The first part of this Entry, covering the basic concepts of Darwinism and Neo-Darwinism, can be found here.

Taxonomy - Uncovering the History of Life

Evolutionary biologists theorise that the life we see today hasn't always been like this, it has evolved from a previous form via the unconscious, automatic processes described in the first part of this article. This raises the question 'So what came before?' Taxonomists are people that like to classify organisms into different categories with the help of impossible-sounding Latin and Greek nomenclature. It can be said that taxonomists stumbled upon the answer to this question.

A rather obsessed Swedish man in the 1700s called Carl Linnaeus had a deep love of plants and was constantly in awe of nature. Around that time it was thought you could understand God's wisdom by studying his creations. Therefore Linnaeus went round happily grouping all sorts of plants and animals together by various features such as anatomy and behaviour. For example, all animals that suckle their young are mammals; all mammals that have continuously growing teeth are rodents; and so on. In fact his system for naming, ranking, and classifying organisms (into groups called Kingdoms, Phyla, Classes, Orders, Families, Genera and Species) is still in wide use today.

Each known species is named in this way, which is a lot of detail for one species to handle. Imagine just how many obsessed Victorian gentlemen there were, and then imagine the amount of information mankind now has regarding the classification of species. It's a lot, in case you didn't know. When all this information is collated together for the entire known biology of Earth, a branching tree emerges. The points at which the branches occur represent events where species have diverged. Common ancestry for any two species can be determined by tracing your way backwards in time, down the tree, until you come across the point at which the ancestor of the two species split.

To illustrate, let's use a human, a chimpanzee, a bird (the brown booby¹), a bluebottle fly and a sunflower, respectively:

All of the above organisms are related. The chimp and the human are grouped most closely together, both being hominids. They are more closely related as they diverged from their common ancestor a relatively short time ago. Compare these hominids to the bird. You can say from this that mammals (Mammalia) and birds (Aves) diverged from a common ancestor that was a Chordate (a vertebrate). The fly has even less in common with the other three, it is an animal, but not a vertebrate so its ancestor diverged at a much earlier time, before backbones or notochords² evolved. The sunflower's common ancestor goes way back even before plants and animals branched. People still share a surprising number of genes with plants - humans share 50% of their genes with bananas. These genes generally code for basic metabolic functions, such as respiration and DNA replication, so it is obvious that we are related in some way.

Classifications of this sort exist for every known life-form, and each fits into its place in the tree of life. With just five organisms we can see a branching tree of relatedness developing, simply from observation of various qualities of living things. Unsurprisingly, recent advances in DNA technology have added a new dimension to the science of taxonomy. The study of phylogenetics uses DNA sequence information to determine the evolutionary relationship of organisms from bacteria to fungi, from animals to plants. The principle is a simple one: the closer the DNA sequences of two different organisms match, the more closely related they are. Phylogenetics has confirmed with hard data the observations and careful painstaking work of taxonomists over the past three centuries.

Speciation

The tree of life branches a countless number of times to produce the most fantastic array of diverse species. The point at which a species forks into two or more is called speciation. Evolution as a whole cannot be observed directly, as it involves about four billion years worth of history. But evolution is still happening all around us, and we can find evidence of speciation everywhere we look.

Species Definitions

This is far more complex than you'd imagine. The commonly used 'biological species concept' by Ernst Mayr states that a species is a species when it does not or cannot interbreed with its ancestors; that it is reproductively isolated from the population from which it arose. This has stood true for many years, but is coming under threat from phylogenetics and cladistics. There are other definitions in the scientific community, although the current consensus is still with Mayr, but only just.

Speciation In Action

The evolution of new species doesn't usually happen in an afternoon, so it's quite difficult to see. And, on the geological scale, mankind has been around for a blink of an eye. Still, we have observed speciation and see its tell-tale fingerprints everywhere, and of course laboratory experimentation has given us a window into the past.

The case of the apple maggot fly (Rhagoletis pomonella) is an interesting one³. It seems that we are witnessing the divergence of one species into two because of the host fruit trees the two emerging races choose to inhabit. The two races of fly are said to be 'sympatric' (ie, they occupy the same geographic areas). One race lives and breeds on hawthorn trees, while the divergent race prefers apple trees. We can witness this speciation event because apple trees were only introduced to North America around 200 years ago. The important thing to note is that the two trees fruit at different times of the year. Natural selection has adapted the 'apple-based' fly race to this difference in timing by matching their emergence to when the apples mature. Consequently the two races never really come into contact with each other - they are reproductively isolated. Hybrids between the two races have been documented, but they were found to have reduced fitness compared to their parents. Natural selection will not favour these unfortunate individuals and a divide is created between the two races of the species.

The naked mole rat of Israel (Spalax ehrenbergi) is another good example of speciation that is underway⁴. Three new chromosomal races have emerged from the main population. From an original diploid number of 52, races with 54, 58 and 60 chromosomes now exist. North Israel is cold, the south is hot; the coast is humid, inland is arid. The races follow these environmental gradients and the chromosomal mutations confer some kind of selective advantage in their respective microclimate. These differences are being reinforced by adaptation to habitat and divergence of mechanisms that reproductively isolate the races by preventing mating. This isolation has come about because of different mating calls and olfactory (smell-based) signals between the chromosomal races that have emerged.

Homeotic Genes

Homeotic genes are genes that control other genes. They encode proteins known as 'transcription factors', transcription being the name given to part of the process by which proteins are assembled from the genetic code. Basically homeotic genes are single entities that can simultaneously switch on or off many genes.

For example, in a well-known experiment with the geneticist's animal model of choice, the fruit fly (Drosophila melanogaster), a mutation in the antennapedia homeotic gene turned the antenna of the fly into a leg. This leads to the fascinating conclusion that this homeotic gene, when it is functioning normally and not mutated, represses many leg genes and that antennae are limbs adapted by evolution for sensory perception.

Some recent experiments⁵ upon homeotic genes have confirmed a theory that the evolution of these so called 'master genes' is responsible for rapid and dramatic changes in a species' morphology (shape). The most recent research has demonstrated how crustacean-like ancestors of insects were dramatically altered with the mutation of a couple of homeotic genes. From having a limb on every body segment, a mutation in the gene that encodes the 'ultrabithorax' and 'abdominal A' proteins suppressed abdominal limb development, resulting in the familiar six-legged insect morphology we see today. It is thought that homeotic genes were responsible for the 'Cambrian explosion', where thousands of species suddenly appeared as if out of nowhere in the fossil record. In a human ancestral species, a single mutation in a homeotic gene responsible for brain morphology probably gave rise to human left-right brain asymmetry, and with it our complex languages, culture, technology and civilisation.

The Selfish Gene Point of View

The Selfish Gene was the title of a book by pre-eminent evolutionary theorist Richard Dawkins. Revolutionary at its time of publishing, it gave new clarity and an exciting new perspective on why organisms behave and evolve in the ways that they do. To summarise, the book argued that the individual organism is merely a transient vehicle for self-replicating entities we know as genes.

This point of view answered a lot of questions that were puzzling biologists for many years. For example, 'kin selection': why do bees sacrifice themselves to aid their siblings, and why do parents of any organism protect their young? By aiding relatives one is helping to propagate one's own genes, as relatives share many genes in common.

Instead of thinking about organisms using genes to reproduce themselves, Dawkins turned it around and came up with the fascinating theory that it is our genes that build and maintain us in order to perpetuate themselves.

Alternative Theories

Lamarckism was a theory that competed with Darwin's natural selection in the mid-1800s. Lamarck theorised that the environment directly changed the individual, and that change was inherited - ie, that acquired characteristics are inherited. For example, Lamarckists would say that giraffes obtained their long neck by stretching for leaves on tall trees. This characteristic was then passed down to the next generation who did the same, gradually extending the necks of giraffes down the generations.

Although this theory had been totally discredited by the tide of support for natural selection, it has rather surprisingly gained some respect in the past decade. For example, heat shock proteins (HSPs) are molecular chaperones that protect the cell's constituents during times of heat stress. It was found that HSP90 in the Drosophila fruit fly prevented some forms of genetic variation from being expressed. When HSP90 was disabled by cold or heat stress, this variation came out in the form of abnormalities. After a few generations of selection, the abnormalities happened independently of the levels of HSP90. Usually evolution works by the environment selecting the individuals that just happen to be the most well adapted. In this example it is the environment (heat or cold stress) that has allowed the normally hidden genetic variation to be expressed by disabling HSP90. A small amount of selection can then lead to the expression of the variant traits, even when HSP function is restored. Hence, a character that was acquired has been inherited. This example of micro-Lamarkism 'assists the process of evolutionary change in response to the environment'⁶.

There are, of course, also the beliefs and theories associated with Creationism. A Creationist viewpoint can be found here.

Conclusions

Evolution acts on the genome of organisms at different levels. 'Junk DNA', such as repetitive elements and non-coding sequences, conspire to increase the amount of DNA in a cell. The sheer amount of DNA in a nucleus can be under selection and has evolutionary consequences. The number of chromosomes in a population can have a dramatic effect: a spontaneous doubling of chromosome number (ploidy) can lead to incompatibilities with the ancestral species, isolating groups of individuals. Recombination of chromosomes at meiosis jumbles up DNA from parents to create unique individuals. Duplication events caused by transposable elements (or 'jumping genes') create multigene families and new genetic combinations. Mutations in homeotic genes can dramatically alter a species, creating new branches of the evolutionary tree. Finally, gene mutations alter protein function and create new genes with new properties, some of which can isolate the individual from a population. This frenetic activity has come to be known as genomic fluidity. These concentric layers of the ever-changing genome are all subject to evolutionary forces at once. Different characteristics and properties are being twisted and morphed by natural selection in an unconscious attempt to find a good combination that will more effectively propagate the genes of the genome.

Imagine a fluid - water perhaps. It is sitting in a square glass beaker, and its shape changes to take on the shape of the container, as any decent, law-abiding liquid should. If the fluid is transferred to a round beaker it would take on the shape of the new receptacle. Genomes are very much like water - they are fluid. If their environment changes, they will change to 'fit' the new 'shape' of the habitat they now find themselves in. They will adapt.

The theory of evolution is just that, a scientific theory. But then again, so is the theory of gravity, quantum theory and the theory that the Earth revolves around the Sun. All of these theories, as far as the scientific method is concerned, are real. The convergent lines of evidence in evolution's particular case make for quite a compelling argument - there are few theories as strong as the theory of evolution. Observations and experimentation from genetics, geology, paleontology, zoology, botany, comparative anatomy, biogeography, genomics, evolutionary-development (or 'evo-devo') and more, all point to the same conclusion: evolution happens.

It would seem that everything has a common ancestor. If you extrapolate this backwards, you'd come across a progenitor: the original organism. Evolution does not explicitly state this in the theory, but it is inferred and supported by DNA evidence and observation. This original 'replicator' competed successfully with other lifeforms to evolve into cellular life, eukaryotic⁷ life and subsequently multicellular life. Cumulative mutation and other microevolutionary forces drove life onwards to ever-greater complexity and diversity. Like fractals, life uses a simple set of rules that, when repeated, create structure, near-infinite complexity and beauty.

Evolutionary theory is a very intellectually-powerful concept indeed. It has pushed biology to the fore of science and it has given answers to questions that would have otherwise gone unanswered or simply put down to an infamous deity's 'mysterious ways'. Mankind has always striven to understand life, the universe and everything; the theory of evolution goes a long, long way to reach this lofty, ambitious goal.

Other Entries in this Project

• Evolution and Creation - an Introduction and Glossary
• The Tension Between Science and Religion
• The 'Genesis' Creation Account
• The Theory of Evolution - Part II
• Creationism - Fundamental(ist) Errors
• Human Evolution - the Aquatic Ape Hypothesis
• Creationism and Creation Science - A Perspective
• Creation - A Mainstream Christian Viewpoint
• Creationism in the UK