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?