What do I do? Why, I thought you'd never ask!

As I have already mentioned in previous posts, one of the motivations for starting Page V was to talk about my research. So what do I do? This is a question I always dread. In trying to explain my work to casual company, I usually do so badly that I come across either as extremely dull or, even worse, vaguely condescending. What better way then to exorcise this demon once and for all than with a 1000-word essay that will bore all 3 of my readers to tears? Brilliant!
 

No, not this kind of modelling...

The short answer to the titular question: Modelling of biological systems! The word "modelling" often brings to people's minds the kind of modelling that Kate Moss or Gisele do. Sadly, nothing could be further from the truth. My kind of modelling is much, much, much less interesting than that, and it means the description of systems or processes with the use of mathematical equations. Why would someone decide to do something as mind-numbingly tedious as describing things with equations? Well, there are a couple good reasons actually: simulating behaviour and making predictions about performance.

Ceci, c'est une voiture...

 Modelling is about creating a representation of an object that you could then run simulated tests on. Think of a car for example. It doesn't have to be a particularly nice one, any old car will do, but to help your imagination along, here is a picture on the left. A car is in fact a pretty sophisticated piece of machinery. Let's say you wanted to find out about the car's performance (speed, turning ability, fuel consumption, when do things start to break down, etc.), and you need this information under all kinds of different conditions (different weather, different terrain, different fuel, or different driving modes). To gather all this data you would have to run hundreds or thousands of tests. If half of those tests required you to blow the engine or crash the car in the process, you would also need hundreds (or thousands!) of cars. That is obviously not the most efficient way to go about it. Instead, you can create a model of a car and simulate the exact same tests. Of course no simulation will give you the same knowledge as actually doing something yourself, so you can then pick a handful of tests that, from the results of your simulations, seem to be the most interesting to perform in real life.

... ceci, n'est pas une voiture.

In addition, your model can be used for predictive purposes, and not only to simulate tests. Think of a Formula One Grand Prix, and how important it is to get the fuel load of the car right. One way of finding out the optimal amount of fuel is to run the full race a few times, until you can safely decide which combination of starting weight and refueling strategy gives you the best chance to win. You also need to remember to run your tests under race conditions, and under different weather conditions, to make sure you consider all possible parameters. The other way, and the way that Formula One teams do it, is to gather information from previous races, from the tests you run on the car in the off-season and from the car specifications, and use it to build a predictive model that can tell you the exact amount of fuel you should have in your tank when the race starts. 

Another thing to consider is the level of detail of your model. Going back to the car example, you can have a model that describes accurately every little part and component of the car, from the engine, to the windscreen, to the tiniest bolt. Putting the parts together, you would end up with a model that can simulate the behaviour of the car (almost) perfectly. On the other hand, you may not have the information, or the computational power, or the need for such a detailed description. Your model can then be as simple as a single equation, relating speed with fuel consumption. That may still be accurate enough to run hundreds of tests that provide you with ample data for your purposes.

Of course, as I mentioned in the beginning, I do not model cars (even though that would probably have been somewhat more exciting!). What I do model is biological systems and, more specifically, cellular metabolism. Metabolism is the set of chemical reactions that happen in living organisms to maintain life. The word means change or transformation in Greek (Note: let's just get it over with and accept that I will always plug Greece in these posts. You will simply have to live with it). Metabolism relates to various processes (reactions, if you remember your chemistry) within the cell, which convert food and other substances into energy and compounds used by the cell, for example as building blocks. It is an essential function that allows cells to grow, reproduce, maintain their working parts, repair damage, heal injury and get rid of toxins. Without metabolism, living organisms, including us humans, would die.

View more of my presentations on SlideShare.

Metabolism is very, very, very complicated as the slide above shows. We use modelling and simulation to try to understand a few things about it. As with the car example, our models can serve diverse purposes: we can test a large number of biological hypotheses computationally, without the need to perform all of the costly and lengthy experiments in the lab, instead picking only a handful of the most promising results for further experimental examination. And we can use the models to make predictions about metabolic behaviour, which then supply the basis for formulating a hypothesis that can be verified experimentally. This interaction between simulation and experiment forms the iterative cycle of knowledge that constitutes the essence of Systems Biology.

What, then, is Systems Biology? A question, perhaps, for another time...

Election time!

I watched the UK election with interest. I even had the chance to vote in the local election for my ward in Hulme, but not the national election, which is a bit of a shame. For the last 7 or 8 years, I have been refraining from voting in the Greek elections*, because I do not live there anymore or pay taxes, and I do not consider it fair that I cast my vote one way or another on issues that will influence someone else’s life, but not my own. Clearly, the exact opposite is true when it comes to the UK elections. I do not believe that I should have a vote; it would be wrong if I had the right to vote in two different countries. But I do think that there should be a common system within the EU, through which citizens could decide to vote at the country where they live instead of their country of origin, like people can do in local elections if they move to a new region. That is the point of a United Europe, and with the technological means available today that should be more than achievable.

It is remarkable how the hung parliament is being made such a big deal. First of all, the term itself shows how strange the concept is in Britain; everywhere else in Europe people talk about a coalition government or a minority government. I absolutely understand the preoccupation; coalition governments are not the norm in Greece either and they are regarded with suspicion and doubt. But the fact is that it's hardly an unusual phenomenon: the only other countries in Europe with strong majority governments are France, Malta and Greece. Not exactly a group to inspire confidence in strong majorities!

The other thing that I find interesting is the discussion about the electoral system. I always thought that the first-past-the-post system is unfair, and the more I find out about it, the more my belief is strengthened. A system in which one party needs 6% or 7% more than another party to get the same number of MPs is wrong. A system in which it is possible to end up with a government that received considerably smaller percentage of the vote than the opposition is wrong. The UK shouldn’t wait until this last -rather unlikely, but entirely possible- scenario happens before something is done to fix the electoral system.

Finally, I am constantly amazed by the fact that most people I know seem to despise the Torries! I guess this is because most of my acquaintances are in Academia, and the academic environment is not conducive to a conservative mindset. But the UK has a two-party system. If Labour is not in, then the Conservatives have to be in. And Labour had a long run since 1997. I am a strong believer in the necessity of change every so often. It is not good for Democracy if the same party rules for more than 2 or 3 terms. People get comfortable. People get sloppy. People get corrupted. You want the people who govern to stay on their toes. And if the idea of a Cameron administration is pure anathema to you and you feel desperation taking over your soul after today’s result, think of it this way: This is still the UK. Coalition governments cannot last long; it is not the British way! The Conservatives managed to turn a clear lead into a constitutional mess after only a few months of campaigning. Imagine what a few months of unpopular administration with all the financial measures the new government will have to take will do for their percentages!

In any case, one thing is certain. We live in interesting times.

*Very fitting anecdote: In 2000, during the Greek parliamentary elections, I was already living in London with my brother. We managed to get ourselves on an Olympic Airlines (the state-owned airplane company) flight back to Greece for free. We voted in the election and also took a short vacation from our studies. That is because the Greek parties (not only the government) arrange for tens of thousands of Greek citizens from all over the world to travel back to Greece to vote. This is the same Olympic Airlines that went bankrupt under mismanagement and was sold last year, and the same Greece with the huge national debt by the way.

i just bought broccolis LOL

So. I have apparently joined the blogosphere. As Duncan Hull pointed out, "what took me so long"? Writing has always been something I enjoy - just take a look at my excruciatingly long emails- and I consider myself a technologically savvy guy, so "blogging" should have fitted like the proverbial glove.

I guess the reason that kept me away for so long was the question "what do I write about"? Looking around, it seems that people on the web are divided into 2 groups: the ones that are really passionate about something and write -well or not so well- about it, and the ones who chatter inanely and eternally about everything and nothing. I don't know if I am expert enough in anything to belong to the first group, and I REALLY don't want to belong to the second!

I think what convinced me to make the leap, is that I can increasingly see the contribution that Web 2.0 technologies and social networking tools are making to science and the way it is performed. Networking has always been a big part of science. What better way to network then for a bunch of scientists who a) probably already possess the expertise required to use all the exciting new "toys" and, b) often do not possess the social skills to do it in person!

So where do I start? My inspiration comes from friends and colleagues who are already very effectively using their blogs, tweets, and so on, to promote their scientific output. Some examples can be seen in the links I have included on the right (look under "Friends"); there are of course others. In trying to emulate their success, I have signed up to a number of services, from which I had been keeping myself away for a long time. I started tweeting. I joined LinkedIn. I signed up for FriendFeed. This was fun, but it also had the opposite effect of what I thought it would: instead of an exhilarating take-off into the free skies of social networking, I am stuck knee-deep in a swamp of technical problems and incompatibilities!

Game on then. I think I am getting there, only a lot slower than I was expecting. At least I have shifted my bottleneck from "what do I write about?" to "how do I make this work?". That is progress. I will keep telling myself that. Now, if I could only link my tweets with my Facebook status...

PS: How is everyone else getting on with their networking? Is your Web 2.0 experience filled with frustration or satisfaction? Post a comment.