Saturday, 21 August 2010

Immortal cells, horizontal gene transfer and the tree of life

Had an interesting phone conversation with Aldo last night, talking about horizontal gene transfer amongst single-celled organisms (yes it also happens in multicellular organisms, but I guess it's not so important there unless the new material gets into the germ cells). He mentioned that the traditional tree-of-life style classification of the prokaryotes is a bit ... can't remember the exact word he used, let's say provisional ... when compared to its application to multicellular organisms. I replied that, with multicellular organisms, there's a clear sense in which offspring are not the same individuals as their parents, but there's no such distinction in the case of single-celled organisms. In a sense, a single-celled organism today is the same individual (or at least, one of many clones of it) as its parent from a billion years ago — a parent which we might not even classify as being in the same species as its "descendant"!

Thursday, 19 August 2010

Interesting post on Chile's pension system

Gonzalo Lira posts an interesting article on how Chile's pension system benefits everyone:

  • By funneling pension contributions into the stock market it increases the amount of risk capital available to companies generally.
  • It keeps employers' hands off their workers' pensions: there's no company-wide fund to raid.
  • Similarly, there's no national fund for the state to pillage either.
  • It increases labour mobility because people can take their pensions with them when they change jobs.
  • Finally, it protects firms from crippling themselves by their own stupidity because they never have to make pension promises that they can't keep.

Wednesday, 18 August 2010

Babies, trees, clones and living forever

Like most nerdy kids, my first introduction to sex was in a library. We're not talking bodies writhing among the books: this was all part of my master plan to acquire All Knowledge before I was thirteen, by reading every book in the local lending library. Amidst all the texts and illustrations, of egg cells, spermatozoa, wombs, pre-natal development, colourful pictures of codpieces throughout the ages and articles on sex-segregated communal living in the South Seas, one question gradually surfaced in my mind: why do we start off microscopic?

Years passed and I didn't acquire All Knowledge, but that question kept coming back to me, and I was reminded earlier today of the answer that I gradually arrived at, when I read an article on declining fertility in clone trees, as reported by the BBC. Trees can't live forever without sex, study shows, they say. The research they're quoting was published in the free, online jounal PLoS Biology: Aging in a Long-Lived Clonal Tree. (Just to make things clear, these trees don't only reproduce clonally. Each tree may be either male or female, and if you put them near each other and supply some bees, they'll reproduce sexually. BUT they can also reproduce by sending out lateral root suckers, and sometimes a single tree can take over an entire location in that way.)

The two things may not immediately seem to be related but they are, and the key is that it's to do with "getting around" the second law of thermodynamics (the one about entropy always increasing with time).

The idea is, the second law says that in a macroscopic object such as a tree or a person, order should always be breaking down. Now animals and plants have repair mechanisms to deal with some of the ways that their bodies break down, and even the cells of which we are made have, themselves, extremely complex and efficient ways of repairing their genetic material when it is damaged. But our bodies consist of billions of cells, and in some of them, inevitably, the repair process fails and they accumulate damage: mutations.

What do we know about mutations? Mostly, they stop things working. Often the things that stop working are critical to the survival of the cell, and the cells die. Sometimes the things that stop working are critical to the body's control over the cell in the environment of the body, and the cell doesn't die when it should, and that can cause cancer. So despite the fact that we owe all the variety of life in the world to mutations, the fact is that most mutations are harmful, and, from the individual's point of view (be it the multicellular being or the cell itself), we don't want them.

Let's put some numbers on this. Each human being inherits about 3 x 10^9 base pairs of DNA from each parent, that's 6 x 10^9 base pairs altogether. Now one estimated is that in humans and other mammals, uncorrected errors occur at the rate of about 1 in every 50 million (5 x 10^7) nucleotides. And note that that's uncorrected errors, true mutations that have survived the repair processes. That mean that each new cell gets about 120 new mutations! The numbers for the Trembling Aspen (the variety of tree that the researchers examined) will be slightly different given its different genome, but from our point of view, essentially similar: the basic point is that every cell is a mutant, no two cells are the same.

Now consider what happens when plants reproduce (if that's quite the right word) clonally. Cells forming a portion of a root produce a bud that starts growing upwards and becomes a new stem or trunk; or, depending on the species, cells forming a portion of a branch produce a bud that starts growing downwards and becomes a new root. In either case, those cells are from the general population and may have been replicated many times since the original seed, accumulating mutations with each fission. It seems to follow from that, that the new individual (trunk, let's say) may already have accumulated significant genetic damage by the time it's "born".

Things aren't looking good for the Aspen. Stands of populus tremuloides can spread asexually for hundreds of thousands of years however, without noticeably degenerating. To some degree this is because of selection at the level of individual trunks or treelets ("ramets", in the parlance), there's also the phenomenon of rejuvenation familiar from coppicing in non-clonal trees, which doubtless applies here too. However the researchers cleverly argued that while surviving ramets in an old clone might maintain genetic fitness due to selection pressure for things like, oh, producing bark, making chlorophyl and so on, there wouldn't be any selection pressure against mutations in sites to do with sexual reproduction. (They are basically saying that if every other tree for a mile around is another male, a clone of yourself, then it doesn't matter if your flowers or pollen work properly or not, there ain't going to be any babies.)

So they looked for evidence of declining fertility amongst male aspen that had been reproducing clonally for a long time, and used that as a proxy for senescence generally. Unsurprisingly, they found it. It seems that, though an individual aspen and its clones may hang around for as long as a million years, they must still find a member of the opposite sex and produce seed before they eventually die.

So what's the connection with microscopic babies? It's just this: that whereas in a macroscopic-sized clone some of its many cells will be viable whereas others won't, in a human baby at the stage of a fertilised ovum either that one cell will be viable or it won't. If the cell isn't viable, then the embryo will not come to term, but if the cell is viable then you have a guarantee that you've started a new cell line without significant accumulated damage. In effect, you've managed to filter out your damaged DNA.

Nothing comes for free though, and it's never really possible to defeat the second law of thermodynamics. In this context it's relevant to consider what might otherwise be a surprising fact: just how frequent miscarriages are even in the developed world. Hunting around the internet I read that one pregnancy in seven miscarries, and it's estimated that the true figure may be as high as one in four: the difference being due to miscarriages that happen before the mother is even aware that she is pregnant.

Today's superplant - the pumpkin

I've been thinking for a while about using the back garden to grow food. Recently, several people I know have also mentioned that they are thinking about doing some vegetable gardening or getting an allotment, so it may be that the idea is in the air (like some mental pollen looking for susceptible brains to pollinate!), perhaps impelled by how broke people seem to be feeling nowadays, what with the double-dip just round the corner...

ENN-EE-WAY I'm looking forward to what I should be planting next year. I want to maximise the utility I get from each type of plant (translation: I'm lazy) and I also like the idea of companion planting to increase productivity, decrease the amount of weeding necessary (see a theme developing here? actually it just appeals on the grounds of basic efficiency, honest) so I'm toying with some kind of variation on the Three Sisters technique.

Now the classical form of Three Sisters calls for growing maize, beans and squash. The maize grows alone until it reaches about 15 inches in height, then ytou plant beans and squash alternately between the maize plants. As the maize continues to grow, the beans grow up it (so, looks like you'll need a strong-stemmed variety of maize!) while the squash vine winds around below, providing ground cover and discouraging weeds. The beans also fix nitrogen, helping to assure fertility from year to year. (I suspect you could also plough in the maize stalks, and bits of the other plants, as a green fertilizer, but then you'd need to carefully rotate locations in order to avoid diseases overwintering in the soil. Maybe it would be best to just burn them or compost them.)

One problem is I'm not quite sure what I'd do with a lot of maize. I can't see myself producing ethanol in the garage, really, and I'm not sure if there is anywhere nearby that could grind them into meal or flour (though it might be worth looking, just in case there is). And would I really be up to putting the maze kernels through the nixtamalization that's necessary to extract all the goodness? — How easy is it to buy relatively small quantities of calcium hydroxide? Then again, maybe I could get by just grinding up some eggshells (mostly calcium carbonate) in a pestle and mortar and adding that to the simmering kernels? And anyway, nixtamalisation is only really necessary if you have maize as the major part of your diet, otherwise you'll get the niacin, lysine and tryptophan you need simply by having a varied diet.

So maize is probably still quite a good possibility, maybe even leaning towards a popcorn variety. Another possibility for the tall-plant role is the occasional sunflower. Beans are, of course, beans: there's any number of varieties that I could try. But what shall I choose for the squash?

Well I'm currently leaning towards the humble pumpkin. If you look at Leaflet No. 12 - 1986 - Pumpkin, you'll see that it's easily grown — the report says an old rubbish heap is ideal! — and that you can eat almost every part of the plant: the fruit (of course), the leaves, the flowers (use the petals, avoid the centres of the flowers), the growing tips of the vine itself, and the seeds.

The pumpkin's vitamin and mineral content is also high, with the leaves being stellar sources of vitamin A and, especially, C. You can eat them with fats (e.g. cream, oil, fatty meat) in order to promote uptake of the vitamin A into the body.