Posts Tagged ‘biology’
“This was not that the subject was simple enough to be explained without mathematics, but rather that it was much too involved to be fully accessible to mathematics.”*…
The idea of ‘biological agency’ — that life devises its own goals and behaves accordingly — complicates our understanding of what it means to be alive. But, Philip Ball asks, does it serve a scientific purpose?…
In 1993, a team led by the planetary scientist Carl Sagan tentatively concluded that there is life on Earth. Not much of a deduction, you might think — except that the researchers confined their evidence to observations made by the Galileo spacecraft, which had flown past our planet three years earlier on a looping journey to Jupiter. So great is the transformative power of life that its presence can be detected just from the light and radio waves our planet emits or reflects into space. Today we scan the cosmos for some of these telltale signatures light-years away.
Life leaves a mark, yet even now there’s no scientific consensus about what makes living things so different from inorganic substances like the rocks, gases, and oceans that are the sole components of dead worlds. Many scientists cite properties such as replication or metabolism. Others speak in more abstract terms about the way life is out of thermodynamic equilibrium with its surroundings. But some give another kind of answer. Living organisms are different because they do stuff for reasons.
It’s not enough to say that life is a nonequilibrium organized state through which there’s a constant flux of matter and energy. That description applies to hurricanes, too. But hurricanes just are. Only living entities have goals: to find food, to reproduce, to survive, sometimes simply to experience good things. (Dog owners will recognize that this is not just a human attribute.)
One way to express this idea is to say that living organisms have “agency.” It’s a hotly contested term. Some biologists reject it outright, at least for any organisms except humans, because we decide on our actions with conscious deliberation. (Whether we’re truly the only species to do so is another issue.) Others think that agency is a fundamental attribute of all life. Since there’s no agreed-upon definition of the term, to some extent it can mean whatever you want it to mean. But the debate about biological agency touches on fundamental issues in our understanding of what it means to be alive, because agency evokes a notion that biologists and philosophers have always wrestled with: teleology, the apparent purposiveness of life. If we admit agency into biology, do we open the floodgates to ideas about design, vitalism, or cosmic meaning? Or is it just a recognition of what makes life such a special state of matter?
To me, the notion of agency indeed speaks to our intuitive sense of what makes living things so special: not mere machines pushed around by environment and circumstance. I suspect that aversion to agency betrays a queasiness about confronting life as something more than some kind of genetic program. But there’s danger in the idea, too: It could so easily derail the work of studying the mechanistic explanations of how life works. I’m not looking to either bury or praise agency, but to explore whether it can be a scientifically productive idea…
[Ball unpacks the idea of agency, then reviews both scientific observations and the theories that they have provoked. He concludes…]
… I’m cautiously optimistic about the prospects of uniting such theoretical ideas with biological mechanisms. It seems unlikely to be coincidental, for example, that organisms that seem to show more agency also have molecular pathways that permit more openness to the influence of context and external information.
If we can get a clearer idea of what makes an agent, this could help us to understand how collective goals arise — as they did when multicellular organisms first arose long ago — and how they can break down, as in cancer. What’s more, a proper theory of agency might give us a clearer idea of what’s needed to make genuine artificial agents, not just computers and machines programmed with our own goals, but ones that can formulate their own. We might then also get a clearer idea of the potential benefits and dangers such truly agential machines might bring. But perhaps the most compelling argument for recognizing agency is that it might help us understand what makes life so different — not just humans, but life — that it is able to shape an entire planet in a manner visible from outer space.
Purpose? Goals? On the idea of “biological agency”: “Is Life Just Different?” from @philipcball.bsky.social in @quantamagazine.bsky.social.
* Erwin Schrödinger in What Is Life? (in which he wrestled, in his way, with Ball’s question, contending that life feeds on negative entropy) Full text here.
###
As we wonder why, we might send frustrated birthday greetings to Ernő Rubik; he was born on this date in 1944. An architect and inventor, he created the Rubik’s Cube (in 1974), which has become the world’s best-selling puzzle game, with over half a billion sold.
A Rubik’s Cube consists of 26 small cubes that rotate on a central axis; nine colored cube faces, in three rows of three each, form each side of the cube. After the cube arrangement is randomized (the highest level of entropy), the player must restore order (that’s to say, practice “negative entropy”), returning it to the original condition of faces with matching colors on each side — which is one among 43 quintillion possible configurations.
“I thought a forest was made up entirely of trees, but now I know that the foundation lies below ground, in the fungi.”*…
As Frank Landymore explains, we’ve been underestimating fungi…
Scientists have mapped the Earth’s entire underground fungal network, showing that it’s so extensive that if it were stretched into a straight line, it would reach other star systems — and span a sizable chunk of the Milky Way galaxy, for that matter.
The groundbreaking work, published in a study in the journal Science, focused on microorganisms known as arbuscular mycorrhizal fungi. Forming the hidden backbone of our planet’s soil, they circulate water and nutrients and regulate the climate by locking away vast stores of carbon.
Altogether, the global fungal network weighs around 300 megatons, the study found, which is four to six times more than the biomass of all human beings. Around 40 percent of that fungal mass resides in high-altitude or flooded grasslands, like the Everglades in Florida.
The authors hope that their work will highlight the indispensable but overlooked role that these fungal networks play in the Earth’s ecosystems, with around 70 percent of all ground-based plant life depending on the fungi.
“People just aren’t paying attention to these ecosystems,” coauthor Toby Kiers, an evolutionary biologist at Vrije University Amsterdam and director of the Society for the Protection of Underground Networks (SPUN), told The New York Times. “What we want to do with these data is really shine a light on some of these hidden patterns underground.”
“I hope this builds into the conversation for their protection because wild grasslands are going away quite quickly,” lead author Justin Stewart, a fellow SPUN biologist, told Live Science. “These are areas that people are really ripping up because it’s much easier to rip up a grass than it is to rip up a tree.”
To unearth this subterranean network, the researchers used data from over 16,000 soil samples across 300 previous papers that calculated the local density of fungal filaments, or hyphae, across the globe. They then fed this data into a machine learning model to predict the density of these hyphal networks per square kilometer of topsoil.
The results were staggering. In all, the model found that the planet is lined with more than 110 quadrillion kilometers of hyphae, or 68 quadrillion miles, which is almost a billion times the distance between the Earth and the Sun. On a cosmic ruler, that equals nearly 12,000 light years, or about a tenth the diameter of our galaxy, which is enough to take you to the Westlund 1 super star cluster.
It’s the clearest picture yet of just how much fungal networks underpin our terrestrial ecosystems. What’s fuzzier from the model, though, is what it says about their health. The density of the fungal networks were lower in soil used for growing crops, but “we don’t know where networks are very healthy and where they’re threatened,” Kiers told the NYT…
“Earth’s Underground Fungus Network Is So Gigantic That If You Stretched It Out, It Would Reach to Other Star Systems,” from @futurism.com.
###
As we muse on the mycorrhizal, we might ponder a different kind of massive spread, as we recall that it was on this date in 1937 that Hormel introduced Spam. It was the company’s attempt to increase sales of pork shoulder, not at the time a very popular cut. While there are numerous speculations as to the “meaning of the name” (from a contraction of “spiced ham” to “Scientifically Processed Animal Matter”), its true genesis is known to only a small circle of former Hormel Foods executives.
As a result of the difficulty of delivering fresh meat to the front during World War II, Spam became a ubiquitous part of the U.S. soldier’s diet. It became variously referred to as “ham that didn’t pass its physical,” “meatloaf without basic training,” and “Special Army Meat.” Over 150 million pounds of Spam were purchased by the military before the war’s end. Indeed, Nikita Khrushchev said that without Spam, the Soviet Army would have starved. And Spam was not only eaten but was also incorporated into many other aspects of the war (e.g., grease for guns, cans for scrap metal).
During the war and the occupations that followed, Spam was introduced into Japan, Korea, Guam, Hawaii, Okinawa, the Philippines, and other islands in the Pacific. Immediately absorbed into native diets, it has become a singular part of the history and effect of U.S. influence in the Pacific region.
Today Spam is regualrly eaten in 50 countries around the world. According to the Spam website, there are 12.8 cans of Spam products consumed every second; over nine billion cans of Spam have been sold (so far). Big Ben is 1,163 Spam cans tall, and it would take 415,469,599 cans of the stuff to circle the circumference of the Earth. Need to know more? There is a museum devoted to anything and everything related to the Spam brand in Austin, MN.
Contrary to rumor, Spam is only made from six ingredients: pork with ham, salt, water, potato starch, sugar, and sodium nitrite.
“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“)
###
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.
###
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.
###
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.
You must be logged in to post a comment.