The Covid-19 virus is a little suckerball around 100 nanometres in diameter. How small is that? It’s around one ten thousandth of a millimetre. One tenth of a millimetre is about the smallest thing you can see. We’re talking about something very small with an enormous impact.
The virus, small though it is, has shown us that it can rule the globe, forcing billions of us into isolation in our own homes, causing over a million deaths worldwide. It must have felt a bit like this for humanity 30,000 years ago, crouched in the caves of southern Europe in the face of an inexorable wall of ice powering down from the north. Our invisible chilly wave has touched on all aspects of our lives, consigning to the waste-bin a year’s worth of our vaunted spectaculars – the Olympic Games, Wimbledon, the Cannes Film Festival. We watched as our cities and towns emptied and the rest of the animal kingdom started to flood back in.
Coming hard on the heels of unprecedented extreme climate events, with persistent floods across the world and the Australian bushfires driving panicked citizens into the sea, the pandemic seemed to carry a message. Was nature teaching us a lesson? An editorial in the Guardian on 23 May seemed to think so:
The coronavirus pandemic and the environmental crisis share the same roots: humans’ success as a species in arrogating global resources for themselves and the consequent ecological disturbance. This is increasing viral exchanges – first from animal to human, then from human to human – on a pandemic scale. Our environmental footprint is too large for the planet, leading to accelerated species extinctions and atmospheric chaos.
If the Covid-19 crisis has seen our world turned upside down by a microbe, the climate crisis is also caused by changes at a microscopic level. This is because microbes are at the heart of nature’s great recycling system, whereby chemical elements flow in and out of living things through the air, water and soil.
If we want to tackle the existentially large challenges facing humanity, we need to start by understanding the tiny processes that underpin everything.
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Since life began, the world has been governed by the power of very tiny living things: micro and nano organisms – especially bacteria and their longstanding enemies the viruses. Within these and all living organisms are the engines of life: large, highly structured proteins that are actually nanomachines. The words “nanotechnology” and “nature” may sound incompatible to your ears. But the great prophet of human-made, engineered nanotechnology, the physicist Richard Feynman, took nature as his example way back in 1959:
A biological system can be exceedingly small. Many of the cells are very tiny, but they are very active; they manufacture various substances; they walk around; they wiggle; and they do all kinds of marvellous things – all on a very small scale.
If you could shrink, like Alice, to explore the wonderland inside a single living cell, you would see that it’s a veritable city with nano analogues of settlements, stores, factories, highways and cars. This is why Feynman famously said, “There’s plenty of room at the bottom” and why I call the proteins in living cells “giants of the infinitesimal”, a phrase coined by my late co-author Tom Grimsey in our book Nanoscience.
Protein nanomachines are highly structured, active assemblies that do all of the work of the cell. They developed over 3.5 billion years ago in bacteria. For over 2.5 billion of those years, the only life on Earth consisted of single-celled creatures: bacteria and the single-celled progenitors of all the higher creatures, including ourselves. While the various species on Earth evolved, the nanomachines inside them have stayed much the same. This is why research into these nanomachines is leading the way in exploring solutions to both climate change and the pandemic.
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All diseases involve malfunctioning protein nanomachines. The Covid-19 virus functions by attacking the human respiratory system. Respiration makes us think about breathing, but the process is much more than that. It’s the primary process of life, involving – for “higher” creatures like us – the “burning” of sugars using oxygen inside every cell in the body. This is achieved through a protein nanomachine that looks like an electric motor, with a spindle inside a ring of proteins that forces it to rotate. (So, nature invented the wheel after all!) This engine is the universal source of energy in all living things. It’s official name is ATP synthase, meaning “the-nanomachine-that-synthesises-the-ATP-molecule”.
Aside from these “electric motors”, the key nanomachines on which all animal and plant life depends are those that perform photosynthesis, using the energy of sunlight to synthesise living matter from carbon dioxide and water. They first evolved in a form of bacteria, cyanobacteria, which still exist today in vast numbers in the oceans and on land. A waste product of the process is the oxygen all animals need. Cyanobacteria in the oceans provide around 50 per cent of the oxygen in the air. Without the oxygen produced by bacteria over billions of years, large mobile creatures (ie animals like us) could not have evolved in the first place.
Besides providing the conditions for animal life, bacteria also transformed the basic rocks into substances that today power our industrial life. Around 2.4 billion years ago, a major Earth cataclysm known as the Great Oxygenation Event occurred as a result of an accumulation of the waste product of photosynthesis – oxygen – in the atmosphere and oceans. Its physical manifestation in the world today is huge bands of iron minerals, the major source of iron ore in the world, which were precipitated in the oceans by the action of oxygen on dissolved iron salts. These precipitates are iron oxides and they were formed by the process we know as rusting – iron cannot resist the attack of oxygen.
Similarly, the great chalk deposits that stretch across Europe to the Middle East and across North America are the shells of countless single-celled photosynthesising marine organisms: coccolithophores. They were laid down in very hot conditions and their formation helped to return the world to a cooler state by removing carbon dioxide from the atmosphere in the form of their calcium carbonate shells. Today, besides its role in shaping our landscape, the chalk of course is a component of our industrial material: cement, the production of which is returning the carbon dioxide stored many millions of years ago once more to the atmosphere.
Fossil fuels are also major products of nature’s photosynthetic nanomachines, in the form of coal, oil and gas. By this time (between 300 and 65 million years ago) the nanomachines were installed inside multicellular organisms: plants and trees. The remains of this vegetal life were then transformed by heat and pressure into the fossil fuels which humanity has found so useful – that is, until we realised their continued use could destroy us.
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Many minerals used in industry today pose environmental problems. Laid down over billions of years by microbial action, they are now being massively exploited, releasing chemicals into the environment over an incredibly short period of time.
Besides creating the oxygenic environment in which plants and animals could evolve, and transforming the rocks into substances we could readily use for our materials needs, microbes are the great recyclers, transforming dead organisms and waste matter into substances fit to sustain future generations. They control the flow of chemical elements through the air, water and soil, maintaining a planetary balance. It is this balance we have disturbed by hogging too high a proportion of the world’s resources.
The most famous global cycle we have disrupted is of course the carbon cycle, resulting in the steady rise in atmospheric CO2 causing global heating. But all the global elementary cycles have been disturbed.
How do these tiny organisms impact the great global cycles? Bacteria are the most versatile chemical processors on the planet. Besides their gift of photosynthesis, in nature only they can convert the useless inert nitrogen in the atmosphere into soluble nitrogen compounds that every living thing needs. Nitrogen is a key element in every protein, every molecule of DNA, every molecule of the universal energy-giving chemical ATP.
Only a few species of bacteria can perform this capture of atmospheric nitrogen, which is performed by a nanomachine called nitrogenase. Some live freely in the soil and can pass on the nitrogen to plants; some live attached to the roots of plants of the pea family. It is a puzzle that this vital process has not evolved more widely in nature.
This weak link is the reason we use artificial fertilisers. Synthetic nitrogen fertilisers, produced from nitrogen in the air by the Haber process, invented in Germany in 1913 and little changed today, now feed about 45 per cent of the world’s population. This input of synthetic nitrogen now outweighs the natural bacterial process, causing pollution through massive run-off into waterways with consequent toxic algal blooms that kill off other forms of aquatic life. Scientists are now trying to introduce the vital nitrogenase nanomachine into crops such as cereals, to avoid the damage caused by artificial fertilisers.
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So, the nanomachines of nature regulate the great global cycles. It’s a marriage of the infinitesimal and the enormous that leaves us humans stranded in the middle, struggling to comprehend what we have done to the planet. One of the main problems is that humans evolved as a species to act on what we can see with our eyes. It’s obvious from the extent of Covid denialism around the world that people find it hard to take invisible threats seriously. We need to develop the imagination to understand what the scientists are telling us about the world of tiny things, and how microbes are linked to enormous cycles that power our environment.
Up to now, we have been no better than the moles in Miroslav Holub’s poem “Brief Reflection on Cats Growing in Trees”. In the poem, the moles decide to investigate the world above. The first intrepid voyager reported that “birds grew on trees”; the next saw only mewing cats; the third ventured forth in utter darkness and reported: “In fact, things above / Were the same as things below, only the clay was less dense. . .”
Unlike the moles, we humans at least have the benefit of science. Yet an appreciation of the importance of the very small has been a long time coming. When, in the 17th century, it first became possible to use microscopes to see beyond the vision of the human eye, many were contemptuous of what was revealed. In his satirical book Citizen of the World (1762), the poet and playwright Oliver Goldsmith pioneered the “Two Cultures” debate, mocking the supposed pedantry of all who study tiny creatures.
Abraham Trembley was one of his targets, a naturalist of the time who had written a paper on the hydra: a transparent primitive freshwater animal about 1cm long with up to 12 tentacles. Goldsmith wrote of Trembley and his kind: “Their fields of vision are too contracted to take in the whole . . . Thus they proceed, laborious in trifles, constant in experiment, without one single abstraction, by which alone knowledge may be properly said to increase.”
It would be hard to devise anything as far removed from scientific truth as the above statement. We now know that DNA and the nanomachines of life are far smaller than the hydra, but they are the architects and executors of the “abstract principle” of life.
But as Goldsmith was writing, the revolution was beginning: from the mid-18th century, the early chemists – Joseph Black, Henry Cavendish, Joseph Priestley, Antoine Lavoisier and John Dalton – were the first to demonstrate that truth does not reside in what we can see. They discovered that the air was not a simple substance, and quickly identified the gases hydrogen, oxygen, nitrogen and carbon dioxide.
Dalton then drew on the prophetic insight of the pre-Socratic philosopher Democritus, as expounded around 2,000 years ago in the great Latin poem De rerum natura by Lucretius, showing that what lies beneath the surface appearance of all matter is something very unlike what we see: tiny atoms, themselves without sensory properties, that constitute everything.
Atoms are smaller than one nanometre, about one third of that size. Chemists knew that atoms were tiny even in the 19th century, thanks to the calculations of the Italian chemist Amadeo Avogadro in 1811. From then on, chemists learnt to manipulate atoms to produce thousands of new compounds throughout the 19th and 20th centuries without ever being able to see the entities they were manipulating, although they could of course see the results – materials that would drive technological civilisation.
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Chemistry is at the root of our new knowledge of nature, challenging that key human adage “seeing is believing”. The structure of DNA and the understanding of how it works only became possible when its relatively simple chemical components – the bases cytosine, thyamine, uracil, adenine, the sugar deoxyribose, the phosphate groups – had been characterised. To finally crack the secret of DNA, James Watson and Francis Crick had to work out how they were assembled in its 3D structure. Chemistry now enables us to know the structure of vastly complicated proteins containing thousands of atoms each in a precise position. This is true knowledge, but it is forever hidden from the sight of the naive eye.
At the other end of the size scale, humans now have the ability to discern the movements of the great global cycles over vast periods of time. Radioisotope dating and other techniques have revealed a very comprehensive and growing picture of the Earth’s state over most of its existence. For instance, ice cores drilled into Greenland and Antarctica can tell us what the composition of the atmosphere was like over the last 800,000 years.
But neither the new knowledge of the very small nor the long history of the global environment is common knowledge beyond the world of the scientists. The early history of the planet does not register strongly in most people’s sense of the world today.
The majority of us have remained like the moles in Holub’s poem, believing that bacteria are purely pathogenic predators of humans and other animals, because that’s the first thing we noticed when we became aware of their existence. In fact, causing disease in humans is a very incidental aspect of bacteria, restricted to a few species.
It’s no surprise that we latecomers to Planet Earth should have so misunderstood the world. Humans have developed rapidly from a species in nature like any other to a geological juggernaut capable of tipping the planet into the Sixth Great Extinction. In terms of the history of the Earth, this happened in the blink of an eye: 10,000 years out of 4.55 billion years of Earth history and perhaps 4 billion years of life.
There is no record of what humans thought was their place in the scheme of things 10,000 years ago, when the invention of farming began the long road to civilisation. We know what our species have thought for at least the last 4,000 years: that we are the point of the whole affair, the pivot of creation, with the Earth ours to use as we wish.This ingrained sapiocentrism is disastrous now that we are confronted with the damage we are doing to nature’s processes – things which we are only belatedly starting to understand.
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Humans are not the pivot of creation. We are merely, as far as nature is concerned, a top predator. That may sound pretty grand, but the real work of planetary balance has always been done at the bottom, by bacteria in particular. It is bacteria that guard the 1,500 or so essential genes that produce the proteins that regulate life’s processes in the cells of every living thing on Earth. As Paul Falkowski puts it in his 2015 book Life’s Engines: “Organisms are transient – even disposable – but the 1,500 core genes are not.”
In the five great extinctions so far, it was the top predators that perished. Life went on, eventually richer than ever. In the last extinction, 66 million years ago, the world of the dinosaurs and limited vegetation (no flowering plants yet) was replaced by the much richer world of mammals, the birds and the luxuriant flowering plants and trees the world has known ever since. But unless we take the right steps now, we will not be here to see whatever new world will emerge following the Sixth Great Extinction.
Humanity has misunderstood bacteria and viruses for too long. We have thought of them solely as our predators, while they have been waging a complex war against each-other. We are just collateral damage, caught in the crossfire. Now that we finally understand the deep chemical interactions between microbes in almost perfect atom-by-atom detail, we can turn their conflicts to our advantage – just as we did with antibiotics, most of which are derived from fungi that can kill bacteria.
This year’s Nobel Prize for Chemistry has gone to two researchers, Emmanuelle Charpentier and Jennifer Doudna, who developed the revolutionary CRISPR gene-editing system, based on a bacterial defence system against phages, which are viruses that prey on bacteria. CRISPR isn’t our only tool derived from the war between bacteria and viruses. Similar techniques are being used to develop vaccines and therapies for Covid-19. They are also at the heart of work on green energy, chemicals and materials production (see my article “Engineering Nature” in the Summer 2020 issue of New Humanist).
We now have, just in time, the tools to fight the two great menaces: Covid-19 and global heating. If humankind is to surmount these immense, complex challenges, we must engage with life at the tiniest of scales.
This article is from the New Humanist winter 2020 edition. Subscribe today.
