Is science sometimes in danger of getting tunnel vision? Recently published ebook author, Ian Miller, looks at other possible theories arising from data that we think we understand. Can looking problems in a different light give scientists a different perspective?

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This will be my last post for 2014, and as is customary at this time of the year, I thought I should survey what I thought were the highlights for me this year. I started this year with posts on how the ancients could have considered the heliocentric theory, largely to support my science fiction trilogy that I had written. The key here was to get this into the plot as a key element, and that gave me the chance to try to explain what I believe science is all about. Now the good news is I have sold quite a few copies, so hopefully there are some more out there that get introduced to the beauty of theoretical science at a level they can understand. (I doubt there is any way you could explain quantum field theory to the general public in a way that makes sense and honestly goes to the basis of the theory.) The key I tried to get across was to ask questions and devise ways to make critical observations that clearly separate possibilities. (In this case, either the Earth moves, or it does not, therefore one needs observations that could be carried out by an ancient Roman that will be different whether it does or does not.)
The next milestone for me was in a sense a negative one. My ebook on "Planetary Formation and Biogenesis" was published three years ago, and its basis is that planetary accretion started through chemical interactions (including physical chemical) in the accretion disk, which has led to the various planetary systems being compositionally different. What is interesting for me is that in the following three years, no observation has been found that falsifies anything of substance toward the theory. Unfortunately, while I made over seventy predictions based on the theory, most are too difficult to carry out. Notwithstanding that, there is one simple chemical experiment that could be done in the lab right now. I shall post on that in the new year, but it is based on an experiment carried out by Carl Sagan's group in the 1960's and which has seemingly been forgotten, or at least its significance not appreciated, since.
The next milestone for me was to produce my ebook on biofuels. I have worked in this area on and off (depending on funding, which has been erratic to say the least) for decades. The conclusion I reached is that by simply looking at the size of the problem (the amount of oil consumed) this cannot be met by biofuels without using the oceans. There are ways to do this, at least in theory, but it would need a significant investment in science to achieve it. I am not holding my breath waiting for funding, but then again I have now reached an age where my personal research involvement is fading away at a serious rate.
What about chemistry as a whole? My impression is that it is very efficient at making new compounds and doing things with them, but I continue to think that we are not so good at sorting and analyzing what we know, probably because of the rate of production of new compounds, etc. I have no doubt that people know a very lot about their specialist field, but in my opinion it is harder to understand the bigger picture. Maybe you do not agree? If so, I welcome your comments.
Meanwhile, I wish you all a very Merry Christmas, and all the best for 2015. I shall be back mid January.
Posted by Ian Miller on Dec 15, 2014 2:01 AM GMT
Chemists are fairly adept at finding out what molecules are present in a sample, but what happens when the sample is light years away? Astronomers have worked out how to do some spectroscopy, but it is not exactly easy to do. One of the interesting reports recently was the announcement of the measurement of an exoplanet's atmosphere (Nature 526: 526 – 529). When starlight passes through the atmosphere, various absorption lines can be seen as long as the atmosphere is basically transparent. While the star is a strong source of light (somewhat too strong, since most of the light does not go through the planetary atmosphere, as the star is very much bigger) the path length of a giant planet's atmosphere is also somewhat longer than the average laboratory cell! In this case, the main signal detected was water, and it was noted that the level of heavier elements in the atmosphere relative to hydrogen was no greater than 700 times that of the star, as would be expected if the planet was a giant that accreted gas from an accretion disk. Not that there would be many other ways of making a gas giant.
Another study (Icarus 243: 39 – 47) considered the chemistry of cometary methanol during impacts. Impacts cause methanol to dissociate into CO and CH4, however the energies are such that methanol should survive accretion onto the large icy satellites, including Callisto, Ganymede, Titan, Ceres and Pluto, although cometary impacts following accretion will produce dissociation. Asteroid impacts onto Ceres would dissociate methanol. However, Callisto could have produced up to 10-2 bar during the late heavy bombardment, while Titan would have acquired 0.1 bar. Since it did not, the authors imply that the methanol concentration in the Saturnian system was much lower than that of comets, or alternatively, some unspecified conversion of CO to CH4 occurred. This supports my mechanism of planetary formation, in which comets were not the source of methanol or other carbonaceous material on the icy bodies. Titan would have contained methanol, but this would be converted to methane by geochemical processes. These authors also show that CH3OH and CH4 abundances on a persistently shadowed part of the moon cannot be of cometary origin.
One of the more difficult questions is what the original earth was like. The standard theory has it that the planet formed as a consequence of giant collisions that led to a magma ocean, but a recent publication (arXiv:1403.0806) throws up interesting constraints. The authors propose at least two giant impacts to generate a global magma ocean based on the ratios of 3He to 22Ne. The depleted mantle has a ratio at least 10, while a more primitive mantle has a ratio of 2.3 - 3. The solar ratio is 1.5.  In-gassing of gravitationally accreted nebular atmosphere will explain the 3, but to get to 10 it requires at least two episodes of atmospheric blow-off and magma ocean outgasssing. The preservation of the low ratio in a primitive reservoir sampled by plumes suggests that later giant impacts, including the moon-forming impact, did not generate a whole mantle magma ocean. Atmospheric loss episodes with giant impacts provide an explanation for Earth's subchondritic C/H, N/H and Cl/F elemental ratios, while preserving chondritic isotope ratios, but if so, a significant proportion of terrestrial water and other volatiles were accreted prior to the last giant impact, otherwise the fractionated elemental ratios would have been overprinted by the late veneer. What is most surprising here is that the collision that caused the moon to form was insufficient, yet the carbon, nitrogen and halogens were determined relative to hydrogen prior to the moon-forming event. That would require the current volatiles were degassed from the earth at a later date.
There were two big events in November. The first involved Philae landing on a comet, and apparently it has made a lot of measurements, and sent the data back to Earth. However, as yet we have no idea what was discovered. The fact it landed and ended up in the shade was bad news because the solar cells will not recharge the batteries adequately. For me the big disappointment was that the device that bored into the comet apparently struck something hard, and when the drill was withdrawn, apparently there was no sample. This is one of the difficulties with robots; whoever designs them has to know what the conditions would be. Why would there be no sample? One possibility is that the ice has clathrated or adsorbed gas in it, and the heat of the drill vaporized the gas, the pressure of which blew out the sample, however I guess we shall never know because "no sample" cannot be analysed.
The second big event involved the European Space Agency, who have studied the star, HL Tauri and found an accretion disk around it. The star is about 1 million years old, and the disk has rings in it, with dark gaps between them. The most obvious cause for such rings would be the formation of planets, although that does not mean there is a planet in every gap, because while a planet will clear out dust on its path, gravitational resonance will also clear out material. One problem is we cannot see the planets. Why would we? We can see four giant planets around the star HR 8799. These are newly-formed giants, and the gravitational energy of the gas falling onto the planet heats it to a yellow-white heat, hence they glow. These are all very much bigger than Jupiter. Similarly, there is a star LkCa 15 that is 3 million years old, and we see a planet much bigger than Jupiter, and significantly further from the star. Planetary growth should be faster the closer to the star, at least for the same sort of planet, because the density of matter increases as it falls into the star. Since we only see one giant, my theory requires there to be three other giants we cannot see, presumably because they are yet of insufficient size to glow sufficiently brightly for us to image them. So, if I am right, 1 My gets you giants of the size we have, and the longer the disk lasts, the bigger the giants get.
Posted by Ian Miller on Nov 30, 2014 8:58 PM GMT
It seems to me there are two purposes for theory: to enable the calculation of things of interest so that predictions can be made, or to lead to understanding so that even if calculations are not practical, at least educated guesses can be made to guide further action. At the risk of drawing flak from the computational chemists, I think the second purpose is of more importance to chemists. The problem is, chemistry is based on a partial differential equation that cannot in general be solved, if for no other reason than the equations relating to a three-body problem involving a central field cannot be solved exactly. That leaves the question, if you cannot solve that, what can you do? What chemists have done is to take solutions from what can be solved (the hydrogen atom) and base models on those. Thus we have orbitals that correspond to the excited state solutions of the hydrogen atom. The perceptive reader of my previous posts will realize I have argued that the actual orbitals do not exactly correspond, nevertheless the wave functions I argue for (essentially superpositions of waves with fewer nodes based on the principle that separation is possible provided all components have quantized action) are essentially the same in terms of angular distributions, so that issue is irrelevant to the present issue, which is what to do with these orbitals relating to dative bonds? Most chemists are familiar with one answer relating to dative bonds: models based on arrows, etc.
Recently, we have seen a debate about dative bonds in Angew. Chem. In. Ed. (2014, 53, 370 – 374; 2014, 53, 6040 – 6046.). There seem to be several points being made, but they tend to boil down to the use of arrows, what the dative bond is, and what model is worth following. This discussion attracted the heretic in me!
First, why models? One of the protagonists (Frenking) used this quote: Bonding models are not right or wrong but they are more or less useful. This raises the issue, what do we mean by "right or wrong", and when can a model that is known to be wrong continue to be used? In the first case a model can be seen to give useful outputs and can be used while there are no known examples of it being wrong, and, of course, there is nothing wrong with using a model that you know to be an approximation, as long as everyone accepts that it is an approximation. Another time when the model is strictly wrong but can still be used (in my opinion anyway) is when it is only wrong when a given external condition is imposed that gives a known effect, in which case it can be used when that effect is absent. The most obvious example is Newtonian mechanics. Newton assumed action at a distance was immediate. It is not, and when that is relevant we have to resort to Einstein's mechanics, but when motion is such that the effects of light speed can be considered as effectively instantaneous, you would be mad not to use Newtonian mechanics.
However, back to the dative bond. What is it? Seemingly Haaland (Angew. Chem. Int. Ed. 1989, 28, 992 – 1007.) considered: The basic characteristics of a dative bond, depicted with an arrow “→”, are its weakness, the substantially longer bond length compared to typical single bonds, and a rather small charge transfer. My personal view is this does not help much. What does " substantially longer bond length compared to typical single bonds" mean? In this sense, it must be recalled that bond lengths vary, and the dative bond does not have a non-dative counterpart. Both parties to this discussion used the example of borazane (NH3→BH3). Right – what is the length of a non-dative nitrogen-boron single bond free of other complications, including lone-pair interactions? The next question, though, is, if we write it like that, what does the arrow mean? What I was taught as an undergrad, and it seems reasonable enough, is that a two-electron bond forms using both electrons from the nitrogen lone pair. Now, part of this discussion then focused on, what does that mean?
A lot of people seem to think that what happens is that the nitrogen transfers an electron to the boron atom, then the two electrons pair. The net result is that the molecule is a zwitterion, with N and B- charges on the relevant atoms, with a little subsequent polarization of the hydrogen atoms. That would seem to contradict Haaland in that such a distribution would give a very strong dipole moment, but note now what Frenking says: "Writing ammonia borane H3N-BH3 as a zwitterion yields a negative charge at boron and a positive charge at nitrogen, while the partial charges exhibit the opposite polarity." What exactly does that mean? From what I can make out from a cursory glance at the literature, borazane has a dipole moment of 5.2 D. Now, which way is that likely to go? I cannot see a sufficient electron transfer to get that dipole moment from boron to nitrogen, so it seems reasonable to me to assign the direction of flow to be from the lone pair of nitrogen towards boron, as the arrow indicates. Accordingly, I find this discussion just a little misleading. However, I also do not feel that the concept of the nitrogen transferring an electron to boron, and the two pairing is very helpful either.
So, how do I see the dative bond? In my picture, the nitrogen atom has a lone pair, and those electrons are described by a wave function that has a barrier at infinity, while boron, if it hybridizes, can create an sp3 configuration with an empty wave function, which I shall describe as a hole. If the nitrogen atom approaches such that the lone pair wave function is directed towards the hole on the boron atom, the boron atom now provides a barrier to the lone pair wave function, perhaps described as the vacant sp3 orbital "capturing" the lone pair and reducing the range over which the electrons can roam by the boron atom providing a turning point. As positional uncertainty is lowered, momentum increases, kinetic energy increases, and by the virial theorem, total energy is lowered. In that picture, the arrow is a great way of describing it, and the lone pair mechanics are now determined both by the nitrogen atom and the boron atom, and to maintain the sp3 hybridization, the lone pair has to spend increased time away from the nitrogen atom, hence the high dipole moment. Note that that is also more valence-bond type thinking than molecular orbital thinking. As to why I put that here, apart from highlighting the debate, the sort of thinking of this last model, which is essentially that the dative bond forms as a cosnequence of the change to boundary conditions applied to a lone pair helps me; whether it helps anyone else is, I suppose, a more interesting question.
Posted by Ian Miller on Nov 9, 2014 8:59 PM GMT
Recently, there have been two themes regarding the Moon's origin. Some unexpected but now well-known results from the samples returned by Apollo included:
1. the rocks were remarkably dry,
2. the isotopes of oxygen and some other elements were essentially the same as those of Earth whereas these isotope ratios differ from other samples, such as chondrites, and from Mars,
3. there was considerable anorthosite, which is a feldspathic mineral, present. Earth is the only planet that we know of that has extensive feldspar. (Mars has a limited amount of plagioclase, but no known extensive granite. Venus may have two granitic cratons, Ishtar and Aphrodite Terra, but we have no means of knowing.)
This information was most easily accommodated by postulating a Mars-sized impactor, Theia, colliding with Earth and sending up massive amounts of silica vapour, from which the moon condensed. Various computations have shown this was possible, it explained the dryness, provided the bulk of the mass came from Earth it explained the isotope levels and the composition, so it became the established theory. Because the condensate was from Earth's surface, radioactivity levels would be low, which explains why the moon has been essentially dead for a long time. The major activity has been considered to have involved massive impacts during the so-called late bombardment. There was always one problem: in detail most impactor computations require much of the moon to have come from Theia, in which case Theia, coming from somewhere else, should have a different isotope and mineral composition. Also, the relative velocity of Theia on impact should not significantly exceed the escape velocity, which means, at a distance where Earth's gravitational field becomes insignificant, it should have little excess energy. There is one largely overlooked option from Belbruno and Gott that I prefer: Theia accreted at one of the Lagrange points to the Earth/Sun system. If we assume the isotope composition of the accretion material is dependent on the solar radial distance, then the composition similarity follows automatically, while there is no problem with the collision energy. If my theory outlined in Planetary Formation and Biogenesis is correct, maximum rates of initial accretion occurred for rocky planets at the Earth distance from the star, and there would be enhanced accretion of calcium aluminosilicates (because as cements, they caused the accretion) and this would explain/require the enhanced anorthosite.
The standard picture is now starting to show signs of wear. First, the moon did not die quite so rapidly, and certain small volcanic areas on the Moon appear to have had eruptions within 100 My BP (before present), and possibly up to 50 My BP. Further, while the Procellarum region has been interpreted as an ancient impact basin of approximately 3,200 km diameter, gravity anomalies show that the region is essentially a massive lava outflow, consistent with the higher concentrations of the heat producing elements uranium, thorium and potassium in the rock. These elements are readily concentrated if the body has melted, because they tend to be the last to crystallize out. But that requires fluid, such as from a magma ocean. Even if the impactor did not form a vapour, a magma ocean still remains very probable. The magma ocean also favours the formation of the aluminous crust, as it would float on basalt. (Interestingly, one review noted that plagioclase only floats on dry magma; where this came from is unclear because basalts usually have a density of about at least 0.7 units greater.)
The issue of whether the moon condensed from vapours is unclear. There is a lack of fractionation among refractory elements, which is strong evidence that the moon did not form by condensation of vapours, yet the moon is depleted in volatile elements such as potassium, which is generally considered to indicate that there were vapours, BUT it turns out the isotopes of potassium are the same as on earth and other solar system bodies, which counts against vapour condensation. Even more suggestive, lithium isotopes are the same as on Earth. Thus it is generally concluded that the Moon has little trace of the impacting body, even though models show the impactor makes a significant contribution to the putative proto-lunar disk. To summarize, the formation of the Moon requires a highly energetic origin, it carries the elemental signature of Earth, but it is depleted in volatile elements and water. Of course, if Theia accreted at the Lagrange point, then the resultant collision will still have been energetic, but maybe not quite as energetic. There may have been sufficient energy to lead to extensive dehydration and moderate loss of potassium, but essentially as a single event, which would not lead to significant isotope fractionation, as opposed to equilibration between vapour/liquid, which would.
Andrews-Hanna, J. C and 13 others. 2014. Structure and evolution of the lunar Procellarum region as revealed by GRAIL gravity data. Nature 514: 68 – 71.
Belbruno, E., Gott, J.R. 2005. Where did the Moon come from? Astron. J. 129: 1724–1745.
Braden, S. E., and 5 others, 2014. Evidence for basaltic volcanism on the Moon within the past 100 million years. Nature Geoscience : doi:10.1038/ngeo2252
Taylor, S. R. 2014. The Moon re-examined. Geochim Cosmochim. Acta 141: 670–676.
Posted by Ian Miller on Oct 26, 2014 10:00 PM GMT
One theme of my posts that I have raised more than once is that while scientists are very good at collecting information and of measuring things, this leaves the problem of interpreting what it means. Scientific theory is based on either propositions or statements. A proposition is of one of two forms:
(1)  If theory P is true, then you will observe A
(2)  If and only if theory P is true, then you will observe A
Failure to observe A falsifies either proposition, but if you observe A, all you can say about (1) is the theory is in play. As Aristotle noted over two millennia ago observing A can only prove P if (2) applies, and it is the "only" condition that is difficult to validate. A statement (and an equation is a statement) carries the implied proposition that it is true.
What brought this thought on was one paper (Science, 345: 1590 – 1593) that has had quite some publicity, even in the public news media. What it claims is that at least some of the water we have is older than the solar system. What does that mean? First, it was deuterium/hydrogen ratios that were measured. We also note the authors were astrophysicists, and I quote: " our emphasis is on the physical mechanism necessary for D/H enrichment: ionization." As stated, that is an "only" statement, but I consider the "only" condition is unjustified. However, before getting to that, all hydrogen and deuterium was made in the Big Bang, and all oxygen atoms were made in supernovae. Water is made in space by oxygen and hydrogen reacting, usually on dust. Deuterium enrichment can arise because the O – D bond is stronger than the O – H bond, mainly because the latter has the larger zero point energy, so any process that breaks an O – H bond, particularly if it just does so, may increase the D/H ratio in what remains. It also arises through sublimation equilibria of ices in space, as heavier molecules sublime slightly less easily and under equilibrium conditions, they become enriched. Under these conditions, the D/H ratio of all water remains constant, and if ice gets enriched in deuterium, the vapour becomes depleted.
What they note is that the highest levels of D/H in water occurs in interstellar ices, and that Earth's oceans have a significant deuterium enhancement over solar hydrogen levels and are similar to comets from Jupiter's orbit, and a little less than that of interstellar water. They then model what they believe happened in the solar accretion disk and note that the deuterium levels we see are inconsistent with the disk physics/chemistry leading to the observed enhanced, with respect to solar, deuterium levels. What they then conclude is that comets could comprise either 14% or up to 100% of accreted interstellar ice, and ~7% or up to 30-50% of earth's oceans originated as interstellar ices. Why the "either" options? Largely because while they have a ratio for interstellar ices, they also have a water signal from the disk of a protostar. In short they believe the nature of the original water may vary from star to star. However, that is irrelevant to their claim that our water predates our solar system formation. They then conclude that provided the formation of our solar nebula was typical, then interstellar ices from the molecular cloud core should be available to all young planetary systems.
The last conclusion seems obvious. If there is water and ice in the cloud, which would be expected as long as the carbon levels do not consume all the oxygen, then the water ice should persist at least to the outer parts of the accretion disk, and indeed my theory of formation of the gas giants relies on this being so, so in one sense the paper supports my theory. On the other hand, provided there were water ices in the cloud, what could possibly happen to them until they reached the ice sublimation temperature, given that the disk is opaque so while the star is forming, ionizing radiation should be absorbed much closer to the star? It is here that they seem to have overlooked that there are three important hydrogen sources: interstellar ice, interstellar water vapour, and hydrogen. The latter is about four orders of magnitude higher than anything else, and determines the initial deuterium levels in the star. Nuclear burning will then decrease the stellar deuterium levels.
However, the conclusion that Earth's water reflects the deuterium content of the water as it was accreted is an "only" statement, and it is not true. There is a further possible mechanism: as water travels through hot rock, and current volcanism shows it does, it may oxidize any reduced species, and in many cases liberate hydrogen, which may then escape to space. Such reactions involving the breaking of the O-H bond will also be affected by the chemical isotope effect, with O-D bonds reacting significantly more slowly, and that in turn will lead to deuterium enrichment. That is my explanation for the Venusian atmosphere, where there is a hundred-fold enrichment of deuterium (Science 216: 630-633). The reactions include water reacting with carbon or carbides as the original source of the carbon dioxide in the Venusian atmosphere. As I showed in Planetary Formation and Biogenesis by reviewing a number of papers, either the gases were emitted from the earth, in which case they had to be accreted as solids, or they were delivered from space, but if the latter were the case, each rocky planet had to be struck by completely different types of bodies, and the Moon, quite remarkably, be struck by only trivial amounts of any of the volatile containing bodies. Note that most asteroidal bodies contain negligible volatiles.
So what do I make of this? Of course water arrived from interstellar space, and this work at least supports my concept of ice accretion. On the other hand, the presence of ices in the disk is generally held to be the reason why the giants form, so in another sense this paper simply supports what was long assumed. I am not convinced it warranted the media attention it received.
Posted by Ian Miller on Oct 13, 2014 1:57 AM BST
There are a number of problems that seem to be looming, one of which is the climatic effects of the so-called greenhouse gases. Science should be able to address such problems, but the question arises when a discovery is made is, is this a solution to the designated problem, could it be a solution to the designated problem if some further problems can be overcome, or is it simply an interesting observation but essentially irrelevant in terms of solving any of our problems? With the problem of getting funding for science, "relevance" often becomes an issue. Accordingly, funding applications frequently make significant claims as to what their research might achieve, and there are advantages in carrying this over into the subsequent papers. Of course some of these papers may truly herald an opportunity. So, what do you make of the following?
Ammonia is an important chemical for fertilizer, and is usually made through the Haber-Bosch process, which involves reacting nitrogen gas with hydrogen under pressure, the hydrogen being made by steam reforming of methane, in turn obtained from natural gas. The oxygen from the steam ends up eventually as carbon dioxide, so it contributes to the greenhouse effect. However, a new process has been claimed (Science, 345: 638 – 640) that involves electrolysis of air and steam in a pressurized molten hydroxide suspension of nano-sized Fe2O3, at temperatures of 200 – 250 oC. This process results in the conversion of nitrogen to ammonia with an efficiency that is apparently 35% of the applied current, the other 65% resulting in excess hydrogen. Hydrogen would remain a marketable product. The chemistry is interesting. Iron/iron oxide is a catalyst for the Haber-Bosch process, but that process uses pressures considerably higher than would be found in this reaction. That comparison is probably irrelevant, as is shown by ball-milling standard iron oxide, in which case the reaction did not go, so the nano-sizing is important. The question then is, is this a solution to a problem or merely an interesting side-issue? That leaves open the question, how likely is it that this reaction will scale up successfully, and if it does, then run successfully?
The first problem that I could see is that the efficiency drops off at higher current, thus the efficiency of one synthesis was >30% at 20 mA, but ~7% at 250 mA. The suggestion was that the conversion is limited by the available area of nano-Fe2O3, which may or may not be fixable during scale-up. From the chemical point of view, the nanoparticles were dispersed throughout the solution, but the electron transfer would presumably occur at the electrodes, so that raises the question, exactly what are the nanoparticles doing? The electrodes were nickel, so they should not be a problem for scale-up, but the area might be. The production rates were in the order of 7 x 10-9 mol NH3 per second per square centimetre. That would require a very large area to get 1t/hr, which is hardly a rate to get excited about. The requirement for nano-sized  Fe2O3 would also worry me because Fe2O3 slowly dissolves in hot sodium hydroxide solution to make sodium ferrite. This was not mentioned in the article. On the other hand, they found conditions that stabilized production for six hours. (Actually, it may not be beyond the bounds of possibility that sodium ferrite is the catalyst, as nano-sized Fe2O3 might well be more reactive than the bulk oxide. That is yet another aspect that at least needs answering.) Is this possibly a commercial process? My guess is no, at this stage at least, but it does provide an interesting new opportunity for research. If they could get the current density up significantly, then perhaps there is something here.
Would that help solve the greenhouse problem? In my view, since this electricity would be the marginal production, no, unless we find a way to make electricity that totally stops the use of fossil fuels to make electricity. Nevertheless, the production of ammonia is required to address the food problem. However, if we really want to do something about global warming through ammonia usage, then a good place to start would be to make nitrogen fertilizers more efficient. A very large amount of such nitrogen finds its way into N2O, presumably through the decomposition of ammonium nitrite.  Accordingly, there is plenty of work remaining for further research. The question then is, how to fund it? Unfortunately, the scientist's first duty is to obtain funding, which encourages flag waving in papers.
Posted by Ian Miller on Sep 29, 2014 3:17 AM BST
The question I am now posing involves how scientific papers should be presented where the author faces a dilemma. On one hand, the author wants to show something that might lead to more widespread use, but on the other hand, the information might have more general use. The first point is obviously desirable if in fact the use proposed makes sense, but even if it does not it might still make sense while reporting to funding agencies. The second point involves the dissemination of knowledge, and the problem is if it is presented in one way, it may not be seen by others for whom it may be more useful. The huge output of scientific papers means that nobody can read any more than a tiny fraction, and everybody has to have some form of very coarse screening otherwise they never get anything done.
These thoughts were started, for me, by a recent paper (Angew. Chem. Int. Ed. 53, 9755 –9760) which claimed to give an interesting approach to biofuel production, but I feel the more interesting aspect of it was the implied underpinning chemistry. The basic process involved three reactions that started with molecules such as furfural and hydroxymethyl furfurals, which are acid degradation products of carbohydrates. Furfural is readily obtained from pentoses because it steam distills out of a reaction in which carbohydrates are acid hydrolysed at higher temperatures, but hydroxymethyl furfural does not do this, and instead it degrades further. It can be isolated, but at a cost, and at only moderate yield. So, before we go much further, this paper will have questionable direct applicability because it involves relatively expensive starting materials that represent only a part of the initial resource.
But it is what happens next that is of interest. The authors carry out an aldol condensation of the furfurals with acetone, thus getting C8, C9, C10, C16, etc materials. Furfural gives the furan ring and the unsaturated ketone. These are now reacted at elevated temperatures and pressures with NbOPO4 in the presence of hydrogen and a Pd catalyst. The interesting part now is that the NbOPO4 has the ability to pull out the oxygens, including the furfural ring oxygen and the ketonic oxygen (although this may be a dehydration reaction as the carbon-carbon double bond becomes hydrogenated), with the result that we end up with linear hydrocarbons.
The niobium phosphate gets a 94% yield of hydrocarbons, whereas aluminium phosphate gets a zero yield of hydrocarbons, while the palladium there catalyses the hydrogenation of the double bonds. Actually, the phosphate is not that important as Nb2O5 gives the same yield of hydrocarbons. According to the authors, what happens is that the bulk Nb – O  – Nb groups break, permitting a Nb – O – C  bond to form, and a nearby hydrogen atom can transfer to the carbon atom.
The question then is, what use is this to biofuels? Superficially, not that much because the problem of getting furans probably makes this uneconomic. Not only that, but while the C16 hydrocarbons would make excellent diesel, linear C8 hydrocarbons are not at all attractive as fuels, as lying in the petrol range and having an octane number approaching zero makes them undesirable. What I would find more interesting, though, is how this catalytic system would function with lignin, or lignin derived smaller molecules. While lignin polymerization has essentially no pattern, nevertheless many of the linkages occur through C – O – C bonds. If they could be hydrogenated, and the methoxyl groups removed, it might be a breakthrough in biofuel development. The question then is, why did these authors not try their reaction on lignocellulose to see what would happen? Perhaps they did, and perhaps there are more papers coming, but I do not feel that is constructive. We need to see the fewest papers presented consistent with getting all information over, so as to reduce the deluge.
Posted by Ian Miller on Sep 14, 2014 10:43 PM BST
The question of how planets form continued to attract attention. Everyone agrees the accretion starting position is the disk of gas falling into the forming star. The gas also contains "dust", ranging in size from a colloidal dispersion to pieces a few millimetres in diameter. It is possible some pieces could be bigger, but we would not see them. The question then is, what happens next? The standard theory is that by some undefined mechanism, this accretes into planetesimals, which are about the size of asteroids, and the resultant distribution of these, which is smooth and continuous with regards to distance from the star, gravitationally collide. The asteroid belt is therefore likely to be the remnants of this process. In my opinion, that is wrong, and the first stages were driven by chemistry, and the distribution of growing bodies is highly enhanced in certain zones of temperature appropriate for the specific chemistry.
There was an interesting paper in Nature 511: 22-24  that surveyed problems with the standard theory of planetary formation, and ends with the question, "Why is our system so different from so many others?" Unfortunately, no answer was provided. As my theory shows, the reason is very simple: the admittedly limited evidence strongly suggests that our star cleaned out its accretion disk very quickly after formation, and this stopped accretion. Other systems kept going, which leads to more massive bodies and stronger gravitational interactions, and this results in what is effectively planetary billiards takes place. Unfortunately, once gravitational interactions get big enough, the resultant system becomes totally unpredictable.
Another interesting problem involved the question of rubble-pile asteroids. One major question is how rocky planets accrete, and the standard theory seems to assume that somehow moderate sized objects form, and gravity makes these come together, and as they get more rubble, they become bigger objects. Eventually they become big enough that they heat up, partly through radioactivity and partly through the loss of potential energy when bodies pile up, and the heated body starts to melt together. Asteroids are often believed to be piles of such rubble. However, two papers were published that make this proposition less likely. In this context, my theory requires rocky bodies accreted while the accretion disk is still present to be joined together chemically, and in the case of the asteroids, by cements similar to those used by the ancient Romans, and which also come from certain volcanoes such as Vesuvius. Such asteroids can still be piles of rubble, but cemented together where the surfaces meet. Effectively, they are very poorly compacted concretes. Also, non-cemented rubble piles would exist if the pieces came together following the disk clean-out.
The first (Nature 512: 174 – 176) involved asteroid (29075) 1950 DA, which has a density of 1.7 0.7. Since the solids are believed to be similar to enstatite chondrite, it should have a density of 3.55, hence it appears to have about 50% space inside it.  However, the rotational velocity is such that if it comprised rubble, the rubble should peel off. The authors argued that it must be held together with van der Waals forces from fine grains between the larger pieces. I have a problem with this. If the spaces are filled, then the density should be higher. Note that van der Waals forces are very weak at a very short range, and according to Feynman's calculations, they fall off inversely to the power of 6 with distance. The second paper (Icarus 241: 358 -372) analysed the size/frequency distribution of small asteroids and compared these with computed collision frequencies, and they found that the assumption of rubble-pile asteroids leads to a significant worse fit with observation than the assumption of monolithic bodies, hence they conclude that the majority of main-belt asteroids are monolithic.
Finally, there is the question of global magma oceans. The standard theory has rocky planets finally accreting through massive collisions, which lead to massive generation of heat, which in turn converts the rocky planet to magma. However, evidence has been presented (Earth Planet. Sci. Lett. 403: 225 – 235) that the geology of Mars is incompatible with this picture. My mechanism for planetary formation does not forbid a magma ocean, but unless there is a giant collision between two massive bodies, there will not be, and planets can form without one. In fact, they probably have to, because the energy of collision of massive bodies is generally such that size reduction occurs as material is shed to space.
Posted by Ian Miller on Aug 31, 2014 9:34 PM BST
An interesting problem is how should scientists present their information to the public. The issue is more complicated because we have to assume that some of the public will be educated enough to understand what is presented, and if there are flaws, to pick on them. The problem then is, as other members of the public see the fallout, science itself gets discredited. One piece of news that I saw was a statement that from analysis of the decay products of heavy isotopes 182Hf and 129I, the gas and dust that formed the solar system was present in a dust cloud isolated from interstellar space for 30 million years before collapse to form the solar system took place. The news item stated that this was quite remarkable, because it only took about 1 My for the star to form once it got going (or so we think) and about 30 My for the rocky planets to finally form (this is almost certainly wrong – Mars took about 3My.)  What would be your reaction to seeing that?
My initial reaction, knowing something about the subject, was to say, "Hold on a minute. We date the early stages of solar system formation through the decay of 26Al, and that has a half-life of about 73,000 years." If we take the half-lives through 30 My, it becomes obvious that there is essentially no 26Al left. As it happens, with what we know to have been present initially, there is insufficient left to be useful for dating after about 3My at best. So, how do we resolve this?
If we look at the actual paper, (Science 345: 650 – 653), what they actually say is that certain radioactive nuclei were formed 100 My and 30 My before the sun started forming. They then produce one of those "pretty pictures that implies just about everything important ended 30 My before star formation, and that is presumably what the writer of the public statement latched onto. This is not helped by the same being presented in an explanation (Science 345: 620-621) which states early on that the gas cloud was isolated for 30 My before stellar formation. However, at the end of the paper, the authors of the paper conceded that additional supernovae were required to put the 26Al into the gas just before star formation. The problem is, such supernovae would also put in more of the other isotopes as well.
Thus the statement that the dust formed 30 My before star formation is just plain misleading. That does not mean it is wrong, and the authors have found something. The problem is, it has since been interpreted as something else by the media who do not have the skill to actually analyse what is there. So, what the story should have said is that the material used to form the solar system was a mix of material from a sequence of supernovae. The basic gas, hydrogen and helium, was, of course, there from the big bang.
This article could be written off as unimportant. The problem is, this sort of reporting is more widespread. Think of climate change. Why is there such a heated debate? Surely we can find some critical results and agree what they mean. Unfortunately, this does not seem to happen. I think that learned societies have a responsibility to present critical fact-stating documents, where everything within them is analysed and its reliability stated. Most topics have only a very limited number of really critical papers; the problem is to get these summarized so that the conclusion is not misleading.
Posted by Ian Miller on Aug 17, 2014 10:50 PM BST
One of the more unusual publications recently involved a theoretical computation of a hypothetical carbonium ion (or at least a very short-lived molecule-ion) C-(CH3)5 . (Angew. Chem. Int. Ed 53: 7875 – 7878.) Computations concluded that the structure was that of a trigonal bipyramid, which effectively had three methyl groups around the central carbon atom, which was in sp2 configuration, and two other methyl groups bonded to the p orbital of the central carbon atom. All methyl groups were in sp3 configuration. The important point about such a computation is that the ion is argued to be sufficiently stable that it exists, albeit short-lived, as it has two computed decay modes. The question now is, is it right? The issue is important because it proposes a type of bonding that so far has not been recognized, or if it has, the recognition passed by me.
There is one important point to note. Computations indicate that the CH5 ion does not follow the same structure. This ion can be considered as a distorted CH3 system that bonds to a H2 molecule. This gives three equivalent hydrogen atoms and two further equivalent, but different atoms. This is supported by the infrared spectrum (Science 309: 12219 – 1222) which shows a fluxional molecule consistent with that structure and with full hydrogen scrambling. Why does the replacement of hydrogen atoms with methyl groups make such a difference? Then again, does it?
The CH5 ion is conceptually simple, in that it is really a carbenium ion making an electrophilic attack on a two-electron bond. Now, if it will do that to the hydrogen molecule bond, why does the same thing not happen with, say the (CH3)3 – C ion which could make an electrophilic attach on the C – C bond of ethane?
The next question is, does it matter? I think it does, because it calls into question a number of bond issues. The first is, where is the formal positive charge? In my view, it starts on the central carbon atom. I argued that the gas phase stabilities of the usual carbenium ions is given quite satisfactorily by assuming the positive charge is first located at the formal ion centre, and it then polarizes the substituents (Aust J. Chem. 26 : 301-310.) That makes the (CH3)3 – C ion considerably more stable than the CH3 ion, and that ion would more readily polarize the bond in ethane. The issue then resolves itself to whether the formation of a two-electron C – C – C bond, plus the polarization energy is lower than the energy of the C – C bond in ethane, plus its polarization energy. A further question then is, is a two-electron C – C – C bond even possible? What we are asking, at least in conventional chemical thinking, is for the two methyl electrons that are separated over that distance to pair, and get the appropriate phase relationship. What disturbs me about this is that there are no other examples that I can think of where a vacant p orbital can bind two electrons in that way. My immediate thinking then makes me ask, is there any equivalent in boron chemistry? I am not sufficiently familiar to say there is not, but I am certainly unaware of any. Therefore the question is, does B-(CH3)5 exist? If the trigonal bipyramid structure for C-(CH3)5 is correct, one would think it should because the troublesome ionic character that leads to rearrangement is missing. If on the other hand, such an ion represents the (CH3)3 – C ion polarizing ethane, then there should be no B-(CH3)5
Posted by Ian Miller on Aug 11, 2014 12:27 AM BST
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