The Mesozoic and Cenozoic Eras — reptiles and mammals

The Mesozoic Era – age of reptiles

The Mesozoic began after the End-Permian mass extinction, 251 Mya, and ended in the less catastrophic but better-known Cretaceous-Tertiary (“K-T”) mass extinction, 65 Mya. Like the Paleozoic, it is subdivided into periods:

  • the Triassic (251-200 Mya),
  • the Jurassic (200-145 Mya) and
  • the Cretaceous (145-65 Mya).

As life in the Mesozoic was dominated by reptiles, including dinosaurs, it is often called the “Age of Reptiles”.


As the Mesozoic opened, there was only one continent, Pangea. Pangea did not just form and then sit stationary for millions of years; tectonic activity continued throughout the era. Evidence from fossils (types of organisms) and sedimentary rocks (formation from sand dunes) indicate that the interior of Pangea was quite arid.

As plates shifted, rifts developed and sea water periodically spilled into the rifts. In between periods of flooding, evaporating water left behind salts (evaporites). Measurement of the ages of these salts gives geologists a calendar of the opening of the rifts and therefore the development of the inter-continental oceans.


Movement of the continents, from “This dynamic earth” via USGS

The main geological event of the Mesozoic was the breakup of Pangea into seven major continents. Around the end of the Triassic, around 175 Mya, Laurentia rifted and what would become the North Atlantic opened up. As the Tethys Sea penetrated into the flank of Pangea from the east, the two seas joined and split the supercontinent into its two major components, Laurentia1Or Laurasia. in the north and Gondwanaland in the south. A huge mountain chain which had stretched diagonally across the great continent left its remains in the Appalachians of North America and the mountains of Ireland, northern Scotland and western Scandinavia. Around the end of the Jurassic, 50 million years later, Gondwanaland rifted and South America and Africa began to separate, the South Atlantic Ocean opening between them. Antarctica and Australia broke loose from Gondwana and India, from Africa.

Note that Laurentia and Gondwana were originally formed at the breakup of Rodinia, then fused to form Pangea, before again breaking apart at the end of Pangea and fragmenting into seven continents.

The resulting changes in continental and oceanic configurations brought about changes in the climate. It is thought that the climate during this era was generally warm, with a reduced temperature gradient between the equator and the poles. This spurred evolution, for instance, through the creation of new econiches.

Life in the sea

The ancient “mascot” of the Paleozoic, the trilobite, did not survive the end-Permian extinction. This diverse group of arthropods had proliferated in the seas for over 250 million years. In terms of longevity, they beat out the soon-to-become-dominant dinosaurs. Nor were there any reefs during the early or middle Triassic. It is amazing anything did survive. The extinction was like pushing the restart button for life on Earth. But survive, it did.

An expansion in the numbers of plankton brought about abundance at the bottom of the food chain. Skeletons of these tiny beings, which precipitate to the sea bottom after death, contain calcium carbonate and silica. They pile up on the sea bed to form chalk, hence the name, cretaceous. The cliffs of Dover have their origin in these minuscule creatures. Elsewhere, along the edges of the Tethys Sea, organic material decayed and metamorphosed to produce the oil found today in places like Russia, the middle East – the source of so much pollution and conflict.

Marine reptiles of new sorts appeared. The ichthyosaur, a giant fish-like marine animal was a land reptile which had returned to the sea but continued bearing its young alive. However, it was not the ancestor of current whales or dolphins.

Life on land

Some land plants survived the extinction. Forests of conifer and ginkgo trees, among others, grew up. Flowering plants (angiosperms) showed up only late in the Mesozoic, around 100 Mya, but quickly spread to all environments. Such plants produce seeds which, like the amniotic egg for animals, are furnished with a protective skin and and plentiful nourishment. Through nourishment and pollination, plants and insects have co-evolved ever since the Cretaceous. Plants developed colors and structures that protected them from all but specific insects. Insects simultaneously developed so as to live off certain flowers. Flowering plants and insects form an inseparable symbiosis. Think ecology.

The acknowledged stars of the Mesozoic were the reptiles, who came to dominate the sea, the land and the air for almost 200 million years. Dinosaurs diversified by occupying econiches left vacant by the animals killed off in the end-Permian extinction. They evolved to eat vegetation, meat, fish and even insects. They lasted so long and went so far that, had they had historians or philosophers, these might well have thought that they were the end product of evolution and, so, eternal. How about that?

So-called stem reptiles2Or captorhinids; ancestors of archosaurs. already had been around at the end of the Permian, having evolved from amphibians. Although their numbers were greatly diminished by the end-Permian extinction, they made a comeback in the early Mesozoic.

At that time, there were principally two types of reptiles which had survived the extinction. The cynodont (of the therapsid group) was one of the lucky survivors from the late Permian. It was a mammal-like reptile and had skin instead of scales. It probably had hair and whiskers and may have been endothermic (warm-blooded). In spite of being a reptile, details of its skull and jaw were mammal-like. It remained small and furtive throughout the Mesozoic, living in burrows by day and sneaking out at night to scavenge or hunt for insects. Among its descendants is the species Homo.

The other surviving reptiles were the archosaurs3Again, there is disagreement as to whether the archosaurs are the animals discussed here or others which appeared only in the early Triassic., whose current descendants include turtles, snakes, lizards, crocodilians and birds. They also evolved into dinosaurs.

The oldest dinosaur fossils date from around the early Triassic, 240 Mya. The fossil record of dinosaurs is extremely incomplete, but it is known that they spanned the globe, largely due to their amniotic egg and scaly skin, which enabled them to live far from the sea. As Pangea started breaking up in the Jurassic, the climate grew moister, making a much greater area habitable by animals.

Dinosaur eggs from Museu da Lourinhã, Portugal. Photo by author.

Dinosaur eggs from Museu da Lourinhã, Portugal. Photo by author.

The boundary between these two periods was marked by the Triassic-Jurassic mass extinction. This extinction occurred in two or three steps across some 18 million years. Although various causes are ascribed, it is known that at least half the species on Earth disappeared, allowing dinosaurs to take over as the dominant species. So the Jurassic was to be the age when dinosaurs ruled.

It is not certain whether dinosaurs were warm or cold-blooded. The biggest ones would have needed high blood pressure in order to pump blood from the heart to the brain, many meters away, maybe even in an upward directions; this would have implied a mammal-like circulatory system, making them warm-blooded.

The first dinosaurs were quite small, about 1 meter long. Many of them were bipedal. In the course of their long reign of almost 200 million years, they diversified and evolved. Many grew larger or developed defensive armor, like the stegosaurus or the triceratops. Dinosaurs did evolve quite a lot, and not all species of them lived simultaneously. The fight between Tyrannosaurus rex and Stegosauras during the excerpts from Le sacre du printemps in the original movie “Fantasia” could not have taken place, as these animals lived at different times.

Paleontologists identify two types of dinosaurs, based on the bones of their hip and pelvis: ornithischian ( “bird-hipped”) and saurischian (“lizard-hipped”). The bird-hipped dinosaurs could be either bipedal or quadrupedal and were all herbivores. The stegosauraus was one of them. The lizard-hipped dinosaurs are in turn divided into two groups: sauropods and theropods. Sauropods were the commonest and were huge, including some of the largest land animals ever, diplodocus. Theropods were all bipedal and carnivorous and included the infamous tyrannosaurus.

Possible family tree of dinosaursk birds and mammals. from Wikipedia

Possible family tree of dinosaursk birds and mammals. from Wikipedia

Characteristics of a  very limited number  of dinosaurs are indicated in the following table.

Name Length/height Weight (kg) Diet Pedalism Time
coelophysis 3m/2m 27 carn 2  late Triassic
megalosaurus 9m/- n/a carn 2 mid Jurassic
stegosaurus 9m/- n/a herb 4 late Jurassic
archaeopteryx 0.5m/0.2m 0.4-0.5 carn 2, flying late Jurassic
diplodocus 26m/8m 20000-25000 herb 4 late Jurassic
triceratops 9m/3m 5500 herb 4 late Cretaceous
tyrannosaurus 12m/5.6m 7000 carn 2 late Cretaceous

Some of these dinosaurs are pictured in the following gallery (not to size).4The links, which I cannot get into the captions without their giving errors are as follows. (1) “Coelophysis size” by Dr. Jeff Martz/NPS, (2)”Seismosaurus” by ДиБгд, (3) Triceratops by Nobu Tamura, (4) “Stegosaurus BW” by Nobu Tamura, (5) Tyrannosaurus rex by Matt Martyniuk,



Birds only evolved in the late Jurassic, 140-150 Mya. One of their reptilian fore-fingers grew long enough to support a web of skin which helped the animal to plane in the air – the first wing. The early pterosaur (“winged lizard”) was a flying reptile, not yet a bird. Birds and pterosaurs evolved from reptiles along separate lines (following figure). The transition between reptiles and birds is thought to be archaeopteryx, which had a reptilian skeleton but possessed feathers formed for flight. This made it a better flyer than the pterosaur. During the Cretaceous, these animals developed hollow bones like modern birds. It is now known that a number of dinosaurs had feathers, which probably served as insulation since they did not have the asymmetric form needed to act as an airfoil.

The world was now enormously different from the Paleozoic, enhanced (from our point of view) by flowers and bird song.

K-T extinction

At the end of the Cretaceous and just before the Tertiary, there was another great extinction. Though much less serious than the end-Permian extinction, this one has captured imaginations more. This is partly due to the fact that it brought about the end of the dinosaurs, except for birds, thereby permitting the rise of mammals and the eventual arrival of humans. It is also due to the explanations offered for the extinction.

One explanation depends on volcanic explosions in the Deccan Traps, in what is now central India. The other explanation cites the crash of a mammoth asteroid into the Earth on the coast of what is now Yucatan, forming the Chicxulub Crater. Both events occurred very near the K-T border. The asteroid would have caused a massive tsunami. Both events would have flung debris and gases (sulfur dioxide and carbon dioxide) into the air, darkening the planet and reducing temperatures.5According to one study, temperatures would have been reduced by at least 26°C, which would have brought about temperatures around -15­C. or Cooling surface waters would have brought up nutrients from below and favored plankton blooms, affecting plant and animal life.

The result was the disappearance of some three quarters of plant and animal species on Earth, including ammonites and dinosaurs. Fossil evidence shows that the extinction was world-wide. But some members of each group of organisms managed to survive into the Cenozoic Era.

Mass extinctions, from Openstax College

Mass extinctions, from Openstax College

Scientists usually count five major mass extinctions, which are summarized in a preceding figure and in the following table. 

Time Approx. date (Mya) Probable cause(s)6Causes from Wikipedia, Ibid., and BBC Nature. “Big five mass extinctions”, Principal victims7Figures from Wikipedia, “Extinction event”,
Ordovician-Silurian 450-440 Climate change (ice age) due to continental movement 60-70% of all species (2nd worst), mainly in sea
Late Devonian 375-360 Asteroid impacts,changes in sea level and chemistry At least 70% of all species, worst in shallow seas
Permian-Triassic (End-Permian, “The Great Dying”) 252 Atmospheric change due to volcanic eruptions – and much more 90-96% of all species (worst), including trilobites and other marine creatures, and insects
Triassic-Jurassic 200 Massive lava floods 70-75% of all species  
Cretacious-Tertiary (“K-T”) 65  Volcanic explosions and basalt floods, asteroid impact 70-75% of all species, including all dinosaurs except birds 

The Cenozoic Era – mountains and mammals

Geology and atmosphere

The Cenozoic Era is considered to be divided into several periods:

  • the “Tertiary” (65-1.8 Mya), commonly broken down into
    • the Paleogene (65-23 Mya) and
    • the Neogene (23-1.8 Mya);
  • the Quaternary (from 1.8 Mya).

Each period is broken down into two or three epochs. Some scientists consider that we now are living in a new epoch, the Anthropocene, dating vaguely from the beginning of the Industrial Revolution (or perhaps the beginning of agriculture), but the term has not yet been accepted by any official geo-chronological body.


The Cenozoic Era has been called the age of mammals, but it could equally well be called the age of orogeny, or mountain-building. The band of mountains running from North Africa to Indonesia, including the Atlas, Pyrenees, Alps, Taurus and Himalayas, was formed during the Cenozoic.

During the Cretaceous, Eurasia and Africa were separated by the Tethys Ocean. When the Atlantic started to spread out and Africa broke loose from Antarctica, it floated northwards towards Eurasia. Initially, small bits of continents within the Tethys (now Spain and Italy) were pushed up and joined to southern Europe, forming the first Alps and Pyrenees. As Africa continued its journey north, the Tethys was closed and the Mediterranean formed. Subduction due to Africa’s continued northward push is responsible for the volcanoes around southern Italy, Sicily and Greek islands like Thira (Santorini).

In a similar way, the Arabian plate moved toward Turkey and pushed up the Taurus Mountains. This plate too is still moving and is responsible for earthquakes in the Middle East.

With the breakup of Gondwanaland, what is now India started moving north. Around 55 Mya, it entered into collision with Asia, administering the coup de grace to the Tethys. The crust of India was too light to be subducted, but some of it slid in under Asia, making the continental crust there almost twice its maximum elsewhere. The result was the chain of the mighty Himalayas and the high Tibetan plateau. In both places, at thousands of meters above sea level, there are sedimentary rocks from the floor of the Tethys, with accompanying fossils, such as the ammonites called shaligrams, which are worshiped by Hindus as an incarnation of the god Vishnu (him again!). India’s encroachment on Asia is still going on at the rate of around 2 cms per year. This process leads to buildup of tension in the rock which, when released, causes enormous earthquakes in China.

Shaligram (ammonite) from the Himalayas, photo by author

Shaligram (ammonite) from the Himalayas, photo by author

As summer heat warms up the high Tibetan plateau, moist tropical air is drawn in. When this precipitates, it brings about the monsoon. This weather phenomenon is both good (irrigation) and bad (flooding and mudslides) for India and Bangladesh.

Since the Earth’s surface maintains a fixed area, the expansion of the Atlantic Ocean causes the squeezing up of the Pacific. As the Pacific plate has subducted almost all the way around its perimeter, volcanic activity has arisen there – the so-called Pacific Ring of Fire.

Climate and the PETM

Geologists originally distinguished the boundaries between different geological ages by relatively sudden observed changes, such as significant modification of the fossil record. Only later did they learn why such changes had occurred. The Paleocene-Eocene boundary is at the “moment” of the Paleocene-Eocene Thermal Maximum, or PETM, also referred to as the Great Warming, which can be seen clearly as a narrow peak on the graph of temperature change in the Figure.

Data from sediment cores of about 55 Mya show a strong “isotope excursion” over a period of around 110,000 years and a lack of carbonate deposits (from dead organisms) over about 60,000 years.8MacDougall 2011, 174. These data indicate that a sudden, huge amount of carbon was added to the atmosphere — as CO2 and methane. Ocean currents were also disrupted. These changes occurred at the same P-E boundary where it was already known that many foraminifera species (of ocean plankton) became extinct. It has since been found that the isotope excursion was world-wide, on land, in oceans and in the atmosphere. It also shows that much of the carbon was ejected in the form of methane, but there is still disagreement as to its source. Nevertheless, the picture which has emerged is that the normal equilibrium of the carbon cycle maintained by volcanic eruption and chemical weathering was overpowered by short-term processes. The result of all this greenhouse gas was an increase in atmospheric and oceanic temperatures between 5°C and 10°C.9MacDougall 2011, 178.

At the beginning of the Oligocene Epoch, about 34 Mya, temperatures started falling steeply, leading to the ice ages of the Quaternary. Temperatures can be deduced from the shape of fossil leaves and from the isotopes of oxygen in limestone formed in the sea. The two methods agree well on the high temperatures of the Eocene epoch and the sharp drop at the beginning of the Oligocene. In the next chapter (Paleontology), we will see the important influence of these climate variations on primate development.

The origins of these temperature shifts are found in plate tectonics. The existence of a large antarctic continent meant that sea waters had to flow around the whole continent. But when Australia and South America separated from Antarctica in the Cenozoic, it became isolated in a circuit of cold waters and a permanent ice cap gradually formed, around 10 Mya. In a similar way, the closing of the Atlantic-Pacific connection by the formation of the Isthmus of Panama 3-4 Mya brought about reinforcement of the warming Gulf Stream, good news for Europe. But this led moisture up to the north, where it precipitated and soon formed a polar ice cap there. Ice caps bring about global cooling. Plate tectonics influences climate which, in turn, influences evolution.

The still-controversial uptake hypothesis suggests that the chemical weathering of recently-exposed rock removes CO2 from the atmosphere. If so, then formation of the Himalayas might in this way have contributed to global cooling.

Since the beginning of the Quaternary, there have been a series of glaciations, or ice ages, with periods of roughly 100,000 years. These cycles, called Milankovitch cycles after the mathematician who first calculated them (without a computer!), have been shown to depend on the Earth’s orbit, its rotation and its distance from the sun. This repeated glaciation has shaped the Earth through erosion and displacement of rocks. The last great ice age started about 130 Kya and left northern Europe and America only around 12-15,000 years ago. We are now living near the peak of a relatively warm interglacial period, but there is no reason to expect that to last indefinitely. Computer models incorporating Milankovitch cycles, continental configurations, atmospheric composition (CO2) and many other factors are currently used to predict the future of global climate.


As the Mesozoic was the age of reptiles, so was the Cenozoic the age of mammals.

During the Tertiary, mammals took over the econiches left empty by the then-extinct dinosaurs, just as these had occupied econiches left vacant after the end-Permian extinction. Like the dinosaurs, mammals rapidly grew in numbers and varieties. They currently range in size from mice to elephants, and of course whales. During the ice ages of the early Quaternary, some grew to be enormously big: a huge rhinoceros-like animal; elephants and mammoths; whales, which include the largest animal ever, bigger even than the largest dinosaurs; various large animals like camels, elks, sloths, bears and so forth. Although their size made them well adapted to cold climates, most of these megafauna died out about 13 Kya, for reasons which are still not understood.

The Earth has been around for 4700 million years and mammals since something like 250 million years but only in great numbers for 65 million years. Man has only been around for at most 4 million years – and even then he did not bear much resemblance to us.

But that is for the next section (What paleontology tells us).

And now…

Plate movements are not finished. At this moment, Africa is on the move. The entire continent is moving slowly northward, causing volcanic activity on mainland Italy (Vesuvius) and Sicily (Etna). One day, Africa will smash (slowly) into southern Europe, raising new mountain ranges and obliterating the Mediterranean Sea. Meanwhile, within Africa, the Great Rift Valley is threatening to break off all of East Africa into a new (small) continent, with a new ocean in between it and the rest of Africa. And who knows what will become of poor little Iceland or the eastern edge of North America? The dance continues.

Temperature and sea-level variations will certainly continue. In the long run, whatever that may turn out to be, there is no reason to expect the climate to remain friendly to the human species. Bacteria, not prokaryotes or eukaryotes are the basis and the necessary ingredient for life on Earth. We depend on them, not the other way around. One day we will go the way of the trilobites and the dinosaurs – and probably much sooner than they.

For more, go find out what paleontology tells us.


1 Or Laurasia.
2 Or captorhinids; ancestors of archosaurs.
3 Again, there is disagreement as to whether the archosaurs are the animals discussed here or others which appeared only in the early Triassic.
4 The links, which I cannot get into the captions without their giving errors are as follows. (1) “Coelophysis size” by Dr. Jeff Martz/NPS, (2)”Seismosaurus” by ДиБгд, (3) Triceratops by Nobu Tamura, (4) “Stegosaurus BW” by Nobu Tamura, (5) Tyrannosaurus rex by Matt Martyniuk,
5 According to one study, temperatures would have been reduced by at least 26°C, which would have brought about temperatures around -15­C. or
6 Causes from Wikipedia, Ibid., and BBC Nature. “Big five mass extinctions”,
7 Figures from Wikipedia, “Extinction event”,
8 MacDougall 2011, 174.
9 MacDougall 2011, 178.


Now we are ready to understand how it is that carbon is such a versatile element. It is at the basis of all organic chemistry and, in particular, biochemistry. The functioning of all living things depends on water and on the versatility of the carbon atom.

We saw that the carbon atom’s electron-shell configuration was

12C: 1s22s22p2

so it has four electrons in its valence shell (n=2). That enables it to share its four electrons with four others from other atoms. The bonds tend to be equally spaced around the carbon atom in the form of a tetrahedron, like those little creamer packets you get in cheap restaurants. For instance, a carbon atom can bond with four hydrogens, sharing each of its four valence electrons with one hydrogen, so each hydrogen has two and the carbon has eight and everybody is happy. This is called methane and looks like this.

"Methane-2D-stereo" by SVG version by Patricia.fidi - Own work. Licensed under Public Domain via Wikimedia Commons.

Methane molecule, CH4 by Patricia.fidi via Wikimedia Commons.

You should see one of the lower-right-hand hydrogens as pointing up out of the page; the other, down into it. The angles between any two adjacent connecting lines (which of course are only imagined by us) are about 109.5°. Carbon’s versatility in binding is illustrated by the examples in this diagram.

Versatiliy of carbon bonding, after Lehninger.

The dots represent valence electrons and the right-hand column is another way of looking at the product in terms of bonds rather than electrons. Each line between atoms is a shared pair of electrons. Note the double and triple inter-carbon bonds in the last two examples. This large number of ways of bonding is the key to carbon’s versatility. In fact, compared to the huge number of such molecules possible, only a relatively small number of the same biomolecules occur in living organisms. This is the first example we see of nature using the same set of techniques or tools all over the biosphere.

Single bonds between carbons also exist, of course, and have the particular advantage that the carbons and whatever is bonded to them can rotate around the axis linking the two carbons. This is more important than one might think. It turns out that some proteins function differently in their left-handed and right-handed versions. Since rotation can change the shape of the molecule, this enables biomolecules with hundreds of atoms to take on specific shapes with definite mechanical or fluid properties. (We will see some of this in the biochemistry chapter.)

The importance of water is not just because we drink it. Let’s go look at that.

Evolution — the modern synthesis

Evolution is most simply defined as descent with modification. Biologists’ understanding of evolution since the 1940s is called the modern synthesis1Or neo-Darwinian synthesis., the synthesis being between evolution through natural selection and the science of genetics.2Or between morphology and genetics.

Population genetics

The modern synthesis employs mathematical (statistical) methods to study what is called a population, the collection of those members of a particular species living in a specified area. Population genetics considers the collective gene pool of such a population, i.e., the sum of all alleles – versions of genes3More specifically, gene variants at the same positions on homologous – corresponding – chromosomes. All this gene business will be explained in a later chapter. – within the population. A given gene may have more than two alleles, such as those for human blood antigens (A, B and O). The link with what we actually see comes about when these alleles are expressed as phenotypes, i.e., observable traits in the organisms of the species. Evolutionary scientists measure the changes in the distribution (frequency) of the alleles in the gene pool across generations. The underlying genetic composition of the phenotype is the genotype.

The modern synthesis merges genetics and morphology and provides mathematical techniques for a quantitative study of evolutionary change. It recognizes four mechanisms of evolutionary change.4Sometimes, they may mention non-random mating as a fifth mechanism.

  1. Natural selection operates when random changes in genes improve the ability of the individuals possessing those genes to survive long enough to reproduce successfully and pass the changes on to their offspring. One then says that differential reproduction has taken place. The superior survival rate of these individuals because of this adaptive trait will assure that, over time, their relative numbers will increase. In terms of population genetics, the frequency of their alleles will increase in the gene pool.
  2. Mutation is a random change in DNA , the genetic material (much more about that later on). Mutations are small and slow. They may disappear quietly without leading to evolutionary change, or lead to the death of the organism (and the allele). Or they may accumulate very slowly. Mutation is the ultimate generator of variation in alleles and so is necessary for the other three mechanisms.
  3. Genetic drift occurs when a chance variation (due to mutation) reproduces itself and then gradually becomes important in the gene pool. According to statistics, the range of values of a trait will be well represented by the normal distribution (the famous “bell curve”) in a large population of samples. Since a large population furnishes numerous possible mates, any variation probably will be quickly diluted. Therefore, genetic drift takes place more often in smaller populations which are less statistically significant. Genetic drift occurs most frequently when a sub-group of a population becomes physically separated from the main group, say, due to emigration to an island or environmental isolation by the forming of a new body of water or a mountain ridge – or even just due to large distances between extremities of a vast landmass. The small group may then change sufficiently to form a different species. Such speciation (formation of a new species) due to an external barrier to gene flow is called allopatric5Also referred to as geographic or vicariant., (Greek for “another country”). Since it is due to chance, genetic drift need not be adaptive. Natural selection, on the contrary, is adaptive and so can not bring about evolution of a lasting trait which is bad for the organism.
  4. Gene flow (or migration) is similar to genetic drift, but involves the immigration of individual organisms or alleles into one population from another. Pollen blown by wind may be an example of gene migration. The result is that genes flow from one population to another.

In all these cases, change is a random, chance occurrence, whereas natural selection is a law which always operates on such changes. In spite of the terms often used to express evolutionary change (“Flowers have colors in order to attract bees.”), it is not teleological (goal-oriented). “Colored flowers attract bees and so survive better.”

Natural selection acts on changes brought about by the other mechanisms cited. In addition, sex is a source of gene mixing, as will be discussed in a later chapter. But the oddest source of change is shuffling of the genetic material when antibodies are created in our bodies. More on that later, too.

Like quantum mechanics, evolution injects the theme of randomness into our understanding of the workings of the universe, but not at all on the same scale.


The notion of species has been much discussed in the history of biology before arriving at the current definition of a species as “groups of interbreeding natural populations, which are reproductively isolated from other such groups”.6Dobzhanksy, cited by Reznidk (2010), 144. This means that members of two different groups do not mate to produce viable offspring for one of two reasons: Either (1) they are geographically isolated by necessity or by choice; or (2) their genetic differences are such that they cannot produce viable offspring, or “fertile hybrids”.7Coyne and Orr, cited by Reznidk (2010), 144.

However, not much is known about the sexual reproduction of, e.g., bacteria or fossils. So in many cases, biologists must fall back on observation of physical or genetic similarities for distinguishing species. It also happens that observed differences do not amount to differences in species. The case is complicated.

Speciation (formation of new species from an older one) may take place when members of a species occupy different niches or habitats and each group evolves rapidly (in geological terms…) to fit into its respective niche, a phenomenon called adaptive radiation.

In the case of genetic drift, members of the changed smaller group may rejoin the larger one (thus becoming sympatric), bringing their variations with them. The change may take place over a time scale less than that of the dates of adjacent rock strata, in which case there would be no intermediate fossils visible between the two states, hiding any continuity in the evolutionary process. The appearance of evolutionary stasis punctuated by discrete changes has been called punctuated equilibrium, abbreviated as “punk-eek”.8Or, more disparagingly, “evolution by jerks”. Some biologists have a strange sense of humor.

Evolution can give rise to two kinds of similar structures. Characters9The word “character” refers to a heritable trait and may be morphological, genetic or behavioral. I would have said characteristics, but nobody asked me. of different species which are inherited from a common ancestor are called homologous. An example is the presence of the four limbs of tetrapods. Similar characters which are not inherited from a common ancestor are analogous, like the wings of bats and birds, and are the result of convergent evolution, the evolution of similar adaptations in species which are at most distantly related.

Fossils and classification

The goal of evolutionary classification is to demonstrate and explain relations among species. The method uses hierarchical grouping of species into larger groups called genera (singular, genus), genera into families into orders into classes into phyla into kingdoms.10There are many mnemonics for remembering these, of which I prefer: “King Phillip Came Over For Good Spaghetti”. This amounts to a road map or genealogy of evolutionary relations. Since two species may be related by being descendants of a long-extinct ancestor, information about that extinct ancestor is necessary. This is obtained primarily through the evidence of fossils.

Classification of modern humans and house cats, after Wikipedia

Classification of modern humans and house cats, after Wikipedia

These classifications will be discussed in more detail in following chapters.

Fossils and fossilization

Fossils are central to our understanding of past species, but they come with problems.

How fossils are formed

If a dead organism does not decay and is not destroyed by predators, it may be covered, all or partially, by sediments. The sediment continues accumulating and, under pressure, eventually may form rock. Shells may dissolve and leave a hole in their own form in the sediment – a mold. Dissolved minerals such as silica may move through the porous rock, fill in the hole and harden, taking on the shape of the organism. Or the dissolved minerals may fill in only the pores in the organism itself, leaving a detailed record. The result is a fossil, entombed within the sedimentary rock.

Fossils may also be found where organisms are frozen (as in Siberia) or dessicated (as in deserts). They may be preserved in amber from pine resin or in tar if they fall into a petroleum swamp. They may leave only impressions, tracks or even footprints which are then preserved, for instance, by falling ash.

From the number of species alive today and the “turnover” seen in fossils, an estimation of the number of species which have existed during Earth’s history gives numbers in the billions. But the fossil record only contains some hundreds of thousands, so the fraction of the number of past species in the fossil record is much, much less than 1%.11Reznick (2010). Where have all the fossils gone?

What can fossilize

Some fossils have indeed gone, but many others were never formed. Organisms consist of parts of differing hardness. Teeth are the hardest and decay slowly enough that they may be fossilized easily. Bones decay faster than teeth, but still slowly enough to be fossilized. However, soft body parts usually decay before adequate sedimentation can take place. Only if sedimentation occurs rapidly can soft parts be preserved, as in the case of the mudslide which preserved the fossils of the Burgess Shale and those of Chengjiang, CHiina..

Many fossils are unable to form because of their environment. The ideal habitat for fossilization is a shallow basin which is slowly subsiding, providing good conditions for marine animals and for an appropriate sedimentation rate. This is no help for terrestrial animals.

Even if fossils are formed, they may be destroyed by subsequent movements of the earth, during which heat and pressure may deform, break, crush or burn them up. No fossils are found in igneous rocks and almost none in metamorphic rocks.

Fossils are often hard to find. Most of the earth has not yet been searched for fossils. They often are found when their enclosing sediments erode or are exposed by geological activity, such as at the East African Rift. Such conditions do not take place everywhere.

For all these reasons and more, the fossil record is a very incomplete history of life on Earth.

Classification – taxonomy and cladistics

According to the theory of evolution, all living organisms of one species have evolved from organisms of a different species, and those from still different species, all the way back to the original Ur-form of life, the first cell or amino acid or whatever it was.12More on this in the geology chapter.

A phylogenetic tree of life, from Wikipedia

A phylogenetic tree of life, from Wikipedia

The branch of biology called taxonomy is the science of defining groups of organisms based on shared characteristics in order to show up their shared evolutionary history. The result may be displayed as a family tree or phylogeny. Biologists use cladistics, or phylogenetic systematics, to diagram the evolutionary steps between species. An example of such a diagram is in the above figure. A clear distinction is made between primitive characters13The word “character” refers to a heritable trait and may be morphological, genetic or behavioral. and advanced or derived characters. Only groups defined by common derived characters are considered valid monophyletic groups or clades, which are groups descended from a common ancestor and which include all descendants of the common ancestor. Monkeys and apes without humans do not constitute a monophyletic group, nor do reptiles without birds. It is important to understand that a phylogeny is a tree, not a ladder, and implies nothing about whether an organism is “advanced” or “primitive”.

Although these phylogenies are based on both morphological and molecular data, new data often leads to slightly different relations, so the tree changes somewhat as time goes by. This is due mainly to the incomplete record presented by the fossils.

Next, atomic physics and chemistry.


1 Or neo-Darwinian synthesis.
2 Or between morphology and genetics.
3 More specifically, gene variants at the same positions on homologous – corresponding – chromosomes. All this gene business will be explained in a later chapter.
4 Sometimes, they may mention non-random mating as a fifth mechanism.
5 Also referred to as geographic or vicariant.
6 Dobzhanksy, cited by Reznidk (2010), 144.
7 Coyne and Orr, cited by Reznidk (2010), 144.
8 Or, more disparagingly, “evolution by jerks”. Some biologists have a strange sense of humor.
9 The word “character” refers to a heritable trait and may be morphological, genetic or behavioral. I would have said characteristics, but nobody asked me.
10 There are many mnemonics for remembering these, of which I prefer: “King Phillip Came Over For Good Spaghetti”.
11 Reznick (2010).
12 More on this in the geology chapter.
13 The word “character” refers to a heritable trait and may be morphological, genetic or behavioral.