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Science

Chemical Evolution of Self-Replicating Molecules Observed In a Lab (nature.com) 172

Posted by Soulskill from the genesis-is-planet-forbidden dept.
New submitter n0w4k writes: Researchers at the University of Groningen have developed a self-replicating system able to not only pass hereditary information from one generation to another, but also mutate (non-paywalled link to the paper). It is a crucial step towards Darwinian evolution of abiotic species and artificial life. According to the authors and perhaps somewhat counterintuitively, in order to fully reach this goal, a death mechanism needs to be implemented in the system. Otherwise new species can only form but not disappear.

Self-replicating chemical systems have been widely studied before; some were even able to mutate. However, this discovery provides the first example of mutating replicators which are fully artificial.

Full disclosure: I am one of the co-authors; you can ask me if you have some specific questions or suggestions — maybe they can be implemented in the lab!
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Chemical Evolution of Self-Replicating Molecules Observed In a Lab More

Chemical Evolution of Self-Replicating Molecules Observed In a Lab

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  • Obligatory (Score:1, Troll)

    by Dunbal ( 464142 ) *
    Where is your god now?

    • Re:Obligatory (Score:5, Funny)

      by Viol8 ( 599362 ) on Wednesday January 06, 2016 @09:50AM (#51248213) Homepage

      I don't know where God is , but I do know the Devil is in the details with this sort of thing.

    • Where is your god now?

      Down at the 7-11, enjoying a Big Gulp

    • Where is your god now?

      In a maze of twisty little passages, all alike.

    • Obviously, if we're created in God's image then it is only natural that we'd be both inclined to and able to "play God".

      However, I think the consensus among Christians is that while we're made in God's image we should in no way act in a Godlike (or was that Godly) manner, particularly when it comes to morality or ability.

  • Movie plot? (Score:5, Funny)

    by Dawn Keyhotie ( 3145 ) on Wednesday January 06, 2016 @09:51AM (#51248219)

    I would ask you to please don't let it get out of the lab.

    You will probably reply: Bwahahahaha!

  • Congratulations on your success n0w4k! I'm reading the article now.
    • All I'm seeing after clicking on the "non-paywalled link" is a page with a spinner icon near the middle and the text "Loading Enhanced PDF..." at the bottom. I'm using the latest version of the Chromium browser packaged for Debian GNU/Linux. It would be nice if there's a pre-print version available at the usual source.

    • Yes, nice article - now that we're more or less back on topic.

      One question. If I understand the first few paragraphs (unlikely) then the major difference between your system and the quasi species model is that your system does not have a death mechanism (no, I'm not going there). But these are aormatic cyclic molecules that I would not think would be particularly stable. Would not just random degradation of the replicators imply death to the 'organism' or would that just be like cooking your hamburger?

  • Counterintuitively? (Score:3)

    by Pegasus ( 13291 ) on Wednesday January 06, 2016 @10:10AM (#51248393) Homepage

    I don't get it... To me death is an obvious part of the life cycle, which is the base for evolution. What way of thinking can bring you to the point where you think evolution is possible without death?

    • Re:Counterintuitively? (Score:4, Insightful)

      by Teun ( 17872 ) on Wednesday January 06, 2016 @10:36AM (#51248615)
      I can think of evolution without programmed self-destruction.
      For example, you can have death of the original caused by the evolved next generation.

    • Re:Counterintuitively? (Score:5, Interesting)

      by n0w4k ( 3643913 ) on Wednesday January 06, 2016 @10:48AM (#51248719)
      To me it's also obvious, but judging from the conversations with colleagues in the field (who are chemists, not evolutionary biologists), destruction of replicators is generally neglected. The challenge has been to just make molecules which can replicate and it is even more difficult to make them evolve because you need at least one bit of information that can assume 0 or 1 state, translated into chemical structures. Such error-prone replication process is enough to generate diversity of replicators but without extinction, the only selection pressure is on the replication efficiency and not survival.

      The idea of reducing with Darwinian evolution to chemical kinetics (replication and destruction of replicators) has been nicely outlined by Addy Pross, who introduced the concept of dynamic kinetic stability [jsystchem.com]:

      dX/dt = kMX - gX,
      where X is the concentration of the replicator, M is the concentration of 'food' and k and g are the rate constants (efficiencies) for the replication and destruction processes.

      So far we only got the first part of the equation and colleagues from the lab got some promising results implementing the second part.

      • Re: (Score:2)

        by hawkfish ( 8978 )

        To me it's also obvious, but judging from the conversations with colleagues in the field (who are chemists, not evolutionary biologists), destruction of replicators is generally neglected. The challenge has been to just make molecules which can replicate and it is even more difficult to make them evolve because you need at least one bit of information that can assume 0 or 1 state, translated into chemical structures. Such error-prone replication process is enough to generate diversity of replicators but without extinction, the only selection pressure is on the replication efficiency and not survival.

        This has also been brought up as a critique of cosmological natural selection.

      • In optimization theory another way to look at diversification and death is the trade in algorithms between exploitation and exploration of a potential surface for local minima. Consider the 3-armed bandit problem where one of the slot machines has a better payoff ratio and one has a worse. Your initial search of a few pulls gives you a crude guess about which is the best and if you are right then it's a waste of resources to pull the lesser bandit arms in the name of exploring further. You should exploit

        • In optimization theory

          ... what follows may or may not be true. However, Nowak and colleagues are chemists at the bench and find it very difficult to simultaneously have reducing conditions in their bucket ("reaction vessel") to promote separation of their macromolecules into monomers ("food") and to have oxidising conditions to promote assembly of monomers into macromolecules under the influence of the existing macromolecules.

          This is an operational constraint, not a theoretical one.

          In a practical system,

    • I'm really not sure why the submitter decided to describe it as counterintuitive, but I did find it interesting that, technically, it may be possible to have a form of proto-life that evolves by mutating during replication and does not die. But if that happens, evolution ends as soon as all available space is taken up. It kind of makes me wonder whether it's possible that there are dead-end planets in the universe where that did, indeed happen. And what the odds would then be of that sort of life startin

      • Bacteria are effectively immortal; in that they just divide and divide and divide.

        That being said, as environmental pressures increase, one would assume that self-replicating units of this nature would soon evolve the ability to gain nutrients from its neighboring proto-life, and you now have a predator-prey situation. Being eaten or being killed by some eternal factor is how bacteria and archaea die. You're applying a concept that mainly applies to multicellular organisms.

        • Bacteria are effectively immortal;

          No they're not. They reproduce, but with a non-zero copying error rate. After separation, the two daughter bacteria from a single parent bacterium are different from each other, and both from their parent. They might be the three most closely related organisms on the planet (even if one of them no longer exists, except as a recorded genome), but the odds are high that none of the genomes will be identical.

          In computing, we like to think that the error rate on digital copyin

      • Chemical reactions like that need some form of energy input, and likely some chemical input. Self-replication will require an environment with the necessary parts (atoms or smaller molecules) available. Deprive the reaction of these, and it can't continue. The molecules might be fine still, and so no more dead than they were while breeding, but they're going to look awful dead, even if they will spring right back into operation with the correct inputs. (That is not dead which can eternal lie / And with

        • Which is why, in their model system, they add monomers ("food") and remove macromolecules ("organisms").

          A real world system would be in an environment which did this. Here the chemists have to put their baby to the tit, and wipe it's arse. You could say, they're taking "baby steps".

    • Because evolution technically doesn't require death to continue to create new species, it just means without a death mechanism the planet would be awfully crowded, and at a very base level you could say that evolution has failed, because the less "fit" species don't die out, and could continue to breed. Evolution doesn't require death at all to function, it just becomes much more transparent with death. Look at it this way. Species A develops a beneficial trait that lets them eat food others can, giving

    • Re: (Score:3)

      by ediron2 ( 246908 )

      Sorry, but you've hit 3 problems.

      First, your definition is twice flawed. It infers that your definition is correct without proof. And your definition requires death, when evolution is a process of transition of traits in organisms. Death is a coincidence, but neither causal nor integral to that transition.

      Your question is equally flawed: questioning research only because the research focuses on a stage, because it doesn't include all stages.

      Last item first: when we study something, science allows focusing

    • Re: (Score:2)

      by Tablizer ( 95088 )

      To me death is an obvious part of the life cycle, which is the base for evolution

      I wouldn't say death is a prerequisite. "Competition for quantity" may be effective in driving evolution also. Those variations that are the most common will be the more efficient or prolific replicators, and that's why they are more common.

      Mutations that produce faster replicators will be more common, creating a feedback mechanism to "reward" them, where the reward is quantity of existence rather than mere survival.

      If you have

    • What way of thinking can bring you to the point where you think evolution is possible without death?

      Humanity's entire success is based on us figuring out how to do just that. Our behaviour has an instinctual aspect but is mostly dictated by surrounding society, and can be "updated" within our lifetime. Death became obsolete as soon as nature invented evolutionary Turing machines. We can only hope it'll become nonexistent, too.

  • n0w4k, first of all: congrats to you and your co-authors on this brilliant achievement ! Second: have you guys thought of the minimal amount of information necessary to represent each of the "elements" (or, as I'd rather say, "individuals") of your system ? I am very bad at chemistry, but not that bad as a programmer ;-) I'd actually love to try and replicate your experiment with pure information. Of course, this is only an idea. One would prolly also need to (en)code the system's environment...

    • This has already been done in many different ways within computer science. Genetic Algorithms is a technique in Artificial Intelligence that has been solving problems in production settings for decades now.

      • Of course, but an accurate digital simulation of the chemical experiment might be interesting to try variations on the chemistry without having to synthesize it.

        What I wonder is how much soup they are cooking, digital simulations - even on machines with 128GB of RAM tend to be pretty limited in their quantity of elements simulated. 100GB of RAM might simulate a couple of drops full of replicating chemicals.

        In the digital simulations I've done, fragmentation of the world into varying environments seemed to

    • Re: (Score:2)

      by n0w4k ( 3643913 )
      Thanks vikingpower!
      Yes, we thought of that and we have been collaborating with physicists/programmers who are interested in chemical kinetics from the origins of life perspective. And the simplified model of our system is based on exactly what you suggested: A and B elements interacting with each other with different strength. We hope that the model can guide further experiments and help us to properly set the conditions to incorporate the 'death' mechanism.

  • First of all n0w4k, congratulations to you and your team on your work at Groningen.
    Every day, there's a lot of tech news, but this is what i consider truly nextgen science. It stands out.

    Second, i clicked the link. I expected to find something insightful to read, but apparently its paywalled.
    http://www.nature.com/nchem/jo... [nature.com]
    This paywall is something i do not understand. So my first question now is, who descided this to be paywalled, and why? Where does the PDF money go?

    • Nature is a for profit magazine. You need to subscribe to it to get the content. The PDF money goes to the publisher. However there is a non-paywall link in the Slashdot summary. I'm not seeing the problem here.

    • Re: (Score:2)

      by n0w4k ( 3643913 )
      Thanks, Barryke.

      Unfortunately, paywalling is a common problem with scientific publishing [slashdot.org]. Making it open access would cost us a few thousand euros and that money is spent better on doing research. Fortunately Nature journals provide a way to share articles freely on the internet [slashdot.org]. This link should work: https://t.co/wMF2wfbJDr [t.co]

      • Might ve a temporary problem, but right now your paywall-free link in the sunmary goes to a nature paywall asking for $22, and your other twitter link goes to a "nature is broken right now, we will charge you later" page. Shame as your article sounds interesting, any chance of putting the pre-submission draft on Arxiv?

      • The issue that smallfries reports seems to have gone away. I could read the "ReadCube"-ed version of the paper.

        Not your problem I know, but the fact that I can't save a PDF of the paper is vastly annoying. I do actually like to go back and think over these things when I'm at work and don't have internet access. It's hugely insulting that Macmillan (IIRC, the international publishing house that own Nature) take the results of publicly-funded research and paywall it. At least in astrophysics, Arxiv has long

  • death system required? (Score:1)

    by Anonymous Coward

    How can a death system be required, when you can have the later generations feed off of the previous generations.

    So they don't die. they just get re-used by the offspring...

  • Eerily similiar, a self replicating and mutating system without DNA or RNA. Only like the Omega Man, man made. Yet in both stories it runs amok escaping the scientists lab.
  • And all this fancy DNA and proteins that we see nowadays are the result of long evolution, starting from something much more simple.
  • Apparently these guys were too busy creating replicators to have watched Stargate SG1, because if they had they'd know that creating replicators was a seriously bad idea; now the sons-of-bitches have doomed us all.
  • $32 per copy otherwise. If you want free suggestions then provide a free readable piece.

  • I know exactly what would happen if I sent this link to my father, who is a creationist. He would tell me that it doesn’t prove anything. When I was a kid (and didn’t know enough to see through his poor logic), he addressed the issue of “what if scientists created new life in a lab.” He explained that having intelligent people spend millions of dollars to design a new life form is not the same as it happening by accident in nature. Of course he’s right, technically. We sti

    • a lot of the vehement creationists I have known are various kinds of protestant fundamentalists who are also rather anti-catholic

      Not untrue, but there are also a LOT of Muslims who don't consider themselves to be particularly "fundamentalist" (for different "Fundamentals" to the Protestant Fundies [wikipedia.org]) , but who are profoundly creationist and if prodded would automatically leap to a YEC stance.

      When I was working in Turkey a few months ago, my Turkish fellow geologists described even more pronounced difficulty

  • There are some strange, broken header pages which curiously enough do not link directly to the actual details. Here is the proper page:

    http://www.nature.com.sci-hub.io/nchem/journal/vaop/ncurrent/full/nchem.2419.html

    • That redirects through something that makes the framework appear in Russian (well, a Cyrillic script anyway).

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