John writes …
Plants and our planet.
My PhD supervisor, Dr (later Professor) Tom ap Rees often quoted the phrase which I have used as the title of this blog. It is actually part of a verse from the Bible: 1 Peter, chapter 1, v 24: All flesh is grass and all its glory like the flowers of the field; the grass withers and the flowers fall … . The verse refers to the transience of human life and my supervisor had doubtless heard his father, a church minister, quote it at various times. However, Tom ap Rees’s use of it in our lab conversations took us in a very different direction. He was referring to our total dependence on plants, which was one of his major motivations for doing research on how plant cells control their metabolism and which has driven my research on plant genes and DNA.
Let us look at this a little more closely. I am very fond of saying that without plants, we would not be here. This may seem rather sensationalist but it is true. It is a statement of the dependence of all animals (and indeed of many other types of organism) on green plants for their very existence. We see hints of a partial understanding of this in the media as they debate ways of mitigating climate change. Planting trees is correctly lauded as a means of capturing carbon dioxide from the atmosphere while at the same time releasing oxygen. Further, these two features have featured strongly in the evolution of life on Earth, as we describe in Chapter 5 of the book: the first occurrence of photosynthesis in simple micro-organisms (similar to modern blue-green bacteria) about 2.8 billion years ago and the invasion of dry land by green plants about 472 million years ago had major effects which have led to the development of the biosphere as we know it today.
However, what is often not emphasised enough in our discussions is that the process which takes in carbon dioxide and gives out oxygen, namely photosynthesis, uses energy from sunlight to drive the synthesis of simple sugars. This process requires light-absorbing pigments, mainly the chlorophylls which are green because they absorb light in the red and blue regions of the spectrum. The mixture of light wavelengths which are not absorbed gives us green. Green plants are thus our planet’s primary producers. This ability of plants to ‘feed themselves’ (autotrophy) is essential for the life of all non-autotrophic organisms, namely animals of all kinds, fungi and some micro-organisms. Non-autotrophic organisms such as ourselves are thus directly or indirectly dependent on green plants for their nutrition. We eat plants or we eat organisms that themselves eat plants. Thus, I repeat ‘Without green plants we would not be here’. ‘All flesh is grass’.
Plants and population.
I now want to look at this in the context of feeding a hungry world at a time of changing climate (1). Current estimates from charities such as TEAR Fund, Christian Aid and OXFAM indicate that about 800 million people are undernourished. In 2020, 9 million people actually died from malnutrition. This compares to the total number of deaths from malaria, HIV, TB and flu combined, of 3.17 million in the same year. Poverty is undoubtedly one of the main drivers of this situation: food needs to be more readily and cheaply available but food production also needs to be increased. Further, current projections suggest that the global population will increase to about 9 billion by 2050, an increase of about 1.05 billion on the current figure (2), with the vast majority of the increase occurring in low and middle-income countries (LMICs). At the same time, agricultural land is being lost to the effects of climate change and there is also some loss in order to house the increasing population. The situation has been described as a perfect storm.
I am going to focus specifically on the tension between two imperatives that I described in the previous paragraph, namely care for planet Earth and care for its human inhabitants. What are the environmental ‘costs’ we incur as we produce enough food for a population which is already fast approaching 8 billion and which is set to reach 9 billion within 30 years? The table below sets out one of those costs, namely the production of greenhouse gases. It is immediately and obviously apparent that farming of animals for food is far more ‘expensive’ than farming of crops. For example, beef production produces more than 50 times the quantity of greenhouse gases per kilogram of food than does wheat production. We need to note in passing that this way of expressing the data (‘per kilogram of food product’) places milk (whether from cows, sheep or goats) in an anomalously low position on the chart because 1 kg of milk is largely water. We get a better idea of the costs of producing the main nutrients in milk – protein and lipid - by looking at cheese production.
I now want to look at two other aspects of the costs of food production, land use and water use. These must both come into our consideration as we attempt to balance the tensions involved in ‘feeding the nine billion’. Firstly, about 75% of the world’s agricultural land is used for animal production. This figure includes land that is used to grow crops for animal feed. Crops for direct human consumption occupy the remaining 25%. However, the yield of food obtained from just one quarter of the total agricultural land exceeds that obtained from the three quarters devoted to farming animals. Indeed, depending on the particular animal under consideration, the average protein yield per hectare of crop land is six times that of land devoted to animal husbandry.
Secondly, there is water usage which, like land use, shows a huge difference between plant- and animal-based food production, as is shown in the following table, taken from Mekonnen and Hoekstra (2010).
Overall then, the data from agricultural science and biogeography indicate that crop growth is ‘better’ for the planet than animal farming and that concentrating more on crops than on animals is likely to be the better route to feeding the burgeoning population. However, I am not forgetting that some land is better suited to animals than to crops, as discussed by Isabella Tree in her book Wilding (3). Nor am I trying to dictate that we should all move to a plant-based diet: in the rich industrialised nations of the world, we are privileged that this is a matter of personal choice. Nevertheless, it is clear that there must be extensive focus on plant science - genetics, molecular biology, biochemistry and physiology - over the next 20 years, both in respect of mitigating climate change and in respect of global food production. That science will be the subject of a future blog.
Graham writes ...
After 25 years in development, and a 10 billion dollar spend, the JWST was finally launched on Christmas Day 2021 (much to the delight, I’m sure, of the families of the army of engineers who had to attend the launch!) as I described in my January 2022 blog post. You might like to have a look back at that post, which discussed the launch and looked forward to the spacecraft deployment and orbit insertion.
A second brief post in January 2022, announced the news of the completed configuration deployment just 17 days after launch, while the spacecraft was still on its way to its operational orbit around the second Lagrange point. The deployment sequence required the successful actuation of over one hundred mechanisms which is unprecedented in the brief history of the space age. In the context of spacecraft engineering, ‘mechanisms’ are essentially moving parts which allow the deployment of things like solar arrays and antennae, which usually need to be stowed in a compact configuration for launch. I remember a time, in the 1980s, and to some degree the 1990s, when it was considered good practise to minimise the number of mechanisms, as each one represented a potential single-point failure that could terminate the mission of a very expensive spacecraft. I think it’s fair to say that the complex deployment sequence of the JWST has finally put that philosophy of ‘mechanism-phobia’ to bed. If you haven’t seen this remarkable sequence there is a link to an excellent video in my first January 2022 post.
After the deployment, the spacecraft continued its journey outwards towards its final operational orbit, which it reached about 30 days after launch. Three mid-course corrections (thruster firings) placed it into a large, sweeping halo orbit around the L2 point about 1.5 million km from Earth. L2 is an equilibrium point in the Sun-Earth-spacecraft three-body system (see January post and (1) for details). However, it is a point of unstable equilibrium, which means that the spacecraft will have to continue to execute course corrections during its operational lifetime to keep it on-station around L2.
The main features of the spacecraft configuration are a 6.5 m (21 feet) primary mirror, consisting of 18 hexagonal, gold coated elements and a tennis court-sized sun shield. The latter is required to passively cool the payload instruments to a temperature of around -230 degrees Celsius, as the telescope is optimised to operate in the infra-red (heat radiation) part of the spectrum – see diagrams. The temperature had already decreased to about -200 degrees C by early January. Since the instruments must be kept on the dark side of the observatory, the telescope can access only 40% of the sky on any specific day of the year, and it will take about 6 months to access the whole sky.
Each hexagonal element of the mirror has 7 actuators (mechanisms again!) to tilt, translate, rotate and deform each mirror surface to ensure they all operate as one ‘perfect’ parabolic surface. Prior to the alignment process, the telescope imaged a single bright star in the constellation of Ursa Major (aka ‘The Plough’ in the UK) called HD84406. The resulting image shows the star in 18 different positions. To undertake the alignment process of the individual elements, a test star in the constellation of Draco (the Dragon) called 2MASS J17554042+6551277 (2) was chosen because it is effectively an easily identifiable ‘lonely star’ with few nearby neighbouring stars. Using this star, each hexagonal element was adjusted so that the 18 separate images were amalgamated into a single point at the telescope’s focus to an accuracy of around 50 nm (1 nm = 1 nanometre = 1 thousand-millionth of a metre). This was a landmark process in the commissioning of the telescope, which was completed successfully in early May 2022.
As I write, the process of collimating each of the observatory’s instruments is underway. The spacecraft has a number of primary instruments (spacecraft engineers love their acronyms!):
Returning to the picture of the test star in Draco, which was acquired using the NIRCam instrument, the alignment team noticed a scattering of galaxies in the background of the image, many of which were estimated to be billions of light years distant. One scientific bonus derived from this commissioning activity is the image of a galaxy which appears to be in the process of ejecting its once-central super-massive black hole (see picture). As described in (3), such super-massive back holes (with masses typically of the order of millions of solar masses) are ubiquitous at the centres of galaxies throughout the cosmos. About 8 billion light-years distant, the galaxy 3C186 is home to an extremely bright galactic nucleus — the signature of an active super-massive black hole. But this one is about 35,000 light-years from the centre of its home galaxy, suggesting it is in the process of being ejected. This object had already been imaged by the Hubble Space Telescope, and this new data from the JWST has reignited debate about what may be causing the ejection of this extremely massive object.
So, when can we expect the first operational images from the new observatory? Best guess at the moment is probably late June or early July. And what can the JWST do in furthering our understanding of the Universe? The answer to this question is related to the characteristic that the observatory is optimised to observe in the infra-red part of the spectrum, as we mentioned earlier. This is effectively heat radiation, which is why the telescope and the payload instruments need to be cooled to very low temperatures. If the JWST operated at the same temperature as the Hubble Space Telescope – around room temperature – the telescope and instruments themselves would produce thermal radiation which would swamp the incoming data from the sky.
So why is infra-red good? First off, it is less prone to scattering from dust and debris (compared to visible light) so the JWST will be able to observe ‘local’ events such as the formation of stars and the development of embryonic planetary systems beyond our own. The infra-red optimisation will also enable the observation of very distant objects, such as the first stars and galaxies. When these were forming, around 13 billion years ago, the light that they emitted in the visible part of the spectrum will have been stretched in wavelength by the subsequent expansion of the fabric of space-time. The JWST will now ‘see’ this radiation in the near and mid infra-red parts of the spectrum. Also, as mentioned above, one of the payload elements has been enabled to observe exoplanets to look for signatures of habitability in their atmospheres – such as water vapour and oxygen.
The JWST is part of a long heritage of astronomical instruments designed to answer the deep questions about the cosmos in which we live, such as
Clearly big questions, and of course no one project such as the JWST can be expected to provide all the answers. Clearly, the quest for understanding is an incremental process. However, we have great expectations that, like its predecessors, the JWST will reveal new findings beyond our hopes and imagination. However, it is also important to realise that all observatories that utilise the electromagnetic spectrum to probe the cosmos are ultimately limited by a fundamental barrier. As described in the book (4), immediately after the Big Bang, and for some 380,000 years afterwards, the energy and matter content of the Universe comprised a dense and very hot soup of charged particles and photons. Because the photons (particles of light) were continually interacting with the particles, the radiation was unable to propagate freely so the Universe was effectively opaque. This state of affairs continued until the temperature of the Universe was low enough for the charged particles to form neutral atoms, at which point the Universe became transparent to light. Consequently, direct observation of the events of the Big Bang using the electromagnetic spectrum are veiled by this early era of universal fog.
Rather than finish on this rather negative note, it should also be pointed out that we have other avenues of investigation to discover the secrets of the Big Bang, the main one currently being the emulation of the physical conditions just a fraction of a second after the Bang using particle accelerators. Another pathway is the utilisation of the new technology of gravitational wave detectors. The era of universal fog presents no barrier to the propagation of gravitational waves, and consequently the cosmos is probably awash with gravitational radiation containing information about the genesis event. However, the science of gravitational wave detectors is very much in its infancy, and nobody quite knows where it’s going and what a gravitational wave observatory of the future might look like. That is a revolution that has yet to unfold.
At the end of the day, after all the talk of science and engineering, our amazing God has given us a rational and creative intellect to envisage and build incredible machines like the James Webb Space Telescope (and the Large Hadron Collider, comes to that). The motivation that drives us to these heights of ingenuity and creativity comes from a God-given curiosity to uncover the secrets of His beautiful creation!
I hope to be showing some JWST images of this in the July blog post.
John writes …
I started to write this blog post on April 25th which is a very significant date in the history of molecular biology. On April 25th 1953, the prestigious journal Nature published the paper that announced the elucidation of the double helical structure of DNA. ‘Landmark’ is a rather over-used term but this was certainly one. Like any major discovery it led to a flurry of further experimental work. In this case, the structure gave some clear clues about the biochemical mechanisms involved in replication of DNA and in the working of genes. Understanding the biochemistry then led to research on the way in which different living organisms control that biochemistry throughout the different phases of their life, research which continues to this day.
In our February vlog I talked about the Golden Age of Genetics; the discovery of DNA structure and the subsequent biochemical research were part of the prelude to that golden age, as was the decoding of the genetic code in the early 1960s. But what actually initiated the golden age was the invention of genetic modification (GM) techniques – genetic engineering (GE) – in the early 1970s, an invention that could not have happened without the biochemical and genetic research of the previous decade. Genetic modification techniques enabled scientists to study individual genes. Combination of biochemical knowledge with possibilities raised by GE techniques led to the development of methods for sequencing DNA. The first full DNA sequence, that of a bacteriophage (a virus that infects bacteria) and consisting of 5365 base pairs (DNA ‘building blocks’) was published in 1977. The golden age was underway.
The developments that I have just described took place early in my career and without a doubt have enabled me and my colleagues to carry out research that previously would not have been possible. Some of our work certainly employed more conventional biochemical techniques (1) but a significant proportion was only possible because we were able to use GE and related methods in our studies of regulatory mechanisms (2). I feel immensely privileged to have contributed in a minor way to the golden age and have also been thrilled in making discoveries that give me insights into the awesome beauty and cleverness of the regulatory mechanisms that operate in living cells
The progress that has been made in our understanding of how genes work has certainly been amazing. Thinking back to the start of my career, I would not even have imagined the possibility of knowing some of the things that are now embedded in our understanding of molecular biology.
That leads to another of my ‘pet themes’. I am all for original research with ‘no strings attached’ because I believe that is a good thing to know and understand more about the universe in which we have been placed. Further, for me as a Christian, it gives more insight in the work of our creator God. However, I also want to see the findings of science used, where possible, for the good of humankind and indeed of the whole planet.
In our February vlog I mentioned several medical applications of our current understanding of DNA and genetics. One example is the development of vaccines for COVID-19 which depends on knowledge of virus genes and, for the Astra-Zeneca vaccine, also on GE techniques. Other examples included rapid genome sequencing to identify gene-based diseases and the use of genome editing (which is in effect another type of GE) to make pig organs suitable for transplant into humans. These are undoubtedly sophisticated applications of our knowledge but they raise questions about world-wide availability, questions about which I have serious concerns. Taking the first example, the development of vaccines, in the UK many people have had three doses of COVID-19 vaccine while some have had a fourth. And yet in many of the poorer countries of the world, fewer than 20% of the population have received any vaccine and even if they been vaccinated, they have had only one dose. In the chart, this situation is illustrated by data from Nigeria and Ethiopia.
I do not have the space here to comment much further on this, except to say that it seems very wrong and surely there must be some way of addressing such glaring inequality.
The other topic mentioned briefly above, on which I want to comment further, is genome sequencing. It is undeniably useful in diagnosis of genetic diseases and in prediction of some possible future health-care needs. However, as with vaccine availability, this is medical technology of the rich industrialised nations of the world and we should not let it, wonderful though it is, blind our eyes to the still widespread occurrence of malaria, TB, HIV, childhood dysentery and so on. These diseases account for many more deaths than can be attributed directly to genetic mutations. Further, even in developed countries it is possible that the wonders of genetic medicine may lead us to take our eyes off the ball with respect other factors that affect our health. An anonymous GP said that for most people, the postal code of where they live gives a better picture of their health than their genome sequence. What did she/he mean? Poverty, poor housing, poor social and physical environments, less access to facilities and so on can all have dramatic effects on our health. In and around all our major cities in the UK, there are huge differences in life expectancy between people living in the most affluent areas and people living in the poorest areas; for example in Glasgow in 2021, the difference between the two extremes was nearly 20%. Amongst the significant factors contributing to these inequalities are differences in air quality. A recent article in New Scientist (3) looked at the effect of environmental pollution on health, including resistance to and recovery from diseases, reaching the conclusion that ‘For most diseases, exposure to pollution plays a far greater part in mortality than genetics.’
So, although I am thrilled to be living in the ‘Golden Age of Genetics’ I am also motivated to apply the imperative to love our neighbour as ourselves in dealing with inequalities, whether internationally or within our own country so that all may benefit from advances in biomedical science.
Graham writes …
Welcome back to this topic, which we discussed back in October’s blog post. As always in physics and biology, significant developments always happen, which have distracted me from writing further about the prospect of new physics. It might be worth revisiting the October 2021 post to remind yourself briefly of some of the fundamentals that are relevant to today’s discussion.
As discussed then, one of the main theoretical pillars of the very small – the world of atoms and subatomic particles – is the standard model of particle physics. On the one hand, we know that the theory is ‘right’ in a very fundamental way, as we can perform detailed calculations to predict the results of experiments very accurately. This is evident from what we shall see later in this post. However, on the other hand, we also know that the standard model is not comprehensive. Again, as discussed in October, the theory of gravity (Einstein’s general theory of relativity) persistently ‘refuses’ to be unified with the standard model. Also, the mysterious ‘dark universe’ – dark matter and dark energy – which is believed to comprise about 95% of the matter/energy in the Universe is missing from the model. So, we know there’s lots to be done, but we really are not sure how to go about it. All we can do is attempt to find experimental results which are not in complete accord with the theory, and then probe what such an anomaly might mean for the model. The reason why I’m blogging today is to talk about a ‘strange’ experimental result, which has been reported recently by a team of scientists working at Fermilab near Chicago, Illinois. Given that this can be referred to as the ‘anomalous magnetic dipole moment of the muon’, or the ‘muon g-2 experiment’, we need to unpack some of the terminology to hopefully reveal something of what’s going on. So, where to start? Firstly, I’d like to look at a property of fundamental particles called spin.
I think we are fairly familiar with the notion of spinning objects. If we spin up a macroscopic object, like a wheel, it acquires something called angular momentum, and the amount of angular momentum depends upon the mass of the object, how the mass is distributed and how fast it is rotating. It is the rotational equivalent of linear momentum. So, in the same way as we avoid standing in front of objects with large amounts of linear momentum, like a car travelling at speed, we also know intuitively not to tangle with an object with a significant amount of angular momentum, such as a large, rapidly rotating wheel. If we reached out and tried to grasp the wheel to slow it down, its significant rotational inertia will cause us grief.
However, scientists also talk about spin when referring to sub-atomic particles such as an electron, for example. However, the properties of the ‘spin’ of an electron are very different to that of a macroscopic body. For one thing the angular momentum is quantised in terms of magnitude and direction. Also, such particles are considered to be infinitesimally small point particles, and as such talking about physical rotation makes no sense. But intriguingly they do possess intrinsic attributes that are usually associated with the property of rotation. Such particles also possess a magnetic field very similar to that produced by a tiny, simple bar magnet. This type of field is referred to as a magnetic dipole field, with the usual so-called north and south poles. You may have seen the structure of this field in a simple school experiment by sprinkling iron filings onto a piece of paper which has been placed on a bar magnet. This type of magnetic field can be generated by the motion of an electric charge around a looped wire. So, we could imagine that electron is rotating, carrying its electric charge in a circular path around its axis of rotation, producing the magnetic field. However, we know that this cannot be so. If we were to envisage the electron as something other than a point particle, and try to use size estimates, its surface would have to be rotating faster than the speed of light to produce the measured dipole field strength! It’s clear that particle spin is a difficult concept for everyone (not just me!) to appreciate intuitively. So, after all that, what is the dipole moment? Well, if we place the electron in an external magnetic field, the north-south axis of the particle’s field will align with the direction of the external field, as a compass needle rotates to align with the Earth’s magnetic field to indicate north. Hence the electron’s field exercises a torque, or moment, on the particles magnetic axis to bring this alignment, and this is referred to as the dipole moment.
Another attribute of the particle which has its counterpart in macroscopic rotation is precession. If you think of a toy gyro and spin it up, then the force of gravity produces a torque which causes the axis of rotation to precess (or ‘wobble’), as illustrated in (the first half of) a video demonstration, which can be seen by clicking here. In a similar way, the magnetic axis of a particle (indicated by the the black arrow in the diagram) will also precess if placed in an external, uniform magnetic field (indicated by the green arrow). This is referred to as Larmor precession, after Joseph Larmor (1857-1942).
I don’t know if you are still with me, but let’s come back to the media assertions about new physics, and the Fermilab announcement which mentions something called the ‘g-2 experiment’. The g here is referred to as the ‘g-factor’, which is a dimensionless quantity (a pure number) related to the strength of a particle’s dipole moment and its rate of Larmor precession. For an isolated electron, g = 2 according to Paul Dirac’s theory of relativistic quantum mechanics (QM), which he published in 1928. Subsequently, this theory has been superseded by the development of quantum electrodynamics (QED), which describes how light and matter interact. Using QED, we can perform the calculation for an electron that is not ‘isolated’. The g-factor calculation is not just about the interaction of the electron with the applied external magnetic field, but it is also influenced by interactions with other particles. This introduces another piece of quantum world terminology called quantum foam. This is the quantum fluctuation of the spacetime ‘vacuum’ on very small scales. Matter and antimatter particles are constantly popping into and out of existence so that the quantum vacuum is not a vacuum at all. For those of you with a bit of QM background, this is due to the time/energy version of the uncertainty principle. This idea was originally proposed by John Wheeler in 1955. Consequently, the electron also interacts with the quantum foam particles, and the influence of these short-lived particles affect the value of the g-factor, by causing the particle’s precession to speed up or slow down very slightly. The experimental value of the electron g factor has been determined as
g = 2.002 319 304 362 56(35)
where the part in brackets is the error. The theoretical value of g-2 matches the experimental value to 10 significant figures, making it the most accurate prediction in all of science.
So, we find that the behaviour of an electron conforms with theory very well, but what about other particles? The recent Fermilab experiment refers to similar work looking at a particle called a muon. So, what is this? The muon is a particle which has the same properties as an electron, in terms of charge and spin, but is 207 time more massive (see the blog post for October again, for details). It is also unstable, with a typical lifetime of about 2 microseconds (2 millionth of a second), but this is still long enough for the scientists to work with them. What the Fermilab team did was measure the muon’s g-factor in the same way that we have described for the electron. This time a difference between experiment and theory was observed,
g(theory) = 2.002 331 83620(86),
g(experiment) = 2.002 331 84121(82).
Of course, the difference is tiny, so why the big deal? Well, the theoretical value describing how the quantum foam influences the value has been determined using our current model of the subatomic world – that is, the particles and forces as described by the standard model of particle physics. The fact that the experimental value differs suggests that there may be new particles and/or forces that are currently absent from our understanding of the quantum world. Another question posed by this result is why does the electron conform and the muon not? In the theory, the degree to which particles are influenced by the quantum foam is proportional to the square of their mass. Since the muon is about 200 times heavier than the electron, it is approximately 40,000 times more sensitive to the effects of these spacetime fluctuations.
At the end of the day, do the Fermilab results have the status of a confirmed, water-tight discovery? Well, actually no. The degree of certainty at present is at the 4.2 sigma level, which suggests that there is a roughly one chance in 100,000 that the result could be a result of random chance. To get the champagne glasses out, and to start handing out Nobel prizes, further work is required to achieve a 5 sigma result (again see October’s post).
So, where does all this take us? The bottom line is that it tells us there are things about the quantum world that we don’t know – which, you could say, we knew already! But this is how physics works. To paraphrase Matt O’Dowd, Australian astrophysicist, “ … to find the way forward, we need to find loose threads in the [current] theories that might lead to deeper layers of physics. The g-2 experiment is just one loose thread that was begging to be tugged. The scientists at Fermilab have just tugged it hard …”. I await further developments!
John writes …
We, my co-author Graham Swinerd and I, have produced a vlog (video blog) focussing on my expertise – biology, and in particular what’s going on in the world of genetics. To see the video, please click here. What follows is a brief commentary on the video’s content.
When I started my Natural Sciences degree I was fairly sure that I would come out the other end as a functional ecologist – someone who studies ecology with an emphasis on plant and animal adaptive mechanisms. How wrong I was. During those three years I became completely hooked on the molecular aspects of genetics and on biochemistry and so it was a natural progression that for my PhD I studied DNA biochemistry (in the context of plant cell division).
It was an opportune time to become involved in that area of science. The ‘golden age’ of genetics was about to dawn. The basic mechanisms involved in the working of DNA and genes were known and there was already some information on control mechanisms, an area that I hoped to eventually get involved in. And then came the invention of genetic engineering techniques (and associated spin-offs) which, as I say in the video, gave us a huge range of research possibilities. It opened up previously impossible (and some cases undreamed of) lines of investigation. Combining our knowledge gained by these new techniques with our knowledge of biochemistry led to DNA sequencing; detailed analysis of individual genes gave ideas about gene control mechanisms, ideas that could be tested with techniques based on genetic engineering.
More recently, invention of new methods for DNA sequencing have very significantly reduced the cost and the time involved in analysing any DNA sample of interest, including whole genomes from individual members of a species (rather than an ‘average’ genome for that species). The applications of this are very widespread, as I mention briefly in the video. And now another technique has entered our tool-kit, namely genome editing* which enables us to knock out specific genes in a highly targeted manner, again as described in the video.
But I need to say one more thing: the more that I know about DNA and genes and the ways in which they work, the more awestruck I become. In my own specific area of research, the beauty and complexity of the mechanisms that a cell uses to control DNA replication are amazing. The psalmist was in awe of the God who made the ‘heavens’ (Psalms 8 and 19) but I am equally in awe of the God of our genes.
* For those who want to know a bit more about genome editing, I have included two papers. One is the uncorrected proof of an article in Biological Sciences Review and the other, at a higher level of understanding, was published in Emerging Topics in Life Science. Please click on the files below to download the files.
Graham writes …
A new age of astronomy is about to begin, with the launch of the James Webb Space Telescope (JWST). The new space observatory, named after the NASA administrator during the Apollo era, lifted off at 12.20 UT on Christmas Day 2021 atop a European Ariane 5 heavy-lift launch vehicle. A video of the launch and ascent (simulated) can be seen here, and another of the separation from the launch vehicle and power array deployment can be seen here. Both these videos are courtesy of Arianespace/NASA.
Apologies once again to those of you who are looking out for the ‘New Physics? Part 2’ blog post, but the launch of the JWST is long-awaited and cannot be overlooked. If the new space telescope works as it supposed to, then it will most likely make history as did its predecessor, the iconic Hubble Space Telescope. This is a truly monumental event for the astronomy and cosmology communities.
At the time of writing, 6 January 2022 (~ launch + 12 days), the JWST is still on its way to its operational location – the Earth-Sun Lagrange point L2, which is about 1.5 million kilometres from Earth. It also has to deploy a significant number of mechanisms during its journey, so there are an awful lot of crossed fingers in the control centre and around the world. The operational configuration has a 6.5 metre aperture telescope and a sun shield about the size of a tennis court (~ 22 m x 12 m), and all this had to be stowed inside the launcher fairing of the Ariane 5. Consequently, there are around 140 release mechanisms that must perform perfectly to shape the final operational telescope. All this is going on while the JWST is in transit to L2, which will take about 30 days. An excellent video of the complete deployment process during the transfer, courtesy of NASA/Northrop Grumman, can be seen here. Once it arrives at the Lagrange point, it will enter its operational orbit, called a ‘halo orbit’, around this location. For more details about this exotic orbit and Lagrange points, see (1).
So, briefly, what is a Lagrange point and why is L2 a good place to operate an astronomical telescope? In any three-body system (for example, in this case, the Earth, Sun and spacecraft) there are in fact 5 Lagrange points, named in honour of the Italian-French mathematician Joseph Lagrange. The second Lagrange point L2 is about 1.5 million kilometres beyond the Earth’s orbit around the Sun (on a line joining the Sun, Earth and spacecraft) where the gravitational and rotational forces cancel to produce a place of equilibrium where the space observatory can be ‘parked’. This an ideal place for a space telescope, as the Earth only subtends an angle of about 0.5 degrees, so the sky viewing efficiency is excellent. The downside of this choice of orbit is that the observatory cannot be visited by astronauts to perform repairs or servicing. You may be aware that the Hubble Space Telescope was visited on five occasions by astronauts, as it was accessible in a low orbit near Earth. The table gives an outline of the main attributes of the observatory.
Table: Summary of spacecraft characteristics
Launch mass: 6,200 kg
Overall dimensions: 22 m x 12 m (sun shield)
Mirror aperture: 6.5 m (compared to 2.4 m for the HST)
Maximum electrical power: 2 kW
Planned operational lifetime: 5 to 10 years
Operational temperature: -230 degrees (on the dark side of the sun shield)
Towards the end of this month (January 2022), the observatory should have completed the sequence of deployment mechanisms, and will enter its operational ‘halo orbit’ around L2 in its final configuration. While on station the sun shield will be directed towards the Sun and the subsystem module will be permanently located on the sunny side of the shield. This will enable the supporting subsystem elements, such as power, data handling and communications, to remain at a sensible temperature to ensure reliable operation. The telescope and associated payload elements will reside permanently on the dark side of the shield so that its temperature will be very low (see the last entry in the table). This thermal constraint indicates that the telescope is optimised to operate in the infrared (IR) part of the electromagnetic spectrum – that is, heat radiation (more about this below). The telescope needs to be at a very low temperature so that its own IR emissions do not interfere with the IR observations. The telescope’s mirror is comprised of 18 hexagonal elements manufactured from beryllium, with a thin coating of gold deposited on the reflective surface. This striking feature of a gold mirror is that it helps improve the mirror’s reflection of IR light. The composite hexagonal pattern of the main mirror has become something of a logo for the JWST project.
So why the emphasis on IR optimisation? This is, of course related to the science objectives of the observatory. It is hoped that the JWST will be able to see the ‘first light’ in the Universe, about 600 million years after the Big Bang, when the swirling dark clouds of hydrogen and helium began collapsing to form the first stars. It is also hoped that the processes involved in the origin of galaxies will be revealed. The ultra-violet and visible light emitted by the first luminous objects in the Universe is significantly red-shifted, due to cosmic expansion, into the IR part of the spectrum. Another objective is to study the birth of stars more locally, and the formation of embryonic planetary systems, which are usually obscured by the debris and dust associated with these events. Short wavelength visible light is appreciably scattered by dust. However, the longer wavelength IR radiation is less affected by this, allowing the telescope to observe these formative episodes.
Needless to say I am very excited by the prospect of all this, but we will have to wait till summer 2022 to see the first output from the JWST. Meanwhile, there is an awful lot of critical moments in the deployment and commissioning of the observatory. I am keeping everything crossed that this ambitious programme will all work out just fine!
(1) Graham Swinerd, How Spacecraft Fly, Springer, 2008, pp. 83-89.
Graham writes …
John and I are offering an additional post in recognition of NASA’s DART mission, which launched recently (24 November 2021). The acronym DART stands for Double Asteroid Redirection Test for reasons which will become apparent. The objective is to crash the spacecraft into a small asteroid to determine the effect the impact has upon the orbit of the asteroid. If all goes well, the impact will occur on 26 September 2022.
So why is NASA deliberately crashing its valuable spacecraft into a lump of rock? The answer to this question goes back some 60 million years, when an asteroid about 10 km across impacted what is now called Central America, creating a global catastrophe which ultimately led to the extinction of the dinosaurs. The impact speed of the object is unknown, but most likely of the order of 10s of kilometres per second, resulting in a hugely energetic event which dwarfs those created by our most powerful nuclear weapons. We discuss this event, and its consequences, in the concluding section of Chapter 5 of the book.
Coming back to the twenty first century, we consider the occurrence of such an event to be very unlikely. However, we also appreciate from consideration of Earth’s history that such catastrophes are inevitable in the future. For example, the 1.1 km diameter Barringer Crater in Arizona, USA was created by the ground impact of a 50 metre diameter asteroid some 50,000 years ago. Also, an air burst of an asteroid in the Tunguska region of Siberia in 1908 flattened forestation over an area about the size of the London M25 orbital motorway. This one was caused by an object about 60 metres across. Clearly, we have to wait a very long time for a 10 km impactor, but the arrival of these smaller objects occurs more frequently, and the devastation that would result if one struck a large city cannot even be imagined. So, we need to take planetary defence, with regard to celestial impactors, seriously.
This is why the DART mission was proposed and implemented. The spacecraft is referred to as a ‘kinetic impactor’, and you could say that the process is a bit like a game of celestial billiards. When the spacecraft hits the asteroid, it will change the asteroid’s speed a little, and this small change will alter the asteroid’s orbit. It is effectively a test to see if the orbit of an asteroid, that threatens to impact the Earth in the future, can be changed sufficiently to prevent a catastrophic collision with Earth.
The target asteroid for the test is a 160 metre diameter object called Dimorphos, which itself is in orbit around a larger asteroid (780 metres across) called Didymos – see images. To discuss asteroid impacts in general, and the DART mission in particular, John and I have attempted a ‘vlog’ – that is a video blog which we have posted on YouTube. If you would like to see this please click here. We have not used this medium before, but nevertheless we hope you find it interesting. Please leave thoughts and comments on this website, or on YouTube.
Francis Collins, a very distinguished medical geneticist, well-known for his Christian faith, has just retired from heading the USA's National Institutes of Health. He was appointed to the post 12 years ago by President Obama and has now reflected on his time at NIH and on related issues, in an interview published in the scientific journal Nature, which can found here.
Some of our readers may also be interested in Collins' own book (Francis S. Collins, The Language of God, Simon & Schuster, 2007). This is one of Graham’s favourite books, helping him to get to grips with aspects of the biology of life, which don’t come easy to a physicist.
Graham Swinerd and John Bryant
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?
(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
John Bryant and Graham Swinerd comment on biology, physics and faith.