synthetic biology

October 4, 2009 1:23 PM

Our biotech century: the noocytes are coming... (previously)
posted by kliuless (25 comments total)

VENTER'S ON A BOAT
posted by grouse at 2:01 PM on October 4 [4 favorites has favorites]

...a future far stranger than Mr. Huxley had been able to imagine in 1948.

Brave New World was written in 1931.
posted by furtive at 2:08 PM on October 4

Fail on my part, he's talking about Ape and Essence.
posted by furtive at 2:10 PM on October 4

Cytation please.
posted by Artw at 2:22 PM on October 4

Hurry up I say
posted by A189Nut at 2:48 PM on October 4

"Edge Master Class 2009"

rut roh...
posted by hal9k at 2:54 PM on October 4 [2 favorites has favorites]

Craig Venter's institute recently published a quite exciting paper in Science along these lines. ("Creating Bacterial Strains from Genomes That Have Been Cloned and Engineered in Yeast" doi:10.1126/science.1173759)

In it, they show that they can synthesize the entire genome of a mycoplasma species in yeast. (Admittedly, mycoplasmic genomes are quite small as such things go, but this is still a DNA molecule that is orders of magnitude larger than those that are routinely synthesized by chemical methods.) Using yeast genetics, they are able to modify it as they please. The kicker is that they can then move the entire genome into the empty shell of another species of mycoplasma, "reboot it," and produce a member of the DNA's species.

This does raise some interesting issues. IANAL, but I'm not sure, for example, how easy it is to patent a bacterial strain that is produced by directed evolution, since you are essentially depending on nature to do the work for you. If, on the other hand, you produce an entire organism synthetically for a particular purpose, I'm fairly certain you could claim that you invented it, and thus patent it.

P.S. I've seen Venter speak a few times, and he's definitely my pick for "most likely to be a movie villain."
posted by dubitoergosum at 4:41 PM on October 4 [1 favorite has favorites]

The nuclear age was just the first of many collective nightmares to be wrought by science over the next few generations. On the plus side there will be fabulous yet undreamt of consumer products and other amazing things that will make your mind tingle with glee.
posted by humanfont at 4:48 PM on October 4

humanfront,

That "tingle in your mind" is a genetically engineered virus chewing through your gray matter, turning you into a Consumer Zombie...
posted by kuatto at 5:14 PM on October 4

Dear Dr. Venter,

It's come to the attention of the legal department here at EDGE Games Inc® that you've recently put forward a lecture on Synthetic Biology as an "Edge Master Class." This use of the word "Edge" directly violates our registered copyright, and as such is in flagrant violation of national and international law.

Futher, we've noticed that elements of your presentation bear an obvious and actionable resemblance to our much beloved and world-renowned video games. To whit, the discussion of "humanized-mice" draws heavily and without attribution from the bipedal rats in the famous "Alley" stage of Garfield: Big Fat Hairy Deal, and your contention that it's possible to resurrect extinct life forms is a direct lift from the ZX Spectrum, C64, Amiga, Sega Master System, and Atari ST versions of Alien Syndrome. We will not allow you to continue this transparent plagiarism.

While I assure you that I desire nothing more than to see posthuman science reach its full potential, the simple truth is that EDGE Games® can't afford to be lax in the protection of its intellectual property. I therefore advise you to adopt one of the following accommodations:

1) Change the name of your presentation to something that does not contain the word EDGE in it within the next 7 calendar days. Be advised that we would need payment for your use of the trademark to the day you change the name. We propose 75 per cent of the revenues you have received since your first use of the word "edge," on March 4, 1949.

2) License the right to use the trademark "EDGE" from us. This would require you to add a subtitle to your presentation, such as "Edge Master Class: an homage to Garfield: Big Fat Hairy Deal and the ZX Spectrum, C64, Amiga, Sega Master System, and Atari ST versions of Alien Syndrome." You would also need to add our company name (EDGE Games Inc®) immediately below yours in all future publications.

If you refuse, we will be forced to pursue our rights in court. You could not hope to win.

Sincerely,

Tim Langdell™
posted by Iridic at 5:15 PM on October 4 [3 favorites has favorites]

Iridic wins. Everyone else: stop being so dramatic.
posted by rxrfrx at 5:51 PM on October 4

IANAL, but I'm not sure, for example, how easy it is to patent a bacterial strain that is produced by directed evolution, since you are essentially depending on nature to do the work for you.

Diamond v. Chakrabarty established the patentability of genetically modified organisms. 35 USC 103(a) straightforwardly provides that "patentability shall not be negatived by the manner in which the invention was made." Further 35 USC 100(a) provides that "the term 'invention' means invention or discovery."

In other words, if X is patentable, then it's patentable regardless of whether it was invented or 'merely' discovered and regardless of whether it was invented or discovered by hard work, dumb luck, scientific genius, a brute force search, etc.
posted by jedicus at 6:32 PM on October 4 [1 favorite has favorites]

The nuclear age was just the first of many collective nightmares to be wrought by science over the next few generations.

Oh sure, it has nothing to do with the moral failing of a world that uses scientific discoveries for nefarious ends. It has nothing to do with the powerful, wealthy, and warlike who hold the reigns.
posted by treepour at 6:42 PM on October 4 [1 favorite has favorites]

Jedicus, I'm not sure if what you said applies or not, and would be interested to know.

The brief you cite refers to a strain that was explicitly constructed to digest oil, where no such faculty existed before. (In biological terms, it seems they introduced the necessary genes on a pair of plasmids, which are self-replicating hangers-on that are not a natural part of the organism.)

What about the following scenario: I take a naturally occurring, oil-eating bacterium. Can this be patented? (My naive guess would be no, as I can't for example patent a dog and ask all dog owners to pay licensing fees.)

Now I subject it to directed evolution, putting it in an environment where it is evolutionarily advantageous to digest oil more quickly. Mutations accumulate, and I now have a strain that better digests oil. Is this patentable?

I guess my question is, when did the species become novel? You likely don't even know all the mutations that made the bacteria better digest oil, and if you ran the experiment several times, you'd get different variants, all of which likely did the job better than before.

I guess I fail to see how a patent would work. Either it would be hopelessly narrow--say referring to the particular genetic sequence--or it would be ridiculously broad--covering say all better oil-digesting variants of a particular species.
posted by dubitoergosum at 7:03 PM on October 4

I guess my question is, when did the species become novel?

Technically speaking it becomes novel as soon as it's different from the prior art species. The bigger question is when does it become a non-obvious advance over existing species. The answer to that is generally 'when a biologist having ordinary skill in the art of genetic engineering would find the difference non-obvious.'

So, for example, if your goal was to make your organism glow in the dark and your directed evolution process duplicated green fluorescent protein, then a genetic engineer might say "that's obvious: we splice GFP into organisms all the time." On the other hand, if your process created bacteria that functioned as little ATP-powered LEDs, then that would probably be non-obvious.

You likely don't even know all the mutations that made the bacteria better digest oil, and if you ran the experiment several times, you'd get different variants, all of which likely did the job better than before.

Knowing the sequence of mutations isn't (necessarily) important. What's important is the end result.

I guess I fail to see how a patent would work. Either it would be hopelessly narrow--say referring to the particular genetic sequence--or it would be ridiculously broad--covering say all better oil-digesting variants of a particular species.

This is something that can be solved with appropriate claim drafting. It may be instructive to look at the claims in the Chakrabarty patent.

The broadest claim is to "A bacterium from the genus Pseudomonas containing therein at least two stable energy-generating plasmids, each of said plasmids providing a separate hydrocarbon degradative pathway." You can see that it's sort of half way. It does not claim a specific genetic sequence, but neither does it claim something like 'all bacteria of genus Pseudomonas able to digest oil.' The narrower claims specify the possible hydrocarbon degradative pathways, particular species, and plasmids.

In the directed evolution context the claims would be similar. You would run your directed evolution process until you had a strain that was commercially viable, scientifically interesting, what-have-you, then analyze it to determine the particular species, genetic characteristics, metabolic pathways, etc. The claims would likely be similar to those in the Chakrabarty patent; only the inventive process would differ.
posted by jedicus at 7:57 PM on October 4

Thank you for explaining that.

For what it's worth, part of my thinking is guided by my suspicion that Venter et al. intend to produce a generic "chassis" bacterium. Once you are freed from using a preexisting organism, it seems to me that patent obligations would be less difficult to satisfy, as you'd always be starting from a novel base. (E.g. Produce mycoplasma craigventerus and patent it. But also mycoplasma craigventerus var withafinehat...)
posted by dubitoergosum at 8:11 PM on October 4

What happens when these oil eating bacteria get loose and eat all our oil, huh!?
posted by delmoi at 8:26 PM on October 4

No scientific achievement has promised so much, and none has come with greater risks or clearer possibilities for deliberate abuse.

Given all the tools and techniques that have been used to fold, spindle and mutilate people over the years, none of which have involved synthetic biology, I'm kind of thinking that the possibilities for deliberate abuse aren't so damn clear or somebody would have gotten around to it by now.

Of course, since you can just culture existing pathogens using the old fashioned kind of biology it's not like you actually have to go to the trouble.
posted by Kid Charlemagne at 8:46 PM on October 4

That "tingle in your mind" is a genetically engineered virus chewing through your gray matter, turning you into a Consumer Zombie...

I was thinking it was more the ADAM kicking in...
posted by humanfont at 9:19 PM on October 4

What happens when these oil eating bacteria get loose and eat all our oil, huh!?

That's when Omni Consumer Products steps in and sells your government doses of the Lipophilomuncher2000Z™ strain. Unfortunately, this anti-bacterial bacteria is no cure, but regular treatments will help "control" or "manage" the problem, and OCP's subscription program has worked well for most nations' budgets, offering protection at only a small percentage of GDP.
posted by Blazecock Pileon at 11:00 PM on October 4

For what it's worth, part of my thinking is guided by my suspicion that Venter et al. intend to produce a generic "chassis" bacterium.

Suspicion? His stated goal is exactly that.
posted by atrazine at 1:57 AM on October 5

Synthetic biologists are convinced that, with enough knowledge, they will be able to write programs to control those genetic components, programs that would let them not only alter nature but guide human evolution as well.

Are we really this good at programming? Could we start with some robot police or something and see how it goes first? maybe an artificial intelligence designed to manage our military systems... just imagining the effect of mistakes and bugs in a program for "altering nature" kinda gives me the creeps... I don't mean to sound like a frankenfood conspiracy nut, but is this a good idea?
posted by ServSci at 9:31 AM on October 5

I just want to toss out that jedicus is awesome and reminds me why I ♥ metafilter. I'm looking forward to more patent-related discussion.

Back on topic... low-level bio tinkering and bio patents in particular creep me out, which creates some cognitive dissonance for me because it makes me feel like a Luddite. I feel like I can resolve that feeling by asserting that my complaint isn't the 'ME AM PLAY GODS' factor, but the very real possibility of dicking over indigenous peoples all over the world as we create our fancy new bio toys. Am I wrong? I could probably just say "Monsanto" instead of all of the foregoing....
posted by tarheelcoxn at 10:39 AM on October 5

Related: bunnie, a hardware hacker, looks at the swine flu genome: How many bits does it take to kill a human?
posted by ymgve at 2:31 PM on October 5

Rudy Rucker on Synthetic Biology.
posted by homunculus at 1:03 PM on October 19