Another month, and my alternative theories on planetary formation are still alive. Most of the information that I could find was not directly relevant, but nevertheless there were some interesting papers.
 
One piece of interesting information (Science 341: 260-263) is that analysis of the isotopes of H, C and O in the Martian atmosphere by Curiosity rover, and comparison with carbonates in meteorites such as ALH 84001 indicate that the considerable enhancement of heavy isotopes largely occurred prior to 4 Gy BP, and while some atmospheric loss will have occurred, the atmosphere has been more or less stable since then. This is important because there is strong evidence that there were many river flows, etc on the Martian surface following this period, and such flows require a significantly denser atmosphere simply to maintain pressure, and a very much denser atmosphere if the fluid is water, and the temperature has to be greater than 273 ^oK. If the atmosphere were gradually ablated to space, there would be heavy isotope enhancement, so it appears that did not happen following 4 Gy BP. If there were such an atmosphere, it had to go somewhere other than space. As I have argued, underground is the most likely, but only if nitrogen was not in the form N₂. It would also not be lost due to a massive collision blasting the atmosphere away, the reason being there are no craters big enough that were formed following the fluvial activity.
 
There was one interesting piece of modeling to obtain the higher temperatures required for water to flow. (Icarus 226: 229 – 250.) The Martian hydrological cycle was modeled, and provided there is > 250 mbar of CO₂ in the atmosphere, the model gives two "stable" states: cold and dry, or warm and wet, the heat being maintained by an extreme greenhouse effect arising from cirrus ice crystals of size > 10μm, even with the early "cool sun". One problem is where the CO₂ came from, because while it is generally considered that Earth's volcanoes give off CO₂, most of that CO₂ comes through subduction, and Mars did not have plate tectonics. Whether this model is right remains to be seen.
 
There was one paper that annoyed me (Nature 499: 328 – 331). The problem is that if Earth formed from collisions of protoplanetary embryos, the energy would have emulsified all silicates and the highly siderophile elements (those that dissolve in liquid iron) should have been removed to the core nearly quantitatively. Problem: the bulk silicates have these elements. An analysis of mantle type rock have chalcogen ratios similar to Ivuna-type carbonaceous chondrites, but are significantly different to ordinary and enstatite chondrites. The authors argue that the chalcogens arrived in a "late veneer", and this contributed between 20 -100% of the water on earth. What has happened is that the authors carried out a series of analyses of rocks and to make their results seem credible, Earth had to be selectively but massively bombarded with one sort of chondrite, but none of the more common ones. Why? The only reason they need this rather strange selection is because they assumed the model in which Earth formed through the collision of planetary embryos. If the Earth accreted by collecting much smaller objects, as I suggest, the problem of the chalcogens simply disappears. It is interesting that the formation of planets through the collision of embryos persists, despite the fact that there is reasonable evidence that the rocky planets formed in about 5 My or less, the Moon formed after about 30 My due to a collision with something approaching embryo size, and modeling shows that formation through such embryo collisions takes about 100 My. The time required is far too long and the evidence is that when there is such a collision, the net result is loss of mass, except possibly from the core.
 
A paper in Angew. Chem Int Ed. (DOI: 10.1002/anie.201303246) showed a convincing mechanism by which hydrogen cyanide can be converted to adenine. This is of particular interest to me because my suggested mechanism for the formation of ATP and nucleic acids is also photochemically assisted. If correct, life would have commenced in vesicles or micelles floating on water.
 
On a positive note (Nature 499: 55- 58) the authors noted that while most stars form in clusters, some are also in loose clusters with stars density at less than 100 per cubic parsec. One problem might have been that stars born in loose clusters might be the only ones that can retain planets, however the authors report transits in two sun-like stars in a dense cluster, which shows that planets can survive in such a cluster, and that the frequency of planet formation is independent of the cluster density. This makes extrasolar planets very much more probable.

I have another blog, to support my literary efforts, and one of the issues I have raised there is climate change. I originally raised this to show how hard it is to predict the future, yet in some ways this is a topic that is clearer than most while in others, I find it more confusing than most. It seems to me there are a number of issues that have not been made sufficiently clearly to the public, and the issue here is, what should scientists do about it, individually, or more importantly, collectively? Is this something that scientific societies should try to form a collective view on?
 
One thing that is clear is that all observable evidence indicates that the planet is warming. Are so-called greenhouse gases contributing? Again, the answer is, almost certainly yes. The physics are reasonably clear, even if the presentations of them to the public are often somewhat deviant from the truth. Are the models correct? My guess is, no; at best they are indications. Are carbon dioxide levels increasing? Yes. Our atmosphere now has 400 ppm of carbon dioxide, up from the 280 ppm at the beginning of the industrial revolution. I think that, on balance, however, most of the public are reasonably well-informed on what the so-called greenhouse effect is.
 
I am not convinced, however, that some of the aspects have made an adequate impact. For me, the biggest problem is sea-level rise. There is considerable net melting of the Greenland ice sheet, and in every one of the last four interglacials, there is evidence that the Greenland ice sheet melted and the sea levels were 7 meters higher. That was when carbon dioxide levels were 280 ppm. Now, check Google Earth and check how much land disappears if the sea is 7 meters higher. It swamps most port cities, and takes out a lot of agricultural land. Check Bangla Desh; a very large part goes. Holland is also in bad shape. Worse, if the climate scientists are correct at their more pessimistic greenhouse estimates, the 400 ppm will take out a significant fraction of the Antarctic ice sheets, and that could lead to something like a 30 meter sea level rise. Now, if such sea level rise occurs, where do all those people go?
 
One option is, do nothing, wait and see, and if the seas rise, tough luck. So now we have an ethical question: who pays? The people who caused the problem and benefited in the first place, or the Bangla Deshis, Pacific Islanders, and other people living in low-level countries? So, what are we doing? Apart from talking, not a lot that is effective. We have carbon trading schemes, which enriches the pseudobankers, we measure everything because some scientists like to measure things, and we devote a lot of jet fuel to having conferences. However, if the levels of greenhouse gases are of concern, we burn ten billion tonne of carbon a year, and d²/dt²[greenhouse gas] is positive for each of them. The second differential is positive! Yet it is the sum of the integrals that is important.
 
We are scientists, so we should be able to recommend something. What do we recommend? To the best of my knowledge, no scientific organization has recommended anything other than platitudinal "decrease greenhouse emissions". Yes, what to do is political, and everything that I can think of meets general objections. Whatever we do, many/most will be adversely affected. The problem is, if we do nothing, a very large number of different people will be adversely affected. So what do you think scientists or scientific societies should do?
 

Our thinking on the Universe changed somewhat towards the end of the 1990s, when it was found that type 1A supernovae at extreme red shift are dimmer than expected. The type 1A supernovae start out as basically white dwarfs that have burnt their fuel to carbon-oxygen, but they have a further companion that they can feed off. If they get above 1.38 solar masses, they reignite and explode, and because they do this at a defined mass from a defined starting position, their luminosity is considered to be standard. Observation has shown this up, at least with nearby 1A supernovae. If they are standard candles, that meant that the expansion of the universe was faster in recent times than in distant times. Thus was born dark energy.
 
I always had a problem with this: what we see is the outer shell, which has a composition that will retain a considerable history of that of the neighbour, because once the explosion gets underway, that which is on the surface will stay there. That would mean the luminosity should depend on the metallicity of the star. However, when I expressed these feelings to an astrophysicist, I was assured there was no problem - metallicity had no effect.
 
Two things then happened. First, I saw a review of the problem from an astrophysicist who left an email address. The second was a publication occurred (Wang et al. Science 340: 170 – 173, 2013) that showed that luminosity could vary significantly with metallicity, and hence I emailed the astrophysicist asked what effect this would have. The reason is, of course, metals in stars are formed in previous supernovae, so it follows that the earlier the stars, the fewer cycles of supernovae would have occurred, and hence the stars would have fewer metals. If so, they should be dimmer, and if they are dimmer, and not standard, then perhaps there is no accelerating expansion or dark energy. Maybe that reasoning is wrong, but all I wanted to do was to find out.
 
Now, the issue for me lay in the response. I was told unambiguously that the lack of metallicity had been taken into account, and there was no problem. This raises an issue for me. Either the lower luminosity resulting from less metallicity was well known or it was not. If not, how as it taken into account? You cannot account for an effect of which you are unaware, and if so, this response was a bluff. If it were known, then how come someone gets a publication in a leading well-peer-reviewed journal when he announces a new discovery? If it were well-known, surely the paper would be rejected, and if it were well-known, surely the peer-reviewers would know.
 
What disturbs me is that there must be a fundamental scientific dishonesty at play here. I do not have the expertise in that field to know where it lay, but I find it deeply concerning. If scientists are not honest in what they know and what they report, the whole purpose of science fails. Just because it is fashionable to believe something, that does not make it true. Worse than that, there are some issues, such as global warming, where scientists have to take the public with them. If scientists start bluffing when they do not know, then when caught out, as they will sooner or later, the trust goes. What do you think?
 
 

One of the most heated and prolonged debates in chemistry occurred over the so-called non-classical 2-norbornyl cation. Very specifically, during reactions, exo-2-norbornyl derivatives solvolysed about 60 times faster than the 2-endo ones. The endo derivatives behaved more or less as you might expect if the mechanism was SN2, but the exo ones behaved as if they were SN1, but there was an additional surprise: the nucleophile was about as likely to end up on C6 as C2. There were two explanations for this. Winstein suggested the presence of a non-classical ion, specifically the electrons in the C1-C6 bond partly migrated to form a "half-bond" between C2 and C6. Thus was born the "non-classical carbonium ion". On the other hand, Brown produced a sequence of papers arguing that there was no need for such an entity, and the issue could be adequately explained by more classical structures, and as often as not, by the use of proper reference materials.
 
That last comment refers to a problem that bedevils a lot of physical organic chemistry. You measure a rate of reaction, and decide it is faster than expected. The problem is, what was expected? This can sometimes border on being "a matter of opinion" because the structure you are working with is somewhat different from standard reference points. This problem is even worse than you might consider. I reviewed some of the data in my ebook Elements of Theory 1, and suggested that the most compelling evidence in favour of Brown's argument was that the changing of substitution at C1 made very little difference to the rates of solvolysis at C-2, from which Brown concluded there was no major change of electron density at C1, which there should be if the C1-C6 bond became a half-bond as Winstein's structure required. As it happened, Olah also produced evidence that falsified Brown's picture, and as I remarked at the end, each falsified the other, so something was missing.
 
In the latest edition of Science (vol 341, p 62- 64) Scholz et al. have produced an Xray structure of the 2-norbornyl cation, which was made from aluminium tribromide reacting with the exo 2-norbornyl bromide, and what we find is equal C1-C6 and C2-C6 distances, as required by the non-classical ion. Also, these are long, at about 180 pm. Case proved, right? Well, not necessarily. The first oddity is that the C1-C2 distance is 139 pm, or about the same length as benzene bonds. Which gets back to Brown's "falsification" of the non-classical ion: while the C1-C6 bond is dramatically weakened, the C1-C2 bond is strengthened, and the electron density about C6 may be not that much changed, despite the fact that the bond Brown thought he was testing was half-broken. Nobody picked that at the time.
 
What do I mean by, "not necessarily"? It is reasonably obvious this is not the classical structure that Brown perceived. That is correct, but there are two other considerations. The first one is that to get a structure, the structure must be in an energy well, which means it does not actually represent the activated state. To give an example, the cyclopropylcarbinyl system would presumably give, as an ion, Cyc-CH2+ would it not? The trouble is, the system rearranges and is consistent with that, as well as a cyclobutyl cation, and an allylcarbinyl cation. The actual cation is probably something intermediate. So the rate acceleration then may not be caused by the intermediate cation, but by whatever is happening on the reaction path. If this cation was the cause of the rate acceleration, it should also operate on the endo cation. Yes, the mechanism is different, but why? A product available to both cannot be the reason. There has to be something that drives the exo derivative to form the cation. My explanation for that is actually the same as that that drives the cyclopropylcarbinyl cation.
 
The second consideration is the structure itself: the two bonds to C6 are equal, and C1-C2 is remarkably short. There is one further way this could arise. Let us suppose we follow Winstein and break the C1-C6 bond. What Winstein, and just about everybody else, thought is that we replace that with two half σ bonds, but suppose no such σ bonds are formed? Instead, rehybridize C1 and C6 so we have two p orbitals. With two p orbitals and a carbenium centre we have the essence of the cyclopropenium cation, without two of the frame-work σ bonds. That gives us a reason why the cation is so stable: under this interpretation, it is actually aromatic, even if two of the bonds are only fractional π bonds.
 
Is that right? If it is, then there is a similar reason why ethylene forms edge-complexes with certain cations. Of course, it may not be correct, but as a hypothesis it seems to me to have value because it suggests further work.

I found a number of interesting papers during June, and I am reasonably pleased that there were no significant contradictions to my ebook Planetary Formation and Biogenesis.  There were three major thrusts. The first one involved fluid flow on Mars, which my work requires, although of course its existence is generally accepted. Observations from the Curiosity rover at Gale crater showed isolated outcrops of cemented pebbles and sand. The rounded pebbles in the conglomerate indicates substantial fluvial abrasion, which led the authors (Williams et al. Science 340: 1068 – 1072) to conclude that sediment was mobilized in water that probably exceeded the threshold conditions (depth, 0.03 – 0.9 meter, velocity 0.2 – 0.75 m/s) required to transport the pebbles. They conclude that sustained liquid water must have flowed across the landscape. Unfortunately, no evidence was available as to why it flowed, or what the fluid was. (It would be water, but such water could either be heated, or it could contain something to depress its melting point.) 
 
Another major issue is, when did rocky planets get their volatiles? Volatiles that are accreted from the stellar accretion disk are almost certainly essentially lot to space due to the high energy emissions of the young star, which persist for about  0.5 Gy. My mechanism of rocky planet formation requires many of the volatiles to accompany feldsic crust formation, and I required that to happen following about 4 Gy BP, in part to ensure that the chemicals required for life were available continuously from about 4 Gy BP for another 1.5 Gy. Pujol et al. (Nature 498: 87-89) measured argon ratios from gas occluded in rock, and concluded that less than 10% of feldsic crust evolved between 170 My and 3.8 Gy BP, 80+10% of the crust formed between 3.8 Gy and 2.5 Gy BP, and < 30% crust was generated from 2.5 Gy BP to today. These results effectively confirm that my requirements were met. Interestingly, Debaille et al (Earth Planet Sci. Lett. 373: 83-92) proposed that early-formed mantle heterogeneities persisted at least 1.8 Gy after Earth's formation. The best explanation is that there was a stagnant lid regime as the crust built up. The major change in geodynamics noted at ~3 Gy BP then reflects the transition to plate tectonics.
 
In my ebook, I argued that there should be significant reduced species emitted geochemically early in a rocky planet's history, and I argued that the components in the Saturnian system would convert methanol and ammonia to methane and nitrogen. I also argued that the planetary systems formed relatively quickly, as opposed to the current theories that require at least 15 My to get a giant. I was pleased to note that Malamud and Prialnik (Icarus 225: 763-774) calculated how serpentinization would produce nitrogen and methane in Enceladus, and argued that for their calculations to be correct, because initiation requires heat from short-lived radioisotopes, the Saturnian moons had to be formed between 2.65 and 4.8 My after CAI formation. Just what I needed! Etiope et al. (Icarus 224: 276-285) showed that methane may be formed at relatively low temperatures by the Sabatier reaction catalysed by chromite minerals. More good reduced materials.
 
Finally, Pringle et al. (Earth Planet Sci. Lett. 373: 75-82) showed from consideration of silicon isotopes in meteorites from 4-Vesta that Vesta differentiated under more reducing conditions than previously considered. Again, just what I wanted.