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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At this point I had difficulties, but since I had made some new amines in order to measure their acid-base equilibrium constants, I did just that. Then, I measured some rate constants for the reaction of the amines with dinitrochlorobenzene. I then had two Hammett lines, but none with mesomeric withdrawing substituents because the para cyano substituent had also refused to make the amine. Part of the reason was because the very aggressive conditions needed to stop urea formation also tended to hydrolyse the cyano group. I was now back to the Hammett rho factor. We knew the rho value for anilines and benzylamines, so we could estimate that for 2-phenylethylamines. The cyclopropyl group enhanced the rho value by about 30% over the ethyl group, which was consistent with my concept of conductance and two routes. This indicated (to me, anyway) an absence of conjugation, but it was hardly a definitive result. Meanwhile, those wretched styrenes had still not put in an appearance, but of course without the mesomeric withdrawing groups it probably did not matter. I had a rho value, and it appeared that it would be impossible to get such amines consistent with having mesomeric withdrawing substituents. (I have no doubt that a more skilled synthetic chemist may have had more success here, but not with the para nitro derivative. I found it interesting that somebody tried to make this a decade later, and reported the same trouble.)
What now? Suddenly, supervisor put in a cameo appearance. (The 9 month sabbatical had extended to over 16 months, by my calculations.) He had an idea: take the acids, which I had already made and measure the rates of reaction with diphenyldiazomethane. Nobody measured rates of reaction of acids with this material, so get data, pad out the thesis! I was a bit skeptical about this comment, but then again, getting a PhD did have a certain attraction, so off I went. Since apparently nobody had bothered to carry out this with any other acids, I also had to measure the reaction rates with benzoic acids, so I could make some estimate of what the rho values should be, and of course to get an idea of how much mesomeric effect could be expected from substituents. The benzoic acids were available, so this meant plenty of measurements. If nothing else, thesis padding would ensue!
The reaction of the acids with diphenyldiazomethane depends on the acidity, so I expected this to merely reproduce existing   data on the phenylcyclopropanecarboxylic acids, but suddenly I realized that supervisor had made a key advance. The reactions were carried out in toluene, and this amplified the differences in acidity. The net result was that all the rho values were much bigger than anybody else had managed to get, and this meant that experimental errors did not have such significance with respect to sigma values. The rho value for the cyclopropane ring was again roughly where I expected it, but now I had some mesomeric donors, the para methoxy and the para fluoro substituent, and furthermore, the para nitro and para cyano substituted acids were available to anchor the line at a greater distance from the rest of the substituents.
Joy to the world! These results were quite unambiguous: the para substitution offered no mesomeric donating properties. I had a conclusion! Thank you, supervisor! Unfortunately, this brought a major problem: the scientific community was coming to the conclusion that cyclopropane conjugated with adjacent unsaturation, and here was me with results saying it did not. The reason for the conclusion that it did were:
(a) Hammett rho values for 2-phenylcyclopropyl-X were about 30% higher than those for 2-phenylethyl-X
(b) Cyclopropyl stabilized adjacent positive charge
(c) Cyclopropyl adjacent to a chromophore such as a benzene ring gave a bathochromic shift to UV signals.
(d) MO theory, and in particular CNDO/2 computations, said it conjugated.
(e) Dipole moments of molecules such as cyclopropyl chloride were about 0.3 Debye less than, say, isopropyl chloride.
All was not bad, because there were also data that indicated that cyclopropane did not conjugate. There were also some almost confusing options, thus the fact that the C-Cl bond in cyclopropyl chloride was slightly shorter than alkyl chlorides could be explained in terms of changed hybridization, but what did that mean in relation to conjugation? So, I had a further problem: I had to write up. No problem with much of the thesis, until the conclusions, where I had to deal with (a) to (e). My choices were simple: I had to show that my results were wrong (most undesirable because that was guaranteed failure, and anyway, I backed them) or irrelevant (again, undesirable, as why had I chosen this project?) or I had to find an alternative explanation for (a) to (e). Welcome to the start of an unusual career! I was happy that I had (a) under control, but . . . To add to my problems, supervisor disappeared again, apparently seeking a better paying job in North America.
How many of other PhD students had to take on an essentially emerging scientific consensus amongst those who had influence, essentially on their own? The problem was, how to do it?
Posted by Ian Miller on Nov 23, 2012 6:01 AM GMT
Ever had trouble making something? Yes, I had further problems. Recall, I needed a sequence of substituted trans-2-phenylcyclopropylamines, and I would get the amine through the carboxylic acid. My aim was to tell whether the para nitro substituent would give the sigma constant typical of conjugation, or no conjugation, which meant I needed the para nitro substituent, and I would prefer the meta nitro substituent to "anchor" the Hammett line.
The para nitro compound would be a straightforward nitration, or so I thought, of the carboxylic acid. The literature suggested concentrated nitric acid at 30 degrees C, to get an awful yield, so I tried fuming nitric in an ice bath. The product melted at 170 degrees C, not the required 198 degrees, and was shown to be the then unknown dinitrophenyl cyclopropanecarboxylic acid. Nitric acid diluted with acetic acid kept below 5 degrees for five hours gave a 75%  yield of the right stuff. So far, so good.
The meta nitro compound was obtainable, in principle, through my standard synthesis, except that after the Friedel Crafts reaction of succininc anhydride with benzene, I nitrated the resultant ketone, and ended up with the meta nitro substituted keto acid. Easy! Then all went well until the cyclization: a zero yield of cyclopropanecarboxylic acid, and a 100 % yield of shog, aka dirty brown rubbish.
It was around about now that supervisor went overseas on a 9 month sabbatical. No advice about what to do. Anyway, I thought I had better make the amines, because these wretched styrenes that I had ordered some time ago refused to turn up. Amine conversion went well, until, disaster, the para nitro compound refused to behave. The Curtius reaction went well enough, and I made the hydrochloride of trans-2-p-nitrophenylcyclopropylamine in good yield. If I dumped this into strong alkali, I got the amine (at least I believe so) but under any conditions near neutral pH, where there could be some of both protonated and base forms present, there was an immediate production of a reddish brown condensed product. By definition, the measurement of a dissociation constant requires both to be present. Using it as a nucleophile to carry out a displacement generally permits some of the protonated form to be present, as you cannot carry out kinetics of a nucleophilic displacement with molar NaOH present. Now what?
My nearest piece of inspiration was to risk some of my p-bromo substituted acid and try to carry out a nucleophilic substitution with cyanide. In this reaction, the cyclopropyl ring retards the reaction, but it worked. The yield may not have been magic, but it was adequate. Whew! Not so fast! Conversion to the amine was again, troublesome. I was in trouble. I was also on my own; supervisor remained absent, not even mail, and nobody else was offering help.
One final piece of amusement, that could have been in the previous blog. As a reward for supervising senior organic undergraduate labs, I was permitted to get some non-critical synthesis done for me, so I got a student to try the Friedel Crafts reaction of succinic anhydride on ethyl benzene. The student worked well (I supervised the first part very closely!) and eventually the student proudly announced he had a good yield of white material. I suggested he do a melting point, so we could see how pure it was. Some time later, he was still measuring the melting point, so I asked him what was taking so long. "It isn't melting," he replied. A quick flame test told me all I needed to know: he had thrown out the product and kept the aluminium oxide. It would take some time to measure the melting point of that!
Posted by Ian Miller on Nov 17, 2012 2:29 AM GMT
As most people who have undertaken a PhD in organic chemistry know, synthesis can take a long time, even when the objective is not primarily synthesis, so to get a sense of proportion in this account, this seems to be time for an interlude, wherein some various tales of, well, you can choose your word, can be told. So, here are some things that should not have happened.
The prequel, and warning that not all is as it should be, happened in the summer when I had been hired for my first taste of research. I came back from lunch and saw water on the floor from the bench behind me. A hose had come off a small condenser, and a small "river" of water was snaking across the bench. By itself, a nuisance, but in two dry bits, enveloped almost by the winding "river", were two sizable lumps of sodium sitting there! Fortunately, I knew where some tongs were, so tongs, then tap, then when the perpetrator returned, some language not befitting an output of the RSC!
I started the PhD in a small “temporary” building called “The Armoury”, a sort of overflow lab because the main chemistry building was “full”. One advantage was it was near the Students’ Union cafeteria, so coffee was at hand. Soon after starting, my supervisor announced he was to do some lab work, a statement not greeted with unqualified enthusiasm by the senior PhD students. His first move was to purify a very large amount of acetic anhydride by distillation, but after a short period into this exercise, there was a yell, an emergency wash,  and a very strong smell of acetic anhydride. No boiling chip or stirring, and not a lot of work for the rest of the afternoon. There was no repeat of this enthusiasm for lab work! It was also suggestive that good advice for lab work might not be forthcoming.
One morning I came in and saw a remarkable sight. There was a small room at one end directly facing the path to the Student’s Union, and on a bench on the far side from the window, someone had carried out a sealed tube pressure reaction. The top had blown, there was a 2 mm hole drilled through the safety shield, and in a direct straight line from the tube, hole in shield, there was a further 2 mm hole in the window about 3 meters away. That did not put me off pressure reactions (I have done quite a number through my career) but I always used steel.
After a year I was moved to the top floor of the chemistry building, and old stone building with basically one entrance. At some point, a Colombo Plan student was brought in and put at the bench behind me. Since nobody knew what his skill level was, I was asked to offer assistance. His first synthesis involved reacting a ketone with a Grignard reagent, so I discussed what would happen and set him off. I had to help him get it started, but soon the magnesium was reacting well. About two hours later, I heard the bleat, "I've got two layers." I pointed out that was expected when he poured his ether into the acidified ice-water. "But I haven't done that yet." Somewhat annoyed, I had to go around the other side of the island to see what he had done, and there were two layers! Had I tried, I could not have done that in a hundred years! He had managed to add the ketone as an ethereal layer on top of the Grignard! His hand shuddered, and as I dived for the floor there was a roar like a rocket motor (OK- slight exaggeration). Fortunately, there was no gas lit in the room. So, I gave him a lecture about the need for stirring or refluxing, and he was at it next day. About three in the afternoon, another bleat, "I've still got two layers!" I succeeded in getting him removed from the lab.  More next week.
Posted by Ian Miller on Nov 9, 2012 7:44 AM GMT
My supervisor finally reappeared, fresh from prolonged summer holidays, and for some reason I could not understand, my brilliant project was not greeted with unqualified enthusiasm. Just maybe he saw problems that eluded my somewhat innocent/inexperienced state but somehow he accepted and so I was off to the bench. The good news was that trans 2-phenylcyclopropylamine was made commercially; it is a monoamine oxidase inhibitor. (Memo to self: emphasize hygiene and clean working! Recalling that baggage, I did not want my brain messed up.) The simplest route was through the Curtius reaction from acids (acid chloride, nucleophilic substitution with azide, thermally decompose azide, acid hydrolysis of isocyanate). So, the problem now was to make the carboxylic acids. The most obvious route was rather long and only gave para substitution: Friedel Crafts with succinic anhydride, borohydride reduction to give the lactone, thionyl chloride to give the 4-(substituted phenyl)-4-chlorobutyroyl chloride, which was then esterified with ethanolic HCl, then cyclization with sodium t-amylate, purified by oxidizing out the olefinic material with alkaline KMnO4. Long-winded, an interesting filtration problem, but seemingly free of big problems.
There were two reasons to look for something else. The first was to get something quicker, while the second was to get some meta substitution. The literature said that ethyl diazoacetate on styrene gave a 5% yield of the desired compound. That did not impress me. I tried the zinc-copper couple/di-iodomethane on ethyl cinnamate, but no significant yield of desired product resulted. This was not unexpected, because that reaction was known to be difficult when the olefin was electron poor. The reaction of the ylide from trimethylsulphoxonium iodide on ethyl cinnamate did not work either, although a little help here from supervisor could have come in handy. The reference was from Corey, in a Tet. Lett. It was only much later, in a J. Org Chem., did I learn that the reaction only really works at minus 80 degrees. Silly me, I never thought of that, but a more experienced chemist might have asked, what were those bubbles – try cooling it until they stop. However, I did get a reasonable yield with alkali, triethylphosphonoacetate and styrene oxide. So, I immediately ordered some meta substituted styrenes. The basic problem with this project, of course, was that the electron withdrawing substituent that could show mesomeric effects would be para nitro, and its sigma value was some distance from the others in the line, which meant that the line had to be well-anchored so that the extrapolated "non-mesomeric" value had as little error range as possible.
The best way to avoid this difficulty was to make the meta nitro substitution, so while making a number of compounds by the "slow" route while waiting for styrenes, I made a lot of the simple reaction of succinic anhydride with benzene, and nitrated it. That gave me a lot of meta nitro substituted acid, so then I took that down the route to the cyclopropanecarboxylic acid, but when trying to form the cyclopropane ring, disaster! There was essentially a 100% yield of dirty brown rubbish. Supervisor had no suggestions, and it appeared that I was down to extrapolation, or doing something spectacular with one of the styrenes. Which raised the question, a year later, just where were those styrenes? It was around about now I started to get nervous. It was also somewhere about now that supervisor went off on a 9-month sabbatical. More soon!
Posted by Ian Miller on Nov 2, 2012 11:44 PM GMT
Again, my theories on planetary formation survive another month, although if I were rewriting I would amend the literature survey a little. There were three papers of particular significance. 
Paniello (Nature, 490: 376) examined zinc isotope evidence from lunar rocks and concluded that the moon had an additional condensation step than Terran rocks. This is in accord with the generally accepted theory that the Moon was formed by the condensate from a collision of a body called Theia with Earth. By itself, this is unexceptional, however there was also a comment by Elliot (Nature, 490: 346) in which he notes that collisional models suggest the Moon should be made predominantly from material originating from Theia, in which case isotope distributions of non-volatile elements should match Theia, but they are essentially identical to those of Earth. Elliot suggests that this requires an extremely rapidly rotating Earth prior to collision, which seems unlikely. Elliot overlooked the option that Theia accreted at an Earth-sun Lagrange point (Belbruno and Gott. 2005. Astron. J. 129: 1724) either L4 or L5, in which case Theia would have the same isotopes. I favour that interpretation, mainly because my theory argues that Earth forms at the most favourable temperature for rocky accretion.
Shcheka and Keppler (Nature 490: 531) did me a favour. One big problem in accounting for earth's atmosphere is why is xenon depleted compared with argon, and to a lesser extent, krypton. One answer is that the initial atmosphere suffered strong hydrodynamic escape to space, which led to an enhancement of heavy xenon isotopes, but that should remove almost all the argon. These authors found that perovskite, which makes up much of the Earth's mantle, can dissolve up to 1% argon. The reason is, anomalies in perovskite (MgSiO3) arise through elements like aluminium getting in, which create holes that are roughly the same size as argon. Xenon, being bigger, does not fit. Under this scenario, the early hydrodynamic escape (powered by intense solar radiation on an atmosphere of retained accretion disk gases) of hydrogen and helium drags off most of the other elements, and subsequent argon is released, without heavy isotope enhancement, by volcanic degassing.
Cassata et al. (Icarus 221: 461) determined isotope ratios of trapped argon from the Martian meteorite ALH84001 and concluded that the atmospheric pressure on Mars at 4.16 Gy BP was < 400 mbar, and accordingly a CO2 atmosphere could not have had sufficient pressure to have sufficient greenhouse gas to permit water to flow. This strongly supports my theory, in which it was ammonia that dissolved in water and lowered the melting point. At first I got excited, because these authors used a C/N ratio that only made sense if the nitrogen ended up underground. That would strongly support my theory, but unfortunately it did not. Closer reading showed they assumed the C/N ratio.
Finally, you may wonder why I got involved with planetary formation theory. In the early 1990s, thanks to a persistent economic downturn, I had some spare time, so I wrote a science-fiction book about the colonization of Mars, in which the bad people were intending to get rich by floating junk shares/stock on Earth. (There were plenty of examples of fraud to learn from in the previous decade!) To expose the fraud, I needed an unexpected discovery, and in my background, I had published one paper arising from the idea that the CO2 atmosphere beloved of geologists would lead to basalt weathering and giving ferrous ions, which, in turn, could photochemically reduce CO2. We did some experiments and it does, but then I became concerned; what happened to the ferric ions? A few experiments showed that ferric ions are very aggressive at photochemically attacking carbohydrates and amino acids. Somehow, CO2 being part of the origin of life became much less attractive.
Accordingly, for my required "unexpected discovery", I tried for a reduced atmosphere, which would lead to massive underground deposits of urea. (Yes, I know it might go further, but . . .) My agent managed to persuade the editor of a major publisher to look at it, but the editor died. The replacement cleared the desk, and rejected my novel on the grounds it was too implausible. I was fairly confident "colonization of Mars" was not too bad for SciFi, with big money around, fraud is hardly implausible, so that left the reduced atmosphere. How dare a literary editor trash my chemistry! So I became involved. The experts say that thanks to UV radiation, ammonia would only last decades and so is irrelevant, nevertheless the only available sample of ocean from about 3.2 Gy BP has levels of ammonia in it approaching those of potassium. I back observations over "experts", even if the observers did not realize the significance of what they found. Incidentally, if anyone is interested, the offending book, Red Gold is now available as an ebook on Amazon, and I have included a précis of the theory in an appendix.
Posted by Ian Miller on Oct 27, 2012 12:24 AM BST
Mid December, and time to select a supervisor and project. That was easy; I selected my supervisor on the grounds he was enthusiastic over a project. I did my background reading, got some glassware to my bench, and was all ready to start, but with two days before time to go away for Christmas, I headed for the library. Then, for a Christmas present, I gave my supervisor the results of the project: it was neatly written up in the latest JACS. Oops! Worse, there was no safety net; apart from these measurements there was nowhere to go with the compounds.
Back from Christmas, my supervisor gave me two new projects. One was to examine solvolyses of a number of substituted acetylacetonates of various metals, to see the degree of electronic effects that could be related to various metals. That seemed a great project, until the literature indicated that the rate constants of at least some were zero. Not promising! The alternative project involved fusing a cyclopropanecarboxylic acid to the 9-10 position of phenanthrene, and examine the possibility of conjugative effects of substitution on the phenanthrene on acidity. At the time, there was a debate as to whether cyclopropane transmitted conjugative effects.
I saw difficulties. To get a starting material, one took 3 kg of refluxing phenanthrene and carefully added about 700 g of ethyl diazoacetate while avoiding using scratched glassware, etc. If things went wrong, bang! The report indicated that it was possible to extract about 25 g of product from the 3.6 kg of resultant tar. As if that were not bad enough, how did one get substitution? Trying to make 3 kg of a substituted phenanthrene did not seem to be particularly attractive, especially since the most reactive carbons of phenanthrene itself are 9 and 10. Substituting the basic product was possible, but there was a risk the 2-position (para to the other phenyl) would be the most reactive. Accordingly, I was fairly dejected when the Head of Department met me walking towards the department. When I explained, he smiled and said, “Why don’t you select your own project?” That was probably just to get rid of me, but I took him up on this offer. (Note to self at time: supervisor not functioning on all cylinders, and most of time so far, he was somewhere else! Little did I know I was getting into the groove!)
At that time, two results had come in from the dissociation of a sequence of 2-phenycyclopropane carboxylic acids, employing the Hammett equation. Recall my baggage? I knew about that. Now the interesting thing about this was the two determinations, one in water and one in aqueous ethanol, came to opposite conclusions! Further, the conclusions were based on the Hammett rho values, which were known to attenuate substitution effects by about a third for every saturated carbon in the chain, but full conjugation, e.g. a double bond, showed little attenuation. The determination in water had substitution effects attenuated by the same as two methylene units, i.e. no conjugation, while the aqueous ethanol results had the rho value about 30%  higher, which led to the conclusion that cyclopropane conjugated about 30-50% as well as a vinyl, as in cinnamic acids. What do you think about that?
I regarded this as hopelessly naïve. Suppose whatever induction measured acted like a fluid. An example might be pushing electron charge, or, dare I think it at the time, enhancing probability? Cyclopropane has two routes to go through, therefore, when you add the second route, it should be 30% higher anyway. More interesting were the sigma values; these represent the ability of the substituent to "push or pull" charge/potential, and each has an inductive value, which is enhanced if the substituent can participate in a mesomeric effect. A quick graphing of the carboxylic acid results showed the rho values were too small to be sure, but if we discarded the para nitro substitution, the water results were also consistent, but with worse scatter, with the rho value being 30% higher. Discarding inconvenient results, I here you say. Well, yes, but there was a reason. The paranitro compound is almost totally insoluble in water, the others are not a lot better, so I considered that it was doubtful if true equilibrium was reached. The ethanol results would be better. The basic problem with considering sigma values was that rho was too small that experimental uncertainty made a conclusion unreliable, but what you could see indicated, based on para methoxy, that there was very little or no conjugation.
So, I could see a project: measure the dissociation constants of the 2-phenylcyclopropylamines. Amines, with one less atom in the road, have higher rho values, which I knew from my previous summer work. Baggage at work for me! So, all I had to do was wait for supervisor to reappear. More to come.
Posted by Ian Miller on Oct 19, 2012 11:07 PM BST
I have seen some blogs from young chemists starting or being involved in their PhD who seem to think they have troubles so I thought that just in case they thought previous times were a golden age, why not disillusion them! This little tale also shows why I got addicted to alternative theories, and has two further messages for young chemists. (1) Give more thought to the importance of beginnings. It makes or wrecks (or lies somewhere in between) the rest of your life, so think! (2) Be careful what you wish for; sometimes you get it! Then it is too late to work out you might be better off without it.
I started my PhD at the end of 1963, but what preceded that is relevant because I started with baggage that most students do not have to carry. During the summer of 1962-3 (southern hemisphere!) I was given employment to assist a little research. The department had been involved with the Hammett equation, and had been looking at some benzylammonium dissociation constants. I had the job of purifying some and making some measurements, which I did, and which introduced me to physical organic chemistry and put my name on a paper for the first time. Then in my honours year, selenium poisoning due to the failure of fume cupboard ducting led to my missing lectures frequently. Then came disillusionment. A lecture on the quantum mechanics of the hydrogen molecule led to an equation across the blackboard, and the lecturer said that he would try to show how progress could be made in solving it. I stopped the lecture to point out the equation had an energy minimum when the internuclear distance approached zero, and where it was supposed to be infinite. (If you want to do theory, it helps if you can mentally determine critical aspects of a function.) The lecturer did not know what had gone wrong (and he was only lecturing QM because someone had to). I suddenly discovered that lecturers did not necessarily understand what they were teaching! And they were going to determine my honours level!
I wanted to understand, so later, once again sick, I thought, if wave particle duality occurs, as in diffraction, electrons do not have an option: they must follow what the wave requires of them. After all, no particle description gets diffraction. So, if the wave determines energy and momentum, why not consider the problem as a standing wave problem? (As an aside, can you think of a good reason why not? Bet you can't!) An important point about stationary waves is that they are single-valued, i.e., they do not self-interfere, which requires the geometry of the problem to fix the location of nodes and antinodes. (In a subsequent paper I submitted, I used an organ pipe as an example. The referee could not understand the relevance.) Now, for a given energy, to a first approximation in the Coulomb field of a hydrogen atom the momentum is independent of the mix of radial/angular momentum, so consider it angular, in which case wavelength is proportional to m(thetadot)r^2. Doubling the interactions (electron pairing) is equivalent to doubling mass, hence at constant frequency (frequency had to be conserved otherwise there would be self-interference and the wave would not be single-valued) the wavelength between the nuclei should be a/root2, where a is the Bohr radius. Then from the Einstein ratio, where energy = h x frequency, the energy of the component on the bond axis, in Cartesian coordinates had to be twice the energy of those components in the free atom, hence the bond energy of the hydrogen molecule was 1/3 the Rydberg energy. Try looking up the observed values – the agreement was extraordinarily encouraging, and I had this weird feeling that I had discovered something. Then, problems! The method did not work for any other bond, so it was wrong, right? Not so fast! For the alkali metals, the errors were a clear function of the quantum number n!
Now what? The next step was to go to the library. Unfortunately, with finals about five weeks away, most of the "good" books were gone. One that was there was by de Broglie, on his "double solution". The good news was that there was someone there who felt that there was a real wave there, which although not necessary for the above reasoning, seemed to be the only way there was a physical cause. The bad news was that it was clear that I needed to learn some more physics to make sense of quantum mechanics. One more thing was clear: I had to avoid quantum mechanics in my finals! So, when finals were over, and my total neglect of quantum mechanics had paid dividends, I had a decision: progress to PhD or go back and do physics. I decided to progress, and put my efforts to learn physics to one side. I could teach myself, so I thought. It turned out to be an interesting decision because I avoided bothering about the mathematical formalism of the state vector approach, which of course specifically forbids factorizing the wave function as I did above. My next problem was simple: choose a PhD project. More soon.
Posted by Ian Miller on Oct 12, 2012 10:54 PM BST
Since I found no papers that falsified the major premises, my alternative theory on planetary formation survived September! Of course the skeptic might say (a) I never found them, or (b) I ignored them. I cannot guarantee that (a) did not apply because I do not have access to every journal (nor the time to read them), but some, having read this month's Chemistry World, may accuse me of (b). This paper (Alexander et al. (2012) Science 337: 721) determined the isotope ratios of hydrogen and nitrogen in various bodies from the solar system with the goal of deciding from where Earth's water came. In particular, they determined that water from the outer solar system has a higher D/H ratio than Earth's water, and since hydrogen on Earth escapes to space, anything that creates hydrogen from water, such as UV photolysis, raises the D/H ratio. There is no known mechanism to lower it. Accordingly, they decided that their determinations falsify some modeling work, which has the volatiles arriving due to the influx of a massive amount of icy bodies during a period when Jupiter and Saturn migrated outwards (having previously migrated inwards!).  (For a planet to migrate outwards, conservation of angular momentum and energy require massive amounts of material from further out to be thrown inwards.)
So, where did Earth's volatiles come from? These authors determined the D/H ratio and the 15N/14N ratio in various types of asteroidal bodies, and found the ratios in CI chondrites closely matched the ratios of Earth's hydrogen and nitrogen. Therefore, on the basis that there were no further possible sources, they decided CI chondrites were the source of Earth's volatiles. If so, that falsified my theory. So, why did I ignore it? Basically because, in my ebook, I devoted a whole chapter with fifty-six references to this issue and most of the critical issues were ignored by this paper, which makes me a little grumpy about both the paper and the refereeing.
What can go wrong with this logic? First, simply matching two ratios runs into the possibility of the fallacy of false cause. The asteroidal bodies have a wide range of results, although the enrichment of one element tends to follow the other. Given a wide range, the value for Earth is likely to match one of them. However, if we compare total mass, the nitrogen/carbon ratios in such chondrites do not match the ratio on Earth by a factor of approximately four, which strongly suggests they are not the origin. Worse, the nitrogen/carbon ratio is almost four times higher on Venus, and two orders of magnitude lower on Mars, which requires each body to be struck almost solely by bodies of different origin and totally different composition. Then, to get the Earth's volatiles, Earth has to be struck by at least 10^23 kg of chondrite, and based on area the Moon would have been struck by about 7x10^21 kg of chondrite. There is no evidence to support this. Of course, CI chondrites are relatively rare in the asteroid belt, so we have to also ask, why did virtually all these collide with Earth, while the other asteroids were not disrupted from their orbits (and the CI chondrites are further out), or alternatively, if the entire asteroid belt was disrupted, why were we not struck predominantly by the predominant silicaceous bodies? Then, previous work by Drake and Righter (Nature 416: 39) showed that, based on isotopes of other elements, no asteroidal body could have delivered Earth's volatiles, and the problem becomes much worse if the predominant asteroids devoid of volatiles also struck Earth. Oxygen isotopes alone characterize both the Earth and the Moon as being different from all other bodies for which data are available.
There is a further problem: why do we think that the D/H ratio on Earth is primeval? On Mars, and particularly on Venus, D enrichment must have occurred, so why did it not occur here? Genda and Ikoma (Icarus 194: 42) showed that there should have been an enhancement of between 2-9 times on Earth; nine times would mean that the current Earth's hydrogen was originally of nebular composition.
The problem with this paper is that conclusions were drawn from a very minor subset of available data, it focused on isotope ratios of hydrogen for water but ignored oxygen, which are known to be characteristic, and worse, the conclusion was reached based on the premise that the set of possible source of water was {comets, asteroids}. The real set is {comets, asteroids, accretion disk}. Just because the current paradigm ignores the accretion disk as the answer does not mean it was not the source. Finally, in my opinion it is extremely wrong to reach a conclusion based on genuinely good analytical data, and then ignore all the previous papers that call the conclusion into question. If referees have any function at all, surely this is one of them?
Accordingly, I ignored it in my claim because it was too complicated to show why in a blog. The chapter in the ebook that dealt with this issue took over 11,000 words, and that assumed that some material from previous chapters had been read. In short, this paper would not have changed that chapter, so as far as I am concerned, the conclusions of the chapter stand.
Posted by Ian Miller on Oct 6, 2012 3:35 AM BST
I believe that society has now become addicted to technology, and accordingly as some of the adverse consequences come to the fore, such as resource depletion, we shall have to address them through science. We cannot just get off the horse and return to a preindustrial lifestyle because there are too many mouths to feed, and too many of these concentrated in cities. To do that, I think we need a greater proportion of the general population to understand how science works. Since I have now essentially retired from lab work, my approach to helping in this has been to publish fiction, with science in the background, and to support that, I have also started a literary blog. My last posting to that involved an answer to the question, why is the science behind invisibility relevant to you? The idea was to show how science does not work with facts, but rather uses them to develop further understanding. Whether I succeeded is a matter of opinion, but more important to me is whether what I wrote is suitable. I am not a teacher, a deficiency that may make what I wrote inappropriate. So, I am reposting that blog below, and I am interested in comments. Also, I rather fancy that many scientists themselves will not have realized the significance of the conclusion. So:
Why put something scientific into a story? If it is merely to impress, in my opinion the effort is wasted. Putting in something necessary to make the story work is much better, however in my writing I would also like to show something about the scientific approach. I feel rather strongly about this latter purpose because we now have so much dependence on technology that we are beginning to create new problems arising from it (such as the dependency on oil, which must run out sooner or later) so we need to know how to address them. An important point about science is that collecting facts and doing mathematics are not the goals; rather the goals are to understand, and to make use of that understanding. Now, let’s reconsider The Invisible Man. In my previous blog, I asked the question, can you think of anything very important relating to invisibility that is relevant to your life? My guess is that most people would shake their heads in despair at that question. How can invisibility have practical use? You simply cannot make people invisible.
The scientific approach looks at problems in a different way. The most common way is to ask and attempt to answer questions. So, why do we see things? Light comes from somewhere, strikes the surface of the object, and is reflected. We then ask, why is it reflected? Because the surface represents a change of refractive index. In The Invisible Man, Griffin became invisible by changing the refractive index of his body to that of air. Assuming that could be done, Griffin would truly be invisible, although there is a subtle price.
Changing a refractive index of an object is generally speaking impossible, but it is possible to immerse it in a medium with the same refractive index, in which case it will disappear, provided it is transparent. So now we ask, what is the difference between transparent and opaque objects? The answer is that opaque things have lots of internal surfaces (such as fractures between crystals) where light is reflected or scattered. We now see the price for Griffin: separate cells have surfaces, which perforce define changes of refractive index, so for Griffin to be invisible, he had to have no cells! That would make life somewhat difficult to maintain. Anyway, now we see we can make transparent objects become invisible by immersing them in a suitable fluid. That still leaves the question, why is this important for the average citizen? The answer is simple. Suppose you put a liquid on the surface of the skin that closely matches the refractive index of skin (about 1.5)? That makes all the roughness of the surface of the skin, which is quite effective at scattering light, invisible, which means that light passes deeper into the body. Now do you see the relevance? Think sunburn and skin cancer!
A number of oils have refractive indices around 1.47. Simply apply oils like coconut oil and you will baste in the sun! Get the skin wet with water (refractive index about 1.33) and your natural protection drops by about 50%. With close matching, very little reflection occurs. This becomes relevant when you apply sunscreens, because the carrying medium provides such matching, and removes almost all the natural reflectivity of the skin. The sunscreen, of course, stops the UV radiation while it is working, but if your sunscreen does not offer UVA protection, putting such screen on your skin may stop you burning, but it may pump the UVA into the lower dermis. Also, while a very high SPF may offer prolonged protection against UVB (which burns) the UVA screen usually decays more quickly. The SPF says nothing about UVA protection, and UVA is presumed to be capable of inducing a cancer. The remedy, of course, is to re-apply frequently, and I also recommend not rubbing it in, but merely smoothly spreading it and letting it dry.
The point I am trying to make is that a little bit of scientific reasoning, together with some necessary information, can lead to a much improved lifestyle. In my opinion, inserting some of these facts into stories, and showing how the reasoning works, is of some value. What do you think? In the meantime, next week I shall provide the answer to the other question that seems to be somewhat troublesome.
Now, is that appropriate? Let me know. Also, did you realize that the carriers in sunscreens by themselves actually promote sunburn and cancer?
Posted by Ian Miller on Sep 29, 2012 12:41 AM BST
In a previous blog, I discussed the case of whether platinum, palladium or gold could form oxo compounds. The argument that they could was published, with mountains of data that allegedly supported the case. Eventually, these assignments were found to be wrong, and one critic blamed the referees for permitting the original publication. Throughout the discussion, however, nobody seemed to come to grips with the problem: what comprises proof? One question that fascinates me is why do undergraduate science courses inevitably omit to address this question? Why do no such courses include the prerequisite for some, even brief, course in logic?
We sometimes see the argument, often attributed to Popper, that you cannot prove a statement in science; all you can do is falsify it. I think that is unnecessarily restrictive. One answer was given by Conan Doyle: when all possible explanations but one for an observation are eliminated, then that one, however unlikely it might seem, must be the truth. The reason why Popper's argument fails in such cases is that there was an observed effect, and therefore something must have caused it.
Set theory provides a formal means of answering the title question. Suppose I carry out some operation that addresses a scientific question and I obtain an observation, and to simplify the discussion, assume I am trying to obtain a structure of a molecule. There will be a set of structures consistent with that observation. Suppose I do another; there will be a further set of structures consistent with it. Suppose we keep making observations. If so, we generate a number of such sets, and because the molecule remains constant, the desired structure must be a member of the intersection of all such sets. The structure is proved when such an intersection contains only one element. Of course, this raises the question of the suitability of data. Simply reproducing the same sort of observation many times merely produces much the same set many times.
The problem, of course, is to ensure that the sets of structures that might give rise to the observation is complete because the logic fails when the truth was not considered, and proof fails when the sets are incomplete. (The truth not being considered may show up if the intersection of all sets is the empty set.) We may now guess at a problem with the oxo compounds: there was an awful lot of data consistent with the argued structure, but it was not definitive. This is one place where it is possible that the referees failed, but then the question arises, is it reasonable to expect the referees to pick it? Referees have general expertise, but only the author really knows what was observed. Should authors have to outline their logic? I think so, but I know I am in a minority.
I should also declare an interest in that last comment. I published a series of papers devoted to determining the substitution patterns on red algal polysaccharides, and I followed that logic. Accordingly, the papers tended to have a large number of set relationships, and a number of matrices. Rather interestingly, eventually the editor told me to desist and write papers that looked like everybody else's. Since I am not paid to write papers, and they made no difference whatsoever to my well-being, I simply desisted.
Posted by Ian Miller on Sep 23, 2012 12:53 AM BST
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