Saturday, 5 January 2008

A Brief Guide to Evolution

Before Darwin

We have seen how Linnaeus laid the foundations of modern taxonomy, but he did not himself believe that species changed and was an adherent to the then-prevalent view of creationism, claiming that “God creates and Linnaeus arranges” (it has to the said that the self-proclaimed “Prince of Botany” was not the most modest of men!). Linnaeus died in 1778. At that time it was widely believed that Earth was less than 6000 years old, having been created in 4004 BC according to Archbishop Ussher, who put forward this date in 1650.

But the existence of extinct organisms in the fossil record represented a serious problem for creationism (about which creationists are still in denial – get over it!). Fossils had been known for centuries and it was becoming clear that they represented in many cases life forms that no longer existed. William Smith (1769-1839), a canal engineer, observed rocks of different ages preserved different assemblages of fossils and that these succeeded each other in a regular and determinable order. Rocks from different locations could be correlated on the basis of fossil content; a principle now known as the law of faunal succession. Unfortunately Smith was plagued by financial worries, even spending time in a debtor’s prison. Only towards the end of his life were his achievements recognised.

Georges Curvier (1769-1832) studied extinct animals and proposed catastrophism which is modified creationism. Extinctions were caused by periodic catastrophes and new species took their place, created ex nihil by God, though his view that more than one catastrophe might have occurred was contrary to Christian doctrine. But all species, past and present, remained immutable and created by God. Curvier rejected evolution because one highly complex form transitioning into another struck him as unlikely. The main problem with evolution was that if the Earth was only 6,000 years old, there would not be enough time for evolutionary changes to occur.

The French nobleman Compte de Buffon (1707-88) suggested that planets were formed by comets colliding with the Sun and that the Earth was much older than 6,000 years. He calculated a value of 75,000 years from cooling rate of iron – much to the annoyance of the Catholic Church. Fortunately the days of the Inquisition had passed; only Buffon’s books were burned! Buffon rejected Noah’s Flood; noted animals retain non-functional vestigial parts (suggesting that they evolved rather than were created); most significantly he noted the similarities between humans and apes and speculated on a common origin for the two. Although his views were decidedly at odds with the religious orthodoxy of the time, Buffon maintained that he did believe in God. In this respect, he was no different to Galileo, who remained a faithful Catholic.

Catastrophism was first challenged by James Hutton (1726-97), a Scottish geologist who first formulated the principles uniformitarianism. He argued that geological principles do not change with time and have remained the same throughout Earth’s history. Changes in Earth’s geology have occurred gradually, driven by the planet’s hot interior, creating new rock. The changes are plutonic (caused by volcanic action) in nature rather than diluvian (caused by floods). It was clear that the Earth must be much older than 6000 years for these changes to have occurred.

Hutton’s Investigation of the Principles of Knowledge was published in 1794 and The Theory of the Earth the following year. In the latter work he advocated evolution and natural selection. "...if an organised body is not in the situation and circumstances best adapted to its sustenance and propagation, then, in conceiving an indefinite variety among the individuals of that species, we must be assured, that, on the one hand, those which depart most from the best adapted constitution, will be the most liable to perish, while, on the other hand, those organised bodies, which most approach to the best constitution for the present circumstances, will be best adapted to continue, in preserving themselves and multiplying the individuals of their race." Unfortunately this work was so poorly-written that not only was it largely ignored; it even hindered acceptance of Hutton’s geological theories, which did not gain general acceptance until the 1830s when they were popularised by fellow Scot Sir Charles Lyell (1797-1875), who also coined the word Uniformitarianism. However, it is now accepted that the catastrophists were not entirely wrong and events such as meteorite impacts and plate tectonics also have shaped Earth’s history.

The best-known pre-Darwinian theory of evolution is that of Jean-Baptiste de Lamarck (1744-1829). Lamarck proposed that individuals adapt during their lifetime and transmit acquired traits to their offspring. Offspring carry on where they left off, enabling evolution to advance. The classic example of this is the giraffe stretching its neck to reach leaves on high branches, and passing on a longer neck to its offspring. Some characteristics are advanced by use; others fall into disuse and are discarded. Lamarck’s two laws were:

1. In every animal which has not passed the limit of its development, a more frequent and continuous use of any organ gradually strengthens, develops and enlarges that organ, and gives it a power proportional to the length of time it has been so used; while the permanent disuse of any organ imperceptibly weakens and deteriorates it, and progressively diminishes its functional capacity, until it finally disappears.

2. All the acquisitions or losses wrought by nature on individuals, through the influence of the environment in which their race has long been placed, and hence through the influence of the predominant use or permanent disuse of any organ; all these are preserved by reproduction to the new individuals which arise, provided that the acquired modifications are common to both sexes, or at least to the individuals which produce the young.

Lamarck was not the only proponent of this point of view, but it is now known as Lamarckism. There is little doubt that confronted with the huge body of evidence assembled by Darwin, Lamarck would have abandoned his theory. However the theory remained popular with Marxists and its advocates continued to seek proof until well into the 20th Century. Most notable among these were Paul Kammerer (1880-1926), who committed suicide in the wake of the notorious “Midwife Toad” scandal; and Trofim Lysenko (1898-1976). With Stalin’s backing, Lysenko spearheaded an evil campaign against geneticists, sending many to their deaths in the gulags for pursuing “bourgeois pseudoscience”. Lamarckism continued to enjoy official backing in the USSR until the after fall of Khruschev in 1964, when Lysenko was finally exposed as a charlatan.

Natural selection.

Not until the middle of the 19th Century did Charles Darwin (1809-1882) and Alfred Russel Wallace (1823-1913) put forward a coherent theory of how evolution could work.

Darwin was appointed Naturalist and gentleman companion to Captain Robert Fitzroy of the barque HMS Beagle, joining the ship on her second voyage, initially against his father’s wishes. Fitzroy, serving as a lieutenant in Beagle, had succeeded to the captaincy when her original skipper Captain Pringle-Stokes committed suicide on the first voyage. Fitzroy was a Creationist and objected to Darwin’s theories. Darwin sailed round the world in Beagle between 1831 and 1836. He studied finches and turtles on the Galapagos Islands – different turtles had originated from one type, but had adapted to life on different islands in different ways. These changes and developments in species were in accord with Lyell’s Principles of Geology. Darwin was also influenced by the work of economist Thomas Malfus (1766-1834), author of a 1798 essay stating populations are limited by availability of food resources.

Darwin developed the theory natural selection between 1844 and 1858. The theory was as the same time being independently developed by Alfred Russel Wallace and in 1858 Darwin presented The Origin of Species by means of Natural Selection to the Linnaean Society of London, jointly with Wallace’s paper. Wallace’s independent endorsement of Darwin’s work leant much weight to it. Happily there were none of the unseemly squabbles over priority that have bedevilled so many joint discoveries down the centuries of which Newton and Leibnitz’s spat over differential calculus and strain placed on Anglo-French relations in the 1840s by John Couch Adams and Jean Urbain Le Verrier’s independent discovery of the planet Neptune are but two examples.

Darwin’s pivotal On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life (usually simply referred to as The Origin of Species) was published in 1859 and promptly sold out. The book caused uproar and a debate was held at Oxford where Darwin and Thomas Huxley (grandfather of Aldous Huxley, author of Brave New World) were opposed by Bishop Samuel Wilberforce (son of the anti-slavery campaigner William Wilberforce), the clergy and Darwin’s erstwhile commanding officer, Captain Fitzroy of the Beagle. Darwin was by now in poor health due to an amoebal infection contracted during the Beagle voyage, but Huxley defended his theories vigorously.

The theory of natural selection states that evolutionary mechanisms are based on four conditions – 1) organisms reproduce; 2) there has to be a mode of inheritance whereby parents transmit characteristics to offspring; 3) there must be variation in the population and finally 4) there must be competition for limited resources. With some organisms in a population able to compete more effectively than others, these are the ones more likely to go on to reproduce and transmit their advantageous traits to their offspring, which in turn are more likely to reproduce themselves.

Evolution is the consequence of natural selection – the two are not the same thing, as evolution could in principle proceed by other means. Natural selection is a mechanism of change in species and takes various forms depends on certain conditions.

If for example existing forms are favoured then stabilising selection will maintain the status quo; conversely if a new form is favoured then directional selection will lead to evolutionary change. Divergent selection occurs when two extremes are favoured in a population.

Adaptation is a key concept in evolutionary theory. This is the “goodness of fit between an organism and its environment”. An adaptive trait is one that helps an individual survive, e.g. an elephant’s trunk, which enables it to forage in trees, eat grass, etc; colour vision helps animals to identify particular fruits, etc (and bright distinctive colour schemes are plants’ adaptations to help them to be located).

Sexual selection, proposed by Darwin in his second work The Descent of Man and Selection in Relation to Sex (1871), refers to adaptations in an organism specifically for the needs of obtaining a mate. In birds, this often leads to males having brightly coloured plumage, which they show off to prospective mates in spectacular displays. In many mammal species, males fight for access to females, leading to larger size (sexual dimorphism) and enhanced fighting equipment, e.g. large antlers.

The Descent of Man also put forward the theory that Man was descended from apes. Darwin was characterised as “the monkey man” and caricatured as having a monkey’s body. But after his death in 1882, he was given a state funeral and is buried in Westminster Abbey near Sir Isaac Newton. A dubious BBC poll ranked Charles Darwin as the 4th greatest Brit of all time, behind Churchill, I.K. Brunel and (inevitably) Princess Diana, but ahead of Shakespeare, Newton and (thankfully) David Beckham!

The main problem with Darwin’s theory was that by itself, it failed to provide a mechanism by which changes were transmitted from one generation to the next. Most believed that traits were “blended” in offspring than particulate – the latter being the view now known to be correct.

Mendelian inheritance

Ironically at the very time Darwin was achieving world fame, the missing link in his theory was being discovered by an Augustinian abbot named Gregor Mendel (1822-1884), whose work was practically ignored in his own lifetime. Between 1856 and 1863, Mendel studied the inheritance of traits in pea plants and showed that these followed particular laws and in 1865 he published the paper "Experiments in Plant Hybridization", which showed that organisms have physical traits that correspond to invisible elements within the cell. These invisible elements, now called genes, exist in pairs. Mendel showed that only one member of this genetic pair is passed on to each progeny via gametes (sperm, ova, etc).

The set of genes possessed by an organism is known as its genotype. By contrast, a phenotype is a measurable characteristic of an organism, such as eye or hair colour, blood group, etc (it is sometimes used as a synonym for “trait” but phenotype is the value of the trait, e.g. if the trait is “eye colour” then possible phenotypes are “grey”, “blue”, etc.). Mendel investigated how various phenotypes of peas were transmitted from generation to generation, and whether these transmissions were unchanged or altered when passed on. His studies were based on traits such as shape of the seed, colour of the pea, etc, beginning with a set of pure-breeding pea plants, i.e. the second generation of plants had consistent traits with those of the first. He performed monohybrid crosses, i.e. between two strains of plants that differed only in one characteristic. The parents were denoted by a P, while the offspring - the filial generation - was denoted by F1, the next generation F2, etc. He found that in the first generation of these crosses, all of the F1s were identical to one of the parents. The trait expressed in the offspring he called a dominant trait; the unexpressed trait he called recessive (the Law of Dominance). He also observed that the sex of the parent was irrelevant for the dominant or recessive trait exhibited in the offspring (the Law of Parental Equivalence).

Mendel found that the phenotypes absent in the F1 generation reappeared in approximately a quarter of the F2 offspring. Mendel could not predict what traits would be present in any one individual, but he did deduce that there was a 3:1 ratio in the F2 generation for dominant/recessive phenotypes. In describing his results, Mendel used the term elementen, which he postulated to be hereditary “particles” transmitted unchanged between generations. Even if the traits are not expressed, he surmised that they are still held intact and the elementen passed on. These “particles” are now known as alleles. An allele that can be suppressed during a generation is called a recessive allele, while one that is consistently expressed is a dominant allele. An organism where both alleles for a particular trait are the same is said to be homozygous; where they differ, it is heterozygous.

For example, consider traits X and y, where X is dominant. A homozygous organism will be of phenotype X and genotype XX and a heterozygous organism will still have phenotype X, but the genotype will be Xy. (Note that the recessive allele is written in lower case.) The recessive trait will only be expressed when the genotype is yy, i.e. it receives the y-allele from both parents. There is a 50% chance of receiving the y-allele from either parent; hence only a 25% of receiving it from both; explaining the 3-1 ratio observed. The Law of Segregation states that each member of a pair of alleles maintains its own integrity, regardless of which is dominant. At reproduction, only one allele of a pair is transmitted, entirely at random.

Mendel next did a series of dihybrid crosses, i.e. crosses between strains identical except for two characteristics. He observed that each of the traits he was following sorted themselves independently. Mendel's Law of Independent Assortment states that characteristics which are controlled by different genes will assort independent of all others. Whether or not an organism will be Ab or AA has nothing to do with whether or not it will be Xy or yy.

Mendel’s experimental results have been criticized for being “suspiciously good” and he seems to have fortunate in that he selected traits that were affected by just one gene. Otherwise the outcome of his crossings would have been too complex to have been understood at the time.

Population genetics

Mendel’s work remained virtually unknown until 1900, when it was independently rediscovered by Hugo de Vries, Carl Correns, and Erich von Tschermak and vigorously promoted in Europe by William Bateson, who coined the terms “genetics”, “gene” and “allele”. The theory was doubted by many because it suggested heredity was discontinuous in contrast to the continuous variety actually observed. R.A. Fisher and others used statistical methods to show that if multiple genes were involved with individual traits, they could account for the variety observed in nature. This work forms the basis of modern population genetics.

The discovery of DNA

By the 1930s, it was recognised that genetic variation in populations arises by chance through mutation, leading to species change. Chromosomes had been known since 1842, but their role in biological inheritance was not discovered until 1902, when Theodor Boveri (1862-1915) and Walter Sutton (1877-1916) independently showed a connection. The Boveri-Sutton Chromosome Theory, as it became known, remained controversial until 1915 when the initially sceptical Thomas Hunt Morgan (1866-1945) carried out studies on the eye colours of Drosophila melanogaster (the fruit fly) which confirmed the theory (and has since made these insects virtually synonymous with genetic studies).

The role of DNA as the agent of variation and heredity was not discovered until 1941, by Oswald Theodore Avery (1877-1955), Colin McLeod (1909-1972) and Maclyn McCarty (1911-2005). The double-helix structure of DNA was elucidated in 1953 by Francis Crick (1916-2005) and James Watson (b 1928) at Cambridge and Maurice Wilkins (1916-2004) and Rosalind Franklin (1920-1958) at King’s College London. The DNA/RNA replication mechanism was confirmed in 1958. Crick, Watson and Wilkins received the Nobel Prize for Medicine in 1962. Franklin, who died in 1958, missed out (Nobel Prizes are not normally awarded posthumously), but her substantial contribution to the discovery is commemorated by the Royal Society’s Rosalind Franklin Award, established in 2003.

How DNA works

With these discoveries, the picture was now complete, and it could now be seen how the genome is built up at a molecular level and how it is responsible for both variation and inheritance which are – as we have seen – fundamental to natural selection.

The genome of an organism contains the whole hereditary information of that organism and comprises the complete DNA sequence of one set of chromosomes. It is often thought of as a blueprint for the organism, but it is better thought of as a set of digital instructions that completely specify the organism.

The fundamental building blocks of life are a group of molecules known as the amino acids. An amino acid is any molecule containing both amino (-NH2) and carboxylic acid (-COOH) functional groups. In an alpha-amino acid, both groups are attached to the same carbon. Amino acids are the basic structural building blocks of proteins, complex organic materials that are essential to the structure of all living organisms. Amino acids form small polymer chains called peptides or larger ones called polypeptides, from which proteins are formed. The distinction between peptides and proteins is that the former are short and the latter are long. Some twenty amino acids are proteinogenic, i.e. they occur in proteins and are coded for in the genetic code. They are given 1 and 3 letter abbreviations, e.g. A Ala Alanine. Not all amino acids can be synthesised by a particular organism and must be included in the diet; these are known as essential amino acids. An amino acid residue is what is left of an amino acid once a molecule of water has been lost (an H+ from the nitrogenous side and an OH- from the carboxylic side) in the formation of a peptide bond.

Proteins are created by polymerization of amino acids by peptide bonds in a process called translation, a complex process occurring in living cells, etc. The blueprint – or to take a better analogy – the recipe or computer program for each protein used by an organism is held in its genome. The genome is comprised of nucleic acid, a complex macromolecule composed of nucleotide chains that convey genetic information. The most common nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). For nearly all organisms, the genome is comprised of DNA, which usually occurs as a double helix.

Nucleotides comprise a heterocyclic base (an aromatic ring containing at least one non-carbon atom, such as sulphur or nitrogen, in which the nitrogen atom’s lone pair is not part of the aromatic system); a sugar; and one or more phosphate (-PO3) groups. In the most common nucleotides the sugar is pentose – either deoxyribose (in DNA) or ribose (in RNA) and the base is a derivative of purine or pyrimidine. In nucleic acids the five most important bases are Adenine (A), Guanine (G), Thymine (T), Cytosine (C) and Uracil (U). A and G are purine derivatives and are large double-ringed molecules. T, C and U are pyrimidine derivatives and are smaller single-ringed molecules. T occurs only in DNA; U replaces T in RNA. These five bases are known as nucleobases.

In nucleic acids, nucleotides pair up by hydrogen bonding in various combinations known as base pairs. Purines only pair with pyrimidines. Purine-purine pairing is does not occur because the large molecules are far apart for hydrogen bonding to occur; conversely pyrimidine-pyrimidine pairing does not occur because the smaller molecules are too close and electrostatic repulsion overwhelms hydrogen bonding. G pairs only with C and A pairs only with T (in DNA) or U (in RNA). One might also expect GT and AC pairings, but these do not occur because the hydrogen donor and acceptor patterns do not match. Thus one can always construct a complimentary strand for any strand of nucleotides.


Such a nucleotide sequence would normally be written as ATCGAT. Any succession of nucleotides greater than four is liable to be called a sequence.

DNA encodes the sequence of amino acid residues in proteins using the genetic code, which is a set of rules that map DNA sequences to proteins. The genome is inscribed in one or more DNA molecules. Each functional portion is known a gene, though there are a number of definitions of what constitutes a functional portion, of which the cistron is one of the most common. The gene sequence is composed of tri-nucleotide units called codons, each coding for a single amino acid. There are 4 x 4 x 4 codons (= 64), but only 20 amino acids, so most amino acids are coded for by more than one codon. There are also “start” and “stop” codons to define the beginning and end points for translation of a protein sequence.

In the first phase of protein synthesis, a gene is transcribed by an enzyme known as RNA polymerase into a complimentary molecule of messenger RNA (mRNA). (Enzymes are proteins that catalyze chemical reactions.) In eukaryotic cells (nucleated cells – i.e. animals, plants, fungi and protests) the initially-transcribed mRNA is only a precursor, often referred to as pre-mRNA. The pre-RNA is composed of coding sequences known as exons separated by non-coding sequences known as introns. These latter sequences must be removed and the exons joined to produce mature mRNA (often simply referred to as mRNA), in a process is known as splicing. Introns sometimes contain "old code," sections of a gene that were probably once translated into protein but which are now discarded. Not all intron sequences are junk DNA; some sequences assist the splicing process. In prokaryotes (non-nucleated organisms – i.e. bacteria and archaea), this initial processing of the mRNA is not required.

The second phase of protein synthesis is known as translation. In eukaryotes the mature mRNA is “read” by ribosomes. Ribosomes are organelles containing ribosomal RNA (rRNA) and proteins. They are the "factories" where amino acids are assembled into proteins. Transport RNAs (tRNAs) are small non-coding RNA chains that transport amino acids to the ribosome. tRNAs have a site for amino acid attachment, and a site called an anticodon. The anticodon is an RNA triplet complementary to the mRNA triplet that codes for their cargo protein. Aminoacyl tRNA synthetase (an enzyme) catalyzes the bonding between specific tRNAs and the amino acids that their anticodons sequences call for. The product of this reaction is an aminoacyl-tRNA molecule. This aminoacyl-tRNA travels inside the ribosome, where mRNA codons are matched through complementary base pairing to specific tRNA anticodons. The amino acids that the tRNAs carry are then used to assemble a protein. Its task completed, the mRNA is broken down into its component nucleotides.

Prokaryotes have no nucleus, so mRNA can be translated while it is still being transcribed. The translation is said to be polyribosomal when there is more than one active ribosome. In this case, the collection of ribosomes working at the same time is referred to as a polysome.

In many species, only a small fraction of the total sequence of the genome appears to encode protein. For example, only about 1.5% of the human genome consists of protein-coding exons. Some DNA sequences play structural roles in chromosomes. Telomeres and centromeres typically contain few (if any) protein-coding genes, but are important for the function and stability of chromosomes. Some genes are RNA genes, coding for rRNA and tRNA, etc. Junk DNA represents sequences that do not yet appear to contain genes or to have a function.

The DNA which carries genetic information in cells (as opposed to mitochondrial DNA, etc) is normally packaged in the form of one or more large macromolecules called chromosomes. A chromosome is a very long, continuous piece of DNA (a single DNA molecule), which contains many genes, regulatory elements and other intervening nucleotide sequences. In the chromosomes of eukaryotes, the uncondensed DNA exists in a quasi-ordered structure inside the nucleus, where it wraps around structural proteins called histones. This composite material is called chromatin.

Histones are the major constituent proteins of chromatin. They act as spools around which DNA winds and they play a role in gene regulation, which is the cellular control of the amount and timing of appearance of the functional product of a gene. Although a functional gene product may be an RNA or a protein, the majority of the known mechanisms regulate the expression of protein coding genes. Any step of gene expression may be modulated, from the DNA-RNA transcription step to post-translational modification of a protein. Gene regulation gives the cell control over structure and function, and is the basis for cellular differentiation – i.e. the large range of cell types found in complex organisms.

Ploidy indicates the number of copies of the basic number of chromosomes in a cell. The number of basic sets of chromosomes in an organism is called the monoploid number (x). The ploidy of cells can vary within an organism. In humans, most cells are diploid (containing one set of chromosomes from each parent), but sex cells (sperm and ova) are haploid. Some plant species are tetraploid (four sets of chromosomes). Any organism with more than two sets of chromosomes is said to be polyploid. A species’ normal number of chromosomes per cell is known as the euploid number, e.g. 46 for humans (2x23).

Haploid cells bear one copy of each chromosome. Most fungi, and a few algae are haploid organisms. Male bees, wasps and ants are also haploid. For organisms that only ever have one set of chromosomes, the term monoploid can be used interchangeably with haploid.

Plants and other algae switch between a haploid and a diploid or polyploid state, with one of the stages emphasized over the other. This is called alternation of generations. Most diploid organisms produce haploid sex cells that can combine to form a diploid zygote, for example animals are primarily diploid but produce haploid gametes. During meiosis, germ cell precursors have their number of chromosomes halved by randomly "choosing" one homologue (copy), resulting in haploid germ cells (sperm and ovum).

Diploid cells have two homologue of each chromosome (both sex- and non-sex determining chromosomes), usually one from the mother and one from the father. Most somatic cells (body cells) of complex organisms are diploid.

A haplodiploid species is one in which one of the sexes has haploid cells and the other has diploid cells. Most commonly, the male is haploid and the female is diploid. In such species, the male develops from unfertilized eggs, while the female develops from fertilized eggs: the sperm provides a second set of chromosomes when it fertilizes the egg. Thus males have no father. Haplodiploidy is found in many species of insects from the order Hymenoptera, particularly ants, bees, and wasps.

Cell division is the process by which a cell divides into two daughter cells. Cell division allows an organism to grow, renew and repair itself. Cell division is of course also vital for reproduction. For simple unicellular organisms such as the Amoeba, one cell division reproduces an entire organism. Cell division can also create progeny from multicellular organisms, such as plants that grow from cuttings. Finally, cell division enables sexually reproducing organisms to develop from the one-celled zygote, which itself was produced by cell division from gametes.

Before division can occur, the genomic information which is stored in a cell’s chromosomes must be replicated, and the duplicated genome separated cleanly between cells. Division in Prokaryotic cells involves cytokinesis only. As previously explained, prokaryotic cells are simple in structure. They contain non-membranous organelles, lack a cell nucleus, and have a simplistic genome: only one circular chromosome of limited size. Therefore, prokaryotic cell division, a process known as binary fission, is straightforward. The chromosome is duplicated prior to division. The two copies of the chromosome attach to opposing sides of the cellular membrane. Cytokinesis, the physical separation of the cell, occurs immediately.

Division in Somatic Eukaryotic cells involves mitosis then cytokinesis. Eukaryotic cells are complex. They have many membrane-bound organelles devoted to specialized tasks, a well-defined nucleus with a selectively permeable membrane, and a large number of chromosomes. Therefore, cell division in somatic (i.e. non-germ) eukaryotic cells is more complex than cell division in prokaryotic cells. It is accomplished by a multi-step process: mitosis: the division of the nucleus, separating the duplicated genome into two sets identical to the parent's; followed by cytokinesis: the division of the cytoplasm, separating the organelles and other cellular components.

Division in Eukaryotic Germ cells involves meiosis, which is the process that transforms one diploid cell into four haploid cells in eukaryotes in order to redistribute the diploid's cell's genome. Meiosis forms the basis of sexual reproduction and can only occur in eukaryotes. In meiosis, the diploid cell's genome is replicated once and separated twice, producing four haploid cells each containing half of the original cell's chromosomes. These resultant haploid cells will fertilize with other haploid cells of the opposite gender to form a diploid cell again. The cyclical process of separation by meiosis and genetic recombination through fertilization is called the life cycle. The result is that the offspring produced during germination after meiosis will have a slightly different genome contained in the DNA. Meiosis uses many biochemical processes that are similar to those used in mitosis in order to distribute chromosomes among the resulting cells.

Genetic recombination is the process by which the combinations of alleles observed at different loci in two parental individuals become shuffled in offspring individuals. Such shuffling can be the result of inter-chromososomal recombination (independent assortment) and intra-chromososomal recombination (crossing over). Recombination only shuffles already existing genetic variation and does not create new variation at the involved loci. Since the chromosomes separate independently of each other, the gametes can end up with any combination of paternal or maternal chromosomes. In fact, any of the possible combinations of gametes formed from maternal and paternal chromosomes will occur with equal frequency. The number of possible combinations for human cells, with 23 chromosomes, is 2 to the power of 23 or approximately 8.4 million. The gametes will always end up with the standard 23 chromosomes (barring errors), but the origin of any particular one will be randomly selected from paternal or maternal chromosomes.

The other mechanism for genetic recombination is crossover. This occurs when two chromosomes, normally two homologous instances of the same chromosome, break and then reconnect but to the different end piece. If they break at the same place or locus in the sequence of base pairs – which is the normal outcome - the result is an exchange of genes.

An allele is any one of a number of viable DNA codings of the same gene (sometimes the term refers to a non-gene sequence) occupying a given locus (position) on a chromosome. An individual's genotype for that gene will be the set of alleles it happens to possess. For example, in a diploid organism, two alleles make up the individual's genotype.

Organisms that are diploid such as humans have paired homologous chromosomes in their somatic cells, and these contain two copies of each gene. An organism in which the two copies of the gene are identical — that is, have the same allele — is said to be homozygous for that gene. An organism which has two different alleles of the gene is said to be heterozygous. Phenotypes associated with a certain allele can sometimes be dominant or recessive, but often they are neither. A dominant phenotype will be expressed when only one allele of its associated type is present, whereas a recessive phenotype will only be expressed when both alleles are of its associated type. This is Mendelian inheritance at a molecular level.

However, there are exceptions to the way heterozygotes express themselves in the phenotype. One exception is incomplete dominance (sometimes called blending inheritance) when alleles blend their traits in the phenotype. An example of this would be seen if, when crossing Antirrhinums — flowers with incompletely dominant "red" and "white" alleles for petal colour — the resulting offspring had pink petals. Another exception is co-dominance, where both alleles are active and both traits are expressed at the same time; for example, both red and white petals in the same bloom or red and white flowers on the same plant. Co-dominance is also apparent in human blood types. A person with one "A" blood type allele and one "B" blood type allele would have a blood type of "AB".

Recombination shuffles existing variety, but does not add to it. Variety comes from genetic mutation. Mutations are changes to the genetic material of an organism. Mutations can be caused by copying errors in the genetic material during cell division and by exposure to radiation, chemicals, or viruses. In multicellular organisms, mutations can be subdivided into germline mutations, which can be passed on to descendants and somatic mutations. The latter cannot be transmitted to descendants in animals, though plants sometimes can transmit somatic mutations to their descendents. Mutations are considered the driving force of evolution, where less favourable or deleterious mutations are removed from the gene pool by natural selection, while more favourable ones tend to accumulate. Neutral mutations are defined as those that are neither favourable nor unfavourable.

It will be apparent from the above how both variety and inheritance of variety arise at the molecular level.

The so-called central dogma of molecular biology arises from Francis Crick’s statement in 1958 that “Genetic information flows in one direction only from DNA to RNA to protein, and never in reverse.” It follows from this that:

1. Genes determine characters in a straightforward, additive way: one gene-one protein, and by implication, one character. Environmental influence, if any, can be neatly separated from the genetic.

2. Genes and genomes are stable, and except for rare, random mutations, are passed on unchanged to the next generation.

3. Genes and genomes cannot be changed directly in response to the environment.

4. Acquired characters are not inherited.

These assumptions have been challenged and they do not hold under all conditions, e.g. horizontal gene transfer (for example, haemoglobins in leguminous plants).

Modes of evolutionary change

Put together, natural selection, population genetics and molecular biology form the basis of neo-Darwinism, or the Modern Evolutionary Synthesis. The theory encompasses three main tenets:

1. Evolution proceeds in a gradual manner, with the accumulation of small changes in a population over long periods of time, due to changes in frequencies of particular alleles between one generation and another (microevolution).

2. These changes result from natural selection, with differential reproductive success founded on favourable traits.

3. These processes explain not only small-scale changes within species, but also larger-scale processes leading to new species (macroevolution).

On the neo-Darwinian picture, macroevolution is seen simply as the cumulative effects of microevolution.

However the extent and source of variation at the genetic level remained a bone of contention for evolutionary theorists until the mid-1960s. One school of thought favoured little variation, with most mutations being deleterious and selected against; the other school favoured extensive variation, with many mutations offering advantages for survival in different environmental circumstances. Techniques such as gel electrophoreses settled the argument in favour of the second school: genetic variation turned out to be most extensive. By the 1970s the debate had shifted to selectionism versus neutralism. The selectionists view genetic variation as the product of natural selection, which selects favourable new variants. On the other hand the neutralists contend that the great majority of variants are selectively neutral and thus invisible to the forces of natural selection. It is now generally accepted that a significant proportion of variation at the genetic level is neutral.

Consequently certain traits may become common or may even come to predominate in a population by a process known as genetic drift. This is the random changes in the frequencies of neutral alleles over many generations, which may lead to some becoming common and some dying out. Genetic drift, therefore, tends to reduce genetic diversity over time, though for the effect to be significant, a population must be small (to explain by analogy, while a group of ten people could throw a die and all fail to get a six with reasonable probability [tenth power of 0.8 = 0.1], but the probability of one hundred people all failing to get a six is far smaller [hundredth power of 0.8 = 2x10e-10]). There are two ways in which small isolated populations may arise. One is by population bottleneck in which the bulk of a population is killed off; the other is the founder effect which occurs when a small number of individuals carrying a subset of the original population’s genetic diversity move into a new habitat and establishes a new population there. Both these scenarios could lead to a trait that confers no selective advantage coming to predominate in a population. More controversially, they could lead to genetic drift outweighing natural selection as the engine for evolutionary change.

With the foregoing in mind, how do new species arise? There are two ways. Firstly a species changes with time until a point is reached where its members are sufficiently different from the ancestral population to be considered a new species. This form of speciation is known as anagenesis and the species within the lineage are known as chronospecies. Secondly a lineage can split into two different species. This is known as cladogenesis, and usually happens when a population of members of the species becomes isolated.

There are several such modes of speciation, mostly based on the degree of geographical isolation of the populations involved.

1. Allopatric speciation occurs when populations physically isolated by a barrier such as a mountain or river diverge to an extent such that if the barrier between the populations breaks down, individuals of the two populations can no longer interbreed.

2. Peripatric speciation occurs when a small population is isolated at the periphery of a species range. The difference between this and allopatric speciation is that the isolated population is small. Genetic drift comes into play, possibly outweighing natural selection (the founder effect).

3. Parapatric speciation occurs when a population expands its range into a new habitat where the environment favours a different form. The populations diverge as the descendants of those entering the new habitat adapt to the conditions there.

4. Sympatric speciation is where the speciating populations share the same territory. Sympatric speciation is controversial and has been widely rejected, but a number of models have been proposed to account for this mode of speciation. The most popular is disruptive speciation (Smith), which proposes that homozygous individuals may under certain conditions have a greater fitness than those with alleles heterozygous for a certain trait. Under the mechanism of natural selection, therefore, homozygosity would be favoured over heterozygosity, eventually leading to speciation. Rhagoletis pomonella (Apple maggot) may be currently undergoing sympatric speciation. The apple feeders seem to have emerged from hawthorn feeders, after apples were first introduced into North America. The apple feeders do not now normally feed on hawthorns, and the hawthorn feeders do not now normally feed on apples. This may be an early step towards the emergence of a new species.

5. Stasipatric speciation occurs in plants when they double or triple the number of chromosomes, resulting in polyploidy.

Rates of evolution

There are two opposing points of view regarding the rate at which evolutionary change proceeds. The traditional view, known as phyletic gradualism, holds that it occurs gradually, and that speciation is anagenetic. Niles Eldredge and Stephen Jay Gould (1972) criticized this viewpoint, arguing instead for stasis over long stretches of time, with speciation occurring only over relatively brief intervals, a model they called punctuated equilibrium. They pointed out that species arise by cladogenesis rather than by anagenesis. They also highlighted the absence of transitional forms in the fossil record (an old chestnut, often favoured by creationists).

Richard Dawkins has pointed out that no “gradualist” has ever argued for complete uniformity of rate of evolutionary change; conversely even if the “punctuation” events of Eldredge and Gould actually took 100,000 years, they would still show as discontinuities in the fossil record, even though on the scale of the lifetime of an organism, change would be immeasurably small, and invisible at any given time due to variation between individuals; if for example average height increased by 10 cm in 100,000 years, that would be 1/500th of a cm per generation – completely masked by the variation in height of individuals at any one time. It follows that the speciation event – be it anagenetic or cladogenetic – would be very slow in relation to the lifetime of individuals. Reproductive isolation would occur only over hundreds of generations.

On the Dawkins view, then, there is no conflict between gradualism and punctuationism; the latter is no more than the former proceeding at varying tempo.

The Physical Context

Three factors are recognized as influencing the evolution of new species and the extinction of existing ones. The first is the existing properties of a lineage, which places constraints on how it can evolve. The second is the biotic context: how members of a particular species compete both in both an inter-specific and intra-specific context for food, space and other resources; how they interact with other species in respect of predation; mutualist behaviours, etc. The third is the physical context such as geography and climate, which determine the types of species that can thrive and the adaptations that are likely to be favoured.

The relative importance of the last two is a matter of ongoing debate. Darwin held that biotic factors predominate. He did not ignore environmental considerations, but he saw them as merely increasing competition. This view is central to the modern synthesis and it is held that natural selection is necessary and sufficient to drive evolutionary change. For example, adaptations by predators to better their chances of catching prey are the driving force for evolutionary change in the prey, where adaptations to avoiding capture are selected for; thus maintaining the status quo in a kind of evolutionary “arms race”. This is sometimes referred to as the Red Queen effect (van Valen, 1973), from the Red Queen in Alice through the Looking Glass.

However in recent years, it has become clear that the history of life on Earth has been profoundly affected by geological change. The discovery of plate tectonics in the 1960s confirmed that continental landmasses are in a state of constant albeit very slow motion across the Earth’s surface, and when continents meet, previously-isolated biota are brought together. Conversely, as continents drift apart, previously united communities are separated. The first introduces new elements of inter-specific competition; the other to possible isolation of small groups. Both scenarios are likely to lead to evolutionary change.

There is also a school of thought that downplays natural selection and emphasises climate change as the primary cause of evolutionary change. There are two ideas associated with this view – firstly, the habitat theory, which states that species’ response to climate change represents the principle engine of evolutionary change, and that speciation and extinction events will be concentrated in times of climate change, as habitats change and fragment; secondly this pattern of evolutionary change should be synchronous across all taxa, including hominins (the turnover-pulse hypothesis) (Vrba 1996).

Units of selection

In the original theory of Charles Darwin, the unit of selection i.e. the biological entity upon which the forces of natural selection acted was the individual; for example an animal that can run faster than others of its kind, and so avoid predators, will live longer and have more offspring. This simple picture does, however, fail to explain altruism in which an individual acts in a manner that benefits others at its own expense.

One answer is that selection may operate at social group level (group selection) as proposed by V.C. Wynne-Edwards (1962). On this picture, a group in which members behave altruistically towards one another might be more successful than one in which they do not. Kin selection, proposed by W.D. Hamilton (1964), posits reproductive success in terms of passing on one’s genes, and that by helping siblings and other relatives, one is doing this by proxy. This view largely superseded the group selection view. Robert Trivers (1971) extended the theory to non-kin in terms of doing a favour in the expectation of it being returned (“reciprocal altruism”). This behaviour is common in species of large primates, including humans. Kin-selection and reciprocal altruism act at individual and not group level, so the latter fell out of favour; though it has been recently revived.

By contrast, the gene-centric or “selfish gene” view popularised by Richard Dawkins states that selection acts at gene level, with genes that best promote the interests of their host organisms being selected for. On this view, adaptations are phenotypic effects that enable genes to be propagated. A “selfish” gene can be favoured for selection by favouring altruism among organisms containing it, even if individuals performing the altruism do so at the cost of their own chances of reproducing. To be successful, however, a gene must “recognise” kin and degrees of relatedness and favour greater altruism towards closer relatives (by, for example, favouring a sibling [where the chance of the same gene being present is 1/2] over a cousin [where it is only 1/8]). The green beard effect refers to such forms of genetic self-recognition, after Dawkins (1976) considered the possibility of a gene that promoted green beards and altruism to others possessing them.

© Christopher Seddon 2008

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