Chapter 2

The molecular, vegetative animalcule

Throughout the centuries, yeast has been an important commodity in domestic and industrial life. Consequently, its fermenting ability has been the focus of many different hypotheses and paradigm shifts. Fermentation was once thought to be the consequence of a chemical reaction by some kind of substance and never imagined to be the metabolic activity of a living organism.  During the Biblical era, due to lack of knowledge, there would have been no conception that microscopic bugs were responsible for fermentation.

Wine merchants display their yeast by-products in Marseille. Image:2whoitmayconcern

Yeasts are abundant in the environment, especially in the soil where they are transferred, by insects or other means, on to the skins of fruit and animals, including humans. There exists a wide variety of naturally occurring yeasts, from those that cause fungal infections (Candida spp.) to industrially important species used in baking and wine production (Saccharomyces spp.). Yeast belongs to the kingdom Fungi and division Ascomycota, derived from the Greek for ascus meaning “sac” or “wineskin”, a name inspired by their characteristic spore cases. In recent times, it has become a major player in biological research and is now one of the most studied organisms on Earth. It was the first eukaryote to have a fully sequenced genome, the majority of its genes have been researched and functionally analysed and many of these genes have analogues in other multicellular organisms. It is, therefore, possible to study molecular processes from mammalian systems within a unicellular, model eukaryote,  making yeast a favourable alternative to animal model systems. Furthermore, the simplicity of its life cycle and the ease in which it is cultured has made it a valuable resource in medical and biotechnological applications. Yeast has make a great impact on 21st century anthropology, which has influenced social behaviour and scientific research. Humanity would most probably have evolved differently if this organism ceased to exist.

The term leaven originates from the latin word levere, the French equivalent being the noun levure meaning to rise. The English term yeast, probably originates from the Greek term for fermenting which was zestos. Derivatives from later European influences resulted in the medieval English terms zeest, which eventually became yest. Leaven when mentioned in the  Bible is probably used to describe fermented dough or sourdough. So called  because, along with yeast cells, it contained acidifying bacteria that produce lactic and acetic acid, giving the bread a unique tangy flavour. Natural microbial contaminants of milled grains and fruit were probably used for alcohol production and leavening in the Biblical era. This microbial flora would have included wild yeasts that were naturally found on cultivated crops. In just one hundred grams of flour there are up to ten billion microbes of these about thirty thousand are natural yeasts.

The historical steps taken to elucidate the metabolic processes and characteristics associated with yeast and fermentation follow an intriguing journey of scientific discovery that spanned nearly four centuries. A journey that commenced with the discovery of microscopy in the 17th century and is now meandering through the complex science of molecular biology in the 21st century. This chapter looks at the history of Science in relation to the discovery of yeast, exploring how Biblical text has influenced the principles and directions of scientific investigation, for instance, the Biblical version of creation greatly differs from scientific theories of evolution. The ensuing debates this creates typically illustrates divides that exist between religious and scientific theory.

It’s generally accepted that for an enquiry to be viewed as scientific it must involve the gathering of observable, empirical and measurable evidence. The scientific method involves the collection of this data to formulate and test hypotheses. A number of proven hypotheses, from various published and recorded sources, can then be strung together in a wider context to form theories. The practice of distributing and therefore sharing data is often referred to as full disclosure as it permits evidence to be scrutinised by others thereby allowing the interpretation of results to be challenged.

The Bible indicates that a divine being must have in some way directed the creation of Life in order to account for its existence on Earth and complexity. An understandable viewpoint, as even a simple single-celled microscopic organism such as yeast is an intricate living structure encoded by over 6000 genes. It’s difficult to visualise where DNA originated and how complexity could have happened gradually over time. The 21st century scientific method would not defend the concept of human origin as presented in the Bible as it’s largely based on theories without the support of tangible evidence. Although the ancient scientific method may well have defended it when it was first written, given the lack of scientific research at the time. Ultimately though, it is impossible for anyone living in the 21st century to know, with any certainty, how the World was created without use of a time-machine.  There is certainly no compelling reason why there should be Life on Earth, so various scientific and theological arguments must be considered before determinate conclusions are reached.

The Creation of Adam. Michelangelo, c1511

Based on archaeological evidence, it is thought that the Earth was created approximately 4.6 billion years ago and that life originated in the form of bacteria 3.8 billion years ago. Multicellular organisms, in various microscopic forms, are thought to have first existed about a billion years ago and are thought to have given rise to simple animals, such as sponges and anemones. More complex forms of animals started to appear 550 million years ago (mya). Arthropods are thought to have appeared first, followed by fish, land plants, insects, amphibians, reptiles, mammals, birds and flowering plants respectively. The first primates that resembled humans arrived on the scene 2.5 mya with humans resembling the present form arriving just 200,000 years ago. Neanderthals disappeared fairly recently, only 25,000 years ago. A short time in evolutionary terms, but still a vast time-scale  for a human with an average lifespan of 62.5 years to visualise. When the Bible was written human lifespan was only 28 years.

The Bible condenses the time-scale that humans arrived on earth within the space of a few days. On the first day God created light which was divided into day and night. The next day, water were divided from the sky and earth was divided into land and sea. It was not until the third day that Life first appeared when God created vegetation. During the fourth day planets and stars were added with time being divided into seasons, days and years. On the fifth day God creates birds and sea creatures,  commanding them to be fruitful and multiply. Finally, on the sixth day he adds wild beasts, livestock and reptiles, creating humanity in his own “image”. The humans are instructed to be fruitful, multiply, fill the earth and subdue it. In the book of Genesis the Bible draws a distinction between animals and humans, with emphasis on human superiority:

God said, ‘Let us make humans in our own image, in the likeness of ourselves, and let them be masters of the fish of the sea, the birds of heaven, the cattle, all the wild animals and all the creatures that creep along the ground.’
[Gen 1. 26]

There are a number of anomalies in the account of creation within the Bible. We now know that the stars and planets must have existed before the introduction of life.  Seasons would  prerequisite the existence of vegetation. We are also aware that reptiles existed before mammalian species on account of dinosaur fossil records. These restrictions in knowledge also resulted in no reference to the creation of microbes within Genesis, but there are several references to disease and of fermentation processes throughout the Bible.

An early reptilian Apatosaurus louisae skeleton in the Carnegie Museum.
Image: Tadek Kurpaski

Ancient civilisations would be completely unaware of the causes to many diseases. In general, injuries resulting from accidents or animal bites were understood and treated by various dressings, including sesame oil, wine and balsams, some of which contained naturally occurring antibiotics. In contrast, the mechanisms behind diseases involving parasites or microbes were a complete mystery and thought to have been placed in the body by evil forces. Consequently, these illnesses were treated by making the body hostile to the invader through intense cleansing with various noxious substances. Diseases were largely viewed as a punishment brought through sin or disobedience:

The Lord said, ‘If you will not obey my commands, you will be punished. If you refuse to obey my laws and commands and break the covenant I have made with you, I will punish you. I will bring disaster on you- incurable diseases and fevers that will make you blind and cause your life to waste away.
[Lev 26.14-16]

As microbes where viewed as some kind of mysterious, unexplained power they were also used to represent the spread of sin and corruption. For instance, in his first letter to the Corinthians, Paul the Apostle uses the permeating character of leaven to illustrate the spreading of corruption within a community:

You know the saying, “A little leaven makes the whole batch of dough rise.” You must remove the old leaven of sin so that you will be entirely pure. Then you will be like a new batch of dough with no leaven, as indeed I know that you actually are. For our Passover Festival is ready, now that Christ, our Passover lamb, has been sacrificed. Let us celebrate our Passover, then, not with bread having the old leaven of sin and wickedness, but with the bread that has no leaven, the bread of purity and truth.
[1 Cor. 5.6-9]

Fermentation procedures and the art of making leavened bread was first introduced by the Egyptians over 4000 years ago. In ancient Egyptbrewing and baking were practiced together on the same premises. Wooden and plaster models depicting Egyptians working in a brewery and bakery have been recovered from a tomb dated around 1975 BC during the reign of Amenemhat I. Egyptian hieroglyphs that show pictures of dough rising next to bread ovens have also been found. The Egyptians were, therefore, aware that both processes used the same substance. To the Egyptians, bread was an important commodity used as a type of currency for trading and for the payment of services. In fact, the workers who built the pyramids were believed to have been paid in bread. Bread was also used to pay homage to Osiris the God of grain. The Egyptians believed that Osiris had given them the gift of leavened bread to make it lighter to carry, especially in the journey to the afterlife.

A funerary model of a bakery and brewery, from Thebes circa 2000 B.C.
Image: Keith Schengili-Roberts.

In contrast to the Egyptians who revered fermented dough, the ancient Palestinians were extremely suspicious of it. Perhaps this could be due to the different methods by which the bread was leavened. Palestinians would reserve a piece of leavened dough from a previous baking to make the next batch of bread. This dough could easily have been contaminated by harmful microbes which may not have been completely destroyed by the baking processes. If a person died all leaven was thrown out of the house and from all neighbouring houses because Palestinians thought that it may have contributed in some way to the individual’s demise, they believed that the angel of death may have thrust his sword into it.

In Britain during the 15th century, as in ancient Egypt, brewing also took place on the premises where bread was baked. The thick layer of dormant yeast cells that sank to the bottom of the brewing or wine vessel was usually referred to as the lees, while froth from the top of beer was known as barm. Barm from a good batch of beer would be reused to make more beer and to ferment bread dough. Barm, the brewer’s equivalent of leaven, used to be referred to as Godisgoode because it was thought to be a gift from God. Yeast used in brewing and baking seemed to be received in a different manner to leaven that was used to make sourdough. In fact, during the 17th century the Paris Faculty of Medicine tried to ban leaven because in the New Testament St. Paul had signified that it was a substance that denoted corruption.

So it seems that fermentation generated through leaven was not viewed in the same way or as a similar process to the fermentation that produced wine. It is clear from passages in the Bible that leaven is used figuratively to symbolise the permeating influence of certain types of human behaviour, especially corruption. Traditionally unleavened bread is used to symbolise the purity of Christ’s body whereas wine symbolises the blood of Christ. This is not without some irony, as wine is made in a similar process and perhaps more likely to lead to acts of sin and corruption when consumed than is bread. Indeed, some religions do recognise this and at the beginning of the 20th century, alcohol became prohibited for a time in a number of Nordic countries and North America due to Protestant led objections. Alcohol is also prohibited in some countries that follow Islamic laws. The contradictory views relating to fermentation in wine and bread will be discussed at greater length in a later chapter.

Although its meaning still may remain a mystery, Life in itself is hard work and requires a lot of energy. It’s now well established that the initial source of this energy is provided by the Sun in the form of light, which is absorbed by a photosensitive pigment called chlorophyll found in plants and other photosynthetic organisms. The energy is then trapped in molecules of glucose, a carbohydrate compound composed by a series of chemical reactions involving carbon dioxide and water. Plant consumers then transfer the energy stored within the glucose carbon source along the food chain. When the glucose is broken down it produces adenosine triphosphate (ATP), the compound required to release the energy that powers most cellular functions. The most efficient way for an organism to synthesise ATP, thereby releasing energy, is by an oxygen requiring process called cellular respiration. In humans, oxygen is transferred into the body from the surrounding atmosphere by respiring, it is extracted from air in the lungs by haemoglobin, which is then circulated around the system in the blood. As it contains the oxygen required for anaerobic energy production humans cannot survive without blood. Blood was, therefore, considered of extreme importance in the Biblical era, as it was the substance thought to contain an animal’s character and life force.

Chloroplasts visible in the cells of Thyme-moss.
Image: Kristian Peters.

Every living thing is a package of consumable energy, but not every organism can boast a sophisticated circulatory system that enables cellular respiration. Microbes and other lower life forms have to adopt fairly basic means to generate their energy. The energy generating processes of yeast produces by-products that have been exploited by human civilisations for centuries. One of the ways yeast requires its solar produced energy is by fermentation; a biochemical transformation that converts carbon sources such as glucose or sucrose into energy, producing alcohol and giving off carbon dioxide in the process.

Fermentation is not as efficient in producing ATP as aerobic respiration, but enables yeast to convert glucose into energy without the aid of oxygen. Scientifically defined, fermentation is a catabolic process that makes a limited amount of ATP from glucose without an electron chain (supplied by oxygen) producing a characteristic end product, such as, ethyl alcohol or lactic acids. During fermentation, yeast not only generates energy from the carbon source but it also breaks it down into an industrially and socially important commodity, namely alcohol. Yeast also has the ability to perform aerobic respiration to give off carbon dioxide, but this process does not produce alcohol. Being able to live with or without oxygen is undoubtedly ecologically advantageous to this microbe. Certainly explaining why it inhabited the Earth long before humans did and why it will still be here long after our fragile species has disappeared.

The mysteries surrounding fermentation were once, and to some extent still are, the subject of great scientific endeavour. It was mainly assumed that the reaction was chemically induced because investigators were unaware that miniscule creatures unseen by the human eye could exist. The yeast commercially responsible for transforming carbohydrate rich ingredients, like flour and fruit juice, into loaves of bread or alcoholic drinks is predominately Saccharomyces cerevisiae also known as baker’s, brewer’s or budding yeast. When sugar is plentiful the metabolic route that this type of yeast chooses is fermentation. During fermentation cells multiply rapidly by budding, when all carbon resources are depleted cells either enter a stationary phase of non-division or produce spores. Budding yeasts can also reproduce sexually. Adjacent cells of opposing mating types fuse together, in response to pheromones, by forming protruded structures called shmoos. The end product is a slightly larger round diploid cell that contains two sets of chromosomes; a method of introducing genetic variability into the cell. This diploid cell can either continue budding or enter meiosis to produce four ascospores.

Performing meiosis to generate ascospores is a risky business to budding yeast as it has to temporarily stop increasing population size. Therefore, it only faces this challenge when nutrients are low and its survival is threatened. Ascospores  and quiescent cells are resistant to stress and can remain dormant for several months, years, decades or even centuries. While dormant they lie at the bottom of the fermenting vessel to form a thick layer of pale brown sediment. Some cells or spores die, but many retain the ability to begin dividing again when conditions improve, for instance when more sugar becomes available. This mode of survival allows them to remain viable in the face of adversity.  They are well suited to harsh industrial conditions and, also,  the arid  environment that forms the backdrop of the Biblical Testaments.

Like other simple life forms, yeasts such as Saccharomyces cerevisiae are fully self-contained within one microscopic cell. S. cerevisiae cells are round and, providing they are well nourished with carbohydrates, spend most of their life cycle reproducing vegetatively by growing buds. Buds separate from the parental cell when they reach a certain size in order to follow an individual pattern of growth. Upon maturity these too can start budding; each cell produces about thirty progeny. The loss of the bud leaves a scar on the parental cell that can be visualised with fluorescent dyes or electron microscopic techniques. The pattern and number of scars can reveal a lot about the condition and age of the yeast cell. Some yeasts do not reproduce by budding, but by forming a cross-wall rather like the mitotic cell division observed in higher eukaryotes. Schizosaccharomyces pombe or fission yeast is an example of this. It divides in a similar way to human cells and therefore is used as a model system to study many human diseases, especially cancer.

Yeast cells stained with calcofluor-white dye and observed under a fluorescent microscope. Newly budded cells take up less dye. Small rings on cell surfaces are budding scars. Image: 2whoitmayconcern

The concept that living organisms produced leaven wasn’t seriously considered until Erxleben, in 1818, proposed that leaven and barm consisted of living vegetative organisms responsible for fermentation. Prior to this, in 1680, Leeuwenhoek, with his early microscope, observed yeast cells in fermenting beer. He referred to most of these single-celled creatures as animalcules because they were believed to be immature forms of larger animals. These first observations of microscopic cells were not further investigated for another century. Leeuwenhoek’s contemporaries were largely preoccupied with the argument centred on spontaneous generation, a belief that animals could materialise from other living or mineral things. Before the groundbreaking experiments by Louis Pasteur in the mid 19th Century, which showed that excluding particles from sterile broth prevented contamination by microbes, many theorists believed in spontaneous generation.

Different theories and speculations concerning the creation of organic things occur in every religion, as most feel that the complexity of the natural world could not have arisen by chance. Many investigators began to challenge the image of creation as depicted in the Bible. Perhaps the most compelling of these arguments was the theory of natural selection presented by Charles Darwin in the mid 19th century. His book entitled the Origin of Species created tensions between the church and science because it questioned a popular and largely accepted image of creation.

Religious devotees perhaps saw science as being not only a threat to their faith but to their social acceptance and respect. Science innovation threatened to ridicule the basis of their fundamental beliefs and values. It is, therefore, understandable that there was a need to retain Biblical teachings in some form. In the 19th century, the paradigm shift that was rapidly evolving science was too extreme to evoke an equally rapid change in religious faith. In order to fully commit to a belief requires a great deal of conviction. This conviction can be impenetrable leading believers to imagine that an evil being is responsible for any deviancy from a steadfast commitment. Any element of uncertainty in religious belief seems to lead to the evolution of new religious theories to give meaning to situations that are too difficult to comprehend. In the New Testament an interesting method is used to quell sceptics and doubting critics. Individuals who questioned the ideals proposed by Jesus were thought to be influenced by the devil:

 After spending forty days and nights without food, Jesus was hungry. Then the devil came to him and said, “If you are God’s Son, order these stones to turn into bread.”
But Jesus answered, “The scripture, says, Man cannot live on bread alone, but needs every word that God speaks.”
[Matt. 4.1-11; MK. 1.12-13; Lk. 4.1-13]

Christ is tempted by the Devil. Mosaic from Monreale Cathedral.
Image: Sibeaster

This  not only discourages doubt from those with religious faith but also prevents others from persuading them away from their convictions. It is not surprising that scientific hypotheses that question religious beliefs are subject to contention.

Through research by evolutionary biologists we have now discovered that humans are more closely related to leaven than early civilisations could have imagined. Many of the human proteins involved in the fundamental functions of the cell, such as DNA replication, are conserved in other organisms, even in yeast and bacteria. In fact, some human DNA can be expressed in bacteria and yeast to produce protein. Proteins that are homologous in different species are known as orthologues. DNA processing proteins, such as Polymerases, are often found in this category. For this reason, the mechanisms of mutation in mammalian cells can be studied equally as well in yeast cells.

The big question is, why did all yeast cells not evolve into complex multicellular organisms like humans or even plants? Why are there still primitive cells like bacteria? As George Carlin, so eloquently put it:

If man evolved from monkeys and apes, why do we still have monkeys and apes?

The answer is that organisms are continually evolving, they are constantly finding new ways to preserve or obtain energy, therefore, new species could arise at any time and, as a consequence, there must always be lower and higher life forms. It is the diversity of Life that encourages adaptations. Through a constant competition to obtain energy, diversity provides the resources on which selection can act. For instance, a group of higher species A are infected by lower species B and some are killed. Some A species were able to survive because they have a mutation that makes them more resistant to species B but it also makes them less resistant to physical stress C. It flourishes until it encounters C. As consequence of  this cycle of adaptations, species A no longer resembles its original form and becomes subspecies D. So evolution depends heavily on a changing environment and the ability of an organism to adapt.  This allows the evolutionary route to continue in a perpetual cycle of various adaptations until many species of organisms evolve. Darwin called this process natural selection or the preservation of favoured races in the struggle for life:

If under changing conditions of life organic beings present individual differences in almost every part of their structure, and this cannot be disputed; if there be, owing to their geometrical rate of increase, a severe struggle for life at some age, season, or year, and this certainly cannot be disputed; then, considering the infinite complexity of the relations of all organic beings to each other and to their conditions of life, causing an infinite diversity in structure, constitution, and habits, to be advantageous to them, it would be a most extraordinary fact if no variations had ever occurred useful to each being’s own welfare, in the same manner as so many variations have occurred useful to man. But if variations useful to any organic being ever do occur, assuredly individuals thus characterised will have the best chance of being preserved in the struggle for life; and from the strong principle of inheritance, these will tend to produce offspring similarly characterised. This principle of preservation, or the survival of the fittest, I have called Natural Selection. It leads to the improvement of each creature in relation to its organic or inorganic conditions of life; and consequently, in most cases, to what must be regarded as an advance in organisation. Nevertheless, low and simple forms will endure if well fitted for their simple conditions of life.

[Darwin, 1859]

Evolutionary selection relies on the chance that an adaptation will occur and that it will improve the fitness of a particular organism. This directly conflicts with early Christian beliefs that organisms do not evolve and remain as they were originally conceived.

Gradual evolution of 21st cent humans.
A schematic representation by José-manuel Benitos.

The discovery of humans at various stages of evolution has diminished the concept that humans were created in their current form or generated spontaneously. Humans are thought to have evolved from primates that first appeared around 5-8 mya and share many similar characteristics to chimpanzees. In fact, 98% of chimpanzee DNA is homologous to human, but one of the greatest anatomical differences is in brain size. The chimpanzee’s brain weighs less than half a kilo while a human brain weighs around three times that much. Archaeological evidence suggests that three or four hominid species lived in the African continent several million years ago. Currently, one of the earliest of these is known as a species called Ardipithecus ramidus.  Modern humans, Homo sapiens are thought to descend from Australopithecus anamensisAustralopithecus afarensisHomo habilis and Homo erectus. There are other early hominids that are thought to be more distantly related: Australopithecus africanuParanthropus aethiopicusParanthropus boisei and Paranthropus robustus The hominid that began to be dispersed around the globe was the bipedal Homo erectus. This species is thought to have evolved into Homo sapiens only 200,000 years ago, a blink of an eye in evolutionary terms.

Common arguments by creationists against evolution theory are if humans evolved from apes why have apes not evolved and how is it possible that life on Earth is so diverse even in similar habitats?  One explanation could be that even though life looks diverse all of it is encoded from just four nucleotides.

Nucleotides play an important role in several biological functions, including metabolism, but they are mostly known for being the base units, thymine (t), adenine (a), guanine (g) and cytosine (c), in DNA. When arranged into predetermined DNA sequences, nucleotides can have very similar patterns even in organisms that appear morphologically different.  In fact, although humans may seem to look very different from chimpanzees there is only a 1.23% difference in nucleotide divergence.

Science has become an ever-advancing, voracious creature, forever trying to satisfy a relentless appetite of knowledge and discovery. Whereas, religion treads warily, fearful of disrupting the balances of nature that are governed by laws preceding civilised life. Like a badly matched couple, these two different entities seem to have drifted further apart, but at one time they were closely entwined. Theologians were once dedicated to deciphering God’s laws. They believed that unravelling these may reveal why life exists and to what purpose it served.  For instance, in the 19th century the Augustinian friar Gregor Mendel was equally committed to religious endeavour as he was to scientific investigation. By breeding and statistically recording the colour and shape of peas, Mendel was foremost in discovering that characteristic traits were inherited. He was the first to record genetic variation. It is this same variation that enables some members of a species to follow different evolutionary routes.

Advances in science at the molecular level have further reinforced Mendel’s experimental work. The mechanisms of molecular evolution attribute the blueprint of characteristic traits to nucleotide code which, when inherited by offspring, leads to the generation of tissues that cumulatively construct a new individual with parental characteristics. Genetic diversity exists to strengthen the gene pool, allowing the plasticity needed to evolve. If there were no nucleotide diversity between individuals there may be no life, as variation gives organisms the ability to survive changing environments.

Comparing the nucleotide variation in protein encoding genes from a variety of organisms reveals a distinct evolutionary history. This complex science, known broadly as Molecular Phylogenetics, can involve the comparison of huge amounts of electronic data, sometimes reaching many terabytes in volume.  The human genome alone is composed of over three billion nucleotide pairs that contain thousands of repeated regions and single-nucleotide variations or polymorphisms, also known as SNPs. Molecular phylogenetics allows species to be characterised into orders and families not only through physical similarity but also through the arrangement of their nucleotides.

Recent developments in faster high-throughput DNA sequencing techniques, whereby hundreds of DNA strands are sequenced simultaneously on microchips, have enabled whole genomes of organisms to be sequenced at a fraction of the time and cost.  The human genome sequence was completed in 2003 using older methods developed by Sanger in 1980. It took more than 3,000 scientists 13 years to complete and cost of over three billion dollars.  Currently a human genome can be sequenced within weeks for under fifty thousand dollars. Consequently, nucleotide pattern variations from thousands of genomes in a large number of species are being compared at an accelerated rate using SNPs and other molecular markers to further refine theories of evolution. A major focus of these studies in human genomes is the identification of variation that gives rise to genetic diseases such as cancer.  If a small variation in the usual DNA of the human genome can lead to a disease altering the survival of an individual then, understandably, it could give raise to variation that can increase survival too. In the beginning perhaps God created nucleotides, the rest is evolutionary history.

The application of molecular archaeology has largely denounced the explanation of creation as proposed by Babylonian type theories recorded in the Old Testament. Several views held at this time have been dispelled by Science. For instance, rain was thought to fall from seas separated from the Earth by a dome structure which the Creator called sky:

Then God commanded, “let there be a dome to divide the water and keep it in two separate places”- and it was done. So God made a dome, and it separated the water under it from the water above it. He named the dome “sky”.
[Gen. 1, 6-7]

Birds and fish were created on the fourth day, while animal life on Earth was created on the fifth. On the sixth day the Creator placed humans on Earth to control the animals that existed in the land and sea. The order in which the animals appear seems to be fairly logical, fish and birds being further down the food chain than the higher animals with humans at the very top. There is no mention of bacteria and parasites. Evolutionary speaking they should appear before the birds and fish in day three.

So God made a dome, and it separated the water under it from the water above it. He named the dome “sky”.
Woodcut by Julius Schnorr von Carolsfeld, 1860

Theories involving the spontaneous generation of living beings were widely accepted for centuries. The Greek philosophers Plato and Aristotle in the 4th century BC held views that contradicted a gradual evolution of life forms. Plato argued that there were two worlds: one was real the other was imaginary. The variations that were present in plants and animals were merely imperfect illusions of an already perfect form. This philosophy was known as idealism or essentialism and ruled out evolution as organisms were already in the form that they were destined to become. Aristotle recognised that organisms could be arranged according to complexity this is often referred to as a scale of nature or scala naturae. He believed that there was an organism at each scale; species were fixed and no evolution occurred. This view persisted for 2000 years and was widely adopted by natural theologists who thought that the Creator had designed each species for a specific purpose.

Linnaeus in the 18th century adopted a filing system for all these species. He was a natural theologian who claimed that he had developed the classification system in order to reveal God’s plan, he clarifies this using the phrase:

Deus creavit, Linnaeus disposuit; God creates, Linnaeus arranges.

During the nineteenth century yeasts were thought to be part of the plant kingdom in the division of Thallophyta because they lacked true roots, stems and leaves. They were eventually classified as fungi because they do not contain chlorophyll or rely on photosynthesis to create energy. Instead, they live a parasitic or saprophytic existence, living off the carbon sources supplied by other organisms. Like other species of fungi, yeast can also form spores.

Jean Baptiste Lamarck was one of the first biologists who proposed a theory of evolution in 1809. As curator of the invertebrate collection in the Natural History Museum in Paris, he observed that insects changed gradually over the centuries. He thought that microscopic creatures were at the bottom of evolution and generated spontaneously from inanimate material. Lamarck felt that creatures evolved towards greater complexity and that higher organisms were aiming towards perfection to become completely adapted to their environment. He proposed that organisms adapted continually thereby some aspects of their physiology grew stronger while others disappeared and that these lifetime improvements could be passed on to their offspring. Lamarck’s hypotheses that inheritable traits could be acquired during a species lifetime have been largely disproved, but his views were revolutionary; he implied that species evolved and that they were not fixed. Darwin’s theory of natural selection was to directly challenge the current viewpoint of fixed design. Natural, or should it be supernatural, theology, was the accepted way of thinking and doing science, each species being allocated a specific niche by a supernatural being.

At an early age Darwin was already a keen naturalist and obtained a degree in theology at Christ College Cambridge where he became the protégé of the botanist Professor Henslow. When he was 22 he joined the crew of  The Beagle, a survey ship whose mission was to chart the South American coastline. During this voyage he collected flora and fauna while other members of the crew surveyed the coast. He was particularly interested in the diversity of species that were present in the Galapagos Islands and recovered over a dozen different types of Finch. Darwin began to understand through his own work, and that of others, that the origin of new species arose from a distant ancestor by the gradual accumulation of adaptations. He saw this within the beaks of the finches that he had collected from the Galapagos Islands. Each Finch had a specialised beak that was adapted to forage for the type of food found on its island of origin. This was visible evidence that selection through environmental factors could contribute to speciation.

Darwin’s drawings of beak variation in Finch species.

Darwin was reluctant to introduce his theories publicly because, being a theologian, he was aware of the controversy that this would cause. He wrote an essay on the origin of species in 1844 that remained unpublished until 1858 when extracts from it were presented to the Linnaean Society. In the same year another naturalist, Alfred Wallace published a paper on the evolution of new species. This prompted Darwin to complete his book the Origin of Species, which was published the following year. The Origin of Species presented a strong argument for natural selection through scientific evidence and became adopted by evolutionists as the primary text on the subject. At the time it was written, molecular genetics and the true nature of genetic inheritance were still undiscovered so Darwin adopted a Lamarckian approach to explain acquired characteristics. Where strengths acquired during the course of a lifetime could be passed down to the next generation.

Mendel and Darwin worked in a parallel universe. They were both theologians whose discoveries emerged at the same time and resulted from a similar method of meticulous observations. Mendel’s work did not cause an upheaval equivalent to that of Darwin’s, as it described the laws of nature and did not directly threaten orthodox beliefs. Attentions were focused mainly on the findings of Darwin and Wallace and, as a consequence, the significance of Mendel’s results remained unappreciated until the beginning of the 20th century. The integration of Mendel’s findings with those of Darwin’s led to a greater understanding of inheritance and evolution, but digressed from the common belief that Earth evolved only a few thousand years ago and that each species was created within a similar time-scale. Similarly, Pasteur’s research  eradicated the idea that organisms could spontaneously generate by demonstrating that microbes could not grow under sterile conditions.

Louis Pasteur made great advances in microbial research especially when it had industrial connotations. His doctorate thesis was in researching the crystalline structure of two compounds found in fermenting wine, these were tartaric and paratartaric acids. The structures of these two compounds were identical, but in solution they rotated polarised light in different ways. Pasteur established that this was due to chirality; he discovered that one structure was the exact mirror image of the other, rather like a left and right shoe. Science has now established that all living organisms only synthesise left-hand amino acids and can only utilise right-hand carbohydrates, left-hand carbohydrate compounds are synthesised artificially. Pasteur suspected that one of the molecules in wine was artificial while the other had been synthesised by a living organism and that it was this organism that was responsible for wine fermentation.

During the time Pasteur was researching chirality, alcohol production was thought to be a chemical reaction. Lavoisier had demonstrated that if a sugar solution was dropped on to heated platinum it produced carbon dioxide, water and alcohol. It was, therefore, reasonably assumed that the production of wine, beer and vinegar was simply caused by a destabilising chemical chain reaction. By transferring some of this destabilised solution to a vat of sugar and grape juice, the momentum of the chain reaction would continue. Yeast cells were known to exist in fermenting wine, but were just thought to be an incidental byproduct. Around about this time, French wine production was inconsistent because spoilt wine contributed to great economic loss. Pasteur was asked to research a problem concerning lactic acid contamination in beetroot fermentation. Pasteur noticed that whenever fermentation took place yeast cells were present. He also noticed that when lactic acid was produced smaller rod shaped microbes appeared. In addition, he observed that compounds other than those formed through the degradation of glucose were present and these tended to be asymmetric.

Louis Pasteur. Albert Edelfelt, 1885

Pasteur deduced that living cells were responsible for wine fermentation and contamination. He also established that if the wine was heated before fermentation commenced, then the microbes were killed and the wine remained free from contamination. The procedure of heating to sterilise came to be known as pasteurisation and is today applied to many foodstuffs. One of its most notable applications, and perhaps most beneficial as far as health management is concerned has been in sterilising milk. Milk as a rich source of protein, was at one time infected by many pathogenic bacteria, including those responsible for common diseases such as tuberculosis and brucellosis. It was through continual development of his knowledge in microbiology and sterilisation methods that allowed Pasteur to disprove the spontaneous generation theory. Using sophisticated equipment he found that he could physically exclude air-borne microbes from a vessel containing boiled meat thereby preventing contamination. His many contributions to science did not finish here he also went on to develop vaccinations against anthrax and rabies infections. The French government funded the Pasteur Institute to allow him to treat rabies victims. His fame transcended the Atlantic where another three Pasteur Institutes were set up.

In 1818 slightly prior to the spontaneous generation experiments conducted by Pasteur, Erxleben put forward a theory that a biological interaction was responsible for fermentation. Renewed interest in this theory led to a number of experiments, in the 1830s, by Cagniard de la Tour, Schwann and Kützing. They proposed that fermentation was caused by a biological organism that used sugar as a food excreting waste substances in the form of alcohol and carbon dioxide. Many chemists of this period disagreed with this theory, they thought that the fermentation process was entirely physical and did not involve any biological activity. Von Liebig proposed that fermentation was completely mechanical involving a substance that continually processed a chemical transformation causing sugars to degrade into ethanol and carbon dioxide. This argument was resolved by the work of Louis Pasteur. In 1876 Pasteur published a book, Études sur la bière, in which he proposed that microorganisms obtained energy in anaerobic conditions by fermentation. His theories were supported by experimental evidence later supplemented by the work of Meyerhof. The fundamental metabolistic behaviour of yeast is now known as the Pasteur-Meyerhof reaction. There was a brief return to von Liebig’s chemical theories following the discovery that the cell-free juice of yeast extracted by a mechanical press could initiate fermentation. This cell-free juice was called zymase and is now known to consist of enzymes. In fact, the word enzyme, derived from the Greek term for yeast, originates from this discovery. This extract was unstable, but still allowed the chemical and catalytic reaction that turns sugar into alcohol and carbon dioxide. It eventually, became generally accepted that this reaction was only sustainable in yeast cells. It was a chemical reaction that provided the yeast cell with the energy of life.

Now, in the 21st cent, there are about 30 yeast factories in the European Union consuming about a million tons of cane molasses per annum. European yeast production alone generates an annual turnover of around800 million Euros. Until the turn of the 19th century yeast was supplied in a liquid form very similar to that found at the bottom of beer barrels. Perhaps, in a similar way to  how bread was made in early Egyptian civilisation from fermenting beer. Pliny the Elder noted in the first century BC that Gallic and Iberian bread was particularly light because it had been made with froth from the top of beer. There are now several forms of yeast, compressed, crumbled and active/instant dried and genetically modified. The task of baking and brewing in earlier civilisations would have been difficult without the knowledge of sterilisation and pasteurisation. In ancient times, leaven or sourdough would have been left to rise in considerably unsterile conditions in a warm temperature. This environment would have been optimal not only for yeast, but for all kinds of microbial growth including those that were pathogenic to humans. It is not surprising that leaven was associated with impurity and corruption. Excessive contamination would have most certainly contributed to disease.

The desired characteristics of the yeast strain used in brewing and baking are different although they use the same species Saccharomyces cervisiae, which is also known as baker’s or brewer’s yeast. Brewing yeast needs to have an agreeable flavour and an ability to flocculate so that the wort can settle quickly to achieve clear beer. In order to achieve these characteristics yeast are selected through generations, so that a specific yeast strain produces a desired flavour. In Darwinian terms this would be known  as directional selection.  Directional selection results in a variety of yeast varies with a particular industrial use. For instance, pizza dough is made with reduced power dry active yeast. Its slow fermentation allows the pizza to be shaped with reduced shrinkage after baking. Yeast for the baking industry is usually supplied as a compressed block because this form has a longer shelf life. Just 2.5 grams of this yeast in 100g of flour divides until it reaches a population size of 25 billion yeast cells.

Package of compressed yeast. Image: Hellahulla.

There is no question that yeast has transformed the structure of modern culture. In the food industry it provides baked goods, yeast extracts and alcoholic beverages. In scientific research it is a major model organism used mainly in molecular biology to discover information about the mechanisms of cellular processes. In fact, early in the 20th century, RNA was called yeast nucleic acid because it was first discovered in yeast.

Disappointingly, no women have been attributed to any of the early scientific discoveries associated with yeast. Understandably, they were less likely to encounter Leeuwenhoek’s animalcule containing sperm or beer during their daily routines, but the more likely reason could be associated with the status of women within religion.  As a consequence, they are largely excluded from early investigations were scientific endeavour was mainly to reveal the complexity of God’s creation in  investigations that were exclusively undertaken by men. Within the Bible it is clear that women were preferred to have a more subordinate role as revealed in a letter from Paul the Apostle to Timothy:

Women should learn in silence and all humility. I do not allow them to teach or have authority over men; they must keep quiet. For Adam was created first, and then Eve. And it was not Adam who was deceived; it was the women who was deceived and broke God’s law.
[Tim (1) 2, 11-15]

In subsequent chapters,  the portrayal of women in the progress of religion and science will be further discussed.

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