Saturday, February 23, 2008

History in our Genes

Via the Wired Science Blog, I found this story about a study of variations in the human genome among different populations. While this has been done before, the new study shows how much data we can get just by looking at people's genes.

"The novel finding is the depth of the resolution we've gone to," said National Institutes of Health neurogeneticist Andrew Singleton, co-author of one of the papers in Nature. "This really lets you start moving towards locating individuals geographically. Previously, we've been able to look at the genome and say, 'This part is from Africa, this is from Asia. Now we can look past that and say, 'It's from this part of Africa or Eurasia.'"

Continued Singleton, "We can use these data to look at other areas of the genome that might have been under particular pressure for survival, and go from there to figuring out what the pressure is. One area that was highlighted was the genes responsible for digesting lactose. In countries where there's milk consumption, that one particular haplotype that allows more efficient lactose digestion has arisen."

They've not only been able to identify populations based on the genome alone, but they've also managed to model how humanity spread around the globe. Our history is encoded in our genes. How cool is that?

And all this was done using only the genomes of about a thousand people. Imagine what will be possible once we have even more data. And on the biology side, we will be able to repeat the same analysis for animals or plants. These are truly exciting times.

The full article that appeared in Science can be read here.

Thursday, February 14, 2008

Evolving Evolution

Okay, that title was too easy a pun. I apologise. But Wired blog had a couple of posts about where evolution (as in, "the theory of...") may be headed. The name for this extension of evolution is complexity theory. I bet that's going to be confused with chaos theory a lot.

What is complexity theory? Let's let Wired explain:

Not a religiously inspired revision -- intelligent designers need not apply. Nobody suggests that genetic mutation and natural selection aren't responsible for the evolution of birds from reptiles or humans from tree-swingers.

But a growing number of scientists do say that neo-Darwinian evolution doesn't explain certain jumps in biological complexity: from single-celled to multicellular organisms, from single organisms to entire communities.

The jumps -- saltations, in complexity parlance -- appear to be non-linear emergent phenomena, the result of networked interactions that produce self-organization at ever higher levels. From this perspective, Darwinian evolution is a mechanism of a higher universal law, perhaps even a variant on the second law of thermodynamics.

There's something that will strike fear into the hearts of mathematicians and computer scientists everyhwere: non-linear emergent phenomena. Everybody knows that that is the last thing you want to be modelling.

Personal fears aside, this seems like a reasonable extension. It is important to find out how certain networked properties emerge, whether they be multi-cellular organisms, or human societies.

Now, some people, including me before I read this article, might think that classic evolution might be all we need to explain these jumps. Just because we haven't figured it out yet, doesn't necessarily mean that we need a new framework, right?

Maybe, but the second Wired article that caught my eye gives more evidence that our current view of evolution may limit our ability to explain certain phenomena.
When Guy Hoelzer runs computer simulations of organisms living in the modeling equivalent of a featureless plain, he sees them break into different species -- even though there's no reason for natural selection to take place.

That preliminary but tantalizing finding hints at some larger phenomenon driving the mechanisms of neo-Darwinian evolution. Hoelzer thinks the phenomenon is self-organization: combine energy with complex networked interaction and order will emerge.

As with all experiments based on simulation, you have to take this with a grain of salt, but it's certainly more fodder for complexity theory.

One thing I don't quite agree with is that they try to relate it back to the second law of thermodynamics. ("The entropy of an isolated system not in equilibrium will tend to increase over time, approaching a maximum value at equilibrium.") That seems doubtful to me (speciation is entropy?) and also a bit premature. Save the unification with physics for when you've worked out the details of your theory.

Thursday, February 7, 2008

It's Started Already

Remember the "telepathic" DNA story? Well, what'd I tell you:

DNA Found to Have "Impossible" Telepathic Properties

[...]No one knows how individual DNA strands could possibly be communicating in this way, yet somehow they do. The “telepathic” effect is a source of wonder and amazement for scientists.

So we've moved from a "telepathy-like quality", that can be explained, to "impossible telepathic properties". I predict that we'll reach alien influences in two more steps.

Tuesday, February 5, 2008

I love Bad Science

Let me clarify: I hate bad science, but I love Bad Science. Ben Goldacre cuts right through the bull and exposes charlatans, cranks and clueless journalists. In his latest column, he dissects a collection of recent articles that are full of bad science.
I know I’m wrong to care. On the BBC news site “crews were hopeful the 20m cubic litres of water could be held back and not breach the dam wall”. And that’ll be a struggle, since “cubic litres” are a nine-dimensional measuring system, so the hyperdimensional water could breach the dam in almost any one of the five other dimensions you haven’t noticed yet.
Seriously, go read it.