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

by Nick Lane

Cells are already microscopic. We had no inkling of their existence for most of human history. Ribosomes are orders of magnitude smaller still. You have 13 million of them in a single cell from your liver.

Ribosomes have an error rate of about one letter in 10,000, far lower than the defect rate in our own high-quality manufacturing processes. And they operate at a rate of about 10 amino acids per second,

We know that complex cells arose on just one occasion in 4 billion years of evolution, through a singular endosymbiosis between an archaeon and a bacterium

We don’t know what forces constrain bacteria and archaea – why they remain morphologically simple, despite being so different in their biochemistry, so varied in their genes, so versatile in their ability to extract a living from gases and rocks.

Essentially all living cells power themselves through the flow of protons (positively charged hydrogen atoms), in what amounts to a kind of electricity – proticity – with protons in place of electrons.

We tend to think of bacteria and minerals as occupying different realms, living versus inanimate, but in fact many sedimentary rocks are deposited, on a colossal scale, by bacterial processes.

Almost all the genes involved (encoding so-called eukaryotic ‘signature proteins’) are not found in prokaryotes. And conversely, bacteria show practically no tendency to evolve any of these complex eukaryotic traits. There are no known evolutionary intermediates between the morphologically simple state of all prokaryotes and the disturbingly complex common ancestor of eukaryotes (Figure 6). All these attributes of complex life arose in a phylogenetic void, a black hole at the heart of biology.

We do not see the historical steps in the evolution of eyes, but we do see an ecological spectrum. From a rudimentary light-sensitive spot on some early worm-like creature, eyes have arisen independently on scores of occasions. That is exactly what natural selection predicts. Each small step offers a small advantage in one particular environment, with the precise advantage depending on the precise environment.

evolutionary theory predicts that there should be multiple – polyphyletic – origins of traits in which each small step offers a small advantage over the last step. Theoretically that applies to all traits, and it is indeed what we generally see.

So what about sex, or the nucleus, or phagocytosis? The same reasoning ought to apply. If each of these traits arose by natural selection – which they undoubtedly did – and all of the adaptive steps offered some small advantage – which they undoubtedly did – then we should see multiple origins of eukaryotic traits in bacteria. But we don’t.

On one single occasion, here on earth, bacteria gave rise to eukaryotes. There is nothing in the fossil record, or in phylogenetics, to suggest that complex life actually arose repeatedly, but that only one group, the familiar modern eukaryotes, survived. On the contrary, the monophyletic radiation of eukaryotes suggests their unique origin was dictated by intrinsic physical constraints which had little if anything to do with environmental upheavals such as the Great Oxidation Event.

Why would a virus not be alive? Because it does not have any active metabolism of its own; it relies entirely on the power of its host. That raises the question – is metabolic activity a necessary attribute of life? The pat answer is yes, of course; but why, exactly? Viruses use their immediate environment to make copies of themselves. But then so do we: we eat other animals or plants, and we breathe in oxygen.

Everything that happens in a living cell is spontaneous, and will take place on its own accord, given the right starting point. G is always negative. Energetically, it’s downhill all the way. But this means that the starting point has to be very high up. To make a protein, the starting point is the improbable assembly of enough activated amino acids in a small space.

Your 40 trillion cells contain at least a quadrillion mitochondria, with a combined convoluted surface area of about 14,000 square metres; about four football fields.

Not only do bacteria ‘eat’ rocks, but they can ‘breathe’ them too. Eukaryotic cells are pathetic in comparison. There is about the same metabolic versatility in the entire eukaryotic domain – all plants, animals, algae, fungi and protists – as there is in a single bacterial cell.

The difference between pathogenic variants of E. coli and harmless common strains is not reflected in the ribosomal RNA, but in the acquisition of other genes that confer aggressive growth – as much as 30% of the genome can vary in different strains of E. coli – that’s 10 times the variation between us and chimpanzees, yet we still call them the same species!

it is almost impossible to know how a bacterium earned its living 3 billion years ago, given that slow rates of transfer could have replaced essentially all of its genes many times over in that period.

genes found in both archaea and bacteria could have arisen in one group and been transferred into the other group by lateral gene transfer. Transfers of genes across entire domains are well known.

Bacteria and archaea share the same environments across the world, yet remain fundamentally different in their genetics and biochemistry in all these environments, despite lateral gene transfer between the two domains.

Different genes in the same eukaryotic organism do not all share the same ancestor. Around three-quarters of eukaryotic genes that have prokaryotic homologues apparently have bacterial ancestry, whereas the remaining quarter seem to derive from archaea. That’s true of humans, but we are not alone. Yeasts are remarkably similar; so too are fruit flies, sea urchins and cycads. At the level of our genomes, it seems that all eukaryotes are monstrous chimeras.

Emotions and personality play a surprisingly big role in science. Some researchers naturally embrace the idea of abrupt catastrophic changes, whereas others prefer to emphasise continual small modifications – evolution by jerks versus evolution by creeps, as the old joke has it. Both happen.

By no means do all the bacterial genes found in eukaryotes branch with a single group of modern bacteria such as the α-proteobacteria, as might be supposed if they all derived from the bacterial ancestors of mitochondria. Quite the reverse: at least 25 different groups of modern bacteria appear to have contributed genes to eukaryotes.

Let me ram home just how odd this is. Cell respiration – without which we would die within minutes – depends on mosaic respiratory chains that are composed of proteins encoded by two very different genomes.