This post is very well written and addresses most of the misunderstandings in Yudkowsky’s biomaterial post. Thanks for that.
There is one point where I would disagree with you but you seem to know more about the topic than I do so I’m going to ask: Why exactly do you think diamond is so hard to synthesise via enzyme? I mean it is obvious that an enzyme cannot use the same path we currently use for diamond synthesis, but the formation of C-C bonds is quite ubiquitous in enzyme catalysed reactions (E.g. fatty acid synthesis). So I could easily imagine repeated dehydrogenation and carbon addition leading to a growing diamond structure. Of course with functional groups remaining on the surface. What makes you think any such path must fail? (That this would not be very useful, very energy intensive and a difficult to evolve multi step process is quite clear to me and not my question.)
Controlled C-C bond formation in mild conditions is always enabled by nearby functional groups. In cells, the most important mechanism is the aldol reaction. Nearby functional groups can stabilize the intermediates involved.
Chemists consider C-C bond formation to be, in general, one of the most important and difficult reaction types, and have extensively considered every possible way of doing it. Here are some C-C coupling reactions. The options here are limited and it’s unlikely they’re just overlooking something very easy.
Also note that coupling a 4th non-hydrogen atom to carbon is especially hard. Many C-C coupling reactions involve H moving and temporary double bond formation, and if there are 3 bonds that can’t move, you can’t form a double bond. So diamond formation requires radicals or something similar, and those are always high-energy.
I failed to properly consider the 4th carbon problem. So you are right, between the steric problems I mentioned with Roger and the stabilisation of the intermediate it is VERY hard to do with enzymes. I can think of a few routes that may be possible but they all have problems. Besides the CDC approach another good candidate might be oxydation of a CH or COH to a temporary carbocation with subsequent addition of a nucleophilic substrate. Generating and stabilizing the carbocation will of course be very hard.
Just wanted to say the same. Though with the diamond occluding more than a hemisphere getting all the machinery in place to provide both the substrate and oxydation at the same time will run into severe steric problems.
Strong oxydation per see is quite possible if you look at e.g. Cyp P450.
This post is very well written and addresses most of the misunderstandings in Yudkowsky’s biomaterial post. Thanks for that.
There is one point where I would disagree with you but you seem to know more about the topic than I do so I’m going to ask: Why exactly do you think diamond is so hard to synthesise via enzyme? I mean it is obvious that an enzyme cannot use the same path we currently use for diamond synthesis, but the formation of C-C bonds is quite ubiquitous in enzyme catalysed reactions (E.g. fatty acid synthesis). So I could easily imagine repeated dehydrogenation and carbon addition leading to a growing diamond structure. Of course with functional groups remaining on the surface. What makes you think any such path must fail? (That this would not be very useful, very energy intensive and a difficult to evolve multi step process is quite clear to me and not my question.)
Controlled C-C bond formation in mild conditions is always enabled by nearby functional groups. In cells, the most important mechanism is the aldol reaction. Nearby functional groups can stabilize the intermediates involved.
Chemists consider C-C bond formation to be, in general, one of the most important and difficult reaction types, and have extensively considered every possible way of doing it. Here are some C-C coupling reactions. The options here are limited and it’s unlikely they’re just overlooking something very easy.
Also note that coupling a 4th non-hydrogen atom to carbon is especially hard. Many C-C coupling reactions involve H moving and temporary double bond formation, and if there are 3 bonds that can’t move, you can’t form a double bond. So diamond formation requires radicals or something similar, and those are always high-energy.
I failed to properly consider the 4th carbon problem. So you are right, between the steric problems I mentioned with Roger and the stabilisation of the intermediate it is VERY hard to do with enzymes. I can think of a few routes that may be possible but they all have problems. Besides the CDC approach another good candidate might be oxydation of a CH or COH to a temporary carbocation with subsequent addition of a nucleophilic substrate. Generating and stabilizing the carbocation will of course be very hard.
I’m not a chemist, but the https://en.wikipedia.org/wiki/Cross_dehydrogenative_coupling looks like the most plausible approach, given the shortage of space. But as you say, that tends to require very strong oxidizing agents.
Just wanted to say the same. Though with the diamond occluding more than a hemisphere getting all the machinery in place to provide both the substrate and oxydation at the same time will run into severe steric problems.
Strong oxydation per see is quite possible if you look at e.g. Cyp P450.