In the beginning there were nucleotides

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

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 Gods 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.

In the book of Genesis, plants were created first, birds and fish appeared on the fifth day, with other animal life, including humans, arriving on the sixth. The order in which animals appear corresponds roughly with evolution theory, fish and birds being more primitive in genetic terms than mammals with humans appearing later. According to the Bible, humans were put on Earth to control the animals that existed in the land and sea, with females being cloned, by the Almighty, from male bone tissue. The genus Homo is thought to have diverged from other primates fairly recently, within the last four to five million years. Therefore, humans are also considered to be at the top of the phylogenetic tree. There is no mention of microbes in the story of creation as their existence only came to light with the advent of microscopy in the last few centuries. Evolutionary speaking they would appear before plants.

Garden of Eden

Garden of Eden – The Garden of Earthly Delights Hieronymus Bosch (circa 1450–1516)

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.

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.

…in the beginning there was chaos from which evolved order

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

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 [Gen. 1, 6-7].

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”.

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 Gods 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. In the case of S. cerevisiae these are found in a sac called an ascus this has earned them the further classification of Ascomycetes.

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 life-time improvements could be passed on to their offspring. Lamarck’s hypotheses 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 others 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 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 life-time could be passed down to the next generation.

…my distant relative is a lower life form

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

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 then why did not all yeast cells 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 species C. It flourishes until it encounters species C. As consequence of  this cycle of adaptations, species A no longer resembles its original form and becomes subspecies Ab. 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 anamensis, Australopithecus afarensis, Homo habilis and Homo erectus. There are other early hominids that are thought to be more distantly related Australopithecus africanu, Paranthropus aethiopicus, Paranthropus 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.

…the metabolic habits of microbes have earned them a bad press

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

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. 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 life span of 62.5 years to visualise. When the Bible was written human life span was only 28 years.

Trilobite fossils, early anthropods that are now extinct. Image Moussa Direct Ltd.

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 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 misconceptions in the account of creation within the Bible. The stars and planets must have existed before the introduction of life.  Seasons would  prerequisite the existance of vegetation. We are now also aware that reptiles existed before mammalian species on account of dinasaur fossil records. These restrictions in knowledge also result 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 by 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]

…big bang, creation and other theories

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

Leaven, the term commonly found in the English translation of the Bible, is often used to describe fermented dough or sourdough. It’s called sourdough because, along with yeast cells, it contained acidifying bacteria that produce lactic and acetic acid, giving the bread a unique tangy flavour. It’s believed 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 associated with cultivated crops. In just 100 grams of flour there are 1 to 10 billion microbes of these about 30,000 are natural yeast.

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 to the 21st century and  in to the complex science of molecular biology. 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 the scientific investigation. For instance, the Biblical version of Creation greatly differs from scientific theories of evolution. The ensuing debate 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; it permits evidence to be scrutinised by others thereby allowing the interpretation of results to be challenged.

The Bible suggests that a divine being must have in some way directed the creation of Life in order to account for its 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 that this 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 being supported by any tangible evidence. Though it may have  been defended when it was written, given the lack of scientific research at the time.

The Creation of Adam, Michelangelo c1511

Ultimately, 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.  Therefore, various scientific and theological arguments must be considered before determinate conclusions are reached.