Why Life Must Start with RNA and not Something Else.

In the previous post, I argued that reproduction had to start with RNA, but that leaves the obvious question, why not something else? The use of purines and pyrimidines to transfer energy arises simply because the purines and pyrimidines are the easiest to form, given the earliest atmosphere almost certainly was rich in ammonia, hydrogen cyanide, cyanocetylene, and urea would soon be formed. Some may argue with the “easily formed”, however leaving a sample of ammonium cyanide and urea to its own devices will get nucleobases. Cytosine is a little more difficult, but with available cyanoacetylene, it is reasonably likely. The important point is that if you accept my mechanism for how rocky planets form, these chemicals are going to be prolific. I shall justify that later. The important thing about these chemicals is that they lead to the formation of multiple hydrogen bonds only with their partners. As explained in the last post, there is no alternative to hydrogen bonds for transferring information, and these are the only chemicals that can provide accuracy under abiogenic conditions.

The polymer linking agent is phosphate, so why phosphate? Phosphoric acid has three hydrogen atoms that are available for substitution, i.e.it can form three functions. Two are to form esters and as I noted previously, the third is to provide solubility. The solubility is important because if there was not anionic repulsion, the strands would bundle together and reproduction would not work. The strands would also not provide catalysis, which occurs because a strand can fold around a cation like magnesium and form the shapes that seem to be needed. The good news is that unlike in enzymes, it can rearrange the magnesium and thus get different effects. Of course, enzymes are hugely more effective, but an enzyme generally only does one thing.

The polymer forms esters by phosphate bonding to a sugar. Think of the reaction as

P – OH  + HO – C    ->  P – O – C  + H2O       (1)

where P is the phosphorus of a phosphate or phosphoric acid, and C is the carbon atom of a sugar. Note that this reaction is reversible, but at room temperature the bonds are quite stable. These ester bonds are very strong, which is important because you do not want your carefully prepared polymer to randomly fall to bits. On the other hand, it must be able to be disrupted or substituted and not be essentially fixed, as would happen if proteins were used for information transfer. The reason is, life is evolving by random trials, and it is important that since many of these trials will be unproductive, there has to be a way to recover an many of the valuable chemicals as possible for further trials, and also to unclutter the system so that something that conveys advantages does not get lost in the morass of failures or otherwise useless stuff. Only phosphate offers these properties. In principle, you might argue for arsenate, but its bonds are weaker, thus less reliable, and worse, arsenic reacts with hydrogen sulphide (common around fumaroles which as we shall see are necessary sites) to form insoluble sulphides. These are the very pretty yellow layers in geothermal areas. No other element will do.

There are a variety of other sugars that if used to link nucleobases to phosphate will form duplexes, so the question then is, why weren’t they used? The ability to catalyse its own scission is the first of two reasons why ribose is so important. Once the strands get long enough to fold around themselves, catalysis starts, and one of the possible catalytic reactions is the promotion of the remaining OH group on the ribose to help water send the reaction (1) into reverse, which would break a link in the polymer chain. Deoxyribose does not have such a free hydroxyl and hence does not have this option, which is why DNA ended up being the information transfer chemical once a life form that had something worth keeping had emerged. What this means is that RNA has the opportunity to mutate, which is a big help in getting evolution going, and when it is broken, the bits remain available for further tries in some rearranged form.

The question then is, how do you form the phosphate ester? You mix phosphate and the sugar in solution and – oops, nothing happens. Reaction (1) is so slow at ambient temperature that you could sit there indefinitely, however, if you heat it, it does proceed. However, the rate of a reaction like this depends on the product of the concentrations on each side, with such a product on the right-hand side determining the rate of the reaction going from right to left. If you look at (1), it probably occurs to you that in aqueous solution, the concentration of water is far greater than the concentration of sugar. You will see people say that life could start around black smokers, but when you check, at the temperatures they require for the forward reaction to go it requires the concentration of water to be less than about 2%. Good luck getting that at the bottom of the ocean. You may protest that nevertheless there is life there, devouring emerging nutrients. True, although the ocean acts as a cooling bath, and the life forms have evolved protective systems. There are no such things when life is getting started. Life has moved to be close to black smokers but it did not start there.

What we need is a more precise way of delivering the required energy to the reaction site. So far, one and only one method has been found to make such initial linkages, and that is photochemical. If adenine is irradiated with light in the presence of ribose and phosphate, you get AMP, and even ATP. We now see why only ribose was chosen. AMP, and for that matter, RNA, link the nucleobases and phosphate through the ribofuranose form. Such sugars can exist in two forms: a furanose (a five-membered ring involving an oxygen atom linked to C1 of the sugar) and a pyranose form (the six-membered equivalent.). Now the first important point about a sugar is it cannot transmit electronic effects arising from the nucleobase absorbing a photon. However, it can transmit mechanical vibrational energy, and this is where the furanose becomes important. While the pyranose form is always rigid, the furanose form is flexible. The reason ribofuranose can form the links, in my opinion, is it can transmit and focus the mechanical energy to the free C-5 which will vibrate vigorously like the end of a whip and form the phosphate ester. Ribose is important because it is the only sugar with a reasonable amount of furanose form in aqueous solution. It is also worth noting that in the original experiments, no phosphate ester was formed from the pyranose form. As the furanose is used, the equilibrium ensures pyranose maintains the furanose/pyranose ratio.

That leaves open the question, how are the polymers formed? It appears that provided you can get the mers embedded in a lipid micelle or vesicle (the most primitive form of the cell wall), leaving these in the sun on a hot rock to dry them out leads to polymers of about 80 units in an hour. This is the first reason why life probably started around geothermal vents on land. Plenty of hot rocks around, with water splashes to replenish the supply of mers, and sunlight to form them. The second reason will be in the following post.

The title statement can now be answered. Life must start with RNA because it is the only agent that can lead to biological reproduction without external assistance. I started the last post indicating I would show what sort of planets might harbour life. The series is nearly there, but some might like to try the last step for themselves.

What do we need for life?

One question that intrigues man people is, is there life in the Universe besides what we see? Logic would say, almost certainly yes. The reason is we know there is a non-zero probability that it can form elswhere because it did here. That probability may be small but there is an enormous number of stars in the Universe (something in excess of 10^22 that we can see) that the conditions that led to life here must be reproduced a very large number of times. Of course, while there are such a large number of stars, by far the most are at such an extraordinarily large distance from us that they are essentially irrelevant. For the bulk of them, it took the light more than ten billion years to get here. But if we were to look for life nearby, where would we look? To answer that, we need to ask ourselves, what conditions are needed to get life started? The issue is NOT where can life exist, but rather where can it form. We know life can be found now on Earth in a wide range of environments, but that does not mean it can form there. It can migrate from somewhere else, gradually evolving systems needed to stabilize it to the new environment. The most obvious example is life emerging from the water to live on land. Nobody suggests life did not start in water because you need a solution to move nutrients around.

The first question to ask is, what are the most difficult things to achieve for life to get started? I think the four hardest things to get started are reproduction, energy transport, solubilization, and catalysis. Catalysis is required to make the chemical reactions that are desirable to go faster, and thus get more of the available resources going in the desired direction. (In this, when I use the word “desired” I mean to get on a right track to where life can get going and then support that choice during subsequent evolution. I do not mean to imply some sort of planning or directing.) Solubilization is required because many of the chemicals with functions that will be needed are not soluble in water, and hence they would simply settle out as a layer of brown gunk, which, as an aside, is what happens in many experiments designed to simulate the origin of life. What needs to happen is that something joins on at a place that does not spoil the function and then conveys solubility. Energy transport is a critical problem: if you do not have something that stores energy, functionality is restricted to microdistances from energy inputs.

Each of these critical functions, as well as reproduction, as I shall show below, depend on forming phosphate esters. Thus energy transport is mediated by adenosine tripolyphosphate (ATP), solubilisation of many of the most primitive cofactors that do not contain a lot of nitrogen or hydroxyl groups is aided by an attached adenosine monophosphate (AMP), initial catalysts came from ribozymes, RNA would be the initial source of reproduction, and both ribozymes and RNA (the latter is effectively just far longer strands of the former) are both constructed of AMP or the equivalent with different nucleobases. The commonality is the ribose and phosphate ester.

Catalysis is an interesting problem. Currently, enzymes are used, but life could not have started that way. The reason lies in the complexity of enzymes. The enzyme that will digest other protein, and hence make chemicals available from failed attempts at guessing the structure of a useful enzyme, has a precise sequence of three hundred and fifteen amino acids. There are twenty different common amino acids used (and in abiogenic situations, a lot more available) and these occur in D- and L- configurations, except for glycine, which means the probability of getting this enzyme is two in 39^315. That number is incredibly improbable. It makes selecting a specific proton in the entire Universe trivial in comparison. Worse, that catalyses ONE reaction only. That is not how initial catalysis happened.

Now, look at the problem of reproduction. Once a polymer is formed that can generate some of whatever requirements life needs, if it cannot copy itself, then it is a one-off wonder, and eventually it will degrade and be lost without a trace. Reproduction involves the need to transfer information, which in this case is some sort of a pattern. The problem here is the transfer must be accurate, but not too accurate initially, and we need different entities. By that I mean, if you just reproduced the same entity, such as in polyethene, you have two units of information: what it is and how long it is, but that second one is rather useless because life has no way of measuring the length without having a very large set of reference molecules. What life here chose appears to have been RNA, at least to start with. RNA has two purines and two pyrimidines, and it pairs them in a double helix. When reproduction occurs, one strand is the negative of the other, but if the negative pairs, we now have two strands that are equivalent to each original strand. (you retain the original.) There are four variations possible from the canonical units at any given position, and once you have many millions of units, a lot of information can be coded.

Why ribonucleic acid? The requirement is to be able to transfer information reliably, but not too accurately (I shall explain why not in a later post.) To do that, the polymer strands have to bind, and this occurs through what we call hydrogen bonds, which each give a binding energy of about 13 kJ/mol. These are chosen because they are weak enough to be ruptured, but strong enough you can get preferences. Thus adenine binds with uracil through two hydrogen bonds, which generates a little over 26 kJ/mol. (For comparison, a carbon-carbon bond is about 360 kJ/mol.) To get the 26 kJ/mol. the two hydrogen bonds have to be formed, and that can only happen of the entities have the right groups in the correct rigid configuration. When guanine bonds with cytosine, three such hydrogen bonds are formed, and the attraction is just under 40 kJ/mol. Guanine can also bind with uracil generating 26 kJ/mol., so information transfer is not necessarily totally accurate.

This binding through hydrogen bonds is critical. The bonding is strong enough to give a significant preference for each mer, but once the polymer gets long enough, the total energy (the sum of the energy of the individual pairs) holding the strands together gets to be those energies above multiplied by the number of pairs. If you have a million pairs, the strength of diamond becomes trivial, yet to reproduce, the strands must be separated. Hydrogen bonds can be separated because as the strands start to separate, water also hydrogen bonds and thus makes up for the linking energy. However, that alone is insufficient because the strand itself would be insoluble in water, and if so, the two strands linked together would remain insoluble (for those who know what this means, entropy strongly favours keeping the strands together). To achieve this, we need something that joins the mers into a chain, adds solubility, forms stable chemical bonds in general but is equally capable of being broken so that if the information creates something that is useless, we can recycle the chemicals. Only phosphate fills these requirements, but phosphate does not bind nucleobases together. Something intermediate is required, and that something is ribose.

In the next posts on this topic, I shall show you where this leads in seeing where life might be.

Homochirality – how I believe it originated

In a previous post I issued a challenge that was issued prior to my talk to the Wellington Astronomical Society: can you work out how homochirality arose in life? To remind you, chirality is what causes handedness. If you have gloves, your left hand has its glove and the right hand its, and one cannot really replace the other. Homo chirality means there is one only form of handedness, thus in your body, sugars are D sugars (right handed) while all your amino acids are L, or left handed. The problem is, when you synthesis any of these through any conceivable route given the nature of the starting materials, which have no chirality, you get an equal mix of D and L. On the other hand, if you synthesize the molecules through a chiral entity, chirality remains. Think of using a left-handed glove. If you use it as a mold for a plaster cast, you will keep making casts of left hands, not right hands.

How did nature select one lot and neglect the others? The real reason for asking this, though, was not to do with chirality. Most people can get through life without stopping to worry about why their proteins are made from L amino acids. Space travellers landing on another planet might, though, because if you landed on a planet where all the amino acids were D, then you could not eat their food and be nourished. However we are here. No, the real reason was, this is a chance to show how to develop a theory.

Everyone develops theories, for example, “Who trashed the letterbox?” is an example I gave in my first ebook, which was about developing theories. The book was mainly about scientific theories, so don’t rush out and buy it unless science really interests you, but that point is valid about life. If you look at the web, you can find many places where people theorize on political matters. That would be very good for democracy, if they did it properly, but not so good if the methodology is very bad. Most simply jump to the first conclusion their prejudices lead to, and if that is the way we intend to run our democracy, then we are in trouble. The reason I picked on this issue of chirality is that it is easy, and it is unlikely to run into prejudiced anger and hence can be considered dispassionately.

There are numerous scientific papers devoted to the question of how homochirality arose: they consider the weak force (which does not apply to chemistry anywhere else); materials adsorbed on special clays (without asking how the material can get off again, or why another clay won’t give the complementary material); polarized light (why is there not the opposite result with oppositely polarized light); and even an assertion there is a weak preference in meteorites.
I believe the answer is strangely simple when instead of starting at the beginning with a mixture of both forms, you stop worrying about how it happened, and start asking why it happened? Why would emerging life discard half of the resources available to it? After all, if it did, why did not some other form use both? By using both, it would have twice the amount of resource, so it should be able to survive better, and should prevail.

The obvious answer is that life chose one form because it had to, so where is homochirality so important? The answer is reproduction. What happens is reproduction is governed by nucleic acids that can form a double helix, or duplex. If you have a strand, complementary nucleobases get absorbed on the strand, and if all the bases can link through the phosphate esters, they form their own helix. When that strand is complete, the strands can separate, and the process starts again. That is the essence of reproduction. Now, the problem is in joining those phosphate esters because the appropriate parts have to be in the right place. The new strand has to have the same degree of twist, in the same direction. This is where the chirality comes in. To get a regular twist, or pitch to the helix, all the ribose units have to have the same handedness. Think of making a bolt, and a nut to fit it. If the bolt has right hand thread, then suddenly lurches every now and again into left hand thread, how can you make a nut to fit it?

If a sugar came in with the opposite chirality, the twist would be wrong, the ends would not match up, and the base could not join the strand. It would then go away and nothing would happen until the correct pitch to the helix could be supplied, and that is with the correct chirality of the ribose. At first, strands with any mix could occur, but duplexes would only form with one chirality, and when one came along, since it could reproduce and the others could not, inevitably it must prevail.

Why does that go out to all the other molecules? Because they are made either directly or indirectly from RNA molecules. (RNA is the generator of enzymes.) Accordingly, everything that comes from the chiral RNA will also carry the appropriate chirality.

Was that so difficult to conceive?

Origin of life, and a challenge!

Here is a chance to test yourself as a theoretician. But do not worry if you cannot solve this. Most people will not, and I predict nobody will, but prove me wrong! And as a hint, while nobody actually knows the answer, as I shall show eventually, getting a very reasonable answer is actually relatively simple, although you need a little background knowledge for the first question.

Just before Christmas, I posted with the title Biogenesis: how did life get started?” (http://wp.me/p2IwTC-6e ) but as some may have noticed, I did not get very far along the track indicated by the title. The issue is, of course, somewhat complicated, and it is easier to discuss it in small pieces I also mentioned I was about to give a talk on this early this year. Well, the talk will come on March 4, so it is approaching quickly. Accordingly, I have put out an abstract, and am including two challenges, which readers here may or may not wish to contemplate. Specifically,
1. Why did nature choose ribose for nucleic acids?
2. How did homochirality arise?
Put your guesses or inspired knowledgeable comments at the end of this post. The answers are not that difficult, but they are subtle. In my opinion, they are also excellent examples of how to go about forming a theory. I shall post my answers in due course.

The question of, why ribose, is a little complicated and cannot be answered without some chemical knowledge, so most readers probably won’t be able to answer that. Notwithstanding that, it is a very interesting question because I believe it gives a clue as to how life got underway. RNA is a polymer in which each mer is made up of three entities: one of four nucleobases, ribose and a phosphate ester. The nucleobase is attached to C-1 of ribose (if you opened it up, at the aldehyde end) and the phosphate is at C-5 (the other end, ribose being a five carbon sugar. The nucleobases are, in general, easy to make. If you leave ammonium cyanide lying around, they make themselves, but that is the only thing that appears to be easy about this entity. Sugars can be made in solution by having formaldehyde, which is easily made, react in water with lime, and a number of other solids. That seems easy, except that when you do this, you do not get much, if any, ribose. The reason is, ribose is a high-energy pentose (five carbon sugar) because all the hydroxyl groups are eclipsing each other in the closest orientation (axial, for those who know some chemistry). In the laboratory, double helix nucleobases (duplexes) have been made from xylose and arabinose, and in many ways these have superior properties to ribose, but nature chose ribose, so the question is, why? Not only did it do it for RNA, but the unit adenine – ribose – phosphate turns up very frequently.

Adenine combined with ribose is usually called adenosine, and the adenosine phosphate linkage turns up in the energy transfer chemical ATP (adenosine tripolyphosphate), the reduction oxidation catalysts NAD and FAD, where the AD stands for adenosine diphosphate, and in a number of enzyme cofactors, to give solubility in water. Giving solubility in water is an obvious benefit, but putting a sugar unit on the group would also do that. Giving an electric charge would also be of benefit, because it helps keep the entity in the cell, nevertheless there are also other ways of doing that. You may say, well, it had to choose something, but recall, ribose is hard to make, so why was it selected for so many entities?

The phosphate ester also causes something of a problem. In the laboratory, phosphate esters are usually made with highly reactive phosphorus-based chemicals, but life could not have started that way. Another way to form phosphate esters is to heat a phosphate and an alcohol (including the hydroxyl groups on a sugar) to about 180 oC, when water is driven off. Note that if water is around, as in the undersea thermal vents that are often considered to be the source of life, the superheated water converts phosphate esters to phosphate and alcohol groups. Life did not start at the so-called black smokers, although with sophisticated protection mechanisms, it has evolved to tolerate such environments. Another problem with phosphate is that phosphates are insoluble in neutral or alkaline water, and phosphate esters hydrolyse in acidic water.
However, notwithstanding the difficulty with using phosphate, there is no real choice if you want a linking agent with three functions (two used up to join two groups, one to be ionic to enhance water solubility). Boron is rare, and has unusual chemistry, while elements such as arsenic, besides being much less common, do not give bonds with as much strength.

Homochirality is different matter. (Chirality can be though of like handedness. If you have gloves, your left hand has its glove and the right hand its, even though they are identical in features, such as four fingers and a thumb. The handedness comes from the fact you cannot put those fingers and thumb on a hand where the top differs from the bottom without making the right hand different from the left.) The sugars your body uses are D sugars (think of this as right handed) while all your amino acids are L, or left handed. The problem is, when you synthesis any of these through any conceivable route given the nature of the starting materials, which have no chirality, you get an equal mix of D and L. How did nature select one lot and neglect the others?
Put your guesses below! In the meantime, my ebook, “Planetary formation and biogenesis”, which summarizes what we knew up to about 2012, is going to be discounted on Amazon for a short period following March 6. This is to favour those going to my talk, but you too can take advantage. It has a significant scientific content (including an analysis of over 600 scientific papers) so if your scientific knowledge is slight, it may be too difficult.