This is my genome. There are many others like it, but this one is mine.

Paul Raven @ 19-01-2011

With the increasing difficulty of getting people to actually sign up for military service in the first place, you’d think the Pentagon would make more of an effort to not treat its soldiery as disposable meatbags. Or at least I’d think that… which is one more reason to add to the list of reasons that I’m not a five-star general, I guess.

Aaaaaanyway, here’s the skinny on a Pentagon report that recommends the Department of Defense get some more mileage out of their human resources by collecting and sequencing the DNA of their soldiers en masse [via grinding.be]:

According to the report, the Department of Defense (DoD) and the Veteran’s Administration (VA) “may be uniquely positioned to make great advances in this space. DoD has a large population of possible participants that can provide quality information on phenotype and the necessary DNA samples. The VA has enormous reach-back potential, wherein archived medical records and DNA samples could allow immediate longitudinal studies to be conducted.”

Specifically, the report recommends that the Pentagon begin collecting sequencing soldiers’ DNA for “diagnostic and predictive applications.” It recommends that the military begin seeking correlations between soldiers’ genotypes and phenotypes (outward characteristics) “of relevance to the military” in order to correlate the two. And the report says — without offering details — that both “offensive and defensive military operations” could be affected.

That HuffPo piece leads off with the privacy angle, and wanders onto the more interesting (if potentially nasty) territory of promotional assessment based on genetic factors – a little like like a version of Gattaca where your perfection entitles you to use bigger and better guns. (Or, if you’re lucky, a job in the generals’ tent instead of the trenches.) More interesting still is the news that the DoD already has over 3 million DNA samples on file…

HuffPo being HuffPo, the piece ends with a blustering condemnation of the report:

Soldiers, having signed away many of their rights upon enlistment, should not be used for research that would not otherwise comport with our values, just because they are conveniently available.

Our enormous military establishment is a whole world unto itself, and there is no good reason why that world should depart from the standards that Congress so definitively banned in the rest of the employment world. Congress should prohibit the military from spending money on sequencing individual soldiers’ genomes (without individualized medical or forensic cause) or carrying out large-scale research on soldiers’ DNA.

Yeah, good luck with that. Frankly, I’d have thought a cheaper and more effective option for selecting the optimum soldierly phenotypes would be taking a more honest approach at the recruitment screening phase…


Garage ribofunk going mainstream

Paul Raven @ 18-10-2010

Interesting to see it’s taken less than a year for coverage of DIY molecular biology to graduate from the comparative fringedom of H+ Magazine to a mainstream science publication like Nature [via SlashDot]. Notable lack of scare-stories and hand-wringing involved, too… though I suspect we’ll have this meme picked up by the tabloids before the end of the year; that’s a nice juicy OMG-terror-security-panic!!1 story just waiting to shift units to the easily frightened, right there.

What’s impressive is the level of sophistication involved, which (as others have pointed out) mimics the enthusiastic adoption of home computing by the cutting edge of geek enthusiasts back in the day:

Many traditional scientists are circumspect. “I think there’s been a lot of overhyped and enthusiastic writing about this,” says Christopher Kelty, an anthropologist at the University of California, Los Angeles, who has followed the field. “Things are very much at the beginning stages.” Critics of DIY biology are also dubious about whether there is an extensive market for garage molecular biology. No one needs a PCR machine at home, and the accoutrements to biological research are expensive, even if their prices fall daily. Then again, the same was said about personal computers, says George Church, a geneticist at Harvard Medical School in Boston, Massachusetts. As a schoolboy, he says, he saw his first computer and fell in love. “Everybody looked at me like, ‘Why on earth would you even want to have one of those?'”

[…]

No one knows how many of those 2,000 are serious practitioners — Bobe jokes that 30% are spammers and the other 70% are law-enforcement officials keeping tabs on the community. But many DIY communities are coalescing: not only in Cambridge, but also in New York, San Francisco, London, Paris and the Netherlands. Some of these aim to develop community lab spaces with equipment that users could share for a monthly fee. And several are already affiliated with local ‘hacker spaces’, which provide such services to electronics enthusiasts. For example, the New York DIYbio group meets every week at the work-space of an electronics-hacker collective called NYC Resistor, which now has a few pieces of basic molecular biology equipment, including a PCR machine.

Of course, there are real risks that come with the growth of a movement like this, but there’s also a whole lot of potential, which I think outweighs the risks if they’re managed sensibly (i.e. by oversight, transparency and strong networked communities, rather than by blanket bans and heavy-handed restrictions that would drive the movement underground, as well as potentially into a position of political radicalism). Viewed in parallel with the surge of interest in 3d printing and electromechanical hacktivism (which really is spreading very fast, alongside the hacker spaces that house them), things don’t look entirely unlike some unpublished proto-prequel to Bruce Sterling’s Schismatrix. Who will you be: Mechanist or Shaper?


The left-wing genes

Paul Raven @ 13-10-2010

Which genes are left-wing? All of them! At least that’s the interpretation Oliver James puts forward in this piece at The Guardian, as he points out that the mapping of the human genome hasn’t delivered evidence for the genetic determinism of mental health and social status that conservative politics – not to mention the pharmacology industries – hoped it would:

This result had been predicted by Craig Venter, one of the key researchers on the project. When the map was published, he said that because we only have about 25,000 genes psychological differences could not be much determined by them. “Our environments are critical,” he concluded. And, after only a few years of extensive genome searching, even the most convinced geneticists began to publicly admit that there are no individual genes for the vast majority of mental health problems. In 2009 Professor Robert Plomin, a leading behavioural geneticist, wrote that the evidence had proved that “genetic effects are much smaller than previously considered: the largest effects account for only 1% of quantitative traits”. However, he believed that all was not lost. Complex combinations of genes might hold the key. So far, this has not been shown, nor is it likely to be.

[…]

Another theory was that genes create vulnerabilities. For example, it was thought that people with a particular gene variant were more likely to become depressed if they were maltreated as children. This also now looks unlikely. An analysis of 14,250 people showed that those with the variant were not at greater risk of depression. Nor were they more likely to be depressed when the variant was combined with childhood maltreatment.

In developed nations, women and those on a low income are twice as likely to be depressed as men and the wealthy. When DNA is tested in large samples, neither women nor the poor are more likely to have the variant. Worldwide, depression is least common in south-east Asia. Yet a study of 29 nations found the variant to be commonest there – the degree to which a society is collectivist rather than individualistic partly explains depression rates, not genes.

Politics may be the reason why the media has so far failed to report the small role of genes. The political right believes that genes largely explain why the poor are poor, as well as twice as likely as the rich to be mentally ill. To them, the poor are genetic mud, sinking to the bottom of the genetic pool.

It’s a rather generalised and sweeping statement, but I think there’s a core of truth to it. Is this why there’s been such a right-wing push-back against genetic science in recent years, perhaps?

[ That said, James is narrativising genetic science in a very similar way, albeit on behalf of the other side of the debating chamber. The political polarisation of science worries me regardless of who’s doing it, because it puts the primacy onto agenda-driven interpretation rather than evidence; nowhere is this more clear than in climate science, where progressive/left-wing attempts to counter the right’s conspiracy theories with their own rhetoric have obscured the facts of the matter even further. ]


Camels and Bulls and Bar Talk: cloning revisited

Brenda Cooper @ 25-08-2010

Two-million-dollar cloned camels running races in the desert with robot riders.  Makes you think of a science fiction story, huh?  But that’s happening now.  In an early version of this column, I wrote about the world’s first cloned camel, Injaz.  I thought I’d check up on Injaz, and I learned about the world’s second cloned camel, and the hope that Bin Soughan will be a racing sensation (see the Al Jazeera YouTube video on cloned camels for more of the story).

In case camels weren’t enough, we now have a cloned fighting bull. At the risk of observing the obvious, cloned racing camels and cloned fighting bulls are all pretty masculine activities.  This feels like cloning for profit and prowess rather than to make the world better.  I mean, what will we be cloning next at this rate? Quarterbacks?  David Beckham?

So that’s how I decided to re-visit cloning for this month’s column. Continue reading “Camels and Bulls and Bar Talk: cloning revisited”


Transhumanist science clash! Kurzweil vs. Myers

Paul Raven @ 18-08-2010

Say what you will about transhumanism, but one thing’s for certain: it really polarises opinion, and nowhere more so than in the halls of academia and scientific research. Observe: Wired/Gizmodo had a chat with Singularitarian-in-chief Ray Kurzweil, who restated his theory (considered unrealistically optimistic by some transhumanists) that we’ll be able to reverse-engineer the human brain and simulate it with computers within a decade or so.

Here’s how that math works, Kurzweil explains: The design of the brain is in the genome. The human genome has three billion base pairs or six billion bits, which is about 800 million bytes before compression, he says. Eliminating redundancies and applying loss-less compression, that information can be compressed into about 50 million bytes, according to Kurzweil.

About half of that is the brain, which comes down to 25 million bytes, or a million lines of code.

Now enter PZ Myers, prominent atheism advocate (I like to think of him as “Dawkins’ Bulldog”, though I’m not sure Dawkins really needs a bulldog in the way that Darwin did) and vigorous debunker of fringe science. Broad claims in the Kurzweil vein are like a red rag to Myers, especially on his home turf of genetic biology, and he’s not afraid of mixing in a little ad hominem disparagement with his rejoinders, either:

Kurzweil knows nothing about how the brain works. It’s design is not encoded in the genome: what’s in the genome is a collection of molecular tools wrapped up in bits of conditional logic, the regulatory part of the genome, that makes cells responsive to interactions with a complex environment. The brain unfolds during development, by means of essential cell:cell interactions, of which we understand only a tiny fraction. The end result is a brain that is much, much more than simply the sum of the nucleotides that encode a few thousand proteins. He has to simulate all of development from his codebase in order to generate a brain simulator, and he isn’t even aware of the magnitude of that problem.

[…]

To simplify it so a computer science guy can get it, Kurzweil has everything completely wrong. The genome is not the program; it’s the data. The program is the ontogeny of the organism, which is an emergent property of interactions between the regulatory components of the genome and the environment, which uses that data to build species-specific properties of the organism. He doesn’t even comprehend the nature of the problem, and here he is pontificating on magic solutions completely free of facts and reason.

Now, I’m not taking sides here*; I don’t know enough computer science or evolutionary biology to cut into either interpretation. But a high-minded slapfight like this is always of interest, because it highlights just how seriously some very intelligent people take the issue. Kurzweil has more than a tinge of the evangelist about him, which is (I suspect) a large part of what bothers Myers about him, but there’s obviously something powerful about the idea (the meme?) of transhumanism/singularitarianism that he feels makes it worth fighting.

Ideas that get people arguing are important ideas. I consider myself a fellow traveller of transhumanism for this very reason; the ways we imagine tomorrow says a lot about where we are today, and vice versa. There’s a lot to learn by listening to both sides, I think.

[ * Yeah, yeah, I know, I’ve got marks on my ass from sitting on the fence. That’s just how I roll, baby; you want clenched-fist advocacy of anything but the right to think for yourself, you’re gonna need to read a different blog. ]


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