Yep, I totally concede that the size and level of detail of exposed metal parts is going to be limited, the discussion would mostly be interesting in terms of whether or not nanomachines would be able to assemble large metal parts as an external product or metal parts that are fully embedded in another material (eg. copper wires embedded in diamond). The discussion about surface coatings and cathodic protection is just “haggling over the price”, so to speak.
I’m not sure what you mean by electrons “sloshing around”.
The thing where if you stick a piece of metal in an electric field, charges build up on the surface of the metal to oppose the field.
Consider the analogous versions of ionic and electrostatic motors, and think about what’s better. Ionic motors use tubes filled with water instead of conductive wires with insulation; those transmit signals slower but are easier to make. Ionic motors can dump ions into solution instead of needing a conductor at a lower voltage. Ionic motors don’t have to deal with possible unintentional electrolysis. Ion gates are much easier to make with proteins than electrical switches.
The original drawback I had in mind for ionic motors is that you need to drag a membrane everywhere that you want to use a motor, which is very inconvenient. Tubes are membranes, but they’re rolled up, which makes them a lot more convenient. Diffusion of ions is very fast on these scales, so I’d guess that ions and electrons are about equally good as power sources, unless the motor is going to be correspondingly very fast at using up lots of ions. On the other hand, I think you’re misunderstanding what I’m saying about the pure electrostatic motor. It doesn’t need any external switching electronics to power the motor, and in particular not silicon electronics. It should just spin given DC power of the correct voltage. The switching would work via proximity, and would happen on the wheel molecules themselves. It’s easiest for electrons to tunnel between two sites when they’re physically close in space. Depending on how the wheels are rotated relative to each other, various sites will be closer to or farther from each other in space, and this changes as the wheel spins.
If the objects bound to the walls of gas-filled compartments have movable arms, on a small enough scale, those arms would also get stuck to (or away from) the walls by electrostatic and dispersion forces.
Aren’t there lots of proteins that undergo conformational changes in ways that don’t look like “having arms”? Alternatively, I can make my arm negatively charged and put it on a tower-thingy made of lots of covalently bonded carbon so that it doesn’t bend. That tower-thingy holds it up away from the surface of the tube so it’s physically too far away to stick. But won’t it just stick to the tower-thingy? I’m one step ahead of you: I’ve also made the tower-thingy negatively charged!
I’m fairly familiar with protein mechanisms and their limitations. Is there some other type of mechanism you’re proposing for low-temperature catalysis, something that enzymes don’t already use?
I guess to start with, let’s say we’re making diamond. We’re building up a block of the stuff from carbon, and the dangling bonds on the edge of the structure connect to hydrogens. My first though would be a condensation reaction: We stick a methanediol onto the structure, replacing two dangling hydrogens with bonds to a new carbon atom. Two molecules of water are produced, made from the hydroxyl groups and those two hydrogens.
I think existing proteins can do condensation reactions okay, but maybe those become impossible when the carbon you’re trying to attach to is already bonded to three other carbons?
Yes, proteins are covalently bonded. They’re also non-covalently bonded. If all their structure was covalent, then they wouldn’t be able to do conformational changes. And because some of it is non-covalent, they denature at high temperature.
You’re correctly pointing out two extremes: very floppy chains with no additional structure, and fully rigid crystals with to flex at all. I’m trying to say that there exists an intermediate zone in between: Molecules that have enough covalent bonds to have structure, but there’s a few pivots where there’s just a single covalent bond that can rotate, and this gives the molecule flexibility to change shape. The structure of the molecule isn’t a chain, it’s a connected graph with lots of cycles.
I think the word for that is “cofactor”.
Yep, I know what a cofactor is. :) I’m saying that we could go farther in that direction than nature has. Normally a cofactor is held in a parent enzyme that still has to be just the right shape and everything. What if even the parent enzyme was just some organic molecule synthesized by other enzymes, rather than a protein itself? You complained above that any solvent that wouldn’t corrode metals would have to denature proteins. What if we could use molecules that aren’t proteins instead?
Also remember that on a molecular scale, energy-efficient = reversible. ATPase spins in both directions.
If we’re reading from RNA, near-reversibility seems fine and good. Maybe sometimes the assembly head takes a step backwards to where it came from and its RNA reader correspondingly takes a step backwards to the previous codon in the RNA sequence. If we’re working directly from electrical signals, maybe we have to just spend the energy needed to make sure that there’s no backtracking. When a tRNA detaches from its amino acid during protein synthesis, that seems pretty darn irreversible, but apparently the energy cost is bearable for the cell. If we’re now assembling larger lego bricks, each of which is an individual protein, probably the cost to make all the walking around on the surface irreversible is not too much compared to the cost to assemble each lego brick in the first place.
In what sense would nanobots have “cheaper genome space” than current cells? What mechanism do you envision being used for information storage?
A few senses. The first is that life is amazingly robust to errors, but not infinitely robust. The larger the genome, the more mutations you get per generation. Life does have some error repair mechanisms, but using information theory it’s possible to devise an error correcting code of arbitrarily high robustness. Life just can’t switch to using such a code because changing things up like that would mess with everything else. That kind of refactor is something that evolution just can’t do. If I recall correctly, evolutionary theorists do seem to think that this is a limiting factor on (coding) genome size.
Another sense is that nanobots can be much more cooperative rather than competitive. Each bacteria has to hold its entire genome, along with all the machinery needed to sustain and reproduce itself. Multicellular organisms have it much better in that their cells can cooperate and specialize, but even there, each cell has its own copy of the genome, even the genes it doesn’t particularly need at the moment. You could imagine that maybe only 1 in 1000 nanobots has to lug around the master copy of the genome, and the rest can just request the specific parts they need for their particular specialty they’re working on. They don’t out-compete the bot with the full genome because the system was designed top down and the presence of the the maser-genome holding bot makes sense from a top-down perspective. No need to worry about the nanobot equivalent of cancer because see above about error correction.
If the point of your nanobots is to be “like current life, but worse, except it also produces a computer” then I think the usual word for that is “neurons”. The resulting computer would need to be better than current systems.
Think about component size. Neurons are huge. Even current transistors are still much larger than individual proteins. The goal here is not “somehow build a computer with nanotechnology”. The goal is to build a computer whose logic gates are literally the size of molecules. (And also to make it reversible and therefore super power-efficient.) I know neurons are quite complex and are much more advanced than a simple transistor, but still, the size difference from neurons to molecules is ridiculous. And small components typically switch faster than large ones.
I guess to start with, let’s say we’re making diamond. We’re building up a block of the stuff from carbon, and the dangling bonds on the edge of the structure connect to hydrogens. My first though would be a condensation reaction: We stick a methanediol onto the structure, replacing two dangling hydrogens with bonds to a new carbon atom. Two molecules of water are produced, made from the hydroxyl groups and those two hydrogens.
I think existing proteins can do condensation reactions okay, but maybe those become impossible when the carbon you’re trying to attach to is already bonded to three other carbons?
Condensation reactions are only possible in certain circumstances. Maybe read about the mechanism of aldol condensation and get back to me. Also, methanediol is in equilibrium with formaldehyde in water.
I realize you don’t know my background, but if you want to say I’m wrong about something chemistry-related, you’ll have to put in a little more effort than that.
Thanks for the detailed reply. Jumping right in:
Yep, I totally concede that the size and level of detail of exposed metal parts is going to be limited, the discussion would mostly be interesting in terms of whether or not nanomachines would be able to assemble large metal parts as an external product or metal parts that are fully embedded in another material (eg. copper wires embedded in diamond). The discussion about surface coatings and cathodic protection is just “haggling over the price”, so to speak.
The thing where if you stick a piece of metal in an electric field, charges build up on the surface of the metal to oppose the field.
The original drawback I had in mind for ionic motors is that you need to drag a membrane everywhere that you want to use a motor, which is very inconvenient. Tubes are membranes, but they’re rolled up, which makes them a lot more convenient. Diffusion of ions is very fast on these scales, so I’d guess that ions and electrons are about equally good as power sources, unless the motor is going to be correspondingly very fast at using up lots of ions. On the other hand, I think you’re misunderstanding what I’m saying about the pure electrostatic motor. It doesn’t need any external switching electronics to power the motor, and in particular not silicon electronics. It should just spin given DC power of the correct voltage. The switching would work via proximity, and would happen on the wheel molecules themselves. It’s easiest for electrons to tunnel between two sites when they’re physically close in space. Depending on how the wheels are rotated relative to each other, various sites will be closer to or farther from each other in space, and this changes as the wheel spins.
Aren’t there lots of proteins that undergo conformational changes in ways that don’t look like “having arms”? Alternatively, I can make my arm negatively charged and put it on a tower-thingy made of lots of covalently bonded carbon so that it doesn’t bend. That tower-thingy holds it up away from the surface of the tube so it’s physically too far away to stick. But won’t it just stick to the tower-thingy? I’m one step ahead of you: I’ve also made the tower-thingy negatively charged!
I guess to start with, let’s say we’re making diamond. We’re building up a block of the stuff from carbon, and the dangling bonds on the edge of the structure connect to hydrogens. My first though would be a condensation reaction: We stick a methanediol onto the structure, replacing two dangling hydrogens with bonds to a new carbon atom. Two molecules of water are produced, made from the hydroxyl groups and those two hydrogens.
I think existing proteins can do condensation reactions okay, but maybe those become impossible when the carbon you’re trying to attach to is already bonded to three other carbons?
You’re correctly pointing out two extremes: very floppy chains with no additional structure, and fully rigid crystals with to flex at all. I’m trying to say that there exists an intermediate zone in between: Molecules that have enough covalent bonds to have structure, but there’s a few pivots where there’s just a single covalent bond that can rotate, and this gives the molecule flexibility to change shape. The structure of the molecule isn’t a chain, it’s a connected graph with lots of cycles.
Yep, I know what a cofactor is. :) I’m saying that we could go farther in that direction than nature has. Normally a cofactor is held in a parent enzyme that still has to be just the right shape and everything. What if even the parent enzyme was just some organic molecule synthesized by other enzymes, rather than a protein itself? You complained above that any solvent that wouldn’t corrode metals would have to denature proteins. What if we could use molecules that aren’t proteins instead?
If we’re reading from RNA, near-reversibility seems fine and good. Maybe sometimes the assembly head takes a step backwards to where it came from and its RNA reader correspondingly takes a step backwards to the previous codon in the RNA sequence. If we’re working directly from electrical signals, maybe we have to just spend the energy needed to make sure that there’s no backtracking. When a tRNA detaches from its amino acid during protein synthesis, that seems pretty darn irreversible, but apparently the energy cost is bearable for the cell. If we’re now assembling larger lego bricks, each of which is an individual protein, probably the cost to make all the walking around on the surface irreversible is not too much compared to the cost to assemble each lego brick in the first place.
A few senses. The first is that life is amazingly robust to errors, but not infinitely robust. The larger the genome, the more mutations you get per generation. Life does have some error repair mechanisms, but using information theory it’s possible to devise an error correcting code of arbitrarily high robustness. Life just can’t switch to using such a code because changing things up like that would mess with everything else. That kind of refactor is something that evolution just can’t do. If I recall correctly, evolutionary theorists do seem to think that this is a limiting factor on (coding) genome size.
Another sense is that nanobots can be much more cooperative rather than competitive. Each bacteria has to hold its entire genome, along with all the machinery needed to sustain and reproduce itself. Multicellular organisms have it much better in that their cells can cooperate and specialize, but even there, each cell has its own copy of the genome, even the genes it doesn’t particularly need at the moment. You could imagine that maybe only 1 in 1000 nanobots has to lug around the master copy of the genome, and the rest can just request the specific parts they need for their particular specialty they’re working on. They don’t out-compete the bot with the full genome because the system was designed top down and the presence of the the maser-genome holding bot makes sense from a top-down perspective. No need to worry about the nanobot equivalent of cancer because see above about error correction.
Think about component size. Neurons are huge. Even current transistors are still much larger than individual proteins. The goal here is not “somehow build a computer with nanotechnology”. The goal is to build a computer whose logic gates are literally the size of molecules. (And also to make it reversible and therefore super power-efficient.) I know neurons are quite complex and are much more advanced than a simple transistor, but still, the size difference from neurons to molecules is ridiculous. And small components typically switch faster than large ones.
Condensation reactions are only possible in certain circumstances. Maybe read about the mechanism of aldol condensation and get back to me. Also, methanediol is in equilibrium with formaldehyde in water.
I realize you don’t know my background, but if you want to say I’m wrong about something chemistry-related, you’ll have to put in a little more effort than that.