User:Armondikov/Now/Mar12

23rd March 2012
The case against the nuclear atom (V).

I will finish this book, I swear I will. Anyway, just as Part IV recapped that Larson had proved his point, Part V recaps that he's proven his point and laid out his central thesis. It's like that old joke about BBC documentaries where in Part 1 we'll be looking forward to Parts 2, 3 and 4, in Part 2 we'll just recap Part 1 and tell you that Part 3 and 4 are coming up that will involve looking back on Part 1 and 2... it's an odd sort of self-referential recursion that would make even Douglas Hofstadter blush!

In Chapter 5, Larson mostly waxes lyrical about the nature of the Bohr atom, but by a long detour into talking about other hypotheses that never had a shred of experimental evidence when predicted but turned out to be justified. Namely the neutrino and the structure of the benzene ring. However, hypotheses like this don't come out of nowhere as Larson seems to imply. The ideas are testable, yes, but they also go toward explaining what we know. The predictions of the neutrino fell out of the need to mathematically balance beta decay, [Neutrino#Pauli.27s_proposal specifically conserving momentum, spin and energy]. Of course, Larson's complete phobia of mathematics might view such balancing as unnecessarily complex, yet still, the idea that something must be making the numbers add up lead to the neutrino. Similarly, so many discrepancies with benzene and the properties of other carbon-based alkanes indicated that something was up there. These hypotheses were justified because they had to account for unusual behaviour, and remained quite open possibilities until experimental verification afterwards. Luck, though, didn't play a part in this sort of scientific development. As I said, something had to account for the data, and that "something" would have to have the properties ascribed by the data!

The rest of the chapter is devoted to some philosophical musings. I think. It's kinda hard to tell. Even trying my best to get into what he's trying to say. He's certainly leading up to his summary dismissal of quantum mechanics as a fudge to make an illogical model work. But here's the main problem that comes up so often in this book that any critic would sound like a broken record: Larson is very unspecific in his criticisms of established theories. We are aware of his opinions on mathematics, and I'm sympathetic to that, but if his model is "correct" and the established model is "wrong" then please propose the experiment to differentiate them. The Schrödinger equation with a fairly simple Hamiltonian for a proton and electron perfectly predicts the spectral absorption lines of hydrogen - Larsons model presents nothing. He seems to expect other to do such legwork now he's made such genius logical deductions from the Marsden-Geiger experiment. Remember, so far he's only working on the premise that a minute atom surrounded by empty space is also coherent with the Marsden-Geiger results, everything else stems from that with no additional evidence being thrown our way.

To prepare for his dismissal of quantum theory, he cites Reichenbach:

Only the interior structure of the atom, in which lighter particles like electrons play a leading part, requires the quantum mechanical duality of interpretations.

If only this was true. Wave-particle duality is observed in the double slit experiment, which is as far from restricted to the atom as it is physically possible to get. This shows the nature of light as a dual entity very clearly, and even so, Larson is writing in 1963, two years after someone demonstrated the exact same effect with electrons. Naturally, though, Larson doesn't believe that electrons are constituent parts of the atom, so may well be able to dismiss this as evidence that doesn't refute him. Which is ironic considering how much of this book he spends slamming physics for allegedly twisting evidence to suit their inferior models!

22nd March 2012
I'm skeptical about...

So, first I get involved with a university atheist club, then out of the blue we get a Skeptics society. Ha, I've gone to university 8 years too early, it seems! Anywho, it's currently just a Facebook group looking for ratification, and so I was amused by the post on "so what are you skeptical about?".

Erm... everything? Right? As someone who has "been" a skeptic for a while, and I suppose a "practicing" one since I got a RationalWiki account in early 2008, I find asking "what are you skeptical about?" a weird thing to say. It seems to misrepresent the concept of skepticism quite a bit. As if it's an attitude you take to things you don't like, rather than a general methodology (skeptical empiricism being effectively synonymous with the scientific method) used to assess claims regardless of their nature or your opinion on them. I have certain focuses, sure, but the idea of being skeptical is more widely encompassing than just picking topics in that manner. I'm as equally skeptical about faster-than-light neutrinos as I am about homeopathy, and of claims of UFO abduction as I am about moon landing hoaxes. Perhaps this is reading too much in to the question. Perhaps it is actually asking for specific interests. Perhaps.

"I'm skeptical about how our government, society and economy works, we should think about alternatives." Or something like that (I don't tend to take exact quotes in certain circumstances), was the continuation of that question. After all, if you're going to ask "what are you skeptical about?" it's only fair to proffer an example response. But really, a primary focus of skepticism is "how society works and that we should look for alternatives"? Hmmm... if that isn't a code-word for "I'm an anarchist!!!" I don't know what the hell is.

So this is the thing, skepticism - much like the highly related and often abused "rationality" - is a methodology. You cannot simply just say "I'm skeptical about this" because you dismiss it or hold an opposing view. "Skepticism" can't as easily be shoehorned into politics and socio-economic decisions and used as code for "I'm right just because". This is really just the "WHY DO YOU CALL IT 'RATIONAL' WIKI" argument again. Why, when you know the first thing about skeptical methodology, would you even think that it applies so easily and so broadly to politics? And in a way that just says "I'm going to dismiss the current system" in such a blasé and carefree manner, too. Sure, we can ask for evidence based policies; drugs, rehabilitation, medicine and so on, can all be trialled and controlled. But what about political systems themselves? Well, we can look at the evidence for what works. When it comes to constitutional democratic republics we have the United States and Europe. When it comes to anarchist paradises, we have Somalia. Oh well. Maybe insufficient randomisation in that one.

Anyway, I'm distracting from my point. I'm not really saying such things as "how does government work" are totally and utterly beyond being appraised with skeptical empiricism and rationality. They probably are. Just that to use "I'm just being skeptical" as a cover for your beliefs is contrary to everything skepticism actually stands for.

17th March 2012
Any Respectable Theologian...

With my weekend trip over and done with, I'll get back to The Case Against the Nuclear Atom soon-ish. However, something else has just bugged me. Often, on either the internet or elsewhere, we might hear a phrase similar to this:

Any respectable theologian could pick apart your arguments with relative ease.

'''Of course, I'm paraphrasing a bit here, but I'm sure we've all seen it at some point in some guise or another. This phrase implies two things:


 * 1) "Any respectable theologian could pick apart your arguments" implies that the person saying this is aware of counter-arguments that could do just that; pick apart the arguments in question.


 * 2) Adding "...with relative ease" indicates not just familiarity with such arguments, but knowledge that they are simple and easy to type or put forward.

Given the two points outlined above, we should expect people to put their money (or at least their typing and speaking time) where their mouth is an explain themselves. Perhaps it is true that a more well-versed scholar would be able to refute an argument, I do accept that as a possibility, but you cannot claim this without awareness of what would do this. For example, while I'm no respected physicist, I can pick apart Dewey B. Larson's work because I at least have awareness of quantum mechanics. I could point you in the direction of people more knowledgeable than myself for higher levels of quantum theory that I know exist, because I've read or been taught it, but have either forgotten the details of or only have a general knowledge of. On the whole, though, I have familiarity with evidence and arguments that would work and I can at least remember the basics. I can say "the standard model refutes this" and give the brief outline that I know the standard model represents, and then defer to someone who I know has a more in-depth knowledge of that theory. Without such awareness, however, I would be forced to admit "I'm not sure, but I can find out". The most intellectually honest route in this case is a dichotomy: it's either "here is the refutation" or "I am not currently aware of a refutation".

Secondly, perhaps such an argument really is trivial, simple and caused by mere lack of awareness as claimed in the Courtier's Reply. But if this was really the case it should be possible to highlight these errors without too much trouble or hassle. At the very least, even if such arguments are actually complicated and specialist, it's strongly implying that the person using this stock phrase is at a level of familiarity that they are, in fact, simple and easy arguments. The conclusion is that if someone does add this "with relative ease" extension to the argument (and for most aloof and argumentative individuals, this is almost guaranteed) they would be best served just outlining such trivial arguments rather than wasting time merely asserting that they're there with no further comment.

Arguably this is the real Courtier's Reply in a fallacious form. If someone like Dawkins wants to argue specific parts of Christian doctrine, then he had best immerse himself in actual Christian theology, there's nothing wrong with telling him to do so and showing where he makes comments that are factually incorrect because of personal ignorance of the topic. However, to do nothing but assert that a more respected thinker would almost certainly be able to do this - without providing such evidence of what this train of thought would actually entail - is a far more insidious red herring argument.

14th March 2012
The case against the nuclear atom (IV).

Part 4 quite literally begins with the assumption that my homeboy Dewey has already so tightly proven his case that any objections can now be ignored and, without a single useful piece of information so far we can move onto bigger and brighter things. Especially ironic is the following quote justifying how he's so sure he's dispelled the myth of an atomic nucleus:

The three preceding chapters have gone directly to the heart of the matter.

Well, if you call a massive tl;dr rant about "thinking critically" and "accepting the evidence" (part 4 continues with similar repetitive musings on what is simply basic philosophy of science, but ignoring the more pressing stuff, like predictions and falsifiability) as getting directly to the heart of the matter, I don't have much hope for the rest of the book. I know I can waffle like a lunatic when I want to, but if tl;dr was an Olympic sport, this man would be taking the gold over me any day. He continues to throw around "it has been shown that", but really he hasn't shown anything. There isn't even a frigging diagram to be found! Never mind equations and calculations, or anything that would make a solid physical theory. By contrast, the Rutherford atom and the quantum theory that it has inspired has produced so many successes; theoretical predictions and technology that have monumentally impacted all of science. However, Larson has an answer to the inevitable comeback of how successful theories are:

This question is easily answered. The same thing is true of all theories that finally have to be given up after a long period of acceptance. It was true of the Ptolemaic theory and all of the others mentioned earlier in the discussion. All of these theories gave the right answers to many questions over a long period of time, but they were ultimately pronounced wrong nevertheless.

Of course, on a technicality Larson is correct. But this is really just a slightly long-winded form of the science was wrong before argument and doesn't really say anything a mainstream scientist wouldn't accept as valid. However, what this bizarre model of the atom lacks is sufficient evidence to overcome the established theory. Newtonian mechanics was refined by relativistic physics precisely because strong evidence showed that it didn't match up. All Larson's model of the atom does is claim that it is consistent with the Marsden-Geiger experiment (in so much that magic pixies transporting alpha particles from side of an atom to the other is also consistent) and then summarily dismissed all of quantum mechanics as unnecessary. To usurp an existing theory requires two things: 1) strong specific evidence that the existing theory is failing and how, and 2) a new theory that successfully explains both the old evidence and the new observations. Larson's model provides precisely neither, no matter how much he can prattle on about remarkably basic philosophy of science such as demarcation and theory building.

This leads me to think of a common modus operandi of the average crank. You see, they probably know that they can't do much better when it comes to hard evidence or laying the groundwork required to make their theory work - so they fireproof it with an excellent distraction to make it appear that to dismiss them would be to dismiss the skeptic's own ideas. In this case, Larson tries to equate dismissing his idea with dismissing the whole notion of open-minded science. He is saying that if you balk at his suggestion then you're simply not being a good scientist, because a good scientist should be willing to change their mind to suit the evidence. It doesn't matter that he hasn't actually presented any evidence, and is just working off the backs of hard-working famous experimenters like Marsden, Geiger and Rutherford. Consider the apparent conspiracy theorist mantra for a comparison; "we just want the truth to come out, why are you against finding the truth?" It makes challenging a crank idea tantamount to a skeptic shooting themselves in the foot by dismissing the entire sketpical and scientific methodology! It's a red herring, of course, but they still get away with it.

The case against the nuclear atom (III).

In the third part, on the electrons, I'm reminded that my homeboy Dewey was writing just before the Standard Model of physics gained most of its momentum. Still, a quick bit of Google-fu shows his fan club citing it as an excellent piece of critical thinking literature - I'd be inclined to agree, if it weren't for his appallingly ass-backwards approach to explaining himself, his question-begging assumptions and his apparent inability to correctly deal with quantum mechanics. And besides, some of these people might believe it.

Anywho, the argument so far is that the emission of electrons from atoms doesn't prove that they were constituent parts of the atom - as we come to a different conclusion given that photons are also emitted. But so far, this appears to ignore that there is a fundamental difference between an electron and a photon. Even by the 1960s we knew a hell of a lot about the nature of the electron and the photon - their mass, or lack of, the fact that electrons have certain energies while photons have others. The inference that different processes lead to their creation when ejected from an atom isn't as far-fetched as Larson implies in this section. If we only knew that photons were sometimes ejected from atoms and sometimes electrons were, then Larson may have a point that we could conclude that both are magically "created" from the atom. But put simply, even in the 1950s we knew far more than just that.

Certainly, from a philosophy of science point-of-view, the proposal offers no observational evidence that would falsify it against conventional atomic structure. This makes it completely indifferent to having magic pixies dance on the surface of the atom to throw out particles of photons and electrons. Larson's continued argument is that we shouldn't accept things uncritically, therefore he is right, and that if he continues to assert that evidence for atomic structure is "unsupported" enough times people will buy this. I am amused by this quote, because I find it so fabulously entertaining:

As long as there is any question at all as to whether or not the electron is actually a constituent of matter, the fact that the atomic electron cannot be reconciled with known physical laws is a strong argument against the existence of any such entity, not a justification for formulating new physical laws.

While this might seem like a fair idea on the face of it, what he is actually suggesting here is that our theories must be right, and therefore the evidence is wrong. Remember that physical laws, no matter how strongly adhered to, whether it's gravity or thermodynamics, are still only how we think the universe works - and if it disagrees with experiment, it is wrong. Throughout the early 20th century, our experimental evidence was mounting to indicate that classical mechanics simply couldn't explain the atom. Whether it be the photoelectric effect, the double-slit experiment, electromagnetism, or anything else. Quantum theory was highly motivated by the need to stabilise the Rutherford atom (it would disintegrate within a nanosecond if modeled classically) but it would be foolish to imply, as Larson very much does here, that there is no other supporting evidence for quantum mechanics and that it was an invention to purely stabilise an unfounded atomic theory.

13th March 2012
The case against the nuclear atom (II).

In hindsight, I should have skipped the preface and introduction to Larson's argument against the existence of the nucleus. Even moving into Part 2; The Nucleus took a while to get going, having banged on about Rutherford for a bit longer.

His main argument seems to be that Rutherford's experiment isn't just consistent with a core surrounded by electrons, but also with the entire atom being confined to the small region of the "so-called" core. Okay, I'll take your point, Larson, but let's remember that you're writing in 1962 here... not exactly the dark ages of physics. Already by this point spin had been proposed and demonstrated, quantum mechanics was fleshed out and people were already looking at how to upgrade it, we were starting to use resonance spectroscopy (nuclear and electron) and molecular-orbital theory had been fully formed for decades and telling chemists exactly how it was that things were going down on the molecular level - MO theory, incidentally, more or less explains all of fucking chemistry as we fucking know it.

Larson's errors in this section alone are multifold, but let's get them out of the way one-by-one. Firstly, he seems to misrepresent the Marsden-Geiger/Rutherford experiment considerably. He seems to imply that the results are consistent with the entire atom being in the "so-called" core, and this explains the Rutherford experiment. However, he seems to completely neglect why it is that the Rutherford experiment works the way it does. It works because you are firing massively heavy alpha particles at the atoms. These are deflected and even reflected by the nucleus not because it is solid, but because it is an extremely strong and extremely dense positive charge - and as alpha particles themselves are positively charged, they are repelled by the nucleus. Otherwise, they pass right through. If the electrons themselves were contained within the atom - which is what Larson is describing - then it would overall be neutral in charge. A neutral entity like this would cause a lot of problems, not least would it fail to deflect alpha particles, it would fail to deflect and resist other atoms. Larson's assertion that inter-atomic distances are just where forces balance makes absolutely no sense in his proposal because an overall neutral atom the size of a nucleus would produce no inter-atomic electrostatic forces to help bind everything together!

But that's a very specific criticism of the idea, his main problem is discussing concepts of solids and liquids and gases and "empty". These concepts don't translate very well to the atomic level. Indeed, states of matter are more to do with inter-atomic bonds and how molecules interact and react to outside pressures and so simply cannot have meaning without multiple atoms interacting with each other. These properties are emergent, and do not exist at the atomic level as we know them. When people say "the atom is mostly empty space" they make this mistake. Indeed, the confined size of the nucleus is small, like a grain of sand in a cathedral, but that's not to say you cannot sense its presence. It's like a grain of sand in a cathedral that emits so much heat you can barely stand it and can't approach it at all. The nucleus is small, but its presence can be felt. Similarly, the charge of the electrons can be felt for a considerable distance too. We cannot get away with imagining at atom as just "empty" in the way we normally think of "empty". The forces are always there, effectively replacing our concept of solid/empty.

The second assertion is to do with the variability of the atomic radius and its apparent "incompatibility" with quantum theory. It's this section that makes me think the author may just be doing an arts project to troll real scientists rather than put forward a serious point because it too makes a considerable misunderstanding of quantum mechanics. According to Larson's straw man quantum theory, the Bohr model of the atom precludes atoms changing their radii because electrons are confined to quantised orbitals - and because no electron can take a form between these orbitals, the atom should never change size under this model.

Oh, Larson, Larson, Larson! I do not use the phrase "straw man quantum theory" lightly, and never thought I'd ever have to write it, but here I am, using it anyway. The Bohr model proposes that the energy levels of the orbitals are quantised to a particular energy - but it doesn't say that this energy cannot change! The energies, the specific energies, change all the time. If they didn't, then electronic spectroscopy simply wouldn't work. We would have atoms that exhibited transitions in the same region of the EM spectrum regardless of their chemical attributes. We don't see that precisely because the specific energy values of an energy level do change and do react to outside forces. That's taken into account and explained by quantum mechanics very nicely. Molecular orbital theory - which one presumes that Larson must completely deny - shows it perfectly, as orbitals alter their energy levels in response to chemical transformations. Quantum mechanics says energy is quantised at no point does it say that quantisation is fixed.

Still, the worst part isn't the poor reasoning against "nuclear theory", but the fact it's taken 8000 words just to get this far.

The case against the nuclear atom.

Currently making my way through this. Of course, I shouldn't be too harsh on something written in 1962, it does admit, of course, that it's "been only 50 years" since the Rutherford experiment - for the uninitiated, the experiment that reassessed the structure of the atom, and being the strongest indicator that it was mostly "empty" with a strong nucleus found at the centre - whereas now we've had 100 years since that experiment.

Now, I'm not expecting anything good from it, I'm just curious to get into what the claim is... but I'm struggling. Scientific documents have things called "abstracts" - perhaps one of the oddest paragraphs an unexperienced undergraduate will ever have to write. This paragraph precedes everything and sums up, in as succinct detail as possible, all the relevant facts and conclusions of the article. Indeed, the abstract is the punchline, it is the data, it is everything and with a good abstract there shouldn't be any need to read the full paper except to check a few experimental details. Larson's screed contains no such thing, instead offering us a considerably long preface filled with whimsy, and an introduction that basically spends most of its time playing the science was wrong before card. In short, I have no idea where it's going and why. As a scientific document it falls hard at the first hurdle.

Take one particular section, where we get tantalizingly close to perhaps some real meat:

Perhaps the most surprising discovery that awaits anyone who turns the light of critical inquiry on the current theory of the atom is...

'''What? Come on! Tell us! Is it that the Rutherford experiment was never reproduced? Is it that further experiments have observed the atom in new ways but were suppressed? Is it how the Rutherford model of the atom (technically we're now on the Bohr model, but "Rutherford" is a quick way of saying nucleus surrounded by electrons) doesn't match with quantum theory? Tell us Larson!

...the extent to which the scientific profession has been willing to sacrifice logic and consistency in order to keep this cherished theory from being destroyed by the advance of knowledge.

ARGH!!

This sort of taunting is common with a lot of conspiracy theorists. They set up to reveal an immense fact, but then don't actually deliver on it. Statements like this seem remarkably profound to the proponent, but they have no substance to them. This statement says little, it doesn't tell us anything of value. No, I'm not pulling a quote mine on this, the rest of the paragraph after this sentence doesn't give us any concrete examples either. It simply labours the point again and again, stating something about electrons completely out of context and saying "ah, but it could be fairies!"

I'll still push on with reading it, if only for comedy value.

12th March 2012
Making the invisible... visible

Finally got around to attending a visitor lecture for the first time in ages, from a researcher who's group apparently gets an average of 1000 citations per paper. I'll have to look that up.

So, how do you solve protein structures? They're vastly convoluted and almost invariably focus on the ground state only, that is, the most stable configuration it can take. It leaves us nothing more than guessing about how they fold, deform, attach to substrates and so on. So, what can NMR do to help? Conventionally, nothing. There is simply too many protons in the average protein to even begin to make sense of the spectrum, if you can even get a spectrum out of it and not a completely collapsed and flat lump of nothing.

The solution? Nothing fancy, just deuterate the entire thing - there, no protons to help wipe out your signal. It's a bit of a brute force approach to the problem, really. Conventionally, the more deuterons you want to introduce to replace protons, the more hideously expensive it is. Hence why undergraduates get to use CDCl3 (only one) or at most heavy water, and the most precious thing I own that I have to guard with my life is fully deuterated heptane, with 16 deuterons. But it's not as bad for proteins than you might think, as they tend to be composed of the same basic building blocks, and deuterated amino acids or suitable precursors are available. Simply introduce them into the mix when you start producing the protein through induced gene expression and hey presto, you have it. The key, then, is to selectively switch out certain groups for protons and carbon-13 labels so you can read it off on a conventional spectrum. As you then build up a stock of proteins with different NMR active sites, you can assign up to 95% of the signals you get, which is a pretty good achievement for structural analysis and doesn't require the $25 million to buy the highest field instrument that's currently on the market.

Assigning structure to the spectrum is the just the start. Starting with a protease enzyme, researchers substituted in 5 such probes, but spotted far more than 5 signals corresponding to what they were expecting. In the course of identifying what signals corresponded to what, it became clear that some amino acids were appearing twice, perhaps three, or four times in some cases. The explanation? The proteins are, in fact, exhibiting multiple forms in solution, and the solution-phase NMR was successfully highlighting them. The methodology for solving structures like this is actually quite fascinating, although it sounds ridiculously painstaking - you have to selectively mutate and distort the protein structure to see what signals disappear. When you know what you've prevented the protein from doing, you know what conformation was responsible for the now missing signals. But that's just trial and error and piecing things together in a fairly logical and methodological way. Then by dropping an electron rich group into different locations on the enzyme, you can test the physical distance that each proton signal is away from that one point by looking at the effect it has, which tails of with distance so perfectly that these can be figured out to excellent precision when computed against models. Using multiple locations for this electron rich group they successfully triangulated the physical position of these moving parts of the enzyme and started doing neat things with that information. Neat things such as exposing the protein to a substrate and watch the protein change its conformation to match. So the protease enzyme being looked at could be seen physically reacting to accept substrate and control its own activity. In another case, they locked in a model substrate into the "holding area" of the fairly large protease enzyme and found NMR chemical shift distortions appear half way across the molecule near the active sites. That tells us a lot, because chemical shift is one of the best indicators of the electronic environment around atoms, and here was direct evidence of a protein quite literally communicating information across itself in order to prepare its active sites.

Anyway, I've probably oversimplified the techniques involved, and there was a lot more to it involving being able to selectively view certain conformations even though they existed in ~0.5% concentration compared to the ground state. I certainly don't envy the guys who have to assemble these jigsaws.

11th March 2012
A problem. It's a Sunday evening, and what the fuck am I doing? That's right, I'm working. So, I've managed to get some marking out of the way - some of the undergrads are, well, a bit special - and now decided to look up some data and get a few other things done. Though with my other/better half in London for the weekend, it's not like I have anything better to do.

So, I can spot two hydrides in the proton NMR spectrum of compound X (it's industrially sensitive so I need to be careful here) under a hydrogen atmosphere, with notably similar chemical shifts. This suggests to me that they're similar compounds, particularly as the solid-state crystal structure is slightly different (it's dimeric) to the accepted solution-state structure and I think I might be observing both forms in solution - although they don't show up on EXSY as inter-converting. Both resonances collapse to doublets upon phosphorus decoupling so I know they're monohydrides attached to rhodium. That's fine. Now, if the bisphosphine ligand is fully co-ordinated to the rhodium center, it should manifest as a further triplet splitting in the proton spectrum, and if the H-P and H-Rh coupling constants are similar this will appear as a pseudoquartet structure. Indeed, this is what is observed so I'm pretty sure I know what I'm looking at there.

But it's the second, minor, resonance that is troublesome. With this one, it appears as a triplet in the fully-coupled proton spectrum. One of these couplings has to be due to rhodium, so one additional coupling would suggest only one phosphorus atom co-ordinated to the complex. And as I can produce this signal out of nowhere by switching on the in situ UV probe, I'm pretty sure I've shown I can photochemically unhook the bisphosphine, making it hemilabile under broadband UV light. Bangin'.

The problem, however, lies in using the HMQC pulse sequence to get the rhodium resonances. If there are two phosphorus atoms coupled to rhodium, then the 103-Rh resonance will exhibit a triplet splitting in the F1 dimension and this is what I see for the major hydride product. If only one phosphorus connected to the rhodium centre as suggested above it should only display a doublet splitting... yet I'm observing a triplet quite clearly. The proton spectrum is telling me I've unhooked the phosphine, the HMQC is telling me the opposite and that it's fully attached and coupled to the rhodium. So how can a the rhodium resonance exhibit a triplet splitting and for this to not manifest in the proton spectrum? I have no fucking idea right now.

Time to order pizza, I think...

I think the two compounds are different oxidation states if the Rh-P couplings are anything to go by. One being Rh(I) and the other being Rh(III). Not that this changes much.
 * Addendum

9th March 2012
Safety first

6th March 2012
The Soul

The soul can't exist. As the soul must be magic. Magic things can't exist, by definition. So the soul can't exist. If it did exist, it would cease to be magic. As the soul is magic by definition, it can't be proved to exist. QED.

I'd like to think I've grown beyond this sort of circular arguing, though I have said this sort of thing in the past. I'm pretty happy to accept that a soul exists, should it be demonstrated. Much in the same way I'm happy to admit ghosts exist, or God, should they be demonstrated. If an idea can be shown to have a meaningful effect, then ipso facto it exists in a meaningful way. I'd also be quite happy to call it a "soul", even if the connotations of it are pretty magical and supernatural because otherwise I'd be guilty of such oddly circular denial as above. The above is arguing "by definition", it basically defines something as impossible, then says its impossible because its defined like that. Hardly impressive logical deduction. It's like saying "all swans are white" and when presented with a black swan to argue that it simply isn't a swan because it isn't white. Demonstrate to me that something that satisfies the observational properties we ascribe to the "soul", and I'll accept it as a soul. I just won't accept it as particularly magical.

So, what if the computational theory of mind proves true - that the pattern inside our heads that makes us "us" and so can be replicated independently of the material making up the brain, and then this is demonstrated either through a simulated AI that passes the Turing Test or somehow we achieve mind-uploading? (no, I'm not positing this as a realistic and imminent possibility, nor am I saying it's anywhere close to a literal computer with a CPU, a RAM chip and a hard drive attached to a couple of USB ports) Then surely, this - although we'd possibly prefer to call it a "mind" - would satisfy all the observable properties of a "soul". It would posses the following properties:


 * Contains the essence of our consciousness
 * Could be made immortal if transferred to a material body that didn't decay
 * Would be independent of our material selves

Yeah, it's sci-fi right now and probably will remain so for long after my particular pattern has stopped working and the neurons that carried it have decayed to dust, but this is just a "what if" for now. That's pretty close to the idea of a "soul" as most people seem to use it, albeit it has the big caveat of "not magic". But, to paraphrase Arthur C. Clarke, what is magic apart from sufficiently advanced technology? Any idea about what "magic" is beyond Clarke's 3rd law basically puts it as non-existent by definition, which is circular and unimpressive as said above.

I'd be happy to call that my "soul", especially if we're able to isolate it, though probably not so happy to say that it can only be saved by Jesus.

6th March 2012
I miss drawing...

It's been about 10 weeks since my graphics tablet finally gave up the ghost and stopped working. Perhaps one day I'll finally be frustrated enough to rip open the back and try my hand at soldering the loose connection, but what to do with the giant crack over the front that's probably damaged the actual tablet part, I don't know. Not that it matters, I've never had any free time at home for weeks to put pen to paper anyway.

Sigh.