Nature's Holism (condensed - 12)
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GENETICS and INHERITANCE

This chapter on genetics is part of a major section of this etext. It provides some background to the science of genetics for those who wish to refresh their basic knowledge, or need to learn more on the topic.

You can skip this and go to the next chapter:  G. PARADIGMS OF BIOLOGICAL SCIENCE:
Genetics
provides a crucial element to our understanding of evolution as inheritance and the generation of heritable variations are necessary conditions for the process of natural selection to occur (Endler, 1985). I will cover some basic principles needed for an understanding of genetic mechanisms.

Brief History and Landmarks:


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Aristotle (384-322 B.C.)  recognised that an organism resulted from sexual reproduction and the contribution from the female egg and male seminal fluid (Strickberger, 1985). This knowledge had little advanced when Harvey (1578-1657) expressed similar ideas. By the 17 and 18 centuries the belief called preformationism prevailed, stating that either the female egg or male sperm contained a perfect miniature form of the entire organism (called "homunculi"). Wolf (1738-1794) provided evidence against preformationism when he showed that the structures found in plants and animals developed from uniform or homogeneous embryonic tissues. von Baer (1792-1876) succeeded Wolf and refined the idea that tissues arose through a gradual transformation and specialisation (Strickberger, 1985) of the original tissue. The idea that plants and animals are made up of  cells developed slowly. In 1838, Mattias Schleiden proposed that all plant tissues consisted of cells. The same idea was strongly expressed for animal cells by Schwann in 1839. Rudolf Virchow stated in 1858 that all cells come from pre-existing cells and formulated the Cell Theory. In 1859 Charles Darwin published "Origin of Species", describing natural selection.  Naturalists knew of cell structure and Brown (1773-1858) named and described the cell nucleus in 1833. In 1840 Albrecht Koelliker realised that sperm from the male and ova from the female were cells.  Cell division involving the nucleus and its  chromosomes was first observed by von Nageli in 1842. He was the first to observe and describe chromosomes from the cell nucleus under the microscope (Mc Farland, 1993). Pringsheim was the first to see a sperm enter and fertilise a female cell in 1856. Friedrich Meischer isolated DNA from fish sperm and the pus of open wounds in 1869 and called it nuclein. In 1876, Oscar Hertwig, on seeing two nuclei in a fertilised cell, realised that one came from the sperm and proposed that chromosomes carry the heritable (genetic) material . Walter Flemming correctly described chromosome behaviour in 1882. By 1885, Eduard von Beneden had shown that the chromosomes remained unaltered from one cell division to the next and that the number of chromosomes in the cell nucleus is fixed for a given species (Mc Farland, 1993).

The origin of genetics as a science and the laws of inheritance are to be found in the works of Mendel which were published in the Brunn Society of Natural Science in 1866 (Mc Farland, 1993), but its real development did not take place until the twentieth century. In 1900 De Vries, Correns and Tschermak independently rediscovered Mendel's work. Hugo De Vries, a Dutch botanist, used the term "mutations " to describe the phenomenon of variants in the evening primrose plants. Sutton proposed that genes reside on chromosomes in 1903 (Brown, 1992). Genetics as a scientific discipline, was only named such in 1905 by the British biologist, William Bateson. In 1909, Johannsen proposed that Mendel's factors are genes (Brown, 1992). An American, T.H. Morgan, started to study the chromosomes of the fruit fly, Drosophila in 1910. He establised that genes are carried on the chromosmes and that some are sex-linked. By 1911 they had mapped five genes on the Drosophila chromosome and by 1915, they had mapped 85 different genes on four chromosomes. Biochemist P.A. Levene analyzed the components of the DNA molecule during the 1920s. He discovered that it contained four nitrogenous bases, (cytosine, thymine, adenine, and guanine), a deoxyribose sugar and a phosphate group. He proposed that the basic unit (nucleotide) was composed of a base attached to a sugar and that the phosphate also attached to the sugar.

In 1926, Herman Muller found he could induce mutations in fruitflies with X-rays. Frederick Griffith found that he could transform non-pathogenic  bacteria to become pathogenic, causing pneumonia. He identified some transforming factor as the cause in 1928. R. A. Fisher promoted his genetic theory of natural selection in the 1930's. This theory provided a mechanism for natural selection. Along with genetics as a mechanistic foundation, came the recognition of population biology. This "population thinking" recognises the uniqueness that genetically distinct individuals are the elements of every population. A population is a gene pool of individuals that makes gradual evolution possible (Mayr, 1978). By 1935, G.W. Beagle and E.L. Tatum established that a gene codes specifically for a single protein. A gene is a segment of the DNA molecule (chromosome) in the cell nucleus that stores a feature of the organism's genetic information in their structure (Ayala, 1978). Many genes make up the genetic constitution of the organism. In the 1940s, Oswald Avery, Colin MacLeod, and Maclyn McCarty identified  DNA as the hereditary material ('transforming factor'). At that time, protein, rather than DNA was considered the hereditary material.

In 1952 Alfred D. Hershey and Martha Chase established that the transmitter of heredity was DNA rather than proteins. Watson and Crick discovered that DNA of the chromosomes, found in the cell nucleus, carries the genetic code and figured out its double helix structure in 1953. Advancement in genetics then accelerated. H. Boyer and S. Cohen used restriction enzymes (1973) to cut and splice animal DNA into bacteria, enabling multiple copies to be made. Scientists studying the genomes of various species in the 1970's, found that chimpanzee and human genomes diverge by only 1.6% and that regulator genes control the expression of thousands of structural genes (King and Wilson, 1975). In 1977, F. Sanger and W. Gilbert developed a method for sequencing DNA. Kary Mullis developed the PCR (polymerase chain reaction) technique that allows  billions of copies of a DNA strand to be made in a few hours. By the 1990's molecular biologists had adopted genetics, and used it to extrapolate the evolutionary history of living organisms from changes in their genes (Sci. Am., Apr. 1992). Capillary sequencing, using gel electrophoresis, was invented by M. Hunkapiller and L. Hood in 1992. By 1995 to be a molecular biologist was a serious career option. In the agricultural field, it is used, for example, in projects of DNA fingerprinting to identify new fruit cultivars. This leads to the creation of new fruit varieties in the deciduous fruit industry. Anthropologists can now use genetic evidence to support their findings on the evolution of humanity. Craig Venter accelerated the advance in 1996 when he  found a shortcut method to identify genes; termed "Expressed Sequence Tags" ("shotgun" sequencing). In 2000, the Human Genome Project, with the aim of mapping the whole of human nuclear DNA, presented its preliminary results. Francis Collins of the Human Genome Project and J.C. Venter of Celera Genomics jointly announced a working draft of the human genome.

Primer on Genetics:

If we work down from the individual to smaller units, the genetic basis of life will become clearer. Our body is made up of various specialised tissues such as the liver, brain, muscles and skin. These tissues are made up of cells that differentiated during embryonic development (Beck, et al, 1991). Most children learn about the structure of the cell in school biology lessons. Our cells have a very complex structure and people have written many books on their function. The cellular material is enclosed in a plasma membrane. Within this membrane is a fluid called the cytoplasm that supports many discrete structures or cell organelles, such as mitochondria, lysosomes, pinocytic vesicles, endoplasmic reticulum, centrosomes, Golgi bodies and so on. These organelles serve various functions. Cells are the fundamental working units of every living plant and animal.
Also contained within the cell is the  nucleus , the organelle containing the chromosomes. A nucleus originates from another nucleus during cell division (mitosis) and is essential for the continued life of most cells. The nucleus is large, often spherical and usually found centrally in the cell. Two membranes enclose a fluid, the nuclear matrix, small bodies called nucleoli and chromatin material. Chromosomes contain chromatin material and are paired, thread shaped bodies made up of DNA, protein and RNA. Humans have 46 chromosomes that contain about 15% DNA, 10% RNA and 75% protein (Lehninger, 1977). DNA (deoxyribonucleic acid) is the most important constituent of the chromosome as it controls the cell's activities and is responsible for the transmission of hereditary traits (Smit and van Dijk, 1972). All the instructions needed to direct cellular activities are contained within the chemical DNA (deoxyribonucleic acid). The two members of each chromosome pair are identical in appearance and are said to be homologous (to each other). The corresponding genes present on each of the pair may however differ in that they may code for different traits, say one for blue eyes and the other for brown eyes. A nucleus has between one and 100 chromosome pairs, depending on the species. Man has 23 pairs, Drosophila has four pairs, a bee has eight pairs and the chicken has 39 pairs (78 chromosomes) (Lehninger, 1977). Chromosomes are usually only visible during cell division (mitosis and meiosis) when they contract in length becoming short thick rods. In the resting nucleus they form fine, extended threads (Abercrombie et al., 1973).

We can visualise chromosomal DNA as a ladder with the struts made up of only four compounds, adenine, thymine, guanine and cytosine. These are molecules made up of atoms and have a specific structure. Thymine, for example, is 5-methyl-2,4-dioxopyrimidine, made up of five carbon atoms, two nitrogen atoms, two oxygen atoms, and six hydrogen atoms, joined into a ring. Each upright arm of the ladder consists of long chains of alternate sugar and phosphate molecules with the organic bases (the base pairs), attached to the sugars as side groups. The cross linking side links can only form by bonds of adenine to thymine and guanine to cytosine.
 

a] base pair linkage:
 

               A T T C G A C T G T A C G
                |  |   |   |   |    |   |   |   |  |   |   |   |
               T A A G C T G A C A T G C
 

b] DNA chain:
   base                    base                          base
      |                              |                                |
-sugar-phosphate-sugar-phosphate-sugar-phosphate-
 

(bases = adenine, guanine, thymine, cytosine)
 

The sugar, deoxyribose and the phosphate are complex molecules. When all joined as a strand of DNA, this ladder-like structure spirals upon itself. They call each pair C-G and T-A a base pair and chemically, they call it a nucleotide. There are thus four kinds of nucleotides in DNA that code for the 20 different kinds of amino acids found in the proteins of our bodies. A single mammalian cell has about 2 metres of DNA, equivalent to about 5.5 * 109 base pairs (Lehninger, 1977). In coding for an amino acid, base pairs operate in triplet units so that the three base pairs in series, UUU and UUC code for the amino acid, phenylalanine and AAA and AAG code for lysine (Strickberger, 1985), (Lehninger, 1977). This code is nearly universal amongst viruses, prokaryotes (bacteria) and eukaryotes (e.g. mammals), with only the nuclear material in mitochondria showing some variation (Strickberger, 1985). They call the triplet unit a codon. Some amino acids such as methionine, only have one codon (AUG), while others, such as arginine has as many as six codons. Life on earth must have had one source as all its forms share the same basic code: CUA for example, codes for leucine in bacteria, viruses and humans!

Genes:

Genes are the smallest units of hereditary and are arranged in linear order along the length of the chromosome DNA (Smit & van Dijk, 1972). A gene codes for a sequence of amino acids that make a protein or part of a protein.. Different forms of the same gene are called  alleles . An individual has a pair of each chromosome. As the genes are found on these chromosomes, an individual can only carry two alleles of each gene. Within a population there may be hundreds of different alleles present. Drosophila, the fruit fly has about 10,000 genes on its four chromosome pairs. Also being the units of inheritance, genes can be considered the units of biological information. An organism's entire complement of genes, found on the chromosomes within the nucleus of the cell, contains the total amount of information needed to construct a living, functional organism (Brown, 1992). Genes make up thegenotype or genetic constitution (DNA) of the animal that is found within the nucleus. The gross effect of this genotype is the physical form of the developed animal, the phenotype. An animal's phenotype results from its genetic inheritance interacting with the environment, so that food availability, light, temperature and so forth, may modify the "ideal" form. A person may not be as tall as prescribed by the genes if nutritional factors retard growth. Our phenotype or physical form, such as eye or hair colour is therefore the result of the interaction of many factors at many levels of development (Strickberger, 1985). This interaction is holistic in nature and it involves many levels of organisation: gene, chromosome, nucleus, cytoplasm, tissue, organ, whole organism and environment. Our genes control our physical form.

When one talks of  mutations as a source of variation, one is referring to changes to this very specific sequence of base pairs. Every imaginable type of mutation can occur, such as the insertion or deletion of a base pair, the replacement of a pair (GC) by another (AT) and so on. This sequence on the chromosomes is the database for the body, God's database of life, specifying the sequence for the manufacture of proteins such as muscle, digestive enzymes, and blood proteins. Mutations change the code that dictates the structure of these proteins and so may sometimes be lethal, but are just as often benign. A changed protein may still be functional and such mutations are called silent mutations. Chemicals such as caffeine may cause mutations. Powerful mutagens are x-rays and other radiation, such as ultraviolet light. Skin cancers caused by sunlight originate as mutations to the cellular chromosomes (Lehninger, 1977). These mutations are not transmitted to the sex cells of the gonads (sperm or ova) and so are not inherited by the next generation.

Mutations are not the only source of variation from one generation to the next. Children have visible traits that come from both parents. There are two forms of cell division. Mitosis is the process of cell division involved in growth and maintenance of the body. This is the splitting of the cell material, including DNA into duplicates. For sexual reproduction, a different process,  meiosis , occurs to form the sex cells, sperm and eggs. Sperm and eggs (gametes or germ cells) have only one of the (homologous) pair of  chromosomes from the parent. A gamete then has half the (called the haploid number, n) number of chromosomes of the body (somatic) cell of the parent. When the sperm and egg fuse, chromosomes pair off (called the diploid number of chromosomes, 2n), so that the new (homologous) pairs in the offspring have half their genes from the egg (mother) and half from the sperm (father) (Beck et al, 1991). Traits from the parent mix in this way, so that the child has a new mix of genes to test in the challenges of life.

This union of homologous parental chromosomes is again not the only source of variation to be found in the next generation. During the meiotic process of forming the gametes (sex cells: sperm and ova) within the parent, the homologous chromosomes pair off. While paired off, the chromosomes often exchange genetic material is so that there is a further mixing of the genes. Gametes formed after this (that is a child) can then carry a wide mixture of chromosome material originating from either grandparent (Strickberger, 1985). Also, in the formation of gametes, such as in humans with 23 homologous pairs of chromosomes in a cell, it is a matter of chance as which chromosome of the pair is separated to form the single gamete cell. It may have originated from the grandfather or grandmother. An animal with four chromosomes can then produce 16 different gametes. With five chromosomes, 32 gametes are possible and humans with 23 pairs of chromosomes can produce 223 different gametes! These two processes, crossing over between chromosomes before the formation of spermatozoa or ova, and the random distribution of parental chromosomes in the sex cells (gametes) are an important source of variation from generation to generation. Natural selection then acts upon this material, the phenotype, selecting those that contribute to future generations. Where two successful individuals breed, there is a mix of successful genes that should have a successful outcome.

When you inherit a trait from your parents, whether it is the fact of your humanity, the shape of your ear lobe, or the colour of your eyes, you have received from your parents, the base pairs or genes on your chromosomes that dictate your total physical being. Genes within a population can be compared with each other as gene frequencies. For gene frequencies to change, mutations, or the appearance of new genes, must usually lead to behavioural, physiological or physical (structural) differences (Beck et al, 1991). Some changes may be completely neutral or ineffective. It is this difference upon which the process of natural selection takes effect. Mutations occur at a regular rate so that geneticists estimate and measure mutation rates of particular genes. Along with this generation of mutations, genes are being eliminated or shift in their proportional representation. If a gene is rare, the probability of its elimination increases. Much mathematical analysis has gone into determining mutation rates and gene elimination.

Natural Selection:

Natural selection impinges on this process of mutation, so that if individuals carrying gene A are more successful than those with gene a' in producing surviving offspring, then the frequency of gene A will increase (Strickberger, 1985). Individuals with gene A are fitter than those with gene a' in that particular environment and are better adapted. We can say that Gene A has adaptive or selective value. Black skin colour in humans is a genetic advantage in places such as Australia, with hot climates. A white baby living almost naked as the aborigines did would be dead of sunburn before maturity.


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Each individual has paired chromosomes and so two possible genes ( alleles ) for each phenotype. When these two genes are identical, they call them homozygous and when they are different they call them heterozygous. Within a population, there may be many genes (alleles) for a particular trait, but each individual can only have two, one on each pair of the chromosome. Such populations with gene variability are polymorphic. Polymorphism is selected for and so stable in some environments, such as a variable habitat.

Several processes exist for gene frequencies within a particular population to change:

[1] One is simply migration from another population. For example, one estimate puts the American black population as genetically 70% black and 30% white in 1985 and this changes at a rate of about 3.6% of genes with each generation.

[2] Random  genetic drift is another form of non-directional change that occurs to gene frequencies. This change in the gene frequencies of a population results from the uneven and random breeding success within the population. In small populations this can be quite effective in changing gene frequencies. People may argue that the shift is in some way due to natural selection and thus directional instead of random.

[3] The original aborigine members to colonise Australia would lead to a population with a gene frequency that the colonisers' genes strongly influence. There was no directional selection of genes here and the genotype has factors that are "founding accidents", conferring no advantage to the population. Aborigine colonisers represent a sample from their original population and will have a different gene frequency to the larger population. They call this change in gene frequencies the  founder effect. When a farmer plants seeds at a new site, the genetic constitution is a sample of the source population and so may lead to a strain of the crop with different features developing.

[4] Superimposed on random genetic drift and the founder effect, is  natural selection . Selection has been in operation upon the Australian population since the colonists arrived at least 60,000 years ago (Strausbaugh & Sakelarisc, 2001) and perhaps as long as 130,000 years ago! Their phenotypes (physical traits) are a compromise and optimum, given the time involved for natural selection to act on the material of the genotype (underlying genetic makeup for the traits).

[5] Another source of genetic change is non-random reproduction (Beck et al, 1991).

That natural selection has acted upon Australian aborigines is clear when we compare some of their adaptations with other human populations adapted to different habitats. Originally and until recently, they lived close to nature and depended on a hunter-gathering lifestyle for their survival. They possessed no form of agriculture. Men traditionally hunted and women collected roots and seeds for food. Their territories in drier areas covered hundreds of square kilometres. Aborigines were skilled managers of their natural environment, with accurate knowledge of food distribution, animal behaviour, seasonal changes and so forth. They used this knowledge to decide when and where to move. As they were nomadic, they often slept in the open, only building a rough windbreak for the night. Aborigines also built simple shelters in some areas, especially when the weather was more harsh - cold and dry or wet. Usually, they wore no clothes except a pubic covering. During extreme cold they would spend much time around their fires to keep warm. Because of this mode of life, so exposed to the elements, often sleeping in below freezing temperatures with little shelter or clothing, aborigines developed adaptations to the cold. When sleeping, blood supplies are directed away from the limbs and the temperature in their legs and feet drop, so conserving heat and they burn less energy. The trunk and vital organs remain warm.

In contrast to this, the Inuit Eskimos have also adapted to cold, but in a different way. They maintain a high body temperature by metabolising fat and protein. Blood is directed to arms legs, fingers and toes keeping them warm and preventing frostbite. This requires much energy in this climate where temperatures can go as low as -40 to -50 degrees Celsius. At these temperatures frostbite is rapid and lethal. They get this energy from the animals, such as seals, that they hunt.

Genetics is a massive and complex field. The above few principles should be enough, for as a science, genetics is very complex and beyond the scope of this book.
 

F.  GENETICS, ECOLOGY & EVOLUTION:

Nature is a complex system that is very difficult to model. Mathematics is a form of modelling overwhelmed by the variables in a complex system. Geneticists use complicated mathematics to understand their science, yet have to admit when dealing with nature, that "the genetic structure of population(s) is quite difficult, if not impossible, to predict mathematically in detail, even by the most elaborate techniques" (Strickberger, 1985). By using super computers we may one day change this, but as nature does not have the predictability of a complex machine such as a jet aircraft - there will still be problems in modelling nature. There are many reasons for this:

[1] populations are not of a constant size,

[2] mating patterns can change,

[3] conditions of mutation, migration and selection are not uniform from place to place or time to time,

[4] multiple alleles are common, so that more than three diploid genotypes may be present for any one locus,

[5] Genotypes of various loci interact, so fitness of one genotype must depend upon genes at other loci (Strickberger, 1985),

[6] A population may be broken into small groups of subpopulations. They call these local populations demes. Differences occur between demes due to the process of random genetic drift, but gene exchange still occurs. Organisms within a deme adapt to local conditions, so changes to gene frequencies in nature become very complicated.

[7] Many genetic factors that affect the evolution of populations may act differently to what is expected when only individuals are considered.

An obvious statement is that organisms live within an environment. Evolution through natural selection over millions of years has led to populations with phenotypes optimally adapted to their environment (Strickberger, 1985). This environment consists of a living component (biotic factors) and a nonliving component (abiotic factors). A duck's webbed feet are optimally adapted to the aquatic habitat (abiotic) of its niche. The water is not the duck and the duck is not water, but together they form an intricate whole. Life forms, through reproduction, are geared to produce variations of the phenotype, as described above. These varieties will tend to cluster around some value at which fitness is highest. As variation diverges from an apparent mean optimum, mortality rates increase. Research has illustrated this trend in various animals from snails, through to lizards, birds and humans.

A simple formula illustrates this trend:

I = (So - Ss)*fs

where I = selection intensity or pressure,

So  = survival rate of an optimal phenotype,

Ss = survival rate of sub optimal phenotypes,

fs = the frequency of sub optimal phenotypes.

When the selection pressure is zero, all the phenotypes are optimal. At fs = 1, all the phenotypes are sub optimal. This formula is again a model, one of many that may reflect a real process. It shows how adaptation through natural selection takes place and its beauty lies in its simplicity.

An animal's environment, made up of biotic and abiotic factors, provides the parameters and constraints that determine optimal fitness. An organism within an ecosystem evolves, defined by the parameters of its interactive realm. A weed plant follows a survival strategy that allows it to survive when interacting within the whole ecosystem. The ecosystem upon it depends, defines its optimal phenotype and it defines part of the whole system by its presence. If the weed's seeds are too light, they may float for too long and drift away from the ecosystem upon which they are dependent for their perpetuity. Seeds that are too heavy will not disperse far enough. If they are too big, they may get entangled in another species or attract the attention of a creature that eats them. They may need to attach onto a mammal or bird for dispersal so are designed for entanglement with hair or feathers. The list of possibilities is endless and nature is full of surprises and wonders. A departure from the optimum phenotype leads to lower survival rates.

Natural selection against sub optimal phenotypes throughout the life cycle of an organism can be very heavy. Data from a London hospital proves that humans are still subject to natural selection. When applying the above formula to the variation of  children from the optimal 8-pound birth class, the following was found for the period between birth and one month old:

born survived percentage

optimal 8 pound 727 718 98.8

other classes   5966 5701 95.6

total 5701

The frequency of the sub optimal class is 5966/5701 babies, or 89.2%. Using the above formula, I = (.988- .956)*.892 = 0.029. Of a total of 4.1% deaths, 2.9% were due to selection against the sub optimal phenotypes, measured by the single parameter of birth weight. Of deaths at birth, selection against these phenotypes caused 70.8 percent! In this research, it was found that average birth weights increased by 1% from 7.06 to 7.13lb, while the standard deviation or variation decreased by 10% from 1.22 to 1.10.  ( see graph ) Evolutionists call this stabilising selection, one of many forms of selection that can occur. Changing conditions can lead to directional selection where the optimal phenotype changes consistently, adapting to the new conditions. Darwin's finches illustrate directional selection that has taken place in various directions from some ancestral form.

As behaviour, form and physiology, has a genetic basis the impact of the genes of an organism may extend into the physical environment. Dawkins (1983) calls this the "extended phenotype". Examples he gives are the dam wall size of beaver dams and the structure and shape of anthills. Such structures evolve through natural selection because of the gene's action via the individual feed back and affect the survival of the beaver itself.

The above formula is a useful tool for understanding and illustrating natural selection. Optimal phenotypes are not represented by one individual, but by a cluster of individuals with a common genetic character. Classical Darwinian and neutralist evolutionary camps accept that the wild type populations will cluster around some specific phenotype. Both theories assume that mutations appear blindly, despite their selective value. No single neutral or advantageous mutation would occur more frequently than any disadvantageous one. That view is not fully correct. It is not part of the modern kinetic theory of molecular evolution, nor is it backed by experiments with viruses (Eigen, 1993). In this field, a model called a sequence space is constructed.

A sequence space, or Hamming sequence space is a multidimensional matrix into which the nucleotide sequences of the genes (of viruses) are mapped. The idea is similar to the binary digits of computer language, so that in a sequence with just one position there are only two possible sequences or possible permutations - like a switch, it is either on or off. With two switches there are four permutations, On-On, Off-Off, On-Off and Off-On. These can form the corners of a square for representation in visual form. The variations on a three-digit sequence become the corners of a cube, the options being, 100, 110, 000, 010, 101, 111, 001, 011. Variations of a four-digit sequence form the vertices of a four-dimensional hypercube. Drawing the previous diagram builds each higher-dimensional space iteratively twice and connecting the corresponding points. In genetics the sequence length is equivalent to the number of triplets on a DNA strand, so the sequence space is very complex! Further, four different nucleotides can occupy each position, the equivalent of a switch with four positions.

In nature, the variation generated through mutation balances elimination through selection. This forms a natural cluster of surviving organisms, each genetically different from the other. Such a self-sustaining population continues to reproduce genetic varieties of a typical wild type of species. In the conceptual sequence space, these form an asymmetric space, like a cloud comprising most sequence spaces represented by the surviving individuals. The population density around or at each point of sequence space represents the fitness value of that particular sequence, describable mathematically.

Expression of the mutations in the phenotype, limited by organism viability has led to DNA along which :

[1] some positions are almost constant because of fitness constraints (a change to these positions causes death or zero viability);

[2] some vary at a normal rate, whereas still

[3] others are very variable and change rapidly in response to the selection pressure imposed on them (Eigen, 1993) by their environment.

Natural selection acts upon the whole organism. In the example of newly born children described above, the researcher used a single parameter to separate his population into optimal and sub optimal phenotypes. Causes of death would have been more diverse and complicated. A human body is a complex genetic entity. A virus such as  HIV has only about 10,000 nucleotides with four possible bases on each nucleotide. This allows 410,000 possibilities, the expression of any of which the environment tests. Some of these "possibilities" survive to contribute to the sequence space of the population. Taking account of organism viability in their predictions is very difficult for mathematicians.

Even among viruses, there are variations in mutation rates. Viruses mutate and evolve at more than a million times the rate for cellular micro-organisms. Influenza A virus mutates so rapidly that it should change completely within a few hundred years. It may have a completely different pathology. In the polio-1 virus, nucleotides of the first and second positions of each codon hardly change, resulting in proteins that do not vary much. This allows the development of effective vaccines for the polio virus, but not the Influenza virus. Immunodeficiency viruses express very random changes on all three codon positions. Only about 20% of the positions are constant, being necessary for HIV to function as a retrovirus. Other positions have an average lifetime of 1,000 years. Differences between HIV-1, HIV-2 and the SIV virus proves that these viruses diverged at least 600 to 1200 years ago, not first appearing in 1979 as epidemiological data shows!

Evolution of cellular organisms will follow the same basic rules. Only mutations that allow a viable organism will be perpetuated. Some organisms will not have evolved much over millions of years, as the environment defines their niche and structure. Within a species some features may evolve more rapidly than others. A species evolutionary history results in a genetic endowment that limits the evolutionary pathways in some directions. Obviously, a vertebrate cannot evolve into an insect. Unique adaptations, on the other hand, open new possibilities. Unique adaptations are the source of the "creativity" of evolution.

Strickberger (1985) notes that "The creativity of evolution, however, does not mean "purposefulness" in the human sense. Except artificial selection (human), there are no observable agents either within or without the organism that are consciously capable of directing evolution. . . ." There is however a form of teleology , originally described by Immanuel Kant . Strickberger continues, "According to the modern view, evolutionary creativity is primarily caused by the opportunistic role played by natural selection as it acts upon available genetic variability and thereby exposes a species to further selection for the same or closely connected environment." He further notes that "mutation alone is insufficient to produce most of the observed complex biological structures . . . " Natural selection is required. Natural selection is an environmental factor, so all organisms are adapting to the environment. In this sense natural selection is teleological, especially when adaptation is to both biotic and abiotic factors, as in ecosystems. Even the slightest adaptation to biotic factors requires that Kantist teleology be recognised within the system. After so many billions of years of evolution, we may not even be able to detect coevolutionary events that define our existence!

Go to next chapter: G. PARADIGMS OF BIOLOGICAL SCIENCE:

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