Saturday, 24 September 2016

Dawkins' and Pinker's gene

The two biggest problem for Dawkins' and Pinker's interpretation of what the gene means as a heritable "element" that affects phenotype. Is that first it is most often not an element but a system of non-local and interacting elements and secondly and most importantly it will not follow Mendelian genetics. It will not be segregating and discrete. There will be a myriad of variations depending on how the system responds to the environment it finds itself.

Mendel was lucky with the characteristics he chose to examine and when you do have genes that segregate then you do have a gene as described by the molecular biologist and geneticist, of they type that Pinker riles against. They are just different alleles corresponding to an expressed region of DNA or possibly their cis regulatory regions. They are not the nefarious and indeterminate objects defined by Pinker and Dawkins. If we are to take their views seriously then we have to go back to before the modern synthesis and try again.

Now that we know that most of the genome can be defined as loosely functional, even if just in terms of spacing between coding regions, then perhaps we do need to look at what the term gene means.

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.

Saturday, 3 September 2016

Big Government should Amazon and Starbucks pay more tax?

Yesterday I posted about beggar my neighbour and why the Ireland/Apple tax case matters for democracy and stability. Today Amazon and Starbucks are he focus of attention. These are two more in a very long list that will also include Google, Vodafone. Microsoft and many others who use their global clout to minimise regulation and taxation.

What was amusing is the posts on social media by neo-cons about the companies being justified because the governments waste money and so they should keep avoiding the tax.

What do governments spend their money on? A lot of it is social security and a lot of that is pensions (much more than unemployment in the UK). So shall we cut pensions because Amazon and Starbucks don't pay up? Should those Daily Mail reading baby boomers who support the neo-con illusion get shafted by their own stupidity? Should we allow them to poke themselves in the eye? Sounds good to me but maybe not.

What else does the government pay for? Healthcare is a big spend as well. We could allow Amazon and Starbucks to use their tax avoided cash to invest in sponsored hospitals and to reproduce the philanthropy of Carnegie or Rockerfeller. Look at Oracle and the billions of Larry Ellison as an example he used all that cash to build - the most expensive racing yacht in history. So maybe expecting billionaires to give away their money is not such a good idea (I know Bill Gates has done amazing things and George Lucas and Warren Buffett as well but they do not run countries).

The government also spends money on defence. From an evidence based view this is often a waste of money and the social media post is correct. Britain is building two stupid carriers to fight the types of war that no longer exist against enemies that are no longer there. We are about the renew nuclear weapons that nobody will ever use and that are also a waste of time. Oddly enough I suspect that the person who made the media post would say that this is NOT a waste of government money as the neo-cons are easily deceived by Eisenhower's military industrial complex that sells what nobody needs at an extortionate price.

Then there is education. We could all do with a lot less of that so that we can all be as stupid as the Daily Mail readers and the neo-con social media enthusiasts. That keeps people from questioning. Yes you need to train an elite to run your business and keep globalisation going but an ignorant population is good for business.

What about the infrastructure paid for by taxes? The roads etc. Well there is lots of mis-mangement of funds there, but is is caused by the neo-con push to privatise all services and to have the market find the best price. Just ask Halliburton how this works for them in the US and ask any local government how it has worked out in the UK. Higher price poorer service and don't mention PPI.

So yes Amazon, Starbucks etc. should be paying taxes and while sometimes government does waste money it is a lot better than the alternative.

Friday, 2 September 2016

Beggar my neighbour: Apple's Tax Problem in Ireland

There is well known economic rule called "beggar your neighbour". It is important in behavioural economics when you consider the model of the repeated Prisoner's dilemma. In that case beggar my neighbour represents the defection strategy. There is also a connection to companies seeking countries with the minimum regulation/taxation. This is when the companies are defecting.

Companies have a duty to shareholders which in the short term and when you do not expect there to be a repeat of the circumstances means that defection is the preferred strategy and politicians often think the same way. This is sib-optimal capitalism. It is sub-optimal because in reality we have longer term interactions and repeat business which are undermined by defection. Axelrod has shown that the best strategy as proposed by Rappaport is Tit-for-tat. You respond to defection by defecting and then you go back to a position of trust. Trust is the essential feature that makes the system optimal. You have to maximise the trust to reduce the costs of regulation and defection.

At a national level a defecting country is one that offers a lower level of regulation and taxation compared to all the other countries as business will move to that country and not pay taxes where they actually are active. This is how the Swiss canton of Zugg has become the European HQ of many multi-nationals. Zugg has a tax rate of 5% which is very attractive to global business. Given the size of the canton this minimal amount of tax from a large number of corporations raises more than enough for the infra-structure and services that the canton has to pay for. In fact they should be making a considerable profit. Levels of taxation elsewhere have to be larger because nations are expensive and levels of tax are set to avoid a deficit. This is why Zugg is beggaring its neighbours and why Ireland with its Apple tax deal was also beggaring its neighbours by removing tax revenues from other countries where Apple was doing business. Apple was unlucky enough to be the first company that was brought to court but it will not be the last and Google and Amazon are two more big names that stand out.

Ireland with a much smaller economy can survive without all the tax that is owed but this deficit is pushed onto all the other EU nations. That is why this sort of tax deal is illegal and why the UK deal with Vodafone also  needs to be investigated. Governments do this because they want to keep the jobs in their countries but if I did this as a small business or as an individual even if I did not do my duty well enough only in the expectation of a future benefit I would be in jail for up to 12 years and face an unlimited fine under UK law. In fact the recent report about the possible dropping of the investigation of BHS in return for Sir Philip Green paying a large sum to the pension fund is also bordering on illegal under the Bribery Act 2010. I begin to see why an Italian mafia judge called the UK the most corrupt country in Europe.

Ireland has been caught cheating but both Ireland and Apple are going to seek to contest the judgement. The only way that you can prevent beggar my neighbour is if we go beyond short term interests or if we promote supra-national agreements. We call these trade deals and although TTIP is a dirty word at the minute there are many others that we rely on everyday. The WTO is the largest agreement to make sure that nations do not deliberately cause economic hardship for each other. But the most successful is the European Union and that is why Ireland and Apple in the end have to lose if we are to have any faith in nations and democracies and if we want to live in a world which has not been taken over by corporations.

So why does not being able to beggar your neighbour matter? History shows that wars are usually about resources and as a response to internal economic challenges. Harming another countries economy has political and social consequences and not just economic ones. If we want a more peaceful and equal world we have to get beyond Brexit and Beggar my Neighbour and start understanding the long term benefits of working together.