Thursday, 22 September 2016

I finally understand what Dawkins means by gene

I was reading a short article by Steven Pinker in the book "This Idea Must Die". There Pinker was saying about how molecular biologists have a different view, a very restrictive view of what a gene is. They only consider the protein encoding region of the DNA as the gene.

That was a Eureka moment as I finally understand what Dawkins was trying to say. He shares exactly the same view as Pinker. To him a gene is a heritable element that produces a phenotype. This is a much older view of the gene than the view I was brought up with. It predates knowing anything about DNA at all.

To the atomistic and DNA based molecular biologists and geneticists this means the sections of DNA that produce the protein that is responsible for the phenotype. That piece of DNA when expressed causes the phenotype. This is why the molecular biologists got such a shock when they found that there were only 20-30 thousand protein expressing segments, genes in their words, in the human genome. This looks the same as Dawkins' gene but it is completely different. Dawkins because he knows very little about genetics and molecular biology is living in the world view before the modern synthesis which linked DNA to genes. Pinker shares the same anti-reductionist perspective. Even though both would consider themselves materialist and reductionist scientists.

Their view of the gene would include all of the regulatory elements, both local and non-local in the genome. It would also include all of the mechanisms for regulation and post-translational modification, for localisation and for every other modifier that affects the process of taking that section of DNA or those multiple sections of DNA to produce a phenotype. In Dawkins' view there are no multi-gene effects to produce a phenotype because the genetic atom is actually that complete system that relates DNA and phenotype.

That is what makes me so strongly critical of Dawkins' work because he has no appreciation of the system at the molecular level. I work with proteins and how they fold and I even dislike DNA. I see the disconnect between the DNA code that can be mutated and the proteins that they produce. There is a huge non-linearity in their connection. The effects of mutations are almost impossible to predict. But if you take Dawkins' and Pinker's way of specifying a gene just as a heritable element then their writing makes a lot more sense.

It makes more sense but they still ignore the fundamental problems with this view. That is that these "atomic entities" these genes are not atomic. They are overlapping, intertwined, non-local and non-linear systems that cannot be approximated by some atomic genetic theory. In each cell-type the networks of connections between regulatory elements and expressed regions is different and that is not even considering spatial effects.

In their world each cell type would have its own set of genes, because each have their own phenotype and own system of expression. Even each of my tissues would become a collective organism and and animal would become a collective of collectives. It is this decision to ignore the relationships between the parts and to impose an artificial genetic atomism on these heritable elements that makes it unrealistic as a view. Playing with my sons' Lego makes it clear. I have all those bricks which are the genes of the model. But unless I put those bits together in the right way I never get my car or my space ship. If you don't think at the systems level you can never understand biology. Atomism and reductionism are doomed to failure.

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