04 April 2007

Open Genomics, Closed Minds

One of the great things about open genomics - or bioinformatics if you prefer its traditional name - is that it provides a completely objective resolution of all sorts of emotional disputes.

For example, by feeding genomic sequences of various organisms into a computer program, you can produce a tree of life that is remarkably similar to the ones proposed by traditional evolutionary biology. But in this case, there is no subjective judgement: just pure number crunching (although it's worth noting that the trees vary according to the depth of the calculations, so this is not absolute knowledge, only an ever-closer approximation thereto).

Another case in point is the closeness of the relationship between the great apes and humans. Indeed, it is only human arrogance that allows that kind of distinction to be made: a computer would lump them all together on the basis of their DNA.

Against this background, it's surprising how much we naked apes cling to our difference from the hairy kinds: perhaps it makes us feel a little better in the face of the genocide that we are waging against them. However, it looks like things here might be changing at last:

He recognises himself in the mirror, plays hide-and-seek and breaks into fits of giggles when tickled. He is also our closest evolutionary cousin.

A group of world leading primatologists argue that this is proof enough that Hiasl, a 26-year-old chimpanzee, deserves to be treated like a human. In a test case in Austria, campaigners are seeking to ditch the 'species barrier' and have taken Hiasl's case to court. If Hiasl is granted human status - and the rights that go with it - it will signal a victory for other primate species and unleash a wave of similar cases.


One of their central arguments will be that a chimpanzee's DNA is 96-98.4 per cent similar to that of humans - closer than the relationship between donkeys and horses.

Sadly, there's a terrible race here: which will we see first - apes recognised as near-equals, or apes razed from the face of the earth? (Via Slashdot.)


Bill Hooker said...

a chimpanzee's DNA is 96-98.4 per cent similar to that of humans

Before you can have the computer crunch the numbers, you have to equip it with a number of assumptions -- judgement calls that a machine cannot (yet?) make about such fundamental questions as what constitutes a significant difference between two sequences, or what sequences to use in the first place. A computer would not lump humans with apes unless you fed it the requisite assumptions -- and you could as easily feed it different, equally valid, parameters which would split the two groups.

While I'm nitpicking, I wouldn't equate "open genomics" with "bioinformatics". I think of bioinformatics as a process or set of tools that can take open or closed information as a substrate, but I would understand "open genomics" to mean something much closer to what I call open science.

I am, however, in favor of expanding the practical definition of "human", and agree that the distinction we make between "us" and "the apes" is an unholy mixture of arrogance and self-absolution.

glyn moody said...

Believe it or not, I did think (albeit briefly) before making my claim about the crunching. I'm not a bioinformatician, but I am/was a mathematician.

What I had in mind was some vague idea of treating genomes as strings, and defining a metric for differences between strings; obviously you can define any number of metrics, but ones based on observed chemical transformations (not just theories of gene evolution, say), seem reasonable ones to take without invalidating my thesis.

You could then use computers to crunch the metrics between genomes: you wouldn't need to "tell" the computer what to look for, or what genomes to use. My thesis is that clusters/patterns would emerge from such number-crunching; those clusters/patterns would change according to the depth of the crunching, but maybe asymptotically with more crunching. (Rounding all this stuff out is left as an exercise left to reader.)

OK, it's vague, but it sounds vaguely plausible to me in terms of constructing evolutionary trees that make no assumptions about evolution (only that there might be connections between genomes that have arisen by changes from one to another).

I agree that open genomics and bioinformatics are not synonymous, but I need to use "open genomics" as often as possible to justify the title of my blog....

Bill Hooker said...

OK, it's vague, but it sounds vaguely plausible to me

Sure, I don't mean to suggest the idea is crazy. My point is really only that it's probably difficult to establish definitions/algorithms that make no reference to existing theories of evolution. I am, of course, thinking as a biologist (and one who, moreover, is not very good at maths and recently read Kuhn for the first time).

It does occur to me that, now that we have entire genomes to work with, it becomes easier to do unbiased comparisons because we don't have to pick and choose among sequences, and because we can now compare large-scale architecture (such as relative positions of particular sequences, large duplications/deletions, and so on) as well as base-by-base sequence information.

glyn moody said...

Bear in mind that I'm making this up as a I go along, but your last point is what I was vaguely groping towards: the fact that with enough genomes, we don't need to load the dice by implicitly assuming anything about phylogenetic trees.

Given a big enough GNU/Linux cluster you could simply throw in a few hundred thousand genomes, stir, sit back and eventually watch evolution pop out.