(Roughly) Daily

Posts Tagged ‘Life

“Attend to mushrooms and all other things will answer up”*…

Travis Boyer: Crush Blue, 2020

The living– and conscious?– infrastructure of the biosphere…

Imagine that you are afloat on your back in the sea. You have some sense of its vast, unknowable depths—worlds of life are surely darting about beneath you. Now imagine lying in a field, or on the forest floor. The same applies, though we rarely think of it: the dirt beneath you, whether a mile or a foot deep, is teeming with more organisms than researchers can quantify. Their best guess is that there are as many as one billion microbes in a single teaspoon of soil. Plant roots plunge and swerve like superhighways with an infinite number of on-ramps. And everywhere there are probing fungi.

Fungi are classified as their own kingdom, separate from plants and animals. They are often microscopic and reside mostly out of sight—mainly underground—but as Merlin Sheldrake writes in Entangled Life: How Fungi Make Our Worlds, Change Our Minds and Shape Our Futures, they support and sustain nearly all living systems. Fungi are nature’s premiere destroyers and creators, digesting the world’s dead and leaving behind new soil. When millions of hair-like fungal threads—called hyphae—coalesce, felting themselves into complex shapes, they emerge from the ground as mushrooms. A mushroom is to a fungus as a pear is to a pear tree: the organism’s fruiting body, with spores instead of seeds. Mushrooms disperse spores by elaborate means: some species generate puffs of air to send them aloft, while others eject them by means of tiny, specialized catapults so they accelerate ten thousand times faster than a space shuttle during launch.

But Sheldrake is most interested in fungi’s other wonders—specifically, how they challenge our understanding of nonhuman intelligence and stretch the notion of biological individuality. Fungi infiltrate the roots of almost every plant, determining so much about its life that researchers are now asking whether plants can be considered plants without them. They are similarly interwoven throughout the human body, busily performing functions necessary to our health and well-being or, depending on the fungi’s species and lifestyle, wreaking havoc. All of this prompts doubts about what we thought we knew to be the boundaries between one organism and another…

ungi themselves form large networks of hyphae strands in order to feed. These strands, when massed together, are called mycelium. The total length of mycelium threaded through the globe’s uppermost four inches of soil is believed to be enough to span half the width of our galaxy. Mycelium is constantly moving, probing its surroundings in every direction and coordinating its movements over long distances. When food is found—a nice chunk of rotting wood, for example—disparate parts of the mycelium redirect to coalesce around it, excrete enzymes that digest it externally, and then absorb it. As Sheldrake puts it, “The difference between animals and fungi is simple: Animals put food in their bodies, whereas fungi put their bodies in the food.”

Fungi are literally woven into the roots and bodies of nearly every plant grown in natural conditions. “A plant’s fungal partners,” Sheldrake writes, “can have a noticeable impact on its growth.” In one striking example, he describes an experiment in which strawberries grown with different fungal partners changed their sweetness and shape. Bumblebees seemed able to discern the difference and were more attracted to the flowers of strawberry plants grown with certain fungal species. Elsewhere he discusses an experiment in which researchers took fungi that inhabited the roots of a species of coastal grass that grew readily in saltwater and added it to a dry-land grass that could not tolerate the sea. Suddenly the dry-land grass did just fine in brine.

Much has been written lately about trees communicating and sharing resources among themselves; healthy trees have been documented moving resources toward trees that have fallen ill. This is often characterized as friendship or altruism between trees, but it is not at all clear whether trees pass information or nutrients intentionally. What is clear, though, is that the fungal networks entwined in every tree root make this communication possible. “Why might it benefit a fungus to pass a warning between the multiple plants that it lives with?” Sheldrake asks. The answer is survival. “If a fungus is connected to several plants and one is attacked by aphids, the fungus will suffer as well as the plant,” he writes. “It is the fungus that stands to benefit from keeping the healthy plant alive.”…

Fungi are genetically closer to animals than to plants, and similar enough to humans at the molecular level that we benefit from many of their biochemical innovations. In fact, many of our pharmaceuticals are borrowed innovations from fungi. Penicillin, discovered in 1928 by the Scottish researcher Alexander Fleming, is a compound produced by fungus for protection against bacterial infection. The anti-cancer drug Taxol was originally isolated from the fungi that live inside yew trees. More than half of all enzymes used in industry are generated by fungi, Sheldrake notes, and 15 percent of all vaccines are produced using yeast. We are, as he puts it, “borrowing a fungal solution and rehousing it within our own bodies.”..

We know that fungi maintain “countless channels of chemical communication with other organisms,” and that they are constantly processing diverse information about their environment. Some can recognize color, thanks to receptors sensitive to blue and red light, though it is not entirely clear what they do with that information. Some even have opsins, light-detecting proteins also found within the rods and cones of the animal eye. One fungus, Phycomyces blakesleeanus, has a sensitivity to light similar to that of a human eye and can “detect light at levels as low as that provided by a single star” to help it decide where to grow. It is also able to sense the presence of nearby objects and will bend away from them before ever making contact. Still other fungi recognize texture; according to Sheldrake, the bean rust fungus has been demonstrated to detect grooves in artificial surfaces “three times shallower than the gap between the laser tracks on a CD.”

Can fungi, then, be said to have a mind of their own? That is, as Sheldrake puts it, a “question of taste”—there is no settled scientific definition for “intelligence,” not even for animals. The Latin root of the word means “to choose between,” an action fungi clearly do all the time. But the application of this kind of term to fungi is loaded with something more mystical than that simple definition and demands a willingness to rattle our sense of where we ourselves fall in the imagined hierarchy of life. If fungi can be said to think, it is a form of cognition so utterly different that we strain to see it.

After all, philosophers of mind like Daniel Dennett argue that drawing any neat line between nonhumans and humans with “real minds” is an “archaic myth.” Our brains evolved from nonmental material. “Brains are just one such network,” Sheldrake writes, “one way of processing information.” We still don’t know how the excitement of brain cells gives rise to experience. Can we really dismiss the possibility of cognition in an organism that clearly adapts, learns, and makes decisions simply based on the lack of a brain structure analogous to ours?

Perhaps there is intelligent life all around us, and our view is too human-centric to notice. Are fungi intelligent? Sheldrake reserves judgment, deferring instead to scientific mystery: “A sophisticated understanding of mycelium is yet to emerge.” Still, after spending long enough in the atmosphere of Sheldrake’s sporulating mind, I began to adopt the fungal perspective. I can’t help now but see something like a mind wherever there might be fungal threads—which is to say everywhere, a mesh-like entangled whole, all over the earth.

Fungi challenge our understanding of nonhuman intelligence and complicate the boundaries between one organism and another: “Our Silent Partners“– Zoë Schlanger (@zoeschlanger) reviewing Merlin Sheldrake’s Entangled Life: How Fungi Make Our Worlds, Change Our Minds and Shape Our Futures in @nybooks.

Why did the mushroom go to the party? Because he was a fungi.” – Lewis Tomlinson

* A. R. Ammons

###

As we ponder partnership, we might spare a thought for Jens Wilhelm August Lind; he died on this date in 1939. An apothecary, botanist and mycologist, he published a full account of all fungi collected in Denmark by his teacher, Emil Rostrup. Combining his pharmaceutical and mycological knowledge, he was early in experimenting with chemical control of plant pathogens.

Lind also collaborated with Knud Jessen on an account on the immigration history of weeds to Denmark.

Gravestone of Jens Lind and wife Gunild, at Viborg Cemetery

source

“Life’s a little weird”…

Needs must…

You may have ridden out the pandemic in compact living quarters without, say, much natural light or air conditioning. Perhaps you lived with roommates or family in an atmosphere that, as time wore on, grew increasingly toxic. 

Things could be worse! You could be a member of the Alviniconcha species—specifically, a small, spike-studded snail who thrives in an environment inhospitable to most aquatic life; mere meters from deep-sea hydrothermal vents that constantly spew toxic chemicals into the water. Think you have limited natural light? Try living nearly 10,000 feet below the surface of the ocean, where complete darkness envelops you 24 hours a day, under pressure so intense all the air pockets in your body would instantly collapse. 

And forget Seamless. Forget food—at least the kind you ingest with your mouth. Your survival hinges on bacteria living in your gills (you have gills!) in a symbiotic relationship that provides you with energy, via a process called chemosynthesis. It’s like photosynthesis, but chemosynthesis is driven by chemical reactions instead of light. As there’s no sunlight and minimal oxygen present, the bacteria that dwell within Alviniconcha use hydrogen and sulfur molecules to produce sugars and other macronutrients that the animals then use as food. “There’s very little food so deep in the ocean,” says Dr. Corinna Breusing, postdoctoral researcher at the University of Rhode Island and co-author of a recent paper on the snails and their symbionts. “Having your own food-producing machine is much better than waiting for it to fall to you.” While chemosynthesis is common around hydrothermal vents, it can occur in places outside of vents, such as in cold seeps and whale falls and even salt marshes: anyplace the proper mélange of inorganic compounds is brewing. 

The researchers studied Alviniconcha living at the bottom of the Lau Basin, in the southwestern Pacific Ocean, and found that the type of bacterial symbiont determined where their particular host species could live. “The symbionts have different metabolic capacities and adaptations, so we think that the symbionts influence the distribution of the animal,” Breusing says, adding that snails with Campylobacteria dominated at vents with higher concentrations of sulfide and hydrogen, while those with Gammaproteobacteria were able to thrive at sites with lower concentrations of sulfide and hydrogen. Meaning: your chef-roommate, who happens to live in your respiratory system, also decides where you hang your hat (so to speak).

Most hydrothermal vent-dwelling animals, such the aforementioned snails and deep-sea anemones, as well as some species of mussels and tube worms, depend on bacteria that they pick up from the environment, but there is a species of deep-sea clam that passes their symbiont down from mother to offspring, like a fancy set of dinner plates. (This is rare in the marine world, Breusing says.) In the case of the deep-sea clams, where the symbiont is inherited, the symbiont cannot thrive outside the host and dies with it. But if a symbiont is taken up from the environment, it can be released back into the environment after its host dies, ready to help feed a brand-new host.

Alviniconcha might not pack the same visual punch as much marine life does much closer to the surface, but their very existence points to the origins of life on Earth. Before oxygen was free and plentiful, microbial life had to work with inorganic compounds like methane and ammonia, which over millennia dissolved into the seas. Much is still murky about how these little snails co-evolved with the bacteria that enable them to survive, but these fascinating ecosystems indicate that our education about life at the margins is just getting started…

Life at the Edge of Impossible“: ten thousand feet under the sea, these snails thrive with a little help from their friends; from Adrienne Day (@adrienneday).

* Dr. Seuss

###

As we examine extremes, we might send redefining birthday greetings to Carl Woese; he was born on this date in 1928. A microbiologist and biophysicist, he made many contributions to biology; but he is best remembered for defining the Archaea (a new domain of life).

For much of the 20th century, prokaryotes were regarded as a single group of organisms and classified based on their biochemistry, morphology and metabolism. In a highly influential 1962 paper, Roger Stanier and C. B. van Niel first established the division of cellular organization into prokaryotes and eukaryotes, defining prokaryotes as those organisms lacking a cell nucleus. It became generally assumed that all life shared a common prokaryotic (implied by the Greek root πρό [pro-], before, in front of) ancestor.

But in 1977 Woese (and his colleague George E. Fox) experimentally disproved this universally held hypothesis. They discovered a kind of microbial life which they called the “archaebacteria” (Archaea), “a third kingdom” of life as distinct from bacteria as plants are from animals, Having defined Archaea as a new “urkingdom” (later domain) which were neither bacteria nor eukaryotes, Woese redrew the taxonomic tree. His three-domain system, based on phylogenetic relationships rather than obvious morphological similarities, divided life into 23 main divisions, incorporated within three domains: BacteriaArchaea, and Eucarya.

source

source

“Man tends to define in terms of the familiar. But the fundamental truths may not be familiar.”*…

Most of us probably do not need to think too hard to distinguish living things from the “non-living”. A human is alive; a rock is not. Easy!

Scientists and philosophers do not see things quite this clearly. They have spent millennia pondering what it is that makes something alive. Great minds from Aristotle to Carl Sagan have given it some thought – and they still have not come up with a definition that pleases everyone. In a very literal sense, we do not yet have a “meaning” for life.

If anything, the problem of defining life has become even more difficult over the last 100 years or so. Until the 19th Century one prevalent idea was that life is special thanks to the presence of an intangible soul or “vital spark”. This idea has now fallen out of favour in scientific circles. It has since been superseded by more scientific approaches. Nasa, for instance, has described life as “a self-sustaining chemical system capable of Darwinian evolution”.

But Nasa’s is just one of many attempts to pin down all life with a simple description. In fact, over 100 definitions of life have been proposed, with most focusing on a handful of key attributes such as replication and metabolism.

To make matters worse, different kinds of scientist have different ideas about what is truly necessary to define something as alive. While a chemist might say life boils down to certain molecules, a physicist might want to discuss thermodynamics…

A comparative survey of the definitions that currently exist concludes…

To properly define life, we might need to find some aliens.

The irony is that attempts to pin down a definition of life before we discover those aliens might actually make them more difficult to find. What a tragedy it would be if in the 2020s the new Mars rover trundles straight past a Martian, simply because it does not recognise it as being alive.

“The definition can actually hinder the search for novel life,” says [Carol] Cleland. “We need to get away from our current concept, so that we are open to discovering life as we don’t know it.”

It is surprisingly difficult to pin down the difference between living and non-living things: “There are over 100 definitions of ‘life’ and all are wrong.

* Carl Sagan

###

As we strive for beginner’s mind, we might send exploratory birthday greetings to John Theophilus Desaguliers; he was born on this date in 1683. A natural philosopher, clergyman, and engineer, he is best remembered as the experimental assistant to Isaac Newton, who went on to popularize Newton’s work in public lectures and publications. On the strength of that work, Desaguliers was elected to the Royal Society and ultimately became its curator.

In his own work he coined the terms conductor and insulator. He repeated and extended the work of Stephen Gray in electricity. He proposed a scheme for heating vessels such as salt-boilers by steam instead of fire. And he made inventions of his own (e.g., a planetarium), and material improvements to others’ machines, such as Thomas Savery’s steam engine (by adding a safety valve and using an internal water jet to condense the steam in the displacement chambers) and a ventilator at the House of Commons. 

source

Written by (Roughly) Daily

March 12, 2021 at 1:01 am

“We are what we pretend to be, so we must be careful about what we pretend to be”*…

There is just something obviously reasonable about the following notion: If all life is built from atoms that obey precise equations we know—which seems to be true—then the existence of life might just be some downstream consequence of these laws that we haven’t yet gotten around to calculating. This is essentially a physicist’s way of thinking, and to its credit, it has already done a great deal to help us understand how living things work…

But approaching the subject of life with this attitude will fail us, for at least two reasons. The first reason we might call the fallacy of reductionism. Reductionism is the presumption that any piece of the universe we might choose to study works like some specimen of antique, windup clockwork, so that it is easy (or at least eminently possible) to predict the behavior of the whole once you know the rules governing how each of its parts pushes on and moves with the others…

The second mistake in how people have viewed the boundary between life and non-life is still rampant in the present day and originates in the way we use language. A great many people imagine that if we understand physics well enough, we will eventually comprehend what life is as a physical phenomenon in the same way we now understand how and why water freezes or boils. Indeed, it often seems people expect that a good enough physical theory could become the new gold standard for saying what is alive and what is not.

However, this approach fails to acknowledge that our own role in giving names to the phenomena of the world precedes our ability to say with any clarity what it means to even call something alive. A physicist who wants to devise theories of how living things behave or emerge has to start by making intuitive choices about how to translate the characteristics of the examples of life we know into a physical language. After one has done so, it quickly becomes clear that the boundary between what is alive and what is not is something that already got drawn at the outset, through a different way of talking than physics provides…

Physics is an approach to science that roots itself in the measurement of particular quantities: distance, mass, duration, charge, temperature, and the like. Whether we are talking about making empirical observations or developing theories to make predictions, the language of physics is inherently metrical and mathematical. The phenomena of physics are always expressed in terms of how one set of measurable numbers behaves when other sets of measurable numbers are held fixed or varied. This is why the genius of Newton’s Second Law, F = ma, was not merely that it proposed a successful equation relating force (F), mass (m), and acceleration (a), but rather that it realized that these were all quantities in the world that could be independently measured and compared in order to discover such a general relationship.

This is not how the science of biology works. It is true that doing excellent research in biology involves trafficking in numbers, especially these days: For example, statistical methods help one gain confidence in trends discovered through repeated observations (such as a significant but small increase in the rate of cell death when a drug is introduced). Nonetheless, there is nothing fundamentally quantitative about the scientific study of life. Instead, biology takes the categories of living and nonliving things for granted as a starting point, and then uses the scientific method to investigate what is predictable about the behavior and qualities of life. Biologists did not have to go around convincing humanity that the world actually divides into things that are alive and things that are not; instead, in much the same way that it is quite popular across the length and breadth of human language to coin terms for commonplace things like stars, rivers, and trees, the difference between being alive and not being alive gets denoted with vocabulary.

In short, biology could not have been invented without the preexisting concept of life to inspire it, and all it needed to get going was for someone to realize that there were things to be discovered by reasoning scientifically about things that were alive. This means, though, that biology most certainly is not founded on mathematics in the way that physics is. Discovering that plants need sunlight to grow, or that fish will suffocate when taken out of water, requires no quantification of anything whatsoever. Of course, we could learn more by measuring how much sunlight the plant got, or timing how long it takes for the fish-out-of-water to expire. But the basic empirical law in biological terms only concerns itself with what conditions will enable or prevent thriving, and what it means to thrive comes from our qualitative and holistic judgment of what it looks like to succeed at being alive. If we are honest with ourselves, the ability to make this judgment was not taught to us by scientists, but comes from a more common kind of knowledge: We are alive ourselves, and constantly mete out life and death to bugs and flowers in our surroundings. Science may help us to discover new ways to make things live or die, but only once we tell the scientists how to use those words. We did not know any physics when we invented the word “life,” and it would be strange if physics only now began suddenly to start dictating to us what the word means.

The origin of life can’t be explained by first principles: “Why Physics Can’t Tell Us What Life Is.”

See also this interview with Jeremy England, the author of the article linked above (and of the book from which it is excerpted): “The Physicist’s New Book of Life.”

  • Kurt Vonnegut, Mother Night

###

As we live and let live, we might spare a thought for Ernest Everett Just; he died on this date in 1941.  A pioneering biologist, academic, and science writer, he contributed mightily to the understanding of cell division, the fertilization of egg cells, experimental parthenogenesis, hydration, cell division, dehydration in living cells, and the effect of ultra violet rays on egg cells.

An African-American, he had limited academic prospects on his graduation from Dartmouth, but was able to land a teaching spot at Howard University.  Just met  Frank R. Lillie, the head of the Department of Zoology at the University of Chicago and director of the Marine Biological Laboratory (MBL) at Woods Hole, Mass.  In 1909 Lillie invited Just to spend first one, then several summers at Woods Hole, where Just pioneered the study of whole cells under normal conditions (rather than simply breaking them apart in a laboratory setting).  In 1915, Just was awarded the first Spingarn Medal, the highest honor given by the NAACP.

But outside MBL, Just experienced discrimination.  Seeking more opportunity he spent most of the 1930s in various European universities– until the outbreak of WW II hostilities caused him to return to the U.S. in late 1940.  He died of pancreatic cancer on this date the next year.

Ernest_Everett_Just

 source

Written by (Roughly) Daily

October 27, 2020 at 1:01 am

“I’m sure the universe is full of intelligent life. It’s just been too intelligent to come here.”*…

 

aliens-1024x576

 

The Fermi paradox, named for physicist Enrico Fermi, is the apparent contradiction between the lack of evidence for extraterrestrial civilizations and various high estimates for their probability (e.g., some of the optimistic estimates for the Drake equation).  Fermi wondered, “where are they?”

By way of context, Tim Urban in his wonderful Wait But Why?:

As many stars as there are in our galaxy (100 – 400 billion), there are roughly an equal number of galaxies in the observable universe—so for every star in the colossal Milky Way, there’s a whole galaxy out there. All together, that comes out to the typically quoted range of between 1022 and 1024 total stars, which means that for every grain of sand on every beach on Earth, there are 10,000 stars out there.

The science world isn’t in total agreement about what percentage of those stars are “sun-like” (similar in size, temperature, and luminosity)—opinions typically range from 5% to 20%. Going with the most conservative side of that (5%), and the lower end for the number of total stars (1022), gives us 500 quintillion, or 500 billion billion sun-like stars.

There’s also a debate over what percentage of those sun-like stars might be orbited by an Earth-like planet (one with similar temperature conditions that could have liquid water and potentially support life similar to that on Earth). Some say it’s as high as 50%, but let’s go with the more conservative 22% that came out of a recent PNAS study. That suggests that there’s a potentially-habitable Earth-like planet orbiting at least 1% of the total stars in the universe—a total of 100 billion billion Earth-like planets.

So there are 100 Earth-like planets for every grain of sand in the world. Think about that next time you’re on the beach.

Moving forward, we have no choice but to get completely speculative. Let’s imagine that after billions of years in existence, 1% of Earth-like planets develop life (if that’s true, every grain of sand would represent one planet with life on it). And imagine that on 1% of those planets, the life advances to an intelligent level like it did here on Earth. That would mean there were 10 quadrillion, or 10 million billion intelligent civilizations in the observable universe.

Moving back to just our galaxy, and doing the same math on the lowest estimate for stars in the Milky Way (100 billion), we’d estimate that there are 1 billion Earth-like planets and 100,000 intelligent civilizations in our galaxy.1

SETI (Search for Extraterrestrial Intelligence) is an organization dedicated to listening for signals from other intelligent life. If we’re right that there are 100,000 or more intelligent civilizations in our galaxy, and even a fraction of them are sending out radio waves or laser beams or other modes of attempting to contact others, shouldn’t SETI’s satellite dish array pick up all kinds of signals?

But it hasn’t. Not one. Ever…

Perhaps. as we’ve mused here at (R)D before, life is there, but we’re not seeing it because it isn’t a form of life that we recognize: c.f., “Two possibilities exist: Either we are alone in the Universe or we are not. Both are equally terrifying” and “That is a very Earthling question to ask, Mr. Pilgrim.”

But there are some who’ve refused to give up on the search for more traditionally-defined life; indeed, a new study quantifies the “fraction” (to which Urban alludes, above) of civilizations that could (should?) be communicating around our galaxy:

One of the biggest and longest-standing questions in the history of human thought is whether there are other intelligent life forms within our Universe. Obtaining good estimates of the number of possible extraterrestrial civilizations has however been very challenging.

A new study led by the University of Nottingham and published [earlier this month] in The Astrophysical Journal has taken a new approach to this problem. Using the assumption that intelligent life forms on other planets in a similar way as it does on Earth, researchers have obtained an estimate for the number of intelligent communicating civilizations within our own galaxy -the Milky Way. They calculate that there could be over 30 active communicating intelligent civilizations in our home Galaxy…

Details at (the slightly misleadingly-titled): “Research sheds new light on intelligent life existing across the galaxy.”

* Arthur C. Clarke

###

As we stay tuned, we might send far-seeing birthday greeting to Fred Hoyle; he was born on this date in 1915.  A prominent astronomer, he formulated the theory of stellar nucleosynthesis.  But he is rather better remembered for his controversial stances on other scientific matters—in particular his rejection of the “Big Bang” theory (a term he coined, derisively, in one of his immensely-popular series The Nature of the Universe on BBC radio) and his promotion of panspermia as the source of life on Earth.

220px-Fred_Hoyle source

 

Written by (Roughly) Daily

June 24, 2020 at 1:01 am

%d bloggers like this: