Sunday, 18 January 2015

Books I have read

When Bacon wrote his dictum about books there were so few that you could not be over-powered by their number. Now more than ever we are over-whelmed by writing and his dictum has become much more significant.

Now we have to distinguish the mundane from the profound, we have to distinguish the books that have an impact on the reader from the general background noise.  Not only are some books more significant, but they also take on a life of their own, moulding the experiences and beliefs of the reader.  Each book has its own time, it has order and it has age.

I keep a list of all of the books that I have read so that I can try and unpick the influences that they have on me. Now I have realised that just knowing what I have read is not enough. I need to know when I read it and in what order. For the last three years I have kept an ordered list, and pushed my reading to 50 books a year.

For example I read Brave New World in my 30s and for me it was a profound book because it struck a chord with my age, my experiences and the world in which I lived, but I doubt that the experiences of anyone else would put it into the same context. Reflecting on it, I think it is a book that is more likely to resonate with older readers with a wider range of experiences and I think that I would have appreciated it less if I had read it as a teenager.  The same is true of Borges, Labyrinths. Now for me it is an amazing book, but I do not think I would have grasped its many different layers and themes if I had read it in my teens or 20s. Reading it later I find that it has so many hidden ideas that make it a greater work of thought than many works of philosophy.

Saturday, 10 January 2015

The Downton Delusion

Downton Abbey seems to be a national obsession but I can't quite understand it myself. Why do we enjoy watching a generation of injustice, inequality and wasted opportunities and celebrate them like they were the "Good Old Days". There was nothing good about them but they seem to be the golden age to the British.

My grandma died this week. She was 95 which is a good age and she had loved through a lot of change. She got her first passport to come to my wedding in Spain when she was 81. She was an impressive and strong woman but I have to think what she would have been . Her parents were servants to the aristocrats. Her dad was the chauffeur and I think that her mother was the upstairs maid. She was born to Downton parents, those that lived at their masters wishes. My grandma went to school at Wyggeston Girls Grammar School where she was even a prize winner. I do not know when she left school and with what qualifications but this was a time when women were still not encouraged to continue their education. She had her teenage years in the depression and her early twenties were the war years. What saddens me most is what she could have been if she was born in 1979 and not 1919.

That is what we are celebrating with Downton, the inequality that wasted potential like my Grandma's. The wealthy had their great houses and the aristocracy had their protected lives, because some ancestor had done some favour to some monarch. But why because my ancestor's were successful should I expect to be successful as well? They had their privilege and success built in. This was first weakened by Lloyd-George's "People's Budget" but mostly the inequality and injustice was a consequence of the post-war second world war settlements. The returning soldiers and the women who had fought and worked at home wanted a different world and so the Downton Age passed. There were still pockets left but the 60's and 70's took care of them. I still remember the sense of deference amongst the farmers to the old aristocrats, who had once been their landlords.

Now we have this return to idolising the gilded Downton Age when we are in the middle of another depression caused largely by the same families who caused the last one. The aristocrats who we thought had been vanquished just became the much more diffuse "Establishment". Why do we idealise a time that was so unfair, so unjust and so unequal. We love Agatha Christie where Miss Marple and Hercule Poirot come from the same Downton world with trips on the Orient Express, or cruises down the Nile. We fantasize about a life that did not exist for most people and forget that it was the nineties and noughties when we really "Never had it so good". Now we are entering another age of inequality and instead of fighting against it we are embracing it. It seems that we want to be back in Downton, knowing our place and doffing our caps again.

Continuing the theme on Evolutionary Biology

Yesterday I was tumbling ideas around in my head but there is something important I missed and that is Monod - Chance and Necessity. Although philosophers have attacked it, it does contain a kernel of truth and the beginnings of an important theme. That is that evolution is random but selection makes necessary choices. So we have some developments which will happen over and over again such as eyes, long necks and photosynthetic systems and then we have accidents that are not required by the environment.

This theme is developed by Ian Stewart and Jack Cohen in all of their books and also by Murray Gell-mann in the Quark and the Jaguar where he talks about the amount of information needed to describe a system. Things that have to happen and that are homogeneous across a set require less description than the unique properties that are heterogeneous.

Where we lack theory is in describing the unique heterogeneous events - we struggle withe heterogeneous entropy or any systems because there are no statistical descriptions of the unique. You cannot average them. This is where we need to build our theories, on the edge of maths.


Monod - Chance and necessity
Ho - The Rainbow and the Worm
Gell-mann - The Quark and the Jaguar.
Stewart and Cohen - Figments of Reality
Stewart and Cohen - The collpase of chaos.
Stewart, Pratchett and Cohen - The Science of Discworld I-IV.

Friday, 9 January 2015

Trying to get my Head Around Evolutionary Biology

My mind goes round and round and round to the same ideas and the same connections but I am finding it very hard to out them all together. There is something very deep and fundamental that we are missing in biology, the reason why theories like relativity do not exist.

First is the stupidity of biologists trying to use statistical methods to "average out" historical events to eliminate "accidents". This all stems from Popper and his view of science, which is alright for physics but not appropriate for Biology. You ignore history in a biological problem at your peril. This was never clearer to me than at an ISMB meeting where I had been subjected to the same talk twice, by two different post-docs from the same group (the P.I. was on the organising committee) where the presenter was asked about how well the method worked on real data. The reply was that it didn't. It only worked on the model data. At that point I gave up on ISMB meetings because they are too incestuous.

The problem is that that synthetic data is all nNormals and Poissons and nothing like reality. Reality has nasty things like extinctions, bottle-necks, frozen accidents etc. Reality has population structures, isolation, incest, dispersion and above all else a richness of history that you cannot average out. This is why Mayr was so sceptical about the "bean counters" like Haldane, Fisher and Sewall-Wright. So trying to impersonate physics in quantitative biology throws the baby out with the bath-water. This is not to deny statistics its role but biology is full of what Taleb calls Black Swan problems. These are the out of the usual events, the unknown unknowns that mean the unexpected has a disproportionally large effect. So our knowledge and possibility of knowledge in biology is limited by the barrier of experience that Hume identified.

The error of ignoring history is compounded by excess reductionism that fails to look at the system. How can I judge the fitness of an organism in isolation from its environment? That is why in vitro and in vivo experiments differ so much (see Holmes on Viral Evolution). There have been those who have worked in solving these problems but usually they have been marginalised by the reductionist, statistical main-stream. Waddington stands out amongst these with his epigenetic landscape for development, but more important than that is extending this to evolutionary landscapes through evolutionary canalisation. Monod made some contributions towards this in Chance and Necessity where he introduced gratuity as a side-effect when there is a change in the landscape so evolution has access to new areas. Kaufman put these ideas into a computational and numerical frame-work. The recent appearance and very rapid disappearance of systems biology also produced a burst of activity particularly in the landscape view from Kitano.

The basis for where we need to go is already written but nobody has put it together in a useful way. There are so many works that are ignored and connections missed. These problems are hard - they frustrated Darwin.


Waddington - Towards a Theoretical Biology 4 volumes (The bible of real systems biology).
Waddington - The strategy of the genes (Canalisation - if an evolutionary biology text does not cite him do not believe them).
Taleb - Anti-fragile (His Magnum Opus about Black Swan problems and solving them).
Haldane - On the Causes of Evolution (One of the three founding works of evolutionary genetics).
Maynard-Smith - Evolution and the Theory of Games (Shows that mixed solutions work - not the message most take from it).
Axelrod - The Evolution of Cooperation (Tit-for-tat is the best and cooperation gives benefits).
Sewall-Wright - Evolution and the Genetics of Populations 4 volumes (His complete work on population genetics).
Kimura - The neutral theory of molecular evolution (An important assumption of coalescence).
Holmes - The Evolution and Emergence of RNA viruses (Quite specific and not always right but some good points).
Kaufman - Origins of Order (Has quite a lot of holes but it is a start).