The Ancestor's Tale: A Pilgrimage to the Dawn of Evolution

by Richard Dawkins

The two most important ones are photosynthesis, which uses solar power to synthesise organic compounds, and oxygenates the air as a by-product; and oxidative metabolism, which reverses the process, using oxygen (ultimately from photosynthesis) to slow-burn the organic compounds and redeploy the energy that originally came from the sun.

Photosynthetic bacteria used to be called blue-green algae, a terrible name since most of them aren’t blue-green and none of them are algae. Most are green, and it is better to call them green bacteria, although some are reddish, yellowish, brownish, blackish or, yes, in some cases bluish-green. ‘Green’ also is sometimes used as a word for photosynthetic, and in that sense, too, green bacteria is a good name. Their scientific name is cyanobacteria.

They are true bacteria rather than Archaea,

In other words, all of them (and nothing else) are descended from a single ancestor which would, itself, have bee...

The green colour of algae, and of cabbages, pine trees and grasses, comes from small green bodies called chloroplasts within their cells. Chloroplasts are distant de...

All the free oxygen in the atmosphere comes from green bacteria, whether free-living or in the form of chloroplasts.

when it first appeared in the atmosphere oxygen was a poison. Indeed, some people colourfully say it still is a poison, which is why doctors advise us to eat ‘anti-oxidants’. In evolution, it was a brilliant chemical coup to discover how to use oxygen to extract (originally solar) energy from organic compounds.

Again as with photosynthesis, eukaryotic cells like ours give house room to these oxygen-loving bacteria, who now travel under the name of mitochondria. We have become so dependent on oxygen, via the biochemical wizardry of mitochondria, that the statement that it is a poison makes sense only when uttered in a tone of self-conscious paradox.

Depriving somebody of oxygen is a swift way to kill them. Yet our own cells, unaided, wouldn’t know what to do with oxygen.

It is only mitochondria, and their bacterial cousins, that do.

Unlike bacteria, our genes are split up into pieces along the genome: the useful protein-coding chunks (exons) are separated by ignored rubbish (introns). There is good evidence that these eukaryotic introns trace back to a particular type of selfish genetic element (called a group II self-splicing intron), which is common in the bacterial relatives of mitochondria.

The theory has it that mitochondria, while providing a useful service to early eukaryotes, also infected their genomes with ultra-selfish DNA parasites. Our original genes, each a continuous string of useful information, would become interrupted by sections of parasitic DNA (which later evolved into our meaningless introns).

Both chloroplasts and mitochondria have their affinities with the eubacteria, not the other prokaryotic group, the Archaea. But our nuclear genes, at least those that have not been imported from mitochondria, are slightly closer to Archaea.

some bits of our cells have a different ancestry from the rest of the genome. But it’s not just that. Because of the way they exchange genetic material, prokaryotes have wantonly promiscuous genes, which can jump between ‘species’ with relative impunity. Indeed, the very concept of a species starts to lose its meaning in these life forms. As we go deeper and deeper in time, we might therefore expect to start tracing more and more genes back through radically different routes.

has been argued that there is a core group of genes, especially those involved in DNA replication, which tend not to jump about, but remain in the same bacterial cell as it goes forth and multiplies. Whether this is true or not, it certainly seems that the majority of our genes do not find their closest relatives among the ‘true’ (eu-)bacteria such as the gut inhabitant E. coli, or the typhus-causing kin of the mitochondrion. Instead, the immediate ancestry of most of our body lies among another major group of prokaryotes, the Archaea.

the Archaea (then called Archaebacteria) in the late 1970s.

The Archaea include species that thrive in different kinds of extreme conditions, whether it is very high temperatures, or very acid, alkaline or salty water. The archaeans as a group seem to ‘push the envelope’ of what life can tolerate.

There are creatures for which we now know the entire genome sequence, but nothing else about them, not even what they look like! Strange times indeed.

Despite all this confusion, it does seem that the Archaea evolved from within the eubacteria,

For the great majority of its career on this planet life has been nothing but prokaryotic life.

Bacteria,

are supremely versatile chemists. They are also the only non-human creatures known to me who have developed that icon of human civilisation, the wheel.

The wheel may have been invented in Mesopotamia during the fourth millennium BC.

Three factors conspire to make bacterial relationships particularly uncertain. First, bacteria exchange DNA with each other, so different genes can show radically different trees. Second, their ancient divergences result in a star-like phylogeny which is difficult to resolve. Third, we have no outgroup to root the tree (other methods of rooting are sometimes suggested).

The wheel may even have been the first locomotor device ever evolved, given that for most of its first 2 billion years, life consisted of nothing but bacteria. Many bacteria, of which Rhizobium is typical, swim using thread-like spiral propellors, each driven by its own continuously rotating propellor shaft.

The bacterial flagellum* is attached to a shaft that rotates freely and indefinitely in a hole that runs through the cell wall. This is a true axle, a freely rotating hub. It is driven by a tiny molecular motor which uses the same biophysical principles as a muscle. But a muscle is a reciprocating engine, which, after contracting, has to lengthen again to prepare for a new power stroke.

The bacterial motor just keeps on going in the same direction: a molecular turbine.

At the deepest level, the diversity of life is chemical.

is the bacteria, including archaeans, who display the fullest spread of chemical skills. Bacteria taken as a group are the master chemists of this planet.

Chemically, we are more similar to some bacteria than some bacteria are to other bacteria. At least as a chemist would see it, if you wiped out all life except bacteria, you’d still be left with the greater part of life’s range.

Thermus aquaticus,

Thermus aquaticus, as its name suggests, likes to be in hot water. Very hot water.

Thermophiles and hyperthermophiles are not taxonomic categories, but something more like trades or guilds, like Chaucer’s Clerk, Miller and Physician.

Thermus is famous in molecular biology circles for being the source of the DNA duplication enzyme known as Taq polymerase.

Of course, all organisms have enzymes to duplicate DNA, but Thermus has had to evolve one that can withstand near-boiling temperatures. This is useful for molecular biologists because the easiest way to ready DNA for duplication is to boil it, separating it into its two constituent strands. Repeated boiling and cooling of a solution containing both DNA and Taq polymerase duplicates—or ‘amplifies’—even the most minute quantities of original DNA. The method is called the ‘polymerase chain reaction’, or PCR, and it is brilliantly clever.

Tempting though it is to think of Archaea and eubacteria as just different sorts of bacteria, they are not close relatives at all. We eukaryotes—most of our genes, at least—are much closer to the Archaea. We may be even closer to some sorts of Archaea than others, and there have been calls to recognise only two (not three) major domains of life: the eubacteria, and everything else.

Ribosomes are cellular machines that read the RNA message ‘tapes’ sent from the genome, and churn these messages out as proteins.

They are miniature protein factories, vital to all cells and universally present. They are themselves made of many specialised proteins wrapped around an RNA core—this core is completely separate from the RNA messages that the ribosomes read and translate.

Not only is the ribosome ubiquitous, but the ‘genes’ that encode both the ribosomal core and its surrounding proteins change very little over time, meaning that even ourselves and bacteria have recognisably similar seque...

The primary source of outside energy is the sun. The sun, through symbiotic green bacteria inside plant cells, is the only begetter of energy for all the life we can see with the unaided eye. Its energy is trapped by green solar panels (leaves) and used to drive uphill the synthesis of organic compounds, such as sugar and starch in plants. In a series of energy-coupled downhill and uphill chemical reactions, the rest of life is then powered by the energy originally trapped from the sun by plants.

Energy flows through the economy of life, from the sun to plants to herbivores to carnivores to scavengers. At every step of the way, not only between creatures but within them, every transaction in the energy economy is wasteful.

If you are a sufficiently ingenious chemist, it is possible to dream up alternative schemes of energy flow on this planet, which do not start with the sun. And if a useful piece of chemistry can be dreamed up, the chances are that a bacterium got there first: maybe even before they discovered the solar energy trick, and that was more than 3 billion years ago. There has to be some kind of external source of energy, but it doesn’t have to be the sun. There is chemical energy locked up in lots of substances, energy that can be released by the right chemical reactions.

Sources economically worth mining by living creatures include hydrogen, hydrogen sulphide, and some iron compounds.

The whole rationale of Darwin’s theory was, and is, that adaptive complexity comes about by slow and gradual degrees, step by step, no single step making too large a demand on blind chance as explanation.

What is unique about the first replicator, the one that sparked life, is that it had no ready supply of anything evolved, designed or educated. The first replicator worked de novo, ab initio, without precedent, and without help other than from the ordinary laws of chemistry. A powerful source of help to a chemical reaction is a catalyst, and catalysis in some form was surely involved in the origin of replication.

All biological chemistry consists of catalysed reactions, the catalysts usually being the large protein molecules called enzymes.

typical enzyme offers the shaped cavities of its three-dimensional form as receptacles for the ingredients of one chemical reaction. It lines them up for each other, enters into temporary chemical liaison with them, matchmakes with an aimed pre...

Catalysts, by definition, are not consumed in the chemical reaction they boost, but they may be produced. An autocatalytic reaction is a reac...

fire has some of the properties of an autocatalytic reaction.

Fire is not strictly a catalyst but it is self-generating. Chemically, it is an oxidation process that gives off heat, and needs heat to push it over a threshold to start. Once started, it continues and spreads as a chain reaction because it generates the heat needed to restart itself.