No, Disco Tute, Chemistry is Not Wrong.

Thanks to a previous post, it’s been pointed out to me that creationist do, albeit on fairly rare occasions, go after the chemical sciences. And what was sent my way was an article almost intelligently designed to piss me off titled ‘If Chemistry Can Be Wrong, How Much More Evolutionary Theory?‘ from the Disco ‘Tute’s media wing, Evolution News and Views (ENAV). The Sensuous Curmudgeon already covered this one a little closer to the time it was published, but that was mostly just a “let’s laugh at the crazies” piece – and rightfully so, as the underlying logic is just that terrible. But I thought I’d cover a little more about the chemistry cited in the ENAV derp-fest.

Violating chemical “rules”

The basic outline is that Artem R. Oganov and team, working out of Stoney Brook University, have discovered some unusual chemical compounds, or more specifically some unusual elemental ratios, of sodium and chlorine that apparently violate chemical intuition but are stable at high pressure. Proving that they never read much further than the press release bumped up to Science Daily, ENAV’s contributors thus concluded that all chemistry was wrong and played the persecution complex card of “therefore evolutionary biology is wrong but they don’t believe us”. So I sat down in the office and got in the mood, I went through Oganov’s work – the paper and press release. As usual, it’s fine enough work and certainly worthy of publication in Science. But, like so much work that gets to that stage, it’s the unfortunate victim of some university press office demanding the academic oversell it for headlines; hence “challenge the foundation of a science” being trumpeted in the first sentence. Let’s be clear as early as possible; it does no such thing. ENAV’s description of it as an “unexpected foundation-shaking paradigm shift” is, in all honesty, hilariously wrong.

Here, hidden about halfway down the press release, is one human-readable explanation why this certainly doesn’t (at least, not really) violate all these rules and laws the press release and all the popular reports claim in their headlines – and therefore this creationist claim of “ZOMG, chemistry is wrong!!!1” is bullshit:

“One of these materials—Na3Cl—has a fascinating structure… it is comprised of layers of NaCl and layers of pure sodium…”

Since we’re dealing with pure inorganic chemistry here, the idea of a discrete molecule is less rigid than it is in organic and organometallic chemistry. An Na3Cl molecule, or a NaCl7 molecule, or any of the others, won’t exist as a lone entity. These formulae represent ratios of elements (stoichiometry) found on a much larger scale than merely a four atoms, and this alone says nothing about the structure. It’s this structure at the atomic level where “rules” tend to hold. In this case, Oganov’s structures still obey known crystal packing rules, and their arrangements aren’t uncommon. So far, so straightforward.

Consider the octet rule; this states that most main group elements want to have 8 electrons in their outer shell. Although based on fundamental electronic structure, this isn’t necessarily some core rule. It’s a “chunked” idea that happens to be useful. It is a nice, simple explanation as to why NaCl exists; sodium has one too many electrons to satisfy the octet rule and chlorine has one too few, making it a match made in chemical heaven. The two transfer an electron to form  Na+ and Cl  and they attract by electronic charge to form ionic bonds. In elemental sodium, however, each individual atom wouldn’t satisfy this rule. Each atom would, formally, still have one too many electrons, which is why it’s metallic and conducts electricity as the spare electron can jump around more freely. If one was to take the octet rule absolutely literally as a precursor to forming a solid state compound, then elemental sodium shouldn’t exist. Indeed, this is why we use different rules for solid state chemistry, and things like band structure to describe electron distributions (Zhang and Oganov go into this aspect of their materials in a fair level of detail in their actual Science article).

What is certainly less shocking about Organov’s results is the detection of NaCl3. As Paul Braterman pointed out in the comments of the Sensuous Curmudgeon blog, KIalready exists (as does NI3, which is a remarkably fun piece of classical chemistry to play with, though it’s only tangentially related to KI3). This is part of a series of compounds involving the triiodide ion (I3) and is (read; should be) isoelectronic with NaCl3 in the solid state. The existence of NaCl3 therefore is not actually precluded by known chemical behaviour. Further adding to the lack of actual surprise that such structures would exist, or be stable, is the fact that Oganov and Zhang et. al. added pure sodium or pure chlorine to NaCl before applying pressure. This means that the charges still balance out. They’re dealing with neutral atoms fitting into a crystal lattice structure without much of a problem – again, see the existence of elemental sodium, each atom is neutral, it forms a crystal structure, nothing special to see here. It’s not like Oganov and Zhang magically formed these structures out of Na+ and Cl with one in excess. Although, in fact, even if they did it wouldn’t be overturning anything we know as charged metal clusters are known. Again, they go into this in the Science paper and analyse the overall partial and formal charges of each atom in the structure. 

Unusual structure of sodium chloride

Crystal structure of Na2Cl. Credit to Oganov, Zhang, et.al. – I can crib this under Fair Use, right?

We can actually violate a lot of chemical “rules” all the time. Someone with a cursory knowledge of organic chemistry will remember that “hydrogen only forms one bond”, such as in methane (CH4); but change that context into an organometallic hydride (hydrogen with a formally negative charge) and we can make effectively two bonds to hydrogen quite easily, making the hydride a “bridging” group. These compounds aren’t particularly uncommon, and I lose track of how many of those I’ve seen. Does that mean a fundamental chemical law has been violated? No. It just means that this particular “rule” has a limited scope where it’s true and other areas where it is not (aka, “science, bitches”). So, just as how bridging hydride ligands within organometallic chemistry does not quite overturn the “rules” of organic chemistry, these sodium chloride results within a field of high pressure inorganic solid-state structures aren’t a massive overturn of all known chemistry, nor are they even threatening to shatter the foundations of it.

At this point I want to reiterate again that I’m not attacking Oganov’s work nor his group, just that this doesn’t really say “all of chemistry is wrong”, and therefore the piece-of-shit ENAV article is, well, a piece of shit. The results are just unusual, and in their way every scientific paper is somewhat usual, or unexpected, or challenging the boundaries of some previously held rule; isn’t that the point?

Impossibility, stability, and finding the right conditions

Anyway, to quote Oganov (as he’s massively quotable):

“You just need to find conditions…”

Which is, dare I humbly suggest, the shortest and greatest description of synthetic chemistry I’ve ever seen. Atoms will just do their thing no matter what, all we need to do is get the conditions right so that what they want to do happily coincides with what we want to do. The trick is whether such products are stable or not, not whether they’re possible – and stability is relative. To quote Oganov again, because ENAV clearly didn’t get this far down the press release:

“For a long time, this idea was haunting me—when a chemistry textbook says that a certain compound is impossible, what does it really mean, impossible? Because I can, on the computer, place atoms in certain positions and in certain proportions. Then I can compute the energy. ‘Impossible’ really means that the energy is going to be high. So how high is it going to be? And is there any way to bring that energy down, and make these compounds stable?”

He’s being a bit of a cheeky git saying chemistry textbooks declare this to be “impossible” – I’m not aware of any that declare such things to be impossible – but overall this is a good description of the interface between experimental chemistry and theoretical chemistry. The question is stability. And sometimes stability can surprise you, but there’s always a good reason for it when you look. Sometimes those conditions are high pressures, sometimes those conditions are a particular solvent, or sometimes you need to bung on a few extra groups to de-localise your charges, but stability is the key and it’s stability that we’re really talking about when we say “impossible”. Carbonium, for example, would be “impossible” by rigid standards; but it’s simply that it’s not particularly stable unless you have the right conditions.

I want to finish by quoting this part of the Science paper itself, because I think this ties it up quite nicely with the creationist mumbo-jumbo that brought it to my attention;

“…we used the ab initio evolutionary algorithm [to] find stable stoichiometries and the corresponding structures in multicomponent systems”.

I.e., they used evolution and natural selection in a theoretical environment. Similar to how Boxcar2D works but with chemicals rather than model race cars. The method uses theoretical calculations on a particular chemical structure to determine a molecule’s “fitness”, and then manipulates the structures with a genetic algorithm to converge on to the “best” structures based on this fitness. It’s a novel idea, and a fascinating approach if you’re into that sort of thing – in this case Oganov’s group have applied it to crystal structures rather than just a molecule, and in this particular case they happened to have been right, too, having theoretically located a predicted structure and found it experimentally (which is probably a far more spectacular result than “finding structures that violate the laws of chemistry” and why it’s in Science).

You don’t see ENAV reporting on that bit. Not least because it’s patently obvious that they didn’t even read much further than the headline.

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Why Do Creationists Not Go After Chemistry?

I’m going to do something somewhat unusual for this blog; I’m going to talk about work. Work work. The stuff I actually do. The stuff I’ve been reared from birth (it seems) to actually do with my life. (the title I’ve given this should become clear later, skip to the bottom if chemistry and occasional sexual analogy doesn’t interest you)

I have a problem. It’s a problem I’ve been hitting with a hammer for about 5 years now. While it’s a little complicated to get into it, I’ll try and distil it down to something readable without any prior knowledge.

One of the core aims in chemistry is to understand the mechanism of a chemical reaction; that is, when you go from A to B, to not just understand what A and B are, but to describe in as much detail as possible how you get there and through what steps, and which intermediates.

So I have A and B, and I have two potential pathways, 1 and 2. Please forgive the shittier-than-usual-ness of these diagrams, I am stuck without a functioning PC and graphics tablet, and have resorted to MS Paint and a mouse – still, it’s more effort than a Buzzfeed article.

chem_fig1Actually, this is a little abstract, so I’ll go into a little more detail because I  damn-well can and people seem to think chemistry is all blowing shit up and poisoning people (that’s only 60% of the time). Not too much detail, however, since this is a) unpublished work and b) potentially industrially sensitive.

I’m looking at how a particular metal (and associated ligands), let’s call her “M“, activates a particular substrate, let’s call her “S“, while under the influence of light. “Activate” here, just means “turn into a more reactive substance”. You can sit Ms. S and Ms. M together as long as you like, but they’ll do nothing – but shine some light on it, and BOOM, some kinky chemical lesbianism occurs! (that’s a technical term, by the way) Add in another chemical at this point and you can readily convert Ms. S into something else – something that wouldn’t happen without Ms. M and some light. All disturbingly erotic, I know. And no, this is not allegorical.

But how?

In pathway 1 we have M losing a carbonyl (CO, carbon monoxide, the same stuff that kills you in your sleep if you don’t check your boiler once a year) group in the presence of ultraviolet light to form an higher energy intermediate that lacks this CO. Now, chemistry is a game; get to the lowest energy and you win the game. So if you increase the energy of, say, M by using light (which is a sort of “cheat” in the game) then the higher energy intermediate is unstable; it will stabilise itself by latching on to whatever you give it that lowers the energy. It lowers in energy to win the game, and just so happens to produce something you want in the process rather than turning to black gunk (the usual end-product of organometallic chemistry). In pathway 2, much the same happens except no loss of CO; the entire thing, Ms. M, with all her sex toys ligands attached, just goes into an excited electronic state. “Excited state” in this case means that only the  electrons, rather than the whole atoms themselves, have rearranged into a higher energy state. But the principle is the same; this highly excited M lowers the energy by activating the substrate, S.

chem_fig2And evidence for either pathway 1 or pathway 2 is contradictory. I can’t figure it out. The odds are it will take someone way smarter than me and with far more time to figure it out (and funding, of course, as Ms. M is an expensive little madam and not some cheap slut like copper or nickel). And that’s if it’s even possible to really sift through the hellish amount of conflicting data on this one single reaction.

In favour of pathway 1 we have the fact that the reaction is slowed down when there is excess CO about, in accordance with Le Chatelier’s principle (oh, just Google it, not that you will). Yet in favour of pathway 2 we have some good kinetic evidence. In favour of 1 we have some fast spectroscopy measurements showing CO loss under light. But in favour of 2, the isomer distribution in the final products isn’t what we’d expect from CO extrusion and recombination. Although some energy calculations suggests this is expected because the isomers we don’t see disappear too quickly to be seen – although I think those calculations are bullshit because, and no offence to the authors of this one, if you’re using B3LYP/6-31G calculations on organometallic complexes by evaluating only hybrid density functionals against a few different relativistic core pseudopotentials without calibrating your transition state free energies to known empirical data you’re a fucking…

*ahem*

Then there’s how the evidence conflicts depending on whether you do it with this or that or at what temperature – oh, and my own computational calculations that suggest that, for reasons I don’t want to go into, that it’s both (one after each other).

Although in a fairly narrow field, this is still a significant scientific disagreement. There’s been head-scratching, there have been arguments, there’s been betting and mind-changing – right now I’m not even going to call it. It’s up in the air. We literally have no fucking idea about what the answer to this little problem is and the evidence is all over the place.

So… what?

So, why don’t we see people declaring that chemistry is bullshit?

Where are the cranks wanting to throw out atoms (okay, Dewey Larson and Archimedes Plutonium excepted…) and saying that it’s all folly?

Why don’t creationists latch onto this as proof that chemistry is flawed ergo the Earth is 6,000 years old?

You might think that this is because chemistry has nothing to say about the origins of the earth nor evolution. But you’d be wrong. Chemistry underpins the laws that governs genetics – how the genome functions at a biochemical level is all about this. Chemistry is what stops Jesus turning water into wine – and a little bit of nuclear physics suggests such a change would produce a catastrophic amount of energy that would have turned Cana into a crater. Chemistry governs the rates and qualities of rock and mineral formation that preclude even the notion that a flood 4,000 years ago covered the entire world in water. The mere properties of water – which are chemical – can prove such an event didn’t happen.

In short, far from being irrelevant, it would be very much in the interests of creationists to debunk chemistry. In fact, it would be very much within the interests of any crank to debunk all of chemistry. Homeopaths, climate change deniers, anti-vaccine twats; the lot of them.

And since a major modus operandi of the crank is to latch onto minor disagreements in science in order to declare the entire discipline to be false, why wouldn’t they take the one I just handed them above? Why wouldn’t any particular crank jump upon that disagreement and extremely difficult problem (I’ve barely scratched the surface of it there, and that’s only one problem I’ve had) to say chemistry is bullshit? Hey, after all, those silly little scientists can’t agree on a single simple detail like that, they mustn’t be very trustworthy or very clever!

I doubt anyone would declare chemistry to be false because of the above. Psychics, mediums, climate change deniers, moon landing hoaxers, grassy knoll enthusiasts, homeopaths, creationists, Scientologists, faith healers, intelligent design proponents, exorcists, bitcoin miners (okay, perhaps not) and Thor knows who else, will all remain very happy with the idea of atoms, molecules, bonds, thermodynamics, kinetics, electrons, photochemistry and so on and so forth until I’ve written out a contents page from an undergraduate textbook. They won’t see it as something for them. They’ll be ‘meh’ at most – never mind that their ideologies, philosophies and crank hypotheses often require that chemistry be overturned and their usual method is to jump on tiny little flaws.

But why? Why isn’t chemistry something they want to discredit? It’s no more different to the disagreements in evolutionary biology, genetics, palaeontology and geology used by creationists to self-justify their position. Or the disagreements in climatology used by denialists. Or the disagreements and open problems in epidemiology used to justify anti-vaccine twats. Hey, biology gets a ton of attention; why not its basis?

I imagine people will think it’s because they’re not qualified to discuss the chemical conundrum above because of a lack of knowledge or the lack of qualification.

Which would lead us to a very important question; why the hell is it okay for Ken Ham to debate Bill Nye on evolution?