Happy Halloween!

November 1, 2006 at 12:15 am | Posted in Uncategorized | 1 Comment

Immunology Fact of the Day

September 11, 2006 at 1:35 pm | Posted in immunology | 2 Comments

I haven’t been posting much here, and nothing science related, so here’s a cool fact I just heard*: there are 100 times as many bacteria in your gut as cells in your body that actually belong to you.

*now I’m hesitant to post this because maybe everyone else already knows this, but I didn’t realise there were quite that many bugs.

A Bad Week for Australian Icons

September 9, 2006 at 2:09 pm | Posted in Uncategorized | Leave a comment

First, the Crocodile Hunter, then author Colin Thiele, and race car driver Peter Brock.  At least Colin Thiele got to live to a decently old age, dying in hospital at 85.  Apparently you have to be killed reasonably young, while doing the dangerous thing that made you famous to be offered a state funeral, though.

I wasn’t a fan of any of theirs, really, especially not Irwin or Brock.  I enjoyed Thiele’s books, but they were too closely tied to schoolwork to be favourites.  Actually, reading the Storm Boy excerpt posted at Sarsaparilla makes me think I should reread some of them, this time without any resentment-inducing book reports hanging over my head.

Now that I live in Boston, the many references to Make Way for Ducklings always remind me of Farmer Schulz’s Ducks (sadly lacking a web presence – it’s about a farmer and his daughter who try to find a way for their ducks to safely cross the new highway that’s been built between their farm and the river).  I think Farmer Schulz’s Ducks is a better book, but whenever I try to explain the story to people, they seem horrified that a picture book would include the carnage that accompanies each failed attempt at a safe crossing.  I was a very easily traumatised kid (I refused to read almost anything by Hans Christian Andersen), but somehow I coped with the ducks’ deaths.

RIP Crocodile Hunter

September 4, 2006 at 3:16 pm | Posted in Uncategorized | Leave a comment

A friend at home instant messaged me when I was still up at 1am this morning, asking if I’d heard the news that Steve Irwin had been killed by a stingray. My first thought was to wonder if he’d been poking it. Something that was put more diplomatically by Victoria Brims in this story:

I am aware he was filming a documentary and his documentaries are usually very hands on. I can only assume that he had some kind of hands on or close contact with the animal who like us when we get afraid defended itself

We used to drive past his zoo on the way to visit my grandparents, back when it was a dodgy little reptile park, but I never went.  I did see him and his wife in person when their tv show was just starting out, though.

I always thought he was supremely irritating and pretty irresponsible, and was embarrassed that he was one of the few Australians people in the US could identify, but it’s still sad.  His two kids are very young.

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?

Ben Barres vs Larry Summers

July 19, 2006 at 9:31 am | Posted in Women in Science | 6 Comments

Last week my advisor forwarded to the lab an article from the Washington Post and the Nature commentary (subscription required) it was discussing. The Nature article is written by Ben Barres, formerly Barbara Barres, about discrimination against women and minorities in science. His arguments are uniquely illustrated by his comparison of his experiences in science during the last 9 years as a man with those prior to that as a woman. He particularly attacks Larry Summers, Steven Pinker and Peter Lawrence for their opinion that the lack of women at the highest levels of science is due to innate differences between men and women.

As I read the Washington Post article, I quickly became frustrated with the arguments put forward by Pinker and Lawrence (Summers declined to comment), because they seemed to be ignoring the issues raised by Barres. For some reason, I initially tried to diminish my anger and convince myself that they were just trying to present actual data, rather than anecdotes.

The problem is, the data they present is nothing to do with discrimination. I’m willing to believe that their research shows differences in performance of various types of tasks between men and women. I’m not willing to believe that those differences are all due to innate ability, however. Not when there are other explanations that seem to be better supported. Why don’t they answer the charge of bias against women and minorities with data from studies that measure the prevalence of discrimination? Maybe they’re not interested in that field of research, which is fair enough. But, they should be aware of the limitations of their results, and leave discrimination out of it altogether, rather than claiming their results show it doesn’t exist.

I didn’t have a blog last year, so I’m going to rant about Larry Summers now. After he made his comments and the media started carrying on about the “hysterical” outrage by women, I heard a number of people say that “really, if you look at the transcript, what he said wasn’t that bad”. I read the transcript prepared to be placated, but instead became even more outraged, not only at Summers, but also the people I’d spoken to. How could they think it was “not that bad”? In my opinion, any quote taken out of context actually sounds less inflammatory to me than the whole. It’s the underlying disbelief that there’s anything wrong with the current representation of women and minorities in science that is so offensive.

This part of the WaPo article made me laugh: “Pinker said both he and Summers relied on “a large empirical literature”.” His key pieces of evidence were anecdotes about his own daughters, a former colleague of his and his recent visit to a kibbutz in Israel! Plus his calculation of how many more men than women there are 3.5-4 standard deviations above the mean: “I did a very crude calculation, which I’m sure was wrong and certainly was unsubtle, twenty different ways.” He cites one book that gives a skewed sex ratio at the high end of 12th grade maths/science scores and then admits that the tests used might not accurately measure ability. He still assumes a less-flawed test would give the same result, however.

For more insightful commentary see Zuska, Dr Free-Ride, Propter Doc, SciMom and MissPrism

Moving In

July 19, 2006 at 2:33 am | Posted in Uncategorized | Leave a comment

I’ve been lurking on a number of cool science blogs for a while now. I often don’t feel qualified to join in the discussion on other people’s blogs, but there are things I’d like to talk about (and need the external motivation to think about) so I decided to start my own blog.

I’m a PhD student in immunology, soon to start my 4th year. I’m getting to the stage where people start asking how much longer I’ll be here (bad people!), but somehow I still feel like I just began. I don’t think I’ll be going into any detail about my research, but I’ll probably be complaining about wrangling enormous data sets quite frequently.

“Sinking the Iceberg” refers to an analogy I originally heard in my first-year basic cell & molecular biology class that first made me think about how wondrous the immune system is. Although disease is certainly not rare, health is taken for granted as the normal state of being and complete health is the goal of research into treatments. Yet, disease really only represents the tip of the iceberg in terms of infections. We are constantly exposed to pathogens and yet the vast majority of these are prevented from actually infecting us, or unable to cause any adverse effect, if they do. We don’t really hear about what an amazing job the immune system does of protecting us.

Most research is focussed on curing/preventing disease, hence “sinking the iceberg”. Of course, it’s impossible to sink an iceberg; part of it will always pop above the surface. Bugs will find a way around the drugs we aim at them and new diseases will emerge from unknown sources. Not to mention the many ways in which the immune system can turn against itself.

The central question I’m interested in is how does the immune system, from its wide repertoire of options, induce the response that is appropriate to the specific pathogen? More specifically, what are the mechanisms that determine which cells are activated and which are switched off? How are friendly stimuli (food, our own cells/antigens, commensal bacteria etc) distinguished from foes?

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