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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Ever wondered why planets rotate the way they do? All the outer ones appear to have prograde rotation, i.e. they rotate in the direction as of they were rolling along. However, Mercury and Venus are exceptions. Mercury has a very slow rotation that is explained by it being in a tidal resonance with the sun, so that is no mystery, but Venus rotates slowly, and the wrong way. Most people have viewed this in terms of the standard theory of planetary accretion, where the central body gets hit by a large number of planetesimals, or even larger bodies, from random directions, and the resultant spin is a result of preferential strikes. Earth may well have included this effect when it was struck by Theia to form the Moon. In this case the Moon's orbit also take sup angular momentum from the collision. Venus has no moon, and it spins slowly so the theory went, it was just unlucky and got hit the wrong way at the end by something big. But if that were the case, why no satellite?
There was a recent paper in Science (346: pp 632 – 635) that put a different picture on this. If the planet has an atmosphere, atmospheric temperatures oscillate from night and day, which creates large-scale mass redistribution within the atmosphere, the so-called thermal tides. The retrograde motion occurs because the hottest part of the day is a few hours after midday, due to the thermal inertia of the ground. Because of this asymmetry in atmospheric mass redistribution, the stellar gravity exerts a non-zero torque on the atmosphere, and through frictional coupling, the spin of the planet is modified. This is why Venus has retrograde spin. Atmospheric modelling then showed that the resultant torques for a planet in the Venusian position with a 1 bar atmosphere are an order of magnitude stronger than for Venus, mainly because the very thick atmosphere scatters or absorbs most of the sunlight before it reaches the surface. As a consequence, rocky planets in the habitable zone around lower mass stars may well have retrograde rotation.
During these posts, the reader may have noticed that I sometimes view computer models with scepticism. Here are two examples that illustrate why. The first is from Planet. and Space Sci. 105: 133 – 147, where two models were made of atmospheric precipitation on Mars ca 3.8 Gy BP. The valley network analysis suggests an average of 1.5 – 10.6 mm/d liquid water precipitation, whereas the atmospheric model predicts about 0.001 – 1 mm/d of snowfall, depending on CO2 partial pressure (which varied from 20 mb to 3 bar in the models) and with global mean temperatures below freezing point. The authors suggest that this shows there was a cold early Mars with episodic snow-melt as a source of the run-off. I rather fancy it shows something is left out of the analysis, i.e. there is something we do not understand, because all the evidence to date makes a persistent 3 bar atmosphere most unlikely, and even then, it only works by a near miss at the extremes. The other came from Icarus 252: 161 – 174. Here, an extensive suite of terrestrial planet formation simulations showed that the rocky planets have overlapping stochastic feeding zones. Worse, Theia, the body that formed the Moon, has to be significantly more stochastic than that of Earth, and the probability that the two would have the same isotopic composition is very small, yet the isotopic composition is essentially identical. The authors state there is no scenario for the Moon's origin consistent with its isotopic composition and a high probability event. Why not concede that the premises behind the model are wrong? And there, in my opinion, is the basic problem. Almost nobody goes back and checks initial assumptions once they have been accepted for a reasonable time. And if you do, as I have done for planetary formation, nobody cares. As it happens, each of these is properly accounted for in my Planetary Formation and Biogenesis.
There is a clear published model from Belbruno and Gott that would permit the Moon to have the same isotopic ratios as Earth, and that assumes Theia accreted at one of the two Lagrange points L4 or L5 (Astron. J. 129: 1724–1745). (Lagrange points are where gravitational effects of two major bodies more or less cancel, and a third body can be at L4 or L5 indefinitely, as long as it does not become big enough to be gravitationally significant. L4 and L5 are actually saddle points, and bodies that fall off the "saddle" have net forces that pull them back, so they carry out motion about the point. Jupiter's Trojans are examples.) So why did these other authors not cite this model as a possible way out of their problem? One possible reason is they have never heard of the model, which is almost never cited, one of the reasons being that within the standard model of stochastic accretion of ever increasingly large bodies, nothing could accrete at the Lagrange points because collisions would knock them off. So now we have a problem. The standard model would not permit the conditions by which one model would explain the observations, but the observations also effectively falsify the standard model. So, what will happen? Because there is no way to have discussions on topics such as these, other than in blogs, the whole issue will be forgotten for some length of time. Progress is held up because the modern method of disseminating information has so much information in it that linking it does not always occur.
Posted by Ian Miller on Apr 5, 2015 11:33 PM BST
Two posts ago, I issued two challenges for readers to try their hand at developing theory, and so far I have received a disappointing response. Does nobody care about theory? Anyway, my second question was, why did nature choose ribose? Recall that ribose is not the easiest sugar to make, and in the Butlerov synthesis, under normal conditions essentially no ribose is made. However, that may be misleading, as there are other options. One that appeals is, providing pH 9 or more is reached, silicates dissolve slightly, and catalyse the condensation of glyceraldehyde and glycolaldehyde to form pentoses, and the furanose form is favoured (Lambert et al. 2010. Science 327: 984-986). This strongly favours ribose.
However, even if we can find a way to make ribose, it is inconceivable that we can do that without making other sugars, so why did nature choose ribose? One answer is, it is the most suitable, but that begs the question, why? It is certainly not that it alone can lead to duplexes once the strand is made, because it has been shown that duplexes based on xylopyranoside or arabinopyranoside, or even ribopyranoside have better duplex binding, and xylose and arabinose are easier to make.
I think the answer lies in part in what is an essentially forgotten paper by Ponnamperuma et al. 1963 (Nature 199: 222-226.) What Ponnamperuma et al. did was to take adenine, ribose and phosphate in aqueous solution, then they shined hard UV light (wavelength about 250 nm) on it. Products included adenosine and adenosine phosphates, including adenosine tripolyphosphate. This was quite a stunning achievement, but it leaves open the question, why did it work? Before addressing that, however, we might see why this has been forgotten, apart from the issue of who reads the literature before computer searching? There is a serious flaw in this being the cause of life, and that is that it is almost impossible to conceive of an atmosphere that will remain transparent to such short wavelength UV. For example, water gets photolysed to oxygen, thence to ozone, which screens out the hard UV. If there are reducing materials there, you get a haze like that on Titan, and again, the hard UV gets screened out.
My recommended way of forming a theory is to ask questions, and in this case, the question is, why does light make the phosphate ester? The adenine is clearly absorbing the photon, and one can see that the link between adenine and ribose may be photocatalysed, but what happens next? All bonds in the ribose are σ bonds, so there should be no extension to the excited electronic state. The next question is, how can one make phosphate esters? This is slightly easier: if you heat a hydroxyl and a phosphate with a hydroxyl to about 200 degrees C, water is eliminated and we get the phosphate ester.
This suggests the answer to the problem should lie in radiationless decay of the excited state, where the energy is dissipated in a sequence of vibrational energy levels decaying to the ground state. We now see that a vibrationally excited hydroxyl could form an ester if it had the same kinetic energy as a hydroxyl at 200 degrees C. If that is the case, we now see why nature chose ribose: the furanose is more flexible, and the 5-hydroxyl on a furanose will behave a little like the end of a whip. Ribose is the only sugar that forms a reasonable fraction of itself in the furanose form in aqueous solution. Now, adenine cannot be the primary absorber originally, but there is another option, and that is, given the appropriate reduced rocks, if the cell wall hydrocarbons contain dissolved porphyrans, or some similar material, the absorption could be through them.
Which brings us to an experiment that could be carried out. Make micelles or vesicles from hydrocarbon alcohols with phosphate esters as the surfactant, and have them with dissolved porphyran, and ensure the water within contains phosphate, adenine, and a mixture of ribose, xylose and arabinose. The prediction is that adenosine phosphates will be formed, but the xylose and arabinose will not participate in forming phosphate esters. If that is true, it is fairly clear why nature chose ribose: it is the only sugar that works
Thus we have a clear possible explanation, and an experiment that would confirm of falsify it. The question now is, will anyone carry it out?
Posted by Ian Miller on Mar 23, 2015 12:17 AM GMT
So, my theory challenge, with three weeks to think about it, got no responses. Perhaps nobody is reading these posts. Perhaps nobody cares about theory. That would be ugly. Perhaps the problems were too hard. Really? Anyway, first, a review of where science is at the moment:  My argument is that none of this review answers the question, but it does give a very large number of references. Given that there was this much activity that failed, maybe this challenge was unnecessasrily hard, but let me give you my proposal on how homochirality occurred.

The way to form theories is to ask questions, and in this case ask why did nature choose to be homochiral, given that it wasted half its resources. Why would not some other life form use both, and gain competitive advantage? The obvious answer is that nature chose homochirality because it had to, i.e. if it did not become homochiral, there would be no life. Now, most of what life requires does not demand homochirality. Sources of chemicals could in principle be of any chirality, light is not chiral, energy transport (ATP) depends on the tripolyphosphate, however there is one part where chirality is critical: reproduction. Reproduction occurs when a strand of nucleic acid allows its complement to form as a second strand, where it forms a duplex (double helix). When the duplex separates later, both single strands can grow further new strands, which in turn can form two new duplexes. Note that the helical nature is imposed by the chirality of C-4 on the ribose. The single strand does not have to form a helix, but the two strands, to be intertwined, must both form a helix with the same pitch.

The second strand does not grow by itself. What must happen is that the second strand forms by the complementary bases, with 5-phosphated ribose attached, form hydrogen bonds with their complementary base on the nucleic acid strand. It is now loosely attached by the few hydrogen bonds, and either the required 3-hydroxyl is close to a 5'-phosphate or it is not. If it is, then the ester bond can form, given an impulse from somewhere to overcome the activation energy. If the ribose chirality is correct, esters can form; if it is not, the two sites never come close enough, no ester is possible, and the base eventually wanders off and sooner or later the correct chirality will appear and the duplex grows. Think of a nut and bolt - you cannot make this work if every now and again the thread changes from left handed to right handed pitch. If there is a wrong chirality on the first strand, no duplex can form either, and the impulse required to bring the groups together is now also the impulse required to unravel the duplex.

RNA strands can form loops held together by magnesium ions and these emerging ribozymes can act as catalysts, and these can hydrolyse exposed RNA strands. It may be that it can preferentially solvolyse parts where the pitch chages. Some work is required to validate that piece of speculation, neveretheless, the duplex is at a lower energy than two single strands, so eventually we expect a double helix to form, especially if errors in the chain can be solvolysed.

Once you have a reproducing chiral molecule that can act as a catalyst, then it uses all the resources more effectively than any other option, and when it catalyses syntheses, it synthesises chiral entities. Thus it is RNA that is critical for homochirality; it is the only molecule that can arise naturally, sort itself out, then reproduce. Reproduction ensures that it prevails. Whether it chooses D for sugars and L for amino acids would be pure chance on this interpretation, and it would be predicted that half of alien life would choose the other.

Is that unnecessarily difficult?
Posted by Ian Miller on Mar 9, 2015 12:23 AM GMT
One of the themes I have persisted with in these posts is that in chemistry, thinking about theory is either dead or in terminal decline. Prove me wrong!
In my last post, I offered a challenge to readers, specifically, can you provide answers to:
1.     Why did nature choose ribose for nucleic acids?
2.     How did homochirality arise?
So far, I have no guesses/inspired answers. Come on! Assuming someone is actually reading these posts, either they don't care or it is too difficult. Now, surely you are not going to concede that I can work out more than you can? So, is anyone going to try?
My first answer next week.
Posted by Ian Miller on Mar 1, 2015 8:38 PM GMT
As I haven't updated for some time, there should be a lot of references summarized, however, many of them turned out to be only of partial interest. There were a few papers discussing the origin of chondrules. Up until recently, while the formation of these had been something of a mystery, the nearest there was to a conclusion was that they were formed in the plume formed by collisions of planetesimals. Fu et al. (Science 346: 1089 – 1092) found that chondrules in one meteorite formed at about 2 – 3 My after the first small bodies. This was supported by Palme, et al. (Earth Planet. Sci. Lett. 411: 11 – 19.) who found that chondrules behaved as if they were formed before any larger bodies, and were not formed by impacts. On the other hand, Johnson et al. (Science 517: 339 – 341) argued that chondrules in CB chondrites probably formed in a plume produce by an impact at a relative velocity of greater than 10 kilometers per second. If so, meteorites are a byproduct of planet formation rather than left-over building material. Of course there may have been more than one route that lead to their formation, but as can be seen, there is no clear answer to this question yet.
The landing on the Jupiter family comet 67P/Churyumov-Gerasimenko probably attracted as much recent public interest as anything in science, and some data are coming in. Examination of the comet's water (Altweg et al. Science 347: 126952-1 to 3) showed that the comet had a D/H ratio that is three times greater than Earth's water, and hence Jupiter family comets could not be a significant source of Earth's water. The reason this is important is that the water has to come from somewhere, and comets were once considered the obvious source. However, the usual distant comets were found to have too much deuterium, so Jupiter-family comets became the choice. The alternative is carbonaceous chondrites, but the problem with these is they are rather rare, and lie on the outer part of the asteroid belt. Had they been the source, why were there so many of them, and so few of what are now the more common asteroids? And if there were that many, why did they not accrete into a small planet? In my theory, neither comets nor chondrites are significant sources of water on earth.
 Meanwhile, spectral data of the surface of the comet was compatible with the presence of opaque minerals associated with non-volatile organic material with C-H and O-H bonds, but with very little contribution from N-H bonds (Capaccioni et al. 2015. Science aaao628 – 1 to 5.). There may have been small amounts of ice, but no ice-rich patches and the surface was generally dehydrated. Similarly, (Hassig et al. 2015 Science 347: aaa0276-1 to 4) showed the outgassing comprised water, CO and CO2. The relevance here is the absence of significant amounts of nitrogen-containing compounds, as required by my theory of planetary formation, as long as the body did originate in the Jovian region. That is pleasant support, even though the supporters do not realize it.
Significant results are beginning to come in from Gale crater, on Mars. Of particular interest to me was that from Bridges et al. 2015 (J. Geophys. Res.: Planets: 10.1002/2014JE004757). The clays found at Gale crater was consistent with the basalt having reacted with a fluid of pH between 7.5 and 12, and further, the reactions did not occur in a setting where exchange with an overlying CO2 atmosphere was possible because had it been so, there would have been deposits of carbonates, and there were not. My theory involved an early methane atmosphere with ammonia in the local water, although of course Gale crater may not be a good example of early Mars, as impact craters could have their own localized geology. Nevertheless, overall all these facts are in accord with what I published, and nothing has been found that contradicts it, so I am tolerably happy.
On a more personal level, on March 4 I have been asked by the Wellington Astronomical Society to give a talk, and include some chemistry. Accordingly, I chose "Origin of life" as a topic and have put out an abstract and issued two challenges, which readers here may as well join in.
1.     Why did nature choose ribose for nucleic acids?
2.     How did homochirality arise?
Put your guesses or inspired knowledgeable comments at the end of this post. The answers are not that difficult, but they are subtle. I shall post my answers in due course. In the meantime, I am offering serious discounts on my ebook "Planetary Formation and Biogenesis" from Amazon (US and UK only) from March 6 for about six days, the discount abating over time, so get in early. (Sorry about that commercial intrusion.)
Posted by Ian Miller on Feb 16, 2015 2:21 AM GMT
Yes, this post will be controversial, but I am doing it for several reasons. The first is my wife was convinced there is, and she was equally convinced that I, as a scientist, would quietly argue the concept was ridiculous. However, as she was dying of metastatic cancer we had a discussion of this issue, and I believe the following theory gave her considerable comfort. Accordingly, I announced this at her recent funeral in case it helped anyone else, and I have received a number of requests to post the argument. I am doing two posts: this one with some mathematics, and one where I merely assert the argument for those who want a simpler account.
First, is there any evidence at all? The issue is complicated in that observational verification can only be answered by dying. If there is, you find out. What we have to rely on is statements from people who did not quite die, and there are numerous accounts from such people \, and they claim to see a tunnel of light, and relations at the other end. There are two possible explanations:
(1)  What they see is true,
(2)   When the brain shuts down, it produces these illusions.
The problem with (2) is, why does it do it the same way for all? There was also an account recently of someone who died on an operating table, but was resuscitated, and he then gave an account of what the surgeons were doing as viewed from above. One can take this however one likes, but it is certainly weird.
What I told Claire arises from my interpretation of quantum mechanics, which is significantly different from most others', and I shall give a brief outline now. If anyone is interested in going deeper, I have an ebook on the subject ( I start by considering the two-slit experiment, and consider the diffraction pattern that is obtainable. Either there is a wave guiding the particles or there is not. Most physicists argue there is not. They just happen to give that distribution. You ask, why? They tend to say, "Shut up and compute!" For the fact is, computations based on what is a wave equation give remarkably good agreement with observation, but nobody can find evidence for the empty wave. For me, there must be something causing this behaviour. Accordingly, my first premise is:
The wave-like distributions found in quantal experiments are caused by a wave. (1)
This was first proposed in de Broglie's pilot wave theory, but modern quantum theory does not assert this.
As with general quantum mechanics, the wave is represented mathematically by
 ψ = Aexp(2πiS/h)    (2)
where A is the amplitude, S is the action, and h is Planck's quantum of action. Note that the exponent must be a number. As a consequence, it is generally held that the wave function is complex, but this is not entirely true. From Euler's relation
exp(πi) =-1         (3)
it follows that, momentarily, when S = h/2, or h, the wave becomes real.
My second premise is
The physics of the system are determined when the wave becomes real.   (4)
This is the first major difference between my interpretation and standard quantum mechanics. The concept that the system may behave differently when the wave function is real rather than imaginary has, as far as I know, not been investigated. This has a rather unexpected benefit too: the dynamics involve a number of discrete "realizations", and the function is NOT smooth and continuous in our domain. If you accept that, it immediately follows why stationary states of atoms are stable and the electron does not radiate when it accelerates as required by Maxwell's laws. The reason is, the position of realization does not change in the stationary state, and therefore the determination of the properties shows no acceleration. From that, it is very simple to derive both the Uncertainty Principle and the Exclusion Principle, and these are no longer independent propositions.
Now, if (1) and (4), it follows that the wave front must travel at the same velocity as the particle; if it did not, how could it affect the particle? The phase velocity of the wave is given by
v = E/p        (5)
Since p is the momentum of the particle, and if the phase velocity is the same as the particle velocity (for the particle, consider expectation velocity), then the right hand side must be mv2/mv = v. (Recall that the term v must equal the article velocity.) That means the energy of the system must be twice the kinetic energy of the particle. This simply asserts that the wave transmits energy. Actually, every other wave in physics transmits energy; just not the textbook quantal matter wave, which transmits nothing, it does not exist, but it defines probabilities. (As an aside, since energy is proportional to mass, and mass is proportional to probability of finding it, in general this interpretation does not conflict directly with standard quantum mechanics.) There are obvious consequences of this that lie outside this post, but what I find strange is that nobody else seems to have considered this option. For this discussion, the most important consequence is that both particle and wave must maintain the same energy. The wave sets the particle energy because the wave is deterministic; the particle is not and has to be guided by the wave. There is now a further major difference between this interpretation and the standard interpretation: waves are both linear and separable, as in standard wave physics. There is no need for a non-divisible wave for the total state of an assembly because there is no renormalization due to probabilities.
Now, what is consciousness? Strictly speaking, we do not know exactly, but examination of brains that are conscious appear to show considerable electrical activity. Furthermore, this activity is highly ordered. While writing this, my brain is not sending random pulses, but rather it is organising some reasonably complicated  thoughts and setting out action. To do that, and overcome entropy, there is a serious expenditure of energy in the body. (The brain uses a remarkably high fraction of the body's energy.) I leave aside how this happens, but I require consciousness to be due to some matrix that remains undefined but evolves and is superimposed on the brain, and it orders the activity. Without such a superimposed entity, simple entropy considerations would lead to the decay of the order required for conscious thought. Such order must involve the movement of electrons an since this is quantum controlled, then the corresponding energy must be found in an associated wave. It therefore follows that when we are conscious and living "here", there is a matrix of waves with corresponding energy "there".
Accordingly, if this Guidance Wave interpretation of quantum mechanics is correct, then the condition for life after death is very simple: death occurs because the body cannot supply the energy required to match the Guidance Waves that are organizing consciousness, but if at that point the energy within the Guidance Wave matrix can dissociate itself from the body, and maintain itself "there", and recall that the principle of linearity is that other waves do not affect it, then that wave package can continue, and since it represents the consciousness of a person, that consciousness continues. That does not mean there is life after death, but it does in principle appear to permit it.
Is the Guidance Wave interpretation correct? As far as I am aware, there is no observation that would falsify my alternative interpretation of quantum mechanics, while my Guidance Wave theory does make two experimental predictions that contradict standard quantum mechanics, and these could be tested in a reasonably sophisticated physics lab. It also greatly simplifies the calculation of some chemical bond properties.
Is there life after death? In my opinion, you only find out when you die, but interestingly, this interpretation gave Claire surprising comfort as her death approached. If it gives any comfort to anyone else, this post will be worth it to me.
Posted by Ian Miller on Feb 2, 2015 1:34 AM GMT
Back again. My wife died on the 16th of January, so my blogging will be a bit erratic for a while, but at the end of last year I had planned some, and one theme included the behavior of the scientific community in the dissemination and discovery of knowledge, so here is the first blog that was written before this unfortunate event.
In a recent essay in Angew. Chem. Int Ed. 52: 118 – 122, van Gunsteren outlined what he considered the seven sins in academic behavior, which he ordered in increasing gravity of the offence. I found this to be quite interesting, and worth exploring further, The least "severe" sin, according to the author was "Poor or incomplete description of the work". As the author says, reproducibility is a critical element of good science.
Why is this not such a sin? The author then argues that with the growth of complexity of equipment and the growth of the sophistication of mathematical analysis aided by computers, the publication and analysis of all data required for others to reproduce the work has become more cumbersome. There is no doubt about that, and there is also little doubt that journal space does not lead itself to providing everything, but this in turn raises an interesting question: is the finding of the experiment that complicated that some simplified version cannot be provided? That leads me to a particular dislike I have for computational chemistry papers, in which the general reader such as me, who has an interest but is not involved, has no idea what key features led to the conclusion because they are not listed. Of course the program details are too complicated, but if there is nothing of general interest, why is it published?
When I was doing my PhD, I tried a synthesis outlined in a report in Tetrahedron Letters, and I could not get it to go. Now first, the substrate was not the same, so maybe the reaction did not go on what I was trying to do, at least that was the conclusion I reached, so I abandoned that route, and instead tried a route that was very much longer, but for which I at least could find enough details to know whether I was doing it properly. Also, while it was time-consuming, at least it had the merit of working, although it did not give me quite the range of substitution patterns I would have preferred. (I also tried an alternative synthesis, and it worked to some extent, but only on the most electron-rich substrates. That gave me more reason to believe the first option would not work.) However, four years after I had finished my PhD I came across a full paper where the real details of that failed option were finally published, and one condition that I doubt a young student would be likely to recognize as important had been left out of the letter, yet this condition was absolutely critical, and it would never have been put in accidentally because it needed a special procedure that was quite outside the usual conditions of organic syntheses. I do not consider that a minor sin. I consider that as likely to be due to an egotist who wanted to get as many papers in this field before others worked the obvious possibilities. In my opinion, a synthesis procedure is useless unless sufficient detail is given so that a tolerably competent chemist can carry it out and make the required product. So, for me, if this is a minor sin, some of the others must be pretty bad.
Van Gunsteren then proceeds to criticize the practice of dumping procedures in supplementary information. His criticism of this is largely based on this being less well reviewed than the main body of the paper. Personally, I do not find this to be terribly important. The fact is, in most papers there is a strict limit to what peer reviewers can be required to find. They may, and I have occasionally found absolutely critical errors of procedure, but basically the whole point of peer review (at least in my opinion) is to ensure the paper is coherent and understandable, and makes a point worth making. The peer reviewer usually will have no more chance of finding a basic flaw in a procedure than anyone else who does not try the procedure, and the peer reviewer cannot be expected to reproduce the work. It is the responsibility of the author alone to ensure that the details are correct, AND all details are there. After all, the author alone actually knows what was done, unless, of course, it was a student who did it
Posted by Ian Miller on Jan 19, 2015 7:04 PM GMT
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
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