Vital Question: Energy, Evolution, and the Origins of Complex Life

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. But ribosomes are not only incomprehensibly small; on the scale of atoms, they are massive, sophisticated superstructures. They’re composed of scores of substantial subunits, moving machine parts that act with far more precision than an automated factory line.

They draw in the ‘tickertape’ code-script that encodes a protein, and translate its sequence precisely, letter by letter, into the protein itself. To do so, they recruit all the building blocks (amino acids) needed, and link them together into a long chain, their order specified by the code-script. 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, building whole proteins with chains comprising hundreds of amino acids in less than a minute.

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. The energy we gain from burning food in respiration is used to pump protons across a membrane, forming a reservoir on one side of the membrane. The flow of protons back from this reservoir can be used to power work in the same way as a turbine in a hydroelectric dam.

We also know that the use of proton gradients is universal across life on earth – proton power is as much an integral part of all life as the universal genetic code.

My argument in this book is that there are in fact strong constraints on evolution – energetic constraints – which do make it possible to predict some of the most fundamental traits of life from first principles.

Crick and Watson had inferred the crystal structure of DNA itself. In their second Nature paper of 1953, they wrote: ‘It therefore seems likely that the precise sequence of the bases is the code which carries the genetical information.’ That sentence is the basis of modern biology. Today biology is information, genome sequences are laid out in silico, and life is defined in terms of information transfer.

Genomes are the gateway to an enchanted land. The reams of code, 3 billion letters in our own case, read like an experimental novel, an occasionally coherent story in short chapters broken up by blocks of repetitive text, verses, blank pages, streams of consciousness: and peculiar punctuation.

Onions, wheat and amoebae have more genes and more DNA than we do.

Genomes do not predict the future but recall the past: they reflect the exigencies of history.

Life, as biochemist Albert Szent-Györgyi observed, is nothing but an electron looking for a place to rest.

Some cells such as amoebae make their living by physically engulfing other cells, a process called phagocytosis. Some are photosynthetic. Others, such as fungi, digest their food externally – osmotrophy.

Any trait present in essentially all the species of all supergroups was presumably inherited from that common ancestor, whereas any traits that are only present in one or two groups were presumably acquired later, and only in that group.

So powered flight arose on at least six different occasions in bats, birds, pterosaurs and various insects; multicellularity about 30 times, as noted earlier; different forms of endothermy (warm blood) in several groups including mammals and birds, but also some fish, insects and plants;6 and even conscious awareness appears to have arisen more or less independently in birds and mammals.

An ecological intermediate is not a true missing link but it proves that a certain niche, a way of life, is viable.

The crucial point is that these two domains, the bacteria and the archaea, are extremely different in their genetics and in their biochemistry, but almost indistinguishable in their morphology. Both types are small simple cells that lack a nucleus and all the other eukaryotic traits that define complex life. The fact that both groups failed to evolve complex morphology, despite their extraordinary genetic diversity and biochemical ingenuity, makes it look as if an intrinsic physical constraint precludes the evolution of complexity in prokaryotes, a constraint that was somehow released in the evolution of eukaryotes.

Once they cast off their bacterial shackles, the eukaryotes became enormously complex and diverse in their morphology. Yet they did not accrue this complexity in an obviously predictable way: they came up with a whole series of traits, from sex and ageing to speciation, none of which have ever been seen in bacteria or archaea. The earliest eukaryotes accumulated all these singular traits in a common ancestor without peer. There are no known evolutionary intermediates between the morphological simplicity of bacteria and that enormously complex eukaryotic common ancestor to tell the tale.

Why did life start so early? Why did it stagnate in morphological structure for billions of years? Why were bacteria and archaea unaffected by environmental and ecological upheavals on a global scale? Why is all complex life monophyletic, arising just once in 4 billion years? Why do prokaryotes not continuously, or even occasionally, give rise to cells and organisms with greater complexity? Why do individual eukaryotic traits such as sex, the nucleus and phagocytosis not arise in bacteria or archaea? Why did eukaryotes accumulate all these traits?

By this analysis, the conditions that best encourage the origins of life are found in alkaline vents.

Rock, water and CO2: the shopping list for life. We will find them on practically all wet rocky planets. By the rules of chemistry and geology, they will form warm alkaline hydrothermal vents, with proton gradients across thin-walled catalytic micropores. We can count on that.

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.

The practical difficulties with hermaphrodites gives away part of the problem: neither partner wants to bear the cost of being the ‘female’. Hermaphroditic species such as flatworms go to bizarre lengths to avoid being inseminated, fighting pitched battles with their penises, their semen burning gaping holes in the vanquished.

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.

In recent years, medical research has come to a rather similar view: we now appreciate that mitochondria are instrumental in controlling cell death (apoptosis), cancer, degenerative disease, fertility, and more.

Hybrid breakdown is not caused by mitochondrial mutations, but by incompatibilities between nuclear and mitochondrial genes, all of which are perfectly functional in some other context.

This whole book has been an attempt to predict why life is the way it is.

All life on earth is chemiosmotic, depending on proton gradients across membranes to drive carbon and energy metabolism. We have explored the possible origins and consequences of this peculiar trait. We’ve seen that living requires a continuous driving force, an unceasing chemical reaction that produces reactive intermediates, including molecules like ATP, as by-products.

If life is nothing but an electron looking for a place to rest, death is nothing but that electron come to rest.

Living needs an unceasing flux of energy. It’s hardly surprising that energy flux puts major constraints on the path of evolution, defining what is possible. It’s not surprising that bacteria keep doing what bacteria do, unable to tinker in any serious way with the flame that keeps them growing, dividing, conquering. It’s not surprising that the one accident that did work out, that singular endosymbiosis between prokaryotes, did not tinker with the flame, but ignited it in many copies in each and every eukaryotic cell, finally giving rise to all complex life. It’s not surprising that keeping this flame alive is vital to our physiology and evolution, explaining many quirks of our past and our lives today. How lucky that our minds, the most improbable biological machines in the universe, are now a conduit for this restless flow of energy, that we can think about why life is the way it is. May the proton-motive force be with you!