No, Scientists Didn’t Do The Thing

I threatened to write this a few posts back, and after I Fucking Don’t Understand Science’s last clusterfuck, I’m going to. So next time a major science story gets reported in the popular press, this is the generic response:


No, despite what you have read, Scientists did not do the Thing that has been widely reported in the media yesterday.

You might have heard that scientists did a Thing. This Thing was pretty world-changing. Certainly, if you were to do the Thing, there would be several Nobel Prizes involved. However, you should note that the Thing is, in fact, so far removed from reality that the universe would probably implode with contradictions if the Thing was indeed true.

What was widely reported as “scientists”, plural, with connections to some big science-y organisation you probably have heard of thanks to a Brian Cox documentary, actually just came from one lone scientist, Scientist. As you can probably tell from a quick Google search of their name, this is not the first time Scientist has done something like this.

In fact, they are prone to talking about doing the Thing quite frequently, which was debunked the last time this blog mentioned Scientist.

Scientist has never so far reported doing the Thing in a peer reviewed, decent journal. In fact, the Thing was originally just a conference poster, presented to five people in Ass-end, Nowhere. They then emailed this to Journalist, who started the ball rolling as every other “journalist” just copy-pasted the press release, word for word, about the Thing. Of course, journalists have no expertise in the Thing, so we can’t quite expect them to know that the Thing overturns almost everything experts in the Thing already know as actual facts.

But spotting a few glaring inconsistencies with Scientist’s insistence that they did the Thing isn’t hard. You will note it was never published in a decent journal. You’ll note that their paper doesn’t even begin to prove that the Thing was done, nor happened, nor even is a thing to start with. Their communication about the Thing is devoid of any experimental details of how they came about the Thing, making replication difficult, and where Scientist did give us information on the Thing, it turned out to be severely lacking.

So, in conclusions, the Thing is not real. Scientists did not do the Thing. Can we please have a bit more fucking skepticism and less clickbait next time, please, is that too much to ask?

The Predictability of Science Churnalism + Bonus Sweary Rant

Ca. 20 hours ago, I dropped the following comment on Facebook:

Currently trending is that the Philae lander has perhaps found life on a comet… yeah, if that turns out to be verified and not just media mis-reporting of one lone nut with an incredibly tenuous association with NASA I will physically eat my shorts.

Now, I should reiterate that as I wrote that I had read absolutely nothing about the story on the Philae lander. I had no idea about the specific claims made. All I knew was the phrase “Trending: Philae: Comet That Spacecraft Landed on Could Have Alien Life, Scientists Say”. That’s all.

How much of it did I get right without even looking? Well, it’s obvious innit?

The pattern has become so predictable it was possible to get pretty much all of it right from seeing the mere fact that the story was trending. “Found alien life”? No. Just no. “Scientists say”? Nope, it was one lone nut, namely Chandra Wickramasinghe. “Evidence”? Smevidence.

The only thing I didn’t get right was “tenuous association with NASA” – not surprisingly, Philae is an ESA project, not a NASA one (idiot – though perhaps I just had the EmDrive on the brain). Still, that tends to fit the pattern; since it employs nearly 20,000 people and is associated with countless others, it’s not hard to have a connection with NASA, and “NASA claims” makes a pretty headline no matter the article content.

Still, the story trended anyway.

ALIEN LIFE? Astronomers say there are signs of possible alien life on Comet 67P, after studying data from the European Space Agency’s Philae Lander.

….ABC7 News said.

Philae’s comet may host alien ‘life’: astronomers

….Some other guy said.

Scientists have spotted what some believe to be evidence of life on the Philae comet.

….I Don’t Fucking Understand the First Thing About Science said.

….

…said the Daily Mail because for the last few months I’ve set AdBlock to kill anything from that site and my life has been so much better ever since. Although I’m told their article was on form.

Mere hours later, the refutation articles finally caught up. Bullshit, called Phil Plait of Bad Astronomy (in a near-identical reflex-action to mine). Nope nope nope said Rachel Feltman in the Washington Post. What a croquembouche of solidified emu excrement declared… well, pretty much anyone who knows even the first thing about the subject.

Why do we even bother with the refutation articles? The pattern is quite literally that predictable. Why not just write the generic post – titled “No, Scientists Didn’t Do The Thing You Read About” – and point to it? We can have a few set phrases like “It turns out that the evidence they presented has a more simple, parsimonious and perfectly expected explanation” and “No, the scientist in question wasn’t actually associated with the research project” and absolutely certainly “The claims weren’t published, they were just mouthed off in an email to the press desk” and words to that effect.

It would save so much time.

— Note, profanity begins here —

Mainstream popular science right now is a fucking shambolic piece of cunting horse bollocks. We thought it was bad before, but it hasn’t got much fucking better. The rise of the internet and – buzzword alert – social media has given us easier and more ready access to experts than ever before, but still these fucking fucktarded fucking newspapers, sites and the people who read them still gobble up any old shite guffed up by fucking moron that tells them something.

Lone Nut: “Hey, I’ve got a fucking PhD, kind-of, doesn’t matter that I’ve spent the years since plucking shit-covered morsels of Wrong out of my hairy anus and flinging them at the fucking internet, I have a crank theory for you to post!”

Shitty Newspaper: “Oh, sweet, dude, just what we needed! We haven’t undermined the public’s trust in science for fucking ages!”

Lone Nut: “Yeah, you take that sweaty morsel of shit I just told you!”

Shitty Newspapers: “Yes, sir, please feed me more of your shit! I love it because I’m a filthy fucking whore!”

That’s basically what happens. Each. And. Every. Fucking. Time.

It has been over a decade since Andrew Fucking Wakefield shat all over our collective consciousness with his outright fucking fraudulent claims about autism and measles jabs – and now people are starting to fucking die because of it – and the shitting papers still haven’t learned their fucking lesson about basic fucking fact-checking before jumping to publish some trumped up fucking dingo’s kidneys coming from some twat-mouthed cockwomble.

Just fucking admit it you cunts – you’re not fucking writing science articles, not even fucking popular science articles. You’re writing fucking clickbait for shit’s sake! Or worse, you’re trying to fuck about with peoples’ perceptions of what science even fucking is so that when you publish your own fucking horseshit like “vaccines cause AIDS” and “climate change isn’t real” people will believe your version of events because “Hey, scientists thought there was life on a comet! What idiots!”

Something needs to fucking change. Fucking pronto.

Magical Narrative Thinking

Before I begin, this focuses on a very specific example – so, if you have time, have a think about how it generalises. There are countless examples out there, in fiction especially, but where it bleeds over into real life we can run into serious problems.


Yes, it’s a post dedicated to Ken Ham, the dumbest person on the planet not named Ray Comfort, who recently said this in “celebration” of the same-sex marriage ruling in the United States:

hambow

Specifically, I want to look the part that says “Well, the president did not invent the rainbow; God invented it.” (emphasis added)

I’m sure many Christians out there think God is the de facto inventor of the rainbow by virtue of being the creator of the universe, but I’m not talking about that. That’s actually fairly self-consistent, and I can’t really fault it much. This is different. Remember: Ken Ham is a literal Biblical creationist.

He genuinely, literally believes the Bible is the historical book of record for all of history. And by extension, all of physics, too.

He honestly, really, genuinely doesn’t believe in any science that contradicts the Bible, never mind any historical fact that contradicts it.

He literally, actually, genuinely, really believes that the Book of Genesis is correct that the atmospheric phenomenon we call a “rainbow” is a sign from God, an apology for taking his anger management issues out on the entire population of the world in the single biggest act of genocide in “recorded” history.

Ken Ham literally, really, honestly, actually, literally, genuinely, properly, really, actually thinks that the rainbow was invented by God after the flood.

It didn’t, therefore, exist before the flood.

This is what Ken Ham actually believes – otherwise his entire world collapses in on itself faster than the rectal prolapse suffered by a homophobic televangelist after too much anal sex with gay hookers on speed.(That’s quite enough of that, Ed.)

Now to cut a long-winded pseudo-intellectual story short; we simply cannot build a universe where a rainbow cannot exist.

Well, we can, but we have to understand its wider effects. I’m perfectly okay with God Almightly clicking his non-corporeal fingers and altering physics in such a way that one moment there was no optical phenomenon in the sky and then suddenly there was… but we have to follow those changes to their logical conclusion. In stories, with their narratives, you can get away with changing one thing, but in real life you can’t.

There are three things you can change in order to stop a rainbow from being physically possible: the light, the principles of optics, and the source (I suppose one could call it the “material cause”?) of the refraction. Remove one of those components, and no rainbow is physically possible.

The details makes a fun and entertaining thought-experiment: what would happen if we stopped a rainbow from happening?

  1. Remove the light – No light, no rainbow. But then we can no longer see, either. Our vision requires light, so any antediluvian civilisation would be blind and incapable of sight. It doesn’t stop there, though. Without photons, chemical reactions that are sensitised by photons or that emit photons wouldn’t happen. Energy level changes at the quantum level would all have to take place non-radiatively. There would be no mechanism to masslessly transfer energy about the universe. Quantum mechanics breaks at the seams as it can’t shed energy around as photons. At the very least, the Earth would freeze solid as the sun was no longer capable of warming it from across the void of space with a massive influx of solar radiation.
  2. Remove the optical effects –  Now we’re cooking! We can keep the light, but let’s kill the concept of refraction. Okay… now we can’t see either, since our (allegedly “intelligently” designed) eyes have to bend light twice in order to focus. Once through the main cornea and then through our squishier lens. Antediluvian civilisation is still blind. Light now travels at the same speed through all media, not slowing down or altering. Light is no longer interacting with matter in the way it should. Quantum mechanics as we know it again shatters into a thousand pieces, the universe dies of entropic heat death before it is even born.
  3. Remove the water – Okay… let’s keep all the physics behind the rainbow! The universe exists, light interacts with matter, let’s just kill the rainbow at its source – the condensed water droplets in the atmosphere. Immediately we all die of thirst and starvation as there’s no water, so let’s put the water back. Oh, wait, the hydrogen bonding between water molecules, as well as the mass of two hydrogen atoms and an oxygen atom give bulk water very specific properties such as its vapour pressure, and its melting/boiling points – that means if we put the water back we’ll have water vapour, and it’ll condense around any particulate matter in the atmosphere… back to the drawing board, let’s alter conditions so that water vapour can’t condense! Aha! Let’s lower the pressure of the atmosphere, that should keep it in the gas phase… oh, wait, now people can’t breathe because the partial pressure of oxygen is too low for haemoglobin to work properly. Let’s up the molar proportion of oxygen in the atmosphere so the partial pressure is still ca.0.2 atm as it is now…. oh great, now not enough nitrogen for nitrogen-fixing bacteria to work with and we all die of starvation and let’s not even start with what the lower pressure does to the boiling point of the oceans and the gases dissolved in them… okay, so let’s boost the temperature above the dew point of water… bah, we’re all dead again… quantum mechanics remains in tact, but chemistry explodes in fireball of icy self-contradicting death and destruction that renders the planet inhospitable to everything that isn’t a self-contained abstract concept.

That’s consistency for you. There isn’t a world where you can’t have a rainbow yet let it still work exactly as it does today. You can’t pick it apart from the rest of the universe and treat it as a narrative block, a piece of magic with its own separate rules. If you change one rule, it changes for everything.

Chemistry by Chance – How Even Qualified Chemists Cease to Understand Chemistry Once They Come Out as Creationists (part 2)

See Part 1 and Part 3

Time to continue slogging through this… so…

4. The Problem of Reactivity

In this 4th section, McComb’s gradually tries to get into a little bit of abiogenesis and evolutionary biology. And again, he seems to mix the two up entirely, applying the conditions and pre-requisites for one to the other. So, let’s get this clear: abiogenesis is how life gets started, evolutionary biology is what happens once it has and natural selection can get involved. Importantly, abiogenesis has no requirement that an amino acid chain that has formed from a hypothetical “primordial soup” has a purpose. Purpose and function is something that comes later, once selection criteria have been able to refine the process. This is why evolutionary biologists that have to defend themselves against creationists and design advocates say that abiogenesis and evolution are different things, and that evolution has no need to explain abiogenesis. One works on refining information (information that exists as an abstract isomorphism with a chemical compound) and the other simply gets us to that chemical compound, and any variant of it that it likes.

So, the core claim of this section can be summed up in this sentence:

The product of natural or random reactions could never provide the precise sequences found in proteins and DNA/RNA.

But, as I said, they don’t have to. At this stage, what we’re calling “life” doesn’t serve a particular function. Now, I could go into how McComb’s is ballsing up reactivity and rates of reaction again, but I actually want to blow my word count on this very important revelation. I will put it in large, centred, capital letters and bold text just to make it clear:

ABIOGENESIS IS A PROCESS NOT AN EVENT

This means that there is no magic sudden spark that generates life. No one studying or theorising the early stages of life (studying it seriously, that is) has ever proposed differently. Life is a continuum, working its way up slowly from simple chemicals to complex chemicals – from disorder to order, from less organised information to more organised information (this is in an “information theory” sense, I direct anyone with a problem with this to this article). There is no sudden barrier that delineates life from non-life, and there certainly isn’t one in abiogensis. This is an important subtly that few really get, and creationists actively exploit this lack of understanding when trying to sell their wares to an unsuspecting population. In fact, “life”, as a thing, is an illusion (yes, this is an extreme over-interpretation of a very subtle point, but it makes headlines). “Life” is really just a mental (and linguistic) short-cut that differentiates between things that we can eat or could eat us, and things that can’t. A rock? Can’t eat us, we can’t eat it; not alive. That deer over there? We can eat it or it could eat us; alive. It serves us well because if we had to apply too much thinking to it, we would die pretty quickly. When it comes to edge cases, our intuitive of what is “alive” breaks down – and we think it’s a problem with reality, when really it’s a problem with our perception.

No more is this evident when it comes to viruses, prions, bacteria, fungus and other edge cases where our simple, intuitive definition of life fails almost completely. We simply cannot define it well enough. So, are self-replicating DNA fragments “alive”? Are organised peptide chains “alive”? Perhaps, perhaps not. The question is, in fact, meaningless. We’re going from a gradual scale of “not alive” at one end and “alive” at the other, with no sudden jump between them.

Forming amino acid chains or RNA chains in a solution has no requirement that they form a particular order. The order is refined later as life increases in complexity and begins to be acted upon by natural selection – and indeed, natural selection can refine things from random noise as a starting point. An argument against amino acids forming at all (as shown in the first three points) would be relevant to abiogenesis, but arguing that they couldn’t magically form a particular sequence is not. Besides, any chain would be a probability defying event, just as any combination of cards in a deck is a trillion-to-one-against order, yet still happens. Once that chain has formed – under the control of chemistry – that’s where we need to look at how it obtains, or at least refines, its information content.

5. The Problem of Selectivity

This is just re-wording no.4. Let’s not bother with it in too much detail. Suffice to say, the most correct bit of chemistry in it is the following quote:

Chemical selectivity concerns where components react.

Yeah, that’s about right.

Overall, this is trying to say that because a peptide chain can grow from both ends, the odds of it generating a “meaningful” sequence is small. Except, I need to just reiterate this, the concept of a meaningful sequence does not exist in the abiogenesis framework. It does for us today because we have an established system for translating DNA sequences to protein chains, and enzyme catalysts to run the show. In a hypothetical primordial soup where our main aim is simply to produce a polypeptide, the exact sequence does not matter.

Though I want to finish this with a curious observation. Throughout numbers 1, 2 and 3 (covered in part 1 of this piece), McCombs focuses on how unreactive amino acids apparently are. He goes to great lengths to say they won’t form chains. Yet here, in point 5, he is talking about the countless hundreds of isomers that should be formed. Surely, if he was under the impression the amide bonds didn’t form at all from a reaction of two amino acids, then the “problem of selectivity” shouldn’t matter at all, right? Such is the nature of a Gish Gallop – creationists are so desperate to pad out their over-bloated lists of arguments they don’t notice when their points actually start to contradict each other.

6. The Problem of Solubility

Again, an apparent Ph.D chemist seems to be displaying a sub-middle-school level understanding of polymer science. While it’s vaguely true that macromolecules have a tendency to be less water-soluble (and less soluble in general) this isn’t purely because of their length. After all – and I’m starting to sound like a broken record here – they are soluble in our cells. Protein chains and DNA chains don’t magically hit a certain length and precipitate out of our bodies and, subsequently, kill us. If solubility was a problem for abiogenesis, it would be a problem for our mere current existence. So, obviously, peptide chains and proteins definitely are water soluble.

But how does nature manage to do this? It’s simple, really, because it’s the same way synthetic chemists get around the problem; by attaching a few water soluble functional groups to the chain. But for this, I need to explain what solubility actually is.

Solubility is the ability for a substance to be broken down into just a single molecule and effectively surrounded by a liquid so that it can move freely inside it. That’s it. This is the solution phase. It’s not a particularly special thing, but it is useful for chemical reactivity because it means every molecule is spread out and open to reaction (i.e., it’s not a solid) but at the same time it’s a nice controlled environment (i.e., it’s not a gas phase). For this to happen you need sites on your molecule where the solvent can bind, so that it can be carried around in solution. In really small molecules this is comparatively trivial – a metal ion like Co(II), for instance, will just coordinate water octahedrally in its inner sovlation sphere and it will dangle around in water quite nicely. For larger macromolecules, however, we can be more specific with sites where a solvent will bind to help bring it into solution. So we need groups that are compatible with the solvent. For water, charge and polarity is important – hence why it can solubilise cobalt with a 2+ charge very easily. Individual amino acids also do this well because of the individual acidic and basic groups on them which hold a high polarity and a potential charge. As a chain increases – as McCombs points out – the number of acidic and basic sites relative to the size of the chain reduce, and eventually the solubility becomes poor. However, and this is the however that McCombs conveniently forgets to add to his list, not all amino acids are common, boring,  aprotic alanine and glycine. Many have sites that will water-solubilise the protein. In fact, in protein folding these are essential as they are what drive proteins to fold up a certain way.

This interesting graphic shows the wide variety of naturally occurring amino acids. What is interesting are the wide variety of ones with charged side chains or uncharged polar side chains. There are those words again, “polar” and “charge”, which happen to be very water soluble. Bung a few of those in your peptide chain and insolubility ceases to be a problem regardless of length. In fact it really doesn’t take many of these groups to solubilise a chain, and that’s a fact abused by polymer chemists and catalytic chemists to get their stuff to be water soluble without much trouble.

And again, I’m going to leave it there and come on to 7 and 8 later, they seem to change track to a different set of chemical principles.

Chemistry by Chance – How Even Qualified Chemists Cease to Understand Chemistry Once They Come Out as Creationists (part 1)

Part 2 and Part 3

I’m going back on a chemistry and creationism kick. You know, because I can. And in this case, I’m going to look at this article* by Charles McCombs, Ph.D – apparently a Ph.D in organic chemistry from UCLA, though you wouldn’t know that from him talking about the basic fucking organic chemistry that I’m about to go through.

Like most creationist listicles,** it’s less like 10 separate points and more 10 vaguely similar points re-worded differently – and all have the same problem; namely, that McCombs doesn’t know what he’s talking about. The second most generic comment I can give on this subject is that all these chemical objections would suggest life doesn’t exist. They don’t say that life couldn’t arise naturally, they say that – if true – life simply couldn’t exist. Life does exist, and we are the giant walking chemical factories that prove it, so there is clearly something up with these objections. This is a recurring theme, remember it.

*“Cite this article: McCombs, C. A. 2009. Chemistry by Chance: A Formula for Non-Life. Acts & Facts. 38 (2): 30.” – No. I won’t cite your ‘article’ this way. Posh-sounding citations are for real actual factual science and academic work, not blog posts from the Institute for Creation Research.

**A portmanteau of “list” and “article”. It unfortunately never looks as good written down as it sounds.

1. The Problem of Unreactivity

In this first section, McCombs attests that amino acids cannot form peptide chains in a watery environment – these reactions must exclude water (and this is basically what his other 9 points say more or less).

But if amino acids can’t react to form peptides in water, one needs to ask: how the hell do they react to form in our cells? The average human, by mass, is about 60% water. Our cells are rammed full of the stuff. Our cells even form because of water, as hydrophobic and hydrophilic sections of the phospholipids that form cell membranes arrange the way they do precisely because we are aqueous creatures. Biological reactions take place entirely in H2O, and entire fields of medicinal chemistry and bio-active chemistry all have to face the fact that their chemistry is water-based. If water was such a problem to the formation of these essential chemicals, we wouldn’t exist. We would fall over and die as the chemical reactions that sustain us refused to take place in the watery environment of our cells. So, no matter how good (or bad, and it is bad) this theory is, the simple fact is that water cannot be a barrier to reaction. In fact, actual factual existent condensation reactions, that form actual factual existent peptides, happen in water every day. Where McCombs declares that the process must be completely water-free, since the activated compounds would react with water”, he either doesn’t understand the chemistry he supposedly has a Ph.D in or is outright lying to the flock to prove creationism true. I cannot comprehend a third option there.

The main assertion in this first part, however, is that these chemicals – amino acids – are naturally un-reactive and that you need to activate them to generate a reaction. Outside the cellular environment where enzymatic catalysis drives peptide formation, these chemicals will sit tight and do nothing. However, this itself isn’t a barrier to the start of life. Evolutionary biology and modern geology postulates we had billions of years for peptides to form, slow reactivity is not a problem here. What would be a problem is if the peptide bond between amino acids was massively unstable – but it isn’t, it’s the opposite in fact, and we’re literally living proof of that. Slightly acidic or basic conditions speed up the condensation reactions required to build a peptide bond, and mineral catalysts or autocatalytic reactions in a hypothetical “primordial soup” also reduce the reaction barrier so that polymerisation can occur. It’s not really a problem except in the creationist imagination.

But once formed, the peptide bond is kinetically stable meaning it will only break down slowly – and honestly, it would help if McCombs actually phrased things in proper chemical terms such as stability, equilibrium and kinetics so I didn’t have to try and second-guess what he was on about and try and translate it for him. It takes a long time to break an amide bond unless you have a strong catalyst in there. The nitrogen in the bond de-localises its electrons and stabilises the bond against acid/base attack far more than in the comparable ester bond – and in fact the breakdown of proteins over thousands of years in nature is a remarkably useful dating technique. So, once formed, even if that formation is slow, the products are similarly inert and stable enough to take part in further reactions (even if these other reactions are slow – but speed is not a problem for evolutionary biology), and McCombs very slyly ignores this fact when he declares amino acids to be unreactive but implies their polymeric products are not.

2. The Problem of Ionization

I’m going to be frank with this section – it makes no sense. McCombs first off conflates “ionisation” with “acid base equilibrium”. In the first case, we’d use that term to describe the mechanical – or perhaps electrochemical – action of stripping electrons away from a neutral molecules. This happens in a mass spectrometer where we use an electric current to start giving these molecules positive charges, or it happens at high temperatures where we form a plasma. This takes a lot of energy because you’re disrupting a strong electrostatic bond between a positively charged atomic nucleus and its surrounding negatively charged electrons.

But this article seems to mix this up with what is really just charge separation, which occurs when an acid and base exchange a proton to form a charged conjugate base and conjugate acid. It’s best demonstrated by example:

HCl +H2O → H3O+ + Cl

Here, hydrochloric acid (HCl) acts as an acid, water (H2O) is acting as a base. H3O+ and Cl are the resulting conjugate acid and conjugate base respectively. These hold formal charges – i.e., they have one too few and one excess electron respectively to balance out the positive charges of the atomic nuclei – but they still balance out with a positive (+1) and negative (-1) on the right hand side of that equation, so overall the chemical system remains neutral. However, I have never, ever, ever, heard this sort of reaction being referred to as “ionisation” – except, perhaps, in an abstract sense where you might use a Hess Cycle to break it down into individual steps; for instance, you’d have a step where you’d “ionise” gaseous Cl to gaseous Cl prior to solvating it, but this isn’t to say the real Cl atom in reality actually goes magically into the gas phase and ionises itself out of nowhere, a Hess Cycle is just a bean-counting exercise in energy conservation. No, what is really happening is that our molecules combine together into an intermediate or transition state, and when they separate again one side takes an extra electron with it because it happens to be more stable that way. The charges are then successfully separated because water, being a polar solvent, binds electrostatically to these ions to keep them apart. And this just happens to be a nice, stable situation. Again, I have never heard of this being called “ionisation” just in case anyone confuses it with something like the formation of a plasma.

But what is his point? To use McCombs’s words:

The amine group is basic and will react quickly with the acid group also present. This acid-base reaction of amino acids is instantaneous in water, and the components necessary for protein formation are not present in a form in which they can react.

So, what he’s referring to is the acid-base equilibrium of a basic amine group and an acidic carboxylic acid group. He seems to be suggesting that because of this reaction, the acid and base groups will protonate/deprotonate and can no longer react (just as in the HCl reaction above).

R-COOH + R’-NH2 → R-COO + R’-NH3+

Actually, the above is slightly more complicated because if it’s in water there will be H2O + H2O → H3O+ + OH playing about in there, too.

BUT, and this is fucking GCSE-level chemistry here, amines and carboxylic acids are not a strong acid/base combination. They do not all protonate/deprotonate in solution. In fact, the pKa value* for the average carboxylic acid is between 2 and 5. McCombs seems to think that this acid dissociation is a problem to the formation of peptide chains – but, and this is a recurring theme, if it was then protein chains wouldn’t form at all. In fact, this protonation is probably quite helpful for formation of peptide bonds because such a reaction is acid (and base) catalysed. These protonated/deprotonated forms that are charged are actually highly reactive – and because they are a weak acid/base combination, have plenty of uncharged and unchanged molecules around them to react with. This sort of thing is, far from a barrier, an essential property of the molecules doing what we need them to do.

*This is a measure of acidity based on the equilibrium constant between the acidic proton being attached and detached. It’s a logarithmic scale, and the fact that these pKa values aren’t negative-infinity suggests that not all – not by a long shot – amino acids are going to be formal ions in solution.

3. The Problem of Mass Action

Here is my favourite one (and this is getting long so I might stop here for now), because McComb’s manages to mess up the explanation of, and then completely misapply, Le Chatelier’s principle. Let’s just quote his conclusion verbatim for now:

This means that any reaction that produces water cannot be performed in the presence of water.

Now, I could give him the benefit of the doubt that he’s not explaining himself well, but let’s not and just take this sentence literally. Think about this for a moment. Suppose we have a completely dry solvent (say, dry benzene that’s been distilled and refluxed over sodium and then cannula transferred to a flame-dried reactant flask that has been flushed with nitrogen – as you do) and we perform an organic reaction in it that condenses out water – peptide/amide/ester bond formation, for instance. As soon as the first molecule – of trillions – reacts, the reaction is now in the presence of water. If you were to take the above sentence literally, then no chemical reaction would ever occur at all. The first reaction would take place, it would then be in the presence of its product, the reaction would stop. But of course, reactions do proceed, so this principle that McCombs is alluding to could not possibly say what he’s trying to claim. So, let me try to explain it.

Le Chatelier’s principle states that a chemical system at equilibrium will adapt to oppose any change imposed on it.

Okay, that’s probably not very nice and pop-sciencey, so let’s break it down further. A chemical equilibrium is where a chemical reaction, say “A + B → C” can reverse so that “C → A + B” happens too. At equilibrium, or in “equilibrium conditions”, the rate of both reactions is the same. It should then be obvious that that relative concentrations of A, B and C will remain the same – C is produced in the first reaction at the same speed it’s consumed in the second reaction and likewise for A and B. Le Chatelier’s principle says that if we change those conditions by, for example, adding a spoonful of C to the system, then the chemical system will oppose that addition and go back to “equilibrium conditions” by consuming C at a faster rate.  This is simply because rate is proportional to concentration, and if you boost the concentration of C, that backwards reaction (C → A + B) will speed up until enough C has been consumed that the rate is the same as the forward reaction again. Aka, equilibrium has been achieved again.

Where McCombs has catastrophically fucked up this explanation and applied it ass-backwards is to assume this is an absolute statement, and that you can tell just by looking at a reaction on paper whether it will go ahead or not in the presence of A, B or C. No. Just no. This is not how it works. A chemical equilibrium is driven by energy and the energy difference between the products and reactants; specifically a little formula that reads “ΔG = -RTln(K)”. If the product is more stable, the equilibrium will lie to the right, if the reactant is more stable it will lie to the left. Concentration does not come into this except when you are talking about changing the conditions at equilibrium.

A + B → C

For instance, an equilibrium concentration might be a 10:1 ratio of A:C at a particular temperature. Le Chatelier’s principle refers only to a change made against those conditions – if we make a system were it’s a 1:1 ratio of A:C by spooning in some C the system will oppose this change and get itself back to equilibrium by consuming C until 10:1 is reached again. This emphatically does not mean that reactions that generate water as a by-product cannot occur in a water solvent. In fact they can, and they do. And there are many where you don’t need to bother drying your solvents or glassware in the lab precisely because the reaction generates water.

Seriously, where the fuck did this guy learn chemistry?

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.