I am reading The Selfish Gene by Richard Dawkins.

I am on chapter two.

He speaks of the observation of the formation of amino-acids when you simulate environmental conditions of primordial earth.

UV light + water + carbon dioxide + methane + ammonia + a couple of weeks time = amino-acids

I understand that amino acids are an organic compound that serve a lot of important functions in our bodies.

Presumably, they are important to all life, because from the context I can derive, they seem to be somewhat of a precursor to life itself.

Dawkins then says:

Processes analogous to these must have given rise to the 'primeval soup' which biologists and chemists believe constituted the seas some three to four thousand million years ago.

He goes on and eventually states:

At some point a particularly remarkable molecule was formed by accident. We will call it the Replicator. ....

Actually a molecule that makes copies of itself is not as difficult to imagine as it seems at first, and it only had to arise once. Think of the replicator as a mould or template. Imagine it as a large molecule consisting of a complex chain of various sorts of building block molecules. The small building blocks were abundantly available in the soup surrounding the replicator. Now suppose that each building block has an affinity for its own kind. Then whenever a building block from out in the soup lands up next to a part of the replicator for which it has an affinity, it will tend to stick there. The building blocks that attach themselves in this way will automatically be arranged in a sequence that mimics that of the replicator itself. It is easy then to think of them joining up to form a stable chain just as in the formation of the original replicator. This process could continue as a progressive stacking up, layer upon layer. This is how crystals are formed. On the other hand, the two chains might split apart, in which case we have two replicators, each of which can go on to make further copies.

A more complex possibility is that each building block has affinity not for its own kind, but reciprocally for one particular other kind.

Then the replicator would act as a template not for an identical copy, but for a kind of 'negative', which would in its turn re-make an exact copy of the original positive. For our purposes it does not matter whether the original replication process was positive-negative or positive-positive, though it is worth remarking that the modem equivalents of the first replicator, the DNA molecules, use positive- negative replication. What does matter is that suddenly a new kind of 'stability' came into the world. Previously it is probable that no particular kind of complex molecule was very abundant in the soup, because each was dependent on building blocks happening to fall by luck into a particular stable configuration. As soon as the replicator was born it must have spread its copies rapidly throughout the seas, until the smaller building block molecules became a scarce resource, and other larger molecules were formed more and more rarely.

As someone with a limited understanding of Biology and Chemistry, I have a couple of questions.

  1. We have observed that the chemical conditions outlined at the top of this question seem to yield more complex organic compounds with time. Do we know (or have theories) as to why this is, or is it merely something we have observed and re-created?

  2. The theory about replicators suggests that they are like a chain of building-block molecules each with an affinity for either its own kind, or some other kind. (positive-positive vs positive-negative). -- Which ever was the case, you could end up with a big chain of molecules that had a fractal nature, because these building blocks were freely available in the soup surrounding the replicator. -- If the chain split apart, you would get two identical copies and each part could go off and replicate further.

    Now, I suppose this question mirrors the first, but why is it that it is so easy to imagine the affinity relationship? What makes molecules want to stick together with other, specific molecules?

  3. Further more, what makes chains of molecules split apart (replicate)?

Can somebody elaborate further on these points, and on what Dawkins is saying here in general, so as to pander to the cravings of someone who is not particularly versed in the parlance?

  • $\begingroup$ Since you're reading about the concept of molecular replication, you might be interested in very relevant and more general chemical term: autocatalysis. A substance that once formed favours the production of more of itself is not unique to life or biochemical compounds. $\endgroup$ – Nicolau Saker Neto Apr 7 '15 at 22:04
  1. We have observed that the chemical conditions outlined at the top of this question seem to yield more complex organic compounds with time. Do we know (or have theories) as to why this is, or is it merely something we have observed and re-created.

A recurring theme in chemistry,and all of your questions, is "lower energy usually equates with more stable structures." Oversimplifying just a bit (see note on time to reach equilibrium below), we can say that all chemical transformations are also equilibria. That means that our starting materials are converted to products and our products are converted back to starting materials - reactions are continually happening in both directions. Once at equilibrium the rate of the forward reaction matches that of the back reaction and the concentrations of starting materials and products will no longer change. At equilibrium the equilibrium constant ($\ce{K_{eq}}$) describing the relative concentrations of our starting materials and products will have the following form $$\mathrm{K_{eq}={\frac{(concentration ~products)}{(concentration~starting~ materials)}}}$$ and the equilibrium constant is related to the free energy difference between our starting materials and products by $$\mathrm{\Delta G = -RT\ln K_{eq}}$$ These equations tell us that the more stable a structure, the more it will predominate at equilibrium.

If we take carbon, oxygen, hydrogen and nitrogen an equilibrium will be set up between these elements and the simple amino acid glycine

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according to the following equation $$\ce{4C + 5H2 + N2 + 2O2 -> 2C2H5NO2~(glycine) + heat}$$ Over 500kJ of heat is produced per mole of glycine formed. This means that glycine is over 500kJ/mol more stable than the elements used to create it!

Bottom line: If a complex molecule is more stable than a simpler molecule, then over time the higher energy "simple" molecule will transform into the more stable (lower energy) "complex" molecule.

Just a word about time. It may take a long or a short time for an equilibrium to be attained on its own. Suffice it to say that with catalysts and\or energy, equilibria can be attained quickly.

  1. ...why is it that it is so easy to imagine the affinity relationship? What makes molecules want to stick together with other, specific molecules?

Again the answer has to do with lowering the energy of the system and making things more stable.

Some molecules have what is called an "active site". It may be an odd-shaped kink or pocket in the molecule. Let's think of this odd-shaped pocket as a lock, only molecules shaped like the key will fit. Further, there are often other functional groups (perhaps hydroxyl groups) around the active site that will bind (hydrogen bonds perhaps) with the key and stabilize it once it is inserted into the lock. Stabilization means lowering the energy of the system. Only the key fits into the lock and once inserted it is stabilized - energy is lowered.

  1. Further more, what makes chains of molecules split apart (replicate)?

By now you've probably guessed that the splitting apart step occurs because it lowers the energy of the system. Perhaps once the molecule reaches a certain size it folds differently - a new lower energy shape is now possible. A protein that was bound to the molecule and stabilizing it can no longer bind to it due to this new folding pattern. The protein is displaced, it is replaced by a different protein that stabilizes the molecule's new folded structure but predisposes it to splitting apart to a smaller size.

  • $\begingroup$ At first, I was disappointed to see an answer like "lower energy usually equates with more stable structures." because I immediately want to know WHY this is, but the answer actually made something click in my head. That is, If I want to know that answer, I need to go much deeper, as I believe its more related to questions about the fundamental forces that cause the atoms themselves to form. And like Dawkins says, No matter what level you're on, It all comes down to "survival of the stable" $\endgroup$ – Luke Apr 7 '15 at 23:45
  • $\begingroup$ This answer is just plain wrong. Biological life happens far from thermodynamical equillibrium, where entropy is maximised. Glycine is more stable than the elements, but far less stable than CO2, water and nitrogen. $\endgroup$ – Karl Dec 22 '18 at 23:00

The situation leading to the formation of amino acids was simulated by Stanley Miller and Harold Urey in their famous experiment and published as A Production of Amino Acids Under Possible Primitive Earth Conditions in Science, 1953, 117, 528-529 (DOI).

Imagine that this formation of amino acids might have happened not just in the sea, but also in shallow pits at the shore that once in a while fell dry and were heated by sunlight. Under these conditions, particularly in the presence of insoluble salts serving as catalysts, amino acids may have undergone condensation reactions, i.e., splitting off water and forming peptide bonds. The resulting molecules are oligopeptides, small brothers of proteines.

Imagine that these pools were filled with water again and that the process repeats. Between oligopeptides of fitting amino acid sequences, hydrogen bonds can form, resulting in $\beta$-sheets or similar aggregates. Upon repetition of the condensation step, free amino acids bound to one chain by hydrogen bonds might preferably undergo condensation in the other. This may be the molecular background of the replicator concept described by Richard Dawkins.


'UV light + water + carbon dioxide + methane + ammonia + a couple of weeks time = amino-acids'

The answers by ron and Klaus are very good, but I'd like to add one additional point which I think is very important.

The key "reactant" in the above equation is, to my mind "UV light". UV light comes from the sun. The sun is very hot. The surface of the sun is at ~5800 Kelvins, or about ~5500 °C, and the light it emits is effectively the equilibrium mixture of photons for that temperature (this equilibrium for photons is called black body radiation). The high temperature for the sun means that the equilibrium mixture of light frequencies it emits has much more UV light than "equilibrium" light at Earth's temperatures.

You can view the formation of complex molecules from simple molecules via UV light as a partial, frustrated attempt for the simple molecules to equilibrate with the blackbody radiation of the sun, i.e., for the simple molecules to equilibrate at temperatures of 5800 K. Those high temperatures favor high entropies or "disorders" among the molecules. You can view a "soup" that contains small amounts of many different amino acids and other molecules (in addition to large amounts of unreacted simple molecules) as having more disorder or entropy than a mix where the simple molecules are present in 100% purity.

An analogy is the frying of an egg. An egg in the refrigerator is ordered and "simple":. When you try to equilibrate the egg with blackbody radiation at a higher temperature (i.e. put it on the stove), the simple mix changes considerably and the result is a complex, solid-like gel of egg white and a pasty solid goo of yolk.

Note that your question mainly seems to be about formation of the primordial soup, and not actually formation of the replicators themselves.


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