October – November 2022

These are chapter-by-chapter notes (with occasional quotes) on Entangled Life: How Fungi Make our Worlds, Change our Minds, and Shape our Futures, by M. Sheldrake. I’m reading this book with KC, a chapter or two at a time, and adding notes for each chapter as I go. Having now finished it, my one line review is that it has some fascinating stuff in it, but it is a lot more focused on cool stuff than on giving a detailed account of the science.

Contents

General questions I have about fungi

Do individuals of the same species differ — that is, by analogy to ant colonies – do different individuals adapt to similar situations using different strategies, which in turn influence their reproductive success?

How do fungi construct different structures out of identical units (hyphae)?

To what extent are hyphae like cells and to what extent are they not like cells. I.e. they have septa that can separate them hyphae, but the septae can open and close and cell ‘nuclei’ can flow along hyphae?

How does a mycelial network coordinate its behavior? What are its signaling mechanisms, and what functions do they preform? Does a mycelium have some sort of equivalent of a memory? If so, how long does it last?
What is the argument for considering lichens to be organisms rather than ecosystems? Since the fungal part of the lichen can reproduce separately, and take on a different species of algae than before as a symbiont, the organism argument seems weak.

Introduction and back materials

Monday, 3 October 2022

We’ve begun with the front and back matter: Prologue, Introduction, Bibliography and Index.

My initial impression is that it will have a good coverage of the science — a lot of serious references and topics in the bibliography and index — but that it may have considerably more about the author and what he’s learned personally through which experiences, than I care for. The Introduction is sub-titled “What is it like to be a fungus, but it would be more accurate to title it “Why I’m interested in fungi and think they’re cool.”

The introduction contains a bunch of fact-oids on fungi: the biggest, the oldest, fungi that consume radiation, that fungi collectively produce 50 megatons of spores a year, mushrooms that grow through asphalt, that there are estimated to by 6 to 10 times as many fungal species as plant species, and so on. We learn about him taking LSD as part of an experiment to enhance his creativity, and about the particular organism he studies, and how thinking about fungi in particular, and biology in general, has destabilized his ontology around what it for something to be an individual, or for something to think. I find his interest in the fact that a slime mold network can be used to determine the most efficient network for connecting a set of nodes and his consequent speculations on intelligence to be naive — one might as well marvel at the ability of a tossed ball to compute a parabola for its flight path, or the ability of a trail of ants to compute a straight line. Life is very good at finding the minimum energy solutions, thanks to the mix of physics and survival of the fittest. Still, hopefully the book will become a bit more focused on the science….

C1: A Lure

Monday, 31 October 2022

This chapter begins with truffles and truffle hunting.

They were scruffy, like unwashed stones; irregular, like potatoes; socketed, like skulls.
– Merlin Sheldrake, The Entangled Life, p 25.

Truffles are the underground fruiting bodies of several types of micorrhizal fungi; the claim is that truffles have an intense odor to attract animals (particuarly pigs), that will dig it up and eat, and spread spores through their feces. It is claimed that the scent of truffles may be produced more by a biome of organisms than by just the truffle (Vahdatzadeh, et al., 2015).

Second, the potential role of the microbiome in truffle aroma formation has been addressed for the same four species. Our results suggest that on one hand, odorants, which are common to many truffle species, might be of mixed truffle and microbial origin, while on the other hand, less common odorants might be derived from microbes only. They also highlight that bacteria, the dominant group in the microbiome of the truffle, might also be the most important contributors to truffle aroma not only in T. borchii, as already demonstrated, but also in T. magnatum, T. aestivum, and T. melanosporum.
Vahdatzadeh, et al., 2015

Besides attracting organisms to disperse spores, predatory fungi use them to attract prey. Predatory fungi use a variety of methods — ‘snares,’ ‘harpoons,’ and toxins to capture nematodes. This predatory behavior only occurs under certain circumstances; if organic material is plentiful, the organisms may not resort to predation.

Fungi produce mycelia networks in which hyphae divide and then later “home” in on other hyphae with which they fuse (anastomosis). I think hyphae fusion occurs between hyphae from different organisms (but am not certain); it can also occur between different species which are not reproductively compatible.) This fusion also occurs between plant roots and fungal mycelia: plant roots can produce plumes of volatile compounds which spread through the soil and cause spores to sprout and hyphae to branch and grow faster; in turn, fungi produce plant hormones that cause roots to proliferate into masses of feathery branches, increasing the surface area for possible interaction.

In areas of exploring mycelium, hyphae usually grow away from other hyphae without ever touching. In more mature parts of the mycelium, hyphal inclinations pivot. Growing tips instead become attracted to each other and start to “home” (Hickey et al., 2002). How hyphae attract and repel each other remains poorly understood. Work on the model organism, the bread mold, Neuraspora crassa, is starting to provide some clues. Each hyphal tip takes it in turn to release a pheromone that attracts and “excites” the other. Through this back-and-forthing” – as if throwing a ball,” write the authors of one study– hyphae are able to entrain and home in on each other by falling into thythm. It is this oscillation – a chemical rally – that allows them to lure the other without stimulating themselves. When they are serving, they aren’t able to defect the pheromone. When the other serves, they are stimulated (Read et al. [2009] and Goryachev et al. [2012]); also see: The mechanistic basis of self-fusion between conidial anastomosis tubes during fungal colony initiation.

C2: Living Labyrinths

Tuesday, 1 November 2022

This chapter goes more deeply into how mycelial networks grow and function; a lot of the better material is in the notes.

Mycelia are found almost everywhere: soil, regolith, dust specs, coral reefs, and animal bodies, dead and alive. Species mycelia have a characteristic shape and branching topology, and range in size from sub-millimeter to multi-kilometer scales; likewise their hyphae can take on various forms (e.g., thin or thick). A mycelium in a gram of soil, if stretched out in a single thread, would span from 100 meters to 10,000 meters.

Fungal hyphae are unlike cells in plants or animals. The hyphae of many species have internal divisions called septae that can be open or closed, and when open cellular contents – including nuclei – can flow between divisions creating what is called a “supra cellular state.” Furthermore, one mycelium may fuse with another and share contents, creating what are called “guilds.” [See note 47, p 242]

The hyphae of some species grow so fast that it is visible to the human eye; within the hyphal tip, vesicles arrive at a rate of 100’s/second, and fuse with it releasing their loads of cellular building materials. Hyphae tip growth is managed by an organelle, called a Spitzenkörper, that receives and sorts vesicles, and distributes them to the hyphae tip. The Spitzenkörper can also cause hyphae to branch, by dividing, and can also release materials that cause one hyphae to fuse with another, creating connections within or between mycelia.

A mycelium can change its shape in response to its environment. For example, in one experiment a mycelium growing out from a block of wood explores its environment using a radial pattern, but when it encounters a second block of (consumable) wood, it thickens the connections with the new block and withdraws material from the other exploratory areas of its mycelia to focus on the new block. In another experiment which began in the same way, once the connection was made with the new block and the mycelium reconfigured itself, the original block was removed, pruned of all external hyphae, and put in a new growing medium. The mycelium it produced grew in the same direction (towards where the second block of wood would have been) as before, rather than using a radial exploratory patterns, showing that somehow a sort of memory or state change had been retained.

Mycelia appear to have various ways to propagate information and material.

The mechanism for signaling the direction of nutrients is one [but how fast do the mycelium adapt?]. Later an experiment shows that the block of would triggers increased action potential signaling.
0.007 cm/minute: substances via microtubule transport
Over short distances substances can be transported via a hyphae’s microtubules
.03 cm/second via fluid transport through hyphae
Over longer distance they can be transported by flows of cellular fluid that include nuclei (it is implied that rate of fluid transport through hyphae is a maximum of .3 mm/min. Also: “In certain large hyphae, the flow of cellular fluid changed direction every few [~3] hours, allowing allowing signaling compounds and nutrients to flow along the network in both directions.” Mechanisms hypothesized to control this are hyphal pores and contractile vacuoles. [Note 56, p 245]
0.9 cm/minute: bioluminescence via ???
Another example is, in a study of a fungus with bioluminescence, injuring one part of the mycelium will cause a wave of bioluminescence to spread across the mycelium at a rate of about 0.9 cm/minute. (Olson tested the possibility that the fungus was signaling via a substance emitted into the air, but an adjacent fungus of the same type did not respond).
2.5 cm/minute: fluid via rhizomorphs
Fungi can also produce cords or rhizomorphs (below) that can move fluid at 2.5 cm/minute.
3.0 cm/minute via action potentials
Action-potential like signals can be transmitted through mycelia at a rate of about 3 cm/minute.

Mycelia are not the only structures formed by fungi. They can produce mushrooms for spore production and distribution, and cords or rhizomorphs –hollow ‘cables’ that range from thin filaments to ‘tubes’ several millimeters thick that can stretch for hundreds of meters. Curiously, these structures are formed entirely of identical units, hyphae.

Here is the best paper I can find on the electrophysiology of fungi:

Fungal cells generate D.C. and A.C. (action potentials) electrical currents during theirgrowth and differentiation. In addition, they exhibit tropic growth (galvanotropism) and tactic responses (galvanotaxis) in applied electrical fields. The natural D.C. electrical currents of fungi are due to clustering of ion channels and pumps in certain regions of the cells, mycelium or thallus. It now seems that these electrical currents per se are not essential for the process of tip growth although the local traffic of calcium ions, which are a component of the currents, may be. Instead, electrical currents and action potentials are concerned apparently with spatial control of nutrient uptake and perhaps in intramycelium communication. Studies of the phenomenon of galvanotropism have been used to explore further the mechanisms underlying apical extension of hyphae and these also implicate localcalcium ion uptake as being important for this process. Motile zoospores of phytopathogenic fungi exhibit galvanotaxis in weak electrical fields of a size comparable to those generated by plant roots. This tactic behaviour predicts the sites of their accumulation in the natural electrical fields generated by roots and suggests that they may utilize the endogenous electrical currents of plants to detect potential hosts. Generating and responding to electrical currents is therefore an important and general aspect of fungal physiology.
Gow & Morris, The Electric Fungus, 2009

C3: The Intimacy of Strangers

Wednesday, 9 November 2022

Lichens are places where an organism unravels into an ecoysystem, and where an ecosystem congeals into an organism.
Merlin Sheldrake, Entangled Life, p 88

Lichens are a symbiosis between one or more types of fungi and an algae (also known as a cyanobacteria); more recently we’ve discovered that lichen’s appear to be composed of at least four symbionts, three being bacterial and one being fungal. They cover as much as 8% of the earth, exist in environments from the sea level to alpine environments, and can live on virtually any sort of surface. They use light for energy, and break down rock and other materials for nutirents; they do this through a process of physical and chemical weathering. Lichens live a long time; the oldest known lichen is in Lapland and is over 9,000 years old. Lichens first appeared in the fossil record 400 Ma; the appear to have evolved independently 9 – 12 times since then.

Lichens are extremophiles, though unusual ones because they are multi-cellular and symbiotic. The BIOMEX consortium (Biology and Mars Experiment) ran an experiment on the International Space Station during 2016 that exposed a variety of extremophiles to raw space conditions. Lichens can survive in space (but go dormant) and are able to repair most types of damage afterwards. Lichens can withstand intense radiation – up to 24,000x the lethal dose for humans. Other experiments have shown that Lichens can survive shocks of 10-50 gigapascals, 100–500 times greater than the pressure at the bottom of the Marianas Trench. This suggests that they would be able to survive being blasted off earth as a result of a meteoric impact; re-entry would be trickier, but presumably they could survive an interplanetary trip and rentry if they were buried within a body of material.

Lichens reproduce both as wholes (a fragment with both fungi and algae being transported to a new site where it multiplies), or as parts (the fungal portion sporifies, is transported and finds a new symbion not necessariy of the same species). One in five of all known fungal species can lichenize — some species have participated in lichen-relationships for part of their evolutionary history, and have then de-lichenized (and vice versa). It is a little unclear to me what leads (some) to treat lichen’s as single organisms rather than tightly coupled ecosystem. The fact that just the fugal component of a lichen can reproduced and then recruit a different species of symbiont seems to me to argue against the case for licehn-as-organism.

Science Mentions

Joshua Lederberg and horizontal gene transfer among bacteria.
Lynn Margulis and the role of endosymbiosis in evolution (e.g., origin of mitochondria and chloroplasts as indepemendent entities).
Toby Spribille — did DNA analysis of lichens and discovered that more than two organisms formed a part of it. The symbiosis of lichens is very open, and include many types of bacteria.

C4: Mycelial Minds

Wednesday, 9 November 2022

This struck me as a weaker chapter – it did not have a lot of science in it, and was a bit more speculative and pop-sciency. Topics included:

LSD and psilocybin as fungal molecules; description of psychedelic experiences; description of current use of psychedelics in medicine and psychiatry; presentation of K. McKenna’s views…
Zombie fungi: Ophiocordyceps Unilateralis infect carpenter ants and secrete chemicals that control their muscles; although 40% of the ants body may be fungal material, its brain is left alone. This fungus appears to date back at least 48 Ma, as indicated by fossilized carpenter ant scars.
Sheldrake puts a lot of emphasis on fungi as “manipulating” plant and animal behavior; I don’t like this language because of its connotation of intent… seems a bit sensationalistic to me.
Fungi control behavior via various chemicals that include immunosuppressants, amphetimines, and psychedelics; one fungus is thought to carry a virus that it uses to infect insects that host it.
Mentions Dawkin’s concept of extended phenotypes, which is defined as external behaviors that (1) are inherited, (2) they must vary, and (3) their variation must affect the organisms fitness for a particular situation and thus be shaped by natural selection.

C5: Before Roots

FOR Wednesday, 16 November 2022

Around 600 Ma green algae moved from fresh water land. The first land plants had no roots, they were mosses. And for the first 50 Ma, they had no roots, but instead struck up partnerships with fungi. Today plants make up 80% of the mass of life on earth, and 90% of them have associations with fungi.
The associations between plants and fungi preserve their differences of form, and their DNA and reproductive mechanisms are separate. That said, fungi do grow their hyphae within the cells of plants, so the association is very fine-grained.
The ability to associate with plants have evolved separately in over 60 different fungal lineages. “There are many ways to form a mycorrhyzial relationship — what are are they?
Mycorrhyzal hyphae are fifty times finer than plant roots, and can exceed the length of plant roots by two orders of magnitude; the hyphae grow and die back quickly – between ten and 60 times a year.
During the Devonian period, 300-400 Ma (50 Ma after they began evolving their own roots), plants spread across the world and evolved larger and more complex forms than ever before. This spread decreased the amount of CO² in the atmosphere by about 90%, leading to a period of global cooling.
Experiments show that varying the fungal associate of various plants (e.g. strawberries) affects a wide range of the plant’s characteristics, from taste to attractiveness. What is the import of this finding? Varying other environmental variables — sunlight, water, soil organisms, nutrients, etc — would presumably also lead to such differences.
There is a lot of anthropomorphic language used in describing fungal-plant associations — trading, managing, negotiating. I don’t care for this. Later, perplexity is expressed because plant-fungal associations don’t always appear to follow “rational” strategies.
“Almost all plants depend on fungi…” — really? Does this mean they can’t survive without them? I’m skeptical.

C6: Wood Wide Webs

Wednesday, 16 November 2022

Question: If mycelial networks are such a boon to plants and made it possible for them to colonize the land, why did plants evolve their own roots within 50 Ma?

C7: Radical Mycology

For Friday, 25 November 2022

In the Carboniferous (360 – 290 Ma), wood-producing plants spread across the world and drew so much CO₂ out of the atmosphere that it led to global cooling and an accompanying extinction. It is claimed that this material did not decompose because lignin-decomposing organisms had not evolved. From Wikipedia: “Before the end of the Carboniferous Period, an extinction event occurred. On land this event is referred to as the Carboniferous Rainforest Collapse (CRC).[14] Vast tropical rainforests collapsed suddenly as the climate changed from hot and humid to cool and arid. This was likely caused by intense glaciation and a drop in sea levels.“
The biochemistry of wood. Cellulose, found in all plants, is composed of orderly polymerized chains of carbohydrates. Lignin is what makes wood wood; it is a disorderly matrix of molecular rings, and as such is not vulnerable to enzymes that work by locking onto particular molecular shapes. Only a few organisms have developed ways of decomposing lignin. The most orderly are the “white-rot fungi” which work by using non-shape-specific proxydases that release a flood of free radicals that chemically attach lignin’s bonds in a process known as enzymatic combustion.
Radical Mycology is the name of a book by Peter McCoy, now applied to a movement of amateur mycologists that emerged from the DIY psychedelic mushroom growing scene catalyzed by Terrance McKenna and Paul Stamets. McCoy has started an online school called Mycologos. There is an annual conference, and in 2009 someone known only as hippie3 introduced a method for fungal cultivation involving injection ports that has now become standard in the community.
Myccoremediation. Fungi can be used to detoxify polluted environments. The book provides an array of remarkable example of materials that fungi can ‘learn’ to break down, from glycophosphate to components of nerve gas.Pleurotus is mentioned in this regard. Fungi can also be used to accumulate heavy metals; a Finnish company uses a fungus to accumulate gold from electronic waste. All that said, it is one thing to make this happen in a controlled conditions of a laboratory, and another to make it happen in the wild.
Radiotrophic fungi. In the ruins of Chernobyl one can find radiotrophic fungi that live off the energy emitted by radioactive material

Radiotrophic fungi were discovered in 1991 growing inside and around the Chernobyl Nuclear Power Plant.^[3] It was specifically noted that colonies of melanin rich fungi had begun to rapidly grow within the cooling waters of the reactors within the power plant, turning them black. […] Further research conducted at the Albert Einstein College of Medicine showed that three melanin-containing fungi—Cladosporium sphaerospermum, Wangiella dermatitidis, and Cryptococcus neoformans—increased in biomass and accumulated acetate faster in an environment in which the radiation level was 500 times higher than in the normal environment. Exposure of C. neoformans cells to these radiation levels rapidly (within 20–40 minutes of exposure) altered the chemical properties of its melanin, and increased melanin-mediated rates of electron transfer (measured as reduction of ferricyanide by NADH) three- to four-fold compared with unexposed cells.[4] Similar effects on melanin electron-transport capability were observed by the authors after exposure to non-ionizing radiation, suggesting that melanotic fungi might also be able to use light or heat radiation for growth.[4]
— Wikipedia, https://en.wikipedia.org/wiki/Radiotrophic_fungus

Fungal enzymes. Enzymes, or even entire metabolic pathways, can lie dormant in fungal genomes for generations. Furthermore, many fungal enzymes are not shape-specific, and thus can be applied to multiple ends.
Macotermes termites. African termites build a “fungus comb” where they cultivate lignin digesting fungi that they feed with a chewed-slurry of wood pulp. Macrotermes build towering mounds that reach 9 meters in height, some of which are as much as 2,000 years old; they have been doing this for 20 Ma. The mounds allow the termites to cultivate the fungus, and they control the temperature, humidity and levels of O₂and CO₂ by opening and closing tunnels with a system of chimneys and galleries in the mound.
Use of Fungi to Produce Materials and Structures. The company Evocative is using fungi to produce materials that replace plastic in packaging, leather in clothing, and brick, concrete and partical board in construction. Hundreds of square feed of mycelial leather can be grown in a week from materials that would otherwise enter the waste stream. Over all, Evocative grows more than 400 tons of furniture and packaging materials every year.

C8: Making Sense of Fungi

For Friday, 25 November 2022

Yeasts are eukaryotic, single-celled microorganisms classified as members of the fungus kingdom. The first yeast originated hundreds of millions of years ago, and at least 1,500 species are currently recognized
This chapter has a lot about the history of use of yeasts in humans for fermentation, etc. He also spends a lot of time discussing cultural attitudes towards fungi.
The yellow stain mushroom can be consumed by some people, but are toxic to others.
The history of the concept of symbiosis.
The use of metaphors and analogies in discussing fungi, and more in scientific thought more generally.
ADH4. Ability to metabolize alcohol 40x more effectively appear at 10 Ma. Sheldrakes experiments with fermentation.

Epilogue: This Compost

For Friday, 25 November 2022

A lyrical end note that evokes Sheldrake’s childhood and how he learned about the decomposition of leaves, which in turn segues into thoughts about compostion and decomposition, and that into the notion of having fungi digest two copies of his book, one to produce mushrooms, and the other to produce sugars that will be fermented into beer.