Thursday, 6 February 2014

Harvesting the Genetic Algorithm

Antibiotic abyss: The extreme quest for new medicines - health - 27 January 2014 - New Scientist

This New Scientist article made me smile, probably because I still remember a time back in the 1990s, before they had really got to grips with the notion of 'intelligent design' when a favourite theme of creationists and other loons was how wonderful antibiotics were.

Apparently, they were gifts from God which could cure just everything from the common cold to cancer and restricting their use was somehow an infringement of the First Amendment - to most creationists the world only consisted of the USA then as now.

All the warnings from biologists that overuse of antibiotics would lead inevitably to the evolution of antibiotic resistance were all alarmist nonsense spread by conspiracies of scientists in the pay of drug companies. Anyway evolution was impossible because it contravened the second law of thermodynamics, as all the biologists knew - which is how you could tell it was a conspiracy.

How those threads in the old Compuserve forums used to go on... and on... and on. Some threads could last for months before anyone mentioned Hitler!

Anyway, enough with the reminiscing. The above article is about how we are now scouring the planet looking for new and exotic species on the off-chance that they may provide us with a new antibiotic because we are on the verge of an apocalypse as one dangerous pathogen after another evolves resistance to the last few remaining antibiotics in our armoury. Diseases like gonorrhea and tuberculosis, which were once relatively easy to treat, are now making a comeback. In 2013 MRSA killed more people in the USA than AIDS, hepatitis B and tuberculosis combined. In the UK, a resistant strain of tuberculosis is making a strong comeback from being on the verge of extinction and world-wide, malaria, which we thought was on the point of extinction a few years ago is enjoying a spirited revival worthy of a 1960s rock band.

Everywhere we have looked, microbial life has surprised us with its tenacity, versatility and abundance. But perhaps no extreme environment is more unexplored – or more promising – than the ocean trenches. While we have made large leaps in understanding deep-sea life, the trenches are the last unknown. It's the largest unexplored biome on Earth.

Tim Shank. Deep-sea biologist,
Woods Hole Oceanographic Institution, Massachusetts, USA
It's turning out that the richest source of likely candidates for not only antibiotics but other useful substances are the extremophiles which live in these remote, inaccessible places. Extremophiles are organisms which live in extreme conditions like very hot, very cold, very alkaline, deep in rocks or deep, dark, hyperbaric ocean trenches. For example, taq polymerase which has revolutionised DNA sequencing, turning it from a long, labour-intensive one to a relatively quick and easy process, so effectively revolutionising the science of genomics, was found in Thermus aquaticus which lives in near-boiling water around geothermal geysers.

There are a couple of reasons why this should be so. Firstly, of course, these are often the hardest for us to find because of the conditions they live in, so we come to them late in the history of biopharmaceutics. It's not that long ago that we discovered organisms not only could but did, and often in abundance, live in these extreme conditions.

The other reason is the one which made me smile. The reason these extremophiles have substances which organisms living in more normal conditions don't have is because of increased evolutionary pressure from their hostile environment. Extreme conditions demand extreme measures and novel solutions - things which only the genetic algorithm can produce given enough time. In effect, we are harvesting the results of a genetic algorithm which, given the time over which it has been running, has produced substances we can't even imagine let alone design.

It's ironic that we are pinning our hopes on the 'designs' of the genetic algorithm to help us combat the products of other genetic algorithms which are 'designing' antibiotic resistance in the first place. It's ironic also that we are quickly reducing the biodiversity on which we are more and more coming to depend to defend ourselves from the biota which is quickly evolving to live on us.

And the same creationists are still telling us that evolution is impossible, although 'antibiotics' has become something of a dirty word in creationist circles of late.

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