The Leaven – Biblical theory in a Molecular era


So here at last – fresh off the press – the completed book.


the Leaven lives

Pharmaceuticals: a science-based industry influenced by profit. Image:bio+ve

I’ve now posted most of the initial stages of a  book that I’ve been working on. It’s about how leaven in the Bible is interpreted through the mind of a slightly deluded, molecular biologist specialising in yeast research.  In many ways, the scientific community is similar to  religion. Many people who work in it are doing so to benefit others in a collaborative effort that is occasionally overidden by other influences.  In fact leaven is used in the Bible to metaphorically represent how influence permeates through society. It has as much relevance in science as it does in religion. Money seems to fuel the same kind of corruption in science  as in religion, leading to conflict and controversy. Also both science and religion seem to discriminate against women. This all seems to have been affirmed by Paul the Apostle.. who seems to be, hypocritically, under a leaven-like influence. Paul wrote a few of the books in the New Testament but seems to have never witnessed the teachings of Jesus first hand. I believe it’s time that a pop science book addressed equality. If you’d like to read my efforts so far and leave any comments (good or bad) please visit the Leaven.

The leaven of the pharmacies

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

Although pharmaceuticals in general provide us with a life span and standard of living that far surpass that in the Biblical era, controversies can still occur. Media that implicates new drugs in compromising the development of children can rapidly ignite public concern. These issues cause outrage because they effect the vulnerable, those individuals that have no choice but to rely on the judgement of others. Who in turn must have faith in pharmaceutical companies and the bodies that govern them. The problem with governing bodies is that individuals within them  are usually specialists who can be influenced by other interests or individuals. Also, responsibility is spread within a group, there is no single individual who has to take account of any misdemeanor.

In 1988 the MMR vaccine was introduced into Britain ten years later Dr Andrew Wakefield and his colleagues at the Royal Free Hospital, London, found that a bowel condition could be associated with autism in a study group of 12 children. Traces of measles virus were discovered in the intestines of these children but the data established an association rather than an effect. There was no evidence that the single measles vaccination would not behave in the same way, however though, the incidence of autism has increased in recent years. Many parents were concerned that the triple vaccine was harming their children. Autism can be related to other conditions and consequently it is fairly difficult for the disease to be linked to a particular vaccine. It is virtually impossible to prove a cause and effect. Even if in reality some individuals were more susceptible to autism after receiving the vaccine, it would be difficult to directly link the vaccine to the disease. Astonishigly, even though Wakefield did not specifically state that the MMR vaccine caused autism, the UK government, pharmaceutical companies and medical research bodies exploded into a retaliation that was completely disproportionate. He was forced to resign, accused of professional misconduct, struck off the medical register and several of his papers have been retracted by journals. This is quite disturbing for researchers, as it prevents them and scientific journals from publishing research that may attract controversy.

If there was an element of uncertainty in vaccinating individuals then why not stop the vaccines and go back to the old methods of vaccination or better still, offer both choices? After all, the old methods seemed to be fairly effective in preventing the spread of measles, mumps and rubella. Additionally, if both methods were available then it would be possible to compare the rates of autism in a greater population and therefore the epidemiology would be clearer.  Apart from the obvious financial considerations, the answer perhaps lies in the statistical way that governing bodies evaluate risk. If the risk of becoming autistic is below a significant level than it would be argued there is no risk in having the MMR vaccination even if that risk is double that of the single vaccinations. Several members of the public found that the potential risk, however small, of being permanently harmed by the MMR vaccine was greater than the risk of temporarily contracting measles and therefore chose not to vaccinate their children. In many areas only two in three children were vaccinated leading to concern that a measles epidemic could occur and result in disabilities or even fatalities. Media reporting had originally alerted parents to the potential of MMR in causing autism. In a survey conducted by the Economic and Social Research Council the majority of people discovered the controversy surrounding MMR by watching the television. In fact television is the most important means of communicating science controversy with science journals providing source information. So, could it be possible that sensational media coverage was responsible for the MMR controversy and that Wakefield was merely used as a scapegoat to counteract this?

The causative agent of Anthrax, Bacillus anthracis bacteria. Image: Centers for Disease Control.

A similar concern, that did not attract as much media attention, was the discovery that the anthrax vaccination, given to armed service personnel in order to protect them from Biological weapons, could cause miscarriages and premature births. If this problem had affected a greater percentage of the public it would naturally have been given more media attention.  As it happens, this could never have occurred as the product was not licensed for general release. Therefore, the only people who were likely to be at risk were also at greatest risk of encountering anthrax spores. Controversially, despite originally being an animal vaccine, the American and British governments claimed that animal reproductive studies had not been carried out. The incidence of birth defects, mainly associated with premature births, and miscarriages in the infants of American and British troops has increased since the anthrax vaccination program began. Initially in the early 1950’s, when the vaccination was licensed for use on humans, only male service personnel would have been vaccinated. In the 1990’s, when troops were vaccinated in order to go to the Gulf,  both men and women received the vaccine. The vaccine had already earned a bad reputation amongst service personnel for causing ill health.   In order to acquire complete immunity over three shots were required and many of those that received the vaccine voluntarily, failed to complete the course with some remaining ill and developing other symptoms. The vaccine was thought to be responsible for Gulf war syndrome, as countries that did not vaccinate their troops also did not have Gulf war syndrome.

Governments and pharmaceutical companies have again refused to acknowledge  accusations against the anthrax vaccine. Despite individuals having been administered the vaccine with no animal reproductive data being carried out those that have been detrimentally effected are again left to fight for justice. An ambivalent relationship between science, the media, regulatory systems and commerce once more creating an atmosphere of uncertainty. A parallel can be drawn by this situation and how Jesus described the leaven of the Pharisees. The persecution that Jesus endured for challenging corruption remains relevant to this day.

Genetically modified leaven

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

Advances in technology can bring significant medical or agricultural benefits but they are also exploited for commercial gain sometimes with a disregard to any negative impact they may have. In general the introduction of new drugs has benefited human health. The early 1900s witnessed many great advances in chemical therapy. Ehrlich developed a treatment for syphilis in 1907; Fleming discovered the first antibiotic, penicillin in 1920; Domagk found that sulphanilamide could cure septicaemia in 1932. Life expectancy has improved as a consequence of these drugs, in 1935 there were 3,690 deaths in Britain from scarlet fever and diptheria compared to just one death in 1970. Thalidomide was introduced hot on the heels of these discoveries when huge profits could be made from a new drug. Especially in Britain were there was very little regulation of pharmaceuticals.

Ironically, because of extensive screening and restrictions now in place to prevent a reoccurrence of an episode like the thalidomide tragedy, it has become increasingly difficult to bring new drugs on to the market. Therefore, re-evaluating harmful or ineffective drugs for other uses has become an ever increasing trend with pharmaceutical companies. The mechanism behind the teratogenicity of thalidomide has still not been established yet this drug is currently being researched as a possible therapeutic agent for other diseases, such as cancer. Celegene are currently remarketing thalidomide to treat the symptoms of leprosy. It is also effective in the treatment of some myeloma. In the documentation they produce to promote the drug, ‘Thalomid (thalidomide): Balancing the benefits and the risks’, they admit that birth defects still occur in countries where controls and monitoring plans have been inadequate. This brings about another form of controversy, where there is tension between the victim of a disease and a social goal to obliterate thalidomide. The Sunday Times article that the High Court tried to ban ended with this emotional statement:

Many of the main characters who figured in this narrative are now in other employment, thalidomide is only a painful memory. Of the original cast of the tragedy only the victims still occupy the stage.

Thalidomide still retains the ability to promote controversy and to raise issues by the public concerned with the morality of scientists under the influence of commercial gain.

So metaphorically speaking, whose leaven should modern society now be aware of? There are a number of candidates that can permeate a corruptive influence in science, including the media, researchers, commercial companies (pharmaceutical, agricultural), academics, and politicians. The majority of science is fairly mundane and straightforward occurring without grabbing news headlines but occasionally something attracts media attention and becomes headline news. On several occasions in the past, trust in science has been challenged by controversy.

The introduction of genetically manipulated or modified (GM) products into the environment before all research has been effectively collated and publicly distributed, can manifest into controversy. The public may be justifiably cautious of GM food, if there is no benefit in eating it why take a risk? An experiment that is restricted to a laboratory can be controlled and environmental conditions can be manipulated. Once the experiment leaves this controlled confinement of a laboratory it is at the mercy of a number of influencing and unpredictable factors, including commercial profit. It was exactly these factors, combined with the lack of governmental policy, that contributed to thalidomide entering the marketplace.

Following the impact of the BSE crisis, Britain is very cautious about the introduction of GM crops. In the United States GM crops are fairly prevalent, accounting for over 90% of all soybean and rapeseed production. Mostly GM crops are resistant to glyphosate herbicides but there are also GM pest resistant crops. In the US 90% of cotton production is GM for pest resistance. In 2010, 10% of the worlds crop production was GM most of which is grown in the US. Invariably, most of us are unwittingly eating some form of GM food.

Peanut plant containing a bacterial pesticide gene. Lesser cornstalk borer larvae damage the leaves of the unmodified peanut plant (top) but die on the GM plant (bottom). Image: Herb Pilcher

In food production, GM yeasts are available for wine production and in baking. In the UK two products have been approved for commercial use. One in baking to reduce leavening time and the other in  brewing to produce low calorie beer. No GM yeast are currently in use in EU countries. In the US and Canada a GM yeast called ML01 is used to improve taste and colour of wine and to reduce the production of histamines. Additionally, a GM yeast that has been produced to reduce the production of ethylcarbamate, a compound that has carcinogenic properties, has been labelled generally recognised as safe for use in the US. Mostly GM yeasts have non-food usage,they are grown in controlled environments to produce pharmaceticals, chemical compounds and enzymes. They are also increasingly being developed to produce biofuels.

Very little research has been carried out on the safety of consuming GM products. The consequence of eating pesticide containing GM crops, such as maize, is largely unknown. Perhaps scientists are wary about publishing research because they face being academically ostracised.  In 1998, researcher Árpád Pusztai reported changes in the intestines of rats who had eaten a GM potato containing snowdrop lectin, to confer pest resistance. Other scientists argued that there were insufficient controls to determine that the toxin and not the potatoes were detrimental to the rats. As a consequence of his research, Puszatai was suspended from his post and his contract was not renewed. This incident,  known as the Pusztai affair, highlights the extent at which scientists and their research are influenced by corruptive factors.

Beware the leaven.

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

Whereas religion uses faith to dispel anxiety caused through uncertainty, science calls upon facts to achieve the same purpose. In the Old Testament, leaven was omitted from sacrifices in order to increase the purity of offerings thereby eliminating the chance of offending a deity. The fact a sacrificial offering was taking place at all accentuates the extent that fear manifested through uncertainty. Individuals would go to enormous lengths and effort in order to eliminate risk. Through scientific evaluation, most of us now rely on facts rather than sacrificial offerings to protect us from disease and other catastrophes. For instance, we are aware that Food and Drug administrative laws exist to protect consumer’s interests. Although, this still doesn’t entirely eliminate uncertainty, as trust in the regulators also relies heavily on faith. The public must rely on scientists and other professionals to have obtained experimental evidence according to the ethics of the law.

In pharmaceutical development, research occurs initially within a controlled laboratory environment until a new drug is released on to the market, at this point there is no barrier between science and the public. Whenever we take a prescribed drug we assume that it is going to be beneficial or, if this were not the case, the consequences to the prescriber would be so detrimental that the risk of malicious activity would be fairly small. Occassionally, drugs are released without all the necessary research being completed, sometimes with catastrophic consequences. A classic example of this was the thalidomide scandal in the 1960’s. Thalidomide still evokes images of human suffering. It earned this reputation because of the deformities it inflicted onto unborn children. Thalidomide was given to pregnant women to assist sleep and prevent morning sickness. The drug interfered with foetal development to produce deformities that included missing or abnormal limbs, spinal defects, cleft palates and the abnormal formation of many vital organs. Forty percent of cases lead to mortality during or shortly after birth.

Consequences of thalidomide. Tony Melendez aged 4. He is now an award winning singer and guitarist who plays with his feet. Image: Reuters

A German pharmaceutical company, Chemie Grünenthal, first marketed thalidomide in 1957 as a hypnotic to induce deep sleep without producing the side effects associated with other barbiturates available at the time. In 1956 the research of Wilhelm Kunz found it depressed the nervous systems of animals without fatalities. It was considered to be a safe alternative to contemporary medicines because its low toxicity could prevent an accidental or intentional overdose. A marked increase in deformities in newborns of patients taking the drug caused physicians to demand it be withdrawn from the world market in 1961. Astonishingly within a relatively short span of time between the first appearance of the drug and its subsequent withdrawal it had adversely affected the lives of more than 10,000 individuals.

Controversy surrounded the way in which the drug companies had marketed and produced thalidomide. It was argued that the disaster could have been averted if correct scientific procedures and protection were followed. Not until after the drug was removed from the market were extensive reproductive tests in animals carried out. Normally the pharmaceutical company would carry out and publish extensive reproductive studies in animals. Yet in the case of thalidomide, a drug that was being prescribed to pregnant women, similar studies had not been undertaken. Controversies such as this reflect the ambivalent relationship between science and other social institutions such as the media, regulatory systems and commerce. The media played an important role in the in the thalidomide case, contributing to legal history when the Sunday Times won an important case against Her Majesty’s Attorney-General in the European Court of Human Rights. The article that evoked this response exposed the shortcomings of the Distillers Company (Biochemicals) Limited, that marketed the drug as Distaval. Lack of experimental studies prevented the drug from reaching the American market as the chronic toxicity data was incomplete. The Food and Drug Administration (FDA) criticized the lack of long-term scientific studies and was concerned about the evidence that the pharmaceutical company were withholding, they were particularly apprehensive about the drugs reported side effect of peripheral neuritis.

The thalidomide controversy immediately led to tighter controls on the introduction of new drugs in the form of an independent Committee on Safety of Drugs. Eventually a Medicines Act was established in 1968 and the Committee on Safety of Medicines was formed in 1971. The USA had the Pure Food and Drugs Act in place as early as 1906. Evaluation to ensure drug safety was established by The Federal Food, Drug and Cosmetic Act in 1938 governed by the FDA founded in 1931. The FDA demanded scientific evidence to evaluate thalidomide, it was not available and therefore the drug was not granted a license to be marketed. If the same procedures had been followed in other countries the number of affected individuals may have been substantially reduced.

The thalidomide controversy drew the attention of the public towards the morality of the pharmaceutical companies and many aspects of scientific research. Tensions existed between public health issues and economic priorities. Pharmaceutical companies exploited scientific discovery for financial gain that appeared to obliterate human compassion, with individuals passing responsibility so that no body was eventually held to account. Not only were the victims facing the physical and mental hardship of overcoming severe disabilities but they also faced a long fight to receive compensation. The science of actually manufacturing the drug was not fully responsible for the thalidomide controversy. If thalidomide occurred naturally, say as a plant extract, and was not synthesized in a lab these problems would still have existed. It was the marketing of the substance as a drug that caused the problems. The lack of scientific evidence that ensured the drug was safe. The public learnt that scientific evidence could be manipulated by financial gain. Controversies such as this cause people to lose faith in science. In this case essential research was not presented in order to release the drug on to the market and the British authorities failed to regulate the pharmaceutical company concerned or compensate the victims.

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.