Why does the left side of the brain control the right side of the body and the right side of the brain the left side of the body?

The retina of the human eye is 'back-to-front':

1. There are blood vessels in front of the retina.
2. Light has to travel through several layers of nerve cells to reach the rods and cones.

The octopus eye evolved independently and doesn't have this 'design flaw'. Did we and all vertebrates really get it wrong, or is there more to it?

Catalase

The efficiency of Catalase is extraordinary, so is the range of reactions which it has a role in.

Evolution

In this article I argue that:

1. IF any mechanisms exist that affect the speed of evolution THEN evolution will modify them.
2. Well known mechanisms in Molecular Biology act in concert to accelerate evolution.

How Thought Works

The suggestions I put forward in this article go only a part of the way towards explaining these aspects of thought.

A related page gives a mini-review of four different researchers' approaches to the mind.

Protein Similarities.

Computer algorithms can compare the chemical structures of different proteins and sometimes find unexpected similarities.

What does it tell us if we find a similarity between a 'camouflage protein' in a moth wing and a 'crystalin' protein in the lens of the eye?

In this article I describe surprising protein similarities I found in a comprehensive database versus database search - and what these similarities may tell us.

A Study in Optimisation

Sequence Alignment Algorithms are the most heavily used algorithms in bioinformatics. Their use for database searching was once restricted to parallel computers because of their high computational cost.

The basic algorithm is O(N²). Whilst not reducing this complexity measure, I wrote an intensively optimised version with a more than fifty fold speed up over what was previously thought possible. Using this optimised version complete protein versus database searches take minutes rather than hours on an ordinary single processor machine.

Dynamic Programming

'Dynamic programming' is an efficient programming technique for solving certain combinatorial problems. It is crucial in bioinformatics as it is the basis of sequence alignment algorithms for comparing protein and DNA sequences.

In that application Dynamic Programming yields a spectacular efficiency gain. It converts an [infeasible] recursive O(2^N) algorithm to a practical O(N²) one.

Less widely known cases where dynamic programming has advantages over pure recursion are in parsing and in programs to play chess; both gain significant benefits from a Dynamic Programming formulation.

Coding Standards

In writing animation software in C++ I have found a number of rules for coding helpful. Nearly every one of these rules arose from mistakes that I made, times when I found myself having to throw away code and/or re-write.

This is a working list of the rules so far. It's a list I hope to add to over time. Comments are welcome.

Also, if you have your own web page with coding standards on it, I would be happy to put a link to them from my coding standards web page.