Showing posts with label Life. Show all posts
Showing posts with label Life. Show all posts

26 November 2025

Togetherness

Twenty years ago, on this day—26 November 2005—I posted the first essay on this blog. Today's post is the 647th essay (and the first one not posted on a Friday). Jayarava's Raves amounts to some millions of words. If you had told me twenty years ago that I would go on to write well over 600 essays, I would not have found that plausible. And yet, here we are.

These essays reflect my self-education not only in Buddhism, but in all the allied disciplines and fields that are required to understand religion, religieux, and religious phenomena, including: history, philosophy (metaphysics, epistemology, axiology), general linguistics, socio-linguistics, translation theory, sociology, and social psychology (none of which were included in my formal education). I've also maintained an interest in science and written about that from time to time. I've been trying to make sense of Buddhism in rational terms. 

Perhaps the most profound thought I have come across in the last 20 years is that we are not only social animals, but each individual is also a community of cells. And our surfaces—inside and out—are coated with numerous symbiotic microorganisms that make a significant contribution to processes such as digestion and immunity to pathogens. Moreover, our eukaryote cells are themselves symbiotic communities of what used to be separate organisms.

Whether we know it or not, every one of us is a community of communities. And if we go up the taxonomic hierarchy, we find humans in dependent relationships within ecosystems at every turn. Ultimately, all ecosystems contribute collectively to Gaia, the Earth's biosphere conceived of as a single (if complex) self-organising and self-regulating system.

Everywhere we look in nature, at whatever scale we choose, we see communities, cooperation, symbiosis, interdependence, and co-evolution. I find this thought both profound and beautiful. Yes, there is some conflict and competition, but Darwinian approaches to evolution massively over-emphasise conflict and almost completely ignore cooperation.

In this essay, I want to dwell on togetherness. It is, ironically, something I have seldom experienced for myself, and less and less as years go by. Nonetheless, I recognise it as the acme of human existence.


Social Animals are Moral Animals

What do you think of this slogan? Does this sound evil to you? Is this a recipe for tyranny?

All for one, and one for all;
United we stand, divided we fall.

What about these?

  • There's no 'I' in team.
  • A problem shared is a problem halved.
  • It takes a village to raise a child.
  • No one gets left behind.—US Military
  • Alone we can do so little; together we can do so much.—Helen Keller
  • Even the weak become strong when they are united.—Friedrich von Schiller
  • We must learn to live together as brothers or perish together as fools.—Martin Luther King, Jr.
  • Coming together is a beginning, staying together is progress, and working together is success.—Henry Ford
  • "Monks," said the Bhagavan, "you have no mother and no father to care for you. If you don't care for each other, then who will care for you? If you would care for me, then tend to the sick."—Vin I 301

In The Road to Serfdom (1944), Friedrich Hayek argued that all forms of collectivism inevitably lead to tyranny. Only robust individualism, especially in commerce, can save us from tyranny and deliver us to an individualist liberal utopia. If Hayek was right, then these collectivist slogans that emphasise cooperation, community, and togetherness ought to be seen as a threat.

To me, this attitude is almost incomprehensible, but Hayek is probably the most influential intellectual of the last century. Along with other prominent neoliberals—like Ludwig von Mises and Milton Friedman—Hayek's views have shaped every capitalist society on the planet. Virtually all modern politicians and businessmen are neoliberals. Revolutions around the world in the late 1970s and early 1980s aimed to implement Hayek's utopian (neo)liberal view of a society of self-sufficient individuals engaged in commerce. While these men were promoting self-interest to intellectuals and economists, mad old Ayn Rand became the patron saint of self-interest amongst technologists (thus validating the neurodivergence that made them somewhat alienated from society). Alan Greenspan, who was a central figure in US monetary policy ca. 1974 to 2006, was a personal disciple of Rand. Making Rand one of the most influential intellectuals of all time.

Of course, the anti-collectivists were helped by the horrific excesses carried out in the name of Karl Marx in the USSR and China. Stalin and Mao were undoubtedly brutal tyrants. But in terms of socialism, Hayek and company seem to ignore all of the democratic socialist nations and the very high standard of living and freedom they attained. Norway, Sweden, New Zealand, Canada, and even post-War Britain all had democratic socialist governments and free people.

The fact is that humans are social; we live in societies. Our sociology determines our psychology, not the other way around (sociology is more fundamental than psychology). And ideological individualism is a pathology for a social animal.

Some birds and most mammals have adopted a social lifestyle. I won't comment here on social insects since they work on different principles. The social lifestyle is one of the most successful evolutionary strategies in the 3.5 billion-year history of life on Earth. Certainly, the success of humans as a species is directly related to our ability to work together in large numbers for a common cause. We actually enjoy working together.

Amish men raising a barn together.

By the way, I don't cite animal examples to drag us down: "we're no better than animals". I cite animal examples to emphasise the universality of these observations about morality and togetherness. I also want to emphasise that no supernatural explanation of morality is needed

As the late, great, Frans de Waal pointed out, a social lifestyle minimally requires two capacities: empathy and reciprocity.

Empathy is the capacity to use physical cues to internally model how other people are feeling. Which means we don't just know what others feel, we also feel it in our own bodies. This is why emotions are contagious. As social animals, we monitor how the group is disposed, i.e. who is feeling what towards whom. This allows us to accurately judge the potential and actual impacts of our actions on others, and to moderate our behaviour accordingly. This is morality in a nutshell. But we don't just respond in the moment. We also keep track of and respond to how people have acted towards us, which requires the capacity for reciprocity.

Reciprocity is the capacity to form relationships of mutual obligation. It is keeping track of these obligations that creates a limit on the size of groups. The famous "Dunbar Number"—150—was derived by comparing primate group sizes with the volume of their neocortex. Robin Dunbar showed there is a strong correlation between these. Humans can keep track of the history of how members of the group interact in groups up to around 150, though there is considerable individual variation. Beyond 150, we can still form groups, but the sense of mutual obligation is more tenuous as the group size increases. With strangers, we typically do not feel a sense of obligation, except where it is imposed on us by nature: for example, the culture of hospitality common to many desert-dwelling societies.

However, reciprocity only holds a group together if there is some tendency for generosity. Someone has to start sharing, or no one would share. Social animals have to be prosocial, or sociality per se doesn't work. At the very least, mammalian mothers have to be willing to care for newborn infants, or they don't survive.

Anyone who reneges on the obligations of reciprocity has created an unfair situation. De Waal and other animal ethologists showed that social mammals are keenly aware of fairness (see especially his TED Talk). We intuitively understand that unequal rewards are unfair. We know it, and we also feel it deeply. Since the survival of the group relies on maintaining the integrity of the network of mutual obligations, we are highly motivated to be fair and to re-establish fairness when it breaks down. We call the latter "justice".

So our concepts of morality, fairness, and justice all emerge naturally from our having evolved social lifestyles and large brains. The rudiments are all visible, at least to some extent, in all social animals, suggesting universality. What may be unusual in humans is ethics, understood as abstract principles on which more concrete moral rules can be based. It is abstract ethics that allows us to adapt moral rules to new situations, for example (note that Buddhism lacks any ethical discourse, so Buddhists generally take a conservative view—no new rules—or they draw on the ethics of the surrounding culture for making ad hoc rules).

Being a member of a social species is not the only form of biological interconnection that we participate in. Let's now look at some others. 


Evolution and Exosymbiosis

I have long been a fan of Lynn Margulis (1938 – 2011). Margulis got a few things spectacularly wrong, especially later in life (notably her views on HIV were badly wrong). But her overall contribution to biology was pivotal for modern science and for my own views.

Notably, Margulis discovered endosymbiosis in 1966, which I will deal with in the next section. Margulis also advocated, in scientific and popular publications, for much greater awareness of the role of symbiosis in biology and evolution.

Margulis, Lynn. (1998). The Symbiotic Planet: A New Look at Evolution. Basic Books.

When I first studied biology, over 40 years ago, symbiosis was presented as something rather rare and unusual. Some organisms, such as lichens, enter into very close relationships in which two or more species rely on each other to survive. Lichens are the classic example. Lichens are a distinctive form of organism, but they are actually made of at least one fungus and one bacterium. Some species of lichens include both a filamentous (or hyphae-forming) fungus and a single-celled fungus (or yeast).

From quite early on, Margulis argued that symbiosis was much more common than allowed by traditional biology. Indeed, Margulis was critical of Darwin's (and the Darwinian) focus on competition and violence amongst animals (a view that Frans de Waal also rebelled against early in his academic career). 

According to Margulis, this jaundiced view was heavily influenced by the preoccupations of Victorian ruling-class men, i.e. patriarchy and imperialism. That is to say, representing nature as "red in tooth and claw" suited the ruling class men of Europe—of which Darwin was a member—because they were busy trying to conquer, appropriate, and exploit the entire world. Darwin was able to spend 20 years developing his ideas on natural selection because he was never burdened by having to work for a living. Nor did he have to accept patronage. Having inherited enough wealth to live on, he could simply focus on his gentlemanly pursuit of science and volunteer work for learned societies. And this was the norm at the time. There were no working-class scientists.

Nor was this the end of the trend. Richard Dawkins, arguably the most prominent biologist of the twentieth century, applied Hayek's neoliberal worldview to biology to come up with the "selfish gene". Cooperation, communities, symbiosis and all that were simply explained away as being "motivated by self-interest". The conclusion is too obviously ideological rather than objective. Later in life, Dawkins is famous for two things: (1) apologetics for his own unreasonable views and (2) unreasonably picking fights with religious people using arguments that are guaranteed not to change anyone's mind. Dawkins, the biologist, never even tried to understand the phenomenon of "belief".

From the time of Thomas Hobbes (1588 – 1679), liberals have seen humans not as prosocial, empathetic, and reciprocating but as vicious loners, forced by circumstances to live together, creating endless conflict and violence. Note that Hayek is clearly Hobbesian in outlook, and it is no coincidence that both of these ruling-class men lived through periods of all-out war and political chaos in Europe. They both attributed the violence of their own class and gender to the common people and argued that their own class provided stability. In psychological projection, a person projects alienated aspects of their own personality out into the world, in order to try to come into relationship with themselves. 

Liberals see competition as the great winnower of species and individuals (social Darwinism has always been part of the liberal schtick). Competition takes on a moral character in which succeeding in competition equates to moral goodness. Hence, liberals expect "winners" in any competition to be moral role models. 

According to liberalism, the apotheosis of competition means that we naturally adopt a kill-or-be-killed attitude. However, liberals also believe in Hobbes' Leviathan. This is linked to the Christian idea that God placed the ruling class in a superior position to other people, i.e. that of gamekeeper or farmer. The ruling class are the only ones who can impose order on the common people, who are otherwise nasty, brutish, and violent, but also lazy.

These views are all too obviously ideas that the ruling class of imperial Britain used to justify imperialist brutality towards societies, including their own. When a society routinely commits genocide in order to steal resources, it has to have some discourse that legitimises this. And liberalism was one of these. 

In fact, symbiosis turns out to be ubiquitous in nature, with humans themselves providing one of the most striking examples.

The "human gut microbiome" is now a household concept. We all know that many beneficial bacteria, fungi, and protists live in our gut. They very obviously contribute to digestion, for example, by breaking down cellulose, which we cannot do without them.

We now know, for example, that when a baby mammal suckles milk from its mother, it is also swallowing bacteria that will become its gut microflora. And that this is vital for the normal development of the gut and the immune system.

I suspect that part of the reason that so many modern people have "allergies" and "sensitivities" is the trend since the 1960s to bottle-feed newborns. Of course, sometimes there is no choice, so demonising bottle-feeding is counterproductive. But there must be a way to introduce bottle-fed newborns to "good bacteria", some other way, rather than leaving it to chance. I suspect that the massive rise in morbid obesity may be related to aberrant gut microflora as well, although eating to stimulate the parasympathetic nervous system (and thus reduce physiological arousal) is a huge factor. That is to say, we eat to calm down because we are hyperstimulated most of the time and have not learned any better ways. 

So beneficial are our gut symbionts that one can now receive a "faecal transplant" in which faecal matter from a healthy person—said to contain "good bacteria"—is introduced to the bowel of an unhealthy person, with a view to restoring their health. Apparently, this can work. Various foods with "good bacteria" are also popular, though whether these survive passing through the stomach is moot. Stomach acids kill the vast majority of microorganisms. 

Another very striking example of ubiquitous symbiosis is the mycorrhizal fungi that grow in and around tree roots. The fungal filaments (hyphae) live partly in the tree roots and partly in the soil. They break down the soil and transport nutrients into the roots, thus nourishing the tree. 

There is some suggestion that mycorrhizal fungi form underground networks in forests that link trees together and allow them to share resources. From what I've read, the full-on clickbait version of this story is to be taken with a grain of salt. Still, we can say that symbiotic mycorrhizal fungi are very important to the thriving of many plants.

All animals have extensive symbiotic relations with gut bacteria. But our outer surfaces are also an ecosystem. Not only are we constantly covered in microorganisms, but we also play host to organisms such as eyebrow mites that live in hair follicles. We are an ecosystem for such critters. 

Margulis also notes that bacteria evolve rapidly. They have generations of about 20 minutes. Every bacterial cell can, at least in principle, share genetic material with any other bacteria, regardless of species. Indeed, Margulis sometimes argued that one can take this to mean that bacteria are all one species. In any case, bacteria are highly promiscuous and routinely swap genes. This is how a trait like antibiotic resistance can spread rapidly in a population of bacteria.

Another feature of evolution that the Darwinists downplay is hybridisation. Again, when I was studying biology, hybridisation was presented as an exception. Fast forward 50 years, and it turns out that all humans are the result of the hybridisation of more than one human species. Most Homo sapiens carry some genes from one or more of Homo neanderthalensis, Homo naledi, Homo longi (aka Denisovans), and/or Homo floresiensis. Possibly others as well.

Margulis pointed out that where organisms fertilise eggs externally, hybridisation is very common. Some 20% of plants and 10% of fish routinely hybridise.

Finally, we can point to many examples of coevolution in which two species evolve a dependence on each other. The most obvious examples are plants and their pollinators. Some of these relationships are so specific that only one species of insect is capable of fertilising a particular flower. The plant puts considerable resources into attracting appropriate pollinators, and pollinators expend considerable resources collecting and distributing pollen. Each benefits more or less equally from the relationship, and they come to rely on each other to survive. This is surely the very opposite of competition. If the dynamic here were competitive, one of the partners would lose out. It would become a form of commensalism or parasitism.

Even parasitism is considerably more complex than it seems. For example, there is a widespread belief, backed up by robust evidence, that eradicating common human parasites in the modern world has led to the immune system being poorly calibrated, which contributes to the rise in autoimmune diseases and "allergies" in modern times. This is sometimes called the "hygiene hypothesis". We evolved to deal with common parasites and, ironically, not having them, which would intuitively be seen as wholly good, is actually a disruption of the normal order of things and leaves us maladapted. Just as faecal transplants are a thing, some doctors have tried infecting patients with relatively harmless roundworm parasites as a way of correcting an immune system imbalance. The jury is still out, but the idea is not completely mad.

While competition is certainly a factor in evolution, it is far from being the only one. Lynn Margulis convinced me that cooperation, communities, symbiosis, hybridisation, and co-evolutionary dependencies are every bit as important to evolution. Species not only diverge, but they also converge, creating evolutionary leaps. Margulis also alerted me to the ideological nature of some scientific conclusions regarding nature and evolution, especially the influence of patriarchy and neoliberalism. The story of how important symbiosis is to evolution is brought into focus by Margulis's 1967 breakthrough article.


Endosymbiosis

In the mid-1960s (around the time I was born), an early career scientist, then known as Lynn Sagan (married to celebrity scientist Carl Sagan), sent a novel paper to a series of science journals. After many rejections, the paper was eventually published as

Sagan. L. (1967). "On the origin of mitosing cells." Journal of Theoretical Biology. 14(3):255-74. Available online in numerous places.

Part of the abstract reads:

By hypothesis, three fundamental organelles: the mitochondria, the photosynthetic plastids and the (9+2) basal bodies of flagella were themselves once free-living (prokaryotic) cells. The evolution of photosynthesis under the anaerobic conditions of the early atmosphere to form anaerobic bacteria, photosynthetic bacteria and eventually blue-green algae (and protoplastids) is described. The subsequent evolution of aerobic metabolism in prokaryotes to form aerobic bacteria (protoflagella and protomitochondria) presumably occurred during the transition to the oxidizing atmosphere.

This hypothesis was subsequently tested and found to be accurate. This process, in which one single-celled organism ends up permanently and dependently living inside another, is now called endosymbiosis. In the meantime, Sagan remarried and changed her name again to Lynn Margulis, which is how I refer to her throughout.

In 1967, endosymbiosis was a radical theory, though some precedents in Russian microbiology were largely ignored in greater Europe because it was the height of the Cold War. Sixty years later, and this idea that organelles within eukaryote cells were once "free-living" is normative. This radical discovery is now such a commonplace that many modern discussions of endosymbiosis do not even mention Margulis or her role in it. Nick Lane, for example, who is at the forefront of abiogenesis research, has repeatedly downplayed the contributions of Margulis. 

It's fair to say that Margulis thought radically differently from most other people and that she was outspoken about her views. For a woman in the 1960s and 1970s, being outspoken (especially towards men) was seen as a serious character flaw. Many men were (and are) intimidated by a strong, intelligent woman. And, unfortunately, Margulis wasn't always right. However, she was right about endosymbiosis, and this is one of the most profound discoveries in the history of science. It is every bit as important as discovering DNA in terms of understanding how life and evolution work.

The prokaryotes are largely represented by bacteria and archaea (previously known as "extremophile bacteria"). Prokaryote cells have no nucleus and little internal structure. Their nuclear material is in a loop rather than a linear chromosome. 

The eukaryotes are fungi, plants, and animals. Eukaryote cells have a nucleus, with chromosomes, and many other internal structures, such as mitochondria.

Prokaryote organisms are far more numerous in biomass and variety. Animals are relatively unimportant to life on Earth; if we all disappeared, the prokaryotes would hardly notice, except those that specialise in living in/on us. Some plants rely on animals for reproduction. But not all, by any means. 

We can diagram the process by which combinations of prokaryotes led to the various eukaryote "kingdoms".

In the standard, neoDarwinian account of evolution, separated populations of a species subjected to differing environmental pressures will slowly diverge over time and become two distinct species. This has now been observed both in the lab and in nature. Evolution, per se, is a fact. Evolutionary theory is our explanation of this fact. Evolutionary theory is taught as a monoculture, at least up to undergraduate level. 

Darwin himself diagrammed the process of evolution as a branching tree, i.e. as a series of splits. This is still by far the most common way of representing evolution. I wrote a critique of this view in an essay titled: Evolution: Trees and Braids (27 December 2013). My suggestion that that we needed to represent evolution as a braided stream, since this allows for convergence and recombination.

I've already commented above on the ubiquity of exosymbiosis and hybridisation in nature. What I want to emphasise here is that endosymbiosis doesn't fit the neoDarwinian view of evolution at all because it is evolution by addition and recombination, rather than an accumulation of mutations. This alone tells us that the Darwinian view is incomplete.

In terms of my view of the world, the fact that our very cells began as small communities of cells within cells is a profound confirmation of the importance of communities and cooperation in nature at every level.

Similarly, our genome can be seen as a community of cooperating genes. The idea of individual genes, let alone "selfish" individual genes, makes little sense. Genes are always part of a genome. Even when bacteria swap genes, they incorporate new genes into their genome. We can talk theoretically and abstractly about individual genes, and we methodologically identify the corresponding function of the gene. But this is an abstract concept. In reality, genes only occur in genomes. A gene simply cannot function outside of a genome and the associated infrastructure.

The concept of the "selfish gene" is nonsensical, even as a metaphor.

So far, I've been delving down the taxonomic hierarchy into the microscopic. This is all too familiar in a reductionist environment and might have passed without comment. However, I am very critical of ideological reductionism. I believe that structure is also real and that structure anti-reductionism is a necessary counterpart to substance reductionism.

In the last section of this essay, therefore, I want to look up.


Gaia

I've already noted that social animals almost invariably live in family-oriented communities (with occasional solitary outliers). But we can also observe that each extended family exists in a network of inter-familial relations, often linked by intermarriage. 

Every human community is part of a network of communities embedded in an environment. We are also part of the local ecosystem. And the local ecosystem is part of the global ecosystem, also called the biosphere or more poetically, Gaia.

The Gaia hypothesis was first proposed by chemist James Lovelock (1919 – 2022) in 1975, with help from none other than Lynn Margulis. The classic statement of the idea appeared in book form in 1979.

Lovelock J (1979). Gaia: A New Look at Life on Earth. Oxford University Press.

The Gaia hypothesis says that the biosphere as a whole is a complex feedback mechanism that "works" to keep the surface of the earth suitable for life, i.e. at maintaining homeostasis. Lovelock introduced the idea of "daisy world" as a simple cybernetic model of how life might achieve homeostasis on a planetary scale.

Interestingly, the Gaia hypothesis emerged after Lovelock was commissioned by NASA to help them figure out how to detect extraterrestrial life. Gaia maintains surface conditions that definitely could not occur in the absence of life. For example, high levels of oxygen in the Earth's atmosphere require constant replenishment by living things. So any planet with high oxygen is a candidate for harbouring life.  

Life causes our planet to exist in a state that is very far from the (chemical) equilibrium that we see on planets with no life, like Mars or Venus.

In order to understand life, we have to take a holistic view. Rather than reducing everything to its base substance and calling that "reality", we have to see that reality includes structure. Everything we can see with human eyes is a complex object with numerous layers of structure, lending it many structural properties (sometimes vaguely referred to as "emergent properties"). To say that complex objects are "not real" or "just illusions" is not helpful (or true).

When it comes to life, every structure is embedded in larger structures, up to Gaia, which is the ultimate living structure for life on Earth. Reality is substantial, but it's also structural and systematic.

From the lowest level of description to the highest, life is structures made of structures and systems within systems. Nothing living ever exists as a standalone or independent entity. Everything is dependent on everything else. The Hobbesian, lone-wolf version of humanity really only applies to sociopaths and psychopaths (who seem to be over-represented in the ruling/commercial class). 

Biologists are generally in a better position to see this than physicists. A biologist may well dissect (or even vivisect) an organism to see what it's made of. They may well quantify what elements are found in an organism. We're mainly carbon, nitrogen, oxygen, and hydrogen. But clearly, elements like iron and magnesium play essential roles in our metabolism, as well as being potential toxins. I grew up in a region that was low in cobalt, and this meant that farmed animals would not thrive on our pastures without cobalt supplements. 

However, if a biologist wants to really understand some organism, they have to observe how it interacts with its physical and social environment. That is to say, how an organism reacts to physical stimulus, how it relates to others of its own species, and how it interacts with other species. And since the local environment is a product of the bulk environment, in the long run, we have to see all life on Earth in terms of its contribution to Gaia.

A common misconception about life is that it breaks the second law of thermodynamics. This law states that in a closed system, physical entropy always increases. The misconception stems from ignoring the words "closed system". A cell is not a closed system, since molecules are constantly entering and leaving. An organism is not a closed system. Gaia is not a closed system.

However, even if we stipulate that the second law might apply, the overall effect of Earth having a biosphere is a local increase in entropy. Visible and UV photons from the sun impact the Earth, where they are absorbed by rocks, water, and living things. Eventually, the incoming energy is radiated back out into space as infrared photons. And for every visible-UV photon arriving on Earth, twenty infrared photons are radiated back into space, with a net increase in entropy for Earth and its environment. So, if the second law applies (doubtful), then it is not broken by life. 

However, simple cybernetic feedback does not give us a complete explanation of life. For this, we have to change up a gear.


The Free Energy Principle

It's apparent, for example, that if the brain operated purely on homeostatic feedback, it would not be able to respond at the speed that it does. For this, we need to introduce the idea of allostasis. And allostasis leads us into the final big idea that is essential for understanding life: the Free Energy Principle. 

The idea of allostasis is that the brain constantly predicts what will happen next based on the present inputs and past experience. And if the expected input does not match the actual input, then the brain has two options: (1) change the prediction, i.e. update the expectation based on the new input; or (2) change the input, i.e. make some change in the world. And this enables a faster, more adaptable response.

Anyone familiar with the concept of Bayesian statistics should already recognise this paradigm. Bayesian statistics is a mathematical formalism that allows a statistician to quantify how their expectations change as new information comes in, as part of an iterative process. And this, in turn, has strong connections to information theory.

Enter Karl Friston, who primarily works on making information gleaned from medical scans into meaningful images. This involves expertise in statistical analysis and information theory.

Making these connections led Friston to propose the free energy principle. There is, as yet, no popular account of the free energy principle and the explanations that are available all rely on background knowledge of statistics and information theory that I don't have. 

See, for example:

Friston, K., et al. (2023) "The free energy principle made simpler but not too simple." Physics Reports 1024: Pages 1-29.

It is not "simple" at all unless you have the appropriate background knowledge.

This is something I'm still trying to understand, and I'm hoping to write an essay on it in the near future. But my intuition tells me that this idea is hugely important. Listening to Friston talk about it, I feel that I glimpse something significant. It's important enough to try to offer some impressionistic notes and encourage readers to follow up.

The free energy principle says that any self-organising system—living or non-living—that has a permeable boundary separating it from the general environment and that persists over time, will appear to take actions that can be mathematically described in terms of Bayesian statistics or in terms of "free energy" (a concept from information theory). Friston has shown these to be mathematically equivalent.

Where a prediction fails to match an input, Friston calls this "surprise". This is mathematically related to the informational property "free energy". Hence, "the free energy principle". It turns out that minimising surprise with respect to predictions is mathematically equivalent to minimising free energy (I suppose we might also relate this to the idea of the "path of least action" from classical physics, but I need to look into this). 

Rather than describing life as simply reacting to the environment, we can now describe all living things as iteratively predicting the future and testing predictions and optimising their responses to minimise surprise, resulting in changing predictions or changing inputs (external actions). Living systems involve both homeostasis and allostasis. 

In a sense, all the brain does is receive millions of input signals, process them in ways that are not fully understood, and generate millions of output signals, most of which are internal and only affect expectations. In her book How Emotions Are Made, Lisa Feldman-Barrett notes that 90% of the incoming connections to the visual cortex are from other parts of the brain, rather than from the eyes. 

This principle turns out to be an incredibly useful way of modelling and thus understanding living systems. It can be used to explain how even simple bacterial cells are apparently able to act intelligently (i.e. move towards food, move away from waste, or join up to form a colony). Whether there is some abstract "intelligence" behind this intelligent action is moot, but it's not an obvious conclusion, and it's not required by the free energy principle. 

I have never been a fan of panpsychism, which says that all matter is "conscious" (by degrees). It's such obvious nonsense that I find it hard to imagine why anyone takes it seriously. The free energy principle makes some broad claims, but it doesn't commit to metaphysical nonsense. The fact is that all living organisms do have a range of behaviours that they employ intelligently, without any evidence of being "conscious" or "intelligent". Intelligent behaviour is universal in living things. Being conscious of the world or self (or both) is rare. And, prior to the advent of the free energy principle, we were at a loss to explain this. This left huge gaps for "gods-of-the-gaps" style arguments for the supernatural. The free energy principle appears to plug those holes. 

I believe that, in the long run, the free energy principle will stand alongside the concepts of natural selection, symbiosis, and Gaia in terms of the history of understanding life. It offers a powerful, but also deflationary, account of the mechanisms that underpin life and mind.


Conclusion

The idea that "there is no society, there are only individuals and families" is arse-about-face. Rather, there are no individuals; there are only societies (and a family is a microcosm of a society). The individual is a mythological figure. We can talk about them in theory, but we rarely meet them in person. As Oscar Wilde said,

Most people are other people. Their thoughts are someone else's opinions, their lives a mimicry, their passions a quotation.

Me too, for the most part, but I do at least try to give credit where it is due. 

We are social animals. We evolved to live in social groups. Which means we evolved the capacity for empathy and the capacity for reciprocity. We evolved to be prosocial and moral. We evolved a sense of fairness and justice. Assuming we have not completely suppressed these capacities, we don't need anyone to tell us how to be moral. 

Competition is certainly a feature of life, but we have massively over-emphasised it for ideological reasons (patriarchy and imperialism). Consider the case of collectively making music. Music-making is not a competition, and turning it into one does not enhance it in any way. Making music actually requires selfless cooperation and is at its best when the egos of the players are not evident at all. And playing music, in an appropriate non-competitive context, brings out the best in people. It is no surprise, then, that in capitalist societies, the collective elements of music get reduced to passive consumption. And competition is enforced on musicians in ways that only detract from the music. 

Sociology is more fundamental than psychology, in the sense that we may be born with an individual temperament and/or personality that is relatively unchanging, but we develop in response to the environment we find ourselves in. We learn to be a member of the local social group in more or less the same way that we learn the language of the group we find ourselves in. 

Looking down the taxonomic hierarchy, our cells—our very genomes—are tiny, symbiotic, cooperative communities in which every component member prospers together. Looking up, we always live in families embedded within communities, embedded in societies, embedded in ecosystems, embedded in the biosphere as a whole, or Gaia.

At every level, living things are generally collectivist. And, left to their own devices, humans are naturally collectivist. Nothing could be more normal than socialism. Every group of friends I've ever been part of was leaderless. We just organised ourselves without much effort. 

I do not deny that individuals and species compete with each other, sometimes violently. However, I emphatically believe that the incidence and importance of competition has been grossly overstated by scientists with ideological—reductive, patriarchal, and imperialist—views.

We might even say the togetherness is what gives human lives meaning and purpose. The many modern people who say that they lack meaning and purpose are inevitably disconnected or alienated from society. What we all need (except for psychopaths) is a sense of connection. And it is precisely this connectedness that modern political discourse—neoliberalism and capitalism—seeks to replace with the ideas of ownership, control, and competition. This is aberrant and abhorrent in a social species. 

We are social.
We are social.
We are social.

~~Φ~~

17 February 2023

What's the Difference Between a Meditator and Corpse?

At first glance, my title this week might seem like an odd question or the opening to a joke. In fact, the question is asked and answered in the Pāḷi Mahāvedalla Sutta (MN 43). This is one of those suttas that seems to be an attempt to comprehensively summarise Buddhism as it was understood at the time, but not in a standard Theravāda way. 

The Mahāvedella is a teaching by Elder Sāriputta for Elder Mahā-Koṭṭhita. The pair are also portrayed as speaking together in the Koṭṭhita Sutta (AN 9.13) and another Koṭṭhita Sutta (SN 35.232).

In this case, the sutta includes some ideas that are rare elsewhere. What the Pāḷi texts repeatedly show is that different ancient Buddhists thought about the same terms in different ways. Not everything that we find in a Pāḷi sutta was incorporated into Theravāda Buddhism, even in theory. 


The Mahāvedalla Sutta

The Mahāvedalla Sutta is a series of questions and answers. For example, the first question asks for a definition of "faulty pañño" (duppañño; Skt duḥprajñā) and compares this with someone endowed with pañño (paññavā; Skt. prajñāvat). Note how these are not quite opposites. The natural opposite of duppañño would be supañño; while the opposite of paññavā would be apaññavā. No doubt there was a story here, but it's lost to time. It's not clear how the Mahāvedalla-kāra understood pañño, the adjectival form of paññā, but in Prajñāpāramitā it seems to connote the knowledge gained by undergoing cessation (nirodha). The series of questions continues. Define "discrimination" (viññāṇaṃ; vijñāna)? What is the difference between viññāṇaṃ and paññā? The answer here is that paññā is to be cultivated; discrimination is to be comprehended (paññā bhāvetabbā, viññāṇaṃ pariññeyyaṃ). 

This explanation leaves me in the dark about the distinction, I think, because I lack the context in which to understand it. There is one other reference to cultivating paññā in Pāḷi. The Rāga Sutta (AN 6.107) describes a group of three things to be abandoned (raga, doha, moha) and three to be cultivated (asubha, mettā, and paññā) in order to eliminate them, i.e. cultivating understanding (paññā) dispels confusion (moha). This one is comprehensible on its own, but doesn't help us to distinguish paññā from viññāṇa. It seems that the Mahāvedalla-kāra did not see viññāṇa as something that could be cultivated or abandoned. But this doctrine was not developed by Buddhists and all we have is this incomplete snapshot. This happens a lot in the Pāḷi suttas. 

Then the sutta asks, what is valence (vedanā) and recognition (saññā)? And are these three—saññā, paññā, vedanā—inseparable? The sutta-kāra says they are not separable because "what one experiences, that one recognises; what one recognises one discriminates" (yaṃ hāvuso, vedeti taṃ sañjānāti, yaṃ sañjānāti taṃ vijānāti MN I 293). Note that the traditional skandha meditation practice is predicated on being able to distinguish these three, while here the three are said to be impossible to distinguish individually (na ca labbhā imesaṃ dhammānaṃ vinibbhujitvā vinibbhujitvā* nānākaraṇaṃ paññāpetuṃ).

* The repetition of vinibbhujitvā here is odd, but seems to be in the original texts. 

Then a change of pace. "Comrade, what can be inferred by purified mental discrimination that dismisses the five [physical] senses?" (Nissaṭṭhena hāvuso, pañcahi indriyehi parisuddhena manoviññāṇena kiṃ neyyan ti?)

* Ñāṇamoḷi & Bodhi "Friend, what can be known by the purified mind-consciousness released from the five faculties?

Interestingly, what can be inferred or understood (neyyan) from this are precisely the āyatana states. From the statement (or thought) "space has no limits" we can infer the stage of limitless space (ananto ākāso’ti ākāsānañcāyatanaṃ neyyaṃ); from "there is no limit to discrimination" we infer the stage of limitless discrimination can be inferred (anantaṃ viññāṇan ti viññāṇañcāyatanaṃ neyyaṃ); and from "there is nothing" we infer the stage of nothingness can be inferred (natthi kiñcī ti ākiñcaññāyatanaṃ neyyaṃ). And we know this phenomenon through the eye of paññā (paññācakkhunā). And what is the purpose of paññā? It is higher knowledge (abhiññatthā), exact knowledge (pariññatthā), and abandonment (pahānatthā). The latter refers to eliminating sensory experience (cf. Pahāna Sutta SN 35.24).

More questions follow on right view (sammādiṭṭhi), being (bhava), first jhāna, the five faculties, and then the section that really interests me.


Life and Heat

The pertinent question is, "On what condition do the five faculties depend?" (pañcindriyāni kiṃ paṭicca tiṭṭhantī ti); where the five faculties are eye, ear, nose, tongue, body. The Mahāvedalla Sutta says that they depend on āyu "life" (Skt āyuḥ; as in āyurveda). Life itself depends on the condition of "heat" (āyu usmaṃ paṭicca tiṭṭhati) but, at the same time, heat depends on the condition of life (usmā āyuṃ paṭicca tiṭṭhati). The relation between the two is explained by an analogy: it's just like how seeing the light of a lamp is dependent on seeing the flame, and seeing the flame is dependent on seeing the light. This mirrors the analogy between mutually conditioning viññāṇa and nāmarūpa in the Mahānidāna Sutta (DN 15) there conceptualised as two sheaves of harvested grain that lean against each other (called a "stook" in English).

Life and heat are not a common topic in Pāḷi; they occur together in just three texts including the Mahāvedalla Sutta, and I will digress briefly to consider the other two. We find life and heat together in a verse at the end of the Pheṇa­piṇḍ­ūpama Sutta (SN 22.95) where death is equated with the absence of āyu, usmā, and viññāṇa (SN III 143). In the Kāmbhū Sutta (SN 41.6), which features a discussion between the patriarch* Citta and the bhikkhu Kāmbhū, we find a similar discussion of the difference between a corpse and a meditator experiencing cessation (Starting at SN IV 294). Here the bodily, verbal, and mental formations (kāya-, vācī-, and citta-saṅkhāra) cease in a meditator undergoing cessation. However, they still have life and heat, and their "faculties are serene" (indriyāni vippasannāni).

*Gahapati refers to the patriarch of an extended household or possibly an extended family within a clan structure. Standard translations like "householder" seem to miss the point.

Note the inconsistency here: a living person in both texts has life and heat, but the third factor is viññāṇa in one account and indriyāni in another. Here we might conjecture that viññāṇa is intended as the function of the indriyāni, i.e. objectification is the function of the sense faculties. We could, at a pinch, see the two terms in this context as synonyms. Though this is a neat solution, we have to consider other possibilities as well. The two texts may be trying to say something different and incompatible that we no longer understand (this is not uncommon between two Pāli texts).

I don't understand how we came to translate viññāṇa as "consciousness" but it seems plain wrong to me. Notably, viññāṇa is an action noun rather than an abstract noun, so viññāṇa and consciousness are not even on the same level of abstraction. It is my view that no Pāḷi word can be translated into English as an abstract noun "consciousness" and that our whole philosophical concept of "consciousness" is absent from ancient Buddhist dialogues (see also The 'Mind as Container' Metaphor). The use of "consciousness" in discussing ancient Buddhist discourses is a Whiggish anachronism (in which we imagine ancient Indians to be primitive precursors of ourselves).

In any case, the gist here is clear. It can be very difficult to distinguish a meditator from a corpse by the usual signs of life that we look for in a conscious and aware person, because we cannot interact with them. We could say that following cessation a person becomes completely unresponsive to the world around them. People undergoing cessation of sensory experience necessarily lack all sense of time, since all of the clues to the passing of time have, by definition, ceased. Hence, perhaps, the Buddhist insistence that the Buddhadharma is akāliko "timeless", though in a culture where death is often referred to as kālaṅkato "having done one's time", akāliko could also be a synonym for amata "deathless" (Skt. amṛta). The phenomenon of people sitting lost in samādhi for days on end is likely related to their undergoing cessation and having no sense of time passing. It is likely that thirst, i.e. a need for water, is what rouses them. Being dragged out of samādhi by thirst may explain why "thirst" (Skt. tṛṣṇa; P. taṇha) became such a key word in the Buddhist lexicon.


Life Force

Coming back to the Mahāvedalla Sutta and moving to the next section the subject is now "life" (āyu) and the "constituents of life" (āyu-saṇkhārā). The sutta explicitly states that these "constituents of life" are not phenomena that one can experience (na kho, āvuso, teva āyusaṅkhārā te vedaniyā dhammā). And then it says that, if the āyu-saṅkhārā were phenomena to be experienced, the one who experienced the cessation of awareness and experience would not emerge from their meditation, that is to say they would die. The logic here is that if āyu and āyu-saṅkhāra were part of the experienced world, then when the experienced world ceased, so too would life. Rather, the text makes the apposite observation that life continues even when all sensory experience ceases. 

What did the sutta-kāra mean by āyu and āyu-saṇkhārā? It is difficult to say, because the terms are not defined. Sujato has blogged about how the words āyusaṇkhāra and jīvitasaṇkhāra are used. There is not a great deal more to be said. In the Mahāparinibbāna Sutta (DN 16) the Buddha mentions jīvitasaṅkhāra in a sense that Sujato interprets as a "will to live". He is, I think, here relying on the traditional idea that saṅkhāra means "volition" because it is explained as the six kinds of cetanā associated with the six sense spheres.

This meaning of saṅkhāra derives from the earlier Brahmanical use of the Sanskrit equivalent. In Vedic ritual, a saṃskāra is a rite of passage. When performing these rites, the Brahmin priests carry out a series of actions (karman). Hence, in Buddhist usage, saṇkhāra/saṃskāra is "an opportunity for doing karma". Keeping in mind that all intentional acts carry a karmic debt. At the same time, the unique but influential passage in AN 6.63 famously says "intention is how I talk about karma, monks" (cetanāhaṃ bhikkhave kammaṃ vadāmi). Thus an opportunity for doing karma becomes an intention to act. 

Whether this meaning can be applied to āyusaṅkhāra is moot and, since Sujato doesn't make this case, we are none the wiser. He finds a way to make sense of jīvitasaṇkhāra as "the will to life" and then retrospectively relates āyusaṇkhāra to this as a kind of "vital force". In the end, however, Sujato concludes that distinction between āyusaṇkhāra and jīvitasaṇkhāra probably emerged later and that the two words are synonyms for "vitality" and "vital energies" and are best translated as "life force". This is a self-consistent explanation and it might be right. But there is presently no way to confirm such conjectures: we are trying to make sense of how a word was used in the absence of any contemporary explanation and from just a few instances that are vague and/or ambiguous. This is a common problem when dealing with older Buddhist texts (in any language). 

Across the ancient world we repeatedly encounter the idea of a "life force", but it is almost always conceptualised as breath. Words indicating breath as life force include: psyche, anima, spirit, qi 氣, and prāṇa. For more on this theme see my 2014 essay: Spiritual I: The Life's Breath. In the Indian context the vital force is āṇa "breath" which itself is caused by the action of the element of wind (vāyu). Vāyu conceptualises all forms of movement. The word āyu, however, does not refer to "breath". Rather, it is related to the words aeon and age, and often refers to lifespan or longevity. Breath (āṇa) is what animates the body (kāya); the resulting animation seems to be called āyu (and is accompanied by usmā). Similarly, jīva is not related to breath but is cognate with Greek bio, Latin vivarus, and Germanic quick; all meaning "life; living".

These are not ideas that were integrated into later Buddhism. Nor does the concept of a life-force as distinct from mind and body ever become mainstream. The reason is obvious, and has also bothered European philosophers. If there were a "life-force", then it would surely have a roll to play in facilitating life after death. And if it is present in all living things, as appears to be implied, then we are in the realms of eternalism: that is to say āyu starts to sound suspiciously like ātman. Not surprisingly most Buddhist schools of thought set the idea of a "life force" outside of their orthodoxy and āyusaṅkhāra never became a mainstream Buddhists' technical term. Moreover, Buddhist knowledge of physiology never really developed beyond this Iron Age conception.


Conclusions

To answer the question in the title, a meditator and a corpse are similar in that signs of life in the form of actions of body, speech, and mind are absent. Even though the meditator is insensate, or even catatonic, they are still alive; still warm. The corpse is cold and lifeless (and decay sets in almost immediately). 

Presumably, this was enough of an issue for the early Buddhists thought that it required some doctrinal explanation. That said, the terms used to explain the difference—like āyu and āyusaṅkhāra—did not seem to need an explanation in the minds of the author(s). Leaving us scratching our heads. 

This sutta is not consistent with Theravāda Buddhism, if only because it unequivocally states that vedanā, saññā, and viññāṇa cannot be distinguished from each other. Nor is this statement consistent with any form of Buddhism I am familiar with. The Mahāvedella Sutta appears to be from an unknown sect of Buddhists, missing from the historical record. Their text was preserved, but the teaching lineage associated with it was not. I suspect this is true in a large number of Pāḷi suttas.

However, that āyu and usmā occur together in three texts suggests that at least some Buddhists believed in some kind of "life force" as distinct from a soul (ātman). A life force (jīva) was also important in Jain theology, where it provided the necessary continuity for rebirth. At least some Buddhists further conceptualised life as composite and posited life-constituents (āyu-saṅkhāra). However, in the end we don't know precisely what words like āyu or āyusaṅkhāra meant to those people then, because they didn't say and there is not enough context to guess.

In this case it is very tempting to smooth over the difficulty by conjecturing an answer that solves all the problems, is plausible, and self-consistent. However, this is not sufficient to establish how the author(s) thought. Any number of plausible, self-consistent answers are possible. But we have no objective facts available to help us choose between them.

~~oOo~~

15 April 2016

The Rocky Origins of Life

alkaline hydrothermal vent
In an essay in my series on Vitalism (Crossing the Line Between Death and Life, 30 May 2014), I mentioned the Miller-Urey experiment in 1953 as a breakthrough in the study of abiogenesis - the emergence of living things from non-living matter. It turns out, however, that having produced amino-acids and some other medium-sized organic molecules, nothing much else happens in these "organic soup" style experiments. Getting a soup of organic molecules to do anything interesting has proved an intractable problem and neither electrocution, bombardment with ultraviolet light, nor physical shocks help. New research has shown that Miller's estimates of the early atmosphere of the earth were probably wrong. He assumed the atmosphere of Jupiter would provide a good model for the early atmosphere of the earth: ammonia, methane and hydrogen. However, the heavy asteroid bombardment during the early epoch of the solar system, during which our moon was formed, blasted off the existing atmosphere and it was replaced with an atmosphere of mainly carbon-dioxide and nitrogen, with only traces of methane and other gases. Similar gases make up the modern day atmospheres of both Mars and Venus. Unfortunately, this mix of gases is very much less likely to get even as far as amino-acids in the Miller-Urey set up. So the idea of a naturally occurring organic soup fails on two counts: it probably never existed, and even if it had, nothing interesting happens in sterile soup (more on this below). Some comets and meteorites have a mixture of water and organic compounds similar to those produced by Miller-Urey and thus some of the building blocks of life may have come from space, but this still leaves us with the organic soup problem.

Another hypothesis of how life emerged from non-living matter has recently emerged and been promoted by British scientist, Nick Lane (amongst others), This is described in his book Life Ascending: The Ten Greatest Inventions of Evolution (2009). This hypothesis is known as the Alkaline Hydrothermal Vent Origin of Life. For the full detail of this hypothesis, see Russell et al (2013) and the "further reading". In this essay I will both paraphrase and embellish the version of the theory set out in Lane (2009).

We begin with a caveat. Even if we show that this theory is possible and plausible, it still won't tell us exactly how life began here. That is impossible to know. But if we can show that the chemical reactions that underpin life can be started in similar conditions, then we may be able to better understand life more generally. There will be general rules that govern the emergence of life and we can specify some of those rules. In addition if we can show that life emerging from chemistry is plausible it further undermines any remaining tendency to explain life through forms of Vitalism.

One thing we can already identify is the basic chemistry of life. For example all life on earth involves reducing carbon-dioxide (CO2) to methane (CH4) and water (H2O). Some organisms do this directly, most do it indirectly, but this is what all organisms do at a minimum. And since this doesn't happen spontaneously in an organic soup, we need to specify the kind of conditions in which it will happen.


Signs of Life

Stromatolite
via Wikimedia
By 3400 million years ago, the signs of life on earth are unequivocal. The first life seems to have been in the form of bacteria or archaea. Taxonomists now recognise five kingdoms of living things: animal, plant, fungi, bacteria, and archaea. On the surface bacteria and archaea can be indistinguishable, but internally, chemically there are major differences (I'll say more on this later in the essay). Archaea are typically found in niches involving high temperatures, extremes of pH (both acid and alkali) or other factors that would kill most organisms. They are sometimes called extremophiles.

We can see in fossils of this early period, and perhaps earlier, the ratio of carbon isotopes that we expect to see from fossilised living things. This ratio, which sets life apart from non-living chemistry, is the basis of Carbon-14 (14C) dating. We also see fossilised structures of a form of life that we still see in shallow oceans today, i.e. the stromatolite. Archaea and bacteria continued to be the dominant forms of life for 2500 millions years before fossils of complex organisms begin to appear. Arguably they still are the dominant form of life, exploiting a vast range of ecological niches and far outweighing any other form of life in terms of biomass.

Replicators, molecules which copy themselves accurately, seem to be essential to any form of life and thus most existing theories have focussed on how such molecules might have been produced, usually in a soup of organic precursor compounds (like Miller-Urey). However, Lane refers to the various "organic soup" theories as "pernicious" because the idea deflects attention away from the underpinnings of life. As Lane says, if you take a tin of actual (sterilised) soup and leave it for a few million years it does not spawn new life, instead all the complex molecules gradually break down into simpler molecules. In other words following the dictates of thermodynamics the soup goes in the wrong direction. "Zapping" it with electricity or radiation only accelerates the degradation. The laws of thermodynamics means that a soup is far too unlikely a route to life. One can never ignore thermodynamics as they govern everything.


Thermodynamics - The Science of Desire

The physics of matter is a story of attractions and repulsions and thus, according to Lane, "it becomes virtually impossible to write about chemistry without giving in to some sort of randy anthropomorphism." (13-14) I'll do my best. Chemical reactions happen if all the participants want to participate or can be forced to. Molecules "want" to exchange elections or can be induced to overcome their shyness.

The molecules in food want very much to react with oxygen, but don't do so spontaneously, fortunately or we'd all go up in flames! Even reactions that result in a net release of energy often require some "activation energy" to overcome their "shyness" or initial reluctance to react. Another way of looking at the chemistry of life is that it boils down to the juxtaposition of two molecules, hydrogen and oxygen, out of equilibrium. They react with a discharge of energy, leaving warm water. And this is the problem with the organic soup theory - nothing wants to react, so nothing happens. There is no disequilibrium that might drive the necessary reactions. Disequilibrium is a key to life. 

Some origin of life theories focus on RNA, the single-stranded counterpart of DNA, which under certain conditions can self-replicate (normally in a cell RNA replication is dependent on large protein complexes called ribosomes). The idea that a very complex molecule like RNA might have come about without a thermodynamic disequilibrium driving the reactions is not credible. Thus although self-replicating RNA is plausible, there must be more to it. RNA is composed of nucleotides which combine an amino-acid, a sugar (ribose) and a phosphate group. As monomers (ATP), dimers (NADH), and polymers (RNA, DNA), nucleotides play several vital roles in living cells. Although we get amino acids from the Urey-Miller experiment, nucleotides are very much more difficult to make. Nucleotides do not just form spontaneously. One cannot just throw amino acids, ribose, and phosphate into a bucket and expect nucleotides to form. In fact it is worse than this because the conditions required for the synthesis of ribose and amino-acids are very different and they could not happen in the same bucket. They must be synthesised separately and then brought together. But then the reaction will not take place in the presence of water. Nor do nucleotides easily polymerise in the absence of a catalyst to form RNA or DNA. Although aspects of RNA based explanations of the origin of life remain plausible, RNA is certainly not the first step in the direction of life. Many conditions had to exist in order for RNA to be synthesised. If life did not evolve in a chemical soup, where did it come from?

An important clue was the discovery of vents on the sea-floor close to the great ocean ridges where the tectonic plates are forced apart by up-welling magma. These vents, known as "black smokers", spew out hot (300-400°C), acidic water, laden with chemicals, particularly metal and hydrogen sulphides (which account for the dark colour). They support a variety of lifeforms at densities rivalling rain forests. Bacteria use hydrogen sulphide (H2S) to power their metabolism. Effectively they detach the hydrogen from H2S and attach it to carbon dioxide to form organic matter and elemental sulphur (and this is one of the most direct processes for reacting H2 with CO2). This conversion requires energy and it comes from the juxtaposition of two worlds in dynamic disequilibrium, i.e. from cold sea water and the hot vent water. The bacteria that sustain this world live at the margins where the two meet and mix. Then some animals graze on the bacteria and a food chain is established. Or else the bacteria live in symbiotic relationships inside the animals. Tube-worms for example host such bacteria which feed them and because of this do not have a digestive system.

These hot vents became a candidate for the origin of life since the disequilibrium solved the thermodynamic problem. Possible mechanisms for life emerging at these hot vent sites were proposed by German chemist and patent attorney, Günter Wächtershäuser. These involved chemistry taking place on surfaces of iron-pyrites. Unfortunately conditions on the early earth make this route unlikely. Oxygen is still central to the metabolism of the vent archaea and bacteria. They still react hydrogen and oxygen, if only indirectly. There is also the concentration problem, that is, bringing enough of the reactants together in open water to make a self-sustaining reaction. For life to come about organic molecules must dissolve in water and somehow react to form polymers like RNA. But this is extremely unlikely if they are not contained (by a membrane) and concentrated.


Alkaline Vents

Serpentenized olivine
A second kind of hydrothermal vent was predicted Mike Russell, now working at NASA's Jet Propulsion Lab. Russell had conjectured that these other vents would be an even better candidate for the origin of life. Alkaline vents are not volcanic, but rely on the reaction between a type of rock called olivine and sea water. Such rock undergoes a process known as serpentinization after a common form of this rock, serpentine, which is green and thought to resemble the scales of a snake. In serpentinization, water becomes incorporated into the structure of the rock which expands and fractures. The volume of water incorporated in this way is believed to equal the volume of the all the oceans. But the water and rock also chemically react, producing highly (chemically) reduced compounds such as hydrogen, methane and hydrogen sulphide and a high pH value, i.e. the water in serpentinized rock is strongly alkaline. The reaction is also exothermic, i.e. heat producing, and so drives the convection that powers the alkaline vents. The reaction can be represented in simplified form as:

olivine + H2O → serpentinite + H2 + heat

or

2Fe2+ + 2H2O → 2Fe3+ + 2OH- + H2

Alkaline vent Structure 
Note that hydrogen and methane were key ingredients in the Miller-Urey experiments in the 1950s. Having been first predicted by Russell in the 1980s, living vents were discovered in 2000 during a submarine expedition to the mid-Atlantic. The vents form spectacular coral-like structures (right) that can be 60m in height.

The water coming from these vents is warm (70-80°C), highly alkaline (ph 9-11) and filled with chemicals produced by serpentinization, particularly hydrogen. By contrast, in the early oceans, the water would have been cool, slightly acid (pH ~5.5), and much richer in CO2 and iron than the present day ocean. As the hot, chemical rich water mixes with the cold sea-water some of the chemicals precipitate out to form porous limestone structures, filled with tiny chambers roughly the size of an organic cell. The compartments could provide a natural means of concentrating organic molecules. While modern vents tend to lack iron, the composition of the ocean 4 billion years ago would have meant that the early vents did have iron and other metal compounds (particularly nickel, magnesium, and molybdenum) with catalytic properties embedded in their walls. Mike Russell has argued that the iron/sulphur minerals in these structures resembled enzymes that some modern living cells, especially archaea, use to catalyse chemical reactions. The flow through these early vent structures replenished basic reactants, carried off by-products, and prevented catalyst surfaces from becoming fouled, while also allowing for organic molecules to concentrate. The thin walls of the chambers provided membranes, one of the essential features of living things, with very different conditions of temperature and especially pH on either side, thus creating exactly the kind disequilibrium required to power living things.


Disequilibria

The vents provide two kinds of disequilibria that can act as drivers of chemical processes. These are quite technical and I'll try to simplify.
  1. highly reduced electron donors
  2. pH imbalance or proton gradient

Electron Donors

1. Bubbling up from the vent are gases like hydrogen and methane produced by the reaction of water with mantle minerals like olivine. In the presence of iron and molybdenum catalysts in the walls of the vent structures, these come into contact with CO2 and nitrogen oxides dissolved in the water. When hydrogen reacts chemically it readily gives away its single electron to another molecule to create a hydrogen ion or proton. In chemical terms this giving away of an electron is called "reduction". Oxygen is the prototypical acceptor of electrons and thus this side of the reaction is called "oxidation". When iron is oxidised to rust, what is happening is that oxygen in the air is accepting electrons from (i.e. is reduced by) metallic iron (Fe) which is converted into ferrous (Fe2+). Red rust can be further oxidised to black ferric (Fe3+) iron. Atoms will tolerate a net positive or negative charge if they can obtain a more stable arrangement of electrons (this is a consequence of the quantum mechanics of electrons). Serpentinization involves water oxidising ferrous iron in olivine to ferric iron, with water being reduced to hydrogen gas and hydroxide ions.

H2 and CO2 react with a little difficulty. Although the overall reaction is exothermic, meaning that it is thermodynamically favoured, some initial energy is required to get the reaction going and a catalyst to help it along. The catalyst in the archaea that do this reaction directly is a complex of iron, nickel and sulphur atoms, which are very like the kind of minerals deposited at vent sites. "This suggests that the primordial cells simply incorporated a ready-made catalyst" (Lane 28). The activation energy seems to come from the vents themselves, which we can tell from the presence of acetyl thioesters. These molecules are the result of CO2 first reacting with free-radicals of sulphur in the vent water, and these free-radicals provide some of the energy. We will return to this observation below.

The combination results in reactions that produce methanol (CH3OH), methanal (CH2O), and ultimately ethanoic acid (CH3COOH) aka acetic acid). Such molecules can accumulate and concentrate in the cells and this allows for more complex molecules to form and polymerise in tiny versions of the Miller-Urey experimental apparatus. This gives us a more dynamic version of the organic soup. The constant flow of water from the vent solves another problem associated with surface catalysts: fouling. As reactions happen on a surface the products of the reaction build up and prevent new reactants getting to the surface. To have a sustainable reaction at a surface one must combine concentration (enough to bring molecules together) with a flow that carries away products and replenishes reactants. The pores of the vent structures seem to provide for both.


Proton Gradient

2. A feature of all living things is the creation of a proton gradient across a membrane. By this we mean that one side of the membrane has a surplus of protons (in other words an acid pH) and the membrane allows them to diffuse to the other side where there is a deficit (an alkaline pH). Since protons are positively charged this is also amounts to an electrical potential (i.e. a voltage) across the membrane.

In our mitochondria for example, this gradient is achieved by a process called electron chain transport involving four complexes of proteins that pump protons across the membrane to create a pH or proton gradient. These protons then diffuse back into the cell by a process called chemiosmosis, via another protein complex called ATP-Synthase, and in doing so power the creation of adenosine triphosphate 

triphosphate - ribose - amino-acid (adenosine)

At first sight ATP-Synthase appears so miraculous that, like the eye, it is often pointed to as evidence of intelligent design. It is difficult to imagine how something so complex could have evolved from simple steps by chance, though its evolutionary path is in fact known to some extent. ATP synthase is a complex nano-machine. A rotary engine in the cell-membrane is made up of a protein complex (with three subunits) and driven by proton diffusion or chemiosmosis; the engine uses a protein-based crank-shaft to deliver mechanical energy to a separate complex of proteins (with three subunits) inside the cell; the deformation and relaxation of this second complex catalyses the synthesis of ATP from ADP and a phosphate ion. Several good animations are available showing how ATP-Synthase works, for example this YouTube video.



ATP is a universal energy currency in all living cells. It is how energy is stored and moved around the to where it is needed. ATP is a nucleotide, the basic unit, or monomer from which polymers like RNA and DNA are produced. The right-hand group is adenine, an amino-acid, and the middle part is ribose, a saccharide or sugar. And on the left is the phosphate. Compare to the units of DNA or RNA (below):

RNA Nucleotide. Wikimedia

ATP adds two more phosphate groups, the last of which is detachable to make adenosine diphosphate with the release of energy. The reaction that powers life thus looks like this.

ATP ↔ ADP + PO42- + energy

The pH difference between the two bodies of water, kept separate by the membranes of the vent structure creates a voltage across the membrane that can drive a similar kind of reaction, the transformation of orthophosphate into pyrophosphate:


Note how the left-hand side of ATP is very like the pyrophosphate molecule. Russell thinks that pyrophosphate might be the precursor of ATP, that it could do the same job of providing energy to power other reactions, though less efficiently.


Scaling Up.

So in these vents we have the following essential ingredients for chemistry related to life (especially if we consider them as they might have been 4 billion years ago).
  • CO2 and nitrogen-oxides (in seawater) + H2 (in vent water) reacting to form organic molecules
  • Iron-sulphur and other metallic ion complexes that can act as catalysts
  • A mechanism for concentration and replenishment
  • A porous membrane formed from calcium carbonate with distinct environments on either side.
  • A proton gradient
  • Potentially, a pyrophosphate based energy transfer mechanism to provide activation energy for "shy" molecules.
Thus the vents provided natural reactors for sustaining chemical reactions that produce organic molecules in a far more dynamic environment than that envisaged in organic soup theories. They also provide the range of environments necessary to create the conditions for replicators like RNA. However the kind of chemical reactions that might take place in such environments are relatively simple compared with even a bacterial cell, let alone a eukaryote cell. How did we get from there to here? In attempting to answer this question Lane switches from a bottom-up to a top-down perspective.

One of the clues to how life might have proceeded can be found in the common elements of metabolism shared by almost all living cells. By comparing all living things we can reconstruct the common elements shared by all life. In this vein, a paper published in Science on 25 March 2016 (Hutchison et al 2016) has attempted to reduce the genome of a bacteria to just those genes essential for it to live. The resulting partly-synthetic organism has just 473 genes. The function of 149 of them has yet to be determined. Lane discusses the last universal common ancestor of all current forms of life, known by the acronym, LUCA. In order to identify what features LUCA might have possessed scientists compared the two oldest forms of life: archaea and bacteria. Archaea appear very similar to bacteria, but there are important differences in metabolism and biochemistry. Features in which bacteria and archaea differ include,
  • Chemical structure of cell membranes structure
  • Methods of lipid synthesis
  • Methods of glycolysis (conversion of sugars to pyruvate)
  • DNA replication
  • Respiration pathways
Features which bacteria and archaea share include:
  • DNA
  • Ribosome (proteins which transcribe DNA into RNA)
  • RNA to protein translation
  • Krebs cycle
  • ATP synthesis
The features that archaea and bacteria have in common are those likely to have been found in LUCA and those features where they differ were unlikely to be features of LUCA. Note that cell membrane structures are not included in the list of shared features. Archaea and bacteria appear to have separately (and in parallel) evolved lipid-based cell-membranes and methods for synthesising lipids. This is consistent with life having evolved as metabolic pathways in a physical substrate and then later having found ways to create membranes, with bacteria and archaea developing independently. In retrospect, the alkaline vent hypothesis predicts multiple parallel solutions to such problems as cell-membranes and some metabolic pathways.

The Krebs Cycle (aka Citric Acid Cycle) is shared by all forms of life. Lane refers to it as "the metabolic core of the cell". It is central to how we take the complex molecules in food and break them down into hydrogen and carbon-dioxide and in the process produce ATP to power other cell processes.

The cycle can also go backwards. In which case it consumes ATP and produces complex organic molecules, which can be used to build the components of a cell. This backwards Krebs Cycle is not common in life generally, but it is common in the archaea that live in hydrothermal vents. Crucially, given appropriate concentrations of the necessary ingredients including ATP, the chemical reactions of the backwards cycle will happen spontaneously. It is what is sometimes called "bucket chemistry", from the idea that one pours reagents into a bucket and the reactions just happen. And as the products of one step of the process build up in concentration they will automatically start to undergo the next step. No genes are required to mediate this process. It is exactly the kind of reaction that could have got started in the pours of vent structures, perhaps powered initially by pyrophosphate rather than ATP. Once this process got going, side reactions would have been almost inevitable producing amino-acids and nucleotides (the units of the DNA or RNA polymer).

We mentioned acetyl thioesters above. These turn out to be very important, because when they react with CO2 they produce molecules called pyruvates. When our cells take up simple sugars these are broken down by enzymes into pyruvates. These then enter the Krebs Cycle where they are transformed into other molecules to form many building blocks for complex chemistry. So the naturally occurring acetyl thioesters could have produced the pyruvates necessary to set off the backwards Krebs cycle to produce complex organic molecules.
"In other words, a few simple reactions, all thermodynamically favourable, and several catalysed by enzymes with mineral-like clusters at their core... take us straight into the metabolic heart of life, the Krebs cycles, without any more ado." (28)
We now hit the limits of the progress of science. Experiments designed to test how accurate this hypothesis is have been proposed. Lane speculates that peptides and small proteins and RNA are likely products. Some experiments have been performed and generally they seem to throw up problems with the model. So the field is still in the phases of repeatedly testing and redesigning to find the right parameters. However, there is reason to be optimistic that refining the model should produce a self-sustaining series of chemical reactions analogous to the first living systems, and that contain metabolic pathways which hold the key to all life: the proton gradient, a phosphate based energy transfer, and the Krebs cycle. Lane concludes that LUCA, the common ancestor of all life was most likely,
"...not a free-living cell but a rocky labyrinth of mineral cells, lined with catalytic walls composed of iron, sulphur and nickel, and energised by natural proton gradients. The first life was a porous rock..."
The conditions required for all this to happen are unusual, but happen to be exactly the conditions that prevailed on the earth 4 billion years ago. Once the conditions were in place, life was more or less inevitable and probably came about quite quickly.

Of course this story is still quite hypothetical. Some parts of the alkaline vent hypothesis are better attested than others. As far as I can tell the experimental results are still ambiguous, though promising. Other models for origins of life do exist and are being explored. See for example, Keller et. al. (2016), though this group also see a vital role for iron compound catalysis. The more we understand the biochemistry of life, the better we understand what the conditions must have been for the beginning of life. Major advances in understanding that biochemistry are still being made. Elucidating the basic structure of ATP Synthase won Paul Boyer and John E. Walker a Nobel Prize in 1997, less than 20 years ago. This is ongoing work, most of the sources cited in this essay are less than five years old (at the time of writing). 


Conclusions

A sceptical Buddhist reader, if they even got this far, may say, so what? What has any of this got to do with Buddhism? By my own admission, I don't usually countenance the idea that science supports the standard kinds of medieval worldview held by Buddhists. In fact here I am doing the opposite. By showing the plausibility, even the thermodynamic inevitability, of biochemistry emerging from geochemistry, I want to try to eliminate the last vestiges of Vitalism. No supernatural element need be added to the organic soup to make it come alive, merely some form of chemical disequilibrium across a permeable barrier (in our case a proton gradient across porous calcium carbonate). There is no equivalent of the Lord breathing life into Adam or Dr Frankenstein pumping electricity into the monster to shock it into life. Certainly energy must be available, but this is simply energy in the normal sense used by scientists, not some supernatural vital spark. Life proceeding in this manner is no less mysterious, but it is entirely natural. There is no need to introduce any supernatural element. The picture above might not be correct in every detail, but it identifies the basic elements that must be in place for life to be thermodynamically feasible: ie. H2 and CO2 in an environment of disequilibrium separated by a porous membrane, with catalysts present, and a replenishing flow that is balanced out by possibility for concentration of ingredients.

If we accept these ideas, and granted many will not or will find them too speculative, then life requires nothing extra in order to be passed on from one being to another. In the simplest terms, cells divide and the daughter cells go on to become other individuals. What is passed on in modern living cells is a copy of the mother-cell's genes, some of her metabolic equipment, and a section of her enclosing membrane. Nothing supernatural occurs during this process. What occurs is certainly incredibly, almost unimaginably complex and at best incompletely understood. But the broad outlines of it are clear.

I have previously argued that any afterlife is by necessity vitalistic and dualistic. The afterlife exists primarily to fulfil the longing for continued existence and as a mechanism for sustaining the Myth of a Just World. Vitalism and Dualism are the price we pay for fulfilling these longings. If the manner in which we lived is important to an afterlife theory, then that theory demands that information about how lived must survive our physical death in some coherent form. This information is then used to determine our post-mortem fate. Thermodynamics precludes the possibility of this information being preserved because, in our living bodies, the information is encoded in arrangements of atoms. Those atoms become disordered almost as soon as life ends. Nor is there a credible way of transmitting this information from one being to another, even if they were in physical contact. The many Buddhist attempts to explain this information transfer, e.g. a mind-made body (manomaya kāya) or gandharva, do not meet modern standards for theories that make accurate, testable predictions. At best they are myths, at worst they are post hoc rationalisations of something we want to believe despite the evidence.

If we eliminate all forms of Vitalism and Dualism with respect to life, it makes these medieval afterlife views considerably less plausible. If nothing is required to spark matter into life, if there really is no matter/spirit duality, then the idea of something immaterial surviving death is considerably less plausible. Buddhism without the inherent matter/spirit duality, without the supernatural elements changes radically. Karma and rebirth go out the window. The focus becomes how we understand experience and how we can explain the experiences we have during the religious exercises associated with Buddhism.

Because of thermodynamics, religion is basically finished. The death throes are certainly taking a long time, but the world is slowly moving away from seeing life through a religious lens. Buddhism, as a religion in the traditional sense of being concerned with continuity, justice, disembodied spirits, and the afterlife, is finished. We have Hamlet's choice: either embrace the situation and take an active role in shaping the future; or hesitate and allow events to overrun us. But we are not Hamlet, we know how the play ends.

~~oOo~~



Bibliography

Hutchison, C. A. (2016) Design and synthesis of a minimal bacterial genome. Science, 351 (6280) DOI: 10.1126/science.aad6253

Keller, MA. et al. (2016) Conditional iron and pH-dependent activity of a non-enzymatic glycolysis and pentose phosphate pathway. Science Advances 2(1) DOI: 10.1126/sciadv.1501235

Lane, N. (2009) Life Ascending: The Ten Greatest Inventions of Evolution. W.W. Norton. [While it lasts there is a YouTube video with Nick Lane reading his own chapter on the origin of life accompanied by relevant graphics https://youtu.be/UGxAB4Weq0U]

Russell, M. J., Nitschke, W., Branscomb, E. (2013) The inevitable journey to being. Phil Trans Roy Soc Lond B. DOI: 10.1098/rstb.2012.0254


Related reading

Herschy B, et al. (2014) An origin-of-life reactor to simulate alkaline hydrothermal vents. Journal of Molecular Evolution 79: 213-227. http://www.nick-lane.net/Herschy%20et%20al%20J%20Mol%20Evol.pdf

Lane N, and Martin WF. (2012) The origin of membrane bioenergetics. Cell 151: 1406-12. http://www.nick-lane.net/Lane-Martin%20Cell%20origin%20membrane%20bioenergetics.pdf

Lane N, Allen JF, Martin W. (2010) How did LUCA make a living? Chemiosmosis in the origin of life. Bioessays 32: 271-280. http://www.molevol.de/publications/188.pdf

Sousa FL, et al. (2013). Early bioenergetic evolution. Phil Trans Roy Soc Lond B 368: 20130088. https://sites.google.com/site/shijulalns/publications

Update 26 Jul 2016
A recent study (by Bill Martin and others) in Nature Microbiology suggests that LUCA was a hydrogen metabolising thermophile. Based on analysis of the common genes in bacteria and archaea it identifies 355 genes as ancestral - i.e. belonging to LUCA.
Weiss, M. C., Sousa, F. L., Mrnjavac, N., Neukirchen, S., Roettger, M., Nelson-Sathi, S. & Martin, W. F. (2016). The physiology and habitat of the last universal common ancestor. Nature Microbiology 1, Article number: 16116. doi:10.1038/nmicrobiol.2016.116.
For a discussion of the article see
Errington, Jeff. (2016). Study tracing ancestor microorganisms suggests life started in a hydrothermal environment. PhysOrg. 26 July 2016. http://phys.org/news/2016-07-ancestor-microorganisms-life-hydrothermal-environment.html

18 Feb 2017
In Daniel C. Dennett's new book From Bacteria to Bach and Back he references a paper which shows how ribo-nucleotides can be synthesised bypassing the phase of having ribose and an amino acid, which in some cases are very difficult to stick together.
Szostak, J.W. (2009) Origins of life: Systems chemistry on early Earth. Nature. 2009 May. Available from the authors website.
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