Posts Tagged ‘biology’
“There are few creatures more remarkable than the lowly slime mold”*…
… nor, perhaps, more beautiful…
We’ve looked before at the at the “intelligent” accomplishments of the humble slime mold, and wondered what they might mean and what they might teach us. Photographer Barry Webb invites us to appreciate their spendor…
Blown wildly out of proportion in large format, the slime molds that British photographer Barry Webb captures seem atmospheric and sculptural. Stemonitis, for example, looks like dozens of thin pieces of wire with their ends coated in colored wax. But this fungi-like form is one of hundreds of kinds of slime mold, and it typically only reaches a height of about two centimeters at the most. Thanks to Webb’s macro photos, we glimpse a phenomenally beautiful world up-close that is otherwise virtually invisible.
Scientists have documented hundreds of these organisms, which aren’t actually related to plants, fungi, animals, or molds—despite the name. They comprise a unique group unto themselves, more closely related to amoebas. And new discoveries are being made all the time. From mottled gray bulbs that look like snow-covered trees to pink, coral-like tendrils, Webb chronicles a huge array of colors and shapes. He also consistently submits images to local and national botanical records so that researchers have access to high-resolution imagery…
“Barry Webb Documents a Marvelous, Macro Array of Colorful Slime Molds,” from @thisiscolossal.com.
More of Webb’s portraits of slime mold on his site.
* Brandon Keim (in “Complexity Theory in Icky Action: Meet the Slime Mold“)
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As we get small, we might send microscopic greetings to William Ian Beardmore (W. I. B.) Beveridge; he was born on this date in 1908. A microbiologist and veterinarian who served as director of the Institute of Animal Pathology at Cambridge, he identified the origin of the Great Influenza (the Spanish Flu pandemic, 1918-19)– a strain of swine flu.
While there is no way to know with certainty the Bard’s birth date, his baptism was recorded at Stratford-on-Avon on April 26, 1564; and three days was the then-customary wait before baptism. In any case, we do know with some certainty that Shakespeare died on this date in 1616.
“The study of taxonomy in its broadest sense is probably the oldest branch of biology or natural history as well as the basis for all the other branches, since the first step in obtaining any knowledge of things about us is to discriminate between them and to learn to recognize them”*…
The Holotypic Occlupanid Research Group (HORG) is a tongue-in-cheek non-profit organization founded in 1994 by John Daniel (a visual effects artist with a background in invertibrate zoology). It playfully researches and classifies plastic bread clips, calling them “occlupanids,” as if they were a species in a scientific taxonomy (Kingdom: Plasticae), documenting their diverse forms from around the world. They treat these common, often-ignored objects as fascinating organisms, collecting specimens and creating a taxonomy and a database of their shapes, colors, and “species”…
This site contains several years of research in the classification of occlupanids. These small objects are everywhere, dotting supermarket aisles and sidewalks with an impressive array of form and color. The Holotypic Occlupanid Research Group has taken on the mantle of classifying this most common, yet most puzzling, member of phylum Plasticae…
Occlupanids are generally found as parasitoids on bagged pastries in supermarkets, hardware stores, and other large commercial establishments. Their fascinating and complex life cycle is unfortunately severely under-researched. What is known is that they take nourishment from the plastic sacs that surround the bagged product, not the product itself, as was previously thought. Notable exceptions to this habit are those living off rubber bands and on analog watch hands.
In most species, they often situate themselves toward the center of the plastic bag, holding in the contents. This leads to speculation that the relationship may be more symbiotic than purely parasitic.
Their stunning diversity and mysterious habits have entranced many a respectable scientist into studying, collecting, and cataloging specimens late into the night.
This site contains several years of research in the classification of occlupanids. For those of you who do not consume sliced bread, occlupanids do not form an important part of your life. For the rest of the world, These small objects are everywhere, dotting supermarket aisles and sidewalks with an impressive array of form and color.
The Holotypic Occlupanid Research Group has taken on the mantle of classifying this most common, yet most puzzling, member of phylum Plasticae.
They’ve even created a handy, free print-your-own set of cut-out identifcation placards “for the excitable amateur scientists out there who want to start their own collection!”
Ready, set, browse: HORG- Holotypic Occlupanid Research Group
For more on HORG, see here and here.
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As we contemplate classification, we might send insightful birthday greetings to a man who revolutionized the understanding of the taxonomy of his field, Harold Varmus; he was born on this date in 1939. A microbiologist and medical doctor, he shared (with J. Michael Bishop) the 1989 Nobel Prize in Physiology or Medicine for discovery of the cellular origin of retroviral oncogenes— a discovery that led to great strides in the understanding, diagnosis, and treatment of a variety of cancers.
“It’s not a bug, it’s a feature”*…
Anna Marija Helt reports that, as global warming challenges tradtional agriculture, scientists are looking to “probiotics” for crops as a new green revolution in agriculture…
Potatoes contain something about which most people are entirely unaware: endophytes, which means “within plants.” Endophytes can also be found in other vegetables, fruits, and grains. In fact, all plants harbor endophytes in the form of bacteria, fungi, and other microbes.
Endophytes eat plant-derived nutrients but typically don’t cause disease. Instead, they bolster plant growth, disease resistance, antioxidant status, or tolerance to stressors such as drought, heat, and cold. Endophytes enable plants to respond quickly to such stressors by expanding their genetic repertoire, according to a review by ecologist Christine Hawkes and colleagues. To improve crop health and sustainability, Hawkes studies how plants, their fungal residents, and such stressors interact.
Given climate-related drought and temperature extremes, declining soil quality, and a decrease in arable land, endophytes, argue Pankaj Trivedi, Chakradhar Mattupalli, Kellye Eversole, and Jan E. Leach, might undergird a sustainable “green revolution” to improve agricultural productivity while lessening reliance on environmentally damaging and health-threatening agricultural chemicals. Endophytes can have an impact, says plant biotechnologist Julissa Ek-Ramos, on “climate change, recovering the soil, and having more healthy food to eat.”…
… “It’s really amazing how strongly these endophytes can combat the fungal pathogens of crops,” [microbiologist Sharon] Doty says. And she notes regarding their growth-promoting effects, “It works in maize, in rice, in tomatoes, in bell peppers, and strawberries.” Her team has also isolated endophytes from sweet potatoes that improve the rooting of poplars, a promising biofuels crop.
Endophytes confer additional traits useful for a changing planet. For example, those from geothermal habitats can confer heat tolerance, based on studies led by geneticist Regina Redman. And crop physiologist K. M. Manasa demonstrated salt-tolerance in rice plants inoculated with an endophyte from seaside plants. Rice is salt-sensitive and one of the world’s main food crops. But increasing soil salinity is impacting a fifth of farmable land globally due to climate change and human water and land use practices…
Nitrogen is often the most limiting soil nutrient for crops, something nineteenth-century farmers recognized. Agronomist and Nobel Prize nominee Johanna Döbereiner discovered nitrogen-fixing endophytes in non-legume plants in the twentieth century that, like rhizobia, might reduce the need for financially and environmentally costly synthetic fertilizers. Many of the endophytes Doty has characterized over twenty-five years fix nitrogen and promote growth in lab, greenhouse, and field trials but have a much broader host range than rhizobia, extending from farm lands to forests…
… Developing real-world endophyte applications is a complicated challenge, but a necessary one given the need for more productive and sustainable agriculture. In the meantime, skeptical farmers are getting onboard.
“There’s a lot of conversations going on between researchers and farmers,” says Friesen, to “move the needle on our understanding of these processes that are so important for soil health but also plant health and the stability and security of our food supply.”…
More at “Better Farming Through Endophytes,” from @ahelt.bsky.social in @jstordaily.bsky.social.
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As we muse on microbes, we might send healthy birthday greetings to John Boyd Orr (1st Baron Boyd-Orr); he was born on this date in 1880. A teacher, medical doctor, biologist, nutritional physiologist, politician, businessman, and farmer, he was awarded the Nobel Peace Prize in 1949 for his scientific research into nutrition and for his work as the first Director-General of the United Nations Food and Agriculture Organization.
“Smell is a potent wizard that transports you across thousands of miles and all the years you have lived”*…
The most under-rated of our senses is also the least understood. But as Yasemin Saplakoglu reports, a better understanding of human smell is emerging as scientists interrogate its fundamental elements: the odor molecules that enter your nose and the individual neurons that translate them into perception in your brain…
… Smell is deeply tied with the emotion and memory centers of our brain. Lavender perfume might evoke memories of a close friend. A waft of cheap vodka, a relic of college days, might make you grimace. The smell of a certain laundry detergent, the same one your grandparents used, might bring tears to your eyes.
Smell is also our most ancient sense, tracing back billions of years to the first chemical-sensing cells. But scientists know little about it compared to other senses — vision and hearing in particular. That’s in part because smell has not been deemed critical to our survival; humans have been wrongly considered “bad smellers” for more than a century. It’s also not easy to study.
“It’s a highly dimensional sense,” said Valentina Parma, an olfactory researcher at the Monell Chemical Senses Center in Philadelphia. “We don’t know exactly how chemicals translate to perception.” But scientists are making progress toward systematically characterizing and quantifying what it means to smell by breaking the process down to its most fundamental elements — from the odor molecules that enter your nose to the individual neurons that process them in the brain.
Several new databases, including one recently published in the journal Scientific Data, are attempting to establish a shared scientific language for the perception of molecular scents — what individual molecules “smell like” to us. And on the other end of the pathway, researchers recently published a study in Nature describing how those scent molecules are translated into a neural language that triggers emotions and memories.
Together, these efforts are painting a richer picture of our strongest memory-teleportation device. This higher-resolution look is challenging the long-held assumption that smell is our least important sense…
[Saplakoglu recounts the history of our understanding of smell; explains the current science on how millions of molecules, often in complex bouquets, enter the nose and are processed by neurons to generate a sense of smell that’s deeply emotional and personal; and explores the ways in which it’s intstrumental in attraction, survival, and memory…]
… Because our sense of smell can be largely subliminal, in surveys many people, given the choice of losing one sense, choose olfaction. But “every day, I experience people sitting in my office and talking about how they are disconnected to the world,” [Thomas] Hummel said. They can’t smell their children or spouses anymore. They cannot detect bad-smelling food or dangerous smoke. They no longer have access to certain memories.
“I know the memory is there, but I don’t have the key to open [it] anymore,” Hummel said. “Life becomes a much more insecure place without a sense of smell in many ways, but you only realize it when it’s gone.”…
Fascinating: “How Smell Guides Our Inner World,” from @yaseminsaplakoglu.bsky.social in @quantamagazine.bsky.social.
* Helen Keller
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As we get to know the nose, we might celebrate the avatar of affecting aromas: today is National Cheese Pizza Day.
“Memory resides not just in brains but in every cell”*…
As the redoubtable Claire L. Evans [and here] reports, a small but enthusiastic group of neuroscientists is exhuming overlooked experiments and performing new ones to explore whether cells record past experiences — fundamentally challenging our understanding of what memory is…
In 1983, the octogenarian geneticist Barbara McClintock stood at the lectern of the Karolinska Institute in Stockholm. She was famously publicity averse — nearly a hermit — but it’s customary for people to speak when they’re awarded a Nobel Prize, so she delivered a halting account of the experiments that had led to her discovery, in the early 1950s, of how DNA sequences can relocate across the genome. Near the end of the speech, blinking through wire-framed glasses, she changed the subject, asking: “What does a cell know of itself?”
McClintock had a reputation for eccentricity. Still, her question seemed more likely to come from a philosopher than a plant geneticist. She went on to describe lab experiments in which she had seen plant cells respond in a “thoughtful manner.” Faced with unexpected stress, they seemed to adjust in ways that were “beyond our present ability to fathom.” What does a cell know of itself? It would be the work of future biologists, she said, to find out.
Forty years later, McClintock’s question hasn’t lost its potency. Some of those future biologists are now hard at work unpacking what “knowing” might mean for a single cell, as they hunt for signs of basic cognitive phenomena — like the ability to remember and learn — in unicellular creatures and nonneural human cells alike. Science has long taken the view that a multicellular nervous system is a prerequisite for such abilities, but new research is revealing that single cells, too, keep a record of their experiences for what appear to be adaptive purposes.
In a provocative study published in Nature Communications late last year, the neuroscientist Nikolay Kukushkin and his mentor Thomas J. Carew at New York University showed that human kidney cells growing in a dish can “remember” patterns of chemical signals when they’re presented at regularly spaced intervals — a memory phenomenon common to all animals, but unseen outside the nervous system until now. Kukushkin is part of a small but enthusiastic cohort of researchers studying “aneural,” or brainless, forms of memory. What does a cell know of itself? So far, their research suggests that the answer to McClintock’s question might be: much more than you think…
[Evans explains the prevailing wisdom, outlines the experiments that have challenged it, and unpacks (at least some reasons for) resistance to the notion of cellular-scale memory, both sociological and semantic…]
… In neuroscience, [biochemist and neuroscientist Nikolay] Kukushkin writes, the most common definition of memory is that it’s what remains after experience to change future behavior. This is a behavioral definition; the only way to measure it is to observe that future behavior. Think of S. roeselii snapping back into its holdfast, or a lab rat freezing up at the sight of an electrified maze it’s tangled with before. In these cases, how an organism reacts is a clue that prior experience left a lingering trace.
But is a memory only a memory when it’s associated with an external behavior? “It seems like an arbitrary thing to decide,” Kukushkin said. “I understand why it was historically decided to be that, because [behavior] is the thing you can measure easily when you’re working with an animal. I think what happened is that behavior started as something that you could measure, and then it ended up being the definition of memory.”
Behavior tells us that a memory has formed but says nothing about why, how or where. Further, it’s constrained by scale. Take Aplysia californica, a muscular sea slug with enormous neurons (the largest is about the size of a letter on a U.S. penny). Neuroscientists love to conduct memory experiments on Aplysia because its physical responses are easy to measure — poke it and it flinches — and they map cleanly to the handful of sensory and motor neurons involved.
The sea slug, Kukushkin said, can complicate neuroscience’s behavioral bias. Say you shock its tail, triggering a defensive reflex. If you shock it again the next day and find that the defensive reflex is stronger than it was before, that’s behavioral evidence that the slug remembers its initial shock. Any neuroscientist would associate it with a memory.
But what if (apologies to the squeamish) you take that sea slug apart and leave only its immobile neurons? Unlike the intact creature, the neurons can’t retract, so there will be no visible response. Is the memory gone? Certainly not, but without external validation, a behavioral definition of memory breaks down. “We no longer call that a memory,” Kukushkin said. “We call that a mechanism for a memory, we call that synaptic change underlying memory, we call that an analogue of memory. But we don’t call that a memory, and I think that it’s arbitrary.”
Perhaps a definition of memory should extend beyond behavior to encompass more records of the past. A vaccination is a kind of memory. So is a scar, a child, a book. “If you make a footprint, it’s a memory,” Gershman said. An interpretation of memory as a physical event — as a mark made on the world, or on the self — would encompass the biochemical changes that occur within a cell. “Biological systems have evolved to harness those physical processes that retain information and use them for their own purposes,” [cognitive scientist Sam] Gershman said.
So, what does a cell know of itself? Perhaps a better version of Barbara McClintock’s question is: What can a cell remember? When it comes to survival, what a cell knows of itself isn’t as important as what it knows of the world: how it incorporates information about its experiences to determine when to bend, when to battle and when to make a break for it.
A cell preserves the information that preserves its existence. And in a sense, so do we. As today’s cellular memory researchers revisit abandoned experimental threads from the past, they too are discovering what memory owes to its context, how science’s sociological environment can determine which ideas are preserved and which are forgotten. It’s almost as though a field is waking up from a 50-year spell of amnesia. Fortunately, the memories are flooding back…
“What Can a Cell Remember?” from @theuniverse.bsky.social in @quantamagazine.bsky.social.
For more on the work that got Barbara McClintock onto the Nobel podium see here.
And, also apposite, a pair of cautionary historical examples of scientists who followed Jean-Baptiste Lamarck, who argued in the early 19th century that an organism can pass on to its offspring physical characteristics that the parent organism acquired through use or disuse during its lifetime– that’s to say that learning (a kind of memory) is heritable… and went astray: Lysenko and Kammerer.
* James Gleick, The Information
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As we muse on memory (and note that one cannot remember– and learn from– what one cannot know), we might recall that it was on this date in 1735 that New York Weekly Journal publisher and writer John Peter Zenger was acquitted of seditious libel against the royal governor of New York, William Cosby, on the basis that what he had published was true.
In 1733, Zenger had begun printing The New York Weekly Journal, voicing opinions critical of the colonial governor. On November 17, 1734, on Cosby’s orders, the sheriff arrested Zenger. After a grand jury refused to indict him, the Attorney General Richard Bradley charged him with libel. Zenger’s lawyers, Andrew Hamilton and William Smith, Sr., successfully argued that truth is a defense against charges of libel… and Zenger became a symbol for freedom of the press.
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