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. . . And Still We Evolve
A Handbook on the History of Modern Science

[This handbook, which has been prepared by Ian Johnston of Malaspina University-College, Nanaimo, BC (now Vancouver Island University), for Liberal Studies students, is in the public domain and may be used without charge and without permission, released May 2000]

[Table of Contents]



Section Five: Heredity and Modern Genetics



The basic questions of heredity are as ancient as civilization itself: Why is it that animal and plant species almost always produce offspring very similar to the parents and only with members of the same general group? Why is it that no exact copies are made, that there is always some variation? What controlling processes guide the determination of physical characteristics? Where do significant aberrations come from? And so on.

At a very practical level, farmers since Babylonian times, about six thousand years ago, have always understood many issues of animal and plant pedigree, recognizing that the characteristics of the parents in sexual reproduction are something of a guarantee of certain characteristics in the offspring. The Ancient Egyptians practiced cross pollination in order to improve the quality and quantity of a crop.

For the most part, this ancient agricultural knowledge, though very widespread, did not move beyond a practical application. At any rate, we have no record of very early theories to account for how characteristics might be inherited. In this, as in so much else, the Greeks provide our earliest records of speculative thought about a natural phenomenon.

Pythagoras (c. 550 BC), for example, in a doctrine which lasted at least until the Renaissance, held that the male semen was created from fluid collected from the entire body. The male parent played the dominant role in determining the form of the child. The mother served as the receptacle for the embryo formed entirely from male material. The obvious objection to this theory, that it had no room for the inheritance of the mother's characteristics, led another Greek thinker, Empedocles (c. 453 BC), to propose the notion of blending between the male and female sexual material in the production of the embryo. Thus the embryo was the result of various combinations of male and female genetic material and showed a variety of traits derived from the mother and the father.

The most influential ancient doctrine of heredity came, not unexpectedly, from Aristotle, who postulated that semen was purified blood. Both parents contributed purified blood to the embryo, but the male semen was more purified than the female menstrual fluid. Thus, the male semen was the source of life and form; the female material was the matter, or the building material. Heredity was a matter, then, of "blood": the male parent contributing the vitality and the blueprint, the female the building blocks. A surviving fragment of this doctrine is our metaphor about "blood" in talking of heredity, as in, for example, the phrase "blue blood" to refer to the aristocracy.

Largely on the strength of Aristotle's authority, this concept of heredity remained the dominant notion of inheritance for almost two thousand years, during which time there was no available systematic anatomical evidence to confirm or disprove it. Only with the development of studies in genetics, embryology, and histology were the arguments which led to modern theories initiated.


Preformation, Incapsulation, and Epigenesis

In the 17th and 18th centuries separate studies by William Harvey (1578-1657) and Anton van Leeuwenhoek (1632-1723) led to the discovery of the production of eggs in female animals and of the union of the egg and the sperm as the creative act forming an embryo, which then went through a series of developmental stages.

The Dutch scientist Jan Swammerdam (1637-1680) proposed that each sperm contained, in miniature, a complete human being (tiny babies were contained in the heads of each of the sperm). This Preformation Theory (which was mentioned above in Section Three) suggested that the mother provided only the location and nourishment for the growth of the embryo, since the male sperm contributed everything else. A century later the Swiss scientist Charles Bonnet (1720-1793) suggested the reverse, that the potential embryos were in the eggs, not the sperm. According to this Incapsulation Theory, each female would contain all the descendants that would have a hereditary link to her (like boxes within boxes).

In opposition to these notions that the embryo (in miniature or in latent form) existed in either the male or female sexual material, some natural philosophers proposed that the reproductive material contained small particles which had the power to organize the body parts. One such scientist, Pierre Louis Moureau de Maupertuis (1698-1759) suggested that in the combination of these particles, the contribution of one parent might exert a stronger influence than the contribution of another (an early anticipation, although without experimental evidence, of the idea of dominant and recessive particles).

Following Maupertuis, Kaspar Friedrich Wolff (1733-1794) proposed a theory of epigenesis, the idea that reproductive cells do not contain embryos preformed but rather particles which have the power to guide the development of the body parts in the growing embryo. According to Wolff, a vital force, a vis essentialis, which operated within the growth period of the embryo, controlled the development of the offspring. He had nothing to offer about how this force worked, but his theory did emphasize the importance of some material "encoded" inside the fertilized egg.

Lamarck, by contrast, offered no comprehensive notion of reproduction. He seems to have assumed that acquired characteristics were transmitted by some mechanism or other.


Darwin's Notion of Heredity

Charles Darwin, as explained briefly in Section Three above, recognized the importance of a comprehensive theory of reproduction, particularly for the origin and transmission of variations, an essential feature of his theory of natural selection. His own ideas of heredity rested on a theory of Pangenesis.

According to Darwin's notion of pangenesis, tiny particles, called pangenes or gemmules, were produced all over the body. These pangenes moved in the blood stream to the reproductive organs and formed similar organs in the developing embryo. Each individual formed his or her own reproductive material from the gemmules, and characteristics acquired in life could affect the gemmules and therefore the offspring. Hence, Darwin's theory, like Lamarck's, made room for the inheritance of acquired characteristics.

Also important in Darwin's notions of heredity was the concept of blending, that is, the combination of characteristics from both parents into a new unique creation. But this idea created logical difficulties for Darwin's theory and was an important factor in its lukewarm reception among many scientists. The notion of blending, as Darwin's contemporary Fleeming Jenkin, a Scottish engineer, pointed out, contradicted one of the central ideas of Darwin's own theory. For if some variation arose by some as yet unspecified mechanical process, future reproduction would require the new trait to be blended in with existing characteristics. Thus, the variation would simply be dissolved away into the older and infinitely larger population.

One did not have to be a biologist to appreciate this difficulty. Mathematical analysis revealed that any distinctively new variation could not last long enough for significant natural selection to occur in the way Darwin's theory required. A bottle of ink, no matter how distinctively coloured, once dissolved in the ocean, would have no appreciable effect on the characteristics of the entire body of water.

Furthermore, towards the end of the 19th century, a German biologist, August Weismann (1834-1914) tested the doctrine of the inheritance of acquired characteristics and found it deficient. Weismann cut off the tails from 22 consecutive generations of mice. He noticed no effect in the tails of the offspring. Weismann could find no evidence that the life experience of one generation had any influence upon the biological structures of the next. This insight led him to postulate a germ plasm theory, which held that the sex cells endure from one generation to the next and are not affected by the bodily experiences of the organism. This hereditary material is, thus, in a sense permanent and immortal. The body structure is derived from it but does not affect it, so that it is passed on unchanged to the next generation (in combination with the sexual material from the other parent).

These severe limitations on Darwin's theory of heredity were, for a considerable time, an important obstacle to gaining wider acceptance for the theory of natural selection. Only as new insight into basic reproductive events at the cellular level came to light and produced a more accurate idea of the processes of heredity did Darwin's theory, many years after its initial publication, emerge as the cornerstone of Western biology.


Gregor Mendel

By one of the curious ironies in the history of modern science, unknown to most 19th century biologists, a discovery that was to prove absolutely crucial for the acceptance of Darwinian theory was taking place in the years immediately after the publication of The Origin of Species (1859). This was the work of Gregor Mendel (1822-1884), who in the 1860's laid the groundwork for modern genetics while in virtual seclusion from the European scientific community in an Augustinian monastery in Brno (now in Czechoslovakia).

Mendel's work was remarkable for its apparent simplicity and staggering in its consequences. Simply put, his experiments involved cross breeding different varieties of garden peas (22 different varieties), following what happened to particular traits in the offspring (height, colour of the flower, texture of the peas, and so on), and keeping a detailed numerical record of the results. On the basis of these studies, Mendel produced a theory which he presented to the Society of Natural Science in Brno in 1865. His results, however, were generally unknown in the scientific community in western Europe and were thus ignored for many years. Hence, the value of his work, which established the fundamental basis for modern genetics, had to be rediscovered in 1900.

The most significant result of his controlled experiments was statistical. Initially Mendel focused on a single trait, crossing different parents and seeing what happened to that trait in the offspring. In these experiments he discovered that, no matter what trait he was following and no matter what the origin of the parents, the results always fell into one of three ratios: sometimes 100 percent of the offspring were like one parent (or like both parents, if the parents were the same for that characteristic); in other crosses 75 percent of the offspring were like one parent; in still other pairings, 50 percent of the offspring were like each parent.

For example, when he crossed a tall plant with another tall plant, sometimes 100 percent of the offspring were tall; sometimes 75 percent were tall and 25 percent short. When he crossed a tall plant with a short plant, sometimes 100 percent of the offspring were tall, sometimes 50 percent were tall and 50 percent were short. When he crossed a short plant with a short plant, 100 percent of the offspring were short.

When Mendel observed a different trait, like whether or not the offspring had smooth or wrinkled peas or purple or white flowers, he obtained the same ratios. No matter what the characteristic, the ratios in the offspring appeared remarkable stable.

His first conclusion was a statistical one: these results could not be a product of chance. The stability of the ratios meant that some controlling mechanism in the heredity of these plants was determining the distribution of the traits in the offspring. Or, put another way, the external appearance of the offspring (the phenotype) was being determined by some hidden genetic factors (the genotype).

This distinction between phenotype and genotype is important, for it reminds us that the genetic make up of a living organism does not always have an obvious one-to-one relationship with its appearance. Mendel's experiments revealed that an organism can carry a gene which does not manifest itself in the phenotype (appearance) but which the organism can transmit to its offspring and which the offspring can display in its appearance. In other words, two organisms which look the same (i.e., have the same phenotype) can carry different genes (i.e., have a different genotype). This point was to provide a vital and decisive answer to the objection of Jenkin about Darwin's notion of blending, because it demonstrated that an organism can transmit genes which have no apparent influence on its appearance but which can persist and affect future generations.


Mendel's Genes

His mathematical conclusions led Mendel to deduce that the genetic control of each characteristic was exercised by a pair of factors in each plant, two genes or alleles for each characteristic. Thus, height was determined by two genes for height. Furthermore, on the basis of the ratios he obtained, Mendel concluded that of these two genes for height, the one for tallness must exert a more powerful influence than the one for shortness, or, in other terms, the gene for tallness must be dominant and the one for shortness recessive.

It is important to remember that Mendel was deducing this result from the statistical information he derived from counting the offspring of many individual cross-breeding experiments. He had no direct knowledge of the physiological basis of inheritance at the level of the cell. His theory of genetics was an attempt to explain the mathematics of his observations, not the product of actual observations of chromosomes or microscopic processes of cell division (which came later).

Using his hypothesis of gene pairs, made up of one dominant and one recessive gene, Mendel could then account for the ratios produced by his experiments. A tall parent could have two different possible genotypes. If we use the letter H to stand for the dominant gene for tallness and the letter h to stand for the recessive gene (for shortness), then a tall plant could be either HH or Hh. The two plants with these different genotypes would look the same, because the H gene is dominant over h. A plant with two recessive genes (hh) will be short.

Thus, for any one trait a plant might have one of three different genotypes: either two dominant genes, one dominant and one recessive gene, or two recessive genes (e.g., HH, Hh, or hh). A genotype where both genes are the same is called homozygous. There are thus two forms of homozygous genotypes: a homozygous dominant (HH) and a homozygous recessive (hh). A genotype with one dominant and one recessive gene is called heterozygous (Hh).

According to Mendel, each parent contributed one of its genes for each trait to each sex cell (sperm or egg); the combination of the one gene from each parent will give the offspring the two genes for that characteristic. The phenotype (appearance) of the offspring will depend upon the combination of genes the offspring inherits (one from each parent).


Punnett Squares

Consider, for example, a cross breeding experiment between two plants heterozygous for height. The father is Hh and the mother is Hh. According to Mendel, the father will produce sex cells, each with one gene, of two kinds: H and h. And so will the mother. Moreover, these two types will be produced in equal numbers. As a result there are four possibilities for the offspring:


Father's sex cells



Mother's sex cells









This form of diagram representing the distribution of genotypes from a particular cross is called a Punnett Square. Notice how it is made up: the top line contains the single gene possibilities from one parent (the father); the vertical line of the second column from the left indicates the single gene possibilities from the other parent (the mother). The cells with two genes represented indicate the possibilities in the offspring for this characteristic. And since each square has an equal chance of appearing, the diagram also indicates the frequency of all the genotypes (HH will appear 25 percent of the time, Hh 50 percent of the time, and hh 25 percent of the time).

In the above Punnett square, consider the distribution of phenotypes. Since H is dominant over h, 75 percent of the offspring will be tall (HH and Hh), and 25 percent will be short (hh). There will be no way of telling from the appearance (the phenotype) which plants are HH or Hh.

Similar crosses with different genotypes in the parents always produce stable Mendelian ratios. For example, a cross between a homozygous dominant for height (HH) and a homozygous recessive for height (hh) produces offspring with 100 percent Hh as the genotype. These heterozygotes will all appear tall (i.e., have the tall phenotype, indistinguishable from the homozygous tall parent).

Notice the basic assumption here. The hypothesis maintains that each parent contributes equal numbers of each of the two genes in that parent and the offsprings' genotypes are produced by equal chances of combining single genes from each of the parents. This basic assumption is Mendel's First Law or the Law of Segregation. It states that the members of a gene pair for a particular trait separate equally into the sex cells of the parent: 50 percent of the sex cells have one member of the gene pair, and 50 percent of the sex cells have the other.


Two Characteristics: The Law of Independent Assortment

Mendel also turned his attention to following two sets of traits at a time (e.g., height and colour of the flower). Here, as usual, according to his hypothesis, there would be two gene pairs in each parent, one pair for height (the dominant H and the recessive h) and one pair for colour (the dominant P for purple and the recessive p for white). In such a cross, the possible genotypes and phenotypes for plants with these two characteristics would be as follows:

HHPP: homozygous dominant for height and for colour (tall with purple flowers);
HhPP: heterozygous for height, homozygous dominant for colour (tall with purple flowers);
HhPp: heterozygous for height, heterozygous for colour (tall with purple flowers);
hhPP: homozygous recessive for height, homozygous dominant for colour (short with purple flowers);
hhPp: homozygous recessive for height, heterozygous for colour (short with purple flowers);
HHpp: homozygous dominant for height, homozygous recessive for colour (tall with white flowers);
Hhpp: heterozygous for height, homozygous recessive for colour (tall with white flowers);
hhpp: homozygous recessive for height, homozygous recessive for colour (short with white flowers).

Notice how the variety in the genotypes arises from combining all the different possibilities for each pair. The different phenotypes are determined by the different genotypes.

Mendel hypothesized that in following two characteristics (i.e., two different pairs of genes), the separating of the members of each pair and the resulting recombinations would occur independently of each other (i.e., the distribution of the genes for height was not affected by the distribution of the genes for flower colour, and vice versa). This principle is called Mendel's Second Law or The Law of Independent Assortment.

For example, in a cross between a plant heterozygous for both traits (height and flower colour) and a plant homozygous recessive for both traits (HhPp x hhpp), one can construct a Punnett Square on the same principle as for one trait, as follows:



Male Sex Cells (Heterozygous for both traits: HhPp)

Female Sex































Since there are four possible combinations of one gene for each trait in each parent, there will be sixteen possible combinations in the offspring (hence the sixteen spaces for the full genotype in the diagram). Since the sex cells from the mother are here all the same, there will be four distinct genotypes (HhPp, Hhpp, hhPp, and hhpp). The first (HhPp) will be tall with purple flowers (25 percent of the population); the second (Hhpp) will be tall with white flowers (25 percent of the population); the third (hhPp will be short with purple flowers (25 percent of the population); and the fourth (hhpp) will be short with white flowers (25 percent of the population) (1).


Linkage and Partial Dominance

Notice that the construction of a Punnett Square for two character crosses assumes that, because of the Law of Independent Assortment, the genes for the two characteristics separate out independently of each other, so that every combination of one gene for one characteristic with one gene for the other characteristic is equally possible.

Mendel was lucky in this respect, because, as we now know, this Law of Independent Assortment applies only to genes on separate chromosomes. Those on the same chromosome will be linked and will not follow the usual Mendelian ratios, since they will not separate out independent of each other. Fortunately for Mendel the characteristics he chose to follow in the pea plant experiments were controlled by genes on different chromosomes, and thus he did not have to deal with the anomalous results produced by linkage.

It is clear also that not all traits are controlled by gene pairs in which one is wholly dominant over the other. In some cases, the one gene is only partially dominant over the other, so that in the heterozygous genotype there is an intermediate phenotype. Hence, the homozygous dominant will not only be clearly different in appearance from the homozygous recessive, but it will also have an appearance different from the heterozygous form.

For example, in human beings, black hair is homozygous dominant for hair colour, and blonde hair is homozygous recessive for hair colour. But the heterozygous individual has brown hair (partial dominance). If the dominance were complete, the heterozygous person would have black hair.


The Basic Cellular Processes of Reproduction: Mitosis and Meiosis

Darwin had demonstrated the need for heritable variations, but had produced no satisfactory theory of heritablity of variations. Mendel had supplied the theoretical basis for particular inheritance, but had contributed no cellular, microscopic evidence for his hypothesis. Following these two figures, the central issues in the twentieth century narrative have been twofold: (a) What is the genetic material? and (b) How does it operate? The answers to these two questions form one of the most exciting and continuing stories in the history of science, the development of microbiology in the twentieth century.

A giant step forward in the understanding of the mechanism of inheritance came with the discovery of the basis for cellular reproduction, the two processes called mitosis and meiosis. The discovery of chromosomes, paired rod-like structures in the nucleus of a cell (by two German biologists Walther Flemming and Eduard Strasburger in 1875), quickly led to an understanding of these two basic processes in cell reproduction (2).

In mitosis a cell makes an exact copy of itself in a process which (simply put) involves each chromosome duplicating itself, a separation of the identical copies to different parts of the cell, and a splitting of the cell, so that each part has the same number of chromosomes as the original parent cell (see Appendix to Section Five for an illustration). Mitosis is thus asexual reproduction, since there is no union of material from two different parents. The process takes place in a single cell and results in two new cells formed from and identical to the parent.

Meiosis, a more complex process, involves the formation of sex cells, each with one half the number of chromosomes as in the normal parental cells. Although there are two cell divisions in the process, there is only one division of the chromosomes. Thus, the chromosomes in the sex cells are not identical to each other and may carry different genetic information (as Mendel postulated). See the Appendix to Section Five for a diagram illustrating this process.

Since meiosis produces sex cells with half the number of chromosomes as the parent, the sex cell must unite with another sex cell in order to produce a new cell with the correct number of chromosomes.


The Search for the Genetic Material

Understanding the mechanism of cellular division and reproduction still left the urgent questions about what material in the cell might be responsible for controlling the process and about its method of doing so.

In 1869 Friedrich Miescher, a doctor in Basel, Switzerland, in 1869 isolated a new substance in the nucleus of the human pus. He called the substance nuclein and postulated that it is present in all cells and must be concerned with heredity. Miescher's nuclein later came to be called nucleic acid. Walther Flemming, in describing the chromosomes, introduced the word chromatin to indicate what they were made of. In 1881 E. Zacharia concluded that chromatin (the stuff of chromosomes) and nuclein (nucleic acid) were the same. Thus, by the 1890's scientists were declaring that nuclein (nucleic acid) was the basic stuff determining heredity.

In the period from 1914 to 1928, geneticists, prominently Thomas Hunt Morgan at Columbia University, worked to link Mendel's Laws to a growing microscopic knowledge of the nucleus so as to produce a Chromosome Theory of Heredity. Morgan began making gene maps, applying Mendel's Laws to the hereditary material in the chromosome and suggesting that genes occurred in a linear sequence on the chromosome.

In the 1930's Hans J. Muller, a student of Morgan's, recognized that genes could be changed (or mutate) under the influence of X-rays. With artificial agents applied to the chromosomes, he could produce characteristics never seen in nature.

At the same time, other scientists, particularly P. A. T. Levene, a Russian-born chemist who worked at the Rockefeller Institute in New York, were studying intensively the chemical structure of nucleic acid. As a result of their work, the basic components were identified and the terms deoxyribonucleic acid and ribonucleic acid (DNA and RNA) came into common use. It is important to remember that at this time there was still no firm evidence that DNA and RNA were, in fact, the material basis of heredity. About that there was still considerable dispute (see below).


The Chemical Structure of the Nucleic Acids (DNA and RNA)

As a result of analytical work in the 1930's and 1940's the chemical structures of the nucleic acids became clear. The basic building block of both DNA and RNA molecules consists of three parts: a sugar ring, a phosphorus-oxygen (phosphate) bond linking one sugar ring to the ones above and below, and base, in a regularly repeating sequence. Note the fundamental parts of the structure, the entire combination of which is called a nucleotide:


When the combination of these building blocks is arranged in a sequence, the DNA model looks like this (in schematic form):

Notice that the phosphate acts as the link between the successive sugar molecules. A single DNA molecule may be made up of thousands of these nucleotides in combination, each unit linked by the phosphorus-oxygen (phosphate) combination, as if they were stacked up one on top of the other.

The same diagram can be transformed into a two-dimensional chemical diagram illustrating the relationships between the various atoms in each of the three parts of the nucleotide. To interpret such a diagram, one needs to remember that different atoms are capable of forming different numbers of bonds: hydrogen normally forms 1, oxygen 2, nitrogen 3, carbon 4, and phosphorus 5. In some cases atoms may be united by a double bond (indicated below by a double line). These bonds are, in a two-dimensional rendition, given as straight lines without regard to their angles or their lengths.


In the above diagram, C indicates carbon atoms, O oxygen atoms, P phosphorus atoms. The hydrogen atoms are the small black circles. Note that the phosphorus atom has four attached oxygens. One of them has lost a hydrogen atom (the one on the left with only one bond) and thus carries a negative charge. The sugar molecule consists of a five sided ring (a pentagon), made up of four carbon atoms and one oxygen atom, with a fifth carbon attached. Hydrogen atoms are attached to the carbon atoms.

The carbon atoms are numbered, starting with the one on the top right and moving clockwise. The numbers appear as superscripts in the above diagram. Thus, the upper phosphorus bond is attached (via the oxygen atom) to the Number 5 carbon atom of the sugar molecule (the number 5 is missing in this diagram). The lower phosphorus bond is attached, via the oxygen atom, to the Number 3 carbon atom of the sugar molecule. These phosphorus-oxygen links connect one sugar ring to the ones above and below it in the sequence.

A similar diagram of a partial molecule of RNA is identical to the above diagram of DNA (both substances are called nucleic acids), except that at the Number 2 carbon atom of the sugar the RNA has, instead of two hydrogen atoms attached, one hydrogen and one oxygen and hydrogen combination, as follows:

Since the sugar with this configuration of hydrogen, carbon, and oxygen is called ribose, the RNA molecule is called ribonucleic acid (hence RNA). Since the DNA molecule lacks an oxygen at the Number 2 carbon atom, its full name is 2-deoxyribonucleic acid (i.e., ribonucleic acid without an oxygen at the Number 2 carbon atom). Hence comes the abbreviation DNA.

Every DNA nucleotide has this same structure of phosphorus-oxygen linking an identical sugar molecule. Thus, the only variety which occurs between one nucleotide and another (and a crucial point to understand in grasping the importance of the structure of DNA) is the base which is attached to the sugar molecule.

There are four different bases, and any one of them may be attached to the Number 1 carbon in the sugar ring. These bases are Adenine, Thymine, Guanine, and Cytosine. In later diagrams these are abbreviated A, T, G, and C.

Although the basic components of the different bases are very similar, each base has a chemical composition and structure different from the others. The following two dimensional chemical diagrams illustrate these differences (the thick lines indicate double bonds):


The Nucleic Acids as the Material of Heredity

Levene, who did much of the work to sort out the basic chemistry of the nucleic acids, was unimpressed with the DNA molecule. He did not see how such a comparatively simple sequence of repeating sugars, phosphates, and bases could carry out the complicated work of the genetic material:

DNA is just a monotonous string of the four bases: adenine-guanine-thymine-cytosine and so on. Therefore, DNA is a very uninteresting molecule.

Many researchers, like Levene, thought that the genetic material was more likely to be found in proteins, very long molecules made up of amino acids and linked together in a chain much more varied than DNA.

In the 1940's Fred Griffith and Oswald Avery apparently demonstrated that DNA was the hereditary material. Avery's conclusions were published in 1944. This claim, however, was not widely accepted. Only in 1952 when Martha Chase and Alfred Hershey showed that the genetic information in a virus is contained in its DNA not in its protein was evidence for DNA as the hereditary material finally widely accepted.

Meanwhile, in what later turned out to be a crucial study, Erwin Chargaff at Columbia University in the early 1950's purified DNA and came up with Chargaff's Rules for its composition: the quantity of Bases A plus G always equals the quantity of Bases C plus T, and the quantity of Base A always equals the quantity of Base T, while the quantity of Base G always equals the quantity of Base C. At the time, these results were not seen as particularly interesting.


Watson and Crick: The Double Helix

One of the most exciting and decisive discoveries in modern science took place at Cambridge University in 1953 when a young American molecular biologist, James Watson, and a graduate student in physics, Francis Crick, together proposed a three-dimensional structure for DNA (i.e., they turned the two-dimensional chemical formula, like the diagrams above, into a three dimensional model). This discovery turned out to have an enormous impact, spurring major developments in genetics from then until the present day.

Watson had come to Cambridge because there was a group there involved in analyzing the structure of large molecules. The head of the Cavendish Laboratory, Lawrence Bragg, had, many years earlier, developed an X-ray method of analyzing structures of large molecules without degrading or substantially altering the macromolecule (3).

Max Perutz, an Austrian, had been hired to head up the Cambridge University team investigating protein structures. Francis Crick was a theoretical physicist working for his doctoral degree on the mathematics of macromolecules and their investigation by X-ray diffraction. Watson joined the Cambridge team on a hunch in 1952.

One great spur to Watson and Crick was the fact that Linus Pauling at Cal Tech, the world's foremost authority on chemical bonding, was also studying protein structures. Pauling in 1952 proposed that protein forms in helical chains and produced a model of such a chain (the alpha helix).

Watson and Crick's model, for which they were awarded the Nobel Prize in 1962, had the following features:

First, the DNA macromolecule consists of two strands of DNA running antiparallel (i.e., in parallel but one going up the other down).

Second, the two segments of DNA are joined in the centre by the matching base pairs (i.e., the series of nucleotides running up is joined, via the base pairings, at each level with the series of nucleotides running downwards) (4).

This may be represented schematically in simplified form by the following diagram (with P representing the phosphorus-oxygen link, S the sugar, and B the base).

Third, the most crucial discovery of Watson and Crick was that the base Adenine (A) could only form a bond with the base Thymine (T) and that the base Cytosine (C) could only form a bond with the base Guanine (G). This insight came to them from a consideration of Chargaff's Rules. Or, schematically put, the only possible combinations for the base pairs holding the two strands of the DNA macromolecule together were A-T, T-A, C-G, or G-C.

Hence the schematic diagram above can be made more informative by substituting particular base pairs, as follows:

Fourthly, the antiparallel strands are twisted around a common axis, so that the overall structure resembles a double helix, which can be represented schematically as follows (in the diagram the helical structures are made up of the sugar and phosphate molecules; the positions of the bases are indicated with the letters A, T, C, and G:



The importance of this three-dimensional model turned out to be enormous. Watson and Crick may have been addressing a single thorny chemical problem (How do these known molecules fit together in a three-dimensional way without violating the laws of chemical bonding?), but the model they produced not only provided a suitable chemical structure. More importantly, it suddenly offered an truly exciting explanation of two key questions concerning molecular genetics: (1) How does the hereditary material make exact copies of itself (as is required in reproduction)? and (2) How does the genetic material control the production of protein outside the nucleus (i.e., guide the growth of the organism in a particular way)?

The model of the double helix prompted some immediate research into these questions and has resulted in a staggering acceleration in our knowledge of the biochemistry of heredity.


Self-Replication of DNA

The basic structure of the DNA macromolecule suggests immediately the method by which the hereditary material can easily make identical copies of itself.

The first step occurs when the double strand separates (under the influence of enzymes), so that the bonds between the bases joining the two nucleotides at each level are opened. In this process, the hydrogen bonds which link the base pairs at each nucleotide separate, and the double helix becomes two separate strands.

The second stage occurs when the many free unattached nucleotides in the nucleus attach themselves to each of the freshly separated bases. The key mechanism is the fact that the base pairs will only unite in specific combination: A always and only with T, and C always and only with G (and vice versa). Because of this fact, the newly attached nucleotides will create with each half of the original double helix a sequence which matches exactly the old sequence, as the following diagrams illustrate.

Original double helix:

Separated helix (two disjoined halves):

Two new combinations from free nucleotides attaching to the separate bases (A with T and C with G):

Note that as a result of the process there are now two double helix macromolecules, that the sequence of bases is identical in each, and that each is identical to the sequence in the original parent molecule.

The same process can be represented in the following diagram (taken from Watson's book The Double Helix).

As a consequence of this mechanism, then, the way in which the hereditary material might chemically form an exact duplicate of itself (as in mitosis or the opening phase of meiosis) becomes a process relatively easy to picture. The crucial fact is the specificity of the base pairings which hold the double strand together.


Protein Synthesis

A second major task of the hereditary material is protein synthesis, that is, the manufacture of all the various protein structures which make up the extremely varied tissues in a developing organism (e.g., bone, muscle, nerve, skin, hair, leaf, root, stem, and so on). Proteins are made up of amino acid sequences. The sequence of amino acids in the very large macromolecules of a protein determines the structure of the protein and the nature of the living tissue formed.

Proteins are made in each cell, but not in the nucleus (where the DNA is located). Protein synthesis occurs outside the nucleus in special centres called ribosomes. Somehow, then, if DNA is to control protein synthesis, as it must if it is the genetic material determining specific phenotypical traits, there must be some way of transmitting the DNA code, the genetic information, outside the nucleus to the ribosomes.

This task is carried out by RNA, which, as we have seen above, has an identical structure to DNA except for the addition of a single oxygen atom at the Number 2 carbon atom of the sugar ring. In addition, RNA does not have the base Thymine. Instead it has the base Uracil (U). However, Uracil is specific to the base Adenine. Thus, an RNA molecule which matches itself against one strand of a DNA molecule will also have a set sequence of bases (with U or Uracil, replacing T or Thymine).

RNA functions as the messenger molecule, carrying the information about the sequence of base pairs on the DNA to the ribosomes. The process occurs as follows:

Step One

The process begins when in a portion of DNA the double strands open up, so that the matching base pairs separate.

Such a separation may occur anywhere along the paired strands of the double helix.

Step Two

RNA nucleotides from the material in the nucleus attach themselves to the disengaged bases, once again following the strict sequence of pairs: A always binds with T, U (Uracil) always bonds with A, C always bonds with G, and G always bonds with C. In the following diagram the nucleotides from the RNA are shown in the smaller font:

Step Three

The RNA strand, formed by the sequence which attaches itself to the exposed strand of the original DNA molecule, detaches itself and takes the coded sequence (the message) out of the nucleus. The structure of the RNA, that is, the sequence of the bases, is itself the message. From the following diagram, the sequence in the RNA is as follows:


This form of RNA, carrying the message from inside the nucleus to the cytoplasm outside the nucleus, is referred to as messenger RNA (or m-RNA). The m-RNA moves to one of the ribosomes (in a number of special locations in the cell outside the nucleus).

Step Four

At the ribosome the m-RNA sequence is "read off" in triplets. Each three-base sequence is coded for a different amino acid. The amino acids lie free in the cytoplasm and are brought to the ribosome by another RNA molecule, the transfer RNA (t-RNA).

Each transfer RNA has a three-base sequence which attaches to the m-RNA when the matching bases are correct. The following diagrams make is more clear.

First, a suitable t-RNA attaches itself to the first three bases on the m-RNA (reading from the left). Notice that the three base code on the t-RNA will have to match the sequence on the m-RNA.

Note in this diagram that the t-RNA, which consists of the A-A-G combination with the attached Amino Acid 1 must have the correct sequence of bases in order to pair with the first triplet on the m-RNA. Here again, the specificity of the base pairings is essential to the process. That characteristic determines the accuracy of the transmitted message.

The two amino acids will bond (that is, Amino Acid 1 will attach itself to Amino Acid 2, freeing the first t-RNA molecule to move out to collect another amino acid. In this way a chain of amino acids will be formed in accordance with the sequence of triplets on the m-RNA.

Each triplet on the m-RNA adds one more amino acid, when the evolving chain of amino acids bonds with the next one formed (in the above diagram, when Amino Acid 3 attaches itself to Amino Acid 4, releasing its t-RNA molecule coded U-U-C). This sequence of protein building stops when a coded message (a specific triplet on the m-RNA) indicates the end of the process.

The final sequence of amino acids is called a polypeptide chain, which may be a protein or which may combine with other polypeptide chains to form a protein. These chains can be extremely long, consisting of several hundred amino acid constituents.

If we think of the DNA sequence which controls the formation of this particular protein as a gene, then the number of DNA bases in the gene will be three times the number of amino acid molecules in the polypeptide chain, since each triplet of bases controls the selection of one particular amino acid molecule (5).

Note the key to the process is the original sequence of bases on the DNA. Each three-base sequence will result in the selection of a particular amino acid in the construction of a polypeptide chain in the ribosome and will thus minutely control the synthesis of protein in the cell. For example, the three-base sequence in the original DNA strand C-C-T will result in a m-RNA sequence of G-G-A, and this will accommodate the t-RNA with the triplet C-C-U.

Modern molecular biology has managed to decode these triplets. The C-C-U combination, for example, is the code for the amino acid glycine.

Since there are four bases possible at each nucleotide in the DNA and since a triplet makes up a complete code for the amino acid, there are 4 x 4 x 4 ( = 64) possible different triplet messages. This is more than sufficient for the relatively low number of amino acids which exist (20). Different combinations of bases can produce the same amino acid (i.e., a particular amino acid can have more than one triplet code).

Hence, the structure of DNA reveals that the molecule is capable of providing a flexible and accurate code, sufficiently complex to control the construction of proteins outside the nucleus. Earlier analysis which had dismissed DNA as being insufficiently complex to conduct protein synthesis missed just how much different information can be transmitted by a base pair sequence determining the arrangement of nucleotides which can attach to it.

To repeat a point made earlier, one needs to stress that the entire process depends upon the specificity of the base pairings. The fact that one base will bond with only one other base means that the genetic information transmitted throughout the process will be accurately coded by the sequence. Obviously, if any base could bond with more than one other base, the transmission of information to the ribosomes could vary considerably and the synthesis of the protein would become quite muddled.


DNA and Mutations

One other important explanatory consequence of the Watson and Crick model is that it helps to explain the physical process of mutation as some form of alteration in the normal sequence of bases. Such damage may be chemical or physical, but it will result in some altered sequence being passed into the sex cells and thus transmitted to the embryo.

A very small change in the message may have minor results in the organism, or the effects might be major. Sickle cell anemia, for example, which can be a lethal disease, is the result of a malfunctioning in the formation of a single protein in the construction of red blood cells.

Mutations, then, we can best understand as garbled messages. For the most part, the changes brought about by these alterations will be deleterious, since they will result in abnormal protein formation. Occasionally, however, such a change might produce a useful variation, of the sort Darwin saw as an essential component in his theory of natural selection.


Some Further Implications of DNA

Every cell of the organism's body carries DNA with the same coded sequence unique to that individual. Hence the analysis of DNA has become a powerful tool for identification of particular people, a key technique in modern forensic science. In the past few years, the use of DNA in the law courts has become increasingly common, as the reliability of the DNA tests has improved.

At present, scientists working on the genome project are seeking to locate every human gene in the sequence of DNA material in the human chromosomes. When complete, this knowledge will provide an unparalleled insight into the factors which control all heritable aspects of human biology.

The extraordinary characteristics of DNA are raising important ethical questions. For we are at the threshold of being able to identify the precise locations of a great many heritable characteristics and to copy or alter these. In the next few years, for example, scientists hope to locate the gene responsible for aging. An ability to alter the effects of such a gene might well extend human life significantly, a development with enormously important social and economic consequences.

Soon we are going to have to deal with demands for samples of our DNA from potential employers and insurance companies. Perhaps educational institutions and police forces will also want access to genetic information from our DNA. These possibilities, so remote only a few years ago, are now raising all sorts of moral and legal issues.

What makes some of the legal and moral issues surrounding DNA research so complex is that alterations we make in our own or someone else's DNA are heritable. We are thus irreversibly tampering with the genetic inheritance of future generations, perhaps often in ways we do not fully understand.


Postscript: Some DNA Developments After Watson and Crick

Without attempting to bring the history of DNA research up to the present, we can consider very briefly some of the developments after Watson and Crick's breakthrough discovery. Some recent research has suggested that the DNA model might not be quite so stable as Watson and Crick first assumed and, thus, that hitherto unexpected processes occur which complicate the full account of heredity.

For example, the work of geneticist Barbara McClintock (Nobel Laureate in 1983), among others, revealed the existence of "jumping genes" or transposons (for transposable genetic elements). These are small sections of DNA which can move within a single chromosome or even from one chromosome to another. The origin of these transposons is unclear. Some scientists have suggested that they may be viruses. But, whatever the cause, transposons obviously introduce new complexities since, by altering the sequence of the base pairs in a DNA double helix, they will alter the accuracy of DNA replication and protein synthesis.

Other researchers have suggested that, in some cases, genetic material can even pass from one species to another, for example, by means of an insect which ingests DNA from one form and deposits it in another. These controversial possibilities obviously challenged the orthodox view of the stable and reliable process by which DNA controls heredity.

Central to Darwinian evolution, as we have seen in Section Three, is the idea that variations are spontaneously produced. The idea of mutations in the DNA provided a molecular basis for such a hypothesis. The presence of transposons or transferred DNA would obviously suggest a variety of ways in which mutations might occur much more rapidly than hitherto suspected.

Particularly controversial in these developments is the notion that the environment may play a vital role in genetic development. It has long been known that radiation and certain chemicals have an effect on mutation rates. However, research has now suggested that certain environmental stresses may induce very specific mutations.

This hypothesis has obviously given new life to the old idea of the inheritance of acquired characteristics. This doctrine was, so many thought, dealt a death blow by the notion that the genetic material is unaffected by the body's experiences, since the germ cells are isolated from normal body cells. However, new research is reviving a modern form of an ancient heresy.

None of these developments amounts to a discrediting the orthodox model of DNA and the processes of replication, reproduction, and protein synthesis. Thus, the extraordinary explanatory power of that model is still at the heart of modern molecular genetics. However, the processes involved are turning out, as usual, to be more dynamic and complex than the original union of Darwinian and Mendelian theories with Watson's and Crick's model indicated.


Notes to Section Five

(1) A cross of the sort we have just considered, in which one of the parents is a homozygous recessive, is called a test cross, because if the genotype of the homozygous recessive parent is known (from its phenotype), then from the ratios in the offspring one can infer the genotype of the other parent. In this way, the genotype of a plant of unknown origin can be discovered. [Back to text]

(2) Different species have different numbers of chromosomes, but typically the chromosomes in any cell form pairs defined by a similar shape. Human beings have 46 chromosomes (23 pairs), hogs 28 (19 pairs), garden peas 14 (7 pairs), and so on. [Back to text]

(3) Sir William Henry Bragg (1862-1942) and his son Sir William Lawrence Bragg (1890-1971) from 1912 onwards pioneered the use of X-ray diffraction to study the structure of large molecules. Their work earned the father-son combination the Nobel Prize in 1915. The most intriguing father-son Nobel laureates were Joseph J. Thomson and George Thomson. The former won the prize in 1906 for demonstrating that the electron was a particle; the latter in 1937 for demonstrating that it was a wave. [Back to text]

(4) This insight was the key to the discovery, since the most puzzling question concerned the nature of the union between the different strands of the DNA. How many strands were there in the macromolecule, and how were they held together? Watson and Crick decided to experiment with the idea that there were two strands. The model for the bonding between the two strands came from the sudden realization that the Adenine-Thymine match had the same physical dimensions as the Guanine-Cytosine match. These pairs could be held together by hydrogen bonds, special intermolecular bonds (weaker than interatomic bonds). A hydrogen bond exists between hydrogen and some relatively small atoms and serves to link molecules together (as in water, for example, where one molecule of H2O forms a hydrogen bond with another molecule; this phenomenon causes, among other things, the relatively high boiling point of water). The two-dimensional chemical diagram of the appropriate base pairs, a scheme which became the blueprint for the three dimensional model, is represented in the diagram below. The hydrogen bonds are indicated by dotted lines. Note that in this diagram the double bonds between certain atoms are not shown as double but as thick black lines):


[Back to text]

(5) The chromosome consists of a very long tightly folded strand of DNA, and the genes are thus the sequences of bases along this single strand. An animal cell contains a great deal of DNA which does not appear to have any particular function in protein synthesis. This so-called junk DNA makes up approximately 90 percent of the DNA in an animal cell. A proposal has been made that this junk DNA duplicates itself without any apparent benefit to the organism and that, therefore, the function of the organism may be simply to permit the duplication of selfish DNA. The function of life, thus, is to produce sites for the creation of DNA; human beings are just survival sites for DNA. See Richard Dawkins, The Selfish Gene.


Appendix to Section Five

The following diagrams and commentary indicate the major differences between the two forms of cellular reproduction, mitosis and meiosis. The important point to notice is that in mitosis, the original cell divides into two new cells, each with the same component of chromosomes identical to the parent. In meiosis, by contrast, the original cell ends up producing sex cells, each with one half of the number of chromosomes of the original parent and with different combinations in the sex cells. For a new organism to appear through meiosis, of course, the sex cells would have to combine, so that new organism had a full complement of the chromosome pairs. In this diagram, the original parent cells have three pairs of chromosomes, six separate chromosomes in all. One member of the original chromosome pair is shaded in; the other is not. The members of each pair have roughly the same shape, but they may carry different genes. Thus, they are not identical in the genetic message they carry.


In the orignal cell (in the diagram on the left below) there are three pairs of chromosomes (the pairs are indicated by similar shapes. In the diagram the similar pairs have the same number. During the first stage (illustrated in the right hand diagram below), each chromosome makes an identical copy of itself (the two parts remain attached at the centre).

In the second stage, the pairs of chromosomes line up at the centre of the cell in an approximate straight line.

The joined members of each replicated pair now separate, and each member of the pair goes to a different end of the cell. The cell then divides to form two cells. Notice that the complements of chromosomes in the two final cells are identical to each other and to the original parent cell:


In the original cell here there are still three pairs of chromosomes. In the first step of Meiosis, each chromosome, as in mitosis, replicates itself. But then in meiosis, the new pair of chromosomes lines up with the corresponding pair, forming a tetrad (a foursome) of similar chromosomes). In the diagrams below, the original cell is on the left. On the right, the chromosomes have divided and aligned themselves with a corresponding pair:

The cell now divides in two, with the originally similar pairs separating (each taking with it the replicated version of itself):

This division thus produces to cells with three pairs of chromosomes each, but the pairs are not the same as in the original cell.

At the second meiotic division, the joined chromosomes now separate into different cells, each with half the total number of chromosomes (one of each pair, but no pairs):

These cells are the sex cells, each with half the required number of chromosomes. Notice that they are not all the same. The new organism will be formed in the union between two sex cells, one from each parent, so that the new organism will begin with the original number of chromosomes (three pairs).



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