Wednesday, July 18, 2012

The world is complicated

Several things recently have prompted me to write this post; I'm not quite sure where its going, but lets start.

In BBC's excellent series 'Secrets of a Living Planet' with Chris Packham, it showed how complex webs of living organisms can create a sort of super organism, with lots of symbiosis and feedback going on.

For example, underground fungi networks connect  up lots of trees and other plants in a kind of living network. The fungi derive sugar from the tree roots, but the trees also benefit by getting various nutrients from the fungi. The fungi get the nutrients from other plants and decaying matter, some of which (in this case) are from decaying salmon which had been left by bears.

Amazingly it is possible to analyze the bear diet (from a single hair) and know that about 80% of their protein comes from the salmon, despite it being a short season when the salmon run. Even more amazing is analysis of the tree cores which shows that they too owe most of their structure to the salmon. Trees made from fish.

Of course it has long been known that complex relations exist between species, but this series really brought home how interdependent all living things are. It begins to make sense to think of the whole earth as a complex genome - Gaia if you like. It is a simple truism to say that no species could exist all by itself, so it is always necessary to consider evolution of a collection of species rather than just one.

Another hot topic at the moment is 'proteomics', or the extended genome. We now know that the human body carries 10 time as much DNA (by base numbers, not weight) in bacteria and fungi, than it does in its own  DNA. We know that there are hundreds (thousands?) of species of bacteria on and in each human individual, that these vary in different parts of the body, and vary between individuals. We know some of what they do, but we don't know the half of it. There is now an ongoing project to find out about all this stuff, which is as big as the human genome project - probably bigger, but thankfully won't take as long because of the huge advances in gene sequencing.

What amazed me though was to learn that some of these bacteria produce messengers that affect the way in which our genes are expressed in the human immune system. So they aren't just hitching a ride, or helping the digestion. They are a part of our genome almost as much as our own DNA is. Our evolution is a kind of co-evolution with our bacterial and fungal partners.

This is similar in a way to the living network idea above. The point is that we have to think about extended genomes, not just the genome in a specific individual or species. Richard Dawkins wrote a book called 'The extended Phenotype' some years back to discuss how we should consider things like artifacts and society as part of the 'phenotype' of a gene - the way it affects the individual's development. Looks like now is the time for one on the 'extended genome'.

On Science Friday I also heard of things called giant viruses. Apparently these have only been found fairly recently. They are as big as bacteria and operate differently from normal viruses - they set up a kind of internal virus factory. And they are  big enough to have their own viruses attacking them - virophages.
Now that we know they exist, all kinds of different ones are being found all over the place, including in arctic ice and underground.

Now The large hadron collider may (or may not) have found the higgs boson - though it seems it is not quite as simple as that. Apparently there are (or maybe) several different flavours of the possible higgs, and it may (or may not) involve some other new particles, in different flavours naturally.

What with the ever elusive dark matter and dark energy, it seems to me that, just as we begin to think that we are beginning to really understand everything, it all gets a lot more complex, and we realize that we don't actually understand it.

Thats why I wrote this post.

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