Tag Archives: genome

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

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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…

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The left-wing genes

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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. ]

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Singularity slapfight: yet more Kurzweil vs. Myers

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In the interests of following up on my earlier post about PZ Myers’ take-down of Ray Kurzweil’s claims about reverse engineering the human brain, and of displaying a lack of bias (I really don’t have a horse in this race, but I still enjoy watching them run, if that makes any sense), here’s some aftermath linkage.

Kurzweil himself responds [via SentientDevelopments]:

Myers, who apparently based his second-hand comments on erroneous press reports (he wasn’t at my talk), goes on to claim that my thesis is that we will reverse-engineer the brain from the genome. This is not at all what I said in my presentation to the Singularity Summit. I explicitly said that our quest to understand the principles of operation of the brain is based on many types of studies — from detailed molecular studies of individual neurons, to scans of neural connection patterns, to studies of the function of neural clusters, and many other approaches. I did not present studying the genome as even part of the strategy for reverse-engineering the brain.

Al Fin declares that neither Kurzweil or Myers understand the brain [via AcceleratingFuture]:

But is that clear fact of mutual brain ignorance relevant to the underlying issue — Kurzweil’s claim that science will be able to “reverse-engineer” the human brain within 20 years? In other words, Ray Kurzweil expects humans to build a brain-functional machine in the next 2 decades based largely upon concepts learned from studying how brains/minds think.

Clearly Kurzweil is not claiming that he will be able to understand human brains down to the most intricate detail, nor is he claiming that his new machine brain will emulate the brain down to its cell signaling proteins, receptors, gene expression, and organelles. Myers seems to become a bit bogged down in the details of his own objections to his misconceptions of what Kurzweil is claiming, and loses the thread of his argument — which can be summed up by Myers’ claim that Kurzweil is a “kook.”

But Kurzweil’s amazing body of thought and invention testifies to the fact that Kurzweil is probably no more a kook than any other genius inventor/visionary. Calling someone a “kook” is apparently considered clever in the intellectual circles which Mr. Myers’ and the commenters on his blog travel, but in the thinking world such accusations provide too little information to be of much use.

Zing! Now, back to Myers:

In short, here’s Kurzweil’s claim: the brain is simpler than we think, and thanks to the accelerating rate of technological change, we will understand it’s basic principles of operation completely within a few decades. My counterargument, which he hasn’t addressed at all, is that 1) his argument for that simplicity is deeply flawed and irrelevant, 2) he has made no quantifiable argument about how much we know about the brain right now, and I argue that we’ve only scratched the surface in the last several decades of research, 3) “exponential” is not a magic word that solves all problems (if I put a penny in the bank today, it does not mean I will have a million dollars in my retirement fund in 20 years), and 4) Kurzweil has provided no explanation for how we’ll be ‘reverse engineering’ the human brain. He’s now at least clearly stating that decoding the genome does not generate the necessary information — it’s just an argument that the brain isn’t as complex as we thought, which I’ve already said is bogus — but left dangling is the question of methodology. I suggest that we need to have a combined strategy of digging into the brain from the perspectives of physiology, molecular biology, genetics, and development, and in all of those fields I see a long hard slog ahead. I also don’t see that noisemakers like Kurzweil, who know nothing of those fields, will be making any contribution at all.

And, a little later still, after linking to some (fairly insubstantial) snark:

There are other, perhaps somewhat more serious, rebuttals at Rennie’s Last Nerve and A Fistful of Science.

Now run along, little obsessive Kurzweilians, there are many other blogs out there that regard your hero with derision, demanding your earnestly clueless rebuttals.

Smacks a little of “this is beneath me”, doesn’t it… or possibly even “can’t win, won’t fight”. Maybe I’m being unfair to Myers, but he’s certainly never backed off this easily when it comes to atheism and Darwin, and just a few days ago he was full of piss and vinegar. (Which isn’t to say I think he’s definitely wrong, of course; just that I expected a rather more determined attack…. not to mention less ad hominem and othering from someone who – quite rightfully – deplores such tactics when used by his usual opponents.)

Finally, George Dvorsky has a sort of condensed and sensationalism-free roadmap for AI from reverse engineering of the brain:

While I believe that reverse engineering the human brain is the right approach, I admit that it’s not going to be easy. Nor is it going to be quick. This will be a multi-disciplinary endeavor that will require decades of data collection and the use of technologies that don’t exist yet. And importantly, success won’t come about all at once. This will be an incremental process in which individual developments will provide the foundation for overcoming the next conceptual hurdle.

[…]

Inevitably the question as to ‘when’ crops up. Personally, I could care less. I’m more interested in viability than timelines. But, if pressed for an answer, my feeling is that we are still quite a ways off. Kurzweil’s prediction of 2030 is uncomfortably short in my opinion; his analogies to the human genome project are unsatisfying. This is a project of much greater magnitude, not to mention that we’re still likely heading down some blind alleys.

My own feeling is that we’ll likely be able to emulate the human brain in about 50 to 75 years. I will admit that I’m pulling this figure out of my butt as I really have no idea. It’s more a feeling than a scientifically-backed estimate.

That’s pretty much why Dvorsky is one of my main go-to sources for transhumanist commentary; he’s one of the few self-identified members of the movement (of those that I’ve discovered, at least) who’s honest enough to admit when he doesn’t know something for certain.

I suspect that with Myers’ withdrawal from the field, that’s probably the end of this round. But as I said before, the greater intellectual battle is yet to be fought out, and this is probably just one early ideological skirmish.

Be sure to stock up on popcorn. 😉

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Genome sequencing for <$5000

digital rendering of DNAThe title says it all, really; Californian biotech company Complete Genomics has announced publicly that it has…

… sequenced three human genomes for an average cost of $4,400. The most recently sequenced genome–which happens to be that of genomics pioneer George Church–cost just $1,500 in chemicals, the cheapest published yet. [via FuturePundit]

“So what?” you might be thinking. Well, for a start, cheaper genome sequencing will pay off fast for the medical field, as it’ll give them more data to study; also, lowering the price to “consumer” levels (albeit the sort of consumer who doesn’t flinch at the idea of laying out a few thousand bucks for a bunch of data that they themselves don’t have the training to do anything with) opens up a whole raft of potential applications, both medical and otherwise.

Other experts are downplaying Complete Genomics’ announcement, however, because the “reagent cost” of the sequencing doesn’t tell the full story:

Calculating the cost of sequencing a human genome is a tricky business–price estimates can vary depending on what’s included in the calculation. One common measure is the cost of the chemicals used, and this is what Complete Genomics used. However, this measure doesn’t incorporate the cost of the machines that do the sequencing, the human labor, or the computational effort required to assemble raw sequence information into a whole genome. “What’s important is not just the reagent costs, but also the cost of analyzing the sequence,” says Jeff Schloss, program director for technology development at the National Human Genome Research Center, in Bethesda, MD. “It’s unclear how computational costs for this method compare to some of the others.”

My guess would be that CG doesn’t really care about that, though. It looks like they’re taking a leaf from the Web2.0 playbook by rolling out the service at the lowest cost possible in order to get a good toe-hold in an emerging market: make sequencing available, and then watch your early-adopter users to see what people will actually use it for. That said, the $5,000 sequence isn’t available to the general public just yet, but I doubt it’ll be long before it is… and I doubt CG will be the only player on the field by that point, either. [image by ynse]

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Sifting through the genes that make humans unique

AnimaBiologists used to think that new genes “could only evolve from duplicated or rearranged versions of preexisting genes.” Now, though:

Scientists have made a crucial discovery of genes that have evolved in humans after branching off from other primates, opening new possibilities for understanding what makes us uniquely human….

Researchers have found genes that arose from non-coding DNA in flies, , and primates. No such genes had been found to be unique to humans until now, and the discovery raises fascinating questions about how these genes might make us different from other primates….

The authors [David Knowles and Aoife McLysaght of the Smurfit Institute of Genetics at Trinity College Dublin] also note that because of the strict set of filters employed, only about 20% of human genes were amenable to analysis. Therefore they estimate there may be approximately 18 human-specific genes that have arisen from non-coding DNA during human evolution.

This discovery of novel protein-coding genes in humans is a significant finding, but raises a bigger question: What are the proteins encoded by these genes doing? “They are unlike any other human genes and have the potential to have a profound impact,” McLysaght noted. While these genes have not been characterized yet and their functions remain unknown, McLysaght added that it is tempting to speculate that human-specific genes are important for human-specific traits.

[Image: Dollar Bin]