Monday 24 June 2013

Metagenetics

Putting words in the mouth of the enthusiastic northern Fast Show character "in't life brilliant".

Once you've got a self replicating molecule that can almost always make perfect copies of itself but, importantly, once in a while makes a little mistake, a sea of ingredients for the molecule to play with and a great deal of time, out pops a sentient being that can try to make sense of how it all happened. Brilliant. Oh ..... plus you need a reliable long term source of energy.

Using four letters to write a string of 3 letter codes that instruct a cell how to function; to know what to make and when to make it; to know which cells to get on with and which to shun; to know, in short, how to build a body that can sustain itself. At least for a while....

Each of the words simply tells the machinery in the cell to add a particular amino acid to a chain. Put those particular words in a mouse and they do the same thing that they'd do in a human, a banana or a bacterium  It's a bit like having a bit of computer code that does the same thing in a Sinclair ZX81 as it would in Tianhe - 2 ; though not as fast or as often.

Each of us, and all of the various life forms that surround us, are simply solutions to the same question. Does this sequence of words produce a self sustaining organism?

Now of course, the environment that an organism finds itself in has an effect on its chances of survival.  Put most bacteria somewhere really hot, like a hydrothermal vent, and they won't stand a chance, but some will (or they might if the new temperature wasn't too far from the one they'd grown used to). 

Organisms are able to adapt to their circumstances but they can only do this by changing and they can only change if the instructions change; if every now and then they make a mistake; i.e if they mutate.

A couple of thousand million years after life first appeared on Earth a new way of bringing about change emerged. Sex. Take two closely related organisms, ones which have almost the same set of instructions and then shuffle the pack so that some instructions are inherited from one parent and some from another. You can now get change, and the possibility of adaptation to changed circumstances, without waiting for a chance mutation. Brilliant.

It also turns out that some organisms, in particular bacteria, are able to directly swap bits of code with each other, and some some bits of code, viruses, don't contain enough information to construct an entire organism but simply get themselves copied by an organism that already exists. 

What I find wonderful is that the variety of life that we see around us, including ourselves, all has a common origin and all makes use of basically the same set of instructions.  Despite ever changing conditions this process has kept the Earth fairly well populated with life for over 3000 million years but, in the process, over 99% of the species that ever existed have now become extinct.

What we know from the paleontological record is that after a big environmental change the number of species dips and that it then takes a while for new species to evolve and fill in the gaps.  The speed at which we're changing the environment means that, for a while at least, life will be less diverse than it has been for a very long time.

But at least our children's children will have all those wonderful Attenborough videos to remind them what's temporarily been lost. Most of them seem to be living life through a screen anyway.

Postscript: This post was going to be in response to the UK Environment Minister's recent comments on Genetically Modified Organisms (GMOs) but I really can't be bothered to say much other than beware of big business and take each case by the each. The big issue is probably land management rather than GMOs per se.











6 comments:

  1. Blogging is a bit like evolution -- you start out with the intention of addressing one question, but end up -- via a process of adaptation -- addressing another. Your idea of revealing what that original intention was is an innovation that may (or may not) spread into the wider gene pool...

    I think the most difficult question in evolution is the "useless intermediate states" thing -- I know Dawkins has explained this using the example of the eye, but I'm not convinced -- there seems to be a sense in which a genuinely advantageous goal is achieved via a series of adaptations which, in themselves, seem to offer no advantage at all. This may be hindsight, of course.

    I also feel that there are certain "paths" down which evolution is obliged to proceed, once "chosen" (bilateral symmetry, say). It would be handy having a third hand, say, but it's never going to happen.

    The Lamarckian thing bothers me, too -- somewhere down the line, someone is going to discover a mechanism for passing on acquired characteristics, and everything is going to make a lot more sense.

    Mike

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  2. A few years ago the doorbell rang during a particularly tedious world cup football match. At the door were two seventh day adventists. Using the strategy of attack being the best form of defence I began to talk about electronic cameras and got them to agree that putting the wiring that carries the signal from the detector between the detector and the lens wasn't a particularly good piece of design. The follow up was that this is the way thew eye is "designed" which suggests that if it was designed it wasn't designed very well. You get the point...

    Making big changes, like undoing bilateral symmetry, would probably mess so many other things up that your unlikely to get a viable intermediate organism. Hence this sort of conservatism.

    There have, however, been quite a few attempts to model the evolution of the eye starting with just a patch of light sensitive cells which then get folded into a shallow cup, then into the equivalent of a pin hole camera which then acquires a transparent cover etc all the way to the complex structure of our own. Each tiny adaptation represents a distinct improvement on the one before and, given the known rate of mutation, the whole process would take less than 200,000 years.

    Having googled a few things, it turns out that there is an advantage of having the wiring in front of the retina in that it makes it easier to get oxygen to the active cells in the retina and thereby maintain their metabolic rate.

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  3. Yes, the "design" thing is not a problem -- do you know Douglas Adams' neat parable about the sentient puddle going on about how perfectly it fits the hole it's in, and must therefore have been designed for it?

    But the "tiny improvement" model seems dodgy, to me. How tiny does an improvement have to be to give you a serious breeding or survival advantage? And what mechanism gets you from the "largest useless mutation but one" to the "smallest useful mutation"?

    And, come to that, why are there separate species, and not just a vast spectrum of interbreeding life-form variations? Hmm, maybe I should finally read that book by Darwin, instead of relying on my built-in bullshit generator...

    Mike

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  4. Whilst there are many successful solutions to the problem of finding a code that produces a viable organism there are far more unsuccessful ones. the bigger the deviation from a successful solution the more likely you are to end up with an unsuccessful one. So tiny changes are preferred for purely probabilistic reasons.

    Most mutations likely to offer no benefit at all or are even positively harmful but we only get to notice the changes which DO bring about a breeding advantage. So it's not that mutations are somehow chosen to be favourable just that we only notice the ones that are.

    Apart from us poor boys who only have one copy each of the X and Y chromosomes all our other genetic information is doubled up. This means that if the information coded in one chromosome doesn't work then there's a reasonable chance that the information in the other will. The key step in sexual reproduction is meiosis. This is a special sort of cell division where the two chromosomes in each pair swap sections of code and the cell then divides so that the germ cells (eggs or sperm) only contain one (now mixed up)chromosome from each pair. When a sperm cell fuses with an egg the pairs of chromosomes come back together again but in different combinations from their parents.

    For this process to work the sperm and egg need to have the same basic chromosomal structure. But this too is the result of the code. So, if the code is so different that it produces a different chromosomal structure then sex doesn't work and you've effectively got a different species.

    None of these details were known to Darwin and I think that his key insight was to appreciate that given "enough" time the gradual accumulation of small changes could bring about enormous differences between life forms with a common ancestry.

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  5. Thanks,Andy. I need somehow to convey this information to my neighbour's dog, who will attempt to have sex with pretty much anything.

    Mike

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  6. I quite enjoy trying to boil basic scientific concepts down to their essentials but I'm not sure that I'm up to doing this for dogs.

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