What Is Life and How Might It Be Sustained?

Reflections in a Pandemic

Jim Lynch

• Editorial: CRC Press
• Año: 2022
• ISBN:
  9781000618563
• Edición: 1
• Categoría: Medizin
• Categoría: Infektiologie

How did the universe and life begin and what are the threats to people and the environment in a pandemic? This book is for anybody with interest in protecting life on the planet. Studies on the origin of life and scientific contributions to safeguarding the planet are examined in light of current thinking on climate change. A major focus is the spread of microbes, put in the context of environmental assessment and management, including descriptions of microbiomes and a consideration of the risks of genetic modifications. Professor Lynch shows how failure to control disease can lead to the collapse of any biotic population. To avoid this, the ethics of management of disease by biological control and by vaccination are discussed, at the practical level and in a moral theological context.

1 Introduction

DOI: 10.1201/9781003304845-1

The most beautiful thing we can experience is the mysterious. It is the source of all true art and science. He to whom the emotion is a stranger, who can no longer pause to wonder, and stand wrapped in awe, is as good as dead – his eyes are closed. The insight into the mystery of life, coupled though it be with fear, has also given rise to religion. To know what is impenetrable to us really exists, manifesting itself as the highest wisdom and the most radiant beauty, which our dull faculties can comprehend only in their most primitive forms – this knowledge, this feeling is at the center of true religiousness.

Albert Einstein, 1879–1955

Look after the land and the land will look after you, destroy the land and it will destroy you.

Aboriginal proverb

If we lose the land, we lose the culture. Lose the culture, lose the peace. Lose the peace, lose the community. Lose the community, lose our way of life. Forever.

Oloiboni Kitok, Maasai spiritual leader.

This book will discuss how was life created, what are the threats to life as we know it, and how might it be managed sustainably to secure life on the planet. The coronavirus pandemic has changed the world as we know it. The scientific world has come together in an unprecedented way to attempt to combat the virus, and there is a new familiarity amongst many with the work of scientists, medical practitioners and epidemiologists, and sociologists. However, discipline boundaries can often seem impenetrable even though breaking them down is critical to our future. The virus has rendered us vulnerable in a way we never thought possible. We have come to realise that life is fragile, especially when our activities have led to global warming to threaten life. This exposure to uncertainty has led many to question what we value as global and local communities, and what is now compromised. Management of land is crucial in this. Some may ponder on the origin of life itself and the threats to its future existence. In the throes of the pandemic, there is a new consciousness of the need for a better world in which human communities and their associated biota can lead a healthy and sustainable life. The age-old conflict between science and religion continues, but is there a way they can work together for the benefit of mankind?

Quantum physics is a key factor in the origin of life. The term quantum physics has entered public consciousness via the work of Stephen Hawking and the television documentaries by Brian Cox. The Grand Design (2010) by Stephen Hawking and Leonard Mlodinow introduced the reading public to the subject. Roger Penrose, Stephen’s PhD examiner, had described how quantum physics shapes the way we think in his book Shadows of the Mind (1995). Penrose received the 2020 Nobel Prize in Physics for his work on black hole formation, one of the most important phenomena of the universe, as a predictor of the general theory of relativity. Stephen addressed the timeless questions of life on this planet in his book published just after his death Brief Answers to Big Questions (2018). My colleague Johnjoe McFadden introduced Quantum Evolution (2000) in which he describes this new science of life and how it may have emerged from the primeval soup. Johnjoe collaborated with another colleague, quantum physicist Jim Al-Khalili, and in their book Life on the Edge (2014) described how very small events in the quantum world can affect creatures such as us.

The great question remains where do we come from? What was the spark to create life? Physical events almost certainly initiate the pathway for a route to life, but the primary trigger is still unclear and remains a mystery. Such events must be followed by chemical organisation of molecules, and I had the opportunity to pursue this topic for my PhD while funded by the oil company BP who had also generously funded my undergraduate studies. Initially, I found that the lipid fraction of fungi is a source of long-chain hydrocarbons. Further research on a methane-utilising bacterium, Methylococcus capsulatus (Figure 1.1), being grown in bulk by Shell as a possible food source revealed that the dominant hydrocarbon, accounting for 0.5% of its cell mass, was squalene with a carbon chain length of 30 in a branched structure made up of six isoprene units. This appeared to be associated with the extensive internal membranes structure of the bacterium. At that time (1971), it was believed that the lowest class of cells, prokaryotes which are bacteria and blue-green algae, had the absence of sterols as a distinguishing chemical feature. Surely squalene in the methane-utilising bacterium could not be metabolised to sterols? Instrumental techniques were inadequate at the time, and although gas chromatography (GC) was an option to separate them, it would not identify the chemical structures. For identification, a mass spectrometer (MS) would need to be coupled to the flame ionisation detector of the GC. The problem was that hardly any such devices were available. At Bristol University, they had just received the samples of lunar rocks from the first Moon Landing and were using combined GC-MS to analyse them. A trip to Bristol was unsuccessful as the sterols which had been analysed by GC on glass columns in my laboratory in London stuck to the walls of the steel columns being used in Bristol. Another GC-MS system became available at Glasgow University which used glass columns and identified the presence of two unusual sterols. This was the first demonstration of sterols in prokaryotes, resulting in a revision of the distinction between eukaryotes and this was published in Nature. This was of great interest to BP because using the new technique with glass capillary columns and working with a group at Strasbourg University they had found some very ancient (2.7 billion years) sediments, the Soudan Shales in Minnesota, chemical structures which were the same as those in the bacterium. This research was therefore indicative that methane-utilising bacteria, which are capable of growth up to 50°C were probably the oldest forms of life on the planet, making use of methane in the primordial atmosphere. Such markers have never been found on the Moon, but they will likely be investigated when Martian samples come to earth. Methane is of great concern today in global warming because it has about 30 times the global warming potential of carbon dioxide. It is perhaps surprising that the methanotrophic bacteria that utilise methane have received little attention in relation to their potential to remove methane from the atmosphere.

FIGURE 1.1 The cells are 1 micrometre in diameter and the cells have a dense internal membrane system containing squalene. (With permission from Anne Fjellbirkeland)

Many ideas have been promulgated to describe how chemical reactions from a big spark in the primordial atmosphere may have led to life on the planet. These were catalogued by Nobel laureate Melvin Calvin in his book on Chemical Evolution (1961) and will be discussed in this volume, alongside more recent ideas by Gaia Vince in her book Adventures in the Anthropocene (2014) and by Michael Marshall in his book The Genesis Quest (2020). Of particular interest are the Miller-Urey experiments in which a spark was generated in a synthesised atmosphere thought to be representative of the primordial atmosphere of the earth and detected biological molecules are present in living cells. Beyond the sparks, I will try to show primitive cells formed, leading to microorganisms which have beneficial impacts on us we evolved, but also discuss some of the harm they can cause.

In the mid-twentieth century, a controversial Jesuit priest, Pierre Teilhard de Chardin, who was a geologist and palaeontologist, excited considerable interest with his ideas on evolution and the origin of life. Palaeontology investigates fossil structures, building from the chemical evidence just described. Teilhard in his book The Phenomenon of Man (1955, English Translation 1959) outlined evolution as the transition from an abiotic to biotic state. He described a synthetic model of evolution linking to cosmic theology. The evolutionary biologist Sir Julian Huxley praised elements of his work, in contrast to the scornful review delivered by the immunologist and Nobel laureate Peter Medawar, and later by the ethologist and evolutionary biologist Richard Dawkins. Teilhard’s views brought him into much conflict with the Catholic Church, just as Galileo Galilei had effectively been isolated by the Church for his views of the Earth and its place in the solar system. In more recent times, Teilhard’s vision of the world has found support from esteemed quarters, notably Cardinal Ratzinger, subsequently Pope Benedict XVI. This volume will delve further into the legacy of Teilhard’s work.

The twenty-first century has brought us a challenge unlike any other we have faced – saving life on earth. We have ignored warning signs which have been clear for at least six decades, and the clock is still ticking. Rachel Carson identified the threads in her book Silent Spring (1962). She described how pesticides threatened the delicate balance of nature, and how irresponsible crop-dusting has decimated countless forms of life. Indeed, human life itself may well be endangered by pesticides. Such a view generated hostility in the agrochemical industry, especially as she was a marine biologist. This was book strongly supported by Julian Huxley in writing the Preface and was influential in Jim Lovelock writing the book Gaia. A New Look at Life on Earth (1979). Lovelock had an outstanding reputation as a scientist, having developed the use of the flame ionisation detector in GC, and worked with NASA in their space programme. As an independent scientist and choosing to work from a cottage in the West of Ireland, he brought knowledge from astronomy to zoology in support of his hypothesis that the earth functions as a single organism which defines and maintains conditions necessary for its survival, developing a radically different model of earth. He had the support of many colleagues, especially Lynn Margulis of Boston University. One of the principal opponents of his hypothesis was Richard Dawkins of Oxford University who argued that there is no way for natural selection to lead to altruism global in scale. His concept of Mother Earth of Gaia as the Greeks called it long ago excited much debate and discussion which continues today. In 2015, Pope Francis, who was a chemical technician by training in Argentina before studying philosophy and theology, wrote a very important Encyclical letter Laudato Si’. On Care for Our Common Home. In the Encyclical, he put the case to protect the environment along the lines of the Gaia hypothesis. Significant individuals who have championed the cause have included David Attenborough with his outstanding television programmes, which include warning of the dangers to wildlife of plastics in the environment. Also, HRH Prince Charles with Tony Juniper and Ian Skelly wrote Harmony: A New Way of Looking at Our World (2010). Attenborough’s latest book A Life on Our Planet (2020) is presented as his witness statement and a vision for the future. His introduction to the book is titled “Our Greatest Mistake” in which he introduces the concept of how the biodiversity of the planet has been compromised by our actions. Much work is needed, with policy development, to prevent global warming and climate change is needed as a major factor in the potential deterioration of the life on earth. Everybody was excited by the Conference of the Parties (COP 24) Intergovernmental Panel on Climate Change Conference in Paris in 2016. Optimism created by scientists and politicians gave hope to the global community for a reduction climate change. This could be by changing industrial practices and lifestyle. However, the decision of the Trump Presidency to withdraw the USA from the agreement extinguished the hope of radical change. Fortunately, President Biden has a different view and optimism was reignited for the reorganised COP 26 meeting in Glasgow in December 2021. Bill Gates has just produced an important work How to Avoid a Climate Disaster (2021) in which he sets out a wide-ranging but accessible plan for how the world can get to zero greenhouse gas emissions in time to avoid a climate catastrophe. Emission reduction has been a key component of the COP meetings since they started in Rio de Janeiro in 1992, and trees are contributory factors in carbon capture leading to the REDD+ (Reduction of Emissions due to Deforestation and Forest Degradation) initiative. One-fifth of the world’s population, 1.2 billion people, is dependent on forestry for their livelihoods. This is of particular significance in tropical countries and an activity which is being heavily compromised by illegal logging. In a paper to Nature in 2010, I argued that the only way to monitor deforestation is with satellite imagery and the application of stochastic models. International agencies, including the COP meetings, have been slow to come to consensus on international agreements for monitoring and reporting. Another unsatisfactory aspect is that the monitoring by earth observation which is done does not address the forest degradation that can result from environmental conditions such as wind or drought or from pests and diseases. Under such conditions, a forest can reach a tipping point from which trees do not recover and ultimately they die. This is possible to assess using non-linear mathematical modelling, but it is frustrating that there has been so little uptake of this approach to such an important global problem. Tipping point analysis of populations could also be relevant to the current pandemic in a very pessimistic scenario.

We humans are heavily dependent on food security generated by agriculture for their survival, and crops and animals can be subject to pandemics. Crops require suitable temperatures to grow and a fertile soil, which promotes the necessary nutrients and water, without being subject to toxins and growth retardants from pollution or adverse natural processes. This is compromised by climate change where some crops will not thrive at higher temperatures. For example, some of my early studies published in Nature investigated how fungi growing on straw in wet anaerobic soils could produce the growth hormone ethylene and retard root growth and crop productivity. Other studies showed how acetic acid could be produced by anaerobic bacteria under similar conditions and become toxic to seedlings. Another paper published in Nature showed how bacteria and fungi could cooperate to enhance fixation of nitrogen from the atmosphere and increase the supply of nitrogen as a nutrient to plants. Clearly, the value of microorganisms, particularly when they are close to roots (the rhizosphere), is a balance between beneficial and harmful effects. The community of microorganisms is now termed the microbiome. Microbiomes were first named for their interaction between plants and microorganisms, but subsequently, the term was applied to human and animal guts. Microbial ecology is the spine of this book, and the cover depicts a mixed population or microbiome of the human gut. Notable harmful organisms in the environment are the pathogens which can affect both roots and shoots of plants. However, it is often not recognised that some bacteria and fungi can effectively attack the pathogens and bring about the process of biological control. One route to achieve this is antibiosis. Indeed, Selman Waksman investigated antibiosis in a soil bacterium which led to the production of streptomycin, a discovery which resulted in a very important pharmaceutical and led to the award of the Nobel Prize. Preparation of biological control agents against pests and diseases for commercial delivery as a route to reduce the input of potentially harmful chemicals into the environment is an attractive option. In 1983 in a book Soil Biotechnology, I defined this new discipline as the study and manipulation of soil microorganisms and their processes to optimise crop productivity. This can be achieved by enhancing natural processes (augmentative) or by new introduction release to the ecosystem (inundative). In many ways, the uptake by industry has been disappointing, and this has in part been due to the agrochemical industry feeling threatened by the prospect of a reduced need for chemicals. There has also been concern because the public have sometimes thought of them as biological weapons which might spread disease in human populations. This is, even more, the case when the microorganisms or the plants with which they are associated have been genetically modified, attracting headlines in newspapers such as “Frankenstein Foods”. In making the first UK release of a free-living genetically modified microorganism, created with my colleague Mark Bailey in Oxford, into soil, we were subjected to rigorous interrogation by government committees, and rightly so. Explaining such opportunities to the public became a huge challenge. It can be very useful to work with psychologists skilled at forming focus groups with the public to deliver messages and seek opinions with a view to developing trust. My colleague, Glynis Breakwell, has published a book in 2021 on Mistrust which is very relevant to pandemics.

When it was recognised by the early investigators that microorganisms could cause infection and spread of disease, and cause food to rot, there has often been a lack of recognition of the beneficial activities of microorganisms. A balanced view was presented by Bernard Dixon in his book Power Unseen. How Microbes Rule the World published in 1994. These benefits include degrading waste, providing nutrients and food products, and attacking pathogens, including bacteriophages in which viruses inactivate bacteria. A microbiologist is trained to show respect for microorganisms and work safely with aseptic procedures. There has also been the ongoing fear that microorganisms might be used offensively as weapons. Consequently, many countries have set up defence programmes to protect against this. At the time of the war in Iraq, it was believed that biological weapons posed a considerable threat and that, along with chemical weapons, was a justification for the invasion of Iraq. The media ran a story that such weapons were being produced at yogurt factory led by a woman they nicknamed Dr Death. I was immediately contacted because the woman had been one of our students and the security services wanted to know if I thought that possible. I thought it extremely unlikely. More importantly, the British weapons inspector Dr David Kelly who had made several official visits wit...