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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."

34 of 240 comments (clear)

  1. theologian's typo? by Anonymous Coward · · Score: 5, Informative

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

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

    1. Re:theologian's typo? by UbuntuDupe · · Score: 4, Funny

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

  2. Car of the future by MillionthMonkey · · Score: 5, Funny

    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

    1. Re:Car of the future by oblivionboy · · Score: 2, Funny

      Wrong!!

      Let me try.

      Figure I. SCHEMATIC: #32 Hot Woman.

  3. Pfftt... by RuBLed · · Score: 2, Funny

    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...
  4. Not completely artifical by timeOday · · Score: 3, Insightful

    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.

    1. Re:Not completely artifical by Angry+Toad · · Score: 4, Interesting

      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.

    2. Re:Not completely artifical by wizardforce · · Score: 2, Informative

      *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 which are known to exist in natural, healthy genetic systems.

      --
      Sigs are too short to say anything truly profound so read the above post instead.
    3. Re:Not completely artifical by MillionthMonkey · · Score: 5, Insightful

      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.

    4. Re:Not completely artifical by wyldeone · · Score: 2, Informative

      *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 protections don't slam them shut), is nowhere near the difficulty of creating an entire organism from scratch, which is what you suggest would require.

      --
      In the beginning the universe was created. This made a lot of people very angry and is widely considered as a bad move.
    5. Re:Not completely artifical by Plutonite · · Score: 3, Insightful

      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.
    6. Re:Not completely artifical by DaedalusHKX · · Score: 3, Interesting

      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 :)

      --
      " What luck for rulers that men do not think" - Adolf Hitler
    7. Re:Not completely artifical by mcrbids · · Score: 4, Insightful

      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.

      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. 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.

      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!

      --
      I have no problem with your religion until you decide it's reason to deprive others of the truth.
    8. Re:Not completely artifical by Yetihehe · · Score: 2

      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.

      --
      Extreme Programming - Redundant Array of Inexpensive Developers
    9. Re:Not completely artifical by Lord+Ender · · Score: 2, Funny
      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.
      --
      A slashdotter who didn't build his own computer is like a Jedi who didn't build his own lightsaber.
    10. Re:Not completely artifical by Chris+Burke · · Score: 2, Informative

      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. And our hydroponics bay can't include oranges in the mix-up... why? And if not oranges, some source of the chemicals we use to make Vitamin C artificially today. Whichever. It'll all be part of solving the much bigger problem of food.

      --

      The enemies of Democracy are
    11. Re:Not completely artifical by crazyeddie740 · · Score: 2, Interesting

      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 surround might actually be more evolutionary fit than yourself? brr!) If organisms could get away from the kind of matter and energy we know of into some kind of strange omni-vector energy, which is in omni-superposition, then that *might* increase their fitness. But then they probably wouldn't need such mundane things as a metabolism. In which case, it might be an open question whether or not these 'organisms' are actually alive.

      Perfection is not really obtainable. Bug fixes are, but this does not change the fact that there will always be one more bug. Perfection might not even be desirable - 'perfection' is relative to a particular environmental niche. Change the environment, change the niche, change what perfection means. Perfection (over-specialization) can get you killed.

  5. Oh come on... by PieSquared · · Score: 5, Insightful

    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.

    --
    Does a line appended to your comment give your post meaning in and of itself, or only in relation to those without?
    1. Re:Oh come on... by QuantumG · · Score: 2, Interesting

      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.

      --
      How we know is more important than what we know.
    2. Re:Oh come on... by heinousjay · · Score: 3, Informative

      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?

      --
      Slashdot - where whining about luck is the new way to make the world you want.
    3. Re:Oh come on... by feepness · · Score: 5, Insightful

      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.
  6. DMCA by Anonymous Coward · · Score: 2, Funny

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

  7. not jsut DNA by wizardforce · · Score: 5, Interesting

    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.

    --
    Sigs are too short to say anything truly profound so read the above post instead.
    1. Re:not jsut DNA by MuLaNLaNg · · Score: 2, Funny

      I've been to California and trust me, there's plenty of artificial TnA running around.

    2. Re:not jsut DNA by aminorex · · Score: 2, Informative

      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 mod DNA -1 overrated. GNA is +1 interesting. Proteome is +1 insightful. FWIW.

      --
      -I like my women like I like my tea: green-
  8. In other news.. by Anonymous Coward · · Score: 2, Funny

    "...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.....

  9. Whoa by jandersen · · Score: 2, Interesting

    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.

    1. Re:Whoa by QuantumG · · Score: 2, Informative

      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 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. How the proteins interact has been studied. There are system schematics.

      This really is like an "operating system" for a cell. The kinds of "applications" you will run on it will likely not be anything like the biological processes. Using standardized parts like Biobricks from MIT, you'll be able to hack together multicellular systems for performing some exotic task. Anything from producing wanted biological products to computation.

      --
      How we know is more important than what we know.
  10. Re:it's tyrell's fault by theonlyaether · · Score: 3, Funny

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

    --
    Graduate students and most professors are no smarter than undergrads.
    They're just older.
  11. And wouldn't it be ironic..... by mark-t · · Score: 4, Interesting

    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.

  12. vaporware by graft · · Score: 4, Insightful

    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.

  13. "Microsoft" of Artificial Life. by ElizabethGreene · · Score: 3, Interesting

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

    -ellie

  14. Defining Life by Doc+Ruby · · Score: 2, Insightful

    "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.

    --

    --
    make install -not war

  15. For the average slashdotter... by Dareth · · Score: 2, Funny

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

    --

    I only look human.
    My mother is a halfling and my dad is an ogre, so that makes me an Ogreling