Evolving Thoughts

Evolution, culture, philosophy and chocolate! John Wilkins' continuing struggle to come to terms with impermanence... "Humanus sum, nihil humanum a me alienum puto" - Terence

Saturday, September 03, 2005

Some more about Katrina

Mike Dunford puts a bit of balance into the issue by noting that not merely the Republicans (but surely they!) but also all politicians and scientists share the blame for failing to assert the priority of reality over politics. And he is right.

Fortunately philosophers are exempt from the strictures of reality. But it's no joke. If we ignore science, people die.

Friday, September 02, 2005

On disaster, bad science, and political thuggery

The dreadful disaster of New Orleans (why, oh why didn't I visit it last trip? Now I'll never see Bourbon Street as God or Anne Rice intended) has raised some interesting matters.

First of all, this was not unforeseen. Paul Myers at Pharyngula notes a Scientific American item from 2001 in which this very possibility was noted. But the funding was, as Brian Leiter reports, withdrawn, and the Army Corps of Engineers in New Orleans was reduced to half its budget this financial year by the Republican Congress and House of Representatives.

Why? To pay for the Iraq "war". Basically the money used to pay for this unnecessary war could have fixed the levees and the conservation problems that were in trouble for years. Of course, it could also have gone to fix schools, hospitals and so on, but we'll leave that to one side now.

Here's the interesting thing, for me: politics overrode science (ecology, geography and so on) for short-term political gain. Yet another reason why government involvement in matters of intellectual integrity ought to be very light. But this is a Big Government administration, which thinks reality is open to political negotiation.

So, how are the conservatives dealing with their failure? By being honest and open, and promising to learn from it? Not bloody likely. Leiter also discusses the moral vacuity that is American conservatism these days, with gross and copious examples.

And this, folks, is why science must be defended. These things have consequences, goddamnit!

Late edit: Leiter's name spelled correctly at last.

Wednesday, August 31, 2005

How did genes evolve?

A long standing problem I have had about Richard Dawkins' claim that "life began when a molecule gained the ability to replicate itself" is, how did that happen? If evolutionary biology is about remove the miraculous from explanations of life and its past, then why posit a miracle of that kind?

Some properties of the chemicals involved had to lead up to the ability to self-replicate. I have a story of my own, which I'll add at the end, but for now, Science is reporting that ribozymes have a feature which will allow them to copy RNA reliably even if there are major mutations made to the molecules.

Here's the difficulty. Without some method of error correction, such as the ones that DNA replication systems have, a genome of RNA can only get so large before mutation rates, which are a relatively constant frequency, render the molecule too error-prone to act as the genetic molecule in a living system. This has been called by Eors Szathmary the "error catastrophe", and it has been a real stumbling block for scenarios of how self-replication could get going in the first instance.

Now Szathmary and his collegues Adam Kun and Mauro Santos, working in Budapest, which is a real centre for Origins of Life research for some reason, have shown in a paper in Nature Genetics that ribosomes, which are the "machines" (it's a metaphor, OK? No ID implications) of nucleotide replication, can withstand a massive amount of sequence change before they cease to do their work. This means that even if mutations sneak into the RNA genome, the ribozymes will still replicate RNA, thus cutting off the error catastrophe. This is a major achievement (and another blow to the God of the gaps devotees). Now we have the capacity to generate genomes up to the size of a transfer RNA in a modern cell, and that is no small thing, forgive the pun.

But it leaves us wondering how genetic fidelity improved. And the answer to that question was, I believe, inadvertently given byNobel Laureate Manfred Eigen in the 1970s. He and his colleague Peter Schuster proposed a closed cycle of chemical reactions, where each products of one step catalysed the next, and called it a Hypercycle. Now suppose the following scenario for the very beginnings of organic life, before there were even cells.

There is a chamber, say an underground volcanic-water fed one, in which the source molecules from which life is made are being fed. It's hot enough to make chemical reactions occur (let's suppose there's a chemical gradient and a thermal gradient), but not so hot that the products denature. Chemical reactions might set up hypercycles.

Now it follows that the physical properties of the molecules involved in a hypercycle will vary in their stability, how well and accurately they catalyse the next step in the cycle, and how much energy they take. There will tend to be chemical selection, therefore, for reaction cycles that have at least one more stable (that is, long-lived), accurate and cheap molecule in the hypercycle.

So our proto-RNA/ribozyme complex will become optimised over time. And this allows genes to evolve. And it's non-miraculous. Straight Darwinian selection, without replicators.

This undercuts the necessity for there to even be replicators before we get a selection process going, and so it has some implications for cultural as well as biological and protobiological evolution.

Some thoughts..., and the hard work on this was done not by me but by Clem Stanyon and Ian Musgrave, in case anyone wants to credit it.

Tuesday, August 30, 2005

God - a career retrospective, by Purple Koolaid

Do go see this. A lovely piece of anti-ID satire.

Monday, August 29, 2005

I had the idea first, dammit!