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May 22, 2010

Synthetic Genome: TL;DR

If you already understand what's happening with the Venter Institute synthetic genome announcement, and just want to see my response, here's the money quote from the end of the previous post:

One suggestion that we know is possible, because a variation appeared in the Venter announcement: all synthetic genomes should be signed. According to Wired:

“They rebuilt a natural sequence and they put in some poetry,” said University of California at San Francisco synthetic biologist Chris Voigt. “They recreated some quotes in the genome sequence as watermarks.”

What Voigt refers to as a "watermark" should instead be thought of as a "DNA signature." We should require that all synthetic genomes include something like this, unique sequences following a designated pattern, identifying the organization behind the genome, the lab responsible, the date, and any other useful bits of information. Multiple copies should appear throughout the synthetic genome, so it doesn't get mutated away.

That way, if something unexpected happens, we know whom to talk to.

Give My Creation... Life!

The Venter Institute announcement that it had successfully crafted the first self-replicating synthetic organism caused quite a stir, even among people who are otherwise pretty jaded about emerging tech.

It's useful to understand exactly what is -- and what isn't -- going on here.

Where we are:

  • Synthetic genome copied from natural genome and transplanted into existing cell structure.

    This is a moderately big deal, but only that; it's a stepping-stone to a real big deal down the road. What the Venter Institute has done is synthesize a genome that reproduces the genome of an existing organism, then insert that genome into the body of an existing cell, replacing its own DNA. That cell was then able to self-replicate, indicating that the synthetic DNA copy was sufficiently complete.

    "Synthetic" here doesn't mean artificial, by the way. The DNA of the synthetic genome comprises the same base pairs and nucleotides as a natural genome, but was synthesized in the lab rather than replicated from an earlier cell. The best analogy I can think of is if, rather than copying the MP3 of your favorite song, you pulled together a really sophisticated music creation application and reproduced the song yourself, exact in every detail. It's the same, but a synthetic version.

    If that sounds like a lot of work to get something that is essentially the same as the natural/original version, you're right. But this step was never the real goal -- it's just preparation. The real goal is to create an entirely novel life form, comprising both entirely new DNA and an entirely new cell. That's still to come.

    Where we aren't:

  • Transgenic synthetic genome (natural genome copy with genetic code from other kinds of organisms).

    The synthetic genome created by the Venter Institute is a streamlined version of the original Mycoplasma mycoides bacteria, containing enough of the original code to replicate and function as M. mycoides. Adding transgenic features -- that is, genetic material copied from non-M. mycoides species -- should be fairly straightforward, as it's essentially doing standard bioengineering.

    In principle, this should actually be somewhat safer than current transgenic biotech, as they'll have much more precise control over the engineered genomes.

  • Novogenic synthetic genome (entirely constructed novel genome).

    The ultimate goal would be to create an entirely new bacterial species by creating genes that do new things, or by combining diverse known DNA sequences to create a functional, replicating bacteria that doesn't mimic any existing species. This will be hard, but clearly not impossible.

    The bonus goal:

  • De novo creation of cell structure.

    The cell in which the synthetic DNA is housed already existed, but with different DNA (it was the cell of a related species of Mycoplasma). One likely future step will be to create an entirely synthetic cell by throwing together the right set of proteins in just the right way. Like the latest breakthrough, that will undoubtedly start out by simply reproducing an existing cell structure. Ultimately, they'll want to create cellular bodies that have novel features, such as (conjecture here) additional mitochondria for added power.

    Where we go:

    So what does this all mean?

    The idea is to turn bacteria into microscopic machines, carrying out designated tasks in massively-parallel operations. Given the extreme range of things that bacteria can do in nature, the extent to which bacterial machines might be used is pretty staggering, particularly concerning environmental response. This would be a perfect platform for methanotrophic remediation of melting permafrost, for example; the Venter folks are already talking about building synthetic bacteria to do carbon capture. Biofuels are also high on the agenda.

    The big concern about synthetic biology is the potential for the creation of hazardous materials -- aggressive, infectious bacteria, for example. We should also consider, at the same time, its biomedical potential. Are there ways of delivering drugs via synthetic bacteria?

    One advantage of the big splash this relatively modest development has made is that it opens up the possibility of laying out the parameters of what ethical, responsible management of this technology would look like before have to confront its fully-developed form.

    Should we require a "shut-off" gene in any novogenic organism, one that kills the cell if certain conditions are (or aren't) met? A reproduction-limiting set of genes that only permits replication in the presence of a rare chemical? Public registration of all novogenic genomes?

    One suggestion that we know is possible, because a variation appeared in the Venter announcement: all synthetic genomes should be signed. According to Wired:

    “They rebuilt a natural sequence and they put in some poetry,” said University of California at San Francisco synthetic biologist Chris Voigt. “They recreated some quotes in the genome sequence as watermarks.”

    What Voigt refers to as a "watermark" should instead be thought of as a "DNA signature." We should require that all synthetic genomes include something like this, unique sequences following a designated pattern, identifying the organization behind the genome, the lab responsible, the date, and any other useful bits of information. Multiple copies should appear throughout the synthetic genome, so it doesn't get mutated away.

    That way, if something unexpected happens, we know whom to talk to.

  • May 18, 2010

    OtF Core: Ethical Futurism (from 2006)

    (This is the original Ethical Futurism piece I wrote for Futurismic in 2006; I intend to update and build on it, but I wanted to make sure the original could be found in its entirety here.)

    What does it mean to be an “ethical futurist?”

    I don’t mean just the basics of being an ethical human being, or even the particular ethical guidelines one might see for any kind of professional — disclosure of conflicts of interest, for example, or honesty in transactions. I mean the ethical conventions that would be essentially unique to futurists. What kinds of rules should apply to those of us who make a living (or a life’s goal) out of thinking about what may come?

    Futurists — including scenario planners, trend-spotters, foresight specialists, paradigm engineers, and the myriad other labels we use — have something of an odd professional role. We are akin to reporters, but we’re reporters of events that have not yet happened — and may not happen. We are analysts, but analysts of possibilities, not histories. We’re science fiction storytellers, but the stories we tell are less for entertainment than for enlightenment. And, much to our surprise, we may be much more influential than we expect.

    It’s not that no futurists have considered ethical issues before. Foresight professionals regularly grapple with the question of what kinds of ethical guidelines should govern futurism, in mailing lists, organizational debates, and academic papers. But — to my surprise — neither of the two main professional organizations for futurists, the World Future Society and the Association of Professional Futurists, have any lists, documents or debates on the subject available to the public. This doesn’t mean that futurists are inclined to behave unethically or amorally, but simply that there seems to be no overarching set of principles for the field, at least none open to the broader community in which futurists act.

    As I gave this some thought, it struck me that futurists are not alone in thinking about tomorrow professionally. Most business consultant types also concern themselves with what may come, with the results of corporate decisions and organizational choices. But the difference between that sort of business consulting and foresight consulting comes down to the difference between outcomes and consequences. Outcomes are the (immediate or longer-term) results of actions; consequences are how those actions connect to the choices and actions of others, and to the larger context of society, the environment, and the future itself.

    As I see it, then, where business professionals are responsible to the client and their various stakeholders, foresight professionals are responsible to the future.

    Here’s what I think that means:

    It means that the first duty of an ethical futurist is to act in the interests of the stakeholders yet to come — those who would suffer harm in the future from choices made in the present. This harm could come (in my view) in the form of fewer options or possibilities for development, less ecological diversity and environmental stability, and greater risks to the health and well-being of people and other species on the planet. Futurists, as those people who have chosen to become navigators for society — responsible for watching the path ahead — have a particular responsibility for safeguard that path, and to ensure that the people making strategic choices about actions and policies have the opportunity to do so wisely.

    From this, I would argue for the following set of ethical guidelines:

    An ethical futurist has a responsibility not to let the desires of a client (or audience, or collaborator) for a particular outcome blind him or her to the consequences of that goal, and will always informs the client of both the risks and rewards.

    An ethical futurist has the responsibility to understand, as fully as possible, the range of issues and systems connected to the question under consideration, to avoid missing critical potential consequences.

    An ethical futurist has the responsibility to acknowledge and make her or his client (audience, collaborators) cognizant of the uncertainty of forecasts, and to explain why some outcomes and consequences are more or less likely than others.

    An ethical futurist has the responsibility to offer unbiased analysis, based on an honest appraisal of sources, with as much transparency of process as possible.

    An ethical futurist has the responsibility to recognize the difference between short-term results and long-term processes, and to always keep an eye on the more distant possibilities.

    Futurists perform a quirky, but necessary, task in modern society: we function as the long-range scanners for a species evolved to pay close attention to short-range horizons. Some neurophysiologists argue that this comes from the simple act of throwing an object to hit a moving target. Chimpanzees and bonobos, even with DNA 98% identical to our own, are simply unable to do so, while most humans can (at least with a bit of experience). It turns out that the same cognitive structures that let us understand where a moving target will be may also help us recognize the broader relationship between action and result — or, more simply, how “if” becomes “then.”

    I’m not sure how many futurists recognize the weight of responsibility that rests on their shoulders; this is an occupation in which attention-deficit disorder is something of a professional requirement. But when we do our jobs well, we can play a pretty damn important role in shaping the course of human history. It’s incumbent upon us, then, to do our jobs with a sense of purpose and ethics.

    May 14, 2010

    My Talk at Lift10 : Wired for Tomorrow

    Watch live streaming video from liftconference at livestream.com

    (My original title was "Wired for Anticipation," hence the video title.)

    Video quality is iffy, and the audio isn't sync'd well, so be warned.

    May 8, 2010

    Our Posthuman Present

    Annalee Newitz at io9.com asked me to contribute something to their "Posthumanity Week" series, and -- despite being in the middle of a conference a couple thousand miles from home -- agreed. My piece went live today under the title "Your Posthumanism is Boring Me."

    "Posthuman" is a term with more weight than meaning; it's used variously to describe people with altered genomes, people with implanted machinery, people with lifespans measured in millennia, and a whole host of descriptors that ultimately boil down to "not us, not now." Enthusiasts and critics alike embrace the term precisely because it advances the argument that the Augmented is the Other - and either an aspiration or a nightmare, as a result. It doesn't illuminate, it disturbs.

    But as augmentations move from the pages of a science fiction story to the pages of a catalog, something interesting happens: they lose their power to disturb. They're no longer the advance forces of the techpocalypse, they're the latest manifestation of the fashionable, the ubiquitous, and the banal. They're normal. They're human.

    I've done variations of this rant before, but I think it's a pretty important concept. It serves us little good to think of plausible future changes solely in the present-day context. To really understand their impact, we have to imagine their role in a world that actually sees them as boring.

    (And, as I said to Annalee, holy crap that's a big picture of me they're using as an illustration for the piece.)

    EVERYONE JUST CHILL THE &%#! OUT

    Keep Calm, Civilization

    WE'VE GOT THIS

    May 5, 2010

    At LIFT10


    Name in Splat

    May 3, 2010

    Rogue Geoengineering Project Underway?

    Last week, Kyle Vandercamp, an atmospheric scientist, blew the whistle on a rogue geoengineering project funded by billionaire Harrison Wyld. Vandercamp was a senior scientist at the Bluebird Lab, and managed to get ahold of some pretty damning documents laying out the extent of what the Bluebird project intends to do.

    In short, Bluebird was supposed to be a research project looking at what geoengineering would entail, but Vandercamp says that they're actually looking at a near-term full-scale deployment.

    Here's the Bluebird website, which apparently had to go public early because of Vandercamp's leak. This is their promo video:

    Stop Bluebird is a web-driven campaign to push back against this geoengineering experiment. Documentary filmmaker Juanita Monte is helping to organize this effort, so the campaign is pretty video-focused.

    Here's Monte's video summary of what just happened:

    Here's Vandercamp's website, as well as the Stop Bluebird website.

    Or, maybe not.

    Bluebird is actually an "alternate reality game," put together by the Australian Broadcasting Company. Here's the home page for the game.

    I'm pleased to say that the producers of Bluebird contacted me last year to serve as an advisor for the game, and they even had me write a few pieces for the project. If the script for the official Bluebird video above sounds familiar, it should -- I wrote it. (Ken Caldeira was another advisor, so I feel pretty confident about the science of the game.)

    As with any near-term science fiction, events kept catching up with the alternate reality we were trying to create. I think the folks at ABC struck a good balance, though, and I like the storyline that they've constructed (and trust me -- what's available now is just the beginning).

    It's a web-based ARG, so you don't have to be based in Australia to play. Give it a shot -- and let me know what you think!

    Jamais Cascio

    Contact Jamais  ÃƒÂƒÃ‚ƒÃ‚ƒÃ‚ƒÃ‚¢Ã‚€Â¢  Bio

    Co-Founder, WorldChanging.com

    Director of Impacts Analysis, Center for Responsible Nanotechnology

    Fellow, Institute for Ethics and Emerging Technologies

    Affiliate, Institute for the Future

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