Chemistry by Chance – How Even Qualified Chemists Cease to Understand Chemistry Once They Come Out as Creationists (part 3)

See part 1 and part 2.

Okay, okay… time to get this over with. Why do I bother? Anyway, to re-iterate again, this is the article I’m going through.

The Problem of Sugar

In this section we’re changing track a little. It’s moving away from directly messing up reactivity trends in amino acids to something even more bizarre – the assertion that the presence of reducing sugars will impede the formation of RNA or protein chains.

Okay, so lets go through this one more time. Sugars are a source of energy for us (indeed, all cellular living creatures). They are oxidised through reaction with atmospheric oxygen to carbon dioxide and water vapour, and the resulting liberation of chemical energy – via a few convoluted steps that aren’t worth going into – is used to power us. As a result, sugars hang around in solution in our bodies all the time. We can nicely store away an excess as fatty tissue (plants store it away as cellulose), but at some point we need to get sugars into solution where they can react. That this process doesn’t immediately kill us by destroying our metabolism, ability for DNA to replicate or RNA to form, or prevent peptide chains forming is pretty compelling evidence that this particular creationist claim isn’t the insurmountable chemical barrier it claims to be. It’s, in other words, false. Like, liar-liar-pants-on-fire kind of false.

Remember, the only thing that our living cells do differently to chemical reactivity in the “outside” world is provide suitable catalysts for chemical reactions. We do not miraculously reverse stability or reactivity trends – enzymes can control the chemistry by altering the rate of selected reactions but they do not work physics-defying miracles. Therefore any chemistry going on in a living cell can be considered as a good proxy for how a hypothetical “primordial soup” would work. That our own cells contain a mixture of sugars, amino acids and nucleic acid bases, but don’t stop functioning, is a clear indication that such a mixture won’t be an immediate problem in this “soup”.

The major problem with McCombs’ assertion here is how absolute it is. It’s a sub-par middle-school understanding of chemistry – it treats reactivity as an all-or-nothing approach. It’s pretending that if you mix components together, you get 100% yield or 0% yield, that you get a reaction or no reaction. This isn’t the case in chemistry. Actual chemistry contains complex equilibria; even if [A] + [B] goes to [C], this doesn’t mean there will be no [A] and [B] left in solution at all.  An equilibrium would be set up where we have a certain amount of products and a certain amount of reactant left – all because of energy and stability. For example (this is a fairly straightforward physical chemistry experiment I’ve done with undergraduates), in the decomposition of ammonium carbonate we get an equilibrium between ammonium carbonate and gaseous carbon dioxide and ammonia above it – if we don’t remove those gases (recall how McCombs abused Le Chatilier’s Principle in a previous part) then that equilibrium will stay the same. The quantity of gas will not increase forever, the quantity of solid will not decrease forever. It will eventually stabilise.

Okay, that’s a fairly unrelated example – but it demonstrates the principle. When McCombs asserts that “If amino acids (to form proteins) and sugars (to form nucleotides) were present in that soup, they would instantly react with each other, thereby removing both components from the mixture” he is not only over-stating the reactivity of those products (which is obvious because this reaction doesn’t immediately kill us by preventing all the life-supporting biochemical reactions he is talking about), but assuming that they will react completely, and totally, and not have any form of back reaction. The presence of a reducing agent only sets up an equilibrium – it is other conditions that say how far it will go. And again, because such an inhibition doesn’t occur in our cells, we can safely assume that it’s not an inhibition in a hypothetical “primordial soup”.

The Problem of Chirality

Chirality is part of a fascinating form of isomerism known as stereoisomerism. It’s basically where chemical structures in three-dimensions form mirror images. In the case of organic chemistry this is where you have a carbon atom surrounded by four different groups. It means they can be re-arranged to be mirror images of each other, but could never be perfectly superimposed. Importantly, they are chemically identical – that is, their reactivity is exactly the same, their spectroscopic properties are exactly the same, there is no way we can tell them apart through chemical means (except there is, but I’ll get to that). The core analogy of this is hands – and therefore is sometimes colloquially known as “handedness”. Take this diagram I thieved from Wikipedia:

In fact, because it’s such a classic example, those molecules are amino acids. Amino acids display such stereochemistry, and the naturally occurring ones all have the same stereochemistry. They’re all of one particular “handedness”. This is important because proteins, as three-dimensional structures, are altered if suddenly the amino acids have different chiralities. In this sense, McComb’s point is valid as if they were a mixture – called a racemic (pronounced “rass-eem-ic”, not “race-mike”) mixture – the vital three dimensional structure of proteins and peptide chains would fail. It’s convenient, therefore, that they’re not like this and come as stereochemically pure substances.

Remember when I said above that there is a way to chemically distinguish them? Well, you can; with another stereochemical centre – which is what we call a diastereomer. Going back to the hands analogy, have you’ll notice that shaking someone’s right hand with your right hand (as you do) feels comfortable, natural, and matches. But what about opposites? Seriously, try it right now; shake someone’s left hand with your right hand, or try to shake your own hand. You’ll notice it feels very different. Uncomfortable, even. If you consider that “comfort” as an analogy with energy and stability, then you’ll quickly realise how things become stereochemically pure – we react with another stereochemical centre, forming something that may be more or less stable.* This change in stability is what causes separation, and what causes us to have stereochemically pure amino acids because it’s a principle that continues whether it’s the biosynthesis of them in our cells or the formation of protein chains. One combination of stereo-centres will work, the others won’t – and natural selection or chemical stability does it for us.

* There is a complication I won’t go into in too much detail here – what if both centres are opposite? E.g., you shaking someone’s left hand with your right hand, and shaking someone’s right hand with your left. In this case we’ve formed a new stereoisomer that is still a mirror image and therefore chemically indistinct. The environments in our bodies are chiral, so the amino acids are chiral – so the chirality is preserved from generation to generation. There are a few interesting theories as to why one form generates over another in nature – such as circularly polarised light influencing the reactivity, or alternatively we can say it was just chance and that chirality was preserved by natural selection, just as how naturally selecting a coin toss can produce “pure” results even if the coin alone would suggest a 50:50 heads:tails – but that isn’t McComb’s objection. He’s objecting based on the fact that chirality merely exists and so racemic mixtures of amino acids would make inferior proteins (solved due to the existence of diastereomers), not its origin as one form or another, which is a different question.

Problems? What problems?

This frustrates me, because these objections are based on a very hard science -both in the sense of “hard and soft” science and the fact that it’s a difficult subject to get to know. Like many creationist claims, these are all very simple sounding objections arranged in a big list to make it seem impressive. But they take a lot of time to unpack, explain, and demonstrate why they’re wrong. If you want to know more, consider enrolling in a chemistry course, flick through Wikipedia, buy a chemistry set, or stare at yourself and think “wow, there’s some atoms in there doing some seriously convoluted stuff and I’m the result” – not “Goddidit”.

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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?