Processing

Started playing with Processing today, following my find of an excellent book on the subject at Foyles today. Will post images when I develop some proficiency...

A long story

Have been away for a while. A lot has happened, including moving house, and, with great effort, making it across to London where I will be for the next few months.

Spent the day in the Science Museum, and the displays there got me thinking: what am I actually doing, and why?

It's a long story, but it begins in my second year of Med School. I read a book by John Gribbin and Martin Rees ("Cosmic Coincidences"), and this got me interested in cosmology, amongst other things. But it started a process which has been ongoing ever since: I realised that really deep questions about reality could be asked, and that answers to many of these questions could be found.

During the next few years I learned a lot about human biology in health and disease, and about many interventions that could improve the health of people. Many explanations given for biological processes were not really satisfactory, but I persisted with a reductionist worldview ("If we only knew what all the parts are, we can figure out how the whole works"). I especially enjoyed the explanatory power of negative feedback systems in homeostasis.

Then came "Jurassic Park". A movie classic, released 1993, introduced me to the concept of "chaos theory", and I started looking for evidence of chaos in biological systems. To my surprise, the biomedical literature was full of references to chaos. I started collecting articles relevant to biology, even though I hardly understood any of them. And I started collecting books on the subject like crazy (e.g. the excellent "Does God play dice?" by Ian Stewart).

During this time I started playing with computers (as well as doing a medical degree). At the time, I didn't understand the notion of computation, but at least managed to use the computer for some productive work; a review of the immunopathogenesis of HIV infection in 1997 stretched my skills quite a bit, but at least I was able to include my beloved network diagrams in the work. I was completing a Diploma in Tropical Health, as I was, even then, very interested in infectious diseases.

The next piece of the puzzle came in 1998, when I worked in the UK for a while. Chaos theory describes dynamics, but a different language is required to describe fully the strange attractors summarising a chaotic system. This is the language of fractal geometry. Again, I collected books on this topic, and with my brand new Pentium II computer set off simulating hundreds of fractals, mainly parts of the Mandelbrot set. I am unsure what that did for my understanding of the subject, but I started to learn that it was possible to bend computers to one's will (even if they were running Windows!)

Not only were chaos and fractals useful in describing biology, but another science had appeared above the horizon that not only acknowledged the difficulty in producing "the whole" from "the parts", but outlining some strategies how this could actually be achieved: the science of "Complexity": descriptions of annealing cement, collapsing heaps of sand and the function of ant colonies all suggested that many complicated phenomena might have simple underlying rules. More books in my library, of course! And a plan to (eventually) do a PhD, learning to actually do the interesting science.

In Antarctica I learned that reasonable alternatives to Windows existed (e.g. Linux, which at the time was a pain, Solaris, and other flavours of UNIX). I also learned that science is a very real career, and that one could have fun while doing it!

The "Millennium" came and went, the world didn't end, and I ended up in Medical Informatics (of sorts). At least I had a job which allowed me to explore a lot of issues regarding the use of computers in medicine.

After a rather long break from clinical medicine, I finally returned to the fray in 2002, armed with a head full of ideas, and a mind open to new ones. Enter Stephen Wolfram's " A New Kind of Science", which, like a sledgehammer, brought home the idea that "computation" is central to complex systems. In parallel, I specialised in Internal Medicine, and developed some skills in programming in Mathematica. I read a lot about neural networks and their use in solving complex problems. The realisation that I needed some serious training in mathematics and computer science to even stand a chance to participate in this new world was a sobering one.

In 2006, in Belgium, I finally crossed the OS Rubicon and bought my first Mac, and a lot of books about bioinformatics and computational biology books. Bioinformatics was the new way of thinking about the questions that interested me. Implementing mathematical algorithms in computer code to solve complex biological questions was the way forward for me!

Back home I completed my internal medicine training, and in 2007 took the opportunity to attend an intensive training course in bioinformatics. After working in the field for a while, I found myself back in the field of infectious diseases, with a plan...