Re-engineering biology

Tom James @ 31-07-2009

roboticsinsiAs I’ve mentioned before, we’re entering a new phase of technological progress: engineers and technologists are not just seeking inspiration in the mechanisms of the natural world, but are actually reverse- and re-engineering biology to improve synthetic technology. In this case researchers in Germany are studying how bow flies perform their incredible feats of aerial acrobatics by creating a wind tunnel for blow flies (pictured):

A fly’s brain enables the unbelievable – the animal’s easy negotiation of obstacles in rapid flight, split-second reaction to the hand that would catch it, and unerring navigation to the smelly delicacies it lives on.

Yet the fly’s brain is hardly bigger than a pinhead, too small by far to enable the fly’s feats if it functioned exactly the way the human brain does. It must have a simpler and more efficient way of processing images from the eyes into visual perception, and that is a subject of intense interest for robot builders.

While researchers use biomimetic inspiration for the development of flying robots other scientists are working to reprogram existing biological technology, in this case altering bone marrow stem cells so that they function as retinal cells:

University of Florida researchers were able to program bone marrow stem cells to repair damaged retinas in mice, suggesting a potential treatment for one of the most common causes of vision loss in older people.

The success in repairing a damaged layer of retinal cells in mice implies that blood stem cells taken from bone marrow can be programmed to restore a variety of cells and tissues, including ones involved in cardiovascular disorders such as atherosclerosis and coronary artery disease.

For all the pessimism about the future of human civilisation, it is exhilerating to live in an era with so many opportunities and challenges.

[both from Physorg][image from Physorg]


Improving Reality

Paul Raven @ 29-07-2013

Improving Reality… that’s an ambitious title, no?

I’d expect nothing less than ambition from Honor Harger and her crew at Lighthouse, though; this year’s IR (Thurday 5th September, Brighton UK; map here; tickets here) will be the third instalment of their ongoing mission to bring together artists and writers and designers and futures people with the intent of finding ways to… well, there’s a clue in the title, isn’t there?

Previous guests at IR have included among their number Warren Ellis, Lauren Beukes, Usman Haque, Anab Jain, Jeff Noon and Joanne McNeil.

This year’s line-up includes Alexandra Daisy Ginsberg, Justin Pickard (late of this parish), Georgina Voss, Simon Ings and Paula Le Dieu, among others.

And among those others is me.

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How did that happen? Well, it had a lot to do with an essay I sent to the good people at Superflux, in which I coined the phrase “infrastructure fiction”. I hope you’ll go read the whole thing (disclaimer: #longread), but I don’t think it’s too much of a spoiler to say that infrastructure fiction was less a new idea than an attempt to encourage people to use the design fiction toolkit on bigger, more tangled problems, such as infrastructure. There are some infrastructure-specific issues involved, of course – and some theory, because I seem these days to produce theory like yeast produces ethanol* – but mostly I was aiming for what in sf criticism we sometimes call the “conceptual breakthrough”: that bit in the story where the characters (and, implicitly, the reader) experience a scalar paradigm shift in how they think about the system of systems that is their world.

That metasystemic perspective fits with IR’s theme this year, so I’ll be talking about it. Do come along if you’re in the area; Brighton in late summer is a glorious place to be, and there’ll be brainfood aplenty. Do come and introduce yourself, too.

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Speaking of publications, while I haven’t written more than a handful of poems and scene sketches since handing in my Masters dissertation (the same week as IR2012, funnily enough, which is why I remember going, but don’t remember anything else), I’ve been cranking out a fair bit of academic material. You can find my name on the author list of this paper at Futures, which talks about the project which inspired the notion of infrastructure fiction, and this one at Energy, which further develops one of the ideas from that project. I’ve also got a solo paper on science fiction prototyping sat somewhere in the bowels of the editorial system at Technological Forecasting & Social Change, which was accepted for publication last week, but appears to not yet be in press.

(My academic bibliography already far outstrips my fiction bibliography… though admittedly that’s not much of a challenge at this point.)

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I’ve also been speaking at other events, which – to my shame – I never got around to mentioning here before they happened. The wonderful folk at Corporacion Fractal invited me out to Medellín, Colombia where we did something I can only describe as “community design fiction” – an experiment in providing ordinary people with information about new technological developments and then helping them tell stories about it. While it was a lot more intellectually comfortable than playing Talking-Head Authorityguy – I remain convinced there are few if any “experts” on futurity, only people with a strong, dry grip on the right tools for the job at hand – it was hard work; trying to help a crowd of a few hundred people piece together a story about synthetic biology in an everyday context would surely be challenege enough, but doing so through the semantic gauze of live translation raised the bar that much further. Luckily our translator was excellent, and we were having too much fun to notice the hard work bit… and the audience got right into it once they’d sussed out what we were trying to do. Team Fractal are developing an interesting new praxis down there – putting futures thinking into the hands of the people whose futures they might be.

Less glamorously, I’ve read Borges stories to civil engineering conferences (over-reliance on computer modelling is leading to a sort of postmodern crisis in engineering, a flood of signifiers without anything to signify; Borges makes explaining this problem comparatively easy); more glamorously, I was on a panel at the WriteTheFuture conference at the Royal Society on May Day. I’m unwilling to assess the glamour factor of the #stacktivism unconference I spoke at earlier this month (it took place near Hoxton, and thus fell well within the glamour-warping field that ripples through East London like gravity through wet concrete), but it was all politics-of-infrastructure in an old warehouse with high ceilings, an exhibition of nude selfportrait photography and a veritable forest of oddly modular laser-cut plywood furniture.

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So, yeah; it’s been quite a year, and we’re still (just) in July. And there’s more on the horizon… which I shall talk about nearer the time, as I get this ol’ battlestation spun up to full power once again. There’s work to be done, ideas to be shared, conversations to have; keep watching the skies.

In the meantime, hope to see some of you at Improving Reality, or elsewhere.


[ * — It’s a by-product of my life-processes which may eventually poison me; this is a strong metaphor. ]


Blue-sky bioengineering on the DARPA drawing-board

Paul Raven @ 08-02-2010

If you’re looking for the sort of bat-shit Faustian gambles that form the back-bone of much military science fiction, following the news from the Pentagon’s science and tech division is like supergluing your lips to a firehose… and Wired’s DangerRoom blog is one of the better consumer-level sources to start with (if you don’t mind a bit of snark on the side).

Here’s DangerRoom‘s Katie Drummond on DARPA’s latest wheeze: immortal synthetic organisms with a built-in molecular kill-switch. SRSLY.

As part of its budget for the next year, Darpa is investing $6 million into a project called BioDesign, with the goal of eliminating “the randomness of natural evolutionary advancement.” The plan would assemble the latest bio-tech knowledge to come up with living, breathing creatures that are genetically engineered to “produce the intended biological effect.” Darpa wants the organisms to be fortified with molecules that bolster cell resistance to death, so that the lab-monsters can “ultimately be programmed to live indefinitely.”

Of course, Darpa’s got to prevent the super-species from being swayed to do enemy work — so they’ll encode loyalty right into DNA, by developing genetically programmed locks to create “tamper proof” cells. Plus, the synthetic organism will be traceable, using some kind of DNA manipulation, “similar to a serial number on a handgun.” And if that doesn’t work, don’t worry. In case Darpa’s plan somehow goes horribly awry, they’re also tossing in a last-resort, genetically-coded kill switch:

“Develop strategies to create a synthetic organism “self-destruct” option to be implemented upon nefarious removal of organism.”

The project comes as Darpa also plans to throw $20 million into a new synthetic biology program, and $7.5 million into “increasing by several decades the speed with which we sequence, analyze and functionally edit cellular genomes.”

That post goes on to quote a professor of biology, who’s keen to point out that DARPA’s view of evolution as a random string of events is going to prove a major stumbling block to any attempts to “improve” the process. As to what sort of genuine advantage over extant military technologies these synthetic organisms would have, the pertinent questions are absent, as are those dealing with the moral and ethical issues surrounding military meddling with fundamental biological processes, and the unexpected ways in which they might go wrong. And to hark back to an earlier post from today: would killing a bioengineered military organism be a legitimate act of war?

Also absent (but somewhat implicit, depending on your personal politics) are any observations that the world’s biggest military budget shows no sign of helping the US gain the upper hand against a nebulous and underfunded enemy armed predominantly with a fifty-year-old machine gun design and explosives expertise that’s a short step up from the Anarchist’s Cookbook… I’m all for wild ideas and blue-sky thinking, but I’m not sure they’re much use as a military panacea any more. The days of peace through superior firepower are long gone, and the more complex you make your weapons, the more likely they are to blow up in your face.


Bacterial computers to solve complex mathematics problems

Tom James @ 24-07-2009

bacteriaWe’ve seen viruses used to help treat cancer, and help building electrical components, now bacteria are being used to solve hitherto intractable mathematics problems:

Imagine you want to tour the 10 biggest cities in the UK, starting in London (number 1) and finishing in Bristol (number 10). The solution to the Hamiltonian Path Problem is the the shortest possible route you can take.

This simple problem is surprisingly difficult to solve. There are over 3.5 million possible routes to choose from, and a regular computer must try them out one at a time to find the shortest. Alternatively, a computer made from millions of bacteria can look at every route simultaneously. The biological world also has other advantages. As time goes by, a bacterial computer will actually increase in power as the bacteria reproduce.

These developments in synthetic biology are really amazing: it is just another example of how researchers are looking at pre-existing biological structures to solve problems (albeit somewhat abstract problems in this case) instead of building technologies from scratch.

[from the Guardian][image from kaibara87 on flickr]


Bacterial Fuel Cells

Paul Raven @ 25-05-2006

One thing’s for sure – burning hydrocarbons has to be done away with, and soon. The race is on to find new energy sources for our multitudinous needs. One of these potential solutions is to use bacteria in fuel cells. After all, they can produce energy from a wide range of materials, such as glucose and sewage, and the growing field of synthetic biology could engineer new bugs that output enough power to be commercially useful.


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