Forest Recovery: A quote by Anastassia Makarieva

 

You see, there is a succession process for forest recovery. We first have shrub grasses after some disturbance like fire, then it takes time for that to be replaced by trees. So if we are lucky, our grand grandchildren will be walking in such a forest, so this dimension should also be stressed. We are working for the future we are not just securing for ourselves some two dozen years of better comfort. Rather, we send a message through centuries such that people will remember us, and walking into this forest along the brooks and rivers they will remember us with gratitude for our care and dedication.

Anastassia Makarieva  

Can HolobiontsThink?

 

My wife, a holobiont called Grazia, hugs another holobiont, a Cupressus Sempervirens, in the hills near Florence, Italy

This is an excerpt from the chapter I am writing for a multi-author book 

I started this chapter by examining trees and forests as holobionts, then looking at human beings. Trees and humans are as alien to each other as we could possibly imagine. Humans are mobile creatures with an extravagantly powerful metabolism that makes them able to sustain protracted efforts longer than any other living animal. That turbo-charged metabolism is also used to maintain their large brains, of which they are very proud. They use their brains to control their muscles and their sophisticated sensory apparatus, as well as to deal with each other in complicated social rituals.

Trees are the opposite in almost all respects: they are immobile, their metabolism is slow: and they can’t even control their internal temperature. They don’t have eyes, nerves, brains, and not even muscles. Yet, they move, they sense their environment mainly by chemical signals, but also visual and mechanical ones -- including vibrations in the acoustic frequency. They "know" what's going on around them, but in ways that are mostly alien to mobile mammals, including humans.

Nevertheless, humans and trees are both holobionts at their core, and they share more than it would seem at first sight. It is not even forbidden to ask whether trees and other plants might be “conscious” in some way. This is a subject of wide debate, nowadays, and it would be out of the scope of the present text to enter into the details of a question whose answer depends primarily on the definition of the entity being debated. For what we are concerned, we can rather ask the question of whether some creatures store somewhere a schematic representation of at least some elements of the outside world, and modify their behavior depending on the sensor input they receive. That implies a certain level of “consciousness.”

In the case of human beings, there is no doubt that this capability exists. Assuming that most of the readers of this text are human, they should be familiar with the typical sensation of being encased in a bodily container. We have no direct perception of having a brain, but somehow we perceive that we are “inside” a body, that we are a sort of "homunculus" that resides someplace behind the eyes. And, surely, we do keep representations of the outside world, sometimes even too much, as when our political leaders claim that they can “create their own reality.”

How about a tree, then? Where would a tree have its representation of the outside world? As I said, trees have no brains and no nervous system, but they can transmit electric signals from cell to cell. It is a still scarcely known field, but it is known that the phloem and xylem cells form a network to transmit electrical signals long-distance within the plant. At the root level, the mycorrhizal system shares chemical signals within single plants and also from one plant to another. Would such a network be able also of storing information, just like a neural network does in animals? There is no reason to deny that it could. In this case, the representation of the outside world would be stored in the plant as a configuration of the network, continuously changed by sensorial inputs, and leading to signals being transmitted to the various parts of the plants instructing them, for instance, to release volatile organic compounds to fight an insect attack.

If that were the case, apart from the slippery concept of consciousness, a plant would not have the sensation of being encased in a bone cage that humans have. Its intelligence would be delocalized all over the structure. The plant would “feel” the conditions of the leaves, and the presence of sunlight. It would “smell” chemicals floating in the air and perceive the sound of living creatures moving in the vicinity. It would also be actively sending and receiving chemical signals through the mycorrhizal system. In short, it might have a representation of the external world of complexity comparable to the one that humans can build in from their sensorial input. Whether plants could also “create their own reality,” that is, dream, is impossible to say. Communicating with trees is a challenge that was never met, at least in terms compatible with the scientific method. Nevertheless, there seems to be a certain empathy between trees and humans. In the photo, the author’s wife, Grazia, communicates with a specimen of Cupressus sempervirens, in Tuscany.

About this encounter of these two holobionts, we may speculate about their reciprocal sensorial experience. For the human, the tree holobiont is perceived mainly as a visual entity -- but her sensorial system has no capability of detecting the underground root system. Nor she can detect the complex chemical signaling that the tree is operating inside and outside itself. For the tree, instead, the human cannot generate as a visual image, but it is possible that the tree perceives the human from the vibrations she generates and, maybe, detecting the chemical signals she produces. Whether the tree knows that it is being hugged is impossible to say, but we cannot completely discount this possibility. As a further note, both humans and trees use sunlight for chemical processing on their surfaces. Trees use it for photosynthesis, while humans need it to synthesize the compound called "Vitamin D" that they need for their survival.   

We can gather from this discussion that creating a representation of the outside world is a fundamental survival element of holobionts. And since holobionts are the main form that life on Earth takes, we should admit that all holobionts have this kind of capability. In other words, holobionts can “think.” Not in the same way as humans think, of course. But the process of thinking is part of the homeostatic adaptation that all living beings tend to attain. To accomplish that, they need to process information: it is the basic idea of the “dissipation structures” as defined by Prigogine. These structures process entropy and dissipate it, and entropy is basically information. So, holobionts are structured in such a way as to modify their internal structure to obtain homeostasis and maintain it despite changes in the structure of their environment. The holobiont itself is the holobiont’s “brain” and its internal structure stores a representation of the outside world.

Seen in these terms, the hypertrophic brain of which humans are so proud is not an exception to the rule that holobionts store information in their networked structure. All the neurons in the human brain are the same: there is no “super-neuron” that controls the other neurons. In a sense, you could say that the brain is a holobiont, possibly the biggest one known in the ecosystem in terms of the units it contains, with a total of some 86 billion neurons. It is still a small number if compared to the genetic information stored by the whole biosphere has been estimated as Thus, the total amount of genetic information stored in the natural biota is of the order of 1016 bit (Gorshkov et al., 2000) and coincides as an order of magnitude with the information stored in a human brain. This similarity may give us some interesting insights about the idea that the world in which we live is a single, extremely large, holobiont to which we sometimes give the name of Gaia, the Earth Goddess (Castell et al., 2019)

Young holobiont and old holobiont

 

 

The young one is named Aurora

Our Holobiont Friends, the Fungi. A road toward the Circular Economy?

 

The Amanita Muscaria, perhaps the most beautiful mushroom in the world. Said to be poisonous, some say it is edible. It can also have hallucinogenic effects. In any case, the bright red color is a signal directed to animals that, basically, says, "eat me." And the resulting hallucinations may well be a further reason for animals (humans in particular) to seek for it. This bright livery and the mental effects of the fungus may be the origin of the myth of a fat man driving a sled pulled by reindeer and dressed in a liver that's exactly of the same colors. But, apart from myth creation, fungi can be the basis of a number of interesting advanced technologies to recycle waste and produce food. (note: in this text, I often use the concept of "holobiont" that may not be familiar to most people. To know more about it, see the blog "The Proud Holobionts")

Fungi as holobionts

Fungi are the quintessential holobionts. Neither plants nor animals, they are a world apart from us. They lack the capability of photosynthesis and so they cannot live except as associating themselves to plant roots (they are called "mycorrhizal") or, sometimes, as scavengers (in this case, we call them "saprophytes"). In both cases, they obtain their food from plants and, in exchange, they provide plants with a variety of services, including the all-important capability of extracting minerals from the soil and turning them into forms that plants can absorb. The relationship between plants and fungi is so strict and intricate that some plants live on fungi: they are epiparasites ("parasites of parasites"). Holobionts have many way to exist!

Fungi, plants, and animals form different "kingdoms" in the biological classification of living creatures. But the separation between fungi and animals is especially sharp. We may see fungi as the specular opposite of animals in terms of their survival strategies. Both depend on plants, but they live on opposite sides of the ground surface. Animals, like us, live mainly above ground, mushrooms underground. What we see of them is the occasional appearance of the "fruiting body," or the "mushroom," the sexual organ of the underground creature. (if you want to know the proper scientific term, it is the "epigeal" part of the creature).

Given the different environments in which fungi and animals live, it is not surprising that the interactions between fungi and animals are usually limited. Although fungal spores pervade the air we breathe, even in towns and inside homes, we do not harbor many fungal species in our bodies. The Candida Albicans is one of the few examples: it is common in human bodies, where it is probably doing a useful job as a saprophyte, removing decayed materials. But, occasionally, the Candida may become a pathogen and do plenty of damage when something goes wrong in the complex equilibrium of the human holobiont. 

Nevertheless, the above-ground manifestations of fungi are part of the human lore, and also of the human diet. But even as food, mushrooms are not so common, and they are surrounded by myths and legends: some are poisonous, some are hallucinogenic, most have no eating value, but some are considered prized food -- think of truffles! 

From the viewpoint of fungi, we animals may be considered exotic and legendary creatures, often causing damage but in some cases useful to spread the spores. Truffles would not smell so good to human (and animal) noses if they didn't "want" to be dug out and eaten. The same is true for the brightly colored mushrooms that advertise themselves as good food (or, in some other cases, carrying the "do not eat me" message). 

So, fungi and humans form the kind of symbiotic relationship of holobionts only occasionally. In particular, humans are not so good at cultivating fungi as food, but by far not as good as they are at cultivating plants and herding animals. To this day, mushrooms remain one of the few human foods that are mainly harvested from the wild. The capability of cultivating them is a recent skill acquired in human history. It is said that the first mushroom cultivations were developed in China during the first millennium AD. By now, several species can be cultivated, mostly of the saprophyte kind, (the Japanese "shiitake" are an example). Cultivating mycorrhizal fungi, such as truffles, is much more complicated because they live in association with a living plant, which must be provided by humans. "Truffiéres" do exist, but they are a recent development. In all cases, cultivating mushrooms is a step upward in complexity with respect to conventional agricultural techniques. 

Despite the problems involved, cultivating fungi is an attractive idea for many reasons. Apart from food, the capability of saprophytes to break down materials that humans consider waste is interesting: if we can turn waste into food, we can "close the cycle" of many agricultural and industrial activities and move in the direction of the "circular economy" that is the only kind of economy that can last a long time. Can fungi be a fundamental tool for that purpose? Maybe, but we are still far away from a truly circular economy. Let me tell you something about my experience in this field.

Cultivating the mushroom holobiont: the circular farm

It was Galileo who said that "knowledge is the child of experience" (la sapienza è figliola della sperienza). So, in order to learn something about fungi and their cultivation, I took a two-day full-immersion class in mushroom cultivation organized by a company engaged in that field. Amazing: there were so many things I didn't know about that, and so many tricks I hadn't even imagined. I don't think I'll ever become a professional mushroom grower, but it was surely an enriching experience. 

First, let me tell you a few things about the "Circular Farm" company created by Antonio Di Giovanni, a spinoff of the "Funghi Espresso" company. One of the many good things that can be said about the company is that it is a real company, one that's making a product and selling it. I say this because, over a career of working with startup companies, I arrived at the conclusion that most of them are scams. They are there to cash in government grants and gullible investors. When they have made enough money, they close shop and good riddance. That's not the case with the Circular Farm company. 

After 10 years of work and development, the Circular Farm company lives on the profits it makes. It is not an easy task: it is a biotechnological feat that requires a certain degree of sophistication and control of the process. It is not large, it is in many respects a family-based enterprise, but it works. And I can tell you that the mushrooms it produces are delicious. 

The objective of the company, as its name says, is to "close the circle" of the resources it uses -- recycling what others call waste. So, the cultivation of mushrooms is made mainly on coffee ground waste recovered from local coffee shops. The process is remarkably efficient: about 20% of the waste is transformed into edible mushrooms. What is left is composted and it could be another sellable product, were it not for the Italian bureaucracy that forbids selling it, or even giving it away for free. But it is not a pollutant, so it can be used to grow the vegetable garden of the company. 

The company is also engaged in developing more products, different kinds of fungi on different substrates, applications of fungi other than food, and other agricultural technologies according to the concept of "urban farm." After all, the idea of cultivating something inside towns is not new: our ancestors often had vegetable gardens, and they derived a substantial fraction of their food supply from them. If it worked for them, it can work for us, too!

Fungi as a tool to attain a circular economy: is it possible on a large scale?

The idea of recycling coffee ground waste appears to be a success story. The Circular Farm company can do that, and it is not the only one. In the UK, the Bio-bean company does the same, although on a larger scale and its products are different -- including, for instance, "coffee logs" to be used as fuel for wood stoves. The question is, what can these successes teach us about the more general problem of waste recycling? 

One good thing about the idea of recycling coffee waste is that it is a commercial activity. That is, it is a real way to make profits while, at the same time, doing something useful for society; in this case getting rid of some waste. But expanding the idea to a much larger scale, well, it is not so easy. 

Waste is a peculiar entity. For one thing, it has a "negative price," in the sense that people are willing (or, more often, are forced) to pay to get rid of it. This generates the problem that would-be recyclers find themselves in competition with waste management companies, whose business is not recycling, but disposal. Since the public is forced by law to pay, these companies have an unfair advantage and they tend to use all their lobbying power to make the state enact laws that make life difficult for recyclers. In some particular cases, the business of waste disposal is so lucrative and exclusive that you risk being sent to sleep with the fishes if you become a nuisance. If you work in this field, you surely have plenty of horror stories to tell. I do, too, but let me skip this subject, here. 

Another problem, and maybe the most important one, is that if something is classified as waste, it means that it is just that: waste. It means that people don't know what to do with it and just want to get rid of it. So, how come you think you can do something useful with it? Either you are especially clever or you are willing to work on the cheap side of the economy. In the latter case, you must accept to work for low profits, a strategy also known as the "church mouse" strategy." 

Most of the recycling done worldwide today is performed by people who live on the edge of survival. You may have seen pictures of the people who live by scavenging landfill in places such as India or Africa. They are so poor that for them even the very modest profits made from the things that other people throw away help them to survive. But you don't need to think in terms of exotic places. You know that you can find plenty of edible food in the waste bins of your local fast food joint. Surely, it is not as good as the food you buy at the counter, but the people called "binners" rely on that food to survive. They are, by all means, good recyclers. Interestingly, though, in many Western countries "binning" is forbidden and sanctioned by law. This illustrates both the problems I was describing: the powers that be do not want you to recycle, and what you recycle is of lower quality than the original product. This is called "downcycling" and it affects most kinds of recycling, not just food found in waste bins. Recycled plastic, for instance, is a poor material in all respects, while recycled paper is good for toilet paper and little else. 

Instead, the approach of the "Circular Farm" on recycling coffee waste is on the other side of the waste recycling strategy: it exploits cleverness. Indeed, they are performing a remarkable feat: transforming something that nobody wants into relatively high-priced goods, edible mushrooms. But can it be expanded? In part, yes. Fungi are nearly miraculous creatures, and they can do things that no other living creature can do. Just think of the possibility of using the chitin that fungi produce (plants don't produce it). Chitin is a solid polymer, typically used in nature by insects for their exoskeleton. Chitin could be grown by fungi inside molds and replace plastic, with the advantage that chitin is a natural substance that can be easily degraded by bacteria. Fungi might also be able to degrade plastic directly, but we are not there yet. 

Overall, we are just starting to explore the many possibilities of biotechnology in many fields. It could do many useful things (and many horrible ones, bioweapons, for instance). Perhaps the most interesting possibility is to reduce the impact of agriculture on the ecosystem. This is a point that's scarcely recognized, but agriculture is one of the most destructive technologies ever devised by humankind. It occupies enormous areas, with the consequent destruction of the natural biota, deforestation, and the destabilization of the whole ecosystem. To say nothing about how, today, most agricultural production is made on soil that has been thoroughly destroyed by the overuse of artificial fertilizers and pesticides so that it has become sterile and inert ("as sterile as the brains of my students" as I say, but let me not harp on that). In itself, the cultivation of mushrooms can't replace agricultural products, but it is part of a revolution that includes "precision fermentation" which promises the production of food using bacteria with a much smaller environmental impact than conventional agriculture. 

Concluding: The Holobiont Strategy

Modern biotechnologies give us hints of revolutionary possibilities, but we are not there yet. In quantitative terms, some ten million tons of coffee are produced every year in the world, practically all of which becomes coffee grounds waste. Now, Circular Farm recycles about 10 tons per year and, even though there are other companies engaged in the same task, the impact on global waste production is minimal. Besides, coffee grounds are not a major source of pollution. So, you see that it is a long road that we have to walk before we can use bacteria and fungi to replace conventional agriculture or even to make a serious dent in the pollution created by waste.

It looks more likely that we'll have to adapt to what we can do rather than dream about things we cannot do. A good strategy in terms of optimizing a production system is to mimic the way the natural system works: It is the "holobiont strategy." Holobionts do not accumulate capital -- they exchange what they produce immediately after they produce it. A good holobiont is a chain of creatures that cycle nutrients down from solar energy all the way to fertile soil, which then is returned to the top. Holobionts don't strive to become rich, they strive for stability. And they strive for efficiency: a good holobiont would never forbid fellow holobionts from getting their lunch from the waste bin of a restaurant. The holobiont way is to help, not to forbid. And so, one step after another, we'll arrive somewhere. Onward, fellow holobionts!

Photos of the Circular Farm Seminar

A Good Holobiont has a Good Immune System. Managing your Microbial Environment

 

An incredible book by Philipp Dettmer: an ambitious attempt to tell the whole story of the human immune system in an understandable form even for the non-specialist. The result is a 345-page tome, lavishly illustrated, and written in an entertaining style. Remarkably well done, but not easy to digest nevertheless. I went through the whole thing once, but I need to restart from the beginning and reread it again. And, probably, I'll need a third pass. Afterward, I may be able to say that I know just a little bit about how the immune system works. 

And think that this is just an introduction that neglects or just mentions several important details. For instance, it mostly skips the role of the microbiome. But that must be hugely important: after all, human beings are holobionts. We can't survive without our microbiome, and it is likely that the huge numbers of small critters that populate our body play a fundamental role in managing the microbial system "holobiont-style." It means that the immune system is not a sort of Nazi militia that shoots down everything it doesn't recognize and doesn't like. It must be able to recognize those parts of the microbiome which are helpful and those which are not. And note that, in some cases, the same species of microbes can play the role of pathogen or symbiont, depending on the general conditions of the rest of the system. That's how good holobionts behave: they adapt to each other. We need to be colonized by microbes in order to survive. It is just a question of being colonized by the good ones. And it is the job of the immune system to ensure that it happens!

Amazing, as I said. It gives you a glimpse of the immense complexity of just a section for the even more immense complexity of the ecosystem -- that some call "Gaia." The goddess gave every one of us a complete defense and management system that kept our ancestors alive for the past 400 million years or so as multicellular organisms, and also a few billion years as single-cell organisms. If we are here, it means that the immune system of our ancestors worked well enough to interact with, and protect them from, the zillions and zillions of microscopic creatures that we eat, inhale, or come in contact with one way or another. 

But, wait.... aren't we supposed to be much smarter than Gaia, that poor old lady? We are so smart that we discovered that we can do better than just relying on that old stuff that uses billions of antibodies, t-cells, macrophages, and more. You know, those squishy things that evolved over a few billion years, what are they for? Instead, just a piece of cloth placed onto your mouth and nose, and -- voilà -- NOW you are safe! 

My Neighbor Holobiont

The most beautiful scene ever created. From Miyazaki's "Tonari no Totoro" (My neighbor Totoro). The true spirit of the holobiont is caught in this scene.

Be a Good Holobiont! Cultivate Mushrooms!

 

A mushroom-based lunch at the class on mushroom cultivation that I attended. The main dish is based on Pleurotus and I can tell you that it was absolutely delicious. Gaia is wise and benevolent in many of her manifestations!

I took a 2-day full-immersion class on mushroom cultivation. I am not sure that I can engage in this activity myself, it is a full-time job, not really suitable as a hobby. But it is surely a welcome respite from the daily, horrible news we are receiving from all over the world. It is fortunate that there are still people who spend their time doing something good and useful, and may Gaia bless them for what they are doing!

Mushrooms are not holobionts themselves, but they are part of many holobionts, not least forming the "rhizosphere," the all-important layer that keeps Earth's "skin", its fertile soil alive. And you may know that fungi are symbionts of the human organism, even though their role is still largely unknown. https://www.sciencedirect.com/science/article/pii/S1369527416301813

To know more about mushroom cultivation, see the site of the "Funghi Espresso" company that cultivates mushrooms using used coffee grounds as substrate.