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.

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.

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.

Interesting Article, Bad Title

LiveScience had an article about a recent discovery in genetics made by some researchers in Maryland. They found out that DNA sequences that are the same are more likely to cluster together than those that are different.

Curiously, DNA with identical sequences of bases were roughly twice as likely to gather together as DNA molecules with different sequences.

[...]

The electrically charged chains of sugars and phosphates of double helixes of DNA cause the molecules to repel each other. However, identical DNA double helixes have matching curves, meaning they repel each other the least, Leikin explained.

It's an interesting discovery, although it remains to be seen how useful it's going to be. But that's not the reason I'm mentioning it here. What made me laugh was the title they gave the article:
DNA Molecules Display Telepathy-like Quality.

How long until the first New Age healer picks up on this and claims he can heal your DNA by telepathy?

Open Source Genetics?

Here's an interesting premise: Wired Blog has an article on "The Open Organism: Genetic Engineering in the Open Source Era". What would happen if you applied the principles of Open Source Software to genetic engineering?

Modularity in computer science has helped unleash crazy amounts of creativity, and new business models derived from user-generated content. Take Google Maps open-API. Or even HTML itself, which allowed users to create graphically sophisticated pages with no real programming knowledge. By putting the hard stuff into a black box and just letting you access what you need to know, user/producers have been able to focus on creating interesting content quickly and easily. What if, in the next decade, the same group of elite users/coders could do the same thing with corn?

They might be a little too optimistic, in my opinion. The allure of Open Source (or indeed any kind of hacking) is that anyone can do it. You don't need much initial investment, beyond the computer which you likely already have. Install Linux, get a GNU compiler of your choice, fire up the text editor and you're in business.

Genetic engineering is not like that. Or maybe it's exactly like that, but at a far grander scale. Instead of a computer*, you need a lab: You need pipettes, petri dishes, microscopes, solutions, PCR machines, microarrays, maybe even a gene sequencer. These things don't come cheap.

But let's assume for a moment that you have all of that already. Then you'll still need the things every programmer takes for granted, the libraries or APIs containing shortcuts to all the common tasks that you don't want to design from the ground up. As a genetic engineer, you'll need promoters, restriction enzymes and specialised vectors, each different depending on what you started with.

It is always possible that in the future, genetics labs and components will become as ubiquitous as computers and code libraries. I'm sure that when we were putting punch-cards into basement-sized supercomputers, open source software development seemed as far away as open source genetic engineering seems today. But the transition still took thirty years. I don't think we have to worry about it just yet.

*Or rather, in addition to.

Three-Toed Sloth has a thoughtful examination of heritability in IQ, complete with disclaimer:

Attention conservation notice: It's long, and it's about something which makes eyes glaze over even as tempers flare up, and it's not funny at all. Worse yet, more is on the way. You could always read it later, but time spent now is gone forever.

The conclusion? IQ may depend much less on your genetic heritage than previously assumed. I find some of his arguments quite convincing.