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My friend Anthony Wilson, poet and educator, has published several ‘thin volumes’ of his own wonderful poems and has also produced a beautiful and wide-ranging anthology of other poets’ work, entitled ‘Lifesaving Poems’ (Bloodaxe Books, 2015). In his commentary on Tides, a poem by Hugo Williams, Anthony alludes to the words of Seamus Heaney who became conscious in his late 40s of his need to ‘credit marvels,’ or in the words of another commentator, John Wilson Foster, to nurture ‘a more conscious receptivity to the wondrous inherent in the commonplace’. This is a theme that emerges in Chapter 5 of our book. There I suggested that our familiarity with the mechanisms involved in the working of genes has meant that those mechanisms seem ‘ordinary’ or even commonplace. Indeed, in some ways they are, taking place during every second of every day in every living cell. And yet, if we look beyond that familiarity, that ordinariness, that commonplaceness, they are indeed marvels.  We can see the same sequence of thoughts when we consider how some of the findings of science are used to benefit human society. The announcement that ‘scientists are now able to …’ (fill in your own favourite here) induces our amazement, our wonder but those emotions fade as the particular innovation becomes embedded in medicine/agriculture/IT etc. And thus it has been with PCR – a three-letter abbreviation that has become very familiar to us during the COVID-19 pandemic. However, for many people, that’s where their knowledge of the process stops, i.e., it’s a method used to test for the presence of the virus but there’s no need to know any more than that. However, I want to say more than that because it is a beautiful example of how the knowledge revealed by scientific research (or, as tabloid newspapers might say – the work of back-room boffins) can be put to a use that benefits society. PCR stands for Polymerase Chain Reaction and those words sum up beautifully the essentials of the process. Let’s start at the beginning. A polymerase is an enzyme (a biochemical catalyst) that makes polymers – molecules built up from many similar smaller molecules. As we describe in Chapter 5, DNA is a polymer and the individual units of which it is made are called bases (1). Enzymes that build DNA are called DNA polymerases (2). The American biochemist Kary Mullis proposed that the stable DNA polymerases from certain heat-tolerant bacteria could be used in a ‘chain reaction’ to amplify (make many copies of) pieces of DNA (3). He successfully demonstrated the technique in December 1985 and it quickly became embedded as a routine tool in molecular biology. Mullis shared the 1993 Nobel Prize for Chemistry in recognition of the importance of this.  Further, we can, in any sample of DNA, direct the reaction so that it only copies the segments that we want to be copied. The detail is not important except to say that this is achieved by use of primer molecules that can be synthesised in the lab to recognise particular DNA sequences. PCR will then amplify the tract of DNA between the two primers. We can build up a stock of any gene or other DNA sequence in which we are interested. Further, as I am sure dear reader you will have realised, if the sequences at which the primers are aimed are not actually present in our DNA sample, then no amplification occurs. The importance of this is immediately apparent when we apply the technique to the detection or otherwise of, for example virus genes (more about this later in this blog).  As mentioned above, it did not take long for PCR to become established as a routine tool in labs working on genes, including my own at the University of Exeter. Prior to the technique’s invention, amplification of particular genes or other sequences was done by growing them in bacteria by a process called molecular cloning. It was certainly more cumbersome and time-consuming than PCR and it was often difficult to clone just the piece of DNA in which one was interested. The small machines (with a footprint smaller than a piece of A4 paper) in which PCR is carried out became part of the standard kit in any molecular biology or molecular genetics lab. The wondrous had become commonplace. At this point a quick reminder of basic mechanisms involved in the way that genes work will help to understand how PCR has been used during the pandemic. When a gene is working, it is not the code in the DNA itself that is read but the code in a copy of that gene. That copy is not made of DNA but of RNA and is known as messenger RNA (mRNA), as described more fully in Chapter 5. However, some viruses, including SARS-CoV-2 (the virus that causes COVID-19) use RNA as their genetic material. It is the genes themselves that act as mRNA, without the need to copy from a DNA template (4) and the unsuspecting host cells use that virus mRNA to make components of the virus. If you have followed this discussion so far, you can see that this might be a problem for PCR, which amplifies DNA, not RNA. Once again however, scientific discoveries come to our rescue. There are some viruses whose ‘life-style’ involves copying RNA into DNA. These include HIV and, in the plant world, cauliflower mosaic virus (CaMV). And of course, there is an enzyme (biochemical catalyst) that does this. It is called reverse transcriptase (RT), a DNA polymerase that makes DNA copies of RNA molecules (5). When we use it in the lab we can again employ specific primers (see above) so that only the RNA of interest is copied. This can then be amplified by conventional PCR which, by using careful changes of conditions, takes place in the same tiny test tube as the RT reaction. Virus RNA (or a specific section of virus RNA) is copied into DNA with RT; DNA is amplified by PCR.
In testing for SARS-Cov-2, a standard is included to make sure the technique is working and the technician will look to see whether or not there has been any amplification of virus-specific sequences. A lack of amplified viral sequences indicates an absence of virus in the original sample, i.e., a negative test result. There are different ways of detecting the amplified DNA. In one method, fluorescent DNA-binding chemicals are used and in larger, more sophisticated PCR machines than the basic machines I mentioned earlier, the detection of the fluorescence can be done in situ as the reaction proceeds. With suitable calibration with appropriate standards, the amount of fluorescence can be related to the amount of RNA in the original sample. In other words, the process can be quantitative – hence the shorthand name for the overall procedure is qRT-PCR. In my lab for example, we used this procedure to compare the amounts of mRNA from two different genes in dividing plant cells (6). So, if my descriptions have been clear enough – and I hope that they have – next time you hear about a PCR test for presence versus absence of SARS-Cov-2, I hope you’ll think about Seamus Heaney looking to ‘credit marvels’ in the commonplace. I hope you’ll remember the skill and inventiveness of Kary Mullis and of the scientists who subsequently tweaked his PCR technique. I hope that you will see the marvels in the ‘commonplace’ but nevertheless beautiful biochemical reactions, reactions that are going on all around us – and indeed within us – that are employed in the PCR procedures. I hope you will see the ‘poetry of nature’ in those reactions. And dare I hope that you’ll also thank God for science? John Bryant Topsham, Devon November 2021 (1) Technically, the building blocks are actually deoxyribonucleotides; a base is part of a deoxyribonucleotide (or, in RNA, part of a ribonucleotide). (2) These are enzymes with which I and my research team are very familiar: e.g., https://doi.org/10.1093/jxb/43.1.31 (3) When working optimally, the process can generate a billion copies from a single piece of DNA in just a few hours. (4) Tobacco mosaic virus (which also attacks tomato plants) also has an RNA genome which acts directly as mRNA (or in technical terms, is a + stranded RNA virus). It was widely used in research as a ‘model’ for viruses of this type, including our studies of how the viral genome is copied: https://doi.org/10.1093/oxfordjournals.aob.a086791, https://doi.org/10.1093/oxfordjournals.aob.a086933 (5) It was a privilege for me to be part of the group that discovered and started to characterise the CaMV reverse transcriptase https://doi.org/10.1093/nar/13.12.4557 (6) https://doi.org/10.1093/jxb/erg079
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 Graham writes … For those of you who are into this kind of thing, there have been rumours in the scientific press recently that new physics is afoot. So, what’s it all about, and should we be excited? I know I will be … But before we talk about the latest developments … the last time that there was a significant engagement between the physics community and the popular press was in 2012, when the discovery of the Higgs boson was confirmed. Looking back on it, it was quite an exciting time. Interest, and confusion, was whipped up by the adoption of an unusual nickname for this elusive sub-atomic particle – the ‘God particle’! This was principally the reason for the media interest, and this unlikely title was first coined by Physics Nobel Laureate Leon Lederman in 1994. He told people that he invented the name because the Higgs boson – then a purely theoretical entity – was ‘so central to the state of physics today, so crucial to our understanding of the structure of matter, yet so elusive’ (1). As it turned out, this rather confusing association of the particle with God turned out to be not such a bad thing, as it got people talking about frontier research in particle physics. I recall a time in the 1960s/1970s when particle physics was in a state of confusion, with the discovery of a plethora of new particles, but without any understanding of the underlying structure of how they fitted together. Over time, as mentioned in Chapter 2 of the book (2), the physicists have developed a ‘Standard Model of Particle Physics’ that hopefully makes sense of it all. This has been a great success, and has allowed a greater understanding of the quantum world. The diagram below shows the current status of the standard model, indicating all the particles that are believed to be fundamental (each of the particles also have a corresponding antiparticle, which are not shown). In other words, the particles listed are considered to be indivisible.  For example, the ‘familiar’ particles that make up the nucleus of an atom – the proton and the neutron – are now known to be divisible. These particles are composed of 3 quarks, (the family of quarks is shown in purple). In this case, the proton is made up of 2 ‘up’ quarks and one ‘down’ quark, and the neutron 2 downs and one up. There are six ‘flavours’ of quark in all. Shown in green, there are six types of particle referred to as leptons – after the Greek leptos, meaning ‘lightweight’ – which are also considered to be fundamental. The most ‘familiar’ of these is the electron. However, this has larger counterparts – the muon and the tauon, which are about 200 times and 3,500 times heavier than the electron, respectively. Associated with each of these, there is a neutrino particle. Remarkably, physicists have not yet been able to measure the fundamental attributes of the neutrinos (such as mass!) because their interaction with matter is so extremely weak. For example, they can pass through our home planet without leaving any tell-tale sign of their presence. All that is known is that the three types of neutrino have a combined mass that is several million times less than that of an electron, but there is sufficient understanding of neutrino behaviour to appreciate that they are not massless.  The red particles are called bosons and have the property of being ‘force carriers’, and have the job of exercising the forces between particles. For example, the electromagnetic (EM) force acts upon charged particles by the exchange of a photon. A similar mechanism is envisaged for the gluon which governs the strong nuclear force, and the W and Z bosons which administer the weak nuclear force.  However, I am aware that our understanding of the quantum world remains incomplete. For example, it is worth remarking upon the significant absence of a boson (‘force carrier’) for the gravitational force (in its absence, it has nevertheless been given the name ‘graviton’). As discussed in the book (3) gravity has evaded all attempts to include it in the standard model. Indeed, there is debate as to whether gravity is a force in the same sense as the other three fundamental forces (EM, weak nuclear and strong nuclear), and this is probably an obstacle to achieving the unification. As described in the book (4), the mechanism through which Einstein’s gravity acts is completely different to those of the other forces. Briefly, a mass (for example, a star) produces a curvature in the surrounding space-time, and objects moving in the star’s neighbourhood move along trajectories that take the shortest distance in the curved geometry. So, it could be summarised by saying that mass shows space how to curve and curved space shows mass how to move. Inherently Einstein’s gravity is a classical theory, involving ‘geodesics in a curved Riemannian geometry’ (this phrase may be meaningful to some readers?), so it is not too surprising that the quest for unification with the other ‘quantised forces’ is proving to be very challenging. It is a problem of attempting to unify an inherently classical theory with its quantum counterparts.  Another rather large hole in the standard model is the notion that so-called ‘normal matter’, as described by the current standard model, comprises only about 5% of the total matter/energy content of the Universe. The other 95% is comprised of dark matter and dark energy (5), and currently we have no idea what these are. So, there is probably a whole new family of particles waiting to be added to the standard model to describe this so-called ‘dark universe’. We know our theories are incomplete, and there is plenty of new physics waiting for a team of new ‘Einsteins’ to show us the way.  However, coming back to the things we think we understand about the standard model, we finally come to the Higgs boson, identified in yellow and sitting all by itself on the right-hand side of the diagram. So, what is the Higgs boson, and what does it do? It all started with some published theoretical work by Peter Higgs in 1964, which first predicted the existence of the particle. It took a remarkable 48 years for the experimental community to catch up with the theoreticians, with the development of the Large Hadron Collider facility at CERN (Conseil Européen pour la Recherche Nucléaire) near Geneva. This remarkable machine produces sufficient energy to allow the creation and detection of this new particle, for which Peter Higgs, now a retired professor at the University of Edinburgh, UK, received the Nobel Prize in Physics in 2013. In order for such a breakthrough to be declared officially as a discovery, it has to be confirmed at the ‘5-sigma level’. A 5-sigma result is considered to be the gold standard for significance, which is just a bit of statistics jargon which translates into a tiny probability (1 chance in about 3.5 million) that the event is a random fluke.
The remarkable property of the Higgs boson is that it gives all the other particles in the standard model the attribute of mass, with the accompanying property of inertia. The Higgs boson has an associated field which has a non-zero value throughout all of space, which is sometimes referred to as the Higgs ocean. As particles traverse this field, they interact with it in proportion to their mass – in other words, each fundamental particle acquires its specific mass. Of course, some particles such as photons of light are massless, because they do not interact with the Higgs field at all. More recently, physicists have continued to uncover further anomalies that point to new particles that comprise quantum reality. I hope you will join me again when I say something more about this intriguing idea in Part 2 of ‘New Physics?’. Graham Swinerd Southampton October 2021 (1) Alister McGrath, Inventing the Universe, Hodder & Stoughton, p. 57. (2) Graham Swinerd & John Bryant, From the Big Bang to Biology: where is God?, KDP publishing, 2020. (3) Ibid., chapter 2, pp. 36-38. (4) Ibid., chapter 3, pp. 52-56. (5) Ibid., chapter 3, pp. 74-76. John writes ...  I have worked directly or indirectly on DNA and genes from my PhD student days and throughout my research career. My focus was at the interface of biochemistry and genetics, an area of science that we call Molecular Biology and with which I am very familiar. It is replete with marvellous molecules and mechanisms, although, for those of us who are practitioners, it is too easy to take those marvels for granted. We need to ‘stand and stare’ perhaps for just a few minutes to remind ourselves that the whole topic is amazing. Let me start with the genetic material itself, DNA. DNA molecules are not really complex, although they can be very long (long in relation the dimensions of living cells). DNA molecules are polymers, that is they are built of many individual components linked together. These individual components are called bases in biochemical shorthand and there are only four sorts – as I said, DNA is not a complex molecule – and they can occur in any order. This simplicity fooled scientists for a long time: how could such a simple molecule carry genetic information? DNA was discovered in 1869 and was shown to be present in chromosomes early in the 20th century but it was not until the end of World War II that this key role of DNA was finally demonstrated beyond doubt. And of course, that demonstration led to extensive further research, including the elucidation of its structure by Watson and Crick – and others – in 1953. All the information required for the development and second-by-second life of all organisms is encoded just in the four bases of DNA, the specific information coming from the order and the number of bases in subsections of DNA molecules that we call genes. Further – and this fact still fills me with amazement – all living organisms on Earth read the code in the same way. Every living organism is related to every other, consistent with the idea that there was just one origin of life (abiogenesis) and all life-forms are derived from that common beginning.  Caption for image: In bacteria, the DNA molecules are circular and, in addition to their main DNA molecule, they often have mini-circles that carry just a few genes. We constructed artificial mini-circles by splicing different pieces of DNA together in order to study the interaction of a particular protein (see below) with particular structures in DNA. The interaction is seen here under an electron microscope. Image copyright © Sara Burton, John Bryant and Jack Van’t Hof.  But there is more. The information in DNA must be passed on. Every new cell needs a faithful copy of the genetic information from its ‘parent’. This is where the famous ‘double helix’ comes in (if you are not sure what a helix is, think of a ‘spiral’ staircase. A spiral staircase is actually not a spiral but a helix). A molecule of DNA consists of two helices wound round each other and which are held together because of specific abilities of the bases to form pairs with each other. Using just the initials of the bases to indicate their names, A in one helix can only pair with T in the other; similarly, G can only pair with C. I’m sure you can see that this immediately provides the means of passing on the code faithfully. If the two helices separate, then each single helix directs the synthesis of a new partner helix. For example, a T in the pre-existing single helix dictates that there must be an A at that position in the new helix. The structure of DNA means that it can direct its own faithful copying. That is both awesome and beautiful in its simplicity. If a human engineer had come up with this, we would say that he or she was a genius. As a Christian I say that the genius here is God. Thus the genetic code is safely passed on from generation to generation, but what does the code actually do? Well, it directs the synthesis of proteins, the cell’s working molecules. There are thousands of different sorts, many of which are enzymes – proteins that carry out biochemical reactions. Proteins are polymers (see above) built with amino acids, of which there are 20 types that vary significantly from each other in shape and size. The shape of a protein, essential for its function, depends on the particular array of amino acids – overall number and the order of different types within the molecule. Some proteins are small and quite simple, others are very large (in molecular terms). A code based on just four bases (read in groups of three) in DNA tells the cell the order in which to put the amino acids in a protein.
How does this happen? How is the code translated? The answer is not ‘Google Translate’ as one school student suggested to me! I’d like you to envisage the code as a row of beads of four different colours and the cell’s pool of amino acids as a pile of LEGO (TM) bricks of several different shapes and sizes. Those bricks do not fit onto the beads. In the same way, an individual amino acid cannot on its own recognise three bases and line up with them. The answer to this conundrum is in the form of adapter molecules which can recognise an individual amino acid and the three-base code that specifies that acid. These adaptor molecules ensure that the amino acids are built into proteins in the right order. It is an amazing mechanism and we have no understanding of how it evolved. This leads back to a point that I made at the beginning of this article. In Chapter 5 of the book, I wrote ‘… I cannot help think that we biologists are so used to this that we have become a little blasé.’ When we pause to think a little more deeply we can only react with awe and wonder at God’s magnificent creation. Note: I wrote a revised version of this blog for the Faraday Institute’s Faraday Churches web page. You can find it here, with a brief introductory paragraph from Ruth Bancewicz. John Bryant Topsham, Devon September 2021 Graham writes … Sometimes when John and I are leading a conference, we ask people to speculate about what is the most complex object we have discovered in the Universe. After a few responses, usually related to celestial objects, we guide the delegates by suggesting that there are many of these objects in the conference venue – the human brain! The working network of the brain has around 100 billion neurons (brain cells), resulting in the order of a million billion neuronal connections. In some way that science has yet to fully understand, this leads to mind and consciousness, as the mechanisms that give rise to these attributes remain a mystery. Given that mind and consciousness are the things that make us human, and are fundamental to our daily experience of ourselves and the world around us, it is remarkable that we have yet to comprehend how this works. One of the biggest scientific mysteries resides inside our head!  Earlier in the year I tuned in to an online meeting of Christians in Science to hear a talk called Am I just my Brain? by Dr Sharon Dirckx. As you may know by now, I am not exactly well-qualified to comprehend the subtleties of neuroscience, but I was delighted that the talk was pitched at my level, and I was also bowled over by what she had to say about our current understanding (or controversy) about ‘mind’. Dirckx (pronounced ‘Dirix’) is currently a Senior Tutor at OCCA (Oxford Centre for Christian Apologetics), after acquiring over a decade of hands-on experience in functional magnetic resonance imaging. Subsequently, I have acquired a copy of a neat little book that she has written with the same title (1). It was a good read, that I can recommend. This little book has much to say about a great many things, but I would like to say something about two topics in particular.  Firstly, that there is still debate about where the human mind ‘resides’. Given the importance of mind, I was really quite excited by the idea that the practitioners and philosophers are still discussing this issue. Afterall, I am effectively my mind. It is where I play out my inner life, it is where my memories reside (and effectively, my memories are what make me me) and it is where I organise and plan my life. The Oxford English Dictionary sums up ‘mind’ concisely as: The seat of awareness, thought, volition, feeling and memory. The debate about where exactly this seat resides has apparently gone on for a very long time, and still continues today. Having said this, it is fair to say that the scientific view is that the mind is the brain. All the complex facets of my inner life are just the firing of neurons, and the seat of mind is just brain chemistry. In this view, I am indeed just my brain. Another option is that the brain generates the mind. Once the brain reaches a certain level of complexity, mind emerges as something new and distinct, the word ‘distinct’ suggesting that the seat of the mind is controversially beyond the brain. In this scenario, given that mind is a product of brain, the mind ceases to exist once the brain dies. A third option offered by Dirckx is that mind is beyond the brain. Mind and brain are two distinct ‘substances’ that can interact, but they can also operate independently of each other. In this scenario, the brain can influence the mind, but the mind can also interact with the brain and the body – there is two-way traffic as, for example, when the body manifests psychosomatic illness. Clearly, this option is not recognised by the materialistic brand of science that pervades contemporary thinking on these things. Neuroscience can only recognise the first option.  The second topic is to do with whether, as human beings, we have free will – again a bone of contention for scientists and philosophers over many years. This discussion continues in the more contemporary setting of YouTube – you will find pages of responses if you just enter ‘free will’ into the search box. Why is this particularly of interest to Christian believers? It is a fundamental facet of the Christian faith that we are free to choose. God is not in the business of interfering with our free will. We can choose to go God’s way, or our own way – in other words we can choose to follow him. As God’s creations, he could have programmed us to follow and love him, but then the notion of love is meaningless in a world full of what effectively would be a population of programmed human ‘robots’. This is made clear by Jesus when he said “So I say to you: Ask and it will be given to you; seek and you will find; knock and the door will be opened to you.” (2) It is our choice whether or not to ask, seek or knock. However, there are many so-called ‘hard determinists’, who refute our ability to make free choices, despite the common human experience that we do this all the time. Hard determinism is a viewpoint that the human brain and the decisions arising from it are wholly determined by prior causes. In other words, the human brain is likened to a mechanism that operates within the confines of fixed processes, and it is this attribute that prohibits the possibility of free will.  In her book, Dirckx dismantles the philosophy of hard determinism in a beautifully concise section of her book (3) by asking three questions – is it internally consistent?, does it have explanatory power? and can it be lived? I do not wish to repeat her arguments here but just give a summary, with an emphasis on her third question. If I lived as a cause-and-effect machine, then any personally held belief is undermined – and this includes a belief in hard determinism itself, of course! Rather my precious conviction would just be the inevitable consequence of my neurons firing. If a determinist says we don’t have free will, and requests that I evaluate the proposition, I am unable to do this freely in the absence of free will. Effectively I would have no rationality – I would not be able to choose freely between concepts. Similarly, if you can’t make a free decision then there are other important consequences. I would effectively have no creativity, as I would be unable to choose freely between creative ideas. I would have no ability to love, as I would be unable to choose freely whether to embrace someone in that way. Perhaps the most significant issue is that I would have no personal culpability. In contemporary society, we are all considered to have moral responsibility, and are therefore accountable for our actions – I have a choice whether to do right or wrong. If this is not so then hard determinism threatens to unravel the cornerstone of moral responsibility and the need for justice. In other words, if you use the consequence of determinism as a defence in a court of law, the judge would most likely tell you, in no uncertain terms, to go away and rethink.  The scientific basis for saying that we do not have real freedom to make choices is the idea that the laws of physics allow us to predict the future based on knowledge of the current initial conditions. In other words, if we have knowledge of the current state of all the particles in your brain, then the laws lead us to a uniquely defined future state, therefore making freedom of choice an impossibility. However, this argument disregards the fact that physics is not yet complete. In fact, all of our laws of science – the mathematics we write down to make such predictions – are very much approximations to the reality, which is governed by the powerful agencies that enact what we call the laws of nature. For more detail, see the discussion in Chapter 2 of the book (4). Also, to make such claims when the path from fundamental physics to understanding mind and consciousness is completely uncharted, is, to me, the height of scientific hubris.
Dirckx’s argument takes the discussion in the opposite direction, based upon the consequences if hard determinism reigns. Either way, the bottom line is that we live in a manner in which the decisions we make mean something and these are made by volitional people, and not by cause-and-effect machines. (1) Sharon Dirckx, Am I just my brain?, The Good Book Company, 2020 (2) The Holy Bible, Luke's Gospel, Chapter 11, verse 9 (NIV) (3) Reference (1), pp 85-88. (4) Graham Swinerd and John Bryant, From the Big Bang to Biology - where is God?, Kindle Direct Publishing, 2020, Section 2.4 Graham Swinerd Southampton August 2021 John writes ... Our friend Dr Ruth Bancewicz is Church Engagement Officer at the Faraday Institute for Science and Religion in Cambridge. She has recently written an open letter to the Church of England Newspaper to which we have also posted a link on our book’s Facebook page. Her letter is entitled ‘Starting new conversations about science and faith’ and her opening discussion is focussed on something that is dear to both my intellect and my emotions, namely connectedness and inter-connections in nature. Ruth focusses on the extensive network of fungal mycelia that exists beneath the woodland floor providing myriad interconnections between the trees, as I also describe in Chapter 8 of our book. The ‘wood-wide web’, as some have called it, is a beautiful example of mutual support and enablement, leading to fruitful growth of both trees and fungi (in the latter, the appearance of mushrooms/toadstools is a sign of their fruitfulness). For readers who are particularly interested in finding out more, I recommend Merlin Sheldrake’s book Entangled Life.  Ruth suggests that a truly effective congregation should be a network of people, often working behind the scenes, perhaps even hidden, but providing extensive support and help in a mutually dependent way. Further, the establishment by the Church of England of the Anglican Science Commission emphasises the roles of scientists in congregations being active members of such networks. In the network beneath the forest floor one of the things that is shared is molecular information, often in the form of what biologists call ‘signalling’ molecules, molecules whose evolved purpose is to elicit a biological response. In the case of the scientist-Christian this may mean interpreting recent scientific findings and helping our fellow-Christians appreciate the beauty and wonder of the created order. We hope that our readers appreciate that aspect of our book and we note that Ruth herself discusses it at length in her recent book, Wonders of the Living World: Curiosity, Awe and the Meaning of Life. Or we may be able to stimulate discussions about the ethics of applying new knowledge or new science-based techniques or inventions (as is currently happening for genome editing and for AI). Or it may simply be a matter of just ‘being there’, one of thousands of members of the scientific community for whom science is not a threat to faith but a stimulus for worship.
John Bryant Topsham, Devon July 2021 Is there life elsewhere? Part 4. What are the theological implications of extra-terrestrial life?21/6/2021 Graham and John write ...  As Graham discussed in Part 2 of this series of posts, astronomers have discovered thousands of planets orbiting other stars; indeed, the number of new discoveries of exoplanets, as they are called, continues to grow on a daily basis. Many of these are located in the habitable zone of their sun, which spurs inevitable speculation about whether intelligent alien life resides there. However, this does not just depend upon the number of suitable planets but also upon the likelihood that life will occur given suitable conditions. The latter question was addressed by John in Part 3: abiogenesis on Earth looks to be extremely unlikely and remains a mystery but life has originated on our planet. Indeed, it has given rise to beings such as ourselves, capable of contemplating such things. Coming at the problem from two different directions, it is fair to say that we came to same conclusion – clearly there is currently insufficient data to say whether we are alone in the Universe or whether the Universe is teeming with life.  As we mull over these issues, our opinions about the abundance or otherwise of life elsewhere change, almost from day to day. At this moment for example, Graham is of a mind that intelligent life is only sparsely distributed throughout the Universe, because of the improbability of abiogenesis. But are we missing something here? John reminds us that there is evidence to suggest that on planet Earth life arose about 4 billion years ago, as soon as conditions became physically suitable. What life there was also survived the bombardment era, when the planet was repeatedly struck by large debris left-over from the birth of the Solar System. Perhaps abiogenesis is not as improbable as first appears. So, we might ask, as Paul Davies did in his splendid book The 5th Miracle (1), if the laws of nature are somehow bio-friendly. In other words, are they rigged in favour of life? Currently, there is no indication that this is so, or if it is, how it would work. So, what issues are posed for the world’s religions, and for Christianity in particular, if intelligent extra-terrestrial (ET) life does exist? This has been discussed in some detail by our friends at BioLogos in an online article by Deb Haarsma: ‘What would life beyond Earth mean for Christians?’. This includes a 90-minute video of presentations from the 2019 BioLogos Conference, featuring Deb Haarsma (theology), Jennifer Wiseman (astronomy) and Stephen Freeland (life sciences), which is well worth the time if you are really into this topic. It is difficult to add insight to the BioLogos article in this brief blog post, but at least we can express opinions and comment on the issues in general.  It is inevitable that many atheists will assert that the discovery of ET intelligent civilisations would put an end to religion and undermine Scripture. Others claim that since the Bible does not mention life elsewhere, it has nothing to say about the discovery of aliens. But then, as the BioLogos article points out, the Bible does not mention life in Australia either! Indeed, the article points to a survey of people who have a religious faith, which found that, actually, most are happy with the idea of life elsewhere and do not see it as a threat to their beliefs. However, a counter-view is expressed by Robert Lawrence Kuhn in a YouTube video, Would intelligent aliens undermine God?. He suggests that ET life poses challenges to Christian theology, but less so for Eastern religions. Among the many aspects discussed by Haarsma and her co-presenters, are on the one hand the universality of God’s created order, and on the other what might be called ‘parochial concerns’, those linked to planet Earth, especially related to the assumed uniqueness of humanity. The Christian Bible is truly universal in scope. It speaks not only of the Earth but of the entire Universe. God’s creation is unbounded and includes all worlds, and whatever forms of life that resides upon them.  However, it is the Earth-bound aspects that are of primary concern. Two thousand years ago Jesus Christ lived among us and experienced human existence ‘first-hand’. The incarnation is central to our Christian faith. The obvious question posed by Haarsma is that if God created intelligent beings on other planets, would Christ have been incarnate in those species too? Or is the incarnation unique to Earth? In other words, is the Bible just the ‘local branch book’? It is a question that has been explored by many authors. In his space trilogy, C. S. Lewis discussed the possibility of intelligent beings who developed a moral code and asked about their relationship with a creator-God. In the Narnia chronicles, Christ is incarnate as a lion, Aslan. The idea here is that God becomes incarnate amongst the created beings in an appropriate form. If that is so and if indeed the Universe is ‘teeming with life’, then is it reasonable to suppose that Christ became incarnate to other civilisations (assuming that abiogenesis can always lead to intelligent life and then to ‘civilisations’) throughout the Universe? For many (but not all) theologians, including C. S. Lewis, the answer is ‘Yes’ (2), while amongst scientists, Christian physicist Russell Stannard says, 'I can't see why the same Son of God, who has existed for all time, can't take on the form of other creatures once they reach the stage where they can communicate with God’ (3). But actually we have to remain agnostic on this topic, albeit with an inclination to agree with C. S. Lewis and Russell Stannard. We have no idea what intelligent ET beings would look like. We have no concept of how their spirituality would be manifest, assuming that they are spiritual beings, or of how they might relate to God. We can only say ‘God knows’, with no hint or intention of irony. God reminds us of this in the book of Isaiah, when he declares – “ … For my thoughts are not your thoughts, neither are your ways my ways. … As the heavens are higher than the earth, so are my ways higher than your ways and my thoughts than your thoughts.” (4).  One memory for Graham which underlined God’s ‘otherness’ concerned a late evening flight many years ago when he was returning to Southampton from Amsterdam. The flight path skirted the southern part of the conurbation of London, and it was a beautiful clear night. The whole of London stretched out beneath him like a huge, glowing living organism. While taking in this awesome sight, a curious thought suddenly flashed into his head. Just in that one city, at that moment, there was probably several hundred thousand of prayers rising to God. As a Christian who believes in the power and efficacy of prayer, it brought into sharp focus Graham’s complete lack of understanding of God’s omnipotence. The memory spurred him to suspect that, if there is a need to redeem a fallen alien civilisation (presumably, not all of them would be in need of this?), then God would find a way to show his redemptive love.
Finally, it has to be said that there are many scientific and theological questions that remain unanswered (some of which are probably unanswerable) and as a consequence there is currently insufficient knowledge and evidence to determine the existence, or otherwise, of life elsewhere. While it is interesting to ponder these questions, it is also important to worship and serve God here on this planet. In the light of current issues, we need to remember that for us Earthlings, ‘there is no Planet-B’ and that God has asked us to look after this one, ‘Planet-A’, our beautiful Earth. Graham Swinerd Southampton John Bryant Topsham, Devon June 2021
“There is a divine purpose behind this fruitful universe.” John Polkinghorne John writes … I am often asked whether, as a biologist, I think there is life elsewhere in the Universe or whether I believe in aliens (the latter more typical of teenage questioners). In last month’s blog, Graham wrote about this question from the point of view of a physicist who is also intrigued by biology. I am now adding my views on that question. One would think that I could simply answer ‘Yes’ or ‘No’ but I cannot. As I weigh up the possibilities, I cannot reach a firm conclusion – sometimes I think ‘Yes’, sometimes I think ‘No’ but mostly I think ‘I just do not know’. It is a question about which I am truly agnostic.  The first point to consider is the definition of life and that turns out to be harder than we might suppose. In a recent panel discussion on Radio Maria (Science and Faith: Episode 6 – The Biology of Human Life – Radio Maria England) we agreed that it is easy enough to describe life in terms of the attributes and activities that we ascribe to living things. Some of our readers may be familiar with the acronym Mrs Gren which helps us to remember the essential activities of living organisms (Movement, including movement within cells; Respiration, meaning the ‘extraction’ of energy by breakdown of particular substrates; Sensitivity – response to environment etc.; Growth; Reproduction; Excretion; Nutrition). So according to this, a living thing is defined as living because it carries out these activities (but not necessarily all the time). However, in our panel discussion we found it impossible to come up with a stand-alone definition of life – any definition that we came up with was effectively dependent on the descriptors/activities mentioned above. Nevertheless, we agreed that we can tell living things apart from non-living things such a rocks and water, although viruses defy a characterisation as either living or non-living. The second point is whether life elsewhere in the Universe would be similar to life on Earth or different from it. The problem here is that we cannot envisage any other system of chemistry that might lead to the development of entities that exhibit the ‘Mrs Gren’ characteristics mentioned above. Further, based on the uniformity of the laws of physics, it seems very unlikely that there exist any locations in the Universe where an entirely different system of potentially life-supporting chemistry exists. That leads me to suggest that if there is life on other planets it will be based on the chemistry of carbon whose structure and reactivity is ideal for formation of a wide range of complex biochemicals. Having said that, we need to think about whether the use of carbon would result in similar biochemistry in a distant alien life-form to that which pertains on Earth. This leads on to my third point, namely what are the essential basic features of chemistry/biochemistry that would enable life to start? As I describe in Chapter 5, many biologists regard the existence of a ‘self-replicating’ molecule (i.e., a molecule that can be copied and passed on to succeeding generations) as an essential pre-requisite for life. However, building larger molecules from smaller molecules requires an input of energy and, as also described in Chapter 5, Nick lane and other biochemists suggest that an ‘energy-gathering’ system (loosely defined as ‘respiration’ in the Mrs Gren acronym) is also an essential pre-requisite. Thus, we have two essentials that must be in place together before there is life. Intriguingly, these two essentials are manifest in the same ways in all living organisms. All possess DNA as their ‘self-replicating’ molecule and, at the heart of all energy-gathering systems there lies the process of creating a gradient of protons (positively charged sub-atomic particles). In seeing these two features we believe that we are getting a glimpse of what the earliest life-forms might have been like. Fourthly, there is a bit more to the simplest living organism than just the two essentials. In order to prevent dilution by and loss to the surrounding medium, there needs to be containment, That is, a cell with a boundary between the inside and the outside. Further, there must be information to ‘run’ the cell. This is provided by the ‘code’ in DNA (which is the same in all organisms) and I have written in Chapter 5 of the improbability of the decoding mechanisms occurring spontaneously. My fifth and final point is the question of whether there are other planets capable of supporting life. We noted in the book that Earth is a very special place with many features that help life to flourish. How likely is it that, amongst the vast numbers of planetary systems that Graham mentioned in our March blog post, there exists ‘another Earth’ or even several other Earths? On the basis of those vast numbers we might suggest intuitively that such planets must exist but actually we have no real means of calculating the probability. And if there is indeed another Earth somewhere, how likely is it that life exists there? I have already pointed out that, even on Earth, the origin of life (abiogenesis) seems improbable and yet it occurred relatively soon in the evolution of our planet. Does that mean that it will occur wherever and whenever planetary conditions permit? I leave you with a thought expressed several times by the late John Polkinghorne, namely that God has created a finely tuned and fruitful universe (For example, Introduction (wordpress.com)). If God the creator has willed it, life is possible on any other suitable planet. But of course we do not know ‘the mind of God’ in relation to our question. John Bryant
Topsham, Devon April 2021  We were very sad to hear of the death, on March 9th, of John Polkinghorne, a leading and influential voice in the science-faith debate. His career in science, working on particle physics and related topics, was very distinguished. He was appointed as Professor of Mathematical Physics at Cambridge University in 1968 and was elected as a Fellow of the Royal Society in 1974. His PhD students included Nobel Laureate Brian Josephson and Martin Rees, the current Astronomer Royal. However, in 1979 he left the world of academic physics to train for the priesthood in the Church of England and thus embarked on a very different style of life.
Over the succeeding years, his contribution to the discussion about the relationship between science and religion has been immense, with an impressive, intelligent, informative and thought-provoking output of books, talks, lectures and videos. But in addition to all this, John Polkinghorne was a wonderful human being – kind, thoughtful and humble. John had the privilege of meeting him on several occasions – on at least two of these we were speakers at the same conferences and have also both contributed to the Faraday Institute’s multi-media resource ‘Test of Faith’. Graham also had the pleasure of contributing, with him, to the ‘God: New Evidence’ series of videos on cosmic fine tuning. A brief tribute from the Faraday Institute may be found here: Revd. Canon Dr John Polkinghorne KBE FRS (16 October 1930 to 9 March 2021) | Faraday (cam.ac.uk). John Bryant Topsham, Devon Graham Swinerd Southampton March 2021 “Two possibilities exist: either we are alone in the Universe or we are not. Both are equally terrifying.” Arthur C Clarke, sci-fi author.  Graham writes … The question as to whether intelligent life exists elsewhere in the Universe is a fascinating one. As someone who was captivated by the sciences, and astronomy in particular, from a young age I have been always intrigued by this mysterious, unresolved issue. Everyone, including myself, is able to express an opinion, but evidence is lacking to be able to arrive at a definitive conclusion. The two major stumbling blocks are, firstly, no one knows how life began on planet Earth, and secondly no direct evidence of alien life has been found despite decades of searching by programmes such as SETI (the search for extraterrestrial intelligence). The first of these issues is that we do not have a working theory or understanding of the process of abiogenesis, which is the means by which living organisms arise from inorganic material (the proverbial ‘primaeval soup’). Despite intense research activity over many years, this has evaded satisfactory resolution. Some authors have expressed a view that ‘evolution did it’, but of course this only comes into play when there is an existing living population for evolution to act upon. Darwin’s process of natural selection can say nothing about the origin of life. So without an appreciation of how life began here, and in particular how likely or unlikely is the process of abiogenesis, it is difficult to assess whether the Universe is devoid of other life, or conversely teeming with life. The second issue related to SETI raises the question – if intelligent life is abundant in the Universe why has there been a total lack of evidence in the form of direct communication. Where are they all?  Our lack of success in making contact is not just about the vastness of space, but there is also a time-related aspect. There is good evidence to suggest that the Earth was formed around 4.6 billion years ago, and it has taken most of that time for intelligent life to arise. The human species, Homo sapiens, arose about 250,000 years ago, and it is only in recent times that we have developed the technology to potentially communicate across interstellar distances. Although we don’t know how typical our development is compared to extraterrestrial civilisations, we can indulge in a hypothetical comparison to make a point. We can suppose that an alien technological society would discover the energy of the atom, and potentially develop the capability to wipe itself out. Also if we assume that their society, like ours, is energy-hungry, this may result in the threat of a run-away greenhouse effect destroying their biosphere. This raises the question – how long typically would a technological civilization exist? It might be only of the order of 200 years between the development of communications technology and a potentially catastrophic demise. So here’s the point. If we collapse the 4.6 billon year history of planet Earth into a 24 hour period, then 200 years would be equivalent to a very brief 4 milliseconds (four thousandths of a second) – much shorter than the blink of an eye. So the window of opportunity, in time, to communicate with an alien society may be very brief indeed. And furthermore, how likely is it that our window of reception is synchronized with their window of transmission, given the huge sweep of cosmic history? Without breakthroughs in both of these areas, we come back to the notion that all we can do is express an opinion. I think at the moment it’s ‘fashionable’ to express a view that intelligent alien life is abundant. And a great many ‘celebrity scientists’ do. The argument goes that given enough planets and enough time, life will happen everywhere, despite the fact that abiogenesis appears to be very unlikely. An example is American astronomer and science communicator Carl Sagan, who presumably believed the view expressed by Ellie Arroway, the lead fictional character in his excellent novel Contact (1). Talking to a group of children, she expressed what has become a commonly held view: “I'll tell you one thing about the universe, though. The universe is a pretty big place. It's bigger than anything anyone has ever dreamed of before. So if it's just us... seems like an awful waste of space. Right?” I have to say that over the majority of my lifetime, I too have expressed this belief.  In recent years, I have attempted to gain more of an understanding of the problem of abiogenesis. It is fair to say that I have spent a career effectively as a physicist, so my background is not exactly ideal in allowing me to understand the complex biological issues associated with the origin of life. However, working with John Bryant in writing the book, and co-leading conferences, has spurred my interest in biology. I now find myself reading books about organic chemistry, life and the origin of life! I do however have to choose the authors I read very carefully, as I don’t have a lifetime’s experience of the topic to determine the authority, or otherwise, of what I read. Having said that, I now find that doubts about a Universe teeming with life have crept in. From what I grasp from my attempts to understand the biology of life, I have begun to appreciate the magnitude of the problem. Even my rudimentary knowledge gives me an appreciation of the beauty, elegance and especially the complexity of the mechanisms involved in the creation and sustenance of a living organism. In trying to understand how it all started are the enigmas of the curious but vital relationship between nucleic acids (information) and proteins (the molecular work horses) and the apparently irreconcilable ‘chicken-and-egg’ type issues that John has explained so well in his contributions to the book. At this stage of our scientific understanding of abiogenesis we have to say that it remains a mystery. So what are the chances of life arising from inanimate material? Many years ago mathematician and physicist Fred Hoyle (of Steady State Theory fame) likened the probability of abiogenesis as comparable to “the chance that a tornado sweeping through a junkyard might assemble a Boeing 747 jumbo jet.” His estimate of the odds of this happening is one in 10 to the power of 40,000 (that’s 1 with 40,000 zeros) – an extremely low probability. I have no idea how he came to such an estimate, but the truth is that we are not able to estimate the probability of abiogenesis occurring on this, or any other planet. Hoyle’s argument is now accepted as erroneous as it considers the unlikely scenario of advanced life forms arising directly from inorganic material.
One thing we do have some idea about is the number of planets in the visible Universe. Our home galaxy The Milky Way comprises around one hundred billion stars, and we can estimate the number of galaxies also as approximately one hundred billion. This suggests the number of stars in the visible Universe is approximately 10 to the power 22 (that’s ten thousand billion billion, if that means anything to anyone). We also know that most stars have a planetary system, so if we suppose that each star has one planet orbiting in the circumstellar habitable zone that is a huge number of planets where, potentially, life may arise. However, this too is not straightforward. As John writes in Chapter 5, cradle Earth that has nurtured complex life is itself special. It orbits a star, the energy output of which has remained relatively stable over billions of years. The Earth is at the ‘right’ distance from its star, so that water may exist in liquid form. Its size is just sufficient to allow it to retain its atmosphere and oceans over billions of years. It possesses a radiation shield by virtue of its magnetic field. It supports tectonic activity which recycles material, especially carbon. The Earth is also accompanied by a relatively large moon, which helps stabilise Earth’s spin axis producing steady climatic conditions. Among the many planets existing in the visible Universe, the Earth may indeed be very rare. The notion of the ‘rare Earth’ was formalised in 2000 by Peter Ward and Donald Brownlee (2). At the end of all this, we really have no other option than to say the existence of life elsewhere in the Universe is still open to speculation. Frank Drake wrote down an equation in 1961 (the Drake Equation) to estimate the number of communicative extra-terrestrial civilisation in our galaxy. And now, after 60 years of effort, we still do not know the values of the parameters in this equation to allow us to make a definitive judgement. Graham Swinerd March 2021 Southampton
 Graham writes … This post is the first in a series looking at the implications of life elsewhere in the Universe. We start by considering our neighbouring planet Mars. Way back in September 2019, a couple of good friends Pat and Sharon surprised me with a ‘Boarding Pass’ for Mars 2020. At first, I had no idea what it was about but they explained that there was to be a NASA launch of a mission to Mars in July 2020. They had registered my name on a data base, and this would be transported to the surface of Mars. As you can imagine, I was quite excited and inspired by the prospect that my name (in whatever form) would forever reside on the Martian surface. I printed out my ‘pass’ (see picture) and pinned it on my office notice board, where it remained unnoticed until this week. Indeed, this week saw the arrival of the Mars 2020 mission. On the evening of 18 February 2021, I tuned into a live broadcast on NASA TV from the JPL Perseverance Rover Mission Control room to watch the events of the rover landing strategy unfold. After its 203 day, 472 million kilometer journey, the conical capsule carrying the rover hit the upper atmosphere of Mars at 20.48 GMT travelling at about 20,000 km per hour (5.6 km per second). Seven minutes later at 20.55 GMT the rover arrived successfully on the surface. Watching the broadcast, the descent time seemed to flash by. To reduce the speed of the rover to effectively zero in such a short amount of time required a pretty brutal and complex sequence of events (see NASA descent videos – animation and actual video coverage). Just 80 seconds after atmospheric entry, peak heating occurred, with the heat shield reaching temperatures of about 1,300 degrees Celsius. Ten seconds after this, the peak deceleration of 10 g occurred. At this rate of deceleration, the capsule speed is sapped at rate of about 1 km per second for each ten seconds of flight. Finally, a combination of parachute and retro thrusters brought the rover to rest on the surface in a 1200 km diameter crater called Jezero.  This particular landing site for Perseverance, was strongly prescribed by the principal mission objective – that is, to investigate the prospect that microbial life still inhabits the surface (or more likely the subsurface) of the Red Planet. So why Jezero Crater? Over decades, an armada of Mars orbiting spacecraft have looked down on the surface and imaged the spectacular landscape. Mars has the distinction of having the largest volcano (Olympus Mons) and canyon (Valles Marineris) in the Solar System.  However, perhaps the most surprising feature of the topography is the unmistakable evidence that water once flowed freely upon the surface. Scientist have estimated that around 3.8 to 3.5 billion years ago, the climate of Mars was warm and wet – effectively, the planet was a water world not unlike Earth today. Evidence of water features – tributaries, river deltas, flood plains – are abundant. So where has all the water gone? As Mars is only about half the size of Earth, with a surface gravity of 38% of ours, the atmosphere of Mars has slowly leaked away into space over the last 3.5 billion years. Current atmospheric pressure is only 0.7% of Earth’s, and any water on the surface would quickly evaporate. So now Mars is dry and arid.   So, all those years ago it is believed that Jezero was lake, with a river inlet and outlet, and Perseverance rover’s landing site is located near the inlet. The rover has the ability therefore to look for likely sites in the lake bed and river delta where Martian microbial life might still reside. This is likely to be found in the subsurface rocks, so the rover has the capability to drill into the surface to produce core samples. These precious samples will subsequently be left on the surface to collected, and returned to Earth for detailed analysis. The methodology of this retrieval process is quite torturous, and is perhaps the subject of another blog. What then is to be learned from all this? It would be truly remarkable if life was discovered, and it was unambiguously based upon biology unlike that found on planet Earth. This would certainly be a paradigm-changing discovery, having great significance for our understanding of life elsewhere. However, another outcome could be that Martian life is found to be based on the same DNA code that is universal on Earth. This is entirely possible due to the fact that Earth and Mars are not biologically quarantined from each other. It has been known for many decades that chunks of rock from Mars can be found on Earth, and no doubt similarly bits of Earth reside on the Martian surface. The main mechanism accounting for this surprising situation is that highly energetic comet or asteroid impacts on Mars can blast rocks into orbit around the Sun, which can subsequently encounter the Earth. Presumably the reverse route is also viable. Of course, another overall mission outcome could be that no convincing evidence of microbial life is found. Only time will tell. For more information about the prospect of life on Mars, I can recommend Paul Davies’s book The 5th Miracle*.
Finally, it is worth pointing out that there are other places in the solar system where life may reside and where biological quarantine conditions are more stringent. Orbiting spacecraft missions to Jupiter (Galileo) and Saturn (Cassini) have shown that Jupiter’s moon Europa and Saturn’s moon Enceladus have significant water oceans beneath a thick surface crust of ice. The heat required to maintain this liquid state in both moons is generated by tidal heating. The source of this heating is likely to be active thermal vents on the ocean bed, around which conditions for the nuturing of life may exist. Although this is an exciting prospect, the opportunity to investigate this hypothesis is likely to be some significant time in the future. The task of delivering a submarine, robotic probe to these distant worlds is an extremely challenging one from the perspective of rocket science and spacecraft engineering. Graham Swinerd February 2021 Southampton * Paul Davies, The 5th Miracle: the Search for the Origin and Meaning of Life, Chapters 8 & 10, Simon & Schuster, 2000. |
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