Leaven continues to evolve

[The Leaven – exploring the relationship between science and religion (cont)]

Yeast has also made a valuable impact in evolutionary biology as it has allowed the mechanisms of evolution to be scrutinised at the molecular level and over short time-scales. In evolutionary terms, fungi, including yeasts, precede mammals and other bilatarians. Bilaterians possess a left and right symmetry of body plan. The two predominate groups, deuterostomes and protostomes, differ from one another in skeletal development. They are believed to have separated in an early stage of evolution estimated to be 670 million years ago. Humans are likely to have diverged from apes only 4 to 5 million years ago. Plants and fungi are thought to have moved from water to land together, the earliest fossils of fungi are in Precambrian rocks dating back 900 million years. Comparing conserved DNA motifs between species of yeasts allows geneticists to estimate the evolution rate of proteins. Yeast can be compared with other yeasts and then with other model organisms such as nematodes or fruit flies. Comparative genomics evaluates the evolution of certain proteins and the processes and complicated pathways that they participate in.

Antibiotic resistance test: Antibiotic impregnated discs are placed on a lawn of Staphylococcus aureus. The width of the halo around each disc represents the efficiency of the antibiotics in clearing the bacterial cells. Image Don Stalons.

Fungal species are susceptible to disease and parasites that they control by producing antibiotics, such as, penicillin. In fact, the microbial world is full of toxins secreted by bacteria and fungi many being used as insecticides and other biological control  agents. Yeast can also be used to study antibiotic resistance. Resistance to antibiotics and other stresses in yeast is often called rapid evolution. As yeast cells can evolve rapidly to overcome environmental challenge they provide a means to study the mechanisms of evolution. In addition the yeast cell susceptibility to mutagens make it an ideal organism to study the effects of mutagenesis and adaptation.

Yeast therefore provides a molecular tool to study cell biology and a model system that can add to our knowledge of evolution. In contrast to yeast in the biblical era, the molecular era now knows a great deal about this organism. In addition to great improvements in disease management, advances in genetics have led to new arguments surrounding the creation of living things, especially in respect to evolution and cloning. Yet, even though it exists as a simple single-celled organism that thousands of researchers have been studying intensely for centuries, a lot remains to be discovered.

Life on earth has evolved over millions of years through a complex network of processes that will take many years to unravel. Whether the molecular information we have derived from yeast is comparable to the corrupt leaven of the Pharisees or the leaven that the women kneaded into the dough to represent the kingdom of heaven (see previous post) has yet to be established.

Yeast produces not only bread and wine

[The Leaven – exploring the relationship between science and religion (cont)]

The last post established why yeast is used as a model organism to study molecular biology but how and what is it used for? The last century saw a molecular enlightenment, yeast was cemented as a key component of that movement. In the 1950’s, molecular biologists constructed a  Saccharomyces cerevisiae strain containing biochemical markers (antibiotic  resistance or amino acid selection) known as S288C from the fig strain mentioned in the previous post, EM93. It was soon discovered that self-replicating elements of DNA found in bacteria called plasmids could also be made to function in yeast. Yeast cells multiply rapidly and the overall effect of a mutation in a certain gene can be measured biochemically or by observation under the microscope. If DNA fused to reporter genes is inserted into the self replicating DNA from bacteria and then introduced into the yeast cell, it can be propagated and then extracted. This technique is called cloning as it replicates an identical copy of a gene, has been used to mass-produce proteins and vaccines. In yeast, cloning was used as early as 1980 to produce Hepatitis B vaccine. Since then it has produced a multitude of proteins and vaccines including: insulin, growth hormone, haemoglobin, oestrogen receptor and interferons.

Cloning can also take place in bacteria such as Escherichia coli, these cells divide faster than mammalian cells but are a lot smaller so there is a limit in the size of the protein that can be cloned. As a consequence of this other cells types are now also used for cloning such as those derived from mammals, insects and viruses. Cloning provides an extremely economical way to reproduce human proteins. They replace the need for animal production and reduce the risk of transferring unwanted diseases, such as, CJD from growth factor. Although great advances have been made, the systems are still not perfect and have their limitations according to the type of protein that can be cloned, as some are toxic to the cell, and introduction of unwanted mutations occurs far more frequently when selection is not acting on the protein. Most organisms, including bacteria, have their own DNA repair systems that detect mutations. Foreign DNA has a higher chance of retaining mutations in a host cell as it is not detected through normal cell function, a problem to biotechnology that is successfully addressed in natural systems by selection. The use of these systems with limitations causes uncertainty and increases risk factors, subjects which are discussed  in future posts. It seems yeast occasionally retains its Biblical ability to behave in a corrupt way.

Protein interactions: Ribonuclease-inhibitor protein grabbing and surrounding the ribonuclease A enzyme. Image by Dcrjsr.

Following the heady days of protein engineering, yeast laboratories, through intra-science communication, successfully completed the enormous challenge to complete the first fully sequenced eukaryotic genome. This was achieved using strain S288C and relatively archaic apparatus compared to the robotic systems used to decode the human genome. Eventually, over 6,000 genes were unravelled from the yeast nucleus. The yeast genome is 200 times smaller than the human genome but almost four times larger than that of E. coli. This achievement marked a milestone in biological history. Yeast biologists did not stop at just sequencing the genome. In a striking example of inter-organisation collaboration, nominated laboratories began deleting single genes from individual yeast cells through advances in polymerase chain reaction (PCR), a technique that can amplify a single gene from the cells DNA. A marker/reporter gene flanked by target DNA is amplified by PCR technique and then inserted into the yeast cell. Non-homologous recombination replaces the genomic gene with the introduced marker/reporter gene. Biochemical tests were then carried out on the mutant yeast strains to uncover the functional analysis of hundreds of different gene products. This work elucidated many gene functions and undoubtedly contributed to the discovery of many analogous human genes. This information has been collated into several databases to provide a plethora of data available for bioinformatics across the internet. Genes placed on microarray slides and subjected to various environmental conditions and variations of DNA recombination techniques have increased the quantity of this information, enabling researchers to compose complicated hypotheses and uncover new cell processes without even entering a laboratory.

Many would expect yeast’s contribution to scientific research to stop at this point. Exhausted by constant, investigative probing. In contrast, the yeast story continues. It has also been used as a vehicle to investigate protein interactions first with native yeast proteins and then later with proteins from any other organism. Genes can be fused to protein tags, introduced into yeast cells and reporter genes within the cell can detect if the proteins produced from the introduced DNA interact. This procedure is known as the yeast 2-hybrid technique. Several variations to this technique exist, again modifying it to be used in other in cell cultures from other organisms. These techniques, in a rudimentary way, can also be used to evaluate post-translational modifications in proteins, to see how gene products are modified by the cell. Compared to the amount of gene sequencing data available the amount of protein interaction data is still fairly incomplete with the function of many gene products still unknown.

From figs trees to laboratories

[The Leaven – exploring the relationship between science and religion (cont)]

The development of yeast molecular biology can literally be used to assess the impact that the application of scientific research has had on 21st century society. Scientific researchers often describe yeast as the workhorse of eukaryotic molecular biology with many laboratories devoted to studying this single-celled organism, as much of the information derived from it can be equally applied to the study of human cells.

Most modern laboratory strains of yeast originate from one particular Saccharomyces cerevisiae strain, EM93, isolated from dried figs in Merced, California in the 1930’s by Emil Mrak. This strain turned out to be heterothallic, meaning that cells existed as two types of sterile haploids, with a single copy of each gene, that when fused together formed a fertile diploid that could perform meiosis in a similar way to that seen in human cells. Up until this point most strains studied were homothallic, this meant that all haploid cells were of the same mating type and capable of fusing together to form a fertile cell known as a zygote. The emergence of a heterothallic strain meant that the genetic stability of a culture could be placed under greater control, as it would remain haploid until the other haploid type was introduced and then through the production of mating phermones followed by cell fusion a diploid cell could be created.

Green Fluorescent reporter gene in yeast cells. Image: bio+ve

So why has yeast become such a popular organism to study molecular biology and why is this microbe chosen in favour of others microorganisms? Firstly, Saccharomyces is non-pathogenic and does not present a threat to human safety. Therefore laboratory workers do not require expensive protective equipment to practice research. Saccharomyces is also easy to contain as is not usually airborne unless transported involuntarily by animals and insects. Another reason  is the ease by which it is cultured. Yeast can be grown easily and only requires a suitable carbon source, nutrients and appropriate physical conditions to continue multiplying. Additionally, these requirements can also be used to control the rate of cell division, for instance, by altering temperature or by creating metabolic mutants. Mutants are generated either through using a mutagen or by manipulating DNA through genetic engineering. Genes involved in yeast metabolism can be mutated and then used as molecular markers. For instance if the genes for the requirement of an essential amino acid are defective then the yeast will not grow without that amino acid added to its immediate environment. If the defective gene is artificially replaced by a functional one then the yeast cell will be able to continue growing without the need for that particular amino acid. Armed with this knowledge researchers are able to introduce fragments of DNA fused to these marker or reporter genes. If the yeast is able to grow without the selected amino acid this means that the DNA of interest to the researcher has been successfully introduced into the cell. This approach has led to the characterisation of countless genes and proteins in yeast and from other organisms.

Another reason why yeast is used as a molecular model system alongside other well-known microbes, such as Escherichia coli, is because it is a eukaryote. E. coli and other bacteria are prokaryotes, in contrast to eukaryotes they only have one chromosome housed in a cell without a nucleus. In yeast cells, DNA is packaged in chromosomes stored in a nucleus in a similar way as in human cells. Yeast has 16 individual chromosomes compared to 23 in humans. Surprisingly, there are only four chromosomes in the multi-celled fruit fly Drosophila another model organism used for biological research. Yeast also has the advantage of being able to grow just as happily with one set of chromosomes, in haploid cells, as with two or more sets of chromosomes, diploid and polyploid respectively. Additionally, as yeast is a single celled organism without the complexity of cellular differentiation it can be used to study the cell-cycle at a fundamental level. It can be used to study mitosis and meiosis. Many mutations that cause human disease are introduced during meiosis. Following cell fusion or mating, two haploid cells form diploids which can produce four individual haploid cells known collectively as an ascospore. After microscopic dissection of the ascospores, researchers can study recessive mutations and the complicated exchange of genetic material during meiosis by counting the numbers of surviving progeny. The information derived from yeast studies aids the study of genes involved in tissue development and cell differentiation in higher eukaryotes, such as Drosophila. Adding to all these factors many of the biochemical and cellular functions in yeast are conserved in human cells. Yeast therefore is a simple and practical system to study the mechanism of human cell division.

Leaven in a molecular era.

[The Leaven – exploring the relationship between science and religion (cont)]

Not only does yeast now serve as one of the most important organisms throughout domestic history, in recent years it has also substantially contributed to biological research. The numerous molecular techniques that have evolved in yeast have allowed it to make an important contribution to a number of areas in science. Through studying various types of yeast and other microbes, scientists now know a great deal about the molecular processes involved in cell division, rapid evolution and disease.

Fortunately, individuals with skin diseases are no longer thought of as unclean and are normally treated within the community. Scientists have greater understanding of disease management and although quarantine and hygiene are still practiced they are now carried out in order to reduce disease transmission. In the majority of cases, people are not ostracised when they are infected by disease, although fears and anxieties can still be generated through sensational media coverage. Nevertheless, even in this molecular age, some transmissible diseases are still associated with sins of the flesh and can lead to social ostracisation.

Yeast colonies in an array. Each spot contains thousands of yeast cells. The plate shows synthetic lethal interactions when the interaction of 2 or more genes cause cell death (shown by colonies with reduced/no growth colonies). Image uploaded by Masur

There are still many diseases that generate fear because they are untreatable. Some of these have evolved through human activities, such as Bovine spongiform encepthalopathy (BSE) which gives rise to a human form of spongiform encepthalopathy called variant Creutzfeldt-Jakob Disease (CJD). The causative agent of BSE is a defective version of a protein called prion that is similar to one found in the brains of sheep with Scrapies. The prion protein is transmitted horizontically and causes disease through disrupting the normal function of the native protein. Studying the molecular mechanisms by which proteins change conformation to become prions in yeast has led to a greater understanding in the pathology of this disease. Many other human diseases, especially cancers, can be researched by studying molecular processes first in yeast.

Cancers arise when cells begin to divide abnormally due to mutations in DNA. Cancer research investigates the mechanisms that encourage these mutations to arise. The mechanism of cell division is often studied in fission yeast, Schizosaccharomyces pombe. Unlike Saccharomyces cerevisiae, which divides by budding, S. pombe divides symmetrically in a similar way to human cells. Fission yeast originates from Africa were it is found growing on banana skins and is used to ferment beer. Through research in this area scientists have reached many milestones in the mechanisms that have caused various cancers leading to greatly improved clinical treatments. Work yeast genetics has greatly contributed to our understanding of cell cycle research and has led to the award of a Nobel prize in 2001 to three scientists who led pioneering work in this area: Paul Nurse, for his work in S. pombe and human model systems; Leland Hartwell, for his work in S. cerevisiae; and Tim Hunt who used sea urchins as a model system. Researchers later found similar cell division genes in human genomes.

Scanning electron micrographs of Fission yeast (Schizosaccharomyces pombe). Image by David O Morgan.

In addition to investigating diseases, yeast is also used as a model system to research ageing. Saccharomyces cells can divide by budding a number of times but the new bud is always physiologically younger than the mother cell. Each cell produces about thirty buds depending on the environmental conditions and other factors. About thirty genes in yeast have already been found to be involved in ageing. The main factors seem to be related to metabolic capacity, resistance to stress, gene dysregulation and genetic stability. Encountering certain environments that would overload any of these factors would also affect longevity. For instance, excessive oxidative damage or radioactivity would lead to a high level of mutations that will reduce the number of times that a cell can bud. Excessive oxidation is associated with the consumption of calories; so caloric restriction should result in increased longevity. This has been demonstrated in yeast, limiting the amount of nutrients and carbohydrates available in growth medium leads to a longer generation time and life span.

The molecular, vegetative animalcule

[The Leaven –  exploring the relationship between science and religion (cont)]

Yeast is a domesticated organism that has become almost indispensable in modern society. Although unessential to the staple diet, supermarket shelves are crammed with products that require yeast fermentation. Bread, chocolate and alcohol production all involve the metabolic activity of these simple single-celled microbes. Restaurants, bars, clubs and many aspects of social behaviour revolve around yeast products.

Throughout the centuries yeast has been the focus of domestic and industrial life. While it’s 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 not the metabolic activity of a living organism. During the Biblical era there would have been no conception that the metabolic pathway of a microscopic bug was the source of fermentation.

Yeasts are naturally 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. The environment contains many different types of yeast, from those that cause fungal infection (Candida spp.) to others that are used in the baking industry and in wine-production (Saccharomyces spp.). Yeast belongs to the kingdom Fungi and the division Ascomycota. 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 eukaryotic organism to have a fully sequenced genome. The majority of its genes have been researched and functionally analysed and, as many of these have analogues in other multicellular organisms, it is therefore possible to study molecular processes from mammalian systems within a unicellular model eukaryote. It is also well established as a favourable alternative to animal model systems.

Large-scale experiments involving computers, robotics and new molecular techniques, such as polymerase chain reaction (PCR) to amplify genes and DNA micro-arrays, that arrange hundreds of these genes onto a small grid, have generated such a large amount of data that new scientific disciplines, eg., genomics, transcriptomics,  have evolved in order to process it all into meaningful results. The simplicity of the yeast life-cycle has made it invaluable to medical and biotechnological research. Certainly, yeast has had a great impact on 21st century society that has inflicted on social behaviour and medical research. Anthropology would have evolved differently if this organism ceased to exist.

…the complexity of simplicity

[The Leaven – exploring the relationship between science and religion (cont)]

Many discoveries in molecular biology have been pioneered in model organisms that are easily and economically grown and, most importantly, are unlikely to threaten the life of the investigator. Such model organisms include; bacteria, yeasts, rodents, amphibians and several plant species, such as Arabidopsis (small flowering plant), members of the potato family, grasses and, following Mendel’s example (see previous post), legumes such as peas or beans. From all of these species, yeast has affectionately been dubbed the workhorse of molecular biology, playing a prominent role in leading to a greater understanding of biological science at the molecular level.

Several characteristics of the DNA molecule and genetic inheritance have been researched through first observing the physiology of yeast mutants. The impact that yeast has had in molecular research was largely due to the emergence of apparatus that could visualise the microscopic universe in which it resides. Early researchers, on first observing these minuscule yeast cells, thought that they appeared to just materialise from substances in their immediate surroundings, this led to the dubious theory of ‘spontaneous generation’. In many ways they were correct, yeast cells do rely on nutrients from the immediate environment in order to multiply. However even the tiniest of cells requires a precise organisation that takes centuries to evolve.

A yeast cell is now known to contain over 6,000 genes encoded by DNA that is organised within sixteen chromosomes. Not all the DNA provides the genetic code to synthesise components for the cell; some plays a structural role and also adds to overall mass rather like packaging material helping to organise the DNA into chromosomes. DNA containing genetic information is neatly condensed into chromosomes which are stored in a nucleus surrounded by cytoplasm enclosed within a cell membrane protected by a carbohydrate cell wall. Hundreds of proteins and metabolic pathways are involved in maintaining the homeostasis of the yeast cell.

Yeast cells viewed by electron microscopy. A condensed nucleus can be seen near the centre in some cells. The contents of each cell are contained within a protective cell wall.

Even the most simple of cells are derived from a great deal of natural complexity. Today theories of spontaneous generation appear ludicrous, as through microscopy, the precise mechanisms which lead to cell division have now been realised.  A long process of evolution  must have given rise to this degree of intricacy. Such complexity could not have been generated purely by chance. In the order of the Universe every process is known to follow certain physical laws, where biological events occur at random rather than by chance. As Stephen Hawking eloquently said:

The whole history of science has been the gradual realization that events do not happen in an arbitrary manner, but that they reflect certain underlying order, which may or may not be divinely inspired.

..finding faith in science

[The Leaven –  exploring the relationship between science and religion (cont)]

In both science and religion accuracy in recording information requires a certain amount of faith, especially when confronted by uncertainty. Take climate change, for instance, none of us, as individuals, can measure with any certainty that the Earth is gradually warming and that this is the consequence of carbon rich gases. Yet many of us believe that this is the case through watching or reading media reports, most of which may or may not be based on legitimate scientific findings. As a consequence of these reports, we are also assuming that all change created by a shift in climate will result in global catastrophe even if this is not the case. There is a widely accepted view that anthropogenic change will have a negative effect on the balance of natural resources.

We can only assume that climate change is caused through the accumulation of carbon-based emissions because a fairly limited amount of research has drawn up this conclusion. However, consider if climate change was caused by some other factor besides carbon emissions. Suppose climate change is a consequence of the Earths gradual movement closer to the Sun or by the Earths core becoming inexplicably hotter or by  hostile aliens beaming powerful rays through the stratosphere. These causes are far more difficult to comprehend and completely beyond our control. So within reason the preferred scenario is that human activity is causing climate change and that we have the ability to control this, to some extent, by restricting carbon emissions.

In reality, carbon emissions are a by-product of energy production therefore the heat created through energy production could be contributing to climate change. Furthermore, by comparing our present use of heat emitting energy to that of a few decades ago this seems to be a reasonable assumption. If this were the case, reducing carbon emissions would have little effect. Solar power, wind power and atomic energy would all be useless in reducing climate change, as only the reduction of energy generation would have any impact. So several factors could be contributing to climate change but all of these factors are based on data presented to us by relatively small groups of scientists working in specialised areas.

Many aspects of science and religion, therefore, are based on assumptions that require an element of faith. To this end we rely heavily on the investigation and integrity of others to provide answers and solutions.

…fear of scientific uncertainty

[The Leaven –  an investigation into the relationship between science and religion (cont)]

Despite lack of knowledge surrounding biological processes, the Bible still manages to relay the message that by changing behavioural patterns quality of life can be improved. One purpose of science and religion could therefore be to raise this awareness. Occasionally however, both science and religion can step out of line to become socially threatening. In the Bible, this kind of corrupt behaviour is compared metaphorically to the permeating effect of leaven in dough. During this era, the properties of leaven were not understood and would have been shrouded in mystery. Through an accumulation of scientific knowledge it is now known that leaven is a substance that contains microbial organisms, such as yeasts, that ferment carbohydrates in dough, producing carbon dioxide and alcohol as by-products. The process of fermentation has become realised over time through countless scientific experiments; a relentless thirst for enlightenment that led to further questions and further experiments to answer those questions. Science seeked answers not only to what caused the process of fermentation but also how it accomplished this and for what reason, furthermore, could this process be exploited for some other purpose?

Through tiny progressive steps rather than a giant leap, yeast has become a commercially important domesticated microorganism and a well-established tool in molecular research. The natural process of leavening or yeast fermentation is now well understood and can be manipulated scientifically by humans. Genetic engineering has advanced to such a level that mere mortals can now achieve processes in days that would have taken natural selection decades to accomplish. However this knowledge is not shared by all and is still feared by communities who cannot influence the outcome of scientific exploitation. It could possibly be the fear of corruptive or erroneous influences behind this scientific manipulation that currently causes social concern.

Uncannily, the philosophical message that is conveyed through leaven in the Bible, over two thousand years ago, could well apply to corruptive influences within modern scientific institutions today. Sometimes, especially through the efforts to secure material needs, other motivation besides scientific enlightenment drives research. This can lead to the controversy that reveals flaws in regulatory systems. Ironically, fear of uncertainty is still present despite the wealth of knowledge that we now have.

..in search of scientific truth

[The Leaven –  an investigation into the relationship between science and religion (cont)… ]

Studying the dynamics of living cells with molecular techniques is a journey fuelled by curiosity but it also requires collaboration between scientists as the techniques themselves are created through scientific investigation. Although a truth in science is normally supported by physical evidence scientists still require some elements of faith, as they rely a great deal on evidence provided by others. Once research has been published it is rarely replicated by another scientist unless it is necesary to do so in order to discover further truths. [nb. I need to provide some examples here].

Through studying the molecular processes of yeast it becomes apparent that this simple organism has contributed enormously to the development of civilisation. It is also apparent that science is an ultra organised entity, arranged into a number of categories and subcategories, preoccupied in what is a global effort to discover the ultimate in scientific truth.

The Biblical text provides a valuable resource of information on the historical route that yeast has taken to finally arrive in the hallowed halls of molecular biology. In fact, science and religion seem to have both emerged through the need to address similar uncertainties, they have co-evolved in a search for truths. The purpose of this book (the Leaven) is not to condemn or favour views held in religion or science but to bring these doctrines together in order to analyse the way in which society deals with uncertainties. Uncertainties that possibly arise from lack of knowledge or evidence.

Yeast cells expressing green fluorescent protein.

By investigating how yeast, as leaven, was interpreted in the Bible there is a surprising insight into how past societies dealt with fear and uncertainty. The biological processes behind leaven were not understood and it was frequently associated with adverse events (perhaps because of contamination) it was therefore often used to symbolise corruption or evil. There are parallels to how uncertainty was viewed by society in the biblical era with views towards science and molecular biology today and, in some instances, there may be a legitimate argument for this comparison.

Religious and scientific truths

(The Leaven –  an investigation into the relationship between science and religion (cont)… )

Science and religion are often in contradictory hemispheres even though they originate from a similar train of thought. Both are the products of curiosity, they are both concerned with discovery and both seek answers to similar questions. It is not then surprising that the outcome of scientific and religious investigation share the same fate, they are both recorded for future reference, in perhaps what is a kind of altruistic obligation to benefit others.

Perhaps one of the most instantly recognised written example is the Bible, a colossal documentation of spiritual endeavour, consisting of around seventy books, arranged within two testaments. The two testaments were written in quite different states of history. The Old Testament emerged during the decline of Egyptian supremacy over the Israelites, while the New Testament was compiled during the height of the Roman Empire.

The doctrines in the Bible were written at a time when there were countless mysteries underlying biological and natural processes. The nature of several of these processes, such as evolution and disease, were not understood and therefore thought to be the intervention of powerful deities. Not surprisingly, advances in science have challenged the logic behind many ancient ideologies. The development of microscopic techniques has revealed the causative agents behind several diseases, while radiocarbon dating and DNA profiling have added new dimensions to archaeological and evolutionary theories. Even so, there are still many uncertainties associated with disease and evolution that science has yet to unravel.