Keynote: Information and Biology (ISMB 2009 Day 1)
From the chair of the session, Gene Myers: He has 4 degrees, at least 2 PhDs and a Master’s in Philosophy – he has a very broad background.
Biodiversity is at the same time a treasure and a danger – the breadth and depth of different types of species is amazing. Biology is such a young science, and things that are considered “old” now really aren’t that old. In the 1600s it was both the beginning of modern astronomy and there were books saying that fish were leaves falling from trees. Many good scientists have had problems with society, but it is not sufficient to have problems with society to be a good scientist.
It’s only in the 18th century that things started to change a bit with Linneaus and similar. Biodiversity from Linnaeus’ POV: “eternal law of reproduction and nultiplication within the limits of their proper types”. Plants and insects get very different, very quickly. With Linnaeus, species are locked into one shape, because that’s how the Creator has made them. Then came the discovery by Cuvier that species become extinct, with the discovery of mastadons (turn of the 18th/19th century). Lamark: some of the things he said were interesting = species are transformed through processes (which we don’t accept any more). Then came Darwin and natural selection (involving reproduction, variation and “choice”), which is a process repeated over long periods. Darwin had problems with society, as usual for many scientists. :) Nature is not species, but individuals: this was a big idea.
So biology could be seen to have been born in 1859, with Darwin’s work. The *only* figure in the book is of the first phylogenetic tree. The moment when 2 lines become 2 species is not a very special moment: “certainly no clear line of demarcation has as yet been drawn between species and sub-species…”
Diversity within species is the study of heredity. Heredity is amnesic, e.g. Weissman saying no inheritance of aquired characteristics (but this statement isn’t strictly true). He thought that each person just reproduces what you were given and didn’t add anything. In this world, you as an individual can only influence things based on the number of your progeny.
Genetics born in 1906, when the term was coined. Genetics produces trees, e.g. coalescence trees. With genetics, could start to look at species from a systematic, genetic point of view. What is the entity which is transmitted through evolution? What is the target of evolution? Many people would say DNA, which makes it the target. Next came the concept that individuals are contingent artefacts invented by genes to be reproduced.
Information will either grow or disappear according to the efficiency of the avatar it produced. Biologists historically have had problems dealing with thinking about material things as information. DNA -> RNA is *not* equivalent to C + O2 -> CO2. The information appears in RNA without any transfer of material.
Matter versus Information. Except for quantum physics, we know what matter is, and we can deal with it well. We aren’t so advanced in our understanding of information. What is information? Where is it? What can it do? Schrodinger and “What is Life?” talks about it in the introduction. Can information act on matter? The same information can take many different forms, and it is still the same information. It has some independence from matter but cannot exist without it. Encoded info can act on matter if there is a system to transform it.
Lots of biologists say “genes produce proteins”, but why? Genes have never produced any proteins. A recipe has never produced a dish. And different cooks will not end up producing the same dish, even with the same recipe. Different kitchens also aid production of different results.
The triple helix of genes, environment and organism. How do these interact? That is an interesting question. Which role for each? Are they of equal importance for the individual? For evolution?
Hybrids of lions and tigers are possible, but not elephants and rhinos… :) Some hybrids are not capable of reproduction, but you can’t know until you’ve done it right now – it’s very difficult to make predictions about it. Nature is neither moral or immoral: it is non-moral. Eugenics was popular in its time, at the beginning. Unfortuntely, the biggest names of science were proponents: Galton, Alexander Graham Bell etc. They wanted to understand why there was disease. In the US and other countries, eugenics unfortunately led to sterilization. Karl Pearson (invented chi-squared) was a student of Galton, and said “the right to live does not connote the right of each man to reproduce his kind”, and Pearson was a socialist (which might seem contradictory). In general, most geneticists of that time were also eugenicists.
Genes are right-wing, and environment is left-wing. How much is genes, and how much is environment? Some seem to be determined, e.g. tongue folding. Which part of the variation I observe is due to variation in genes, and to variation in environment? All we can do is partition the variation as it is. It is very important that everyone understands this.
We should not simplify epigenetic information too much – it is important, and it is a real challenge, to really include all three components of the triple helix in their thinking. For him, information must have a meaning. We are working with concepts that are still too fuzzy – we need interaction with biologists, computer scientists, and physicists.
Please note that this post is merely my notes on the presentation. They are not guaranteed to be correct, and unless explicitly stated are not my opinions. They do not reflect the opinions of my employers. Any errors you can happily assume to be mine and no-one else’s. I’m happy to correct any errors you may spot – just let me know!