Is there any possibility of a general theory which would allow prediction of possible alternate molecular systems capable of reproduction?
We, supramolecular chemists, generally use our 'chemical intuition', which can be supported by simulations (molecular dynamics, DFT). But usually synthesizing the molecules in question and checking what they do is faster than the simulations. Serendipity plays a very important role here. Many replicators discovered in our lab were not designed to replicate; people just observed strange things happening and were smart enough to figure out what was going on.
Thanks for your perspective. Indeed, the lab has points 1 - 3 covered, and has been working on point 4.
Selection (non-random death) isn't strictly needed for evolution, but without it the population will only evolve via drift. Selection definitely makes for a far more interesting evolutionary system.
I think selection should be still possible if death is fully random, but the fitness of the replicators (Addy Pross calls it dynamic kinetic stability - a chemist's perspective) can be still defferent because of different replication rates.
All of this doesn't say anything about the evolvability of the system, how long it will continue to evolve. I suspect the system described in the posted paper to have a limited evolvability, but the researchers don't seem to discuss the topic.
Indeed, it's evolvability is limited. We listed all possible replicators in the paper; there are 7 different compositions possible (13 different structures if you include sequence isomers). However, their mutation rate is quite high and cross-replication events happen quite often. This fits well into the quasispecies concept developed by Manfred Eigen. In our system we have two such sets of replicators where one is a descendant of the other.
Regrettably, it does not depend on me only and the preprint culture is not very common among chemists. I will ask what can be done about that.
AFAIK, the free-view link (https://t.co/wMF2wfbJDr) does not work on mobile systems but desktop browsers supporting HTML5 should be fine. I tested it with Firefox 43.0 and Chrome 47.0.2526.106 on Ubuntu 15.10.
Great to see a fellow chemist here! Yes, reducing agents indeed work as you expect and the group used this approach in other work. But we need to have replication AND destruction working at the same time. An issue that seems quite minor is that oxidation of thiols to disulfides is not 100% perfect. There are some side products (sulfenic and sulfinic acids) which accumulate if you constantly oxidize and reduce the mixture. So instead of recycling my colleagues have been working on supplying the 'food' molecules by flowing their solution into a vial containing replicators and withdrawing replicators 'out'. The first author of the paper (Jan Sadownik) calls it "death by withdrawal";-)
Still, it's not that easy to get everything right.
It's been an ongoing project and we have collaborations with several people (we don't have much experience with programming in our group) so I need to talk with my boss first. I'll contact you when I get the answer, OK?
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?
Yes, we can degrade them (not by cooking but using reducing agents which selectively break sulfur-sulfur bonds in the molecules, reverting them back to food. One of the issues here is that this process has to work simultaneously with self-replication. We (Elio, to be more specific) tried to do that, but it is very difficult to get it right because waste is accumulated in the system and unwanted side products accumulate significantly over several turnovers. Instead, Jan and other colleagues have been studying flowing 'food' in and removing the replicators by flowing the solution out (death mechanism).
But seriously, no 'grey goo' scenario to worry about. These molecules require very specific, synthetic 'food' to replicate. Moreover, their evolution is not open ended; there are just 7 bits of information per one molecule, so it can't just mutate into whatever it wants. It still needs a lot of effort to make something that could grow outside lab settings.
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.
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:
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.
It might not get millions of viewers, but I still enjoy factorio, dwarf fortress, and EU4 streams.
I also play and watch EU4 from time to time. And it can be a really slow game. But it's up to the player to make it enjoyable to watch. Nothing beats a 5 min long deliberations which idea group goes next and why, while the game itself sits paused.
The main problem with the current model of scientific publishing is that every publisher is effectively a monopolist. Because scientists can't publish the same results twice (it's unethical), each piece of scientific advancement is held by one journal published by one publisher. Therefore, university libraries don't have a choice and have to get subscription to all reputable journals. It's not surprising that a bunch of monopolistic publishers can charge excruciating fees. The most prestigious journals like Nature or Science can sell a small number of papers for exorbitant fees, knowing that everyone will subscribe anyways, and then use that money for god knows what: Philip Campbell, editor-in-chief of Nature, estimates his journal's internal costs at £20,000–30,000 ($30,000–40,000) per paper.
On the other hand, open access publishing brings more free market into the system. A scientist can decide which journal to choose (based on the licence, prestige, reviewing time, target group, etc) and how much money to pay for it. Thus, publishers will have to compete for scientists' money, which should bring down the costs of open access publishing.
Your statistics is broken. You assumed that $120 trillion is equally distributed among the top 70 million. The distribution of wealth among the top 1% is also uneven. Which means that the poorest of the top 1% has significantly less than your $1,714,285.
Nobody argues about obsolescence of physical journals. But even in electronic format they provide the added value: they curate the most valuable content. Nobody has time to check (not even read) thousands of papers in their discipline. As the most selective journals generally publish the most innovative work, I can keep up to date by just checking ~10 RSS feeds.
How else would you identify majority of the most important advances in the field? I agree, the system is far from perfect, many great papers get published in lower-tier journals because the reviewers don't see their significance, but do we have anything better than peer-review?
The authors call them "micromotors". And that's perfectly justified; they have autonomous propulsion, but it's quite random. It's more or less like a car without a driver, just moves here and there randomly and gets stuck in a wall if it hits one. And that's how the delivery works in the paper; it's not directed at all.
It will be insanely difficult to make active micro/nanobots which can be programmed or controlled in real time. It's just like making a living cell, inventing new biology.
It will be way easier to create micro/nanoparticles which have some recognition units on their surface and attach/penetrate specific cells or tissues and then release their cargo. In fact there's been lot of progress in that field in recent years (nanoparticles conjugated with antibodies and stuff like that). But that is still a diffusion-based delivery. When it comes to active delivery, I guess the easiest way to "drive" them inside a human body is by magnetism (using magnetite nanoparticles).
The main cause of scientific publishers charging excessive fees is their monopoly. While there are many different scientific publishers, a reader is usually interested in specific articles he cannot find elsewhere (publishing same results in more than one journal is nothing more than plagiarism). This puts university librarians into a weak position since they have to provide access to basically almost all journals publishing useful papers.
With open access publishing, sooner or later we should get some healthy competition. Scientists will be the ones who pay and will have a choice where to publish. Probably journals with high impact factors (yeah, I know...) will be in a comfortable position to charge more. There's not much competition yet (scientists generally don't care/understand that OA=higher visibility) so we will have to wait for lower prices till most articles in major journals become open.
Slashdot Mirror
What characteristics in a molecular system are required for it to be capable of reproduction?
I suggest a review on self-replicating chemical systems written by a pioneer of the field, Gunter von Kiedrowsky: http://www.arkat-usa.org/get-f...
What characteristics does this system have in common with DNA/RNA/Proteins(DRP)?
What's different from DRP?
If the article seems too complicated, you can watch a short video describing our research on self-replicators.
Is there any possibility of a general theory which would allow prediction of possible alternate molecular systems capable of reproduction?
We, supramolecular chemists, generally use our 'chemical intuition', which can be supported by simulations (molecular dynamics, DFT). But usually synthesizing the molecules in question and checking what they do is faster than the simulations. Serendipity plays a very important role here. Many replicators discovered in our lab were not designed to replicate; people just observed strange things happening and were smart enough to figure out what was going on.
Selection (non-random death) isn't strictly needed for evolution, but without it the population will only evolve via drift. Selection definitely makes for a far more interesting evolutionary system.
I think selection should be still possible if death is fully random, but the fitness of the replicators (Addy Pross calls it dynamic kinetic stability - a chemist's perspective) can be still defferent because of different replication rates.
All of this doesn't say anything about the evolvability of the system, how long it will continue to evolve. I suspect the system described in the posted paper to have a limited evolvability, but the researchers don't seem to discuss the topic.
Indeed, it's evolvability is limited. We listed all possible replicators in the paper; there are 7 different compositions possible (13 different structures if you include sequence isomers). However, their mutation rate is quite high and cross-replication events happen quite often. This fits well into the quasispecies concept developed by Manfred Eigen. In our system we have two such sets of replicators where one is a descendant of the other.
Regrettably, it does not depend on me only and the preprint culture is not very common among chemists. I will ask what can be done about that.
AFAIK, the free-view link (https://t.co/wMF2wfbJDr) does not work on mobile systems but desktop browsers supporting HTML5 should be fine. I tested it with Firefox 43.0 and Chrome 47.0.2526.106 on Ubuntu 15.10.
Great to see a fellow chemist here! Yes, reducing agents indeed work as you expect and the group used this approach in other work. But we need to have replication AND destruction working at the same time. An issue that seems quite minor is that oxidation of thiols to disulfides is not 100% perfect. There are some side products (sulfenic and sulfinic acids) which accumulate if you constantly oxidize and reduce the mixture. So instead of recycling my colleagues have been working on supplying the 'food' molecules by flowing their solution into a vial containing replicators and withdrawing replicators 'out'. The first author of the paper (Jan Sadownik) calls it "death by withdrawal" ;-)
Still, it's not that easy to get everything right.
It's been an ongoing project and we have collaborations with several people (we don't have much experience with programming in our group) so I need to talk with my boss first. I'll contact you when I get the answer, OK?
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?
Yes, we can degrade them (not by cooking but using reducing agents which selectively break sulfur-sulfur bonds in the molecules, reverting them back to food. One of the issues here is that this process has to work simultaneously with self-replication. We (Elio, to be more specific) tried to do that, but it is very difficult to get it right because waste is accumulated in the system and unwanted side products accumulate significantly over several turnovers. Instead, Jan and other colleagues have been studying flowing 'food' in and removing the replicators by flowing the solution out (death mechanism).
Bwahahahaha!
But seriously, no 'grey goo' scenario to worry about. These molecules require very specific, synthetic 'food' to replicate. Moreover, their evolution is not open ended; there are just 7 bits of information per one molecule, so it can't just mutate into whatever it wants. It still needs a lot of effort to make something that could grow outside lab settings.
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.
It's a proprietary reader but it works for onFirefox and Google Chrome for Ubuntu.
Thanks, Barryke.
Unfortunately, paywalling is a common problem with scientific publishing. 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. This link should work: https://t.co/wMF2wfbJDr
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:
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.
It might not get millions of viewers, but I still enjoy factorio, dwarf fortress, and EU4 streams.
I also play and watch EU4 from time to time. And it can be a really slow game. But it's up to the player to make it enjoyable to watch. Nothing beats a 5 min long deliberations which idea group goes next and why, while the game itself sits paused.
There is a gossip that #icanhazpdf works better than torrent for scientific articles ;-)
The main problem with the current model of scientific publishing is that every publisher is effectively a monopolist. Because scientists can't publish the same results twice (it's unethical), each piece of scientific advancement is held by one journal published by one publisher. Therefore, university libraries don't have a choice and have to get subscription to all reputable journals. It's not surprising that a bunch of monopolistic publishers can charge excruciating fees. The most prestigious journals like Nature or Science can sell a small number of papers for exorbitant fees, knowing that everyone will subscribe anyways, and then use that money for god knows what: Philip Campbell, editor-in-chief of Nature, estimates his journal's internal costs at £20,000–30,000 ($30,000–40,000) per paper.
On the other hand, open access publishing brings more free market into the system. A scientist can decide which journal to choose (based on the licence, prestige, reviewing time, target group, etc) and how much money to pay for it. Thus, publishers will have to compete for scientists' money, which should bring down the costs of open access publishing.
Your statistics is broken. You assumed that $120 trillion is equally distributed among the top 70 million. The distribution of wealth among the top 1% is also uneven. Which means that the poorest of the top 1% has significantly less than your $1,714,285.
Nobody argues about obsolescence of physical journals. But even in electronic format they provide the added value: they curate the most valuable content. Nobody has time to check (not even read) thousands of papers in their discipline. As the most selective journals generally publish the most innovative work, I can keep up to date by just checking ~10 RSS feeds.
How else would you identify majority of the most important advances in the field? I agree, the system is far from perfect, many great papers get published in lower-tier journals because the reviewers don't see their significance, but do we have anything better than peer-review?
The authors call them "micromotors". And that's perfectly justified; they have autonomous propulsion, but it's quite random. It's more or less like a car without a driver, just moves here and there randomly and gets stuck in a wall if it hits one. And that's how the delivery works in the paper; it's not directed at all.
It will be insanely difficult to make active micro/nanobots which can be programmed or controlled in real time. It's just like making a living cell, inventing new biology. It will be way easier to create micro/nanoparticles which have some recognition units on their surface and attach/penetrate specific cells or tissues and then release their cargo. In fact there's been lot of progress in that field in recent years (nanoparticles conjugated with antibodies and stuff like that). But that is still a diffusion-based delivery. When it comes to active delivery, I guess the easiest way to "drive" them inside a human body is by magnetism (using magnetite nanoparticles).
The main cause of scientific publishers charging excessive fees is their monopoly. While there are many different scientific publishers, a reader is usually interested in specific articles he cannot find elsewhere (publishing same results in more than one journal is nothing more than plagiarism). This puts university librarians into a weak position since they have to provide access to basically almost all journals publishing useful papers.
With open access publishing, sooner or later we should get some healthy competition. Scientists will be the ones who pay and will have a choice where to publish. Probably journals with high impact factors (yeah, I know...) will be in a comfortable position to charge more. There's not much competition yet (scientists generally don't care/understand that OA=higher visibility) so we will have to wait for lower prices till most articles in major journals become open.