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(bio)logical

Organic computing, anyone? Ars Technica reports on a paper published in Nature, wherein the authors describe the creation of bacterial colonies that can act as logic gates:

The key to the new work is stretches of DNA that act as logical OR and NOR functions. Both of them rely on small stretches of DNA called promoters that control the activity of nearby genes. In this case, the authors used promoters that activate nearby genes in response to simple chemicals (arabinose and tetracycline for these two promoters). By putting both promoters next to a reporter gene, the system acted as an OR gate: when either of the chemicals was present, the reporter was on.

[…]

… the authors set up small clusters of bacterial colonies (small lumps of genetically identical cells). Each colony had a single logic gate (the authors used NOR, OR, and NOT gates). Depending on the arrangement of the colonies, each one could signal to only one or two neighbors, and each could only take input from one or two. The authors demonstrated a functional XOR gate built from four colonies, showing that all logical functions can be built from similar combinations.

The nice thing about using populations of cells is that this averages out some of the chaotic behavior typical of systems based on single cells. At a minimum, the systems they tested showed a five-fold difference between their on and off states. The downside is that, relative to a single cell, these systems are huge. The authors suggest that it might be possible to adapt their system to single cells, but it’s not clear that the same sort of performance could be maintained.

Boole meets biology. Maybe one day we’ll grow computers instead of building them from silicon slices…

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The perils of science hyperbole

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The fallout from the NASA paper on arsenic-eating critters has taught us a lot more about the life-cycle of exciting science stories than it has about the life-cycle of the critters themselves. Molecular biologist and super-sharp sf commentator Athena Andreadis does a post-mortem:

This is not the first or only time NASA administrators have been callously cavalier.  Yet even though the latest debacle didn’t claim lives like the Challenger incident did, it was just as damaging in every other way.  And whereas the Challenger disaster was partly instigated by pressure from the White House (Reagan needed an exclamation point for his State of the Union address), this time the hole in NASA’s credibility is entirely self-inflicted.  Something went wrong in the process, and all the gatekeeping functions failed disastrously.

[…]

NASA spokespeople, as well as Wolfe-Simon and Oremland, have stated that the only legitimate and acceptable critiques are those that will appear in peer-reviewed venues – and that others are welcome to do experiments to confirm or disprove their findings.

The former statement is remarkably arrogant and hypocritical, given the NASA publicity hyperdrive around the paper: embargoes, synchronized watches, melodramatic hints of “new life”, of a discovery with “major impact on astrobiology and the search for extraterrestrial life”.  This is called leading with your chin.  And if you live by PR, you cannot act shocked and dismayed when you die by PR.

As for duplicating the group’s experiments, the burden of proof lies with the original researchers. This burden increases if their claims are extraordinary.  The team that published the paper was being paid to do the work by a grant (or, possibly, by earmarked NASA money, which implies much less competition). For anyone else to confirm or disprove their findings, they will have to carve effort, time and money out of already committed funds — or apply for a grant specifically geared to this, and wait for at least a year (usually more) for the money to be awarded.  It’s essentially having to clean up someone else’s mess on your own time and dime.

Hyperbolic science PR is nothing new, of course, but it’s damaging and counter-productive in these politically-charged times:

By disbursing hype, NASA administrators handed ready-made ammunition to the already strong and growing anti-intellectual, anti-scientific groups in US society: to creationists and proponents of (un)intelligent design; to climate change denialists and young-earth biblical fundamentalists; to politicians who have been slashing everything “non-essential” (except, of course, war spending and capital gains income).  It jeopardized the still-struggling discipline of astrobiology.  And it jeopardized the future of a young scientist who is at least enthusiastic about her research even if her critical thinking needs a booster shot – or a more rigorous mentor.

There’s some sort of deep sad irony in here: our hunger for exciting new truths can jeopardise our chances of discovering them.

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Aliens among us: Charlie Stross on the corporate invasion

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More challenging ideas from Chateau Stross (or should that be Schloss Stross?) – he’s not the first to frame the corporation as a non-human entity with an alarming degree of power and control over human affairs, but – given the current economic and political climate – it’s a conversation worth revisiting.

We are now living in a global state that has been structured for the benefit of non-human entities with non-human goals. They have enormous media reach, which they use to distract attention from threats to their own survival. They also have an enormous ability to support litigation against public participation, except in the very limited circumstances where such action is forbidden. Individual atomized humans are thus either co-opted by these entities (you can live very nicely as a CEO or a politician, as long as you don’t bite the feeding hand) or steamrollered if they try to resist.

In short, we are living in the aftermath of an alien invasion.

The comment thread is fantastic reading too, but very long; set aside an hour or so to really dig into it properly.

Here’s a counterpoint from the NYT‘s Paul Krugman:

These days, we’re living in the world of the imperial, very self-interested individual; the man in the gray flannel suit has been replaced by the man in the very expensive Armani suit. Look at the protagonists in the global financial meltdown, and you won’t see faceless corporations subverting individual will; you’ll see avaricious individuals exploiting corporate forms to enrich themselves, often bringing the corporations down in the process. Lehman, AIG, Anglo-Irish, etc. were not cases of immortal hive-minds at work; they were cases of kleptocrats run wild.

And when it comes to the subversion of the political process — yes, there are faceless corporations in the mix, but the really dastardly players have names and large individual fortunes; Koch brothers, anyone?

I find myself somewhat on the fence here, principally because I’m painfully aware that I know enough about economics to know that I don’t know enough about economics. I’m not sure that the corporation as a concept is inherently bad, but I’m very sure that the current protectionist set-up is a root cause of many of our current problems, at both the global and local scales.

What do you think?

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Walden3.0, or “why can’t we be citizens of the internet?”

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Yeah, I know the versioning-suffix gag went stale in 2008, but I think it fits here. Two posts where people think aloud about post-geographical communities; the first is from Ian “Cat” Vincent, who wants to be considered a citizen of the internet (emphases mine):

I do not trust the government of the country of my birth. I do not feel any loyalty to them, or any other country, whatsoever. At best, I see them as an especially powerful mafia I have to kowtow to and buy services from. The closest thing to patriotism I have ever felt is to the Internet.

So, why can’t I take Internet as my nationality?

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My own country’s government – run by a weak coalition government which is acting like they have a landslide mandate – is cutting vital services to the poor and disadvantaged to pay for deficits caused by their banking pals’ having been caught running the largest Ponzi scheme in human history… and their representatives have the gall to blame those poor and disadvantaged for the financial mess. Students are taking to the streets in protest. They are not my rulers, except by virtue of monopoly of violence and general habit.

When we’re at the point where The Economist refers to Anonymous as “a 24-hour Athenian democracy” I think it’s time to at least consider the idea.

[…]

Citizenship implies abiding by, and contributing to, a social contract. Doing Your Bit. I have to tell you I’m far happier doing that for the internet than for any state. It’s rules, customs and rituals make more intuitive sense to me than any state I have ever heard of. And yes, I would cheerfully give up my right to vote in the UK and EU for the rights and responsibilities of Internet Citizenship. (Dear David Cameron – that’s what a Big Society really fucking means.)

I am completely with Vincent on pretty much everything in that post… which will come as no surprise to regular readers, I suppose. But I’m sure we’re not alone, even if the urge to join a community where one feels one truly belongs may express itself a little differently. Jeremiah Tolbert:

I never seem to have much trou­ble find­ing com­mu­nity online.  This year, my com­mu­nity online seems to be cen­tered around Twitter.  I have some qualms about hav­ing my major sense of belong­ing tied to some­thing that is lim­ited to 130 char­ac­ters at a time, but it does work.  And when you work from home alone day in, day out, hav­ing some way of feel­ing like you’re not alone is help­ful.   Twitter fills that role for me now.  In the long run, I would like a “real world” com­mu­nity to belong to—something Rockwellian, only full of artists and cre­atives maybe. John Joseph Adams and I have talked sev­eral times about his notion of Geektopia—a com­mu­nity pop­u­lated entirely by geeks who relo­cate to cre­ate a com­mu­nity of their own.   If such a place existed—I would seri­ously con­sider mov­ing there.  We’ve been eye­balling the parts of the coun­try where you can get free land.   Problem is, build­ing an entire town from scratch costs mil­lions.  So until we get some mil­lion­aire back­ing the idea, it will remain a pipe dream.  But it’s one that I would love to see become a real­ity.  Some day.

Until then, the inter­net is my com­mu­nity, for bet­ter and worse.

I suspect Jeremy’s not alone in feeling that way… and think about it: if an increasing number of people dissatisfied with the meatspace communities available to them all flock to the internet – which is, as if we needed reminding, a non-dimensional space largely defined by its proliferation of tools for community-building and its corrosive effect on geography – they’re in the best possible position to start building and planning a world that runs on their own terms.

And I suspect that’s exactly why the deep implications of the Wikiwars are so terrifying to authoritarians and nation-states; it’s the same reason the beech tree fears the ivy.

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