Posts Tagged ‘archaea’
“But somewhere, beyond space and time / Is wetter water, slimier slime”*…
Scientist’s have long marvelled at the “intelligent” accomplishments of the humble slime mold (and here). Noting that certain slime molds can make decisions, solve mazes, and remember things, Matthew Sims ponders what we can learn from the blob…
During the COVID-19 pandemic, some people took up baking, others decided to get a dog; I chose to grow and observe slime mould. The study in my partner’s flat in Edinburgh became home to two cultures of Physarum polycephalum, an acellular slime mould sometimes more casually referred to as ‘the blob’.
I began a series of experiments investigating how long it would take for two separated cell masses from the same bisected Physarum cell to stop fusing with one another upon reintroduction. Hours turned into days, and days into weeks, and, due to time constraints, the experiment eventually fizzled out around six weeks. This, however, was only the beginning. Over that following year (unbeknown to our unsuspecting neighbours), I conducted several more experiments. Although none of them were published, each inspired new philosophical questions – which to this day continue to shape my thinking. One of the core questions was: what can the behaviour of slime mould teach us about biological memory?
The differences between P polycephalum and humans may seem vast, but slime mould can reveal a remarkable amount about various aspects of how we remember. While many people might assume that our memories are primarily stored within our brains, some philosophers like myself argue that – along with some other aspects of cognition – memory can extend beyond the confines of the body to involve coupled interaction with structures in the environment. At least some of our cognitive processes, in short, loop out into our surroundings. Slime mould is an intriguing candidate to explore this idea because it doesn’t have a brain at all, yet in some cases can apparently ‘remember’ things without needing to store those associated memories within itself. In other cases, memories acquired via learning by one individual can even be acquired by a separate individual through physical contact. The behaviour of this strange form of life suggests that some of our ideas about how memories are acquired may need a rethink…
[Sims explains how slime mold “remembers”– via slime trails– and explores the questions that this raises…]
… So, what can slime mould teach us about biological memory? One lesson is that spatial memory needn’t be confined entirely within an organism (á la HEC). Moreover, what becomes memory traces when used (eg, extracellular slime) needn’t be the result of learning by the external trace-producer. Another takeaway is that, in some cases, an individual can acquire such memory without having engaged in learning itself. This raises an intriguing parallel in the human case. We do, after all, routinely read and act upon instructions, maps and manuals written by others, drawing on information acquired through their experiences, not our own. Although such externalised sources of information are typically declarative in structure – designed to represent facts explicitly – we often act upon them automatically, without needing to consciously recall or reflect on the information they convey. In this way, they guide behaviour in ways that functionally resemble non-declarative memory. While the analogy shouldn’t be pushed too far, both the human and slime mould cases illustrate how memory can become decoupled from individual learning, instead becoming accessible to others through environmental structures.
These conclusions, of course, remain contentious within traditional cognitive science and psychology where memory is often defined as the result of learning on the part of the same individual whose memory it is. Despite important concerns raised by the likes of Francis Crick in 1984, memory storage is still often attributed to synaptic plasticity – changes in strength of connection between neurons – quashing the very possibility of external memory traces. That said, some like the psychologist C Randy Gallistel – who has long argued that memory may also be stored in molecules like RNA within the brain – have remained vigilant in thinking outside the box. However, given the accumulating empirical evidence that memory-guided behaviour is exhibited in non-neuronal organisms like Physarum, then even this outside-the-box thinking remains firmly planted in traditional views about the requirements of brains for memory and the kind of strict internalism HEC suggests needn’t always be the case. Both HEC and memory without learning are not easy pills to swallow, but then again, neither is the very idea that a non-neuronal organism can learn in the first place – an idea that Physarum’sbehaviour unequivocally seems to support.
Whether it’s the subject of experiments carried out in a lab (or in a cramped study of an Edinburgh tenement flat) or it’s the subject of empirically informed, armchair philosophising, Physarum provides a valuable model organism to inspect, challenge and refine some of our most fundamental biological concepts – concepts like memory…
Fascinating: “Memories without brains,” from @philosobio.bsky.social in @aeon.co.
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As we reckon with recall, we might send microscopic birthday greetings to Carl Woese; he was born on this date in 1928. A microbiologist and biophysicist. Woese is famous for defining, in 1977, the Archaea (a new domain of life, distinct from the previously-recognized two domains of bacteria and life other than bacteria). To accomplish this feat, he pioneered phylogenetic taxonomy of 16S ribosomal RNA, a technique that has revolutionized microbiology. Microbiologist Justin Sonnenburg of Stanford said “The 1977 paper is one of the most influential in microbiology and arguably, all of biology. It ranks with the works of Watson and Crick and Darwin, providing an evolutionary framework for the incredible diversity of the microbial world.”
Woese originated the RNA world hypothesis in 1967, although not by that name. And he also speculated about an era of rapid evolution in which considerable horizontal gene transfer occurred between organisms. With regard to Woese’s work on horizontal gene transfer as a primary evolutionary process, Professor Norman R. Pace of the University of Colorado at Boulder said, “I think Woese has done more for biology writ large than any biologist in history, including Darwin… There’s a lot more to learn, and he’s been interpreting the emerging story brilliantly.”
“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
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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: Bacteria, Archaea, and Eucarya.
“Such is the essential mystery”*…
For about a billion years, life on earth was a relatively simple proposition: it was composed entirely of single-celled organisms (prokaryotes) in either the bacteria or archaea families. Then, about 2.1 billion years ago, one of those single-celled critters crawled inside another; the two merged, and a new kind of life– multi-cellular (eukaryotic) life– was born…
This inner cell—a bacterium—abandoned its free-living existence and eventually transformed into mitochondria. These internal power plants provided the host cell with a bonanza of energy, allowing it to evolve in new directions that other prokaryotes could never reach.
If this story is true, and there are still those who doubt it, then all eukaryotes—every flower and fungus, spider and sparrow, man and woman—descended from a sudden and breathtakingly improbable merger between two microbes. They were our great-great-great-great-…-great-grandparents, and by becoming one, they laid the groundwork for the life forms that seem to make our planet so special. The world as we see it (and the fact that we see it at all; eyes are a eukaryotic invention) was irrevocably changed by that fateful union—a union so unlikely that it very well might not have happened at all, leaving our world forever dominated by microbes, never to welcome sophisticated and amazing life like trees, mushrooms, caterpillars, and us.
Read the extraordinary story of how one freakish event may well account for all sophisticated life on earth in “The unique merger that made You (and Ewe, and Yew).”
* Lao Tzu
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As we fill out our family trees, we might send microscopic birthday greetings to Carl Woese; he was born on this date in 1928. A microbiologist, Woese recognized and defined (in 1977) the existence of archaea as a third domain of life, distinct from the two previously-recognized domains, bacteria and “life other than bacteria” (eukaryotes). The discovery revolutionized the understanding of the “family tree” of life. And the technique he used to make it– phylogenetic taxonomy of 16S ribosomal RNA— revolutionized the practice of microbiology.
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