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Biotech Science

The Los Alamos Bug 389

Kannappan writes "'You somehow have to forget everything you know about life', says Steen Rasmussen, a colleague of Norman Packard. Packard and his team are working on creating life artificially, nicknamed The Los Alamos bug (pdf). It will be created out of a molecule called Peptide Nucleic Acid(PNA), with a blend of three different factors crucial to life, viz. containment, heredity and metabolism. The researchers believe that the synthetic lives so created will have an enormous practical value in producing clean fuels, healing injured bodies and acting as tiny diagnosticians roaming our bodies."
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The Los Alamos Bug

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  • PNA? (Score:4, Funny)

    by Punboy ( 737239 ) on Sunday October 23, 2005 @11:44PM (#13861576) Homepage
    Are there any other lifeforms based on PNA? Why aren't they using DNA?

    Do I just need to RTFA?
    • Re:PNA? (Score:2, Informative)

      by Anonymous Coward
      PNA is catalytically active-- you know enzymes. DNA is not. RNA may be(ribozyme), but is rather quickly degraded in the environment, and rather a bitch to work with.
    • Re:PNA? (Score:4, Informative)

      by caenorhabditas ( 914198 ) on Monday October 24, 2005 @12:31AM (#13861771)
      Normal nucleic acids are composed of sugar, base and phosphate. PNA as described in the article replaces the sugar and phosphate with a peptide (I assume with the R group replaced with the A, T, G or C). The replacement of the sugar-phosphate backbone with a peptide makes the nucleic acid soluble in fat, rather than soluble in water -- the ultimate goal of using PNA rather than DNA or RNA.

      And no, I do not believe there are other life forms based on PNA.
      • Run that past me once again in English?
        • Re:PNA? (Score:5, Interesting)

          by Thomas Miconi ( 85282 ) on Monday October 24, 2005 @05:45AM (#13862504)
          Run that past me once again in English?

          OK. "They're fscking cheating"

          They're using PNA because it does fancy stuff "on its own", just because the out of it is soluble in oil, but the inside of it is repelled by oil and prefers water. So it goes up and down according to whether it's "single-stranded" or "two-stranded" (i.e. whether the inside is expopsed or not). You don't need the complex machinery of metabolic reactions which is necessary for "real" life to cut, assemble and move stuff around.

          The whole thing is a fraud, at least if TFA from the New Scientist is an accurate description. Never mind that the genome is essentially random bits of PNA that don't code for any chemical machinery. TFA says that it does influence "metabolism" directly, through electromechanical influence. Wow, that leaves a lot of degrees of freedom for evolution to play with, doesn't it ? (Hint: no, it doesn't). I could mention the utter lack of self-regulation (that thing just grows and divides when it's too big, period), removing the essential computational component of life (wonder what Packard's friend Stuart Kauffman would say about that).

          The worst part is the thermodynamics. Apparently all the reactions that occur within the bug are "downwards", degrading reactions. The bug doesn't relly "build" anything. The miracle of life lies precisely in its self-constructing aspect: life is able to couple downwards, energy-releasing reactions and upwards, constructive reactions so that the former "feed" the latter. Thus living systems really construct themselves. That "bug" just uses hand-tailored, pre-activated, energy-packed components which are fed to it by the experimenter and degrades them according to a carefully hand-defined pathway. Evolution of the inner processes is utterly impossible because, essentially, there is no real "inner process". It's just like fire - a downwards, energy releasing reaction without any self-regulation. .

          If this thing is alive, then so were Sydney Fox' "protocells" [wikipedia.org] from 40 years ago !

          That thing is about as relevant to understanding life as Deep Blue was to understanding intelligence - i.e. it gives a good example of what life is not.

          Thomas.
          • Re:PNA? (Score:3, Interesting)

            by vertinox ( 846076 )
            That "bug" just uses hand-tailored, pre-activated, energy-packed components which are fed to it by the experimenter and degrades them according to a carefully hand-defined pathway. Evolution of the inner processes is utterly impossible because, essentially, there is no real "inner process". It's just like fire - a downwards, energy releasing reaction without any self-regulation.

            What you just described is a virus.

            Like a fire a virus burns resources without aquiring them. Doens't mean both a virus and fire ca
    • Re:PNA? (Score:4, Funny)

      by JumperCable ( 673155 ) on Monday October 24, 2005 @01:44AM (#13861951)
      They want to lock in all future life into a proprietary format. With current DNA being patented our only hope left is to create our own truly open source life form.

      No word yet on which format Microsoft and Sony intend to back. In related news, Bush is working heavily with Monsanto to ensure that the DMCA is found to be applicable to current life forms. Scientists caught attempting to reverse engineer life should expect to be raided by the FBI by the end of year.
  • I41 (Score:2, Funny)

    by aapold ( 753705 )
    cmon, you know you want to bow down before them....
  • by FlyByPC ( 841016 ) on Sunday October 23, 2005 @11:46PM (#13861587) Homepage
    With our increasing knowledge of the mechanics of life, it's a matter of time until somebody succeeds in creating life from scratch. I don't think it's very controversial these days to say that if we don't already have the power to create life in vitro, we someday will.

    For my money, a much more interesting question is, can we create *intelligence* from scratch? Humor aside, I think creating something with recognizable intelligence (not just programming) will be much more difficult -- and have much more profound implications -- than "merely" creating life.

    Such experiments should help narrow down the various factors in the Drake Equation. Life, I suspect, is fairly commonplace. I have no idea if intelligence is.
    • by ZachPruckowski ( 918562 ) <zachary.pruckowski@gmail.com> on Sunday October 23, 2005 @11:58PM (#13861642)
      We are certainly moving towards artificial intelligence. We actually have programs that can write themselves to a limited degree. And so we'll probably have artifical intelligence shortly. But making a new biological species with our level of intelligence sounds tough because of our limited knowledge of the brain.

      I'd recommend you read things by Ray Kurzweil on this topic. In particular, "The Singularity" seems relevant. Apparently there is a short collection of essays by him online, but I don't know if it'll have what you're looking for.
      • by gfody ( 514448 ) on Monday October 24, 2005 @01:59AM (#13861986)
      • by localman ( 111171 ) on Monday October 24, 2005 @02:51AM (#13862109) Homepage
        We are certainly moving towards artificial intelligence. We actually have programs that can write themselves to a limited degree. And so we'll probably have artifical intelligence shortly.

        Care to take a bet on that? :)

        I don't believe there is anything magical about the brain, and I believe it can be reproduced in a man-made form. But I think it is far far more complex than we yet realize. Even the most advanced neural nets of today are nowheres near the level of complexity of even a rodent brain. And I'm not just talking about the number of neurons. I'm talking about the secondary effects -- the self-organizing nature of the brain, and how different parts, with slightly different layouts are used for vastly different processing tasks. We're still a long ways off. If I had to guess I'd say not within the next 50 years. Perhaps much longer.

        And I don't believe that we'll achieve intelligence through direct programming, even through self modifying programs. If you can look at the low level and tell what's happening at the top level (like with a program) then it's far to simple to encode intelligence. Intelligence requires layers of meaning.

        Nonetheless, an interesting topic.

        Cheers.
        • I don't believe there is anything magical about the brain, and I believe it can be reproduced in a man-made form. But I think it is far far more complex than we yet realize.

          Oh we realize how complex it is. All the computers on the planet combined would still not have enough transistors to emulate a single brain's quadrillion synapses!

          However, creating a virtual analog self organizing neural network with as much or more capacity as a human brain is technically feasible with today's technology. It's the cogni
    • You're right about the 'humor aside'; it could be argued that intelligence has yet to be created.
    • Ahh the Drake Equation. Tell me, is it fair to call a star surrounded by a Dyson sphere 'dark matter'? You can't see it.. What's the current estimate for how much of the universe is made up of dark matter? 23% or something right? Hmmm. That's an aweful lot of Mind.
    • "With our increasing knowledge of the mechanics of life, it's a matter of time until somebody succeeds in creating life from scratch."

      Probably, but I doubt it will be in a U.S. government funded lab. As soon as the religious fundamentalists, who once again dominate the U.S., figure out government scientists are trying to create life without God or screwing this will get shut down. Not sure that would be a bad thing in this case.

      We know just enough about biology and nanotechnology at this point to be reall
      • There is one thing you are failing to see. Immortality has been sought after nearly as long as recorded history has existed. References to immortality occur as early as 2500 BC in the Gilgamesh Epic. Humans are unique in the respect that they have a conscious understanding of their own mortality. Although self-preservation can be observed in the majority of the animal kingdom, there is no evidence that any other species has self-awareness of their own mortality.

        Among humans, self-preservation is probably th
      • by Shihar ( 153932 ) on Monday October 24, 2005 @01:56AM (#13861976)
        And the most insidious unintended consequence of our advance in medicine, most people don't appreciate, we have extended our life spans, if you have the money, to the point that we live much longer than we should, we have people living a poor quality of life for decades in their 80's and 90's draining societies resources, and worse we are producing an exploding population. I'm not sure near technology synthesized immortality is such a great thing. There is benefit in the renewal that comes with the old dieing and letting young, fresh people take over.

        I think you are looking at life expansion from entirely the wrong perspective. First, life expansion does NOT create a population boom. All of the rich western European nation are in a death cycle right now. Their populations are shrinking. Wealth and the ability to live a long time causes people to simply choose to not have as many children. This is an extremely well documented correlation. The US itself would be in a death cycle like Europe if it wasn't for its influx of immigrants.

        Life expansion does not result in a drastically lower standard of living. Being old isn't what makes being old suck. Having your organs fail, your bones become brittle, mental illness, and muscle loss are the reasons why being old is no fun. Fortunately, extending life requires dealing with all of the above. If you have ever watched a National Geographic on a tribe with low life expectancy, you will notice that a 35 year old man looks like an 80 year old American or European. That isn't to suggest that we keep people alive beyond what they would be able to be naturally in the same state, but it isn't right to assume that when people were dying at the age of 40 they were dying looking and feeling like a 40 year old of today.

        More importantly, life expansion these days almost entirely revolves around "solving" old age. If someone was to live to be 200 years old, you can bet that they have 'solved' old age and that 200 year old person probably looks about 30. You simply can't extend peoples' lives much longer without curing the natural degradation that your body suffers as you get older.

        Finally, I think you drastically overlook the social good that old age offers. In a society where people become older and older, you have people building up vast reservoirs of experience and knowledge. The only social ill old age brings is retirement, and as you see people living longer and healthier lives, you are going to see the retirement age kicked out further. I wouldn't be surprised in a decade or two when life expansion hits its next big surge that our way of thinking about retirement gets radically altered. I wouldn't be surprised if one day the normal mode of 'retirement' is to take a few years off from work every decade or two, but never permanently retire.
    • by ShimmyShimmy ( 692324 ) <`bplennon' `at' `gmail.com'> on Monday October 24, 2005 @01:06AM (#13861868) Homepage Journal
      can we create *intelligence* from scratch?

      I think I fundamentally disagree with you in saying that intelligence is hard to create, given life in the first place. At this point in time, science has (almost) undisputedly proved the theory of common descent. I pretty well believe that humans eventually came from single-celled organisms, and so does most of the world.

      So assuming that is true, intelligence more or less created itself, through life, by a glorified trial-and-error system. Although it seems surprising at first, if you consider how many many different orananisms there are (were) at any given time, and how many trials (generations) there have been, it becomes much more down to Earth.

      Actually I think even 'intelligence' today is still a glorified system of trial and error. Think about solving an elementary algebra problem. What's your first intuition (or was when you were learning)? Isolate the variable, etc? Hell no! Trial and error. It's intuitive and doesn't take much mental 'work'. Example: Mary and Sue have a combined age of 15. Mary is 5 years older than Sue. How old is Mary?

      Spit this problem at an average 5th/6th grader and I promise you won't get anything along the lines of x + (x + 5) = 15. You'll just get 3 + 8 = [crossed out], 4 + 9 = [crossed out], 5 + 10 = 15 !! And that's how the problem is solved by a (we'll say) 10 year old.

      Now, I know I don't seem to be really getting at anything big, but consider this: the average 10 year old has solved a LOT of 'problems' in his/her lifetime, from how to balance to stand up, how much food to eat so you aren't hungry anymore but don't throw up... I could go on forever, but I will call one example: pouring.

      Is it hard to pour water from a pitcher into a cup? I'm pretty sure most of you have figured out how to do this reasonably well by now. To do this problem systematically is EXTREMELY difficult. I'll simplify the problem slightly and boil the problem down to two varibles: The height of water in the cup (we'll say % full), and the tilt on the pitcher (an angle between 0 and 180). There is ABSOLUTELY no simple, one-line algebraic equation to solve this one. You can't simply say, when the cup is 100% full, put the angle to zero. You have to correct for how much water is out of the pitcher already and is about to fall into the cup (a time delay), and also the time it takes to move the pitcher from say, 20 degrees to 0 degrees (more time delay). Even better, the flow of the water within the pitcher depends not only on the angular position (zeroth derivative), and the rate and acceleration (first and second derivatives), but also the "jerk" of the pitcher (third derivative of angular position). Wow. That's hard.

      To solve this problem analytically, you would need a lot of math. A LOT. In fact, even more than we know today. Using LaPlace transforms and 3rd order differential equation solvers, this can be done, but even the DE solvers are written in trial-and-error form to some extent. If you've read this far, you're probably asking: What exactly am I getting at?

      YOU ALREADY SOLVED THIS PROBLEM! Ever fill up a cup and not spill? Not bad. Basically, your mind (body?) has already found at least some solution to this problem without you knowing it. You have subconciously short-circuited hundreds of PhD's worth of math with a magic black-box of trial and error. Remember when you were a kid? You tilt the pitcher little and tilt it back. Not enough. You do it again. Not enough. You tilt the pitcher until the cup is full. Crap. Spilled it. Note to self: stop before the cup is full.

      So there you have it. Our 'intelligence' has solved math problems than most college graduates could do (even with Maple) to save their lives. If it works, do it again, and if it doesn't work, do something different. That's all our 'intelligence' is.

      I really don't think this whole 'intelligence' thing is a very novel concept at all.
      • YOU ALREADY SOLVED THIS PROBLEM!

        no I didn't. The problem you described was to pour water with mathematically perfect precision. When I pour it's not perfect. If my brain really did all that math you described I would never spill a drop and I could confidently fill glass after glass with the same exact amount of water from the same pitcher.

        Nope, thats not what my brain does. The "black box of trial and error" solves the problem with enough precision to be practical and that's where it stops. For all intents

    • It is far easier for us to create true intelligence from scratch within a software simulation than in wetware. We can literally run millions of generations of evolution very quickly there, and have very fine-grained control over the natural selection process. If we managed to create intelligence, the first place we'll create it will be in software. We might move on to apply the techniques to wetware and let it evolve a little slower in a little more natural environment, but probably by then SkyNet will a
      • but probably by then SkyNet will already have enslaved us all

        Oh come on, as a California resident, we've seriously mitigated this risk by electing as Governor Humanity's protector from Terminator 2 and 3...

    • "Life, I suspect, is fairly commonplace. I have no idea if intelligence is."

      Of course we have an idea if intelligent life is common place out side of our solar system and the answer is: it is not. If it were very common then we would have likely picked up a signal by now if they were within a few hundred light years.

      Why isn't it common place? There are many possible answers, one of them which I think is that it is much easier to destroy then create so any intelligent civilization eventually reaches the poin
      • it is not. If it were very common then we would have likely picked up a signal by now if they were within a few hundred light years.

        First of all you should remember that you can't use the absence of evidence to disprove something (only to show that it may be less likely). Second, you hit it right on the head when you said "we would have likely picked up a signal.

        Whether we're going to pick up a signal depends on a lot of factors. For example: how common is common? the universe is a *big* place, even if t
    • by Hado ( 923277 )
      First, define intelligence for me. I dare say there is not much more to our own supposed intelligence than can be accomplished with programming. Of course, I do not mean the rule based AI-like systems used for instance in games and most industrial applications. I mean self organising and/or learning systems powered with algorithms like Reinforcement Learning [ualberta.ca] and/or Neural Networks [stir.ac.uk]. I have myself programmed such algorithms to find solutions on tasks I would have never been able to find. Usually these tasks a
  • by inode_buddha ( 576844 ) on Sunday October 23, 2005 @11:47PM (#13861589) Journal
    Well. that's one way to get a life.
  • by account_deleted ( 4530225 ) on Sunday October 23, 2005 @11:53PM (#13861614)
    Comment removed based on user account deletion
  • by commodoresloat ( 172735 ) on Sunday October 23, 2005 @11:58PM (#13861638)
    We have the opportunity to create life and the first thing these guys think of making is a freakin' bug?? Like there aren't enough annoying insects on this miserable planet -- we need science to develop new roaches, new fruit flies, new mosquitos so we can spend our time swatting at them and invest our money in new poison products to kill them.

    Freakin scientists. Go cure cancer or something, will ya?!

  • We've known for a long time that extremophiles (organisms capable of surviving in extreme conditions, often incapable of surviving under human-friendly conditions) exist, and speculated that such life is the kind we'd find on other planets. However, this type of thinking (not necessarily PNA life; I think the slower diffusion inherent to fatty acids relative to water will mean that this new life-form is only useful as a test) allows us to produce extremophiles more exotic than what we see on Earth. All know
  • by autopr0n ( 534291 ) on Monday October 24, 2005 @12:00AM (#13861649) Homepage Journal
    Some people think that before DNA evolved, everything was done with RNA. Both hereditary information and the physical catalysts. Like proteins, RNA molecules can fold up into odd shapes and perform catalytic reactions. The only difference is that Protein based system work faster. The Ribosome, which converts RNA into Proteins is actually made from RNA, rather then proteins, and is almost exactly the same in all life.
  • by N8F8 ( 4562 ) on Monday October 24, 2005 @12:00AM (#13861650)
    Maybe it was a dream but I remember taking the tram ride for a few minutes into a secret lab where an experiment had gone horribly, horribly wrong.
  • Some people have already made comments about intelligent design here, but I thought I should add something. This week I was approached by a creationist/intelligent-design group on campus and they talked a bit about their ideas. One of the main things they mentioned is how unlikely it was that cells could have evolved out of random chemicals. To them, cells are far too complex to have been anything but a conscious creation, and they dispute that such a thing could have evolved out of less complex parts.

    While
    • Simple - the first life wasn't a cell. It was a bit of DNA or RNA floating in a sea rich in organic chemicals. Eventually the bits of what we'd call genes which created proteins that formed a crude shell were more likely to survive (some insulation against changing conditions). Then this little viruslike thingy got in and started making ATP and the cell ended up using that for fuel; The virus-thingy became a mitochondria. Then these simple cells competed and started adding dongles to help them compete. And
      • Time is a factor (Score:3, Insightful)

        by WindBourne ( 631190 )
        The fact that it took about the planets lifetime to form the first cells (BILLIONS of years) smacks of evolution rather than creationism. or did god simply take billions of years to think that he might like life here?
    • by Vellmont ( 569020 ) on Monday October 24, 2005 @12:42AM (#13861809) Homepage

      While I am not a creationist, I did see the point of their argument - how simple amino acids and organic chemicals were first formed into cells, I have no idea.

      I think this is an important question in biology, and I'm sure no biologist would deny it. The problem comes when the creationists merely assume god must have done anything we can't explain. It's the "god in the gaps" argument that's been popular probbably since we first learned to communicate. The problem of course is that science marches on and when you try to find your god in the gaps of science, science eventually closes those gaps. Religion always fights like mad because they've invested much of their belief structure in the argument. The gaps used to be in evolution. Those gaps have closed and now the gaps have moved to the creation of life itself.

      The point that people like you were talking to seem to miss is that assuming the existence of a god to explain current lack of scientific understanding of scientific questions has always been a losing proposition. Where religion always fails is when it gets mixed up with scientific questions. Science adapts, and religion tries to cling to dogma. Religion changes too perhaps.. no one is seriously pissed off about heliocentrism anymore, it just takes about 100 times longer.
    • You really need to look no further than the virus. It is little more than a small bit of DNA or RNA and a protective coating. They generally are parasites on cells since they don't have some of the machinery to reproduce on their own, but as you can tell from the epidemics and pandemics they cause they are a quite successful form of life at its most elemental level.

      One things people who fall for intelligent design refuse to appreciate is that life has had hundreds of millions of years to evolve and perfec

      • You really need to look no further than the virus. It is little more than a small bit of DNA or RNA and a protective coating. They generally are parasites on cells since they don't have some of the machinery to reproduce on their own, but as you can tell from the epidemics and pandemics they cause they are a quite successful form of life at its most elemental level.

        Viruses aren't usually defined as being alive. This is because they don't have any mechanism to reproduce themselves, but rely upon the host in
    • Eugene Koonin and William Martin just came out with a fascinating paper on the LUCA (Last Universal Common Ancestor). Link to Article on Pubmed [nih.gov]

      In brief: the RNA/DNA/protein worlds evolved at hydrothermal vents in inorganic chambers. At some point, the information molecules sheathed themselves in lipids and sugars, and free-living cells emerged from the vents.

      In response to at least one of your questions: the LUCA to cell transition may have taken 500 million years (primordial soup = 3.5bya, 1st eviden

    • Ok, then obviously talking about cells isn't going to get us anywhere. So let's talk about the analogy that ID makes: the mouse trap.

      The modern mouse trap has four parts. A base, a spring, a crushing wire and a trigger lever. If you take away any of the parts it doesn't work. The ID argument is that it must have been designed as any small change that removed one of these critical components would render the mouse trap ineffective.

      This is a powerful argument, and it is what gets most people suckered into
    • While I am not a creationist, I did see the point of their argument - how simple amino acids and organic chemicals were first formed into cells, I have no idea.

      Maybe so, but it doesn't address the issue of where their creator came from. Unless the creator is inherently less complex than the system it created, you need to explain how this earlier step came into being.

      These people seem to take their existance of their god as a given, not requiring explanation.

  • by clambake ( 37702 ) on Monday October 24, 2005 @12:16AM (#13861710) Homepage
    Just to remind everyone, it's not playing God if you aren't creating life with pure will power alone...
  • About PNA.. (Score:3, Informative)

    by QuantumG ( 50515 ) <qg@biodome.org> on Monday October 24, 2005 @12:34AM (#13861781) Homepage Journal
    peptide nucleic acid [wikipedia.org] apparently. See also this page [horizonpress.com]. Hopefully this research will at least develop new techniques for handling and monitoring chemical systems. As for the religious implications, *yawn*.
  • "So now we've carefully put everything from the checklist in so that we know exactly what's in there and what's not. Next we put the lid o...ah...aaaaah CHHHOOOO!!"

    "Oh shit"
         
  • The researchers believe that the synthetic lives so created will have an enormous practical value

"Pull the trigger and you're garbage." -- Lady Blue

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