The Notebook.

A bunch of possibly interesting things.

Some Project Updates.

Since I began this blog I have mentioned many projects I planned to start, but have not yet followed up on them. I thought I would take this time to just give a brief overview of the main ones: SERO, Coulomb, and DeepNeurone. I am also going to talk about a new project of mine.


Recently my internet connection dropped out so I had a chance to work on DeepNeurone. Unfortunately due to the scope of the project it is unlikely I will get a working worm brain, let alone a human brain. I have, however, managed to write a computer program which is able to have neurones, synapses, spikes, rebalancing and reduction. If you look at the largeish output file below you can see the output of one of the runs.

In the run I aimed to create 50 neurones with synapses between them. The program prints out this layout but it is largely rubbish - it is just a random network the machine came up with. It then generates the thing you see in the file. This takes about 5 minutes to run. In initial runs it generally worked itself to a stable area (after about 30 runs) in which the most neurones it could fire were firing, but every neurone fired another which fired another which fired the original - basically, it wasn't moving. Then I thought that maybe it needs some random firings added in - so I made it randomly flip a neurone every once in a while. This produces the pattern you see.



This has largely gone on the back burner - I do not have the time, energy, or money to work on this project. It does not seem to have much use at the moment, as any components for it I am able to fabricate will generally not be powerful enough. Maybe in the future.


Yet again, mainly on the back burner. I might revisit this, but the majority of the code has just become unorganised. The simulation basically devolved very inaccurately due to the floating point issues I ran into.

And finally, some good news - TBD CHemkit.

The final entry on this list is a new project. I have no idea what to call it yet, but it is quite an interesting idea. I do chemistry, and occasionally I need to balance an equation, calculate a reactions products or do atom economy/percentage yield calculations. This can get a bit overwhelming (and I have a paper shortage :D), but the majority of tools I have found are generally either expensive or just drawing tools. My idea is to write a custom built chemistry program whereby you can enter some products, some reactants, and it can calculate the molar ratios. It can then operate on this and work out atom economies, etc. Eventually I hope to make it be able to work out reaction products (but this could be hard - I can see how I could do it for simple compounds, but as you get larger it would be difficult). I have no idea if this will be a command line program, a website (might be nice?) or a GUI app. Should be fun regardless.

Life on the Edge: The Coming of Age of Quantum Biology


I know I said I would do books two at a time, but this one took me about 20 days to read (due to circumstances out of my control), and so I am going to do it standalone.

Life on the Edge: The Coming of Age of Quantum Biology.



Price (As of writing): £13.60 in Amazon (reduced from £20)

Publishers Synopsis: 

Life is the most extraordinary phenomenon in the known universe; but how does it work? Even in this age of cloning and synthetic biology, the remarkable truth remains: nobody has ever made anything living entirely out of dead material. Life remains the only way to make life. Are we missing a vital ingredient in its creation?

Like Richard Dawkins' The Selfish Gene, which provided a new perspective on how evolution works, Life on the Edge alters our understanding of life's dynamics. Bringing together first-hand experience of science at the cutting edge with unparalleled gifts of exposition and explanation, Jim Al-Khalili and Johnjoe Macfadden reveal the hitherto missing ingredient to be quantum mechanics and the strange phenomena that lie at the heart of this most mysterious of sciences. Drawing on recent ground-breaking experiments around the world, they show how photosynthesis relies on subatomic particles existing in many places at once, while inside enzymes, those workhorses of life that make every molecule within our cells, particles vanish from one point in space and instantly materialize in another.

Each chapter in Life on the Edge opens with an engaging example that illustrates one of life’s puzzles – How do migrating birds know where to go? How do we really smell the scent of a rose? How do our genes manage to copy themselves with such precision? – and then reveals how quantum mechanics delivers its answer. Guiding the reader through the maze of rapidly unfolding discovery, Al-Khalili and McFadden communicate vividly the excitement of this explosive new field of quantum biology, with its potentially revolutionary applications, and also offer insights into the biggest puzzle of all: what is life? As they brilliantly demonstrate here, life lives on the quantum edge.


This is possibly one of the best written books I have ever read. It is written in a nice easy to read manner that still pushes across the complexity of the topic. It is a relatively large book (not as long as some, but certainly longer than The Sixth Extinction and Nothing) but I felt a sort of conciseness while reading it - it never appeared to drag on any longer than it needed to. The chapter on photosynthesis and others had nice analogies and anecdotes to go along with them such as the anecdote about the MIT Researchers trying to make a Quantum Computer. This book really opened my mind to biology and the interlinking of the sciences. It also explains the Quantum stuff very well to someone who may not have read about it before. I would recommend it to anyone who enjoys biology or physics.