Posts Tagged ‘slime mold’
“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.”
“Nature is full for us of seeming inconsistencies and glad surprises”*…
George Musser talks with biologist Michael Levin about his practice of uncovering the incredible, latent abilities of living things…
Michael Levin, a developmental biologist at Tufts University, has a knack for taking an unassuming organism and showing it’s capable of the darnedest things. He and his team once extracted skin cells from a frog embryo and cultivated them on their own. With no other cell types around, they were not “bullied,” as he put it, into forming skin tissue. Instead, they reassembled into a new organism of sorts, a “xenobot,” a coinage based on the Latin name of the frog species, Xenopus laevis. It zipped around like a paramecium in pond water. Sometimes it swept up loose skin cells and piled them until they formed their own xenobot—a type of self-replication. For Levin, it demonstrated how all living things have latent abilities. Having evolved to do one thing, they might do something completely different under the right circumstances.
Not long ago I met Levin at a workshop on science, technology, and Buddhism in Kathmandu. He hates flying but said this event was worth it. Even without the backdrop of the Himalayas, his scientific talk was one of the most captivating I’ve ever heard. Every slide introduced some bizarre new experiment. Butterflies retain memories from when they were caterpillars, even though their brains turned to mush in the chrysalis. Cut off the head and tail of a planarian, or flatworm, and it can grow two new heads; if you amputate again, the worm will regrow both heads. Levin argues the worm stores the new shape in its body as an electrical pattern. In fact, he thinks electrical signaling is pervasive in nature; it is not limited to neurons. Recently, Levin and colleagues found that some diseases might be cured by retraining the gene and protein networks as one might train a neural network. But when I sat down to talk to the audacious biologist on the hotel patio, I mostly wanted to hear about slime mold…
Read on for a fascinating conversation: “The Biologist Blowing Our Minds,” @drmichaellevin and @gmusser in @NautilusMag.
* Margaret E. Barber
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As we’re amazed, we might send tidy birthday greetings to Irwin Rose; he was born on this date in 1926. A biologist and biochemist, he shared the 2004 Nobel Prize in Chemistry for the discovery of ubiquitin-mediated protein degradation.
Ubiquitin is a small protein molecule that attaches to other proteins, tagging them for removal, which are thus recognized by the cell’s proteasomes. These structures are the cell’s waste-disposal units, allowing the proteins to be broken down into tiny pieces for reuse; this ubiquitin-mediated process cleans up unwanted proteins resulting during cell division, and performs quality control on newly synthesized proteins… which matters, as faulty protein-breakdown processes lead to such conditions as cystic fibrosis, several neurodegenerative diseases, and certain types of cancer.
“Nothing from nothing ever yet was born”*…
Lacy M. Johnson argues that there is no hierarchy in the web of life…
… Humans have been lumbering around the planet for only a half million years, the only species young and arrogant enough to name ourselves sapiens in genus Homo. We share a common ancestor with gorillas and whales and sea squirts, marine invertebrates that swim freely in their larval phase before attaching to rocks or shells and later eating their own brain. The kingdom Animalia, in which we reside, is an offshoot of the domain Eukarya, which includes every life-form on Earth with a nucleus—humans and sea squirts, fungi, plants, and slime molds that are ancient by comparison with us—and all these relations occupy the slenderest tendril of a vast and astonishing web that pulsates all around us and beyond our comprehension.
The most recent taxonomies—those based on genetic evidence that evolution is not a single lineage, but multiple lineages, not a branch that culminates in a species at its distant tip, but a network of convergences—have moved away from their histories as trees and chains and ladders. Instead, they now look more like sprawling, networked webs that trace the many points of relation back to ever more ancient origins, beyond our knowledge or capacity for knowing, in pursuit of the “universal ancestors,” life-forms that came before metabolism, before self-replication—the several-billion-year-old plasmodial blobs from which all life on Earth evolved. We haven’t found evidence for them yet, but we know what we’re looking for: they would be simple, small, and strange.
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Slime molds can enter stasis at any stage in their life cycle—as an amoeba, as a plasmodium, as a spore— whenever their environment or the climate does not suit their preferences or needs. The only other species who have this ability are the so-called “living fossils” such as tardigrades and Notostraca (commonly known as water bears and tadpole shrimp, respectively). The ability to become dormant until conditions are more favorable for life might be one of the reasons slime mold has survived as long as it has, through dozens of geologic periods, countless ice ages, and the extinction events that have repeatedly wiped out nearly all life on Earth.
Slime mold might not have evolved much in the past two billion years, but it has learned a few things during that time. In laboratory environments, researchers have cut Physarum polycephalum into pieces and found that it can fuse back together within two minutes. Or, each piece can go off and live separate lives, learn new things, and return later to fuse together, and in the fusing, each individual can teach the other what it knows, and can learn from it in return.
Though, in truth, “individual” is not the right word to use here, because “individuality”—a concept so central to so many humans’ identities—doesn’t apply to the slime mold worldview. A single cell might look to us like a coherent whole, but that cell can divide itself into countless spores, creating countless possible cycles of amoeba to plasmodium to aethalia, which in turn will divide and repeat the cycle again. It can choose to “fruit” or not, to reproduce sexually or asexually or not at all, challenging every traditional concept of “species,” the most basic and fundamental unit of our flawed and imprecise understanding of the biological world. As a consequence, we have no way of knowing whether slime molds, as a broad class of beings, are stable or whether climate change threatens their survival, as it does our own. Without a way to count their population as a species, we can’t measure whether they are endangered or thriving. Should individuals that produce similar fruiting bodies be considered a species? What if two separate slime molds do not mate but share genetic material? The very idea of separateness seems antithetical to slime mold existence. It has so much to teach us…
More at: “What Slime Knows,” from @lacymjohnson in @Orion_Magazine.
See also, “Slime Molds Remember — but Do They Learn?” (from whence the image above) and “Now, in addition to penicillin, we can credit mold with elegant design.”
* Lucretius, On the Nature of Things
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As we contemplate kinship, we might send insightful birthday greetings to Johann Hedwig; he was born on this date in 1730. A botanist noted for his study of mosses, he is considered “the father of bryology” (the study of mosses… cousins of mold).
Now, in addition to penicillin, we can credit mold with elegant design…
Quoting Science, Jim Nash at True/Slant reports on researchers at Hokkaido University who have used mold (Physarum polycephalum, a slime mold often found inside decaying logs) to design a transit system… and found that our fungal friends did a very good job indeed.
The Physarum polycephalum built a replica of the Tokyo train system in 26 hours that’s just about as efficient, reliable and “expensive” to run as the real thing.
Slime mold expands from “Tokyo” to connect to oat flakes representing surrounding cities
…the scientists created a map of the Tokyo metro area using oat flakes for the major cities. Then they put a gelatinous blob (technically, a plasmodium) of Physarum on “Tokyo,” and sat back to see what would happen.
Within about 12 hours, the mold had covered the area with a thin and wet veined sheath of itself. By the 26th hour, the sheath was gone, replaced by mushy tunnels connecting the flakes. The tunnels mimicked Tokyo’s transit system…
…scientists think they can take what they’ve learned about self-organization from the slime mold and apply it to the construction of communication networks and other similar systems.
The whole story is here.
As we revel in the excuse to continue to put off cleaning our refrigerators, we might recall that it was on this date in 1812 that the largest (non-subduction zone) earthquake in U.S. history was recorded. One the last in a series of roughly 1,000 tremblers to hit the New Madrid, MO area, the February 7 quake measured 8.3 on the Richter Scale; it destroyed New Madrid, and was felt as far away as New York City and Boston, Massachusetts, where church bells were made to ring. (The 1906 San Francisco Quake registered at about 7.8, and was felt over a much smaller area.)
New Madrid. MO
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