The Vital Question: Why is life the way it is?

by Nick Lane

Second, and more telling, a major distinction between bacterial and archaeal membranes seems to be purely random – bacteria use one stereoisomer (mirror form) of glycerol, while archaea use the other.

There are also challenging problems with the idea that chemiosmotic coupling arose very early in evolution. One is the sheer sophistication of the mechanism. We have already paid our dues to the giant respiratory complexes and the ATP synthase – incredible molecular machines with pistons and rotary motors. Could these really be a product of the earliest days of evolution, before the advent of DNA replication? Surely not! But that’s a purely emotional response. The ATP synthase is no more complex than a ribosome, and everyone is agreed that ribosomes had to evolve early.

The second problem is the membrane itself. Even putting aside the question of what type of membrane it was, there is again the issue of disturbing early sophistication. In modern cells, chemiosmotic coupling only works if the membrane is almost impermeable to protons. But all experiments with plausible early membranes suggest that they would have been highly permeable to protons. It’s extremely difficult to keep them out. The problem is that chemiosmotic coupling looks to be useless until a number of sophisticated proteins have been embedded in a proton-tight membrane; and then, but only then, does it serve a purpose. So how on earth did all the parts evolve in advance? It’s a classic chicken and egg problem. What’s the point of learning to pump protons if you have no way to tap the gradient? And what’s the point of learning to tap a gradient, if you have no way of generating one? I’ll put forward a possible resolution in Chapter 4.

I will argue that natural proton gradients drove the origin of life on earth in a very particular environment, but an environment that is almost certainly ubiquitous across the cosmos: the shopping list is just rock, water and CO2.

How to make a cell What does it take to make a cell? Six basic properties are shared by all living cells on earth. Without wishing to sound like a textbook, let’s just enumerate them. All need: a continuous supply of reactive carbon for synthesising new organics; a supply of free energy to drive metabolic biochemistry – the formation of new proteins, DNA, and so on; catalysts to speed up and channel these metabolic reactions; excretion of waste, to pay the debt to the second law of thermodynamics and drive chemical reactions in the correct direction; compartmentalisation – a cell-like structure that separates the inside from the outside; hereditary material – RNA, DNA or an equivalent, to specify the detailed form and function.

Without a high flux of carbon and energy that is physically channelled over inorganic catalysts, there is no possibility of evolving cells. I would rate this as a necessity anywhere in the universe: given the requirement for carbon chemistry that we discussed in the last chapter, thermodynamics dictates a continuous flow of carbon and energy over natural catalysts.

that rules out almost all environments that have been touted as possible settings for the origin of life: warm ponds (sadly Darwin was wrong on that), primordial soup, microporous pumice stones, beaches, panspermia, you name it. But it does not rule out hydrothermal vents; on the contrary, it rules them in. Hydrothermal vents are exactly the kind of dissipative structures that we seek – continuous flow, far-from-equilibrium electrochemical reactors.

The beneficiary of all these metals dissolved in the ocean was another type of vent known as alkaline hydrothermal vents (Figure 12). In my view, these resolve all the problems of black smokers. Alkaline hydrothermal vents are not volcanic at all, and lack the drama and excitement of black smokers; but they do have other properties that fit them out much better as electrochemical flow reactors.

But these vents are certainly not giving rise to new life forms today, nor even forming a rich milieu of organics by thermophoresis. That’s partly because the bacteria already living there hoover up any resources very effectively; but there are also more fundamental reasons.

there were two main differences that must have had a big effect: oxygen was absent, and CO2 concentration in the air and ocean was much greater.

Now we are getting close to a real flow reactor: hydrogen-rich fluids circulate through a labyrinth of micropores with catalytic walls that concentrate and retain products while venting waste. But what exactly is reacting? Here we are reaching the crux of the matter. This is where the high CO2 levels enter the equation.

the formation of organic matter from H2 and CO2 is thermodynamically favoured under alkaline hydrothermal conditions, so long as oxygen is excluded.

But – and this is a big but – H2 does not easily react with CO2. There is a kinetic barrier, meaning that although thermodynamics says they should react spontaneously, some other obstacle stops it from happening right away. H2 and CO2 are practically indifferent to each other.

CO2 can only accept electrons in pairs. Addition of two electrons gives formate (HCOO–); two more give formaldehyde (CH2O); another two give methanol (CH3OH); and a final pair gives the fully reduced methane (CH4). Life, of course, is not made of methane, but it is only partially reduced carbon, roughly equivalent in its redox state to a mixture of formaldehyde and methanol. This means there are two important kinetic barriers relating to the origins of life from CO2 and H2. The first needs to be overcome, to get to formaldehyde or methanol. The second must not be overcome!

Even ramping up the pressure to the intense pressures found several kilometres down in hydrothermal vents at the bottom of the oceans does not force H2 to react with CO2. That’s why Wächtershäuser came up with the idea of ‘pyrites pulling’ in the first place. But there is one possible way. Proton power

For now, all we need to know is that bacteria growing from H2 and CO2 can only grow when powered by a proton gradient across a membrane. And that’s a helluva clue.

In fact, the reduction potential increases by about 59 mV for each pH unit of acidity. The more acidic the solution, the easier it is to transfer electrons on to CO2 to produce formate or formaldehyde. Unfortunately, exactly the same applies to hydrogen. The more acidic the solution, the easier it is to transfer electrons on to protons to form H2 gas. Simply changing pH therefore has no effect at all. It remains impossible to reduce CO2 with H2.

But now think of a proton gradient across a membrane. The proton concentration – the acidity – is different on opposite sides of the membrane. Exactly the same difference is found in alkaline vents. Alkaline hydrothermal fluids wend their way through the labyrinth of micropores. So do mildly acidic ocean waters. In some places there is a juxtaposition of fluids, with acidic ocean waters saturated in CO2 separated from alkaline fluids rich in H2 by a thin inorganic wall, containing semiconducting FeS minerals. The reduction potential of H2 is lower in alkaline conditions: it desperately ‘wants’ to be rid of its electrons, so the left-over H+ can pair up with the OH– in the alkaline fluids to form water, oh so stable. At pH 10, the reduction potential of H2 is –584 mV: strongly reducing. Conversely, at pH 6, the reduction potential for formate is –370m V, and for formaldehyde it is –520m v. In other words, given this difference in pH, it is quite easy for H2 to reduce CO2 to make formaldehyde.

Under alkaline hydrothermal conditions, H2 should react with CO2 to form organic molecules. Under almost any other conditions, it will not. In this chapter, I have already ruled out virtually all other environments as workable settings for the origin of life. We have established on thermodynamic grounds that to make a cell from scratch requires a continuous flow of reactive carbon and chemical energy across rudimentary catalysts in a constrained through-flow system. Only hydrothermal vents provide the requisite conditions, and only a subset of vents – alkaline hydrothermal vents – match all the conditions needed.

That leaves us with the final barefaced option. The apparent paradox is not a paradox at all: LUCA really was chemiosmotic, with an ATP synthase, but really did not have a modern membrane, or any of the large respiratory complexes that modern cells use to pump protons. She really did have DNA, and the universal genetic code, transcription, translation and ribosomes, but really had not evolved a modern method of DNA replication. This strange phantom cell makes no sense in an open ocean, but begins to add up when considered in the environment of alkaline hydrothermal vents discussed in the previous chapter. The clue lies in how bacteria and archaea live in these vents – some of them, at least, by an apparently primordial process called the acetyl CoA pathway, which bears an uncanny resemblance to the geochemistry of vents.

The fit between the geochemistry of alkaline vents and the biochemistry of methanogens and acetogens is so close that the word analogous does not do it justice. Analogy implies similarity, which is potentially only superficial. In fact, the similarity here is so close that it might better be seen as true homology – one form physically gave rise to the other. So geochemistry gives rise to biochemistry in a seamless transition from the inorganic to the organic.

even by standard methods, roughly one-third of eukaryotic genes do have equivalents in prokaryotes.

Around three-quarters of eukaryotic genes that have prokaryotic homologues apparently have bacterial ancestry, whereas the remaining quarter seem to derive from archaea.

at least 25 different groups of modern bacteria appear to have contributed genes to eukaryotes. Much the same goes for archaea, although fewer archaeal groups look to have contributed.

It looks like the first eukaryotes picked up thousands of genes from prokaryotes, but then ceased to ply any trade in prokaryotic genes. The simplest explanation for this picture is not bacterial-style lateral gene transfer, but eukaryotic-style endosymbiosis. On the face of it, there could have been scores of endosymbioses, as indeed predicted by the serial endosymbiosis theory. Yet it is barely credible that there could have been 25 different bacteria and 7 or 8 archaea all contributing to an early orgy of endosymbioses, a cellular love-fest; and then nothing for the rest of eukaryotic history.

fermentation is the only known alternative to chemiosmotic coupling.

The beauty of chemiosmotic coupling is that it transcends chemistry. It allows cells to save up ‘loose change’. If it takes 10 protons to make 1 ATP, and a particular chemical reaction only releases enough energy to pump 4 protons, then the reaction can simply be repeated 3 times to pump 12 protons, 10 of which are then used to make 1 ATP. While this is strictly necessary for some forms of respiration, it is beneficial for all of us, as it allows cells to conserve small amounts of energy that would otherwise be wasted as heat. And that, almost always, gives proton gradients an edge over plain chemistry – the power of nuance.

The more deeply rooted a mechanism, the more it can become the basis of quite unrelated traits. So proton gradients are widely used to drive the uptake of nutrients and excretion of waste; they are used to turn the screw that is the bacterial flagellum, a rotating propeller that motors cells about; and they are deliberately dissipated to produce heat, as in brown fat cells. Most intriguingly, their collapse ushers in the abrupt programmed death of bacterial populations. In essence, when a bacterial cell becomes infected with a virus, it is most likely doomed. If it can kill itself quickly, before the virus copies itself, then its kin (nearby cells sharing related genes) might survive. The genes that orchestrate cell death will spread through the population. But these death genes have to act quickly, and few mechanisms are faster than perforating the cell membrane. Many cells do exactly this – when infected, they form pores in the membrane. These collapse the proton-motive force, which in turn trips the latent death machinery. Proton gradients have become the ultimate sensors of cellular health, the arbiters of life and death, a role that will loom large later in this chapter.

it suddenly dawned on us that the key to the evolution of eukaryotes lies in the simple idea of ‘energy per gene’.

eukaryotes have up to 200,000 times more energy per gene than prokaryotes. Two hundred thousand times more energy! At last we had a gulf between the two groups, a chasm that explains with visceral force why the bacteria and archaea never evolved into complex eukaryotes,

cells spend as much as 80% of their total energy budget on protein synthesis. That’s because cells are mostly made of proteins; about half the dry weight of a bacterium is protein. Proteins are also very costly to make – they are strings of amino acids, usually a few hundred of them linked together in a long chain by ‘peptide’ bonds. Each peptide bond requires at least 5 ATPs to seal, five times as much as is needed to polymerise nucleotides into DNA.

equalising for both genome size and cell volume means that giant bacteria have 125,000 times less energy per gene than eukaryotes.

You might think this is just playing trivial games with numbers, that it holds no real meaning. I must confess that worried me too – these numbers are quite literally incredible – but this theorising does at least make a clear prediction. Giant bacteria should have thousands of copies of their full genome. Well, that prediction is easily testable. There are some giant bacteria out there; they’re not common, but they do exist. Two species have been studied in detail. Epulopiscium is known only from the anaerobic hind gut of surgeonfish. It is a battleship of a cell – long and streamlined, about half a millimetre in length, just visible to the naked eye. That’s substantially larger than most eukaryotes, including paramecium (Figure 23). Why Epulopiscium is so big is unknown. Thiomargarita is even larger. These cells are spheres, nearly a millimetre in diameter and composed mostly of a huge vacuole. A single cell can be as big as the head of a fruit fly! Thiomargarita lives in ocean waters periodically enriched in nitrates by upwelling currents. The cells trap the nitrates in their vacuoles for use as electron acceptors in respiration, enabling them to keep respiring during days or weeks of nitrate deprivation. But that is not the point. The point is that both Epulopiscium and Thiomargarita exhibit ‘extreme polyploidy’. That means they have thousands of copies of their full genome – up to 200,000 copies in the case of Epulopiscium and 18,000 copies in the case of Thiomargarit...

Why don’t the same problems of scale prevent eukaryotes from becoming complex? The difference lies in the mitochondria.

I mentioned that endosymbioses are rare between prokaryotes, which are not capable of engulfing other cells by phagocytosis. We do know of a couple of examples in bacteria (Figure 25), so plainly they can occur, if only very occasionally in the absence of phagocytosis.

Gene loss makes a huge difference. Losing genes is beneficial to the endosymbiont, as it speeds up their replication; but losing genes also saves ATP. Consider this simple thought experiment.

So the energy savings accruing from endosymbiotic gene loss (just 5% of their genes) could easily support the evolution of a dynamic cytoskeleton, as indeed happened. Bear in mind, as well, that 100 endosymbionts is a conservative estimate. Some large amoebae have as many as 300,000 mitochondria. And gene loss went much further than a mere 5%. Mitochondria lost nearly all their genes.

Mitochondria are just as good at making ATP as their free-living ancestors, but they reduced the costly bacterial overheads massively. In effect, eukaryotic cells have multibacteria power, but save on the costs of protein synthesis. Or rather, they divert the costs of protein synthesis.

Two questions remain, and they are tightly linked. First, this entire argument is based on the issue of surface-area-to-volume ratio in prokaryotes. But some bacteria, such as cyanobacteria, are perfectly capable of internalising their bioenergetic membranes, twisting their inner membrane into baroque convolutions, expanding their surface area considerably. Why can’t bacteria escape the constraints of chemiosmotic coupling by internalising their respiration in this way? And second, why, if gene loss is so important, did the mitochondria never lose their full genome, taking the process to completion and maximising the energetic benefits of gene loss? The answers to these questions make it clear why bacteria remained stuck in their rut for 4 billion years.

mitochondrial genes can respond to local changes in conditions, modulating the membrane potential within modest bounds before changes become catastrophic. If these genes were moved to the nucleus, the hypothesis is simply that the mitochondria would lose control over the membrane potential within minutes of any serious changes in oxygen tension or substrate availability, or free-radical leak, and the cell would die.

On the few occasions that cells lost genes from the mitochondria altogether, they also lost the ability to respire. Hydrogenosomes and mitosomes (the specialised organelles derived from mitochondria found in the archezoa) have generally lost all their genes, and have lost the power of chemiosmotic coupling into the bargain.

In sum: sex arose very early in eukaryotic evolution, and only the evolution of sex in a small unstable population can explain why all eukaryotes share so many common traits. That brings us to the question of this chapter. Is there something about an endosymbiosis between two prokaryotes that might drive the evolution of sex? You bet, and much else besides.

But what connects these ancient genetic parasites with the structure of eukaryotic genes? Little more than the detailed mechanism of the RNA scissors that splice out mobile bacterial introns, and simple logic. I mentioned the spliceosomes a few paragraphs ago: these are the protein nanomachines that cut out the introns from our own RNA transcripts. The spliceosome is not only made of proteins: at its heart is a pair of RNA scissors, the very same. These splice out eukaryotic introns by way of a telltale mechanism that betrays their ancestry as bacterial self-splicing introns (Figure 27).

The positions of many introns are conserved across eukaryotes.

The trouble is that spliceosomes are slow. Even today, after nearly 2 billion years of evolutionary refinement, they take several minutes to cut out a single intron. In contrast, ribosomes work at a furious pace – up to 10 amino acids per second. It takes barely half a minute to make a standard bacterial protein, about 250 amino acids in length. Even if the spliceosome could gain access to RNA (which is not easy as RNA is often encrusted in multiple ribosomes) it could not stop the formation of a large number of useless proteins, with their introns incorporated intact. How could an error catastrophe be averted? Simply by inserting a barrier in the way, according to Martin and Koonin. The nuclear membrane is a barrier separating transcription from translation – inside the nucleus, genes are transcribed into RNA codescripts; outside the nucleus, the RNAs are translated into proteins on the ribosomes. Crucially, the slow process of splicing takes place inside the nucleus, before the ribosomes can get anywhere near the RNA. That is the whole point of the nucleus: to keep ribosomes at bay. This explains why eukaryotes need a nucleus but prokaryotes don’t – prokaryotes don’t have an intron problem.

Even though it is clear from the genes that the host cell was a bona fide archaeon, which must have had characteristic archaeal lipids in its membranes, eukaryotes have bacterial lipids in their membranes. That’s a fact to conjure with. For some reason, the archaeal membranes must have been replaced with bacterial membranes early on in eukaryotic evolution. Why?

This is roughly what happens to the Y chromosome in men – the lack of recombination means that most genes are in a state of slow degeneration; only the critical genes can be preserved by selection. In the end, the entire chromosome can be lost, as indeed has happened in the mole vole Ellobius lutescens.

These two processes – accumulation of mildly damaging mutations, and loss of variation in selective sweeps – are together known as selective interference. Without recombination, selection on certain genes interferes with selection on others. By generating chromosomes with different combinations of alleles – ‘fluid chromosomes’ – sex allows selection to act on all genes individually.

So bacteria enjoy the benefits of sex (fluid chromosomes) along with the speed and simplicity of cloning. But they don’t fuse whole cells together, and they don’t have two sexes, and so they avoid many of the disadvantages of sex. They would seem to have the best of both worlds. So why did sex arise from lateral gene transfer in the earliest eukaryotes? Work from the mathematical population geneticists Sally Otto and Nick Barton points to an unholy trinity of factors that conspicuously relates to circumstances at the origin of eukaryotes: the benefits of sex are greatest when the mutation rate is high, selection pressure is strong, and there is a lot of variation in a population.

One of the deepest distinctions between the two sexes relates to the inheritance of mitochondria – one sex passes on its mitochondria, while the other sex does not. This distinction applies equally to humans (all our mitochondria come from our mother, 100,000 of them packed into the egg)