Synthetic DNA About To Yield New Life Forms

mlimber sends along a Washington Post story about the immanence of completely artificial life: "The cobbling together of life from synthetic DNA, scientists and philosophers agree, will be a watershed event, blurring the line between biological and artificial — and forcing a rethinking of what it means for a thing to be alive... Some experts are worried that a few maverick companies are already gaining monopoly control over the core 'operating system' for artificial life and are poised to become the Microsofts of synthetic biology. That could stifle competition, they say, and place enormous power in a few people's hands."

theologian's typo?

[by Anonymous Coward]

That is _imminence_, or the quality of being imminent...

Immanence is almost another entirely: http://en.wikipedia.org/wiki/Immanence [wikipedia.org]

Re:theologian's typo?

[UbuntuDupe (970646)]

I don't think it effected understanding of the summary.

Car of the future

[MillionthMonkey (240664)]

What kinds of organisms will scientists, terrorists and other creative individuals make?

[broken image]

Figure I. SCHEMATIC.
Modified design for a low-pH respiratory engine. 1) monobasic phosphate buffer tank. 2) ADP-GDP reservoir. 3) primary ADP-GDP feed line. 4) NAD/FAD reservoir. 5) pyruvate feed line. 6) Deinococcus culture chamber. 7) ADP-GDP return line. 8) NADH-FADH2 return line. 9) pasteurizer. 10) sodium-potassium pump. 11) NaCl/KCl reservoir. 12) actin filament membrane. 13) myosin-hydroxyapetite cylinder. 14) axle. 15) flywheel. 16) dilute H3PO4 reservoir. 17) intake port. 18) myosin generator. 19) proton pump. 20) ATPase membrane. 21) secondary ATP feed line. 22) electrophoresis cartridge. 23) pH regulator. 24) UV sterilizer. 25) transmission. 26) +12VDC battery. 27) radiator coil assembly. 28) CO2 exhaust vent. 29) fan. 30) phosphate return line. 31) brake assembly. 32) generator. 33) amylase generator. 34) glycolysis chamber. 35) fibrolytic culture chamber array. 36) microcontroller. 37) compost chamber. 38) thresher. 39) lid. Cit. L. Xu et al, Cellulosic Artificial Muscle Engines (2057), Biomech. Eng. Letts. 21 599-612

Re:

[oblivionboy (181090)]

Wrong!!

Let me try.

Figure I. SCHEMATIC: #32 Hot Woman.

Pfftt...

[RuBLed (995686)]

And while some industry groups have talked about policing the field themselves, the technology is quickly becoming so simple, experts say, that it will not be long before "bio hackers" working in garages will be downloading genetic programs and making them into novel life forms.

SPORE hype...

Not completely artifical

[timeOday (582209)]

Anything still based on DNA is re-using nature's building blocks. It's like in Photoshop, using the clone tool vs. drawing a photorealistic texture freehand - there's a huge difference. Nature has been searching the space of DNA recombinations for a long time.

Re:Not completely artifical

[Angry Toad (314562)]

True but nature's selection criteria aren't the same as man's. We can probably hit maxima that would be outcompeted in nature in a second. There are probably lots of unique and useful solutions out there when survival constraints are relaxed.

Re:Not completely artifical

[MillionthMonkey (240664)]

We can probably hit maxima that would be outcompeted in nature in a second.

That depends on your definition of "maxima".

Even with survival constraints as the basis for a successful design, it can't be denied that an intelligent designer could have come up with much better designs than the ones you see. Attributing evolutionary designs to an intelligent being is practically an insult when you look at some of the shoddy work evolution has come up with. Our testicles, for example, hang from our undersides dangerously exposed, just because some protein denatures at core body temperatures. Apparently something needs to be redesigned that can't be made to work better with slow incremental improvements. Evolution's fix: make them hurt like hell when struck so you learn not to mess with them. A Microsoft-style hack. If we threw a bunch of supercomputers at the problem we might come up with a completely different protein design that would allow reproduction with undescended testicles.

Disregarding survival constraints as a parameter, a world of possibilities opens up. There is nothing in physics or chemistry that prevents the existence of almost any organism you can imagine, so long as fundamental physical constraints are adhered to such as conservation of energy, rising entropy, etc. I'd like an animal with wheels that I can drive to work, with chlorophyll in its skin so I don't have to feed it. Maybe it can sun itself on the roof while I'm at meetings, and ooze a delicious health drink from a special orifice so I can catch dinner on the way home. (Don't spit up your milk laughing, it's quite possible.) A creature like that would go extinct pretty quickly but it would sure be convenient to have one, and no law of nature prevents such a thing from existing.

Re:Not completely artifical

[Plutonite (999141)]

Our testicles, for example, hang from our undersides dangerously exposed, just because some protein denatures at core body temperatures. Apparently something needs to be redesigned

Please speak for yourself, I like my testicles where they are thankyouverymuch. You might at well argue that we should have our genitals protectively hidden deep back in our throats and that we inseminate the females by spurting out the damn seed while we french kiss. or something. Wait, that was awful, sorry.

While there is probably a lot that can be improved in the engineering of human bodies, I find it slightly disheartening that after thousands of years of learning we are still unable to create a single complex living cell without help from nature. When we do, it will be the greatest feat of engineering ever, and I will party like hell.

Re:

[ResidntGeek (772730)]

When we do, it will be the greatest feat of engineering ever, and I will party like hell.

It'd be more of a triumph for analytical and organic chemistry, really. Analytical chemistry provides the high-resolution structure of the various components, and organic chemistry provides the reactions to synthesize them - all the engineers would be doing, is putting everything in the right order. It would require precision, certainly, but I'd assign more credit to the chemists.

For the average slashdotter...

[Dareth (47614)]

... "the praying mantis routine" with a bug-woman-hybrid that looks like Natasha Henstridge may be a really good deal!

Re:

[blahplusplus (757119)]

"Our testicles, for example, hang from our undersides dangerously exposed,"

Existing is dangerous in and of itself, I'm sure next you'll claim "existing is dangerous" kill me now! The design or non-design of something is totally arbitrary. If we look at entropy and the laws of nature, it's a double edged sword, you can't have one thing without the other, it falls out of the geometry naturally.

A perfectly designed being would be a *god* by definition, and hence not natural, not made of the kind of matter an

Re:

[crazyeddie740 (785275)]

Existing is dangerous. That is what drives evolution. Evolution happens when chaos (mutation) and destruction (natural selection) conspire to create order. Who says destruction is a bad thing?

A 'perfectly designed' being, in this case, would be one that its perfectly suited to its environmental niche. It might be an ant (ant species are stable over deep time, so they must be doing *something* right), or a bacteria. It might not be terribly complex or intelligent. (Have you ever wondered if the hicks that su

Re:Not completely artifical

[DaedalusHKX (660194)]

You seem to know little about this subject.

Testicles are among the least of our concerns... what SHOULD concern you, especially in a "SURVIVAL" related subject, is that man seems to have been meant to stay on Earth (until man gets over this particular problem.)

See, man is one of TWO mammalian species that requires an external source of vitamin C... otherwise we get scurvy... and eventually kick the bucket. Interesting that Earth's apex predator is range limited by something so simple as carrying a satchel of oranges or lemons on the ship... (okay, not all specimens of homo sapiens qualify for more than "monkey" classification, granted, and some are not capable of even surviving in society, nevermind without said crutch.)

However, a voyage to the stars, without a good supply of replenishable vitamin C would become a trip delimited by a few days/weeks past the day when the vitamin C runs out.

Pretty sad, when you think about it, every schmuck is looking at all these "big" problems, instead of looking at the fundamentals. Testicles and their placement on the body is nowhere nearly as bad as the fact that every single instance of homo sapiens in space would be cut short by the vitamin C supply. Ironic really, perhaps "intelligent design" might warrant a second look, unless of course, evolution and any supernatural forces others might attribute evolution to "realized" that man was a plague, and should be limited to Earth until it managed to kill itself off, whether by grey goo, killer designer virus, or just plain good ole' nuclear warfare.

If that isn't a vote for intelligent design or intelligent forces of evolution, I don't know what is :)

Re:

[Yetihehe (971185)]

Your post is a little moot. EVERY organism on earth is meant to stay on earth. Every voyage to the stars is limited by water, food and oxygen. Vitamin C is least of your worries as you can just take a few kilograms of pure Vit C. It's so cheap it is even used as a preservative in many many foods. But you can't live JUST on it.

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[Chris Burke (6130)]

However, a voyage to the stars, without a good supply of replenishable vitamin C would become a trip delimited by a few days/weeks past the day when the vitamin C runs out.

Uh... replace "vitamin C" with "food" and maybe the irrelevance of this issue will become apparent?

It's not like minus vitamin C our bodies are self-sustaining. We still must intake sustenance. Any journey me take will be limited by the supply of food we can bring, which means for any truly lengthy journey we will need to grow food. An

Re:Not completely artifical

[mcrbids (148650)]

Our testicles, for example, hang from our undersides dangerously exposed, just because some protein denatures at core body temperatures. Apparently something needs to be redesigned that can't be made to work better with slow incremental improvements. Evolution's fix: make them hurt like hell when struck so you learn not to mess with them. A Microsoft-style hack. If we threw a bunch of supercomputers at the problem we might come up with a completely different protein design that would allow reproduction with undescended testicles.

Which explains the survivability of so much hackish, clumsy, but real-working software. See, software, or life organisms persist to the degree that they solve real-world problems. How "elegant" the solution is is rather secondary. Often, real-world problems are ugly, pseudo-random nasty problems that don't have a clear, simple, ivory tower style solution. I maintain a large, complex, beautiful software codebase that has the ugliest, most horrible hack of a pile of regex and scripting as its very center. The nasty hacks have been amazingly stable for years now, and work well, even if they are a serious pain to edit during the (very rare) need to edit.

It's carefully sandboxed - the ugly part sits in a single file that is itself wrapped inside a handler function, so the "pretty" part of the codebase is *never* contaminated by the ugly, "written in a day or two" hack that got the whole shebang started.

Sometimes, no matter how much you kick and scream, you have several screens of ugly case statements littered with random function calls, and you end up with a great big ball of mud [laputan.org].

Guess what!?!?! Look in the mirror - YOU ARE A GREAT BIG BALL OF MUD. Your body is a complex set of unclear, un-abstracted dependencies without clear boundaries. For example, we've long thought of the pancreas as a key component of blood sugar control. But recent research shows that the bones (yes, bones!) of the body also contribute to positive blood-sugar control [nytimes.com]. As a borderline type-II diabetic, I pay attention to things like this...

Millions of years of evolution (or a few years of hard work by a half-drunk God) have resulted in your body, which is a festering pile of weird dependencies. For example, if you don't get exposed to enough dirt as a baby, you end up with asthma [bbc.co.uk].

If Microsoft's software is truly evolutionary in nature, that would explain its dominance in today's marketplace - it's well adapted to survive in the software environment we've seen so far, and like the dinosaurs, it will only be beaten back when the basic environment changes. (which it is)

Get used to the world of "dirty" evolutionary solutions - it's the basic building block of life itself!

Re:

[somersault (912633)]

Evolution's fix: make them hurt like hell when struck so you learn not to mess with them. A Microsoft-style hack.

Either that or it shows that God has a sense of humour? Or is just giving a convenient way for girls to protect themselves in situations where they are usually at a gross disadvantage because the man is already stronger.. you can go at it with a bunch of supercomputers if you'd rather have to beat someone senseless with a heavy implement (or perhaps just shoot them?) rather than just kick them in the nuts and run away.

Re:

[Lord Ender (156273)]

Let me paraphrase that so people with little time can still get the gist of your statement without having to read much.

testicles ... exposed ... protein ... ooze a delicious health drink from a special orifice so I can catch dinner on the way home. (Don't spit up your milk laughing, it's quite possible.)

flexibility.

Re:

[aliquis (678370)]

Maxima of the species in question or for our purpose? Evolution doesn't happen for the benefit of other species you know ..

In other news..

[by Anonymous Coward]

"...a few maverick companies are already gaining monopoly control over the core 'operating system' for artificial life ..."

Roman Catholic Church cites Genesis in Prior Art claim.....

Re:

[wizardforce (1005805)]

*ahem* there's no reason why we would need to specifically build artificial life based on DNA or RNA for that matter, there are several analogues that do jsut as well. maybe in time we'll find a completely different way of doing things that doesn't require anything remotely resembling the sugar phosphodiester backbone common in genetic systems today. even if we decided to base things on the DNA backbone, we could and probably will be using entirely different nucleotide bases to encode everything- none of

Re:

[wyldeone (785673)]

*ahem* there's no reason why we would need to specifically build artificial life based on DNA or RNA for that matter, there are several analogues that do jsut as well

Yes, there is. Doing so allows synthetic biologists to use all the cellular machinery, vastly simplifying their job. In case you didn't read the article, all the team referenced has done is create an artificial genome which, while still a very important achievement that will open many new doors in synthetic biology (assuming patent protection

Re:

[wizardforce (1005805)]

yes, I should have rephrased that. there's no reason why we couldn't [eventually] build "life" based on entirely synthetic genetic systems. or for that matter, use it in lesser roles in lifeforms as they exist now. certain bacteria already modify their phosphate backbone with a sulfur based group which allows them to alter expression of their genes. morpholinos are already being used to temporarily modify gene expression; from there it would likely be a much shorter hop to replacing a much larger set of

Oh come on...

[PieSquared (867490)]

How exactly does this blur the boundaries of life? I could see some people questioning if a virus was really alive, but adding more things like viruses wouldn't *further* blur the line, and anything as complex as bacteria would be life regardless of if they were natural or not.

I suppose if you let religion define "life" for you this might cause trouble, but definitions shouldn't be the job of religion.

Re:

[QuantumG (50515)]

the term "life" has zero meaning and will continue to have zero meaning. Any sensible definition you care to give will also classify computer programs, tractors and aeroplanes, unless you specifically exclude them. For a while, people have gotten around this by saying "oh, I mean biological life" but now that we're making machines out of biological "stuff" that trick doesn't work anymore.

Re:

[heinousjay (683506)]

Pretty much every definition of life I've ever seen included reproduction. I don't recall ever seeing tractors and airplanes reproduce. Software is only virtual anyway, and the arguments aren't very interesting unless one is in the mood to get very abstract. Do you have any more bad examples?

Re:

[sholden (12227)]

So a mule isn't life?

Re:

[QuantumG (50515)]

So you're saying that sterile animals are not alive?

How about sterile amoeba?

Re:Oh come on...

[feepness (543479)]

Pretty much every definition of life I've ever seen included reproduction. I don't recall ever seeing tractors and airplanes reproduce.

Maybe human beings are tractors way of reproducing.

I sure hope so

[QuantumG (50515)]

In fact, government controls on trade in dangerous microbes do not apply to the bits of DNA that can be used to create them. And while some industry groups have talked about policing the field themselves, the technology is quickly becoming so simple, experts say, that it will not be long before "bio hackers" working in garages will be downloading genetic programs and making them into novel life forms.

We've only been waiting, forever. It's hard to imagine the megacorps coming up with something even remotely innovative to do with this technology. We need hackers.

Competition?

[istartedi (132515)]

They're worried about competition? As in BUSINESS competition? This kind of tech makes me worry more about competition in the true Darwinian sense of the word. What happens when "the Microsoft of DNA" codes an airborn AIDS virus into the system? Kinda puts all that Wall Street crap into perspective, doesn't it?

Re:

[timeOday (582209)]

What happens when "the Microsoft of DNA" codes an airborn AIDS virus into the system?

My doomsday pick is on Sony, due to the length of their rap sheet. They don't mind infecting customers to control them [wikipedia.org].

DMCA

[by Anonymous Coward]

Just be glad that God hasn't invoked the DMCA on reverse-engineering his DNA Code yet.

not jsut DNA

[wizardforce (1005805)]

who says artificial life needs to be based on DNA? The earliest forms of life probably used RNA instead or one of its cousins like TNA, GNA, PNA or LNA. DNA is only special in the fact that it is missing a key hydroxyl group in the 2 position. this makes DNA more stable because there's no nucleophillic group there toi assist in self-cleavage of the phosphodiester bond. GNA has a backbone of glycerol rather than ribose [RNA] or deoxyribose [DNA]. PNA uses a reperating serine polypeptide backbone and because the whole thing has no charge like DNA does it has a much higher melting temperature [can withstand more heat] which may make it superior to DNA or RNA in some applications in biology. TNA on the other hand, has a synthetic polymerase enzyme that has to my knowledge, been able to create strands 1000 bases long. then there's alternative nucleotide bases, there are similar molecules to the naturally occuring 5 that also can encode for proteins and act in genetic systems. there's a lot that can be done with this, it's just a pity that it will probably be encumbered in patents if and when any of it is realized.

Re:

[aminorex (141494)]

Cogent, thanks. I think it's also worthwhile to point out that the original WaPo article is just wrong when it says that DNA contains "all of the instructions" necessary to construct a living organism. The proteome contains the "instructions", the program. The DNA is mere "data" which the proteome operates upon. The proteome is the interpretive mechanism for constructing a living device from the DNA blueprint, and contains all of the "intelligence" in the analogy to a -> house construction process.

I

I can see how too

[rucs_hack (784150)]

That could stifle competition, they say, and place enormous power in a few people's hands

Only if they allow these companies to patent the technology so broadly as to stifle competition. By 'only' I of course mean 'when'.

It's crazy talk anyway. The 'Microsoft of DNA'? To Paraphrase Paul Graham, only if there's someone to bend over and be the IBM of DNA.

Seriously though, that's highly unlikely at this stage unless effective monopolies are granted via patent and maintained in perpetuity so as to prevent any c

Our good friends

[Terminal Saint (668751)]

No doubt our good friends at Monsanto would kill to be the main maverick company in question.

look mom, here's my new virus

[wikinerd (809585)]

Considering that many people choose to apply their programming skills in writing computer viruses, should we expect like-minded people to disseminate real synthetic viruses once the technology becomes sufficiently mainstream?

Re:

[Grey_14 (570901)]

Scarier than that, computer viruses have taken a drastic turn towards being used for nefarious means, greater than just trashing data, When the zombie revolution comes, they will be chanting "Buy... Viagraaaaa"

Whoa

[jandersen (462034)]

Hold it, hold it! We're not quite there yet. It was only yesterday, on the historical timescale, that we discovered DNA and now we are beginning to get some vague ideas about how some of the things actually work. We can even theorize about correcting errors in people's genetic code, but creating a living cell from scratch? Not even the best biologists know more than a tiny fraction of what goes into making a living cell function. IOW, we are far, far out in the world of science fiction here nobody is just on the threshold to discovering how to create living cells from scratch, or even mostly from scratch.

If and when that ever happens, I don't think any of the readers of /. will be around. The problem with absurd, sweeping patents will have solved itself by collapsing completely, capitalism is likely to have been left behind as yet another temporary absurdity in human culture, the climate change crisis will have run its course and found its solution, and if humanity is still around, we will have found a role as the guardians and preservers of the planets.

Re:

[QuantumG (50515)]

It was announced this year that most of the genes of ecoli are now "understood" to the degree that we can now remove the genes we don't understand and still get a working system. It really is amazing how fast biotech is moving..

J. Craig Venter [wikipedia.org] is still the leading force. Next year he plans to publish a full artificial genome for a "minimalist" microbe. This thing can metabolize a feedstock and reproduce. All the genes are well understood. The structure of the proteins they make have been described. Ho

And wouldn't it be ironic.....

[mark-t (151149)]

<troll>If many hundreds of thousands or millions of years from now when humanity is a thing of the past, descendants of the synthetic DNA creatures start debating about whether or not they evolved naturally, or were created by a long-forgotten designer? Of course the former would obviously be a more acceptable conclusion, since the latter creates additional complexity.</troll>

Re:

[BiggerIsBetter (682164)]

It would only answer so much... If they (or we) were designed, it only changes the question to, "How did the designed come to be?"

vaporware

[graft (556969)]

It should be pointed out that the technology described is largely fictitious. The best labs haven't even managed to create a single artificial cell, and those technologies ALL use cobbled-together bits stolen from other lifeforms - nothing truly from scratch. There are a few good examples of proteins being engineered to specific functions (mostly DNA binding specificity), but we're ages away from being able to say, "Okay, I want to synthesize a protein that does this random function; here's how I would do it." And as for more complex lifeforms? Forget it. We don't even understand the development process of any multicellular organism in any detail, never mind being able to manufacture our own. So, on the whole, I think this story is akin to worrying about who is going to get control of, say, shrink-ray technology. Scary when it happens, but it ain't happening any time soon.

"Microsoft" of Artificial Life.

[ElizabethGreene (1185405)]

There may be a "patent troll" of artificial life, but there will be no Microsoft. DNA is, by definition, open source.

-ellie

Defining Life

[Doc Ruby (173196)]

"Life" is a system that transduces energy to maintain local entropy reductions that perpetuate its operation: homeostasis. Recognizable life replicates itself, or is replicated, from identical or nearly identical instances: reproduction.

FWIW, "intelligence" is an information model of the physical world at least minimally accurate and at least minimally inclusive (perhaps solely at initialization) of new information that it adds to itself, and that includes representation of itself in its model.

No difference

[Tony (765)]

Would you prefer that we place enormous power in everybody's hands? Regardless of their level of skill or ethics?

That's effectively the same thing.

What you describe is similar to "security through obscurity," the hope that not enough people will have the knowledge and information needed to cause damage. As soon as one person has the knowledge and power, you have compromised security. The whole point is to design a system that is resistant to knowledge and power.

Unfortunately, since we didn't design the syst

Re:

[MidnightBrewer (97195)]

Would you prefer to limit it to a few people whose only differentiating trait is that they're incredibly rich or happen to be in power? People with wealth and power are not typically known for their high moral standards.

Re:

[theonlyaether (1146549)]

I thought the line between biological and artificial was already blurred in Los Angles O.o