22 June 2017

Crown Estates

Her Maj opening parliament
with her pro-EU hat on.
Partly just because they're in the news again, there are the usual complaints about the Royal family sponging of the taxpayer. I'm always surprised that British people believe this. As far as I can tell it's simply not true.

As I understand it, a badly indebted George III, on his accession in 1760, signed over all rents and other income from his portfolio of land and forestry holdings, currently valued at ~ £12 billion. In return the govt administer it all and pay the monarch a stipend. In 2016 the Crown Estate earned the UK government about £305 million in profit.

The Queen gets about £45 million a year to run the Royal household, most of which is not discretionary. Leaving HMRC roughly £260 million better off. Prince Charles has his own private income of ~ £20 million p/a from lands in Cornwall. Both of them now pay taxes.

The Royal family make a large net contribution to the UK economy and the tax base without even considering factors like tourism. And they don't get to hide their money offshore like other rich people.

I'm inclined towards republicanism and redistribution of the vast unearned wealth of the ultra-rich, though seeing the Queen out there comforting victims of the tower block fire (at her age) and wearing that EU hat to parliament yesterday, I feel well disposed towards her personally.

Its a bit depressing how much of British public opinion seems to come from the gutter press. And the negative impact this has on how Brits feel about themselves and their countries.

18 June 2017

HIV and Intelligent Design

If I was going to provide evidence for an intelligent design argument, then I might well choose the Human Immunodeficiency Virus (HIV). It really is a finely honed and efficient system for killing human beings.

HIV attacks the immune system. Our immune responses mostly come in the form of various types of white blood cells. Amongst this variety are the Helper T-cells. When they come across a pathogenic cell in the body, say a bacterial cell, it is T-cells that release chemicals to attract the other kinds of white blood cells that clean up the infection. Plus it releases another chemical to induce other white blood cells to multiply, so that there are plenty of them. And a third type of chemical, an antigen, which marks the pathogen and makes them easy for other white cells to find, identify, and destroy it.

In short the T-cells coordinate the body's immune response to pathogens. HIV infects various white blood cells, but infecting T-cells is crucial to understanding how HIV kills humans. By disabling T-cells, HIV gives rise to Acquired Immune Deficiency Syndrome or AIDS. A person with AIDS becomes susceptible to every other type of infection - viral, bacterial, fungal, and even parasitical. Normally the body just swats down infections. We only occasionally succumb. And even then our body's immune response helps keep the disease from killing us. What kills the host is not HIV per se, but the range of opportunistic infections that benefit from the weakened immune response.

HIV has a long incubation period. Once infected it can taken anywhere from two years to two decades before any symptoms begin to manifest. In that time the host can be infecting other people. The one limiting factor is that it only spreads in direct exchanges of body fluids - through sex, sharing needles, childbirth, breast-feeding. Were it spread like influenza, we'd all have it by now.

The virus has two layers. The outer layer is made from the bi-lipid outer layer of a human cell - creepily the HIV virus drapes itself in a human "skin". It is studded with proteins that recognise and bind to T-cells. The inner layer is a protein capsule containing two copies of the viral genome and some, plus some protein-based enzymes: e.g. reverse transcriptase, integrase, ribonuclease, and protease.

When the HIV attaches to a T-cell, proteins contract drawing to two together so that their cell walls merge, and then inserts the inner capsule which breaks up releasing the strands of genetic material and enzymes.

Since human cells use DNA to code genetic material, in order to hijack the human cell, the virus needs to produce DNA. The enzyme reverse transcriptase is what does this. But here's the thing. HIV reverse transcriptase is inherently buggy. The HIV genome is about 10,000 base pairs, coding for just 19 proteins. By contrast the human genome codes for tens of thousands of proteins. Crucially, when converting RNA into DNA the enzyme makes on average 1-10 errors every single time it copies the viral genome. Since each infected cell makes billions of copies, this means billions of random variations on the HIV virus.

Darwinian evolution is driven by random mutations. Most organisms have mechanisms for preventing copying errors and suppressing localised mutations which might otherwise, for example, cause cancer. As our cells produce proteins from DNA templates, they proof-read as they go and correct mistakes. Mutations caused by radiation damage can be repaired up to a point. HIV goes in the other direction and creates mutations, by design. Of course many of these mutations will be dead ends. They will not be viable. But many of them are viable and so HIV quickly and constantly evolves into new forms. This helps to defeat any immune response to HIV itself, but it also makes the disease very difficult to fight with drugs.

Having turned the viral RNA into a strand of DNA, another enzyme transports the DNA into the nucleus where another enzyme inserts it into our genome. Viruses that do this are relatively rare and are called retroviruses. Quite a large chunk of our genome is junk DNA, some of it inserted by previous retrovirus infections. In theory these ancient retroviruses could be reactivated. It's a science fiction trope. But in practice the process is complex, that its unlike to happen.

Once it becomes part of our genome, the viral genome is copied in the normal run of things, though it can remain dormant for a period as well. Our standard cellular machinery starts to produce the building blocks of new viruses - strands of RNA, the 4 enzymes, and the proteins that encapsulate the package, as well as some other proteins involved in identifying host cells and infecting them. Finally a last enzyme helps to assemble viral capsules inside the cell, which is transported to the cell wall. As they leave, the virus particles take a little of the cell wall to wrap around themselves, studded with the proteins needed for infecting more cells. The fully formed virus is now in the body fluids and waits for a chance encounter with another T-cell, preferably in another host.

This presentation is obviously simplified. For example, it's likely that HIV first infects another kind of white blood cell that is less detrimental to the host, building up numbers so that when the assault on T-cells begins it is devastating. And the whole process is now understood in a good deal more detail.

At present only one person has even known to have been cured of HIV. Out of 70 million cases. Although drug treatments do exist, they can only slow the disease down, rather than cure it.

One of the fascinating things about these kinds of pathogens is how non-specific they are. It is true that some people are resistant to some strains of HIV, but on the whole the virus can infect any human. If we get the wrong type of blood in a transfusion, we die because the body rejects it as foreign. Patients who receive transplants have to artificially suppress their immune responses for the rest of their lives to prevent rejection. The virus however is not at all choosy about blood type or tissue type or any of these factors. Indeed we really get into trouble when viruses from animals mutate to infect humans. For example, when an influenza virus in birds and/or pigs mutates and jumps the species barrier, we get influenza epidemics.

All in all HIV is devastating pathogen, seemingly engineered to kill humans. A number of conspiracy theories exist which suggest that it was engineered, though I don't find any of the plausible. We still don't really have the depth of understanding to design and make something like this. On the other hand some of the conspiracies suggest that it was a mistake that came from attempts to create Frankenstein's monster bugs by breeding different viruses together. This might work with bacteria, which can share genetic material, but it wouldn't work with viruses which cannot. So, it looks like HIV just evolved.


Intelligent Design?

If you were sceptical about evolution, however, and were looking for an organism to support an intelligent design argument, HIV is certainly a great candidate. The specificity of the mechanism is complex enough to be astounding and yet simple enough for most people to understand it. A series of events have to occur in just the right order, in just the right way, for the virus to be effective, but they do happen. It's almost too perfect, hence the conspiracies.

In particular HIV seems designed to defeat medicine. It can rapidly counteract an effective drug.  The standard treatment in wealthy countries, or for wealthy people in poor countries, is a cocktail of three drugs which target three different aspects of the viral life cycle. This makes it much harder for the virus to circumvent the effects. But it's not enough to kill it outright. The viruses DNA is copied into our DNA where it is very difficult to get at - it's difficult enough to get drugs into the cell, but near impossible to get them into the nucleus of the cell. The cell itself acts to prevent this molecules that disrupt our DNA are almost always detrimental - retroviruses being a case in point.

In the West, the communities who were most affected by HIV happened to be hated by Christians, so they could rationalise it as God's punishment. This is tricky because the Christian God is supposed to love everyone, and having people die horribly, but not before infecting dozens of other unsuspecting, often entirely innocent people, is difficult to reconcile with this view. Why is God using a shotgun to remove a splinter? There's far more collateral damage, e.g. AIDS babies, than actual punishment for evil.

However, the real twist is that HIV in the West is tiny compared with Sub-Saharan Africa. In some countries in Africa, HIV infection rates are one in four of the population. In Africa roughly ten times as many people have AIDS and have so far died from AIDS as in Europe and the Americas combined. And final irony? A large number of these Africans are conservative Christians. They are the Christians fighting the modernisation of the Church of England for example, resisting the ordination of women or homosexuals. AIDS is more prevalent in countries where homosexuality is illegal, than in those countries where it is legal.

So if HIV is an example of intelligent design, what is the designer telling us? First of all the designer seems to be a homicidal, but highly intelligent psychopath. Secondly he is targeting poor Christian people, who often live in crushing poverty, with little education; while the wealthy capitalists of the world continue to steal all the wealth from poor countries. If an intelligent designers was going to loose a plague on us, why would he target Africa of all places? Is he racist? And lastly, very many of the people who contract AIDS now are babies, born to infected mothers. Why is the designer killing babies?

I suppose one might still argue that the HIV virus is too specialised to have evolved through random mutations. The specificity, the argument goes, requires a designer; and this design would have required considerable intelligence. But that intelligence is utterly lacking in empathy. The designer, if we believe in it, is chillingly inhuman and following an agenda that does not include any thought for our well-being. HIV may well be intelligently designed, but it is intelligently designed to kill human beings indiscriminately and wantonly. Worshipping such a designers would be as pointless as a fly worshipping the child that is pulling off its wings.

In fact when it comes down to it, the situation makes an intelligence seem extremely unlikely. Intelligence completely without empathy could hardly have created anything, because it would have lacked the motivation to do so. Things like HIV make random chance seem by far the most likely explanation, but random chance can be productive, but it doesn't care about the outcome. Given how indifferent the universe is to human values and desires, a process which had no view to a particular outcome seems the only plausible explanation for how we got here.

15 June 2017

Reasons

I'm reading a completely fascinating book at the moment: The Enigma of Reason by Mercier and Sperber. It's about reasoning. It's been known for most of my lifetime that we're not very good at solo reasoning tasks. In the classic experiment to test how reasoning works, the Wasson Selection Task, only 10% of people were able to reason through a fairly basic logic problem. And yet 80% of the participants were 100% sure about their method.

The authors argue that the main purpose of reasoning is for coming up with reasons. Yep, the reason we reason is to produce reasons.
"Why do you think this? Why do you do that. We answer such questions by giving reasons, as if it went without saying that reasons guide our thoughts and actions and hence explain them." (p.109)
The authors point out, though again this is not news, that in fact most of our reasons are after-the-fact rationalisations. We decide first, based on criteria we're mostly not even aware of, and then we come up with reasons that we hope make that decision seem reasonable. Reasons are how we explain things to ourselves and others. But on the whole, our reasons are fictions that we make up to explain ourselves to ourselves and the world.

Simplistically, in a court of law, reasons are sought and given and then tested and weighed for veracity. A reason has to be consistent with the physical facts. But it also has to be consistent with the psychological facts, i.e. how the jury think they might act in similar circumstances (for which they ask themselves how the reason feels).  If we the jury find the defendant's reasons plausible then they are not guilty. If not then they are guilty and owe us and/or society a debt.

Ask yourself... Why do I believe the things I believe? You've probably got reasons already. But now ask, Why is that reason a justification for believing anything? What is it about the reason that makes your belief reasonable.

For instance, I believe that the UK is probably better off in Europe so I voted to remain in it. The reasons are actually a little vague. I don't like the Tories. I think the world is safer if we work together more closely. But those who voted to leave also had reasons. Maybe their reasons were less vague - the EU is an inefficient bureaucracy, with too many unelected officials making decisions, it costs us too much, it's run by foreigners, it allows too much immigration, and so on.

If reasoning was anything like the classical view of it, then this kind of divided opinion couldn't happen. We'd all weigh up the evidence and decide the most rational course to take, and most of the time there would be broad agreement. But we don't do this.

What we do is have a feeling about it, and then fish about for reasons, which the media provide for us. Or we're confused, then we hear a reason that resonates and stick with that. Which is why when people give reasons for political decisions, they often unconsciously repeat, word for word, a  political slogan, like, "I want my country back" (a line uttered in a TV program around the time - but ironically uttered by a spy who was helping the Nazi's subjugate his country).

We're all doing this. Deciding on what feels right, then producing reasons ourselves, or reproducing reasons we've heard from third parties. And since we also accept the myth that reasoning and "being rational" are the highest faculty of humans, we assume that our reasoning must be the best. We think that our reasons are good. And why? Well for reasons. And the criteria for judging those reasons? Well they are also reasons. And so on down into the unconscious functioning of our minds that we cannot yet fathom.

Things happen for a reason. Yeah, right!