An antelope might run faster, and be more likely to escape a leopard, if its legs were a little longer. But a rival antelope with longer legs, although it might be better equipped to outsprint a predator, has to pay for its long legs in some other department of the body’s economy. The materials needed to make the extra bone and muscle in the longer legs have to be taken from somewhere else, so the longer-legged individual is more likely to die for reasons other than predation. Or it may even be more likely to die from predation because its longer legs, although they can run faster when intact, are more likely to break, in which case it can’t run at all. A body is a patchwork of compromises. 

Much of the initial domestication of the dog was self- domestication, mediated by natural, not artificial, selection. We can imagine wild wolves scavenging on a rubbish tip on the edge of a village. Most of them, fearful of men throwing stones and spears, have a very long flight distance. They sprint for the safety of the forest as soon as a human appears in the distance. But a few individuals, by genetic chance, happen to have a slightly shorter flight distance than the average. Their readiness to take slight risks – they are brave, shall we say, but not foolhardy – gains them more food than their more risk-averse rivals. As the generations go by, natural selection favours a shorter and shorter flight distance, until just before it reaches the point where the wolves really are endangered by stone-throwing humans. The optimum flight distance has shifted because of the newly available food source.

Flowers again 

A male Euglossine bee is attracted to the orchids by the smell of the substances that he needs in order to manufacture his sexual perfumes. He alights on the rim of the bucket and starts to scrape the waxy perfume into the special scent pockets in his legs. But the rim of the bucket is slippery underfoot – and there’s a reason for this. The bee falls into the bucket, which is filled with liquid, in which he swims. He cannot climb up the slippery sides of the bucket. There is only one escape route, and this is a special bee- sized hole in the side of the bucket (not visible in the picture that appears on colour page 4). He is guided by ‘stepping stones’ to the hole and starts to crawl through it. It’s a tight fit, and it becomes even tighter as the ‘jaws’ (these you can see in the picture: they look like the chuck of a lathe or electric drill) contract and trap him. While he is held in their grip, they glue two pollinia to his back. The glue takes a while to set, after which the jaws again relax and release the bee, who flies off, complete with pollinia on his back. Still in search of the precious ingredients for his perfumery, the bee lands on another bucket orchid and the process repeats itself. This time, however, as the bee struggles through the hole in the bucket, the pollinia are scraped off, and they fertilize the stigma of this second orchid.

The measured age of our planet is about 4.6 billion years, or about 46 million centuries. The time that has elapsed since the common ancestor of all today’s mammals walked the Earth is about two million centuries.

Radioactive decay clocks are available for short timescales as well, even down to fractions of a second; but for evolutionary purposes, clocks that can measure centuries or perhaps decades are about the fastest we need.

A tree-ring clock can be used to date a piece of wood, say a beam in a Tudor house, with astonishing accuracy, literally to the nearest year. You can age a newly felled tree by counting rings in its trunk, assuming that the outermost ring represents the present. Rings represent differential growth in different seasons of the year – winter or summer, dry season or wet season.

A reference collection of rings for  ancient times can be built using the overlap principle. You take the reference fingerprint patterns whose date is known from modern trees. Then you identify a fingerprint from the old rings of modern trees and seek the same fingerprint from the younger rings of long-dead trees. Then you look at the fingerprints from the older rings of those same long-dead trees, and look for the same pattern in the younger rings of even older trees. And so on. You can daisychain your way back, theoretically for millions of years using petrified forests, although in practice dendrochronology is only used on archaeological timescales over some thousands of years.

Unfortunately, we don’t have an unbroken chain, and dendrochronology in practice takes us back only about 11,500 years. It is nevertheless a tantalizing thought that, if only we could find enough petrified forests, we could date to the nearest year over a timespan of hundreds of millions of years. Most of the other dating systems that are available to us, including all the radioactive clocks that we actually use over timescales of tens of millions, hundreds of millions or billions of years, are accurate only within an error range that is approximately proportional to the timescale concerned.

Radioactive clocks

Radioactive clocks cover the gamut from centuries to thousands of millions of years. Each one has its own margin of error, which is usually about 1 per cent. So if you want to date a rock which is billions of years old, you must be satisfied with an error of plus or minus tens of millions of years. 

There are about 100 elements. Examples of elements are carbon, iron, nitrogen, aluminium, magnesium, fluorine, argon, chlorine, sodium, uranium, lead, oxygen, potassium and tin. The atomic theory, which I think everybody accepts, even creationists, tells us that each element has its own characteristic atom, which is the smallest particle into which you can divide an element without it ceasing to be that element.

We can use analogies or models to help us visualize an atom. The Bohr model of the atom, which is now rather out of date, is a miniature solar system. The role of the sun is played by the nucleus, and around it orbit the electrons, which play the role of planets. As with the solar system, almost all the mass of the atom is contained in the nucleus (‘sun’), and almost all the volume is contained in the empty space that separates the electrons (‘planets’) from the nucleus. Each electron is tiny compared with the nucleus, and the space between them and the nucleus is huge compared with the size of either.

When we look at a solid lump of iron or rock, we are ‘really’ looking at what is almost entirely empty space. It looks and feels solid and opaque because our sensory systems and brains find it convenient to treat it as solid and opaque. It is convenient for the brain to represent a rock as solid because we can’t walk through it. ‘Solid’ is our way of experiencing things that we can’t walk through or fall through, because of the electromagnetic forces between atoms. ‘Opaque’ is the experience we have when light bounces off the surface of an object, and none of it goes through.

Three kinds of particle enter into the makeup of an atom, at least as envisaged in the Bohr model. Electrons we have already met. The other two, vastly larger than electrons but still tiny compared with anything we can imagine or experience with our senses, are called protons and neutrons, and they are found in the nucleus. They are almost the same size as each other. The number of protons is fixed for any given element and equal to the number of electrons. This number is called the atomic number. It is uniquely characteristic of an element, and there are no gaps in the list of atomic numbers – the famous periodic table.* Every number in the sequence corresponds to exactly one, and only one, element. The element with 1 for its atomic number is hydrogen, 2 is helium, 3 lithium, 4 beryllium, 5 boron, 6 carbon, 7 nitrogen, 8 oxygen, and so on up to high numbers like 92, which is the atomic number of uranium.

Protons and electrons carry an electric charge, of opposite sign – we call one of them positive and the other negative by arbitrary convention. These charges are important when elements form chemical compounds with each other, mostly mediated by electrons. The neutrons in an atom are bound into the nucleus together with the protons. Unlike protons they carry no charge, and they play no role in chemical reactions. The protons, neutrons and electrons in any one element are exactly the same as those in every other element.

A proton is a proton, and what makes a copper atom copper is that there are exactly 29 protons (and exactly 29 electrons). What we ordinarily think of as the nature of copper is a matter of chemistry. Chemistry is a dance of electrons. It is all about the interactions of atoms via their electrons. Chemical bonds are easily broken and remade, because only electrons are detached or exchanged in chemical reactions. The forces of attraction within atomic nuclei are much harder to break.

Igneous rocks typically contain many different radioactive isotopes, not just potassium-40. A fortunate aspect of the way igneous rocks solidify is that they do so suddenly – so that all the clocks in a given piece of rock are zeroed simultaneously.

Only igneous rocks provide radioactive clocks, but fossils are almost never found in igneous rock. Fossils are formed in sedimentary rocks like limestone and sandstone, which are not solidified lava. They are layers of mud or silt or sand, gradually laid down on the floor of a sea or lake or estuary. The sand or mud becomes compacted over the ages and hardens as rock. Corpses that are trapped in the mud have a chance of fossilizing. Even though only a small proportion of corpses actually do fossilize, sedimentary rocks are the only rocks that contain any fossils worth speaking of.

The graph above shows data from the Uganda Game Department, published in 1962. Referring only to elephants legally shot by licensed hunters, it shows mean tusk weight in pounds (that dates it) from year to year between 1925 and 1958 (during which time Uganda was a British protectorate). The dots are annual figures.  You can see that there is a decreasing trend over the thirty-three years. And the trend is highly statistically significant, which means that it is almost certainly a real trend, not a random chance effect.

Forty five thousand generations of evolution in a lab

E. coli is a common bacterium. Very common. There are about a hundred billion billion of them around the world at any one time, of which about a billion, by Lenski’s calculation, are in your large intestine at this very moment. If we assume that the probability of a gene mutating during any one act of bacterial reproduction is as low as one in a billion, the numbers of bacteria are so colossal that just about every gene in the genome will have mutated somewhere in the world, every day. As Richard Lenski says, ‘That’s a lot of opportunity for evolution.’

Every day, for each of the twelve tribes, a new virgin flask was infected with liquid from the previous day’s flask. A small sample, exactly one-hundredth of the volume of the old flask, was drawn out and squirted into the new flask, which contained a fresh supply of glucose-rich broth. The population of bacteria in the flask then started to skyrocket; but it always levelled off by the next day as the supply of food gave out and starvation set in. In other words, the population in every flask multiplied itself hugely, then reached a plateau, at which point a new infective sample was drawn and the cycle renewed the next day.

Lenski and his team have continued this daily routine for more than twenty years so far. This means about 7,000 ‘flask generations’ and 45,000 bacterial generations – averaging between six and seven bacterial generations per day. To put that into perspective, if we were to go back 45,000 human generations, that would be about a million years, back to the time of Homo erectus, which is not very long ago.

How did the scientists know this? They could tell by sampling the lineages as they evolved, and comparing the ‘fitness’ of each sample against ‘fossils’ sampled from the original founding population. Remember that ‘fossils’ are frozen samples of bacteria which, when unfrozen, carry on living and reproducing normally. And how did Lenski and his colleagues make this comparison of ‘fitness’? How did they compare ‘modern’ bacteria with their ‘fossil’ ancestors? With great ingenuity. They took a sample of the putatively evolved population and put it in a virgin flask.

We have a new experimental flask containing two competing strains, ‘modern’ and ‘living fossil’, and we want to know which of the two strains will out-populate the other. But they are all mixed up, so how do you tell? How do you distinguish the two strains, when they are mixed together in the ‘competition flask’? They could use the colour markers to assay the competitive abilities of each of the evolving tribes, using fossilized ‘ancestors’ as the competitive standard, in every case. All they had to do was simply plate out samples from the mixed flasks and see how many of the bacteria growing on the agar were white and how many red. In all twelve tribes the average fitness increased as the thousands of generations went by. All twelve lines got better at surviving in these glucose-limited conditions.

What this evolutionary change suggests is that becoming larger is, for some reason, a good idea when you are struggling to survive in this alternating glucose-rich/glucose-poor environment. But there are lots of different ways to become larger – different sets of mutations – and it looks as though different ways have been discovered by different evolutionary lineages in this experiment. That’s pretty interesting. But perhaps even more interesting is that sometimes a pair of tribes seem to have independently discovered the same way of getting bigger. Lenski and a different set of colleagues investigated this phenomenon by taking two of the tribes, called Ara+1 and Ara−1, which seemed, over 20,000 generations, to have followed the same evolutionary trajectory, and looking at their DNA. The astonishing result they found was that 59 genes had changed their levels of expression in both tribes, and all 59 had changed in the same direction.

The data are at least compatible with the idea that the evolutionary change that we observe represents the stepwise accumulation of mutations.

Up to about generation 33,000, the average population density of Tribe Ara−3 was coasting along at an OD of about 0.04, which was not very different from all the other tribes. Then, just after generation 33,100, the OD score of Tribe Ara−3 (and of that tribe alone among the twelve) went into vertical take-off. It shot up sixfold, to an OD value of about 0.25.

Having discovered what was special about the Ara−3 tribe, Lenski and his colleagues went on to ask an even more interesting question. Was this sudden improvement in ability to draw nourishment all due to a single dramatic mutation, one so rare that only one of the twelve lineages was fortunate enough to undergo it?

What if the necessary biochemical wizardry to feed on citrate requires not just one mutation but two (or three)? On this hypothesis, you really would need both mutations before there is any improvement whatsoever. The hypothesis,  is that, at some time unknown, Tribe Ara−3 chanced to undergo a mutation, mutation A. This had no detectable effect because the other necessary mutation, B, was still lacking. Mutation B is equally likely to crop up in any one of the twelve tribes. Indeed, it probably did. But B is no use – has absolutely no beneficial effect at all – unless the tribe happens to be primed by the previous occurrence of mutation A. And only tribe Ara−3, as it happened, was so primed.

"Some of these Lazarus clones will ‘discover’ how to deal with citrate, but only if they were thawed out of the fossil record after a particular, critical generation in the original evolution experiment."-Lenski

You will be delighted to hear that this is exactly what Lenski’s student Zachary Blount found, when he ran a gruelling set of experiments involving some forty trillion – 40,000,000,000,000 – E. coli cells from across the generations. The magic moment turned out to be approximately generation 20,000. Thawed- out clones of Ara−3 that dated from after generation 20,000 in the ‘fossil record’ showed increased probability of subsequently evolving citrate capability. No clones that dated from before generation 20,000 did. According to the hypothesis, after generation 20,000 the clones were now ‘primed’ to take advantage of mutation B whenever it came along. Tribe Ara−3, before generation 20,000, was just like all the other tribes.

So, here’s the set-up: guppies were assigned randomly to ten ponds, five with coarse gravel and five with fine gravel. All ten colonies of guppies were allowed to breed freely for six months with no predators. At this point the experiment proper began. Endler put one ‘dangerous predator’ into each of two coarse gravel ponds and two fine gravel ponds. He put six ‘weak predators’ (six rather than one, to give a closer approximation to the relative densities of the two kinds of fish in the wild) into each of two coarse gravel ponds and two fine gravel ponds. And the remaining two ponds just carried on as before, with no predators at all.

After the experiment had been running for five months, Endler took a census of all the ponds, and counted and measured the spots on all the guppies in all the ponds. Nine months later, that is, after fourteen months in all, he took another census, counting and measuring in the same way. And what of the results? They were spectacular, even after so short a time. Endler used various measures of the fishes’ colour patterns, one of which was ‘spots per fish’. When the guppies were first put into their ponds, before the predators were introduced, there was a very large range of spot numbers, because the fish had been gathered from a wide variety of streams, of widely varying predator content. During the six months before any predators were introduced, the mean number of spots per fish shot up. Presumably this was in response to selection by females. Then, at the point when the predators were introduced, there was a dramatic change. In the four ponds that had the dangerous predator, the mean number of spots plummeted. The difference was fully apparent at the five-month census, and the number of spots had declined even further by the fourteen-month census. But in the two ponds with no predators, and the four ponds with weak predation, the number of spots continued to increase. It reached a plateau as early as the five-month census, and stayed high for the fourteen-month census. With respect to spot number, weak predation seems to be pretty much the same as no predation, over-ruled by sexual selection by females who prefer lots of spots.

So much for spot number. Spot size tells an equally interesting story. In the presence of predators, whether weak or strong, coarse gravel promoted relatively larger spots, while fine gravel favoured relatively smaller spots. This is easily interpreted as spot size mimicking stone size. Fascinatingly, however, in the ponds where there were no predators at all, Endler found exactly the reverse. Fine gravel favoured large spots on male guppies, and coarse gravel favoured small spots. They are more conspicuous if they do not mimic the stones on their respective backgrounds, and that is good for attracting females. Neat!

The biggest gap, and the one the creationists like best of all, is the one that preceded the so-called Cambrian Explosion. A little more than half a billion years ago, in the Cambrian era, most of the great animal phyla – the main divisions within the animal world – ‘suddenly’ appear in the fossil record. Suddenly, that is, in the sense that no fossils of these animal groups are known in rocks older than the Cambrian, not suddenly in the sense of instantaneously: the period we are talking about covers about 20 million years. Twenty million years feels short when it is half a billion years ago.

There are more than four thousand species of free-living turbellarian worms : that’s about as numerous as all the mammal species put together. Some of these turbellarians are creatures of great beauty. They are common, both in water and on land, and presumably have been common for a very long time. You’d expect, therefore, to see a rich fossil history. Unfortunately, there is almost nothing. Apart from a handful of ambiguous trace fossils, not a single fossil flatworm has ever been found. The Platyhelminthes, to a worm, are ‘already in an advanced state of evolution, the very first time they appear. It is as though they were just planted there, without any evolutionary history.’

Probably, most animals before the Cambrian were soft-bodied like modern flatworms, probably also rather small like modern turbellarians – just not good fossil material. Then something happened half a billion years ago to allow animals to fossilize freely – the arising of hard, mineralized skeletons, for example.

Hippopotamuses do not descended from dogs, or vice versa. Chimpanzees are not descended from elephants or vice versa, just as monkeys are not descended from frogs. No modern species is descended from any other modern species (if we leave out very recent splits). Just as you can find fossils that approximate to the common ancestor of a frog and a monkey, so you can find fossils that approximate to the common ancestor of elephants and chimpanzees. 

Zoologists have traditionally divided the vertebrates into classes: major divisions with names like mammals, birds, reptiles and amphibians. Some zoologists, called ‘cladists’,* insist that a proper class must consist of animals all of whom share a common ancestor which belonged to that class and which has no descendants outside that group. The birds would be an example of a good class.† All birds are descended from a single ancestor that would also have been called a bird and would have shared with modern birds the key diagnostic characters – feathers, wings, a beak, etc. The animals commonly called reptiles are not a good class in this sense. This is because, at least in conventional taxonomies, the category explicitly excludes birds (they constitute their own class) and yet some ‘reptiles’ as conventionally recognized (e.g. crocodiles and dinosaurs) are closer cousins to birds than they are to other ‘reptiles’ (e.g. lizards and turtles). Indeed, some dinosaurs are closer cousins to birds than they are to other dinosaurs. ‘Reptiles’, then, is an artificial class, because birds are artificially excluded. In a strict sense, if we were to make reptiles a truly natural class, we should have to include birds as reptiles. Cladistically inclined zoologists avoid the word ‘reptiles’ altogether, splitting them into Archosaurs (crocodiles, dinosaurs and birds), Lepidosaurs (snakes, lizards and the rare Sphenodon of New Zealand) and Testudines (turtles and tortoises).