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What the Vai Script Reveals About the Evolution of Writing

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Peirs Kelly in Sapiens describes an interesting example of the evolution of a set of memes. He writes:

In a small West African village, a man named Momolu Duwalu Bukele had a compelling dream. A stranger approached him with a sacred book and then taught him how to write by tracing a stick on the ground. “Look!” said the spectral visitor. “These signs stand for sounds and meanings in your language.”

Bukele, who had never learned to read or write, found that after waking he could no longer recall the precise signs the stranger revealed to him. Even so, he gathered the male members of his family together to reverse engineer the concept of writing. Working through the day and into the following night, the men devised a system of 200 symbols, each standing for a word or a syllable of their native Vai language. For millennia, varieties of the Vai language had been passed down from parents to children—but before this moment no speaker had ever recorded a single word in writing.

This took place in about 1833 in a region that would soon become the independent nation of Liberia. Vai, one of about 30 Indigenous languages of Liberia, has nearly 200,000 speakers today in the Cape Mount region that borders Sierra Leone.

Within just a few generations, Bukele’s invention was being used for penning letters, engraving jewelry, drafting carpentry plans, keeping personal diaries, and managing accounts. Vai people manufactured their own ink from crushed berries and even built schools for teaching the new system. The script was so successful that other Indigenous groups in the region were inspired to create their own; since the 1830s, at least 27 new scripts have been invented for West African languages.

Today the Vai writing system is taught at the University of Liberia and is even popular among students who are not themselves ethnically Vai. The Vai script has been included in the Unicode Standard, which means Vai speakers with smartphones can now exchange text messages in the script.


As a linguistic anthropologist, I am fascinated by the Vai discovery—and especially how the script has become critical for understanding the evolution of writing itself.

It’s not the first time in recent history that a new writing system has been invented from scratch. In the 1820s, the nonliterate polymath Sequoyah created a special script for his native Cherokee language, and similar Indigenous inventions have emerged elsewhere in the world on the margins of expanding colonies. But the evolution of Vai has been especially well-documented, making it a useful case study for researchers of writing.

In a recently published paper, my colleagues and I show that over the past two centuries the letter shapes in the Vai script have evolved via “compression”—a process by which written signs are gradually reproduced with less visual detail while conveying the same amount of linguistic information.

The theory that written signs compress over time has a long history with several versions. For instance,

Continue reading.

Written by Leisureguy

20 May 2022 at 8:21 pm

The web of life

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Ernst Haeckel’s illustration of the Tree of Life in The Evolution of Man (1879). Courtesy the Wellcome Collection

Juli Berwald, an ocean scientist and science writer whose work has been published in The Guardian, National Geographic and Nature, among others, and author of Spineless (2017) and Life on the Rocks (2022), writes in Aeon:

Iremember standing at the front of a biology classroom at the University of Southern California sometime in the 1990s and placing an acetate film on an overhead projector. The words cast onto the white screen read something like:

Species: a group of organisms that interbreed to produce fertile offspring.

More than a century earlier, Charles Darwin’s On the Origin of Species (1859) was published. Its central hypothesis held that, because populations contain variety, some members were born with characteristics, or adaptations, that made them more fit – better able to produce offspring. Others were less fit and they, along with their adaptations, were winnowed away as they added fewer and fewer offspring to future generations. This variation coupled with the winnowing was the fuel that drove changes in populations, eventually leading to populations that could no longer interbreed with each other and produce fertile offspring. Thus, new species evolved.

Darwin’s revolutionary idea was well summarised by the German biologist and artist Ernst Haeckel in the graphic form of a tree. Every one of its twig-tips symbolised a different species. The crook between two twigs represented an ancestral species that diverged into two (or more) modern ones. While many branches were pruned away, others grew ever longer, diverging into the future.

In that southern California classroom, I told my students that once a species diverged from its ancestor – when it became unable to interbreed and form fertile offspring – those branches were separate, forever isolated. But, even as I spoke the words, I knew something wasn’t exactly right.

I was studying phytoplankton at the time. Single-celled creatures such as phytoplankton reproduce by cell division, which makes the question of what’s an offspring tricky. When you clone yourself, which one is the ancestor?

Graduate students down the hall in a microbiology lab regularly used viruses to transfer genes from one species to another. And gene shuffling wasn’t just happening by manipulation. I’d heard seminars about how different species of bacteria naturally perform a kind of sexual reproduction called conjugation, transferring genes from one to another. How did that kind of gene-hopping fit into the concept of a branching tree?

What I didn’t know then was that, even as I ambivalently placed the overhead film on the projector, the concept of the tree of life had begun to wilt. Four decades on, it’s morphed entirely.

‘That whole abstraction of evolution as being a tree, we always knew was a little inadequate,’ Rasmus Nielsen, a geneticist at the University of California at Berkeley and co-author of the book An Introduction to Population Genetics (2013), told me by video call. ‘But now we know it’s really inadequate.’

After I finished graduate school, I fell off the academic path and became a science writer. Three years ago, I started writing a book about the future of corals and discovered the research of the Australian scientist John E N Veron. Veron, nicknamed ‘Charlie’ after Darwin by a gradeschool teacher who noted his predilection for nature, is an icon of the field of coral taxonomy, the science of identifying and describing species. Reading his definitive work Corals of the World (2000), co-authored with Mary Stafford-Smith, my questions about evolutionary-tree inadequacies came flooding back.

In 1972, Veron was the first full-time researcher on the Great Barrier Reef off the northeast coast of Australia, and two years later he earned the distinction of being the first full-time employee of the Australian Institute of Marine Science (AIMS). Veron had completed his doctorate, with award-winning work on colour change in insects, but he knew almost nothing about coral. Yet, he set out to tackle the project that AIMS hired him to do: describe all the corals of the Great Barrier Reef.

The Great Barrier Reef is the most massive biologically built structure on our planet. Composed of around 3,000 smaller reefs, it covers an area greater than Italy. Cataloguing its species was no less monumental. It took nearly a decade of diving, visiting museums across Europe, and studying the work of others for Veron to inventory the more than 400 coral species of the Great Barrier Reef.

Then Veron visited the other side of Australia. There, on Ningaloo Reef, the corals he saw seemed more or less identifiable at first. But, as he looked at them longer, he wasn’t so sure.

‘Eight years on the Great Barrier Reef, and I knew all the species at a glance,’ Veron told me when we talked by Zoom. ‘When I was on the Great Barrier Reef, X and Y are two distinct species. But when I went to western Australia, I found a species that combined the characters of X and Y.’

It would be like . . .

Continue reading.

Later in the article:

Does data support the hypothesis that species don’t just separate, they also merge? The answer is a resounding yes.

‘It’s not just rare freaks or accidents, it’s happening all the time. And in quite divergent species too,’ said Nielsen. Roving genes have been found in every branch of the tree of life where geneticists have looked. Today, the technical terms for the process of genes moving between populations are introgression or admixture.

Introgression occurs in plants such as maize and tomatoes. In mosquitoes, the entire genome except for the X chromosome can be swapped with other species. In a tropical genus of butterfly called Heliconius, gene jumping has been found to cause critical changes in the patterns of their colourful wings. Introgression has been documented in finches, in frogs, in rabbits, in wolves and coyotes, in swine, in yaks and cows, in brown bears and polar bears. And in us.

Nielsen and his colleagues found that Tibetans (and a few Han Chinese) carry a very beneficial gene called EPAS1. The protein EPAS1 gives a boost to haemoglobin, the molecule that ferries oxygen in our blood. EPAS1 makes high-altitude living easier. In 2014, the researchers discovered that the EPAS1 gene was also in the DNA of an extinct group of humans called Denisovans, known from bone fragments in Siberia and Tibet.

The prevailing hypothesis is this: ancient humans left Africa moving northward along temperate plains. When they encountered the Himalayas and their cold, high altitudes, it literally took their breath away. Those oxygen-poor conditions should have kept humans near the base of the mountains. But the ancient humans also encountered Denisovans and interbred with them, receiving the EPAS1 gene. Only those humans with the EPAS1 gene moved up the mountains, and their offspring also carried the EPAS1 gene, giving the ancestors of today’s Tibetans a critical advantage at higher altitudes.

‘I think that process of splitting up and merging back together again, and getting a bit of DNA from here to there, that’s happening all the time, in all of the tree of life,’ Nielsen said. ‘And it’s really changing how we’re thinking about it, that it really is a network of life, not a tree of life.’ . . .

John Veron’s hypothesis of reticulate evolution from Corals in Space and Time (1995). Courtesy John E N Veron

Written by Leisureguy

18 April 2022 at 1:45 pm

Posted in Evolution, Science

What Does the End of Beef Mean for Our Sense of Self?

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An article by Ligaya Mishan (with photographs by Kyoko Hamada) in the NY Times Magazine discusses the on-going evolution of our dietary preferences. (Gift link: no paywall) The article begins:

MEAT IS PRIMAL, or so some of us think: that humans have always eaten it; that it is the anchor of a meal, the central dish around which other foods revolve, like courtiers around a king; that only outliers have ever refused it. But today, those imagined outliers are multiplying. The United Nations Food and Agriculture Organization reports that the consumption of beef per capita worldwide has declined for 15 years. Nearly a fourth of Americans claimed to have eaten less meat in 2019, according to a Gallup poll. The recipe site Epicurious, which reaches an audience of 10 million, phased out beef as an ingredient in new recipes in 2020. Diners at some McDonald’s can now sate their lust for a Quarter Pounder with a vegan McPlant instead. Faux meat products are projected to reach $85 billion in sales by 2030, according to a recent study by UBS, and Tyson Foods, one of the biggest beef packers in the United States, has hedged its bets by introducing its own plant-based line.

Even in the stratosphere of the world’s most expensive restaurants, where multiple-course tasting menus often rely on the opulence of a marbled steak as their denouement, a few notable exceptions have abandoned meat within the past year, including the $440-per-person Geranium in Copenhagen (still serving seafood) and the $335-per-person Eleven Madison Park in Manhattan (save for the puzzling persistence of a tenderloin on its private dining room menu through this past December). Could this be the beginning of the end of meat — or at least red meat, with its aura of dominion and glory?

Those who believe humans are born carnivores might scoff. Indeed, archaeological evidence shows that we have been carnivores for longer than we have been fully human. As the French Polish Canadian science journalist Marta Zaraska recounts in “Meathooked” (2016), two million years ago, early hominids in the African savanna were regularly butchering whatever animals they could scavenge, from hedgehogs and warthogs to giraffes, rhinos and now-extinct elephant-anteater beasts.

Yet it wasn’t necessarily human nature to do so. Meat eating was an adaptation, since, as Zaraska points out, we lack the great yawning jaws and bladelike teeth that enable true predators to kill with a bite and then tear raw flesh straight off the bone. To get at that flesh, we had to learn to make weapons and tools, which required using our brains. These in turn grew, a development that some scientists attribute to the influx of calories from animal protein, suggesting that we are who we are — the cunning, cognitively complex humans of today, with our bounty of tens of billions of cortical neurons — because we eat meat. But others credit the discovery of fire and the introduction of cooking, which made it easier and quicker for us to digest meat and plants alike and thus allowed the gastrointestinal tract to shrink, freeing up energy to fuel a bigger brain.

Whatever the cause of our heightened mental prowess, we continued eating meat and getting smarter, more adept with tools and better able to keep ourselves alive. Then, around 12,000 years ago, our hunter-gatherer ancestors started to herd animals, tend crops and build permanent settlements, or else were displaced by humans who did. Our diet changed. If we narrow our purview to more recent history, from the advent of what we call civilization in the fourth millennium B.C., the narrative of meat eating shifts.

“For nearly all of humanity’s existence, meat was not a central component of people’s diets,” the American historian Wilson J. Warren writes in “Meat Makes People Powerful” (2018). Far from being essential, for most people around the world, meat has been only occasional, even incidental, to the way we eat: craved and celebrated in certain cultures to be sure, showcased at feasts, but not counted on for daily nourishment. This was true outside of the West well into the 20th century, but even in Europe before the 19th century, the average person subsisted on grains (cakes, ale) that made up close to 80 percent of the diet. The Old English “mete” was just a general word for food.

The rich were different, of course, with the resources to dine as they pleased. And not just royals and aristocrats: In 18th-century England, as incomes rose, an ambitious middle class began to claim some of the same privileges as their supposed betters. The Finnish naturalist Pehr Kalm, in a 1748 account of a visit to London, reports, “I do not believe that any Englishman who is his own master has ever eaten a dinner without meat.” The caveat was key. Those not so fortunate as to control their own lives had to make do, as the British poor had done for centuries, with mostly gruel, perhaps enlivened by vegetables, although these were perceived, the late British urban historian Derek Keene has written, “as melancholic and terrestrial and in need of elevation by the addition of butter or oil.”

So meat was both sustenance and symbol. To eat it was to announce one’s mastery of the world. No wonder, then, that the citizens of a newborn nation, one that imagined itself fashioned on freedom and the rejection of Old World hierarchies, should embrace it. “Americans would become the world’s great meat eaters,” the former Librarian of Congress Daniel J. Boorstin writes in “The Americans: The Democratic Experience” (1973). And the meat that would come to define Americans was beef: a slab of it, dark striped from the grill but still red at the heart, lush and bleeding, leaking life. . .

Continue reading. (Gift link = no paywall)

Update: The end of beef might come suddenly for those are bitten by a lone-star tick.

Written by Leisureguy

6 March 2022 at 5:43 am

What animals are thinking and feeling, and why it should matter

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Written by Leisureguy

23 February 2022 at 11:13 am

What are animals thinking and feeling?

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Written by Leisureguy

22 February 2022 at 12:10 pm

Genetically engineered immune cells have kept two people cancer-free for a decade

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A decade after two blood cancer patients received a novel type of immunotherapy involving immune cells called T-cells that had been genetically engineered, the cells are still in the people’s bodies and their cancer is still in remission. A T-cell (orange) is shown attacking a cancer cell (blue) in this illustration.ROGER HARRIS/SCIENCE PHOTO LIBRARY/GETTY IMAGES PLUS

A common characteristic of tools is that they are ethically neutral and can be used for good or for evil. Take knives: I would not be without my knives, given how frequently I chop, slice, peel, and dice vegetables, but then I read about a stabbing, in which a knife is used for evil.

So also with genetic engineering: using genetic engineering to enable rice to store beta-carotene (“golden rice”) will eventually be a green benefit to millions who subsist on rice and whose vision is blighted by diet deficiencies, but using genetic engineering simply to boost sales of toxic pesticides and boost corporate profits is the tool twisted to an evil end. 

In Science News, Erin Garcia de Jesús reports:

In 2010, two blood cancer patients received an experimental immunotherapy, and their cancers went into remission. Ten years later, the cancer-fighting immune cells used in the therapy were still around, a sign the treatment can be long-lasting, researchers report February 2 in Nature.

California resident Doug Olsen was one of the patients. “From a patient’s viewpoint, when you’re told you’re pretty much out of options, the important thing is always to maintain hope. And certainly, I hoped this was going to work,” Olsen said at a February 1 news briefing.

The treatment, known as CAR-T cell therapy, used the patients’ own genetically engineered immune cells to track down and kill cancerous cells (SN: 6/27/18). Based on the results, “we can now conclude that CAR-T cells can actually cure patients with leukemia,” cancer immunologist and study coauthor Carl June of the University of Pennsylvania said at the briefing.

Olsen and the other patient had chronic lymphocytic leukemia. Both responded well to initial treatment. But it was unclear how long the modified cells would stick around, preventing the cancer’s return.

Cancer doctors and researchers “don’t use words like ‘cure’ lightly or easily,” said oncologist and study coauthor David Porter of the University of Pennsylvania at the briefing. But with both patients remaining cancer-free for more than a decade, he said, the therapy has performed “beyond our wildest expectations.”

The biggest disappointment is . . .

Continue reading.

Written by Leisureguy

12 February 2022 at 1:03 pm

E.O. Wilson Saw the World in a Wholly New Way

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David Sloan Wilson, SUNY Distinguished Professor Emeritus of Biology and Anthropology at Binghamton University and president of Prosocial World, a new spinoff of The Evolution Institute, and author of Does Altruism Exist? Culture, Genes, and the Welfare of Others and This View of Life: Completing the Darwinian Revolution and Prosocial: Using Evolutionary Science to Build Productive, Equitable, and Collaborative Groups (with Paul W.B. Atkins and Steven C. Hayes) has a very interesting article in Nautilus. From the article:

. . . While Ed played a prominent role in modernizing whole organism biology, he was by no means alone. Evolutionary theory was proving its explanatory scope and many people were taking part in the effort, leading the geneticist Theodosius Dobzhansky to coin the oft-repeated phrase, “Nothing in biology makes sense except in the light of evolution.” What this meant to me as a graduate student was that I could choose any topic, begin asking intelligent questions based on evolutionary theory (often with the help of mathematical models), and then test my hypotheses on any appropriate organism. I didn’t need to become a taxonomic specialist and I could change topics at will. In short, I could become a polymath based on a theory that anyone can learn.

In Sociobiology, Ed claimed that evolutionary theory provides a single conceptual toolkit for studying the social behaviors of all creatures great and small. It combined the authority of an academic tome with the look and feel of a coffee table book, complete with over 200 illustrations by the artist Sarah Landry. Its publication was noted on the front page of The New York Times.

It was Sociobiology’s last chapter on human social behavior that landed Ed in trouble—in part for a good reason. For all its explanatory scope, the study of evolution was restricted to genetic evolution for most of the 20th century, as if the only way that offspring can resemble their parents is by sharing the same genes. This is patently false when stated directly, since it ignores the cultural transmission of traits entirely, but it essentially describes what became known as the Modern Synthesis. There was a large grain of truth to the critique that Sociobiology was genetically deterministic. On the other hand, it’s not as if the critics had a synthesis of their own to offer!

Only after the publication of Sociobiology did evolutionary thinkers begin to take cultural evolution seriously. Ed was among them with books such as On Human Nature, and others.2 Today, Darwinian evolution is widely defined as any process that combines the three ingredients of variation, selection, and replication, no matter the mechanism. This definition is true to Darwin’s thought (since he knew nothing about genes) and can accommodate a plurality of inheritance mechanisms such as epigenetics (based on changes in gene expression rather than gene frequency), forms of social learning found in many species, and forms of symbolic thought that are distinctively human.

While human cultural inheritance mechanisms evolved by genetic evolution, that doesn’t make them subordinate, as if genes—in one of Ed’s metaphors—hold cultures on a leash. On the contrary, as the faster evolutionary process, cultural evolution often takes the lead in adapting humans to their environments, with genetic evolution playing a following role (gene-culture co-evolution).

Part of the maturation of human cultural evolutionary theory is the recognition of group selection as an exceptionally strong force in human evolution—something else that Ed got right. According to Harvard evolutionary anthropologist Richard Wrangham in his book, The Goodness Paradox, naked aggression is over 100 times more frequent in a chimpanzee community than small-scale human communities. This is due largely to social-control mechanisms in human communities that suppress bullying and other forms of disruptive self-serving behaviors, so that cooperation becomes the primary social strategy (this is called a major evolutionary transition).

Nearly everything distinctive about our species is a form of cooperation, including our ability to maintain an inventory of symbols with shared meaning that is transmitted across generations. Our capacity for symbolic thought became a full-blown inheritance system that operates alongside genetic inheritance (dual inheritance theory). Cultural evolution is a multilevel process, no less than genetic evolution, and the increasing scale of cooperation over the course of human history can be seen as a process of multilevel cultural evolution. . .

Read the whole thing.

Written by Leisureguy

30 January 2022 at 2:24 pm

Newsletter Natural Selection

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Slime Mold Time Mold has a very interesting post, which begins:

Apparently, Substack wants to destroy newspapers. And maybe that would be good — maybe it would be good for journalism to be democratized, for bloggers to inherit the earth. Of course we’re bloggers and not newspapers, so maybe we’re biased.

Obviously it would be great if someone came up with a set of blogging and newsletter tools that were just amazing, that were the clear front-runner, that outperformed every other platform. We’d love it if the technical problems were all solved and we just had a perfect set of blogging tools.

But if everyone ends up on the same platform, well, that’s kind of dangerous. If one company controls the whole news & blogging industry, they can blacklist whoever they want, and can squeeze users as much as they want.

Even if you think Substack has a good track record, there’s no way they can guarantee that they won’t squeeze their writers once they control the market. Even if you trust the current management, at some point they will all retire, or all die, or the company will be bought by, and then you’re shit outta luck.

Substack just can’t make a credible commitment that makes it impossible for them to abuse their power if they get a monopoly. You have to take them at their word. But since management can change, you can’t even really do that. They just can’t bind their hands convincingly.

But there may be some very unusual business models that would fix this problem. 

On the Origin of Substacks

Imagine there’s a “Substack” company that commits itself to breaking in half every time it gets 100,000 users (or something), creating two child companies. Each company ends up with 50,000 users. All the blogs with even-numbered IDs go to Substack A, and all the blogs with odd-numbered IDs go to Substack B. The staff gets split among these two companies, and half of them move to a new office. Both companies retain the same policy of breaking in half once they hit that milestone again — an inherited, auto-trust-busting mechanism.

(Splitting into exactly two companies wouldn’t have to be a part of the commitment. They could equally choose to break up into Substack Red, Substack Blue, and Substack Yellow: Special Pikachu Edition.)

In addition, a core part of the product would be high-quality, deeply integrated tools to switch from one of these branches to another. Probably this would involve an easy way to export all your posts and a list of your subscribers to some neutral file format (maybe a folder full of markdown, css, and csv files), and to import them from the same format into a new blog. If you end up in Substack B and you want to be in Substack A instead (your favorite developer works there or something), the product would make it very easy to switch, maybe to the point of being able to switch at the push of a button.

To help with this, the third and final commitment of the company, and all child companies, would be to . . .

Continue reading. There’s much more — and no paywall. And it’s intriguing — and something a company could easily do.

What I like is that it harnesses the power of cultural evolution in a way that supports the common welfare.

Written by Leisureguy

23 January 2022 at 5:25 pm

Flying in miniature: Secrets of the featherwing beetle

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Written by Leisureguy

21 January 2022 at 7:55 pm

The Psychedelic Jelly

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This is quite cool. When I lived in Monterey, the Monterey Bay Aquarium was a great local institution, and the Monterey Bay Aquarium Research Institute (MBARI) was very active. After I moved to Pacific Grove (adjacent to Monterey, a move of about 6 blocks), I was just a block from MBARI offices.

Written by Leisureguy

13 January 2022 at 4:20 pm

‘Feeling & Knowing’ explores the origin and evolution of consciousness

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In Science News J.P. O’Malley interviews Antonio Damasio about his lates book:

Feeling & Knowing
Antonio Damasio
Pantheon, $26

Neuroscientist Antonio Damasio believes that the link between brain and body is the key to understanding consciousness. In his latest book, Feeling & Knowing: Making Minds Conscious, he explains why.

Consciousness is what gives an individual a sense of self; it helps one stay in the present, remember the past and plan for the future. Many scientists have argued that consciousness is created by vast networks of nerve cells, or neurons, in the brain. While it’s clear that the brain plays a major role in conscious experiences, it doesn’t act alone, argues Damasio, director of the University of Southern California’s Brain and Creativity Institute.

Instead, he argues, consciousness is generated by a variety of structures within an organism, some neural, some not. What’s more, feelings — mental experiences of body states — help connect the brain to the rest of the body. “The  feelings that we have of, say, hunger or thirst, or pain, or well-being, or desire, etc. — these are the foundation of our mind,” Damasio says. In his view, feelings have played a central role in the life-regulating processes of animals throughout the history of life.

In Feeling & Knowing, Damasio suggests that consciousness evolved as a way to keep essential bodily systems steady. This concept is also known as homeostasis, a self-regulating process that maintains stability amid ever-changing conditions. Consciousness emerged as an extension of homeostasis, Damasio argues, allowing for flexibility and planning in complex and unpredictable environments.

Science News spoke with Damasio about why feelings are crucial to understanding consciousness, why consciousness is not exclusive to humans and whether it’s something a computer could ever have. The following conversation has been edited for clarity and brevity.

SN: Why is understanding homeostasis so crucial to understanding consciousness?

Damasio: Homeostasis is central to the entire operation. It’s why we developed consciousness. Once we access feeling, we can then get a mental picture of how the state of life really is in our organism. So, we can get a warning that things are going wrong, and we get suffering. Or, we get a signal that things are reasonably OK, and we can afford to do other things, which is what happens with positive feelings. So I can afford to have this conversation with you because I’m not having a fever; I’m not terribly thirsty, hungry, or I’m not in pain.

SNHow do feelings help an organism manage life?

Damasio: Feelings are . . .

Continue reading.

Written by Leisureguy

6 January 2022 at 7:28 pm

Flying Fish and Aquarium Pets Yield Secrets of Evolution

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Flying fish can glide over the surface of the ocean because of adaptations in their body proportions. Surprisingly few genetic changes were needed for these adaptations.

Viviane Callier writes in Quanta:

o escape predators beneath the waves, a flying fish can shoot out of the water and glide long distances because its paired pectoral and pelvic fins, longer and more rigid than those of other fish, act as airfoils. In a quirky triumph of evolution, creatures that were once strictly aquatic transformed into temporarily airborne ones through a few modifications in body shape.

Recently, a group of researchers led by Matthew Harris of Harvard Medical School and Boston Children’s Hospital reported the genetic basis for the evolution of those unusual fins: Through an innovative combination of techniques, they discovered that changes in just two genes were sufficient to create the distinctive body shape of flying fishes. When those mutations occurred in a species of common aquarium fish, its proportions began to shift in similar ways.

“When we started out in evo-devo, there was no thinking that we would be able to make these large jumps in form with such simple rules,” Harris said. The study appeared in the November 22 issue of Current Biology.

The findings are noteworthy in part because they hint that bioelectric signals within developing tissues, not just “morphogenetic” chemical ones, can regulate the growth and shape of developing fins and possibly other structures. This study and earlier work also clearly illustrate how small genetic changes can sometimes produce big morphological changes that have important evolutionary consequences.

Much of the unfathomable diversity of animal forms in nature arises from natural selection’s tinkering with the genetic programs that control development. Tweaks to the timing and speed of tissue growth can stretch or shrink structures, or even insert and delete bones, to create novel adaptations that open new niches for species. Evo-devo, the biological study of this process, has a long history, but only relatively recently have researchers been able to start probing for the genes responsible for specific changes.

To search for the genetic basis of the flying fish’s body shape, researchers in the Harris lab began by . . .

Continue reading.

Written by Leisureguy

5 January 2022 at 6:30 pm

Posted in Evolution, Science

A big timeline of milestones in evolution and history

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Take a look at this lengthy timeline. The link takes you to the bottom, so you have to scroll a while to get to the top (or use the slider at the right). As noted:

Ages: following the big bang 13.8 billion years ago, time passed two-thirds of the way to the present before the formation of the Sun 4.57 billion years ago. Rescaled to a calendar year, starting with the big bang at 00:00:00 on 1 January, the Sun forms on 1 September, the Earth on 2 September, earliest signs of life appear on 13 September, earliest true mammals on 26 December, and humans just 2 hours before year’s end.

For a year that starts with the earliest true mammals, the dinosaurs go extinct on 17 August, earliest primates appear on 9 September, and humans at dawn of 25 December.

For a year that starts with the earliest humans, our own species appears on 19 November, the first built constructions on 8 December, and agricultural farming begins at midday on 29 December.

Written by Leisureguy

26 December 2021 at 8:05 am

Posted in Evolution, History, Science

Freaky Flowers: Echinopsis Cacti in Bloom 

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Greg Krehel describes his Vimeo video:

A montage of a dozen types of Echinopsis cactus flowers blooming. And wilting. And just generally showing off their mind-blowing colors. My favorite cactus flowerings from the 2014 blooming season.

Echinopsis cactus flowers bloom overnight and the flowers last for only a day. Actually, the flowers are at their peak beauty for an hour or two at the most. That’s what turned me from a cactus enthusiast into a cactus photographer … the desire to try to preserve some aspect of their freaky beauty. Prior to becoming an Echinopsis addict a few years back, I had never owned a DSLR or image/video editing software.

The cacti shown in this video come from my collection. The evening when it looks like a plant’s flowers are about to bloom, I bring it indoors to image. Most of the clips in this montage show approximately 8 hours of change as the flowers open and bloom. A little more than halfway through the montage, there’s a series of three clips showing different views of a 24-hour period in the life of a yellow-flowered ‘Daydream’ plant. Six flowers that opened the night before I started filming wilt to nothingness and another 4 flowers grow dramatically and then open. This series of ‘Daydream’ clips is followed by another three showing other types of flowers wilting. These additional wilting clips are also taken over a daylong period.

The question I’m asked most often about my cactus flower still images and timelapses is whether I’ve “Photoshopped” them, that is, have I used editing software to juice things up and create the flowers’ intense colors. I do, of course, use Photoshop and Lightroom and other editing software. But not in the way most suspect. Rather than using these tools to overstate reality, I actually use them to reduce the intensity of the colors my camera captures. I have reduced the color saturation in every timelapse clip in this video by a minimum of 10% and some (‘Yes’, ‘Cabaret’ and ‘Antimatter’) by 30% or more in order to have something that wasn’t just completely blown out.

I hope you enjoy “Freaky Flowers” and invite you to contact me via my Vimeo account and/or visit where you’ll learn more than you ever wanted to know about these cacti and also be able to reach me via a contact form should you wish. . .

Written by Leisureguy

10 December 2021 at 6:57 pm

Posted in Daily life, Evolution, Science

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The first living robots that can reproduce

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The article by Josh Brown of the Wyss Institute includes a video of the little buggers at work making their offspring. The article begins:

To persist, life must reproduce. Over billions of years, organisms have evolved many ways of replicating, from budding plants to sexual animals to invading viruses.

Now scientists at the University of Vermont, Tufts University, and the Wyss Institute for Biologically Inspired Engineering at Harvard University have discovered an entirely new form of biological reproduction—and applied their discovery to create the first-ever, self-replicating living robots.

The same team that built the first living robots (“Xenobots,” assembled from frog cells—reported in 2020) has discovered that these computer-designed and hand-assembled organisms can swim out into their tiny dish, find single cells, gather hundreds of them together, and assemble “baby” Xenobots inside their Pac-Man-shaped “mouth”—that, a few days later, become new Xenobots that look and move just like themselves.

And then these new Xenobots can go out, find cells, and build copies of themselves. Again and again.

“With the right design—they will spontaneously self-replicate,” says Joshua Bongard, Ph.D., a computer scientist and robotics expert at the University of Vermont who co-led the new research.

The results of the new research were published November 29, 2021, in the Proceedings of the National Academy of Sciences.

Into the Unknown

In a Xenopus laevis frog, these embryonic cells would develop into skin. “They would be sitting on the outside of a tadpole, keeping out pathogens and redistributing mucus,” says Michael Levin, Ph.D., a professor of biology and director of the Allen Discovery Center at Tufts University and co-leader of the new research. “But we’re putting them into a novel context. We’re giving them a chance to reimagine their multicellularity.” Levin is also an Associate Faculty member at the Wyss Institute.

And what they imagine is something far different than skin. “People have thought for quite a long time that we’ve worked out all the ways that life can reproduce or replicate. But this is something that’s never been observed before,” says co-author Douglas Blackiston, Ph.D., the senior scientist at Tufts University and the Wyss Institute who assembled the Xenobot “parents” and developed the biological portion of the new study.

“This is profound,” says Levin. “These cells have the genome of a frog, but, freed from becoming tadpoles, they use their collective intelligence, a plasticity, to do something astounding.” In earlier experiments, the scientists were amazed that Xenobots could be designed to achieve simple tasks. Now they are stunned that these biological objects—a computer-designed collection of cells—will spontaneously replicate. “We have the full, unaltered frog genome,” says Levin, “but it gave no hint that these cells can work together on this new task,” of gathering and then compressing separated cells into working self-copies.

“These are frog cells replicating in a way that is very different from how frogs do it. No animal or plant known to science replicates in this way,” says Sam Kriegman, Ph.D.,  the lead author on the new study, who completed his Ph.D. in Bongard’s lab at UVM and is now a post-doctoral researcher at Tuft’s Allen Center and Harvard University’s Wyss Institute for Biologically Inspired Engineering.

On its own, the Xenobot parent, made of some 3,000 cells, forms a sphere. “These can make children but then the system normally dies out after that. It’s very hard, actually, to get the system to keep reproducing,” says Kriegman. But with an artificial intelligence program working on the Deep Green supercomputer cluster at UVM’s Vermont Advanced Computing Core, an evolutionary algorithm was able to test billions of body shapes in simulation—triangles, squares, pyramids, starfish—to find ones that allowed the cells to be more effective at the motion-based “kinematic” replication reported in the new research. . .

Read the whole thing — and check out that video.

This is evolution in action — in a way. Humans evolved, and as they evolved they gave rise to memes — the units of human culture — and the memes propagated and evolved, and now the result is a new life form that came into being as a result of tha evolution.

Written by Leisureguy

1 December 2021 at 6:19 pm

Could One Shot Kill the Flu?

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Matthew Hutson has an interesting article in the New Yorker:

In 2009, global health officials started tracking a new kind of flu. It appeared first in Mexico, in March, and quickly infected thousands. Influenza tends to kill the very young and the very old, but this flu was different. It seemed to be severely affecting otherwise healthy young adults.

American epidemiologists soon learned of cases in California, Texas, and Kansas. By the end of April, the virus had reached a high school in Queens, where a few kids, returning from a trip to Mexico, had infected a third of the student body. The Mexican government closed its schools and banned large gatherings, and the U.S. considered doing the same. “It was a very scary situation,” Richard Besser, who was then the acting director of the Centers for Disease Control and Prevention, told me. Early estimates suggested that the “swine flu,” as the new strain became known, killed as many as fourteen per cent of those it infected—a case fatality rate more than two hundred times higher than typical seasonal flu. The virus soon spread to more than a hundred and fifty countries, and the Obama Administration considered delaying the start of school until after Thanksgiving, when a second wave could be under way. Manufacturers worried about vaccine supplies. Like most flu vaccines, the one for the swine flu was grown in chicken eggs. “Even if you yell at them, they don’t grow faster,” Tom Frieden, who replaced Besser as the director of the C.D.C., said, at a press conference.

In the end, the world got lucky. The early stats were misleading: although swine flu was extremely contagious, it wasn’t especially deadly. Sometimes the reverse is true. Avian flu, which spread across the world during the winter of 2005-06, is not particularly transmissible but is highly lethal, killing more than half of those it infects. Each flu virus has its own epidemiological profile, determined by its genetic makeup, and flu genes shift every year. Howard Markel, a physician and historian of epidemics who, in the early two-thousands, helped invent the concept of “flattening the curve,” compared influenza’s swappable genetic components to “two wheels of fortune.” A double whammy—ease of spread combined with lethality—could make covid-19, or even the 1918 flu, which killed between forty million and a hundred million people, look like a twenty-four-hour bug.

After the swine flu’s relatively harmless nature became apparent, many people asked if the alarm it provoked had been warranted. A Swiss survey found that trust in institutions had decreased. Some scientists and officials accused the World Health Organization of stirring up a “faked” pandemic to justify its budget. But most drew the opposite conclusion from the experience. Trying to prepare for a deadly flu pandemic had left them more alarmed. “There was just a sense of overwhelming relief,” Besser said. “If this had been like 1918, we sure weren’t ready.”

In truth, we’re never fully ready for the flu. We know it’s coming, like the first fall leaf, and yet three times in the past century—in 1918, 1957, and 1968—it has flattened us, killing a million or more each time. Even in ordinary years, the disease infects a billion people around the world, killing hundreds of thousands; one study estimated that it costs the United States economy close to a hundred billion dollars annually. Our primary weapon against the virus, the flu vaccine, is woefully inadequate. Over the last decade and a half in the United States, flu vaccines have prevented illness only forty per cent of the time; in particularly bad years, when vaccines were less fine-tuned to the strains that were circulating, they were only ten-per-cent protective. Today, the coronavirus pandemic is rightfully the object of our most strenuous efforts. And yet, as the infectious-disease specialists David Morens, Jeffrey Taubenberger, and Anthony Fauci wrote, in a 2009 article in The New England Journal of Medicine, that “we are living in a pandemic era that began around 1918,” when the flu used shipping networks to traverse the world. Since the 1918 pandemic, this century-long, multi-wave pandemic has killed roughly the same number of people.

We’ve controlled a vast number of diseases with vaccination—chicken pox, diphtheria, measles, mumps, polio, rabies, rubella, smallpox, tetanus, typhoid, whooping cough, yellow fever—and, to some degree, we’ve added covid-19 to the list. But the pathogens behind those diseases tend to be relatively static compared with the flu, which returns each year in a vexingly different form. For decades, scientists have dreamed of what some call a “universal” flu vaccine—one that could target many strains of the virus. A universal vaccine would save countless lives not just this year but every year; as those numbers add up, it would become one of the greatest medical breakthroughs in history. Until recently, it’s been beyond the reach of molecular biology. But new technologies are extending our abilities, and researchers are learning how to see through the flu’s disguises. Without knowing it, we’re living on the cusp of a remarkable scientific achievement. One of the world’s longest pandemics could soon be coming to an end.

What we call “the flu” is really plural. Every season, several strains circulate. When it’s summer in one hemisphere, flu infections surge in the other. Virologists at the W.H.O. investigate the viruses and share what they learn with pharmaceutical companies; pharmaceutical researchers then often develop quadrivalent vaccines, which target four separate strains simultaneously. It’s the shotgun approach.

It takes more than six months to design, test, and manufacture a season’s worth of flu vaccine. In that time, a lot can change. Out in the world, strains mutate, jostling for dominance; prevalent varieties fade away, and sleepers come to the fore. Arnold Monto, an epidemiologist at the University of Michigan who has advised the Food and Drug Administration on flu-vaccine targeting, told me that choosing strains to target requires “science and a little bit of art.” The selected flu viruses mutate further as a result of vaccine manufacturing. By the time a needle reaches your arm, there’s a good chance that the vaccine might be off target or obsolete.


Each strain of the flu can be seen as plural, too. Morrens, Taubenberger, and Fauci explain that “it is helpful to think of influenza viruses not as distinct entities but as eight-member ‘gene teams.’ ” A flu virus, they write, “must sometimes trade away one or more team members to make way for new gene ‘players’ with unique skills.”

The surface of a virus is covered by a forest of . . .

Continue reading.

Written by Leisureguy

22 November 2021 at 4:25 pm

Evolution never stops

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This experiment observes evolution in action. It’s odd to me that some people continue to deny that evolution is a fact, but then there are some who deny that the Earth is a globe.

Written by Leisureguy

15 November 2021 at 1:42 pm

Ancient History Shows How We Can Create a More Equal World

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David Graeber and  are the authors of the forthcoming book, The Dawn of Everything: A New History of Humanity, from which this NY Times essay is adapted. Mr. Graeber died shortly after completing the book. The links are gift links, which bypass the paywall, so you can read the entire essay, which begins:

Most of human history is irreparably lost to us. Our species, Homo sapiens, has existed for at least 200,000 years, but we have next to no idea what was happening for the majority of that time. In northern Spain, for instance, at the cave of Altamira, paintings and engravings were created over a period of at least 10,000 years, between around 25,000 and 15,000 B.C. Presumably, a lot of dramatic events occurred during that period. We have no way of knowing what most of them were. This is of little consequence to most people, since most people rarely think about the broad sweep of human history anyway. They don’t have much reason to. Insofar as the question comes up at all, it’s usually when reflecting on why the world seems to be in such a mess and why human beings so often treat each other badly — the reasons for war, greed, exploitation and indifference to others’ suffering. Were we always like that, or did something, at some point, go terribly wrong?

One of the first people to ask this question in the modern era was the Swiss-French philosopher Jean-Jacques Rousseau, in an essay on the origins of social inequality that he submitted to a competition in 1754. Once upon a time, he wrote, we were hunter-gatherers, living in a state of childlike innocence, as equals. These bands of foragers could be egalitarian because they were isolated from one another, and their material needs were simple. According to Rousseau, it was only after the agricultural revolution and the rise of cities that this happy condition came to an end. Urban living meant the appearance of written literature, science and philosophy, but at the same time, almost everything bad in human life: patriarchy, standing armies, mass executions and annoying bureaucrats demanding that we spend much of our lives filling out forms.

Rousseau lost the essay competition, but the story he told went on to become a dominant narrative of human history, laying the foundations upon which contemporary “big history” writers — such as Jared Diamond, Francis Fukuyama and Yuval Noah Harari — built their accounts of how our societies evolved. These writers often talk about inequality as the natural result of living in larger groups with a surplus of resources. For example, Mr. Harari writes in “Sapiens: A Brief History of Humankind” that, after the advent of agriculture, rulers and elites sprang up “everywhere … living off the peasants’ surplus food and leaving them with only a bare subsistence.”

For a long time, the archaeological evidence — from Egypt, Mesopotamia, China, Mesoamerica and elsewhere — did appear to confirm this. If you put enough people in one place, the evidence seemed to show, they would start dividing themselves into social classes. You could see inequality emerge in the archaeological record with the appearance of temples and palaces, presided over by rulers and their elite kinsmen, and storehouses and workshops, run by administrators and overseers. Civilization seemed to come as a package: It meant misery and suffering for those who would inevitably be reduced to serfs, slaves or debtors, but it also allowed for the possibility of art, technology, and science.

That makes wistful pessimism about the human condition seem like common sense: Yes, living in a truly egalitarian society might be possible if you’re a Pygmy or a Kalahari Bushman. But if you want to live in a city like New York, London or Shanghai — if you want all the good things that come with concentrations of people and resources — then you have to accept the bad things, too. For generations, such assumptions have formed part of our origin story. The history we learn in school has made us more willing to tolerate a world in which some can turn their wealth into power over others, while others are told their needs are not important and their lives have no intrinsic worth. As a result, we are more likely to believe that inequality is just an inescapable consequence of living in large, complex, urban, technologically sophisticated societies.

We want to offer an entirely different account of human history. We . . .

Continue reading. There’s more — and no paywall.

Written by Leisureguy

5 November 2021 at 8:54 am

How do tall trees get water to the top?

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Written by Leisureguy

4 November 2021 at 1:08 pm

The weirdness of the world

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Perhaps it’s just me, but this morning the world seems very odd and a little off.

When I arise, it’s generally too early to start the day, so I open my laptop and browse my email and then the internet. The first thing that I chanced upon was Cory Doctorow’s review in Medium of Daniel Pinkwater’s Crazy in Poughkeepsie. (Perhaps the title was a clue that things were about to go off-track.)

The review is an entertaining look at the bizarre events and plot in Daniel Pinkwater’s new Young Adult novel. The story was strange enough that I read the Wikipedia entry for Daniel Pinkwater. Some things I learned that struck me as odd. Here are a few snippets from the article:

Born Manus Pinkwater in Memphis, Tennessee, to Jewish immigrant parents from Poland. He describes his father, Philip Pinkwater, as a “ham-eating, iconoclastic Jew” who was expelled from Warsaw by the decent Jews. 
. . . 
A moment of fame came when he posed as Inspector Fermez LaBouche for the fumetti strip that ran in the final issues of Help! (September 1965); he had been spotted at a party by Terry Gilliam. Pinkwater rode in a Volkswagen convertible to a photo shoot with Gilliam, Robert Crumb, and Help’s creator Harvey Kurtzman—none of the men had any interest in the others. He met a children’s book editor by chance at a party; he invited her to his studio to promote an African artist’s cooperative, and she suggested that he illustrate a book. Pinkwater received a $1,500 advance for his first book, The Terrible Roar (1970), after replying that he would try to write the book himself.

With his wife Jill, Pinkwater published a dog training book and ran an obedience school while living in Hoboken, New Jersey. At the time, he was training to become an art therapist, but found he was unsuited to the work and dropped his studies. However, he attended a meeting of an unspecified cult with a therapy client, and later joined the cult. Pinkwater says “the quality of the [cult’s] rip-off was so minor you could ignore it”, although both he and Jill later left the cult. 
. . .
He adopted the name Daniel in the 1970s after consulting his cult’s guru, who said his true name should begin with a “D”. 
. . .
Pinkwater authored the newspaper comic strip Norb, which was illustrated by Tony Auth. The strip, syndicated by King Features, launched in 70 papers, but received nothing but hate-mail from the readers. Auth and Pinkwater agreed to end the project after 52 weeks.[2] The daily strips were released in a 78-page collection by MU Press in 1992.

Pinkwater was a longtime commentator on All Things Considered on National Public Radio. He regularly reviewed children’s books on NPR’s Weekend Edition Saturday. For several years, he had his own NPR show: Chinwag Theater. Pinkwater was also known to avid fans of the NPR radio show Car Talk, where he has appeared as a (seemingly) random caller, commenting, for example, on the physics of the buttocks (giving rise to the proposed unit of measure of seat size: the Pinkwater), and giving practical advice as to the choice of automobiles. In the early 1990s Pinkwater voiced a series of humorous radio advertisements for the Ford Motor Company.

I wondered whether Pinkwater had concocted his entry as a kind of surrealistic exercise, but on reading one of the source articles linked in the Wikipedia footnotes, it seems to be about right. (That article says that Pinkwater’s father was expelled from Warsaw not so much for eating ham as for being a gangster.)

A little discombobulated, I next read the Doctorow article I had meant to read in the first place. (The Pinkwater article was the first article in the list, and so had caught my eye.) My original goal was an article about the power that large tech companies — YouTube, Twitter, Tik Tok, Instagram, et al. — have to decide whether to allow content to remain on their platforms. 

Consider a content creator who suddenly finds that work developed over months or years of effort is suddenly gone, with no good appeal procedure to get it restored. Doctorow’s article is well worth reading. A few snippets:

After Novara’s channel was deleted, the group tried to find out more. The email that Youtube sent announcing the removal was terse (“YouTube said Novara was guilty of ‘repeated violations’ of YouTube’s community guidelines, without elaborating”). Novara editor Gary McQuiggin “filled in a YouTube appeal form,” which disappeared into the ether.

Then McQuiggin went to YouTube’s creator support chatbot, which introduced itself as “Rose.” What happened next is the stuff of Kafka-esque farce:

“I know this is important,” [Rose said,] before the conversation crashed.

The Times’s story quite rightly homes in on the problems of doing content moderation at scale without making errors. It notes that YouTube deletes 2,000 channels every hour to fight “spam, misinformation, financial scams, nudity, hate speech.” . . .

The platforms remove content in the blink of an eye, often through fully automated processes (such as copyright filters). Takedown systems are built without sparing any expense (YouTube’s copyright filter, Content ID, cost the company $100,000,000 and counting).

But the put-back processes — by which these automated judgments are examined and repealed — are slow-moving afterthoughts. If you’re a nightclub owner facing a takedown of the promo material sent to you by next week’s band, the 2.5-year delay you face in getting that content put back up is worse than a joke. . .

The reality is that there is no army of moderators big enough to evaluate 2,000 account deletions per hour. . .

YouTube’s takedown regime has to contend with 500 hours’ worth of new video every minute, in every language spoken. It has to parse out in-jokes and slang, obscure dialects, and even more obscure references.

In such a seemingly dystopian system, what do content creators do? For one thing, they face challenges — see “8 Challenges Even Millionaire YouTuber Ali Abdaal Faces,” by Amardeep Parmar. That article describes the strange (to me) work situation of a modern-day content creator. Their lives seem to be unceasing effort to move faster and do more, while overhead hangs a sword of Damocles: that a twitch of a corporate algorithm can delete in an instant all the work they’ve posted. 

I myself am involved in this same ecosystem of software, information, creation, and business practices, but at a very low level with little at stake. Having my livelihood depend on such an unstable and slippery amalgam of forces would make me uneasy indeed.

Reading the above collection of weird expressions of human culture — memetic evolution creating very odd results — made me want to read something about nature, something calming and restorative. I happened on the article “Do Not Eat, Touch, Or Even Inhale the Air Around the Manchineel Tree,” by Dan Nosowitz — a tree that likely played a role in the death of Ponce de Leon. It was interesting, but did nothing to dispel this morning’s fog of weirdness. It did make me recalll that natural evolution, just like cultural evolution, can go in strange directions — for example:


Written by Leisureguy

3 November 2021 at 10:45 am

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