care and feeding of graduate students (life as a professor)

Second in a series of posts about evolution and the “laws” of biology.

It is sort of amusing to see what kinds of issues helped the chaplain and captain’s companion of the Beagle towards the theory of natural selection. Today we can measure things with such high precision – count individual molecules, read the genetic code of almost any organism, measure distances to 10^-11 meters, time things with errors in seconds per thousands of years while timing intervals that are billionths of a second, that it is hard to image what it was like in, say, 1820 where the very idea of an atom or molecule was controversial, let alone having no real understanding of how biological systems work.

Putting on our 19th century hats, and maybe holding a flower to our noses to mask the 19th century smells (they weren’t overly careful about hygiene) we can identify several related problems that needed to be addressed:

1. The earth was old. Measurements in the late 1700’s and early 1800’s by Lyell were suggesting that the erosion of stones to form canyons and gorges would have taken 100,000’s if not millions of years. A very simple experiment – go to Hadrian’s wall and find a piece of stone (like a Roman column) that is half buried. We know when it was buried so we can measure the difference in size between the exposed part and the buried part. Dividing that by, say 1700 years, gives us a mean rate of erosion. If we look at an erosion feature, like Cheddar gorge, then we see can estimate the length of time it took to make it. While the number won’t be very accurate – it will be much larger than the 6000 years or so we get from biblical histories.
2. Fossils. When we look at some rocks, the sedimentary ones that are deposited by erosion we see traces of extinct animals. We find sea and land animals so they can’t have all perished in the flood. We find traces of extinct plants in the Devon coal beds. The deeper, and presumably older, layers have animals and plants that are more different from those that exist today than the higher and more recent layers. But it is clear that they are related to organisms that live today. The vertebrate animals follow the same basic building plans that modern animals follow. There are shellfish and odd shrimp-like creatures and ferns and starfish. They seem to form sets of organisms that are comparable to modern sets.
3. Why are things the same? There are patterns in animals and plants. Grouping life by physical similarities yields a simple, yet compelling, indexing of every species we know about (thank you Linneaus). Even more amazing – as our navies go on voyages of discovery – rather than conquest – they find new species which (mostly) fit into the same index. Those new groups, which contain things like kangaroos and platypuses, fit into well defined sets that easily fit into our indexing.
4. Why are things different? This one took a while for the European (mostly English and American) scientists to notice because for some reason the animals and plants of eastern north America are similar to those of northern Europe (in 2008 we know why). We Americans have Oaks, Pines, and Maples – and so do the Brits. We have crows, eagles, deer, foxes, wolves, bears, bison and elk, and so do they. It isn’t until the plants and animals of other parts of the world are described (by devout Church of England scientists who are “describing the glory of God’s creation”) that these differences are noticed. Even though there are different animals and plants in different parts of the world they fit together into a functioning system with different animals performing similar roles. Indeed, the results from small islands in the pacific (does the Galapagos spring to mind?) and isolated continents (Australia, Tasmania and New Zealand) show that the animals and plants are quite different from European ones and yet have similar ecological roles.

There are somethings that we don’t (as of 1820) understand. We do not understand inheritance at all. Can a trait or property be passed from a parent to a child? How? We have anecdotal evidence that there must be some mechanism because our children look like us and we look a bit like our siblings, but how this happens is a mystery. It doesn’t appear to be a simple blending of mom and dad. Further anecdotal evidence can be seen with some of the domestic animals where we have selected for some traits – it is the dawn of “scientific” agriculture – but we don’t have a clear picture of what is going on. Some traits seem to be passed on simply – like blue eyes in people – blue eyed parents have blue eyed children – but then not always – sometimes brown eyed people have blue eyed children (and no the milkman isn’t to blame). But then there are weird effects like differences in calf size that depend on the size of the mother (Maternal effect) – and some people believe that there is a “paternal effect” as well. We have no idea why different species can’t interbreed, nor why common interbreeds like mules are not fertile. (again remember this is 1820 – in 2008 we have a pretty good idea of what is going on). Sometimes animals can be very different physically – say bulldogs and greyhounds – but still the same species, but sometimes they can be very similar -say blue tits and great tits (real English birds) and not interbreed.

Darwin’s brilliance was to realize that problems of time, fossils, similarities and existence of difference required the existence of some sort of selection mechanism and inheritance mechanism. His hypothesis of natural selection – namely that those organisms that are better fitted to produce children that survive will tend to dominate and that those variations will accumulate over time to produce new species forms the basis of modern (2008) biology where we call it a theory. Had he formulated it a few years earlier we’d call it a law – but that is so 18th century. The time delay between his forming this hypothesis and publication was spent trying to understand the mechanisms of selection and inheritance – which he didn’t quite get and would take another 60-80 years for the beginnings of a solid theory.

There are some very simple predictions of the 1820 -type theory that have been borne out over time. The idea that there is a biochemistry of life is truly central – this wasn’t explicitly formulated because chemistry itself wasn’t well understood – has been confirmed by repeated experiments. The way bacteria handle glucose is (mostly) the way we handle glucose. We use the same amino acids, and the same genetic code as bacteria. The mechanism of inheritance – via nucleic acids -seems to be universal on our planet.

One of Darwin’s explicit predictions was that the oldest fossils of humans would be found in Africa because the most similar animals to us are native to there. I think his theories would have had an easier time had he said we evolved in Europe – but that would have been dishonest.

Another surprising thing is that we need to have pre-existing variation to have selection and life goes to a great deal of difficulty to produce variation. One of my favorite examples is in retroviruses such as the human immunodeficiency virus (HIV). Viruses are barely life, because while they reproduce – they use the mechanisms from other creatures to do it. Unlike snakes and wasps HIV can’t run, hunt or flee, yet it is subject to the same selective pressures that any other life is. However, when your progeny is measured in moles, there is another alternative – just make lots of errors when reproducing and some of them will be better than others. So HIV when challenged with effective drugs, evolves by selection to produce viruses that can reproduce in the presence of those drugs. For that matter so do bacteria when challenged with antibiotics (they actually have a split genetic system where essential functions vary slowly but non-essential functions are on small “plasmids” which can have lots of variations quickly) and mosquitoes when challenged with pesticides.