Wednesday, August 11, 2021

Holobiont: An Introduction to the Concept


God must be incredibly fond of holobionts, since He created so many of them. And He (or She) may be a holobiont as well. 


It once happened, that the other members of a man mutinied against the stomach, which they accused as the only idle, uncontributing part the whole body, while the rest were put to hardships and the expense of much labour to supply and minister to its appetites. The stomach, however, merely ridiculed the silliness of the members, who appeared not to be aware that the stomach certainly does receive the general nourishment, but only to return it again, and redistribute it amongst the rest. (Plutarch, “Life of Coriolanus”)

In guerrilla warfare, select the tactic of seeming to come from the east and attacking from the west; avoid the solid, attack the hollow; attack; withdraw; deliver a lightning blow, seek a lightning decision. When guerrillas engage a stronger enemy, they withdraw when he advances; harass him when he stops; strike him when he is weary; pursue him when he withdraws. In guerilla strategy, the enemy's rear, flanks, and other vulnerable spots are his vital points, and there he must be harassed, attacked, dispersed, exhausted and annihilated. (Mao Zedong, 1937)


Maybe it happened to you to spend hours waiting for a flight in a busy international airport. You are blocked there and, after having had enough coffee to make you walk like a shuffle dancer, you have nothing else to do but to wander aimlessly from one shop to another. Bookstores offer something to read but, perhaps more interestingly, they give you a chance to get hints of what other people read. A rare chance of a glimpse of other people’s minds in our busy world.

So, what are people reading, nowadays? A lot of magazines and books that you can find in an airport bookstore are about the two primeval human interests: food and sex (the latter usually not so explicitly presented as the former). Apart from that, you find plenty of material on everyday matters: cellphones and other electronic gadgetry, cars, travel, religion, and more. In addition, the typical international airport bookstore has a section on how to deal with other people. They are self-help books that claim to train you on how to manage your relationship with your coworkers, your friends, and your family.

Evidently, many people find that dealing with others is a difficult matter, enough that they need help and guidance. It is a little strange, because we are all the result of at least three hundred thousand years of evolution of the species called homo sapiens. Our ancestors survived because they were good enough at creating and keeping relationships with their neighbors that would help them in times of need. But, perhaps, living in the modern society, so bewilderingly complicated, is more difficult than living in a tribe of hunters and gatherers.

Are these books really useful? There are good reasons to be skeptical. The books often seem to be a mishmash of this and that, they are not quantitative, not based on solid theories, not related to experimental evidence. The latest fad in management theory is a book titled “Reinventing Organizations.” The title may be interesting, but the substance of the book may be criticized. According to the author, good management has something to do with a hierarchy of colors. Infrared is primitive and bad, while the shade of blue called “teal.” is modern and good. Why that should be the case, is not explained anywhere in the book. That doesn’t mean to disparage a book that may have good points, but maybe you will agree with us that such a classification is a little arbitrary, to say the least.

So, can we make some order in this chaos? Maybe yes. And we can try to do that using the concepts of “holobiont” and the related one of “empathy.” The idea is that human societies of all kinds are the result of evolutionary pressure and that those you find in our world exist because there is a reason for them to exist. Just as biological holobionts are a feature of the biosphere, there exist societal holobionts, a feature of the human social sphere. Societal holobionts are an example of “Complex Adaptive Systems,” (CAS) that is, systems that develop a condition of stability called “homeostasis” and that tend to maintain it when perturbed. These holobionts are virtual, unlike the microbes in your gut. So, we may also call them “virtual holobionts.

Let’s start with an example. The simplest kind of human organization is the least organized one: the crowd (you can also call it a “mob” or a “band”). It has no leaders, no hierarchy, no specializations. Yet, you recognize a crowd when you see one. Perhaps the first time when crowds were dealt with as something worth of interest was with the book by the French author Gustave le Bon “Psychologie des Foules, (1895) that was translated into English as « The Crowd, A study of the Popular Mind. ». Reading it today, you would probably judge it to be a poorly made political pamphlet. And, indeed, it had a certain success with right wing politicians. Nevertheless, it was one of the first studies of complex systems in sociology.

Crowds are not just a feature of human society; equivalents exist with many animal societies. They go with different names: storms (or flocks) of birds, schools of fish, herds of sheep, prides of lions, and there are other examples (for instance, a bacterial mat). In any case, they share the same characteristics: they are loosely bonded groups of individuals who may stay together for a while and dissociate back into single units at any time. But, as long as they exist, crowds (just like all human organizations) are groups of people linked together.

Let’s go deeper into the matter. If a crowd is an organization, albeit the simplest possible one, it could be described using those “organizational charts” that purport to describe how a company is organized. These charts are maps designed to describe the hierarchical territory of the company. They have also been used to describe the organization of entities such as the Sicilian Mafia and Drug Cartels. They can also map the relationships in a band of Chimps or Bonobos.

But an organizational chart can be much more than simply a static map that tells you whom you should see, for instance, to organize a shipment or to order a supply of something (or, if you are a male bonobo, where to find an available female). The chart tells us a lot on how the organization works and also something about how it developed over time. It is part of the field called “management science.”

A good way to interpret organizational charts is to see them as networks.  Network science is a relatively recent development that derives from a field called “graph theory.” It is something that deals with how points in space (called “vertices”, plural of “vertex”) are arranged in space in terms of pairwise links with other vertices. You see an example of a graph in the figure


You note that there are 6 vertices (also called “nodes”), each one connected to its nearest neighbors. In this case, the connections (“links” or “edges”) are not directional, but that may be explicit in some kinds of graphs. It may also be possible that a node is connected to several other nodes.

Graph theory is a branch of pure mathematics, and it deals only with geometric arrangements. Instead, “Network theory” (or “network science”) deals with applications of graph theory to the real world. In this case, the nodes are real entities: people, departments, servers, combat units, and much more. Also, the links are related to real methods of information exchange: documents, orders, radio signals, fiber optics, and more.

Armed with this a basic knowledge, let’s go back to the example of the crowd. The simplest crowd network we may imagine is one formed of just three people (or bonobos). Here is the graph.

You see that each node (one member of the group) is connected to his/her neighbors. Information flows from each node to the closest one. There is no hierarchy: all the nodes are the same, which is one of the characteristics of crowds/bands/flocks, etc. You can say that the relationship between the elements of this crowd is horizontal, as opposed to the vertical kind seen in hierarchical organizations such as companies, armies, etc, as we’ll see later on.

We can expand the graph to describe a system where there are more than three nodes. You see below several possible arrangements


In the first case (a), each node is connected only to its two nearest neighbors. It is a little like being squeezed in the crowd in a busy subway station – if you have ever visited Tokyo, you know what that means. In such a condition, you can only move together with the crowd, and you don’t see anything more than your nearest neighbors.

Things may be more complicated than that and, in the other images, you see how nodes may be connected to more nodes than just their near neighbors. In case (b) each node is in contact with 4 neighbors. It is still a crowd, but not so dense as case (a). Case (c) shows the possibility of long-range connections for some of the nodes. Maybe someone in the crowd is in contact with a friend in the same crowd, but using a cell phone. Case (d) refers to a kind of network that is called “fully connected,” meaning that every node is connected to every other node. In the real world, it is a rare occurrence, even though it may exist for very small networks. For instance, the 3-nodes example seen before is a fully connected network. All these arrangements are non-hierarchical, or “horizontal”.

All these examples are special cases where all nodes are not only identical, but have all the same number of connections. In most cases, this is not true and each element is connected to a different number of nodes.

The figure illustrates the variations in the number of connections. The left examples shows a network where every node has 4 links. The central one is called the “small world” network. Most connections are to the close neighbors, but some are long range. The right one has more links, randomly arranged, but it is not fully connected.

The reason why the central diagram is called “small world” deserves some explanation. It has to do with the distance (in terms of number of links) between nodes. In this kind of network, it grows proportionally to the logarithm of the number of nodes, so it is not as large as it would be if you had to crawl every node, one after the other, to reach a node on the other side of the circle. In a small world network, if you wanted to contact, say, the president of the United States, it is said that you need to go through no more than six steps, starting with a person you are in contact with. It is not exactly like this, but it is a long story. Let’s just say that it is a “natural” way in which networks tend to arrange themselves.

You may say that the number of connections provide an embryonic form of hierarchy in these networks. If knowledge is power, then more connections mean more knowledge and therefore more power. This hierarchical relationship is especially evident on the Internet. A site such as, say, the CNN is defined by an URL (Uniform Resource Locator) just like any other blog or site on the web. But the CNN has a hugely larger number of connections than the average web site and there is no doubt that it has much more power in terms of pushing memes in the memesphere. But, overall, these systems remain horizontal in the sense that CNN doesn’t have the possibility to order to bloggers what to publish or not to publish in their sites (so far). Many internet “bubbles” are relatively egalitarian, although some nodes (people or groups) carry more weight than others.

These non-hierarchical networks are the general representation of the concept of “holobiont.” The way Lynn Margulis described holobionts was in terms of a group of individuals of different species that moved together in the condition called “symbiosis,” a mutual relationship that provides advantages to all the creatures engaged in it. Holobionts imply an intricate network of relationships among the various member of the community, but no fixed hierarchical structure although, obviously, some members have more prestige and power than others. Margulis was thinking of microbial communities, but we can enlarge the definition to ensembles of animals (if you prefer the formal term, we could say “ensembles of metazoa”). But the organizational diagrams in the form of circles could describe them nicely.

But what is the advantage for an individual to be part of a crowd? (or a flock, or a herd, or a pride?). Are these individuals in a symbiotic relationship? Yes, they are, by all means. Symbiosis is a condition of mutual help that in systems is generated by the way the system is organized, NOT by the good will of the individuals (it would be hard to speak of good will among bacteria, for instance). The beauty of symbiosis is that all the creatures engaged in it strive for their own benefit but, in the process, they manage to benefit every other creature.

Said in this form, it sounds as an extreme version of Adam Smith’s “invisible hand,” still today the basis of liberalism as a political ideology. The idea of the invisible hand has been much ridiculed over the years (you know how many economists it takes to replace a light bulb? None, it is done by the invisible hand!). But the idea is good if it is applied with a grain of salt.

Ugo Bardi (yours truly) and his coworker Ilaria Perissi discussed this issue in a paper that they titled “The Sixth Law of Stupidity,” where we argued that the opposite of stupidity is when human beings enter in a condition of symbiosis with other people. We also argued that stupidity is temporary while intelligence is long term, which means that people tend to learn from their mistakes. Even creatures not especially known for their large brains (say, bacteria) tend to learn from their mistakes – and those who don’t learn are eliminated by natural selection.

So, humans in a crowd are in a symbiotic relationship even though they may not recognize that. The crowd offers a certain refuge to its members. Maybe for humans it is not a general rule: when you are being shelled or shot, the worst possible idea would be to form a crowd that would attract the enemy fire. But, if you look at crowds in the animal kingdom, their utility is evident. Have you ever observed the behavior of a storm of birds? You may see them landing on a patch of grass to feed. If you get close, one of the birds may see you, be scared, and fly off. Immediately, the nearby birds will be alerted and fly off, too. In a moment, the whole storm will be flying away. In this case, the crowd (the storm) offers a danger-detection service that a single bird cannot have. 

More in general, a storm/flock/herd/crowd offers statistical protection. A predator is not interested in destroying the whole flock, only at capturing as many individuals as it needs. So, if the flock is large, the probability for an individual to be captured is low. Of course, humans tend to destroy even things they don’t need, but this is part of the 6th law of stupidity .

We have now a definition of how a holobiont is structured according to the network theory. We may want to represent it as a triangle and, thinking about that, there could be a relation with the triangular symbol “the eye of God.”

And, indeed, a triangle can be seen as the icon for both a holobiont and God (or the Goddess Gaia). But let's not go into theology, this introduction should be enough to understand what a holobiont is. The next step is the concept of hierobiont, a network partly or completely structured in a hierarchical manner. But we'll see that in another post.

Tuesday, July 27, 2021

When the Ice Will be Gone: The Greatest Change Seen on Earth in 30 Million Years.



An image from the 2006 movie "The Meltdown," the second of the "Ice Ages" series. These movies attempted to present a picture of Earth during the Pleistocene. Of course, they were not supposed to be paleontology classes, but they did show the megafauna of the time (mammoths, sabertooth tigers, and others) and the persistent ice, as you see in the figure. The plot of "The Meltdown" was based on a real event: the breakdown of the ice dam that kept the Lake Agassiz bonded inside the great glaciers of the Laurentide, in the North American continent. When the dam broke, some 15,000 years ago, the lake flowed into the sea in a giant flood that changed Earth's climate for more than a thousand years. So, the concept of ice ages as related to climate change is penetrating the human memesphere. It is strange that it is happening just when the human activity is pushing the ecosystem back to a pre-glacial period. If it happens, it will be the greatest change seen on Earth in 30 million years


We all know that there is permanent ice at Earth's poles: it forms glaciers and it covers huge areas of the sea. But is it there by chance, or is it functional in some way to Earth's ecosphere? 

Perhaps the first to ask this question was James Lovelock, the proposer (together with Lynn Margulis) of the concept of "Gaia" -- the name for the great holobiont that regulates the planetary ecosystem. Lovelock has always been a creative person and in his book "Gaia: A New Look at Life on Earth"  (1979) he reversed the conventional view of ice as a negative entity. Instead, he proposed that the permanent ice at the poles was part of the planetary homeostasis, actually optimizing the functioning of the ecosphere. 

Lovelock was perhaps influenced by the idea that the efficiency of a thermal engine is directly proportional to the temperature differences that a circulating fluid encounters. It may make sense: permanent ice creates large temperature difference between the poles and the equator and, as a consequence, winds and ocean currents are stronger, and the "pumps" that bring nutrients everywhere sustain more life. Unfortunately, this idea is probably wrong, but Lovelock has the merit to have opened the lid on a set of deep questions on the role of permanent ice in the ecosystem. What do we know about this matter?

It took some time for our ancestors to realize that permanent ice existed in large amounts in the high latitude regions. The first who saw the Northern ice sheet was probably Eric the Red, the Norwegian adventurer, when he traveled to Greenland around the year 1000. But he had no way to know the true extent of the inland ice, and he didn't report about them.

The first report I could find on Greenland's ice sheet is the 1820 "History Of Greenland", a translation of an earlier report (1757) in German by David Crantz, where you can find descriptions of the ice-covered inland mountains. By the early 20th century, the maps clearly showed Greenland as fully ice-covered. About Antarctica, by the end of the 19th century, it was known that it was also fully covered with a thick ice sheet. 

Earlier on, in the mid 19th century, Louis Agassiz had proposed a truly revolutionary idea: that of the ice age. According to Agassiz, in ancient times, much of Northern Europe and North America were covered with thick ice sheets. Gradually, it became clear that there had not been just one ice age, but several, coming and going in cycles. In 1930, Milutin Milankovich proposed that these cycles were linked to periodic variations in the insulation of the Northern Hemisphere, in turn caused by cycles in Earth's motion. For nearly a million years, Earth was a sort of giant pendulum in terms of the extent of the ice sheet. 

The 2006 movie "An inconvenient truth" was the first time when these discoveries were presented to the general public. Here we see Al Gore showing the temperature data of the past half million years.

An even more radical idea about ice ages appeared in 1992 when Joseph Kirkschvink proposed the concept of "Snowball Earth." The idea is that Earth was fully covered by ice at some moment around 700-600 million years ago, the period appropriately called "Cryogenian."

This super-ice age is still controversial: it will never be possible to prove that every square kilometer of the planet was under ice and there is some evidence that it was not the case. But, surely, we are dealing with a cooling phase much heavier than anything seen during relatively recent geological times.

While more ice ages were discovered, it was also clear that Earth was ice-free for most of its long existence. Our times, with permanent ice at the poles, are rather exceptional. Let's take a look at the temperatures of the past 65 million years (the "Cenozoic"). See this remarkable image (click to see it in high resolution)

At the beginning of the Cenozoic, Earth was still reeling after the great disaster of the end of the Mesozoic, the one that led to the disappearance of the dinosaurs (by the way, almost certainly not related to an asteroidal impact). But, from 50 million years ago onward, the trend has been constant: cooling. 

The Earth is now some 12 degrees centigrade colder than it was during the "warmhouse" of the Eocene. It was still ice-free up to about 35 million years ago but, gradually, permanent ice started accumulating, first in the Southern hemisphere, then in the Northern one. During the Cenozoic, Earth never was so cold as it is now.

The reasons for the gradual cooling are being debated, but the simplest explanation is that it is due to the gradual decline of CO2 concentrations in the atmosphere over the whole period. That, in turn, may be caused to a slowdown of the outgassing of carbon from Earth's interior. Maybe Earth is just becoming a little older and colder, and so less active in terms of volcanoes and similar phenomena. There are other explanations, including the collision of India with Central Asia and the rise of the Himalaya that caused a drawdown of CO2 generated by the erosion of silicates. But it is a hugely complicated story and let's not go into the details.

Let's go back to our times. Probably you heard how, just a few decades ago, those silly scientists were predicting that we would go back to an ice age. That's an exaggeration -- there never was such a claim in the scientific literature. But it is true that the idea of a new ice age was floating in the memesphere, and for good reasons: if the Earth had seen ice ages in the past, why not a new one? Look at these data:

These are temperatures and CO2 concentrations from the Vostok ice cores, in Antarctica (you may have seen these data in Al Gore's movie). They describe the glacial cycles of the past 400,000 years. Without going into the details of what causes the cycles (solar irradiation cycles trigger them, but do not cause them), you may note how low we went in both temperatures and CO2 concentrations at the coldest moments of the past ice ages. The latest ice age was especially cold and associated with very low CO2 concentrations. 

Was Earth poised to slide down to another "snowball" condition? It cannot be excluded. What we know for sure is that during the past million years or so, the Earth tethered close to the snowball catastrophe every 100,000 years or so. What saved it from sliding all the way into an icy death?

There are several factors that may have stopped the ice from expanding all the way to the equator. For one thing, the sun irradiation is today about 7% larger than it was at the time of the last snowball episode, during the Cryogenian. But that may not have been enough. Another factor was that the cold and the low CO2 concentrations may have led to a weakening -- or even to a stop -- of the biological pump in the oceans and of the biotic pump on land. Both these pumps cycle water and nutrients, keeping the biosphere alive and well. Their near disappearance may have caused a general loss of activity of the biosphere and, hence, the loss of one of the mechanisms that removes CO2 from the atmosphere. So, CO2 concentrations increased as a result of geological emissions. Note how, in the figure, the CO2 concentration and temperatures are perfectly superimposable: the reaction of the temperature to the CO2 increase was instantaneous on a geological time scale. Another factor may have been the desertification of the land that led to an increase in atmospheric dust that landed on the top of the glaciers. That lowered the albedo (the reflected fraction of light) of the system and led to a new warming phase. A very complicated story that is still being unraveled. But how close was the biosphere to total disaster? We will never know.

What we know is that, 20 thousand years ago, the atmosphere contained just 180 parts per million (ppm) of CO2 (today, we are at 410 ppm). That was close to the survival limit of green plants and there is evidence of extensive desertification during these periods. Life was hard for the biosphere during the recent ice ages, although not so bad as in the Cryogenian. Lovelock's idea that permanent ice at the poles is good for life just doesn't seem to be right.

Of course, the idea that we could go back to a new ice age was legitimate in the 1950s, not anymore as we understand the role of human activities on climate. Some people maintain that it was a good thing that humans started burning fossil hydrocarbons since that "saved us from a new ice age." Maybe, but this is a classic case of too much of a good thing. We are pumping so much CO2 into the atmosphere that our problem is now the opposite: we are not facing an "icehouse Earth" but a "warmhouse" or even a "hothouse" Earth. 

A "hothouse Earth" would be a true disaster since it was the main cause of the mass extinctions that took place in the remote past of our planet. Mainly, the hothouse episodes were the result of outbursts of CO2 generated by the enormous volcanic eruptions called "large igneous provinces." In principle, human emissions can't even remotely match these events. According to some calculations, we would need to keep burning fossil fuels for 500 years at the current rates to create a hothouse like the one that killed the dinosaurs (but, there is always that detail that non linear systems always surprise you . . .)

Still, considering feedback effects such as the release of methane buried in the permafrost, it is perfectly possible that human emissions could bring CO2 concentrations in the atmosphere at levels of the order of 600-800 ppm, or even more, comparable to those of the Eocene, when temperatures were 12 degrees higher than they are now. We may reach the condition called, sometimes, "warmhouse Earth."

From the human viewpoint, it would be a disaster. If the change were to occur in a relatively short time, say, of the order of a few centuries, the human civilization is probably toast. We are not equipped to cope with this kind of change. Just think of what happened some 14,500 years ago, when the great Laurentide ice sheet in North America fragmented and collapsed. (image source) (the 2006 movie "Meltdown" was inspired exactly by this event). Earth's climate went through a series of cold and warm spells that is hard to think we could survive. 


Human survival concerns are legitimate, but probably irrelevant in the greater scheme of things. If we go back to the Eocene, the ecosystem would take a big hit during the transition, but it would survive and then adapt to the new conditions. In terms of life, the Eocene has been described as "luxuriant." With plenty of CO2 in the atmosphere, forests were thriving and, probably, the biotic pump provided abundant water everywhere inland, even though the temperatures were relatively uniform at different latitudes. A possible mental model for that period is the modern tropical forests of Central Africa or Indonesia. We don't have data that would allow us to compare Earth's productivity today with that of the Eocene, but we can't exclude that the Eocene was more productive in terms of life. Humans might well adapt to this new world, although their survival during the transition is by no means guaranteed. 

Again, it seems that Lovelock was wrong when he said that ice ages optimize the functioning of the biosphere. But maybe there is more to this idea. At least for one thing, ice ages have a good effect on life. Take a look at this image that summarizes the main ice ages of Earth's long history

 (image source)

The interesting point is that ice ages seem to occur just before major transitions in the evolutionary history of Earth. We don't know much about the Huronian ice age, but it occurred just at the boundary of the Archean and the Proterozoic, at the time of the appearance of the Eucaryotes. Then, the Cryogenian preceded the Ediacaran period and the appearance of multicellular life that colonized the land. Finally, even the evolution of the Homo Sapiens species may be related to the most recent ice age cycle. With the cooling of the planet and the reduction of the extent of forested areas, our ancestors were forced to leave the comfortable forests where they had lived up to then and take up a more dangerous lifestyle in the savannas. And you know what it led to!

So, maybe there is something good in ice ages and, after all, James Lovelock's intuition may have hinted at an important insight in how evolution works. Then, there remains the question of how exactly ice ages drive evolution. Maybe they have an active role, or maybe they are simply a parallel effect of the real cause that drives evolution, quite possibly the increasing concentration of atmospheric oxygen that has accompanied the biosphere over the past 2.7 billion years. Oxygen is the magic pill that boosts the metabolism of aerobic creatures -- what makes possible creatures like us. 

In any case, it is likely that ice ages will soon be a thing of the past on planet Earth. The effect of the human perturbation may be moderate and, when humans will stop burning fossil hydrocarbons (they have to, one day or another) the system may reabsorb the excess CO2 and gradually return to the ice age cycles of the past. That may occur in times of the order of at least several thousand years, possibly several tens of thousands. But the climate is a non-linear system and it may react by reinforcing the perturbation -- the results are unknowable. 

What we know for sure is that the cycle of Earth's ecosystem (Gaia) is limited. We still have about 600 million years before the sun's increasing brightness takes Earth to a different condition: that of "wet greenhouse" that will bring the oceans to boil and extinguish all life on the planet. And so it will be what it will have to be. Gaia is long-lived, but not eternal.

Friday, June 11, 2021

The Word for "Forest" is "Holobiont:" Reviewing a few Books on the Subject


The idea of "holobionts" is making inroads just about everywhere, although sometimes people describe the concept without using the term. But we are learning from what we see around us, and the best example from which to learn about holobionts is the forest. 

Just like no man is an island, a single tree doesn't make a holobiont. Not even several trees planted together make a good holobiont. They are a plantation, a completely different thing. And the naive faith that planting trees will solve all our climate problems is just that: a naive idea that plays straight into the hands of the logging companies which get to be paid twice: once for planting trees (to save the environment) and once for cutting the trees (selling the wood on the market). 

A true holobiont is not a single tree, not many trees stuck together in nice rows. It is a forest. And a forest needs to be born, to live, to grow, to mature, and to become a full-fledged holobiont. A living being. A creature of the planetary ecosystem that lives with it and gives life to much more than itself. Forests are part of the "biotic regulation" of the whole system, which includes controlling climate and managing the atmospheric rivers by means of the biotic pump mechanism. We cut forests at our own risk. Forests may not survive humans, but humans will surely not survive without forests. 

So, a quick review of 4 books about the forest as a holobiont, none of them mentions the term, but all of them are infused with it. 

The Hidden Life of Trees. Peter Wohlleben.(2016). A popular science book that had a remarkable success. It deserves it. It is timely, well done, and overall understandable, although at times a little too long. Wohlleben cites the biotic pump and one of its discoverers, Anastassia Makarieva, although, curiously, he doesn't use the term, always saying "water pump." But it is a fine book, by all means recommended. 

Finding the Mother Tree, Suzanne Simard, (2021). I had big expectations for this book, but I must say I was disappointed. There is nothing wrong with enlivening a text with personal stories about the author but, if one exaggerates, the book is no more a scientific text, but an autobiography of the author. This book should have been titled "An Autobiography of Suzanne Simard." Some people like biographies, personally I found this one completely flat. The stories about discovering the way trees communicate with each other are interspersed in a mass of uninteresting details about Simard's personal life told in a style that reminds that of a second-rate novel. Too bad, because Simard surely has interesting things to say. But, here, the idea just didn't work. 

The word for world is Forest, by Ursula K. Le Guin (1972). Not the best novel by Ursula Le Guin, it has an ideological overtone that harms the story, but it is still a gem -- as just about everything that Le Guin wrote. The Forest in the book is a metaphor for human consciousness: truly an anticipation of the concept of holobiont that came much later, but that Le Guin clearly had in mind. This novel also was at the basis of the later movie "Avatar" which also used some concepts by Suzanne Simard in describing inter-tree communication in forests.

Il Segreto del Bosco Vecchio, (The Secret of the Old Woods). By Dino Buzzati (1935). This is not a science book, it is a novel. But if you want to read about a true holobiont, do read it. The story of someone who inherits a wood and plans to cut it to make some money. Then, he discovers that the forest is inhabited by invisible spirits. In my modest opinion, it is one of the best novels ever written in the world. Too bad it doesn't seem to have been ever translated into English. A splendid movie was made out of it but, again, only in Italian.


And if you have some time, take a walk in the woods and discover the great holobiont yourself! Humans can be friends with trees even in difficult conditions. Here is a photo taken in Florence a few months ago, this lady made a little garden for herself and for everybody out of a small patch around a tree growing in front of her house, near a busy avenue. 

Wednesday, May 26, 2021

The Descent of Man: How Collaboration Made us What we are




150 years ago, Darwin published "The Descent of Man" -- another great intuition by one of the greatest scientists in history. Today, we understand how humans are what they are because they collaborate with each other -- something that we tend to forget in our current views that emphasize cutthroat competition. Here is how Richerson, Gavrilets, and De Waal comment on this point in their recent article on "Science"

"What makes us different is that our ancestors evolved greatly enhanced abilities for (and reliance on) cooperation, social learning, and cumulative culture—traits emphasized already by Darwin. Cooperation allowed for environmental risk buffering, cost reduction, and the access to new resources and benefits through the “economy of scale.” Learning and cumulative culture allowed for the accumulation and rapid spread of beneficial innovations between individuals and groups. The enhanced abilities to learn from and cooperate with others became a universal tool, removing the need to evolve specific biological organs for specific environmental challenges. These human traits likely evolved as a response to increasing high-frequency climate changes on the millennial and submillennial scales during the Pleistocene. Once the abilities for cumulative culture and extended cooperation were in place, a suite of subsequent evolutionary changes became possible and likely unavoidable."

Tuesday, May 25, 2021

The Secret of Holobionts: How Excessive Efficiency can Kill


Five minutes are enough to take a look at this amazing video. It is extremely well done and it tells you about things that you would never have suspected. How can it be that trees exist? Well, it turns out that their metabolism is truly alien and it exploits physical phenomena that you wouldn't have imagined could be used in that way. But Mother Gaia has many tricks!

One point that has fascinated me most is how this behavior of threes highlights a fundamental characteristic of holobionts: the individual organisms that form the holobiont do not act with a purpose, they do not have "in mind" to benefit the group. But, if it is true that what's good for the hive is good for the bee, also the reverse is often true. And especially in this case. 

Trees pump water by evaporating water, which means they lose most of it. From the video, you'll learn that just about 5% of the pumped water is used by the tree for its needs. The rest evaporates away -- it is the process of evapotranspiration. 

So, trees are highly inefficient pumping machines. But, curiously, this inefficiency is what benefits the forest. This huge evaporation is what puts in motion another pump: the biotic pump. It is a mechanism that generates a depression that, in turn, pulls water from the humid atmosphere near the sea all the way to the inner areas of the forest. Without this mechanism, forests could hardly exist inland. 

If trees were 100% efficient, they would evaporate nothing and the forest would die. I think there is a deep message here, not valid just for forests: too high efficiency can kill. Living is sharing, and if there is no sharing there is no life.




Sunday, April 18, 2021

How I cured my Stiff Neck: Holobionts and Health.


This is a reflection on epistemology in medicine. It deals with my personal case of a bad stiff neck that lasted for more than a year, until I found the trick to make it go away. Please understand that I am no doctor and I don't claim to be able to cure anyone. I am just pointing out that you should always remember that you are a holobiont. So, if you treat your biome well, your biome will treat you well.


About two years ago, I developed a bad case of stiff neck. Sometimes it meant so much pain that I had to stop whatever I was doing and clench my teeth to avoid screaming. And sometimes I really screamed aloud. Then, I had to trust God every time I crossed a street because I couldn't turn my head to see if a car was running in my direction. 

There are various medicines you can take to ease the pain of a stiff neck and I tried several of them. Aspirin, NSAIDs, creams, exercises, acupuncture, massages. But, apparently, my case was bad enough to be resistant to pills, creams, and manipulations. What the hell was happening to me?

I tried to reason it over and I thought I had found an explanation. More or less in coincidence with the start of my neck pain, I had relocated to a new home. It was partly underground, and the humidity inside was much higher than in my old home. On the right, you see one of the windows of my new home. No, not the big one. Look at where my wife, Grazia, is pointing. Yes, that one! The hygrometer in the new home consistently marked over 70% humidity, whereas in the old home the needle would normally stay between 40% and 50%.

I know that correlation doesn't mean causation, but the logical inference was that humidity was the reason for my stiff neck. I found that it is commonly written on the Web that indoor humidity should be between 40% and 60% for optimal comfort, and that seemed to confirm my suspicion: my home was too humid. Even my hygrometer said that there was something wrong when the needle went over 70%. It was made in Germany, and their boffins are said to know what they say. Humidity could have been the reason of my stiff neck. 

So, I bought a professional dehumidifier, It made a lot of noise and it considerably raised my electricity bill, but it did lower the humidity level at home. Not so much, but it could bring it below 70%. But the effect on my neck was nil. During that period, I also happened to visit Iran for a couple of weeks. Tehran is a very dry city, I had brought my hygrometer with me: humidity was around 20%. I thought that it would have some good effect on my stiff neck, but I noted no improvement at all. 

In the meantime, I searched the literature to try to understand why the "perfect" humidity is situated exactly in the middle of the scale. I found very little. Plenty of people say that if humidity goes above 80%, it is bad for your health. And they say that, above that level, you should see green mold appearing on the walls of your home. I saw that happening at home, but did it have anything to do with my stiff neck? I couldn't find a serious study on the effect of high humidity on human health and, in particular, on neck pain.

About one year and a half of pain had gone by when I had one of those serendipitous moments that change your life. Wait one moment..... something HAD changed about two years before: I had bought a new pair of glasses with bifocal lenses. As soon as I started thinking about that, I also noted that in moving to the new apartment I had set up my desk on a table that was a little higher than the one I was using before. And I noted that in order to focus my eyes on the screen, I had to strain my neck backward.

This noted, this done. I got rid of my glasses, discovering that I didn't really need them to read text on screen. And the improvement was rapid: I felt better after just a few days. Completely getting rid of the stiffness took at least 4-5 months, but I can report to you that now it is gone. Zero pain, it is wonderful! I can turn my neck as much as I like and I can cross the street in safety. 

So, what did I learn from this experience? That medicine is a complicated matter. I am trained as a scientist and I am a firm believer in the experimental method. But that's very difficult to apply to medicine. In my case, I found a trick that cured my neck, but does it have a general validity? Does it prove that humidity doesn't cause health damage? Does it prove that my stiff neck was caused by my new glasses? Would that apply to other people? How could I tell?

It is the general problem of "evidence based medicine." The golden standard in medicine is the "randomized controlled trial." That means a complex series of procedures to evaluate a significant number of patients while trying to control all the multiple parameters that might affect their health. 

Seen in this light, my experience with neck pain doesn't count anything. How can I prove that my neck improved because I stopped wearing my glasses? How can I exclude other factors, maybe a special astral conjunction? Or something else? 

The interesting point of this story is that it would be practically impossible to carry out a randomized controlled trial on whether excessive humidity causes a stiff neck. Think about that: how do you find a standardized set of patients? How do you standardize the humidity conditions? How do you define the intensity of one's stiff neck? In addition, who would pay for such a study? Since it doesn't involve pills, no pharmaceutical company would sponsor it. 

The result is that everybody says that medicine is a science, but it is a peculiar kind of science where the "scientific method" is often applied in a creative way (to say the least). That was seen very well with the recent Covid epidemics, where most of the actions that governments took were not based on hard data, but on haphazard evaluations taken on the spur of the moment. Just as an example, we saw everyone suddenly disinfecting everything, everywhere, all the time. Do we have proof that all that has any effect on the spread of the Covid epidemic? No, as you can read on "Nature" -- not normally so unreliable as a source.

Does that mean that randomized control studies are a bad idea? Not at all, and I invite you to follow the blog by Dr. Sebastian Rushworth, a true gold mine of ideas, suggestions, and data, all useful for your health. He is specialized in evaluating randomized control studies and he is very good at translating the dry and incomprehensible language of scientific papers into something that normal people can understand. 

It is, just, that medicine is a world that deals specifically with the most complex system we know: the human body. And complex systems, it is known, can't normally be described in terms of "causes" and "effects." No, complex systems only know forcings and feedbacks. And a small forcing applied on a complex system can generate a chain of feedbacks that sends the system to a completely different state. Just like when a pair of new glasses pushed me from a state of "healthy neck" to a state of "stiff neck."

In the end, I think that always asking for proof in medicine is a double-edged weapon. It may help in many cases, but in others it may lead you completely astray. If you ask me (and let me repeat, I am not a doctor) I would say, "try what looks reasonable and keep what works." And always remember that you are a holobiont. Treat your biome gently (don't try to kill it using disinfectants) and your biome will treat you gently. And onward we go, fellow holobionts!

(on a line completely opposite to that of trusting randomized control studies, you may be interested in the work of Dr. Natasha Campbell-McBride, who wrote the book “Gut and Psychology Syndrome." She never mentions the concept of holobiont in her book or in her talks, but her whole approach is very, very holobiontic!)

Wednesday, April 7, 2021

The Vaccine of Ancient Times: Sharing Water

 The "Old Normal" was an age that spanned from the end of the last Ice Age to the start of the Covid Age. One of the weird things that the people used to do during those remote times was to collectively dip their fingers into a horrible soup of bacteria and viruses called "holy water." Then, they engaged in a ritual gesture that involved touching one's own face with their fingers still wet with that water. How could they survive that remains a mystery. (image source)


Last week, I stopped to visit a church in my neighborhood. An eerie silence reigned among the benches where no one seemed to have been sitting for ages. The holy water bowls at the entrance of the deserted church were completely dry -- not even a trace of humidity! They had been replaced by disinfecting gel bottles. You see both the empty bowl and the gel bottle in the picture. Maybe the priest had blessed the gel?

The elimination of the holy water dispenser would seem to be an obvious thing to do. Think of the unhygienic condition of the water: with people dipping their fingers into it, it must have rapidly become a cocktail of viruses and bacteria, maybe holy, but surely unhealthy

But, amazingly, these "stoups" of holy water are a very ancient tradition. They go back to the very origins of Christianity. Were our ancestors so stupid to pass germs to each other in this way?

It is a diffuse hobby to think that our ancestors were ignorant and superstitious. But if they had been really so ignorant and superstitious, we wouldn't be here. If the holy water rituals were killing people, that would have been noted and people would have stopped using them

But all the variants of Christian religiosity include this kind of ablution rituals. Islam does, too, although in different forms. And many other religions include communal ablutions. These rituals go very deep into the very essence of religion. Whether it is water, wine, or bread, it doesn't matter: it is the sharing that counts. And if those habits were supposed to be purification rituals, they had to purify something.

There is a good reason why purification rituals were good for the health of the faithful. They were early forms of vaccination. 

Think about that: the idea of a vaccine is to put a person in contact with some forms of pathogens in order to stimulate one's natural resistance. An early form of vaccination was called "variolation" (from the Latin term "variola," "smallpox"). It goes back to several centuries ago and it consisted of actually infecting people with smallpox. The idea was to have them develop a mild infection that would then protect them from more dangerous forms. Later, variolation was replaced with vaccination using a live form of the smallpox virus, taken from cows. And, of course, our modern vaccines are small miracles of molecular biology, but they do basically the same thing. They put our bodies in direct contact with some forms of the pathogen we want to fight.

You see that our ancestors were doing the same with their ablution rituals. Of course, they knew nothing about bacteria and viruses but, again, they were not stupid. They tried many things and they kept what worked. The idea of communal ablutions was to put everyone in contact with the skin biome of the whole community, sharing the "good" germs and stimulating an immune reaction that would protect the person from worse infections. That was done also outside religious practices -- in Buddhist countries, for instance, there is no equivalent of the holy water basin of the West, but they do have a tradition of communal bathing.

These old traditions could also go beyond ablution. Look at the picture: it is the "Madonna del Parto" in the Church of St. Augustine in Rome. If you go there, you are supposed to kiss the foot of the statue for good luck. Imagine many people kissing it, one after the other. Can you imagine a better way to transfer bacteria and viruses to one another? Actually, the foot is in silver, known to have some bactericidal properties. The idea may have been that, yes, it is good to share germs in this way, but let's not exaggerate. But, surely, if you didn't want bacteria to spread, you'd better avoid that people would kiss the Madonna's foot, rather than making it in silver! They wanted some germs to be transferred!

So, the ancients had empirically understood the concept that today we call "holobiont."  Our bodies are not single organisms, we are colonies of microscopic creatures: our microbiome. These creatures are part of us and, among the many good things they do for us, one is to protect us from the external microbes that tend to invade our bodies. The microbes living on our skin are the first line of defense we have, but we are protected by multiple defensive layers. The active immune system, the "adaptive" one, is the final layer. It enters into action only after that the other lines have been breached. Your microbiome makes sure that it rarely happens. It is part of the good thing that is being a holobiont!

But there is more than sharing water in being holobionts. It is a deep and significant way to show that we belong to a community, which we can see as a higher-order holobiont. The basic idea of religion, any religion, is sharing. Sharing is the essence of the great planetary holobiont we call sometimes Gaia, from which we came and to which we return. Without sharing, there is no God/Goddess, no community, no life. 

Something of this attitude has filtered through the rather anodyne ritual of modern vaccination, with many people reporting a feeling of spiritual completeness after receiving their vaccine against the Covid pandemic. They felt they had done their duty in protecting not just themselves, but the whole community and they were proud of having shared the burden with everyone else. Which is the way any good holobiont should feel! 

Of course, this kind of feeling depends on trusting that you are doing the right thing. One thing is dipping one's finger in a bowl of holy water: you trust your local community. Another is to have synthetic RNA being delivered inside one's cells to operate the molecular mechanisms of protein creation: you trust science.  

Is science an entity worth our trust? Trust is not bestowed by definition, it must be earned. And we must say that the composite entity we call "science" has not been always up to the standards that would make it deserve everyone's trust. Especially in recent times, scientists have shown attitudes involving petty squabbles, greed, ignorance, subservience to power, arrogance, political partisanship, and more. That explains the diffuse resistance against the modern forms of vaccination, perceived as a violation of one's body. Scientists must do much better than they are doing now if they want to maintain the trust that the community still places on them.

In the end, we keep making the same mistake we have been doing for quite some time: contrasting religion with science, as if the former were superstition and the latter the truth. It is not like that. They are different forms of understanding ourselves and the world (and, eventually, understanding is sharing). 

Even in health care, we are creating a schizophrenic situation by creating an artificial contrast that doesn't need to exist. Are we sure that we did well in abolishing the basins of holy water? They were ways to "prime" our skin microbiome against infection. With our emphasis on molecular vaccines, we forgot that the human defense system is multilayered. And if this first line of defense works, we are not necessarily forced to recur to more invasive ones.

Worse, we are forgetting that being human means sharing with others. Saint Francis would kiss lepers when he met them. We don't need to go to such extremes, but we still need to remember that we are human. Masked, disinfected, and isolated, as we all are nowadays, we are declaring that we are not willing to share anything with anyone. Are we still human? And, if we are, why we treat each other as if we weren't?


Ugo Bardi is a member of the Club of Rome, faculty member of the University of Florence, and the author of "Extracted" (Chelsea Green 2014), "The Seneca Effect" (Springer 2017), and Before the Collapse (Springer 2019)