenesis of prion diseases (eg mad cow disease), but also about systems biology and Big Science in general.  The results he showed were pretty exciting, but I was most interested in the general discussion of different ways of approaching scientific problems.

Unsurprisingly, Dr Hood is a strong advocate for systems biology.  He talked about the need for sophisticated methods for measuring large numbers of outputs simultaneously, and about some very cool nanoscale systems that are currently being developed to do this.  His vision of the future of medicine is one where the optimal state of each protein and gene regulatory network is known, and any perturbation can be detected from a small blood sample and corrected with appropriate drugs.  This all sounds very exciting, but as someone working at the smaller end of big biology, and struggling to figure out how to deal with my (only a few) thousands of data points, my first thoughts were of the data management issues.
He mentioned that he’d met with Sergey Brin and Larry Page at Google, to discuss ways of handling such large amounts of data.  I’m sure Google is a good place to find the right kind of expertise, but I already have issues with letting Google have access to information about my internet usage, let alone trusting them with medical records…  There were understandably a number of concerned questions about the ethical issues that arise when such detailed information becomes available.  Dr Hood mentioned that physicists he’s spoken to have stressed the importance of thinking about the ethical implications of research, given their experience with research that led to the development of nuclear weapons.  Hopefully, biologists will learn from previous mistakes.

As I was listening, I thought of the other science bloggers who would probably have enjoyed the talk a lot.  Particularly, Dr Free-Ride for the ethical questions.  Alex Palazzo at The Daily Transcript also had a post a little while ago about the impact of “Big Biology” on science, especially for young investigators.  I commented then that I could see the value of funding large consortiums in order to accomplish projects that were larger than the scope of an average lab, but not as something that would produce the most innovative results (at least, that was what I was aiming to express).

I’ve been trying to reconcile that opinion, which I still believe in, with the fact that my project could easily be considered “big biology”, although I’m lucky to be getting in at the stage where the initiative is small enough that nobody is in danger of feeling like a cog.  Perhaps it depends on the definition of “big biology”.  Large consortiums that just allow PIs to expand their research empires without using dramatically different techniques definitely don’t seem like the best use of funding to me.  I do believe that individual labs offer great opportunities for innovation, but at the same time, systems biology approaches that allow you to get a sense of how a whole network fits together can also result in important discoveries and speed up the process of identifying key genes.  In this way, such systems approaches also create fodder for many smaller projects.  I think ideally, big biology and small biology would complement each other to build up knowledge of how organisms work on different scales, just as eg structural, biochemical and cell biological approaches can work together.  The challenge is obviously to find the right balance.

Journey or Destination?

July 23, 2006 at 1:33 pm | Posted in research | Leave a comment

I’m going to a conference in Edinburgh in September and I’m excited for a few reasons. For starters, it will be my first conference presentation. Also, this conference is more specialised than the only other one I’ve been too, so it will be good to hear more talks that are related to my research. More personally, my Dad’s side of my family is all from Scotland and I’ve never been there before, so I’m looking forward to taking some time off to go exploring once the conference is over.

Yesterday, I spent some time thinking about the non-scientific part of the trip. I borrowed a couple of guidebooks from the library and spent most of the day picking things I’d like to see and planning potential itineraries. To begin with, I just made a list of everything I thought might be fun, but the list quickly grew far too long and I realised there was no way I could fit everything in.  I tried to choose just the places I was really interested in, but they were spread out all over the country. Although I did figure out a possible way to get to all of them, it would involve a lot of time just travelling between points and only superficial visits. Then, I tried to pick out places that were near each other within a couple of nearby regions. At first, it seemed like a more reasonable itinerary, but I kept adding things that didn’t make the previous list, just because they were right there, on my way. Plus, I’m still longing to squeeze in some of the further places, too.

I’m still working on designing a perfect itinerary (with room to change my mind once I’m there, of course), but I realised that I’m having a similar problem with my research.

My project has been following a fairly defined path since I started in the lab, but now it’s at a stage where I have to choose what direction(s) to take next and I’m feeling somewhat unfocussed. So far, I’ve tried a few things, just because they’re “right there”, so to speak, and while they’ve given me some information, I don’t really think they’ve moved the project forward.

Planning the perfect itinerary is half the fun of travel, since it’s a way of enjoying the trip before it’s time to get on the plane. Research doesn’t have that delay between planning and execution. I’ve been putting off putting the same kind of thought into my research plan, because it seemed more important just to keep moving. I hadn’t realised I’d gone out of range of my old map, though. I guess it’s time to draw up a new one.

But, what’s the right approach to take? When travelling, I’d usually prefer to see a smaller number of things in depth, than rush around all the major places with barely enough time to take a photo. Both could potentially be useful strategies for this stage of my project, however. Maybe it would be good to get a general idea of how my system works by looking quickly at a range of different situations. I can always come back once I know what’s most interesting. Or maybe I’ve spent too long already looking at the big picture and I should start to focus.

One way of choosing an itinerary is to map out the figures of a potential paper, and do the experiments to fill in the blanks. This seems like a good way to make sure the experiments I do are actually adding to the story I’m trying to build up, but I wonder if I would miss anything along the way. Is there scientific merit to just wandering the backroads where my fancy takes me? I suppose there’s no guarantee my experiments will keep me on the track I was aiming for, anyway.

I guess there’s also a question of whether, as a graduate student, it’s an appropriate time to wander. Perhaps it’s better to have a plan that lets me get some results and publications and get out of here.

Actually, designing experiments to fit a paper doesn’t really solve my problem. There are papers that describe one path in detail and others that try to map a whole country. Maybe aiming for a particular journal would help. It would have to be a pretty uncharted country to make a high-impact paper, for example.

Maybe I should’ve have drawn up a map for this post, too, because I think I may be going in circles. Anyone have any advice for me? Do you have a preference for a particular style of scientific journey?

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