Beginner’s guide to DNA sequencing

Paul Raven @ 28-09-2009

Model DNA moleculeGenetic engineering and DNA sequencing are regular features in our news posts here at Futurismic, and in many other venues much less explicitly future-focussed. The technology of life’s tiny building blocks is steadily becoming ubiquitous – hell, you can even buy a DNA synthesizer on eBay [via Paul McAuley] – but it’s still a pretty hardcore scientific discipline, one that takes years of study and research to fully understand.

Luckily for us curious laypersons, Ars Technica is running a series of articles aiming to explain the basics of genetic science in terms that we should be able to grasp – though a basic high-school level understanding of science is probably still a prerequisite to get the best out of it. The first instalment is all about the basic principles of DNA sequencing – the underlying ideas that the latest and greatest methods are built upon. Some of the diagrams and chemical names might be a bit intimidating, but it’s a well-written piece and worth persisting with if you’re genuinely curious about how it all works. [image by net_efekt]


Games and economic misbehaviour

Tom James @ 03-08-2009

wolfram_fractalsGeorge Dyson has an excellent and compelling essay on game theory, economics, information theory, computer science, banking, finance, technology, and John von Neumann:

We are surrounded by codes (some Turing-universal) that make copies of themselves, and by physical machines that spawn virtual machines that in turn spawn demand for more physical machines. Some digital sequences code for spreadsheets, some code for music, some code for operating systems, some code for sprawling, metazoan search engines, some code for proteins, some code for the gears used in numerically-controlled gear-cutting machines, and, increasingly, some code for DNA belonging to individuals who serve as custodians and creators of more code. “It is easier to write a new code than to understand an old one,” von Neumann warned.

The monograph over on Edge discusses von Neumann’s intellectual antecendants and the development of game theory and statistical modelling. It also includes some interesting commentary on our recent economic difficulties. Definitely worth a read.

[image from kevindooley on flickr]


Consumer DNA screening is here; what happens next?

Paul Raven @ 21-07-2009

digital rendering of DNAI’ve recommended Jan Chipchase’s Future Perfect blog before as a great source for near-future speculation with a street-level twist, and it looks like it’s time I did so again. Chipchase has just purchased one of the $99 DNA testing kits from 23andme, inspiring the following thoughts:

With an increasing number of medical and judicial proceedings pulling on DNA data and a continious trickle of whose-the-father paternity testing DNA is slowly but surely moving mainstream. Who’ll be the first to take individual’s DNA data and mash it up with dating profiles? Nature versus nurture? Bring on the hucksters.

The rise in adoption/use of DNA is particularly interesting because it affects people, families deeply and retrospectively. Your dad for the last 40 years? He’s not, y’know. (For source stats head over to Measuring paternal discrepancy and its public health consequences by Mark A Bellis et al. – they cite ~0.8% to 30% paternal discrepancy, median 3.7%)

Roll forward 20 years when you can obtain a DNA test for the cost of a packet of gum – hell, it might even come in the form of a stick of ‘DNA Brand’ gum where the consumer is encouraged to spit out and stick after use.

Can you think of any Gibsonian street uses for ubiquitous affordable DNA testing? [image by ynse]


Biotech to the stars

Tom James @ 28-05-2009

dendritesCentauri Dreams discusses a DNA-based self-replicating interstellar probe:

Think of a probe that gets around the payload mass problem by using molecular processes to create cameras and imaging systems not by mechanical nanotech but by inherently biological methods.

A Von Neumann self-replicating probe comes to mind, but we may not have to go to that level in our earliest iterations. The biggest challenge to our interstellar ambitions is propulsion, with the need to push a payload sufficient to conduct a science mission to speeds up to an appreciable percentage of lightspeed. The more we reduce payload size, the more feasible some missions become

This is similar to Robert L. Forward’s starwisp concept (popularised by Charlie Stross in Accelerando).

I suspect that if and when we do get round to interstellar exploration it will involve sending small-mass packages that are capable of bootstrapping themselves to a broadcast/exploration mode using local materials on arrival in the target system.

It remains to be seen what kind of space-based molecular replicating systems become viable. Will we be able to create space-hardened bioware, or good ol’ fashioned machine phase fullerene nanotech?

[image from neurollero on flickr]


Culture is carried by DNA?

Paul Raven @ 05-05-2009

pair of Australian zebra finchesIt sometimes feels like you can’t go two weeks without some new aspect of human life or behaviour being declared as being related to our DNA. The latest attempted conquest of genetic determinism? Why, our very culture itself!

You see, male zebra finches usually learn their courtship song patterns from their fathers, but it turns out they can generate the same songs spontaneously after a few generations without influence:

“It’s the classic ‘chicken and the egg’ puzzle,” Mitra said. “Learning may explain how the son copies its father’s song, but it doesn’t explain the origin of the father’s song.”

Mitra’s team wanted to find out what would happen if an isolated bird raised his own colony. As expected, birds raised in soundproof boxes grew up to sing cacophonous songs.

But then scientists let the isolated birds give voice lessons to a new round of hatchlings. They found that the young males imitated the songs — but they tweaked them slightly, bringing the structure closer to that of songs sung in the wild. When these birds grew up and became tutors, their pupils’ song continue to conform, with tweaks.

After three to four generations, the teachers were producing strapping young finches that belted out normal-sounding songs.

Uhm. Well, if you’re thinking that seems a little tenuous, you’re not alone:

Mitra admits that the analogies between bird culture and human culture are tenuous. “But there are resemblances. Culture is just learned behaviors. The motivating scenario is, if you isolate human babies from culture, put them on an island and come back after a few generations, what would their culture be like? What sort of language would they have? What sort of politics would evolve?”

That experiment probably won’t take place in the near future. In the meantime, Fitch says we can learn valuable lessons about human culture from songbirds, both at theoretical and mechanistic levels.

“Social learning is shared between the two, and songbirds are a well-understood and experimentally tractable system,” he said. “These biologically-grounded studies will lead us beyond the tired ‘nature versus nurture’ or ‘biology versus culture’ dichotomies which dominate the social sciences today.”

With the caveat that I’m not a geneticist or behavioural scientist, I don’t really see how birdsong and human politics are supposed to be different expressions of the same thing; the former is a biological imperative, while the latter is an emergent phenomenon. As Brian Eno once said, “culture is everything we don’t have to do”; a zebra finch that doesn’t sing sweetly won’t pass on its DNA, making its songcraft a matter of reproductive necessity, but I don’t think you can declare the same thing about, say, a great human painter or poet or politician.

That said, I’m all for getting beyond the nature/nurture dichotomy – knowing how culture emerges from biology is one of the most tempting grails of knowledge I can imagine. But in the same way that everything from alcoholism to sexuality seems to be blithely written off as being primarily a function of our genetic code, declaring such a nebulous and complex phenomenon as human culture to be passed along by DNA on the basis of some songbird studies seems… well, it seems pretty daft, really.

If there’s someone in the audience who can set me straight on this subject, I’d be very glad for them to speak up and tell me where my reasoning is wrong, but this story seems to me like just another instalment in our ongoing fetish with genetics as the key to all unsolved mysteries. [image by Lip Kee]


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