Predrag B. Slijepčević
Microbial Language
Ever since life emerged on Earth, there has been constant communication amongst organisms. But this communication is deceptive. These are no talking heads, but the communication is not unlike our language. Instead, organisms communicate through exchanging biological signals and semiotic signs – chemical messages, electrical impulses, scents, body movements, etc. Bacteria were the first organisms to speak up. Unfortunately, we are deaf to their conversations. Bacteria ‘talk’ to each other and to all other organisms on the planet. For example, bacteria from our microbiome – the collection of bacteria, viruses, archaea and fungi inside and on the surface of our bodies – talk to us behind our backs. They bypass the conscious part of our intellect and talk to the unconscious. Scientists have discovered ‘conversations’ between bacteria living in our guts and cells in our brains. This type of talk is called the gut–brain axis. Bacteria from our guts direct our brain cells to secrete serotonin, which improves mood.22 Gut bacteria drug our nervous systems without us even being aware that it’s happening.
Language is a set of symbols that convey meaning. Every linguistic sign reflects the superiority of mind over matter. When we utter a word, we launch a non-material abstraction full of meaning into the semiotic stratosphere. There, our symbols mix with bacterial, viral, plant and animal symbols in true Tower of Babel fashion, with the crucial difference that the number of languages in the semiotic stratosphere is far greater than in the biblical story. This fascinating biosemiotic construction intrigued the celebrated writer Umberto Eco, who was once impressed by the thought of a biosemiotician friend: ‘Instead of thinking whether cells speak like us, the question should be asked whether we speak like cells’.23
How do bacteria talk to each other? James Shapiro discovered their semiotic symbols – i.e. the ‘words’ of bacterial language. He identified a large group of chemicals that bacteria exchange in communication with each other.24 There are linguistic chemicals used in the communication of bacteria of the same species. There are also linguistic chemicals exchanged between bacteria of different species, in the manner of constructed international languages such as Esperanto or the true global language, English.
Conversations between bacteria and people, or bacteria and plants, are conducted in a language that scientists call cross-kingdom communication. The most successful communicators, including cross-kingdom communicators, are bacteria – true biological polyglots. Bacteria speak and understand all the languages of the world, from their own mother tongues, to plant and animal languages, to cross-kingdom communication that reverberates with the biosphere in the most complex music the universe has ever known. Bacteria also talk to viruses, semi-living biogenic structures, by detecting the words of a viral language – only recently discovered – based on arbitrium, which consists of a peptide composed of six amino acids.25 Thus, mostly thanks to bacteria, the biosphere becomes the semiosphere – a compendium of biological signs and the domination of mind over matter.
The Microbial Mind
We know from experience that words don’t make sense without the mind to decode and interpret them. The mind unites spoken words into sentences, then into stories, or perhaps into algorithms (if words are replaced by mathematical symbols). Without the mind, there is no storytelling, and this is also true of the biosphere and the Gaian mind. In other words, if bacteria have no mind, their talk is pointless; it represents little more than a form of mindless chatter. Mainstream biology, in a true Cartesian manner, does not allow for the existence of a bacterial mind. Even when leading scientists are willing to get into details of bacterial language, the idea of a bacterial mind controlling bacterial language is considered off-limits.26
Non-conventional scientists such as Eshel Ben-Jacob, Gregory Bateson and Lynn Margulis, however, have argued against the shortsightedness of mainstream biology, and especially against the prejudices that scientists cultivate towards non-human organisms – a kind of evolution-based anthropic racism rooted in modern culture. Ben-Jacob developed the concept of the ‘bacterial brain’, which is complete only when combined with Bateson’s concept of the natural mind.
Ben-Jacob argued, similarly to Shapiro, that bacteria are multicellular communities (or colonies), with a typical colony consisting of 109–1012 individual organisms, and with the entire bacterial population connected into a global bacterial superorganism or bacteriosphere. Bacterial colonies are constantly using language to solve the problems presented by their environments. A colony will assess a problem – for example, food shortages – through the collective examination of the environment and collective gathering of information using bacterial language. Once the nature of the problem is determined, bacterial colonies use information about past problems, stored in the colony’s collective memory. In this manner, the colony begins distributed information processing to solve the emerging problem. The problem-solving process transforms the colony into a structure most similar to the human brain. Bacterial colonies become ‘super-brains’ that perform acts of natural computation.27 When we look from this perspective at the planetary bacteriosphere, in which bacterial colonies are connected through bacterial language – a living equivalent of the internet (see ‘The Internet of Living Things’, page 16) – we see glimpses of a planetwide bacterial brain that has maintained biogeochemical balance for billions of years.
Gregory Bateson would probably agree that a bacterial colony constitutes a form of the natural mind. Bateson often reminded his audience that the mind exists in nature in many more places than just inside our heads. To assess whether a biogenic structure meets the requirements of the natural mind, Bateson applied six criteria28:
1. The mind is the unity of the parts that communicate with each other;
2. The mental process creates feedback;
3. Communication between parts is driven by the ‘difference that makes a difference’ or biological information;
4. The mental process requires energy;
5. Biological information directs changes in the physical environment;
6. Biological hierarchy is constrained by both bottom-up (cells to ecosystem) and top-down (ecosystem to cells) forces.
Bacterial colonies and the planetary bacteriosphere meet all of Bateson’s criteria of the natural mind. More than a century prior, Darwin stated the following about the mind: ‘The difference in mind between man and the higher animals, great as it is, certainly is one of degree and not of kind.’30 Bateson, however, was much more radical. For Bateson: ‘Mind is the essence of being alive.’ Interestingly, Bateson considered Lamarck to be the greatest biologist in history, not Darwin. Presumably because, amongst other things, Lamarck sensed the intelligence of bacteria.
Microbial Memory
The collective memory of microbes goes back almost four billion years to the moment when these tiny and invisible organisms emerged on Earth. How is this possible? The first line of memory is the microbial genome that stores blueprints for the oldest protein constructs. This is no exaggeration but simply a consequence of the biological postulate of vertical gene transfer. Since bacteria and archaea were the first organisms in the history of life, all organisms that evolved from them, including humans, share their four-billion-year genetic heritage.31
But genes are only one line of memory. The other line of memory is much more important: the organism as a biological construct that incorporates genes. Genes are important, but they are secondary. The emblem of neo-Darwinism – ‘the selfish gene’ – is becoming an obsolete concept. How can a gene be selfish when it lacks a self? This is a question Lynn Margulis asked Richard Dawkins at a meeting. No one has yet come up with a convincing answer.
Margulis argued that the basic unit of life, and therefore of memory, can only be the simplest cell – a microbe such as a bacterium or an archaeon. Each bacterium is an open thermodynamic system that exchanges matter, energy and information with its environment. Each bacterium has an instinctive sense of its own body in the context of the external environment. It has perception, memory and the ability to make decisions, plan the future and communicate. These characteristics are to be expected from a biological system that has a sense of its own body.
A gene or a piece of a DNA molecule, on the other hand, is a simple biological code that serves the bacterium as an aid in the transmission of biological information, and in the process exchanges matter and energy with the environment. This code is meaningless without the context of the bacterial ‘body’ as an open thermodynamic system. The DNA code is a form of bacterial ‘thought’ – a hypothesis subjected to an evolutionary test.
Interestingly, the source of genes, which are biological ‘thought’ material, is not only bacterial or archaeal genomes, but viruses, plasmids, naked genes and other DNA pieces involved in horizontal gene transfer (HGT). Some scientists argue that viruses may be a precursor to life – a position supported by the fact that bacteria, the most dominant form of life in the biosphere, cannot exist without viruses.32 The bacteriosphere needs an auxiliary biogenic structure. Scientists call this structure the virosphere. The virosphere and the bacteriosphere are the foundations of life. The most numerous viruses in the virosphere are those that infect bacteria (although bacteria developed a system of defense against unwanted viruses, or, metaphorically, unwanted ‘thoughts’, so that they can preserve their own ‘common sense’).33
Eshel Ben-Jacob defines the nature of bacterial memory as follows: a combination of (a) internally stored information in the genome of each bacterium and (b) information that the bacterial society, which makes up the colony, collects from its environment and stores in the structure of the colony. In other words, genetic memory by itself is not enough for the process of wiring bacteria to the environment. Genetically stored information only serves to trigger more complex collective information-processing abilities, which then create new knowledge that bacteria need to learn about new conditions in the environment. Thanks to this memory, the bacterial colony turns into a brain-like entity capable of natural learning, and thus becomes a form of Bateson’s natural mind. The conclusion is self-evident: the ability of bacterial colonies to remember past events transforms the planetary bacteriosphere into the collective memory of the biosphere.
No matter how much Homo sapiens might deny the dominance of microbes on Earth, and artificially impose human dominance, reality refutes us. The COVID-19 pandemic is one example amongst many that ruthlessly revealed the holes in our understanding of biological reality. The bacteriosphere and virosphere are the basis of life (see Chapter 2). Although we can’t deny the usefulness of the term in revealing the destructiveness of human impact, the Anthropocene is little more than an anti-Copernican delusion of modern civilisation.
The First Scientists
But how did humans get to a point where we are so enamored of a faulty interpretation of the biological world – the delusion of the Anthropocene? It may sound paradoxical, but the delusion was inspired in part by some of the greatest achievements of modern civilisation, many of which occurred during (or would not have occurred without) the Enlightenment. Enlightenment thinkers introduced a sweet but dangerous idea: Homo sapiens is the most sophisticated organism in the history of life. Human sophistication has no limits. Transhumanism and man-made machines will help us conquer the cosmos and transform us into a cosmic deity.34
Today, the term used to justify the superiority of the human mind is ‘post-biological evolution’ – the idea that humanity and its machines will dominate the world. Or perhaps that machines will turn against humanity and establish mechanical dominance of the world through the Machinocene (a term coined by Huw Price on the portal Aeon) or superintelligence.35 I suspect Bateson would have questioned this possibility. He thought of machines as mindless. Indeed, in my opinion, post-biological evolution falls into the same category of delusion as the Anthropocene.
Of course, the Enlightenment was enormously useful for the development of civilisation. Without the Enlightenment, there would be no science in the modern form. However, one should also acknowledge, in the manner of far-sighted thinkers such as Bateson, Margulis and others, its major fallacy: anthropic arrogance towards all other life forms, especially microbes. At its worst, this arrogance becomes a form of anthropic racism – our technologies are responsible for a biocide of planetary proportions, recently dubbed ‘biological annihilation’ or even the ‘Necrocene’.36 The fallacy, if one can rely on psychiatry, may be a consequence of the unresolved Copernican complex. Although Nicolaus Copernicus, the 16th-century Polish priest turned scientist, showed us that we live on an insignificant planet that orbits around an insignificant star, we have not given up the comforting but dubious idea that Homo sapiens is the peak of evolution around which the entire cosmos revolves. This is apparent, for example, in the concept of the anthropic argument that places humanity at the center of the thinking universe.37 Anthropic exaggerations, despite the rationalism of the Enlightenment and Copernican caution, only serve to add weight to the validity of Shapiro’s position. Actually, Shapiro’s position is probably the best-articulated form of Copernicanism in biology.
If we adopt Copernicanism in biology – the position that there is nothing special about the human species – then the only relevant yardstick of the two competing options – Mayr’s deeply anthropocentric option and Shapiro’s biocentric one – is evolutionary scale. Although we are unable to experience the temporal scale of evolution, we have ample evidence to conclude that Homo sapiens is a young and inexperienced species whose modern civilisation is not yet aware that, in Bateson’s words, by destroying its environment, it destroys itself. The same thesis in a different context was advocated by Chief Seattle: ‘Man did not weave the web of life, he is merely a strand in it. Whatever he does to the web, he does to himself.’38 Likewise, Lynn Margulis ended her book Symbiotic Planet with a passage containing the following sentence: ‘We cannot put an end to nature; we can only pose a threat to ourselves.’39
Although Shapiro’s position is not anthropocentric, it is deeply humanist in a nuanced and particular sense – it accepts humanity’s place in the world. This form of humanism allows for a constructive criticism of Cartesian science, as well as of the Enlightenment itself. As I will show in this book, microbes have been practicing science (as well as engineering, farming, art, medicine and more) since long before the Enlightenment; indeed, long before the appearance of Homo sapiens at all.
The Artful Science
Flipping the prevailing narrative has two purposes that will make the journey into the world of biocivilisations more comfortable. First, as Gregory Bateson thought, turning the human world upside down is a valuable metaphor that can help us understand our place in the world better. The consequence of this metaphoric turning is not trivial. It may help us realize that we are lost in the jungle of a wrong epistemology, without being aware of how this causes us to misconstrue the human place in the world.40
Second, it can help us find a road into the evolutionary past on which we can discover the origin of biocivilisations, and by doing so identify a way out of the jungle of wrong epistemology. The key person here is Lynn Margulis and her serial endosymbiosis theory (SET).41 SET interprets life as an interconnected mosaic of living organisms that together form the Gaian superbiosystem, one in which viruses coevolve with bacteria, bacteria and archaea complexify into protists, protists complexify into plants and animals, and all these organisms integrate into the Gaian mind (see Chapter 2). SET allows us to argue that the mind-like structural coupling between organisms and environments that sparked the emergence of biocivilisations started with, and is still dominated by, microbes.
Kenneth Clark, a British art historian and broadcaster, remarked at the beginning of his hugely successful TV series Civilisation: ‘What is civilisation? I don’t know. I can’t define it in abstract terms yet. But I think I can recognize it when I see it.’42 Clark was referring to art as the peak of human civilisation. Lynn Margulis was able to discover for us the art behind biocivilisations, which in many respects surpasses everything human civilisation has ever produced, and likely everything it ever will.
Likewise, I view Gaia as an artistic system, one that constantly creates itself in the autopoietic sense described by Humberto Maturana and Francisco Varela: by encouraging viruses here and there, nudging plants from one habitat into another, attracting bacteria and fungi to an insect ecosystem, or directing big changes in its body by converting evolutionary catastrophes into new forms of biogenic art.43 Gaia is the totality of all biocivilisations that defies the mechanistic view of life increasingly imposed on us by AI enthusiasts and their physicalist view of the world. We can call the totality of the Gaian mind the cognitive multiverse – a truly vast artistic system in which mind is more than computation.44 Just as the sculpture of David is the product of an artist’s mind, the oxygen-rich atmosphere is the product of an artistic spark that occurred when cyanobacteria discovered how to eat the Sun. Ever since then, Earth’s atmosphere has been a huge planetary canvas on which artistic sparks thrive, leading to an endless cascade of new plant and animal biocivilisations that constantly enrich the complexity of the Gaian mind.
When we merge Bateson’s and Margulis’ ideas, we get a huge evolutionary theatre of perpetual mind-like mergers of organisms and environments over the course of four billion years. The name of this evolutionary play is biocivilisation. It consists of countless streams – individual biocivilisations that represent the cognitive spaces of individual species – joined together into the big river of the Gaian mind.45 We humans are not able fully to capture or copy the art behind the Gaian mind. We can only admire it by trying to discover, like Bateson, Margulis, Shapiro, Ben-Jacob, Maturana, Varela and others, the streams in the river that can take us out of the jungle of mistaken epistemology.
Allow me to recapitulate: if you want to understand a biocivilisation, you must try to build a model of it in your mind, as Feynman so aptly described: ‘What I cannot create, I do not understand.’ My attempt to build a model of biocivilisation has revealed its three crucial elements: language, mind and memory – essential elements in all biocivilisations that have appeared as streams in the Gaian river ever since microbes started to merge.46
But building a biocivilisation with a human model offers only a limited glimpse into the complexity of the Gaian mind. Nevertheless, this is perhaps what true humanism represents. This is the humanism that makes life worth living – by catching glimpses of the Gaian mind, we integrate into it. We become part of the huge river that started flowing four billion years ago. Gaia is neither a mechanical system nor a giant biological machine. The next time you meet passionate adherents of modern computational concepts such as the Machinocene, AI-based superintelligence or post-biological evolution, please tell them that Gaia is a Heraclitean river that defies the mechanics of physicalism (see Chapter 2). Their machines will simply sink to the bottom of the Gaian riverbed. There, they will serve as meals for countless microbes – those that can eat even metals. After a while, these microbes will return the digested wreckage to the immortal Gaian flow.
For this reason, I have to correct myself. I said earlier that every single piece of evidence that I will use in the book will be based on science and this will make the book scientific. This remains the case. However, the way I will use the evidence to lead you through the story of biocivilisations will defy the classical science that is traditionally dominated by physicalism. I will use scientific evidence to integrate scientific evidence into the artistic Gaian mind. Inevitably, this process may offend hard-core mechanistic scientists. My angle, however, is different. It represents a badly needed avenue for the reconciliation of arts and sciences, whose relationships are poisoned by the high priests of both realms. A scientist-turned-poet friend articulated this false dichotomy in an interview on my blog: ‘Science, art, music and literature explore the same world but using different tools.’47
My goal is to show that the seemingly separate worlds of art and science are, in reality, one, but perhaps with different faces, like the Roman god Janus. Both faces are essential. The scientific face will help us explore and survive our increasingly uncertain future, but only if we tone down the mechanistic reductionism. The artistic face will always remind us that we are not gods but tiny parts of the Gaian mind – a truly creative system that, like an artist, cannot predict its next iteration.48
So, the story of biocivilisations perhaps represents a form of artful science – the science that escapes the grips of physicalism and finds its true habitat: biology. This also means we cannot fully understand life through a physicalist science that mechanizes everything from atoms to biosystems. This mechanophilia, or love for the machine, is a symptom of the ‘pathologies of epistemology’. The only antidote to this pathology is the true science of life, a description of which you will hopefully find in the pages of this book.
This excerpt is taken from Biocivilisations: A New Look at the Science of Life (2023) by Predrag B. Slijepčević and used with permission from Chelsea Green Publishing.
Published December 16, 2023
About the Author
Predrag B. Slijepčević is a senior lecturer in the Department of Life Sciences at Brunel University London. He is bio-scientist interested in the philosophy of biology. In particular, Predrag investigates how biological systems, from bacteria to animals and beyond, perceive and process environmental stimuli (that is, biological information) and how this processing, which is a form of natural learning, affects the organism–environment interactions. He aims to identify those elements in the organization of biological systems that lead to forms of natural epistemology, or biological intelligence, that might qualify those systems as cognitive agents. He has published widely in peer-reviewed journals across all areas of this book. Biocivilisations is his first book.