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 the atomic level where “rules” tend to hold. In this case, the structure 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, KI₃ already 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. 

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.