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.

How Earth Cools

As you may have seen at the end of my last post, I received an objection to the existence of a greenhouse effect on the grounds that it violated the thermodynamics of heat transfer, and if you read what it says it is essentially focused on heat conduction. The reason I am bothering with this post is that it is an opportunity to consider how theories and explanations should be formed. We start by noting that mathematics does not determine what happens; it calculates what happens provided the background premises are correct.

The objection mentioned convection as a complicating feature. Actually, the transfer of heat in the lower atmosphere is largely dependent on the evaporation and condensation of water, and wind transferring the heat from one place to another, and it is these, and ocean currents, that are the problems for the ice caps. Further, as I shall show, heat conduction cannot be relevant to the major cooling of the upper atmosphere. But first, let me show you how complicated heat conduction is. The correct equation for one-dimensional heat conduction is represented by a partial differential equation of the Laplace type, (which I would quote if I knew how to get such an equation into this limited htm formatting) and the simplest form only works as written when the medium is homogenous. Since the atmosphere thins out with height, this clearly needs modification, and for those who know anything about partial differential equations, they become a nightmare once the system becomes anything but absolutely simple. Such equations also apply to convection and evaporative transfer, once corrected for the nightmare of non-homogeneity and motion in three dimensions. Good luck with that!

This form of heat transfer is irrelevant to the so-called greenhouse effect. To show why, I start by considering what heat is, and that is random kinetic energy. The molecules are bouncing around, colliding with each other, and the collisions are elastic, which means energy is conserved, as is momentum. Most of the collisions are glancing, and that means from momentum conservation that we get a range of velocities distributed about an “average”. Heat is transferred because fast moving molecules collide with slower ones, and speed them up. The objection noted heat does not flow from cold to hot spontaneously. That is true because momentum is conserved in collisions. A molecule does not speed up when hit by a slower molecule. That is why that equation has heat going only in one way.

Now, suppose with this mechanism, we get to the top of the atmosphere. What happens then? No more heat can be transferred because there are no molecules to collide with in space. If heat pours in, and nothing goes out, eventually we become infinitely hot. Obviously that does not happen, and the reason becomes obvious when we ask how the heat gets in in the first place. The heat from the sun comes from the effects of solar radiation. Something like 1.36 kW/m^2 comes in on a surface in space at right angles to the line from the sun, but the average is much less on the surface of earth as the angle is at best normal only at noon, and if the sun is overhead. About a quarter of that is directly reflected to space, and that may increase if the cloud cover increases. The important point here is that light is not heat. When it is absorbed, it will direct an electronic transition, but that energy will eventually decay into heat. Initially, however, the material goes to an excited state, but its temperature remains constant, because the energy has not been randomised. Now we see that if energy comes in as radiation, it follows to get an equilibrium, equivalent energy must go out, and as radiation, not heat, because that is the only way it can get out in a vacuum.

The ground continuously sends radiation (mainly infrared) upwards and the intensity is proportional to the fourth power of the temperature. The average temperature is thus determined through radiant energy in equals radiant out. The radiance for a given material, which is described as a grey body radiator, is also dependent on its nature. The radiation occurs because any change of dipole moment leads to electromagnetic radiation, but the dipoles must change between quantised energy states. What that means is they come from motion that can be described in one way or another as a wave, and the waves change to longer wavelengths when they radiate. The reason the waves representing ground states switch to shorter wavelengths is that the heat energy from collisions can excite them, similar in a way to when you pluck a guitar string. Thus the body cools by heat exciting some vibratory states, which collapse by radiation leaving them. (This is similar to the guitar string losing energy by emitting sound, except that the guitar string emits continuous decaying sound; the quantised state lets it go all at once as one photon.)

Such changes are reversible; if the wave has collapsed to a longer wavelength when energy is radiated away, then if a photon of the same frequency is returned, that excites the state. That slows cooling because the next photon emitted from the ground did not need heat to excite it, and hence that same heat remains. The reason there is back radiation is that certain frequencies of infrared radiation leaving the ground get absorbed by molecules in the atmosphere when their molecular vibrational or rotational excited states have a different electric moment from the ground state. Carbon dioxide has two such vibrational states that absorb mildly, and one that does not. Water is a much stronger absorber, and methane has more states available to it. Agriculture offers N2O, which is bad because it is harder to remove than carbon dioxide, and the worst are chlorocarbons and fluorocarbons, because the vibrations have stronger dipole moment changes. Each of these different materials has vibrations at different frequencies, which make them even more problematical as radiation at more frequencies are slowed in their escape to space. The excited states decay and emit photons in random directions, hence only about half of that continues on it way to space, the rest returning to the ground. Of that that goes upwards, it will be absorbed by more molecules, and the same will happen, and of course some coming back from up there with be absorbed at a lower level and half of that will go back up. In detail, there is some rather difficult calculus, but the effect could be described as a field of oscillators.

So the take-away message is the physics are well understood, the effect of the greenhouse gases is it slows the cooling process, so the ground stays warmer than it would if they were not there. Now the good thing about a theory is that it should predict things. Here we can make a prediction. In winter, in the absence of wind, the night should be warmer if there is cloud cover, because water is a strong greenhouse material. Go outside one evening and see.