Friday Links

1. False Positives from Next-Generation Sequencing

2. What I look for in software papers

I [frequently review] software papers which I define as publications whose primary purpose is to publicize a piece of scientific software and provide a traditional research product with hopes that it will receive citations and recognition from other researchers in grant and job reviews. To me this feels very much like hacking the publication recognition system rather than the ideal way to recognize and track the role of software in research communities, but a very practical one in the current climate.

3. On the organic movement and charlatanism

Unfortunately, charlatanism sells. When I was last in Portugal, I was disappointed to find out that one of the organic stores I used to patronize for their premium produce and hard to find food items had gone over to mostly selling small bottles of holy water at €1000/litre and “natural pills”. Their salespeople went from scruffy to dressing in white coats as “pretend doctors”. Ugh.

4. I read Mind and Cosmos: Why the Materialist Neo-Darwinian Conception of Nature Is Almost Certainly False by Thomas Nagel.

Someone wrote about What Money Can’t Buy that it was wrong, but wrong in a way that many people are wrong. Therefore, it is a useful contribution to articulate exactly that argument. [1] In fact he writes:

I would like to defend the untutored reaction of incredulity of the reductionist neo-Darwinian account of the origin and evolution of life.

For example, here he is again:

In the available geological time since the first life forms appeared on earth, what is the likelihoo that, as a result of physical accident, a sequence of viable genetic mutations should have occurred that was sufficient to permit natural selection to produce the organisms that actually exist?

In the conclusion he calls neo-Darwinism a heroic triumph of ideological theory over common sense.

Perhaps it is the task of philosophy (which we may as well call the science of the gaps) to articulate common sense. But the celebration of ignorance that is behind these claims is a bit silly.

5. Here is a good comment on the book. I think this is very much in line with if you care about winning, belittle your opponents arguments; if you care about truth, you improve their arguments for them (I think this was originally a Milton Friedman quote).

Neo-Darwinism perfectly explains why there are zombies. Once you have RNA, zombies are just a matter of time. To explain conscienceness is a harder problem.

[1] Of course, they are wrong in different ways. Michael Sandel is perhaps morally wrong in that his ideas cause a lot of unnecessary suffering and death (although, in another moral conception, those deaths are necessary and just—this is not something we can decide scientifically by looking at the world, but morally by deciding whether it is better that we preserve purity in some conception or that we avoid the deaths of others). Or he is philosophically wrong in that his ideas are contradictory. On the other hand, Thomas Nagel is scientifically wrong.

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