4 ms·

I disagree. Things bump into each other randomly but that is it. An enzyme conformational changes are anything but random. And the thing can work at the speed o

I disagree. Things bump into each other randomly but that is it. An enzyme conformational changes are anything but random. And the thing can work at the speed of a thousand molecules per second. That is not slow and I guarantee you an engineered nanomachine is nowhere near that speed. Get down to the molecular level and biology is at the machine phase.

adastra22 3y ago
Biology is not machine phase at any level. Machine phase means directed motion, often carried out in vacuum by parts highly constrained to follow rigid paths. Like a factory. That does not describe biology. The kind of systems described in Drexler’s Nanosystems would comfortably operate at gigahertz speeds. So yes, a few thousand reactions per second is sloooooow.
- tomohelix 3y ago
  >directed motion, often carried out in vacuum by parts highly constrained to follow rigid paths. Like a factory That sounds exactly like biology to me. That is how any enzyme operate. Why do you think it isn't? How else do they literally pluck an electron from a molecule and move it to another molecule at precise atomic positions? How else does biology reliably produce polymers with polydispersity of 1 if it isn't controlled by highly directed parts? Regarding the speed, I would like some clarification. In my field, when I mention an "operation", it means the machine has to work on a physical object, process it, and output a product different from the output. These are often molecules like drugs or some chemicals. So when you mentioned Ghz operation speed, are you talking about a current nanotech that can actually produce billions of products per second? Or did you mean it just vibrate or have some repeated motion? I am interested to know that. Here is an enzyme with 2Mhz operation speed whose parts are just exactly one atom: https://en.wikipedia.org/wiki/Catalase https://en.wikipedia.org/wiki/Catalase And for a more apple to apple comparison, the fastest moving nanomachine I know moves at around 100nm/minute https://www.advancedsciencenews.com/new-dna-origami-motor-breaks-speed-record-for-nano-machines/ https://www.advancedsciencenews.com/new-dna-origami-motor-br... Compared to a kinesin, which isn't the fastest protein, it is over 800nm/*second* http://book.bionumbers.org/how-fast-do-molecular-motors-move-on-cytoskeletal-filaments/ http://book.bionumbers.org/how-fast-do-molecular-motors-move...
  - adastra22 3y ago
    Yes, gigahertz operation speeds. This is a straightforward result from mechanical scaling laws. A machine scaled down by 1/10th in each linear dimension is able to operate at 10x speed. So a machine operating at 10Hz in ~1m regime (perfectly reasonable in an industrial setting) will be able to operate at 1GHz speeds when scaled down to be ~10nm in size. Biology operates by means of Brownian motion. Enzymes randomly jiggle around as they are bombarded in solution, until by totally random chance one of the reactants they catalyze hits in the right spot and sticks, then waits until the other reactant hits the other spot. This can take a very, very long time to happen. Animations you might watch showing their operation are lies: they show reactants sliding into place, reactions happening, and products being ejected. This is not what happens. If you actually watched a molecular dynamics simulation of a typical enzymatic reaction, and slowed it down just enough that you could see molecules moving around, it would take YEARS to watch typical reactions happen. For the fastest reactions, the ones you mention, maybe weeks or months. Biology works by molecules just randomly jostling around, sometimes moving forward and sometimes moving backward, but a small set of one-way reactions driving things forward over extended time. Kinesin, for example, has no process that drives its motion forward. It relies on random jostling to move its "feet" into the next position, at which point it can react with ATP to prevent being moved back. But only if an ATP molecule happens to be there, otherwise it gets jostled out of place again. Your 800nm/s speed is a random-walk average. Machine phase chemistry, on the other hand, is like the assembly line of a fully-automated factory. Parts can, in principle, move at up to the speed of sound--thousands of meters per second in typical gemstone materials. But to minimize friction and heat dissipation requirements, actual speeds will probably be in the mm/s or cm/s range. Reactants are attached to machinery that moves them into position at >GHz operational speeds, and each reaction happens as directed according to a preprogrammed sequence of events. This is a rather dated video that shows the idea: https://www.youtube.com/watch?v=zqyZ9bFl_qg https://www.youtube.com/watch?v=zqyZ9bFl_qg
    - tomohelix 3y ago
      Please give me an actual example, not a 17 years old video of a theoretical assembler that is still not a reality yet. From what I know, all of this is purely science fiction and worth nothing. Although to be honest, there are indeed molecular assemblers already, except they are biological... From what I read in your post, I must ask: what is your credential in this field and are you discussing this with good faith? It seems you have a very basic understanding of the mechanisms going on at the molecular level if you think enzyme is just about things randomly bumping into each other. Also, your description of kinesin mechanism is completely wrong. Kinesin doesn't move backward without ATP. It doesn't move at all without ATP. And it moves in one direction only unless its substrate was modified or external forces applied to it. Calling it random walk is ignorant at best and dishonest at worst. >This is not what happens. If you actually watched a molecular dynamics simulation of a typical enzymatic reaction, and slowed it down just enough that you could see molecules moving around, it would take YEARS There are so many things wrong with your claim. First, the same binding based on Brownian motion would happen regardless of a biological or synthetic nano assembler. All of them requires the substrates to reach them first before they can proceed to the next step and this depends on the kinetics of the reaction. Thermodynamic doesn't care if you are a polymerase or a tube of graphene. DeltaG is all that matters. But an enzyme can have specific interfacial and hydrophobic interactions built into its structure that promote binding and increase the distance it can "grab" another molecule. An enzyme is a catalyst that lower the activation barrier. A regular reaction, which may take a day to proceed based on random chance a molecule gets a quantum fluctuation in its energy state to overcome the barrier, would get over it in an instant with an enzyme. It positions and moves the atoms around such that the reaction becomes much more favorable. That is the whole point of catalysts. An enzyme conformational changes are deliberate and extremely precise. I have said this multiple times but you keep ignoring them. Please look up the word if you don't know what conformational mean. These happens extremely fast, at femtosecond timescale, at the length scale of a few angstroms. https://pubs.rsc.org/en/content/articlehtml/2018/cc/c8cc02426j https://pubs.rsc.org/en/content/articlehtml/2018/cc/c8cc0242... I didn't go too much into this because we in the catalysis field work with turnover events, which is the operation definition I gave you above. Going down to the elementary reactions is often too fast and difficult to work with. You literally can't do MD at the precision required to model some of the enzyme conformational changes. And what do you mean by slow them down and weeks and months? If I slow any video down they will take longer to play. What matter is how long does it take in realtime. I gave you a Mhz speed enzyme. That is its real speed. It literally processes a million molecules per second by ripping out a single atom on each molecule. What do you mean by weeks and months? How are you alive if reactions take weeks to run in your body? In fact, please show me a Ghz synthetic assembler that can do the same to a molecule. I am ignorant of any but it has been some time since I was last involved with this type of research. Honestly, I tried to give you some benefits of the doubt. But after typing all this out I afraid you and I are not talking on the same level here. So here is a simple ask: give me a real, proper, actually proven, example of a Ghz synthetic nanoassembler, a nanomachine that actually take a molecule and move it somewhere, the same way an enzyme works. No "theoretical videos" or baseless claims.

adastra22 3y ago

Biology is not machine phase at any level. Machine phase means directed motion, often carried out in vacuum by parts highly constrained to follow rigid paths. Like a factory. That does not describe biology. The kind of systems described in Drexler’s Nanosystems would comfortably operate at gigahertz speeds. So yes, a few thousand reactions per second is sloooooow.

tomohelix 3y ago
>directed motion, often carried out in vacuum by parts highly constrained to follow rigid paths. Like a factory That sounds exactly like biology to me. That is how any enzyme operate. Why do you think it isn't? How else do they literally pluck an electron from a molecule and move it to another molecule at precise atomic positions? How else does biology reliably produce polymers with polydispersity of 1 if it isn't controlled by highly directed parts? Regarding the speed, I would like some clarification. In my field, when I mention an "operation", it means the machine has to work on a physical object, process it, and output a product different from the output. These are often molecules like drugs or some chemicals. So when you mentioned Ghz operation speed, are you talking about a current nanotech that can actually produce billions of products per second? Or did you mean it just vibrate or have some repeated motion? I am interested to know that. Here is an enzyme with 2Mhz operation speed whose parts are just exactly one atom: https://en.wikipedia.org/wiki/Catalase https://en.wikipedia.org/wiki/Catalase And for a more apple to apple comparison, the fastest moving nanomachine I know moves at around 100nm/minute https://www.advancedsciencenews.com/new-dna-origami-motor-breaks-speed-record-for-nano-machines/ https://www.advancedsciencenews.com/new-dna-origami-motor-br... Compared to a kinesin, which isn't the fastest protein, it is over 800nm/*second* http://book.bionumbers.org/how-fast-do-molecular-motors-move-on-cytoskeletal-filaments/ http://book.bionumbers.org/how-fast-do-molecular-motors-move...
- adastra22 3y ago
  Yes, gigahertz operation speeds. This is a straightforward result from mechanical scaling laws. A machine scaled down by 1/10th in each linear dimension is able to operate at 10x speed. So a machine operating at 10Hz in ~1m regime (perfectly reasonable in an industrial setting) will be able to operate at 1GHz speeds when scaled down to be ~10nm in size. Biology operates by means of Brownian motion. Enzymes randomly jiggle around as they are bombarded in solution, until by totally random chance one of the reactants they catalyze hits in the right spot and sticks, then waits until the other reactant hits the other spot. This can take a very, very long time to happen. Animations you might watch showing their operation are lies: they show reactants sliding into place, reactions happening, and products being ejected. This is not what happens. If you actually watched a molecular dynamics simulation of a typical enzymatic reaction, and slowed it down just enough that you could see molecules moving around, it would take YEARS to watch typical reactions happen. For the fastest reactions, the ones you mention, maybe weeks or months. Biology works by molecules just randomly jostling around, sometimes moving forward and sometimes moving backward, but a small set of one-way reactions driving things forward over extended time. Kinesin, for example, has no process that drives its motion forward. It relies on random jostling to move its "feet" into the next position, at which point it can react with ATP to prevent being moved back. But only if an ATP molecule happens to be there, otherwise it gets jostled out of place again. Your 800nm/s speed is a random-walk average. Machine phase chemistry, on the other hand, is like the assembly line of a fully-automated factory. Parts can, in principle, move at up to the speed of sound--thousands of meters per second in typical gemstone materials. But to minimize friction and heat dissipation requirements, actual speeds will probably be in the mm/s or cm/s range. Reactants are attached to machinery that moves them into position at >GHz operational speeds, and each reaction happens as directed according to a preprogrammed sequence of events. This is a rather dated video that shows the idea: https://www.youtube.com/watch?v=zqyZ9bFl_qg https://www.youtube.com/watch?v=zqyZ9bFl_qg
  - tomohelix 3y ago
    Please give me an actual example, not a 17 years old video of a theoretical assembler that is still not a reality yet. From what I know, all of this is purely science fiction and worth nothing. Although to be honest, there are indeed molecular assemblers already, except they are biological... From what I read in your post, I must ask: what is your credential in this field and are you discussing this with good faith? It seems you have a very basic understanding of the mechanisms going on at the molecular level if you think enzyme is just about things randomly bumping into each other. Also, your description of kinesin mechanism is completely wrong. Kinesin doesn't move backward without ATP. It doesn't move at all without ATP. And it moves in one direction only unless its substrate was modified or external forces applied to it. Calling it random walk is ignorant at best and dishonest at worst. >This is not what happens. If you actually watched a molecular dynamics simulation of a typical enzymatic reaction, and slowed it down just enough that you could see molecules moving around, it would take YEARS There are so many things wrong with your claim. First, the same binding based on Brownian motion would happen regardless of a biological or synthetic nano assembler. All of them requires the substrates to reach them first before they can proceed to the next step and this depends on the kinetics of the reaction. Thermodynamic doesn't care if you are a polymerase or a tube of graphene. DeltaG is all that matters. But an enzyme can have specific interfacial and hydrophobic interactions built into its structure that promote binding and increase the distance it can "grab" another molecule. An enzyme is a catalyst that lower the activation barrier. A regular reaction, which may take a day to proceed based on random chance a molecule gets a quantum fluctuation in its energy state to overcome the barrier, would get over it in an instant with an enzyme. It positions and moves the atoms around such that the reaction becomes much more favorable. That is the whole point of catalysts. An enzyme conformational changes are deliberate and extremely precise. I have said this multiple times but you keep ignoring them. Please look up the word if you don't know what conformational mean. These happens extremely fast, at femtosecond timescale, at the length scale of a few angstroms. https://pubs.rsc.org/en/content/articlehtml/2018/cc/c8cc02426j https://pubs.rsc.org/en/content/articlehtml/2018/cc/c8cc0242... I didn't go too much into this because we in the catalysis field work with turnover events, which is the operation definition I gave you above. Going down to the elementary reactions is often too fast and difficult to work with. You literally can't do MD at the precision required to model some of the enzyme conformational changes. And what do you mean by slow them down and weeks and months? If I slow any video down they will take longer to play. What matter is how long does it take in realtime. I gave you a Mhz speed enzyme. That is its real speed. It literally processes a million molecules per second by ripping out a single atom on each molecule. What do you mean by weeks and months? How are you alive if reactions take weeks to run in your body? In fact, please show me a Ghz synthetic assembler that can do the same to a molecule. I am ignorant of any but it has been some time since I was last involved with this type of research. Honestly, I tried to give you some benefits of the doubt. But after typing all this out I afraid you and I are not talking on the same level here. So here is a simple ask: give me a real, proper, actually proven, example of a Ghz synthetic nanoassembler, a nanomachine that actually take a molecule and move it somewhere, the same way an enzyme works. No "theoretical videos" or baseless claims.