The prize appears to have been given for work that leads to the modeling of how enzymes work. If I follow the information I have seen correctly, the modelling involves three different levels. The very inner site of reactivity involves a quantum mechanical evaluation of the reaction site and the reactivity. Outside this, where the protein strands fold and interact, the situation is simplified with simple (in comparison) classical physics, while outside this there is further simplification by which the situation is considered simply as a dielectric medium.
 
All of that seems eminently sensible, and there is little doubt that even with such simplifications there remains some serious work that has been done. However one thing concerns me: up until this award, I was totally unaware of it. Yes, this might indicate a lack of effort on my part, but in my defence, there is an enormous amount of information available, and for matters outside my immediate research interests, I have to simply rely on more general articles. Which gets me to the point: assuming this work has been successful, it is obviously important, but why has more not been made of it? Again, perhaps this illustrates a fault on my part, but again I feel there is more need to promote important work.
 
I guess the final point I would like to make is, could someone highlight the principles that this modeling work has uncovered? The general chemist has little interest in wading through computations of the various options open to such a complex molecule as an enzyme, but if some general principles are uncovered, could they not be better publicized? After all, they may have more general applicability.

There was a recent comment to one of my posts regarding the formation of rocky planets, so I thought I should outline how I think the rocky planets formed, and why. The standard theory involves only physical forces, and is that dust accreted to planetesimals, then these collided, eventually to form embryos (Mars-sized bodies), then these collided to form planets. First, why do I think that is wrong? For me, it is difficult to see how the planetesimals form by simple collision of dust, and it is even harder to see how they stay together. One route might be through melting due to radioactivity, but if that is the case, one would need very recently formed supernova debris to get sufficient radioactivity. Then, as the objects get bigger, collisions will have greater relative velocities, which means much greater kinetic energy in impacts, and because everything is further apart, collisions become less probable and everything takes too long. The models of Moon formation generally lead to the conclusion that such massive impacts lead to a massive loss of material.
 
The difference between the standard theory and mine is that I think chemistry is involved. There are two stages involved for rocky planets. The first is during the accretion of the star, and near the star, temperatures are raised significantly. Once temperatures reach greater than 1200 ^oC, some silicates become semi-molten and sticky, and this leads to the accretion of lumps. By 1538 ^oC, iron melts, and hence lumps of iron-bodies form, while around 1500 – 1600 ^oC. calcium aluminosilicates form separate molten phases, although about 1300 ^oC a calcium silicate forms a separate phase. (The separation of phases is enhanced by polymerization.) Material at 1 A. U., say, reaches about 1550 - 1600 ^oC, while near Mars it reaches something like 1300 ^oC. Of particular relevance are the calcium aluminosilicates, as these form a range of materials that act as hydraulic cements. Also, the closer the material gets to the star, the hotter and more concentrated it gets, so bigger lumps of material form. One possibility is that Mercury is in fact essentially formed from one such accreted lump that scavenged up local lumps. Another important feature is that within this temperature range, significant other chemistry occurred, e.g. the formation of carbides, carbon, nitrides, cyanides, cyanamides, silicides, phosphides, etc.
 
When the disk cooled down, collisions between bodies formed dust, while some bodies would come together. Dust would form preferentially from the more brittle solids, which would tend to be the aluminosilicates, and when such dust accreted onto other bodies, water from the now cool disk would set the cement and make a solid body that would grow by simply accreting more dust and small bodies. Because there is a gradual movement of dust and gas towards the star, there would be a steady supply of such feed, and the bodies would grow at a rate proportional to their cross-section. Eventually, the bodies would be big enough to gravitationally attract other larger bodies, however the important point is that provided initiation is difficult, runaway growth of one body in a zone would predominate. Earth grows to be the biggest because it is in the zone most suitable for forming and setting cement, and because the iron bodies are eminently suitable for forming dust. The atmosphere and biochemical precursors form because the water of accretion reacts within the planet to form a range of chemicals from the nitrides, phosphides, carbides, etc. What is relevant here is high-pressure organic chemistry, which again is somewhat under-studied.
 
Am I right? The more detailed account, including a major literature review, took just under a quarter of a million words in the ebook, and the last chapter contains over 80 predictions, most of which are very difficult to do. Nevertheless, an encouraging sign is that the debris of a minor rocky planet around a white dwarf (what remains of an F or A type star) shows the presence of considerable amounts of water. Such water is (in my opinion) best explained by the water being involved in the initial accretion of the body, because it is extremely unlikely that such an amount of water could arrive on a minor rocky planet by collision of chondrites because the gravity of the minor planet is unlikely to be enough to hold such water. Thus this is strongly supportive of my mechanism, and it is rather difficult to see how this arose through the standard theory.

Leaving aside the provision of employment for modelers, I am far from convinced that the climate change models are of any use at all. As an example, we often hear the proposition that to fix climate change we should find a way to get carbon dioxide from the atmosphere, or from the gaseous effluent of power stations. This sounds simple. It is reasonably straightforward to absorb carbon dioxide: bubble the gas through a suitable base. Of course, the problem then comes down to, how do you get a suitable base? Calcium oxide is fine, except you broke down a carbonate at quite high temperatures to get it. Amines offer an easier route, but to collect a power station's output, regenerate your amine, and keep the carbon dioxide under control will require up to a third of the power from your power station. Not attractive. The next problem is, what to do with the carbon dioxide? Yes, some can be sunk into wells, preferably wet basaltic ones as this will fix the CO₂, and a small amount could be used as a chemical, say to make polycarbonates, but how many power stations do you think will be accounted for by that?
 
The problem for climate change is that we currently burn about 9 Gt of carbon per annum, which means we have to fix/use something like 33 Gt of CO₂ per annum just to break even, and breaking even is unlikely to fix this carbon problem. The problem is, CO₂ is not a very strong greenhouse gas, but it does stay around in the atmosphere for a considerable time. One point that nobody seems to make in public is that even if we stopped emitting CO₂ right now, the additional carbon we have already put in the atmosphere will remain for long enough to do a lot more damage. Everybody seems to behave as if we are in a rapid equilibrium, and that is not so. The Greenland ice sheet is the last relic of the last ice age. If we have created the net warming to melt so much per annum, that will keep going until the ice retreats to a position more resilient, at which point our climate will change significantly because we have a much different albedo over a large area. We cannot "fix" climate change by simply stopping the rate of increase of burning carbon; we have to actively reduce the total integrated amount, and not simply worry about the rate of increased production. I suggest that to fix the climate problem, assuming we see it as a problem, we would be better to put more effort into something with a stronger response than fixing CO₂.
 
In the previous post, I attempted (unsuccessfully!) to irritate some people relating to how climate change research is spent. When money becomes available for this, what happens? What I believe happens is that we see numerous proposals for funding to make more accurate measurements of something. My argument is, just supposing we do get more accurate data on, say, the methane output of some swamp, what good does that do? It provides employment for those measuring the output of the swamp, but then what? Certainly it will add more to the literature, but the scientific literature is hardly short of material. Enough such measurements will help models account for what has happened, perhaps, but the one thing I am less confident about is whether such models will be able to answer the question, "Exactly what will happen if we do X?" For example, suppose we decided to try to raise the albedo of the planet by reflecting more light to space, and did this in a region that would lower the temperature of cold fronts coming into Greenland, with the aim of increasing snow deposition over Greenland, how much light would we need to reflect and where should we reflect it? My argument is, until models can give an approximate answer to that sort of question, they are useless. And unless we do something like geo-engineering, we are doomed to have to accommodate the change, because nobody has suggested any alternative that has the capacity to solve the problem. We can wave our hands and "feel virtuous" for claiming that we are doing something, but unless the sum of the somethings solves the problem, it is a complete waste of effort. Worse than that, such acts consume resources that could be better used to accommodate what will come. The only value of a model is to inform us which actions will be sufficient, and so far they cannot do that.

Currently, NASA is asking for public assistance for their astrobiology program, or they were up until the current government shutdown, and in particular, asking for suggestions as to where their program should be going. I think this is an extremely enlightened view, and I hope they receive plenty of good suggestions and take some of them up. This is a little different from the average way science gets funded, in which academic scientists put in applications for funds to pursue what they think is original. This is supposed to permit the uncovering of "great new advances", and in some areas, perhaps it does, but I rather suspect the most common outcome is to support what Rutherford dismissively called, "stamp collecting". You get a lot of publications, a lot of data, but there is no coherent approach towards answering "big questions". That, I think, is a strength of the NASA approach, and I hope other organizations take this up. For example, if we wish to address climate change, what questions do we really want to have answered? What we tend to get is, "Fund me to set up more data gathering," from those too uninspired to come up with something more incisive. We do not need more data to set the parameters so that current models better represent what we see; we need better models that will represent what will happen if we do or do not do X.
 
So what are the good questions for NASA to address? Obviously there are a very large number of them, but in my view, regarding biogenesis, I think there are some very important ones. Perhaps one of the most important one that has been pursued so far is how do the planets get their water, because if we want life on other planets, they have to have water. The water on the rocky planets is often thought to come from chondrites, as a "late veneer" on the planet. Now, one of the peculiarities of this explanation is that, as I argued in my ebook, Planetary Formation and Biogenesis, this explanation has serious problems. The first is, only a special class of chondrites contains volatiles; the bulk of the bodies from the asteroid belt do not. Further, the isotopes of the heavier elements are different from Earth, the ratios of different volatiles do not correspond to anything we see here or on the other planets, so why is such an explanation persisted with? The short answer is, for most there is no alternative.
 
My alternative is simple: the planets started accreting through chemical processes. Only solids could be accreted in reasonable amounts this close to the star, unless the body got big enough to hold gravitationally gases from the accretion disk. Water can be held as metal and silicon hydroxyl compound, the water subsequently being liberated. This, as far as I know, is the only mechanism by which the various planets can have different atmospheric compositions: different amounts of the various components were formed at different temperatures in the disk.
 
If that is correct, we would have a means of predicting whether alien planets could conceivably contain life. Accordingly, one way to pursue this would be to try to understand the high temperature chemistry of the dusts and volatiles expected to be in the accretion disk. That would involve a lot of work for which chemists alone would be suitable. Now, my question is, how many chemists have shown any interest in this NASA program? Do we always want to complain about insufficient research funds, or are we prepared to go out and do something to collect more?