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...

The reference frame

The term "reference frame" has two meanings in physics. First, there is the observational reference frame, where emphasis is on the state of one or more objects relative to the reference frame. Second we have the concept of a coordinate system, which is concerned with positions, not motion 1.

An inertial reference frame, in Newtonian mechanics is an observational reference frame in which Newton's first law is valid 2.

This is not a physics blog, however, and I intend to use the term reference frame primarily as the foundation for mental processes, in which incoming data is compared to the sum-total of past experience and is categorised in that context. For example, a child growing up in rural India will by necessity have a different set of experiences compared to a child growing up in suburban America, and by extension, their set of core values and beliefs may differ dramatically. Therefore, the two individuals may interpret the same event differently. More on this later.

Parking issues

Parking may be challenging at times, as illustrated below. Although the connection to the general theme of this blog may appear to be tenuous, consider this: the coordinate system used by the captains of these vessels to determine their position actually is a fixed reference frame, and this will lead us nicely to a more general discussion of reference frames, and why they are important.

Gallery

From time to time I will post some photographs. We humans have an innate appreciation for beautiful things. Why that might be so will be explored some time in the future. It has to do with symmetry, health and reproductive fitness, amongst others. I would just like to share an image here and there of things and places I consider beautiful. I fully realise that beauty is in the eye of the beholder; in fact here is a practical example of a frame of reference: our reference frames for what should be considered beautiful may overlap, but will likely be non-identical.

FOOTSTEPS

TABLE VIEW

Why deep concepts?

"Concept" is defined in the American Oxford Dictionary as "an abstract idea, a general notion". The Wikipedia article also defines concept as "a mental symbol", or "a unit of knowledge built from characteristics". In short, concepts are the hooks on which you hang your ideas, and thought heavily depends on concepts for structure. 

Deep concepts are thought constructs that are fundamental to a lot of other, more specific thought constructs. In some of the next posts I will explore notions of "time", "causality" and "good and evil" as examples of deep concepts that underlie our worldviews. 

So why are deep concepts important? Well, they really set the scene for us to develop a worldview, and in many cases shape our frame of reference.

For us, the deep concepts that form our frame of reference appear universally true, and many probably are. But not all, and the challenge is to find out which, and why not. But even if some deep concepts are not universally true, they may be useful, and even essential, in allowing us to model the world around us in our minds.

Introduction to this blog

Dear Reader

Everything you internalise is, by necessity, observed by you. The observations that make it all the way to be perceived by your conscious mind are heavily filtered, and integrated into your model of reality. This model in turns depends on your frame of reference. By way of examples I have come across over the past few years I would like share some reference frames with you. By doing this, I hope to share with you my absolute passion for accumulating knowledge about and insight into the world around us.

It is my intention to build my postings around several themes that are of interest to me. I list them here, without promise of expanding on any particular theme any time soon. I will probably change this list as time moves on.

• Deep concepts
• Microbes
• Computers and computation
• Physics
• (The new) biology
• Medicine in the 21st century
• Antarctica
• The universe and cosmology
• The ultimate reality
• Photography
• Publishing
• Literature
• Music and Noise

WARNING: Some of these musings are not for the faint-of-heart. You are certain to hold particular convictions about life, the universe, and everything, and you might find that I challenge some of those. Of course you are welcome to challenge me in turn, but please remain polite.