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Connections - James Crook / Ideas History

Where an interest in the mind takes you...

There is a common theme to the technical articles on this site which is probably not at all obvious. It's my strong interest in understanding how the mind works.

This one interest generated other interests: Mathematics

Interest in the mind took me first into mathematics, particularly the Theory of Graphs, a branch of mathematics which studies connections. Mathematics also provides formalisms for working with symbols, and understanding 'how symbols are used' I felt would be a help towards understanding the mind. Computing

At much the same age as I was learning about mathematics I became interested in computers. I'd seen a computer program in the Science Museum in London which improved as you used it. It showed a very limited ability to learn.

As I saw it, computers provided a starting point for looking at the problem of 'knowledge'. What is knowledge? How is it organised? The limitations of computer learning showed some of the difficulties. The limitations could tell us something about how very differently the human mind is organised. Memory Architecture

Over time I learned more about how computers work through writing programs. It struck me that many of the stock tools of programmers, such as sorting algorithms, linked lists, B-Trees, can be seen as workarounds to overcome limitations in the design of the hardware.

In thinking about computer design, it is usual to focus attention on the processing elements. I realised that some of the biggest design problems are actually in memory. Using 'linear' RAM memory is an extraordinarily wasteful use of circuitry.

When you retrieve data from RAM only one 'cell' is actively providing information. All the others lie idle. One way to look at it is that in 1 Mb of computer memory, at any moment you can actively be working with only 16 millionths of its capability. Other ways of looking at it show computer memory in a better light, nevertheless, a huge improvement in computers could come about simply from improving the structure of computer memory.

I could see how to make that improvement and wanted to do it myself. Integrated Circuit Design

A  first step in improving computer memory is to make it work associatively. People have chains of associations of ideas, one thought links to another. After a mathematics degree, which in spite of my long standing interest I found difficult going, I gained a place on an MSc in Integrated Circuit design at Edinburgh to learn the electronic design techniques I would need.

As it happens, Integrated Circuit design is a rich field for Graph Theory. Because in Integrated Circuit design the routing and processing of signals are so important, Integrated Circuit design could be said to be the applied end of Graph Theory. Mathematics came in handy in other ways too. There are constantly trade offs to be made between speed, size and power. Sometimes mathematical trickery could simplify the design and give improvements in all three. The MSc year was fun, perhaps it was too easy, but it was enjoyable and productive. Molecular Scale

As well as electronic engineers, at Edinburgh I met researchers working on biological sequence data. They were using parallel computers to find similarities between proteins and between DNA sequences. The comparisons they needed to make were computationally demanding, hence the use of parallel computers. The researchers were looking into the possibility of integrated circuits that could do the work faster, or with greater sensitivity.

One researcher, Dr Andrew Lyall, was particularly important for me at that time. In his researches he had found important results by using his own parallel software. He showed me some of the incredible subtleties of design at the molecular scale, design in a different league from the logic structures we were designing in Silicon.

Before starting at Edinburgh, I had worked for a few months at the MRC laboratory for Molecular Biology in Cambridge, so I knew some of the essential background. The combination was enough for me to embark on a PhD in computational molecular biology at the Biocomputing Research Unit in Edinburgh. During the three and a half years there I learned a lot about molecular biological designs. I saw things a bit differently from people around me, for I looked at Molecular Machinery from a background of Mathematics and Computer Science.

Evolution optimises itself too

The now accepted idea that DNA has elements that move about, so called 'transposable elements', took thirty years to become mainstream - it ran counter to the then prevalent dogma. A number of ideas that I came up with in my time at Edinburgh amount to heresy too. I looked at the efficiency of the evolutionary process, the mechanisms by which it optimises itself. It's really beautiful. The accepted dogma is that evolution is a random process and that's the long and short of it. I felt there was more too it. One of my technical articles on this site documents how mechanisms that optimise evolution actually work. It's not quite such a heresey as I once thought it was for a special case of it goes by the name of the Baldwin Effect and is seen as a worthwhile elaboration of the basic idea of evolution.

...avoiding one heresy

However, my ideas were certainly unacceptable in the environment I was in in the late 1980's and could well still be unacceptable there today. As I wanted a PhD, my PhD thesis instead stayed on the safe ground - a dramatic optimisation to an important algorithm in molecular biology .

...finding another

After completing the PhD and moving to Dublin I started to learn about co-counselling and, at workshops in Hungary, I started to learn my girlfriend's therapy for changing muscles in the body. The latter shows very clearly that mental states such as stress are reflected in the body in habits of tension in muscles.

The therapeutic work gives a completely different and more human point of view for understanding how the mind works. Through trading and receiving co-counselling and MET I started to understand where my very strong desire to understand the mind comes from.

Why is 'The Mind' interesting?

If one experiences traumatic events in childhood, one reaction can be to block memory of them. It's possible also that related thoughts that lead to the blocked memories can become blocked too.

I'd experienced thoughts disappearing into a 'black hole', and decided I had to do something about it. My interest in the mind came from trying to repair my own mind.

For many years I had even forgotten that the disappearing thoughts were the origin of my interest in the mind, for that was one route that led back into those thoughts and it was pulled into the black hole with them!

Exchangine ideas, the Web and e-mail.

The journey so far has taken me into technical areas, subjects which I still find fun and interesting. It has lead to ideas and questions that I want to share with others. By writing the technical articles and publishing on the Internet I'm looking for people to challenge the ideas and to build on them. So in short - I'm using the net to trawl for people with interests that overlap with my own. That's what these articles have in common.

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"Connections - Biology, IC Design and Mathematics." page last updated 5-July-2003