Later On

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Archive for the ‘Evolution’ Category

Q: Why Are Plants Green? A: To Reduce the Noise in Photosynthesis.

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Rodrigo Pérez Ortega writes in Quanta:

From large trees in the Amazon jungle to houseplants to seaweed in the ocean, green is the color that reigns over the plant kingdom. Why green, and not blue or magenta or gray? The simple answer is that although plants absorb almost all the photons in the red and blue regions of the light spectrum, they absorb only about 90% of the green photons. If they absorbed more, they would look black to our eyes. Plants are green because the small amount of light they reflect is that color.

But that seems unsatisfyingly wasteful because most of the energy that the sun radiates is in the green part of the spectrum. When pressed to explain further, biologists have sometimes suggested that the green light might be too powerful for plants to use without harm, but the reason why hasn’t been clear. Even after decades of molecular research on the light-harvesting machinery in plants, scientists could not establish a detailed rationale for plants’ color.

Recently, however, in the pages of Science, scientists finally provided a more complete answer. They built a model to explain why the photosynthetic machinery of plants wastes green light. What they did not expect was that their model would also explain the colors of other photosynthetic forms of life too. Their findings point to an evolutionary principle governing light-harvesting organisms that might apply throughout the universe. They also offer a lesson that — at least sometimes — evolution cares less about making biological systems efficient than about keeping them stable.

The mystery of the color of plants is one that Nathaniel Gabor, a physicist at the University of California, Riverside, stumbled into years ago while completing his doctorate. Extrapolating from his work on light absorption by carbon nanotubes, he started thinking of what the ideal solar collector would look like, one that absorbed the peak energy from the solar spectrum. “You should have this narrow device getting the most power to green light,” he said. “And then it immediately occurred to me that plants are doing the opposite: They’re spitting out green light.”

In 2016, Gabor and his colleagues modeled the best conditions for a photoelectric cell that regulates energy flow. But to learn why plants reflect green light, Gabor and a team that included Richard Cogdell, a botanist at the University of Glasgow, looked more closely at what happens during photosynthesis as a problem in network theory.

The first step of photosynthesis happens in a light-harvesting complex, a mesh of proteins in which pigments are embedded, forming an antenna. The pigments — chlorophylls, in green plants — absorb light and transfer the energy to a reaction center, where the production of chemical energy for the cell’s use is initiated. The efficiency of this quantum mechanical first stage of photosynthesis is nearly perfect — almost all the absorbed light is converted into electrons the system can use.

But this antenna complex inside cells is constantly moving. “It’s like Jell-O,” Gabor said. “Those movements affect how the energy flows through the pigments” and bring noise and inefficiency into the system. Quick fluctuations in the intensity of light falling on plants — from changes in the amount of shade, for example — also make the input noisy. For the cell, a steady input of electrical energy coupled to a steady output of chemical energy is best: Too few electrons reaching the reaction center can cause an energy failure, while “too much energy will cause free radicals and all sorts of overcharging effects” that damage tissues, Gabor said.

Gabor and his team developed a model for the light-harvesting systems of plants and applied it to the solar spectrum measured below a canopy of leaves. Their work made it clear why what works for nanotube solar cells doesn’t work for plants: It might be highly efficient to specialize in collecting just the peak energy in green light, but that would be detrimental for plants because, when the sunlight flickered, the noise from the input signal would fluctuate too wildly for the complex to regulate the energy flow. . .

Continue reading. There’s more.

Written by LeisureGuy

30 July 2020 at 2:31 pm

Music in Human Evolution

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Kevin Simler has a very interesting review and summary of the book Why Do People Sing? Music in Human Evolution:

I just finished the strangest, most disconcerting little book. It’s called Why Do People Sing?: Music in Human Evolution by Joseph Jordania.

If the title hasn’t already piqued your interest, its thesis surely will. The thesis is wild, bold, and original, but makes an eerie amount of sense. If true, it would be a revolution — and I don’t use the term lightly — in how we understand the evolution of music, cooperation, warfare, and even religion.

I have my reservations about Jordania’s theory (and his book), but I’ll save them for a later time. As Daniel Dennett once wrote about another remarkable theory:

I think first it is very important to understand [the] project, to see a little bit more about what the whole shape of it is, and delay the barrage of nitpicking objections and criticisms until we have seen what the edifice as a whole is. After all, on the face of it, [the project] is preposterous… [but] I take it very seriously.

These are exactly my feelings about Jordania’s project. Seemingly preposterous, but worth taking very seriously.

0. STYLIZED FACTS

I’m going to share Jordania’s theory with you, but first I want to present a set of “stylized facts” — curious, disparate, and nearly inexplicable phenomena that would seem to have little relation to each other. Then I’ll present the theory that (uncannily) links them all together and explains everything.

OK, brace yourself. Here come the facts:

  • When our ancestors [1] first moved from the forest to the savannah, we were not yet capable of making tools. But early hominid evolution tended away from a physiology that would have helped us hunt and/or defend ourselves from predators. Our canine teeth receded, we became slower and weaker, and we didn’t develop tough skin (in fact the opposite).
  • Lion evolution and migration seems to have mirrored early hominid patterns, both spatiotemporally and (in some ways) behaviorally and morphologically. Lions, for example, are the only social species of cat.
  • Humans are the only ground-dwelling species that sings. There are over 4000 singing species — mostly birds, but also gibbons, dolphins, whales, and seals. But they all sing from water or the trees. When a bird lands on the ground, it invariably stops singing.
  • Of all singing creatures, humans are the only ones who use rhythm.
  • When we sing, we almost always dance, even if it’s just nodding along or tapping a foot. Both singing and dancing (whether together or separate) are group activities used across the world in tribal bonding rituals. Isolated ethnic groups have remarkably similar styles of song and dance.
  • Rhythmic chanting and dancing induce trance states.
  • Early hominids quite possibly ate their dead, and (some while later) definitely started burying them. The instinct to preserve a dead human body from mutilation, and then to dispose of it, is fairly universal. E.g. we strive to retrieve corpses even from a battlefield.

I hope you are intrigued. Each of these facts is hard to explain even in isolation. So a theory that can unify and account for all of them will have to be either profound or crazy — or both.

At this point I’m going to present Jordania’s theory as clearly and comprehensively as I can. I’ll interpolate a bit and add my own explanatory flare, but the ideas come straight out of his book.

1. HUNTERS OR SCAVENGERS?

When human ancestors first descended from the trees and stepped out onto the grasslands, they faced two critical problems: acquiring food and defending themselves from predators. We’ll discuss food acquisition in this section and defense in the next section, but as you’ll see they’re linked by a similar mechanism.

I hadn’t thought deeply about these problems until I read Jordania’s book. I always imagined, naively, that early humans had been “hunter-gatherers.” While this is true of later humans, it’s almost certainly not true of our earliest savannah-dwelling ancestors. Gathering? yes. But hunting, especially big-game hunting, was out of the question. As I mentioned, our earliest ancestors hadn’t yet learned how to make or use tools beyond simple rocks and sticks, and we were fairly weak.

Yet we certainly ate meat — the archaeological record is pretty clear on that. So there’s a growing consensus that we were actually scavengers (or perhaps “scavenger-gatherers”).

Now there are two types of scavenging, two strategies for “carcass acquisition”: passive and confrontational. . .

Continue reading.

Written by LeisureGuy

24 July 2020 at 7:57 pm

Some Animals Have No Microbiome. Here’s What That Tells Us.

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I find this fascinating, but it shows again not to generalize from a small sample. In this case, that means not to jump to the conclusion that what is true for one animal (humans) is true for others. Jordana Cepelewicz writes in Quanta:

In the summer of 2011, the microbiologist Jon Sanders, then a graduate student, found himself in Peru’s tropical rainforest for the second time in as many years, lugging 60 pounds of lab equipment — a bulky fluorescence microscope and the generator to power it — up the Amazon River. Upon arriving at the remote field site, he quickly set about catching as many different ants as he could, eager to peer at the microbes that populated their guts.

In some of those ant species, he saw “this amazing, dense, packed cloud. It was like a galaxy of microbes,” he said. “They’d explode in your eyes when you looked at them” under the microscope. Which is what you might expect to find, given the extent to which we and so many other animals depend on the trillions of bacterial cells that reside within us — for processing food that we can’t otherwise digest, for providing key nutrients, for training our immune system to act effectively against infections. The microbiome is so critical to our health and survival that some researchers even find it useful to think of animals as the sum of their microbial parts.

But when Sanders turned to the rest of the ants — about two-thirds of the different colonies and species he had collected — he was surprised to find that “you would be hard-pressed to find any cells in the gut that you could readily identify as bacteria,” he said. Food, debris, the cells of the insects’ gut lining — all were present. Microbes that might be engaged in the symbiotic relationships we take for granted — not so much.

As the tools to measure and analyze microbial communities have improved, it’s gradually become clear that the microbiome is nowhere near as ubiquitous and important across the animal kingdom as it’s often portrayed to be. Many animals seem to have more flexible or less stable associations with microbes; some don’t seem to rely on them at all. And ironically, it’s these animals that are now allowing scientists to gain new insights into the mystery of how and why the microbiome evolves — its real importance, and the nuanced balancing act of pros and cons that lies at its core.

Microbes Gone Missing

In the early 20th century, biologists began to uncover fascinating relationships between complex organisms and their microbes: in tubeworms that had no mouth, anus or gut; in termites that fed on tough, woody plants; in cows whose grassy diet significantly lacked protein. Such observations generated excitement and prompted follow-up experiments. In those years, the absence of microbial helpers in an animal wasn’t considered particularly surprising or interesting, and it often received little more than a passing nod in the literature. Even when it was thought to merit more than that — as in a 1978 report in Science that tiny wood-eating crustaceans, unlike termites, had no stable population of gut bacteria — it ended up flying under the radar.

And so expectations quietly began to shift to a new norm, that every animal had a relationship with bacteria without which it would perish. A few voices protested this oversimplification: As early as 1953, Paul Buchner, one of the founders of symbiosis research, wrote with exasperation about the notion that obligate, fixed and functional symbioses were universal. “Again and again there have been authors who insist that endosymbiosis is an elementary principle of all organisms,” he seethed. But counterexamples drowned in the flood of studies on the importance of host-microbe symbioses, especially those that drew connections between human health and our own microbiome.

“The human microbiome has completely driven a lot of our thinking about how microbes work,” said Tobin Hammer, a postdoctoral researcher in ecology and evolutionary biology at the University of Texas, Austin. “And we often project from ourselves outwards.”

But the human example is not a good model for what’s going on in a diverse range of species, from caterpillars and butterflies to sawflies and shrimp, to some birds and bats (and perhaps even some pandas). In these animals, the microbes are sparser, more transient or unpredictable — and they don’t necessarily contribute much, if anything, to their host. “The story is more complex,” said Sarah Hird, an evolutionary biologist and microbial ecologist at the University of Connecticut, “more fuzzy.”

A transient, almost nonexistent relationship with bacteria was what Sanders saw in his tropical ants. He brought his samples back to his lab (then at Harvard University, although he is now at Cornell), where he sequenced the insects’ bacterial DNA and quantified how many microbes were present. The ant species with dense, specialized microbiomes had approximately 10,000 times more bacteria in their guts than Sanders found in the many other species he had captured. Put another way, Sanders said, if the ants were scaled to human size, some would carry a pound of microbes within them (similar to what humans harbor), others a mere coffee bean’s worth. “It’s really a profound difference.”

That difference, reported in Integrative & Comparative Biology in 2017, seemed to be associated with diet: Strictly herbivorous tree-dwelling ants were more likely to have an abundant microbiome, perhaps to make up for their protein-deficient diet; omnivorous and carnivorous ground-dwelling ants consumed more balanced meals and had negligible amounts of bacteria in their gut. Still, this pattern was inconsistent. Some of the herbivorous ants also lacked a microbiome. And the ants that did have one didn’t seem to have widespread, predictable associations with particular species of bacteria (although some sets of microbes were common to individual genera of the insects). That result marked a clear departure from mammalian microbiomes like our own, which tend to be very specific to their hosts.

The reasons why would become clearer as case studies of other organisms started to trickle in.

The Tip of the Iceberg

At around the same time that Sanders was examining ants in Peru, Hammer was in Costa Rica on an independent search for a microbiome in caterpillars. (“What better insect to have obligate relationships with bacteria than these cows of the insect world?” Sanders commented.) But try as he might, Hammer couldn’t find much bacterial DNA in the gut and fecal samples he collected. “Something really weird was going on,” he said.

When, after months of “frustrating lab work,” he realized that the animals might simply not have a stable microbiome, “it was a shift in thinking for me that was not expected at all.” He and his colleagues ultimately found that, like so many of Sanders’ ants, caterpillars had much, much lower quantities of microbes than was considered the norm. Moreover, those microbes were simply a subset of the ones found in the animals’ plant diet — “which supports the idea that they’re transiently passing through and some of them are getting digested, essentially,” Hammer said. “They’re not establishing stable populations within the gut.”

To determine whether those transient bacteria benefited the caterpillars, the researchers . . .

Continue reading.

 

Written by LeisureGuy

14 April 2020 at 4:33 pm

Posted in Evolution, Health, Science

Cut the calorie-rich-and-processed (CRAP) foods

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Written by LeisureGuy

13 April 2020 at 10:58 am

Unified theory of evolution

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Michael Skinner,professor of biological science at Washington State University and the principal investigator at the Skinner laboratory with research interests that include environmental epigenetics and disease etiology, writes in Aeon:

The unifying theme for much of modern biology is based on Charles Darwin’s theory of evolution, the process of natural selection by which nature selects the fittest, best-adapted organisms to reproduce, multiply and survive. The process is also called adaptation, and traits most likely to help an individual survive are considered adaptive. As organisms change and new variants thrive, species emerge and evolve. In the 1850s, when Darwin described this engine of natural selection, the underlying molecular mechanisms were unknown. But over the past century, advances in genetics and molecular biology have outlined a modern, neo-Darwinian theory of how evolution works: DNA sequences randomly mutate, and organisms with the specific sequences best adapted to the environment multiply and prevail. Those are the species that dominate a niche, until the environment changes and the engine of evolution fires up again.

But this explanation for evolution turns out to be incomplete, suggesting that other molecular mechanisms also play a role in how species evolve. One problem with Darwin’s theory is that, while species do evolve more adaptive traits (called phenotypes by biologists), the rate of random DNA sequence mutation turns out to be too slow to explain many of the changes observed. Scientists, well-aware of the issue, have proposed a variety of genetic mechanisms to compensate: genetic drift, in which small groups of individuals undergo dramatic genetic change; or epistasis, in which one set of genes suppress another, to name just two.

Yet even with such mechanisms in play, genetic mutation rates for complex organisms such as humans are dramatically lower than the frequency of change for a host of traits, from adjustments in metabolism to resistance to disease. The rapid emergence of trait variety is difficult to explain just through classic genetics and neo-Darwinian theory. To quote the prominent evolutionary biologist Jonathan B L Bard, who was paraphrasing T S Eliot: ‘Between the phenotype and genotype falls the shadow.’

And the problems with Darwin’s theory extend out of evolutionary science into other areas of biology and biomedicine. For instance, if genetic inheritance determines our traits, then why do identical twins with the same genes generally have different types of diseases? And why do just a low percentage (often less than 1 per cent) of those with many specific diseases share a common genetic mutation? If the rate of mutation is random and steady, then why have many diseases increased more than 10-fold in frequency in only a couple decades? How is it that hundreds of environmental contaminants can alter disease onset, but not DNA sequences? In evolution and biomedicine, the rates of phenotypic trait divergence is far more rapid than the rate of genetic variation and mutation – but why?

Part of the explanation can be found in some concepts that Jean-Baptiste Lamarck proposed 50 years before Darwin published his work. Lamarck’s theory, long relegated to the dustbin of science, held, among other things, ‘that the environment can directly alter traits, which are then inherited by generations to come’. Lamarck, a professor of invertebrate zoology at the National Museum of Natural History in Paris, studied many organisms including insects and worms in the late 18th and early 19th centuries. He introduced the words ‘biology’ and ‘invertebrate’ into the scientific lexicon, and wrote books on biology, invertebrates and evolution. Despite this significant academic career, Lamarck antagonised many of his contemporaries and 200 years of scientists with his blasphemous evolutionary ideas.

At the start, Lamarck might have been pilloried as a religious heretic, but in modern times, it is the orthodoxy of science – and especially Darwin’s untouchable theory of evolution – that has caused his name to be treated as a joke. Yet by the end of his career, Darwin himself had come around; even without the benefit of molecular biology, he could see that random changes were not fast enough to support his theory in full.

The question is this: if natural selection isn’t acting on genetic mutations alone, then what molecular forces create the full suite of variation in traits required for natural selection to finish the job? One clue came almost a century after Darwin proposed his theory, in 1953, just as James Watson and Francis Crick were unravelling the mysteries of DNA and the double helix. In that year, the developmental biologist Conrad Waddington of the University of Edinburgh reported that fruit flies exposed to outside chemical stimulus or changes in temperature during embryonic development could be pushed to develop varying wing structures. The changes the scientists induced in that single generation would, thereafter, be inherited by progeny down the lineage. Waddington coined a modern term – ‘epigenetics’ – to describe this phenomenon of rapid change. Notably, before Watson and Crick had even revealed their DNA structure, Waddington recognised the potential impact his discovery could have on the theory of evolution: the single-generation change in the fruit-fly wings were supportive of the original ideas of the heretic Lamarck. It appeared that the environment could directly impact traits.

Although Waddington described the general role of epigenetics, he was no more aware of the molecular elements or mechanisms involved than Lamarck or Darwin. But the more molecular biology decodes the workings of life, the more Waddington’s concepts – and Lamarck’s – make sense. Indeed, although the vast majority of environmental factors cannot directly alter the molecular sequence of DNA, they do regulate a host of epigenetic mechanisms that regulate how DNA functions – turning the expression of genes up or down, or dictating how proteins, the products of our genes, are expressed in cells.

Today, that is the precise definition of epigenetics: the molecular factors that regulate how DNA functions and what genes are turned on or off, independent of the DNA sequence itself. Epigenetics involves . . .

Continue reading. There’s much more. Later in the article:

Environmentally induced epigenetic transgenerational inheritance has now been observed in plants, insects, fish, birds, rodents, pigs and humans. It is, therefore, a highly conserved phenomenon. The epigenetic transgenerational inheritance of phenotypic trait variation and disease has been shown to occur across a span of at least 10 generations in most organisms, with the most extensive studies done in plants for hundreds of generations. One example in plants, a heat-induced flowering trait first observed by Carl Linnaeus in the 18th century, was later found to be due to a DNA methylation modification that occurred in the initial plant, and has been maintained for 100 generations. In worms, . . .

For I the LORD your God am a jealous God, visiting the iniquity of the fathers upon the sons to the third and fourth generation of those who hate Me . . .”

Written by LeisureGuy

11 April 2020 at 10:29 am

Posted in Evolution, Science

A Rapid End Strikes the Dinosaur Extinction Debate

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Joshua Sokol writes in Quanta:

The last time the world was ending, two cataclysms aligned. On one side of the planet, a wayward asteroid dropped like a cartoon anvil, punching through the edge of the Yucatan Peninsula and penetrating deep into Earth’s crust. Around the same time — 66 million years ago — a million cubic kilometers of lava were in the process of bubbling up to the surface, releasing climate-altering carbon dioxide and sulfur into the atmosphere and forming what would become the Deccan Traps of modern-day India.

Rock layers around the world show what happened next. No dinosaurs besides the birds made it out. Neither did the squidlike ammonites that curled like rams’ horns, or marine reptiles including the plesiosaurs (Loch Ness conspiracies notwithstanding). But because of the close timing of the asteroid and the volcanism, geologists have spent years staking out increasingly acrimonious positions on which one deserves the blame for the ensuing carnage. In 2018, The Atlantic called the debate “The Nastiest Feud in Science.”

Until recently, Pincelli Hull kept out of the fray. In her subfield, marine plankton fossils, the impact was considered the obvious sole cause of what’s called the Cretaceous-Paleogene extinction. Instead, she focused on understanding how life bounced back, not on what had almost snuffed it out. “There was a lot to be done without really ruffling any feathers,” said Hull, a paleontologist at Yale University.

That changed over time. First, a paleontologist friend who worked on other time periods argued that of course both the asteroid and volcanism were responsible. “I remember feeling so irritated,” Hull said. “This isn’t your topic of study; how do you have an opinion on this?”

But once she realized that researchers looking at other records of the extinction considered the volcanism theory an open question, not just a minority view, Hull started reaching out to them. Many of these scientists were working on more accurate ways to date when exactly the Deccan Traps erupted, and she wanted to understand their emerging evidence.

Researchers had long known that the Deccan Traps erupted within a few million years of the asteroid strike. But in 2015, a group based at Princeton University significantly narrowed the timing. They found that the lava began squishing out of the earth only 250,000 years before the impact and continued for 500,000 years afterward. Then last year, they estimated that a major pulse of lava erupted just tens of thousands of years before the strike. (At the same time, a Berkeley group argued instead that a big pulse began right after.)

It may seem like an obscure chronological feud, but this one matters: If the Deccan Traps released lava and gas just before the asteroid fell, at least some of the subsequent carnage could be attributed to climate change from the volcanoes. “It made me start to think, ‘OK, this is an open question,’” Hull said.

She didn’t think that for long. Hull went on to lead a global collaboration that, early this year, published a definitive timeline of how the mayhem played out in small ocean fossils. The team tracked changes in global temperature over time. The planet did warm up before the impact, Hull found, but then cooled back down before the asteroid arrived. And while that warming event didn’t seem to correlate to marine extinctions, over 90% of plankton species abruptly vanished after the impact. The study suggests that the major influence of the Deccan Traps was to guide the post-apocalyptic evolution of surviving species — not to drive the extinction itself.

Quanta spoke with Hull about that cataclysm — often abbreviated as the K-T extinction — her deep love of planktonic creatures, and the ways in which the K-T extinction resembles what’s going on today. The interview has been condensed and edited for clarity.

Do you remember first learning about the extinction of the dinosaurs? In my own childhood, it was always blamed on the asteroid impact.

I have to admit that as a child, I wasn’t obsessed with dinosaurs at all. I came into all of this pretty backward. I’m from Ohio, and I grew up without ever seeing the ocean. I remember the first time I saw the ocean and I looked at plankton, at the stuff in the water, under magnification. I was enamored of their strangeness; they’re just crazy weird. So I went off to grad school to study modern ocean ecosystems, and it was only there that I came into studying mass extinctions, essentially from the present back.

You’ve also mentioned in talks that you left high school early to go sailing.

The root of that story is that I am a chronic procrastinator. When I should have been doing my high school project, I was online looking at how I could go sailing around the world. And then I left halfway through my senior year and went to the Sea Education Association in Woods Hole and did some training in oceanography, maritime history and literature. I headed out on an oceanographic vessel and I liked it so much that I didn’t want to go to college. My parents were like, could you please try college out for a semester? I was like, no, I’d rather be a deckhand. But I tried college out for a semester and decided to stick it out.

You started your career trying to understand modern-day ecosystems, only to jump to the extinction that killed the dinosaurs. Is that a logical place to leap, 66 million years back?

People have been wondering whether or not we’re in the middle of a mass extinction right now. The most recent big mass extinction is the K-T mass extinction, and its influence is so big that you actually see it profoundly. Another reason why it’s helpful to study the most recent big mass extinction is that as you go further back in time, you have exponentially fewer fossil archives, because the whole world is basically a gigantic rock recycling factory.

Does that mean it’s rare to drill a seafloor sample that spans even this extinction?

Yeah, I’m a biologist, and when the cores are coming up, it’s sort of intriguing, but in the way that staring at clouds is intriguing. Usually you’re like, oh, there’s another tube of brown mud. There’s another tube of grayish-blue mud. But when you come across a boundary like the K-T boundary, it’s blaring. It’s awesome.

For your new paper, do you remember getting those specific cores? . . .

Continue reading.

Written by LeisureGuy

25 March 2020 at 9:02 pm

How immune systems work

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Alex Danco writes in his newsletter:

Hi everyone, in keeping with last week’s theme on antifragility amidst the global COVID-19 crisis, this week we’re going to talk about a specific example of an antifragile system that’s probably on a lot of your minds right now: your immune system. If you have a biology background you may already know all of this, but I’m guessing most people who read this newsletter don’t. So I hope you enjoy and learn something from this quick overview on how your immune system works, and why it’s such a great example of an antifragile system that gains from disorder.

The immune system: three lines of defence

What are we talking about when we say “The immune system?” First of all, you don’t have one immune system, so much as you have three layers of defence who work to protect you from pathogens and disease. They all work together, particularly the second and third layers who coordinate their work a lot. Still, we can still think of them as three distinct systems that have their own strengths and weaknesses. . .

Continue reading.

Written by LeisureGuy

23 March 2020 at 4:29 pm

He Was Dying. Antibiotics Weren’t Working. Then Doctors Tried a Forgotten Treatment.

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Thanks to JvR for pointing it out: Maryn McKenna reported in Mother Jones in May/June 2018:

Steffanie Strathdee hunched over her laptop, fretting. She barely noticed the kittens asleep next to her or the serene Buddha figure across the living room, anchored next to the glass doors that looked toward the gleaming Pacific. Her mind was 20 miles away in the intensive care unit of the University of California-San Diego’s medical center, where her husband, Tom Patterson, lay in a coma.

Patterson was 68; Strathdee was 49. They had been married 11 years, after meeting in a grant review group convened by the National Institutes of Health. He was a psychologist and she was an infectious-disease epidemiologist; when they fell in love, they also formed a powerhouse research team, studying the effect of the AIDS virus on vulnerable people in Tijuana, Mexico.

But it was a bacterium, not a virus, that was bedeviling them now. Three months earlier, on the last night of a Thanksgiving vacation in Egypt, Patterson had suddenly fallen ill, so severely that he had to be medevaced to Germany and then to UCSD. There were several things wrong—a gallstone, an abscess in his pancreas—but the core of the problem was an infection with a superbug, a bacterium named Acinetobacter baumannii that was resistant to every antibiotic his medical team tried to treat it with. Patterson had been a burly man, 6-foot-5 and more than 300 pounds, but now he was wasted, his cheekbones jutting through his skin. Intravenous lines snaked into his arms and neck, and tubes to carry away seepage pierced his abdomen. He was delirious and his blood pressure was falling, and the medical staff had sedated him and intubated him to make sure he got the oxygen he needed. He was dying.

Strathdee’s friends knew she was desperately searching for solutions, and one told her about an acquaintance with an intractable infection who had traveled to Eastern Europe to seek out a century-old cure. Strathdee spent days reading whatever she could find about it, and now she was composing a last-ditch email to the hospital’s head of infectious diseases, the person who would rule on whether they could use it to help her spouse.

“We are running out of options to save Tom,” she wrote. “What do you think about phage therapy?”

Strathdee didn’t realize it at the time, but her attempt to save her husband’s life would test the bounds of the American medical system—and throw its limitations into stark relief.

The treatment Strathdee had fixed on as a last-ditch hope is almost never used in the United States. The Food and Drug Administration has not licensed phage therapy, keeping it out of pharmacies and hospitals. Few physicians have used it even experimentally, and most civilians have never heard of it. But phages are a natural phenomenon, frequently deployed in the former Soviet Union. When used properly, they can save lives.

To understand how phage therapy works, it helps to know a little biology, starting with the distinction between bacteria and viruses. Most of the drug-resistant superbugs that cause medical havoc are bacteria, microscopic single-celled organisms that do most of the things that other living things do: seek nutrition, metabolize it into energy, produce offspring. Viruses, which are much smaller than bacteria, exist only to reproduce: They attach to a cell, hijack its reproductive machinery to make fresh viruses, and then, in most cases, explode the cell to let viral copies float free.

Phages are viruses. In the wild, they are the cleanup crew that keeps bacteria from taking over the world. Bacteria reproduce relentlessly, a new generation every 20 minutes or so, and phages kill them just as rapidly, preventing the burgeoning bacterial biomass from swamping the planet like a B-movie slime monster. But phages do not kill indiscriminately: Though there are trillions in the world, each is tuned evolutionarily to destroy only particular bacteria. In 1917, a self-taught microbiologist named Félix d’Herelle recognized phages’ talent for targeted killing. He imagined that if he could find the correct phages, he could use them to cure deadly bacterial infections.

That was a gleaming hope, because at the time, nothing else could. (Sir Alexander Fleming wouldn’t find the mold that makes penicillin, the first antibiotic, until 1928.) Treatments were primitive: aspirin and ice baths to knock down fever, injections of crude immunotherapy extracted from the blood of horses and sheep, and amputation when a scratch or cut let infection burgeon in a limb and threaten the rest of the body with sepsis. Phages—whose full name, bacteriophages (or “bacteria eaters”), was given by d’Herelle in 1916—did something that medicine had never before been able to accomplish: They vanquished the infections for which they were administered without otherwise harming patients. A medical sensation and a cultural phenomenon, they provided the key plot device in the novel Arrowsmith, about an idealistic doctor, that won the Pulitzer Prize in 1926, and they saved the life of the Hollywood cowboy actor Tom Mix, a 1930s superstar. . .

Continue reading.

At the link is an podcast of the article.

Written by LeisureGuy

9 March 2020 at 8:06 pm

Machine Learning Takes On Antibiotic Resistance

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Antibiotic resistance is a problem only because evolution is a fact (not a hoax, as some conservatives — particularly evangelicals — maintain). Katharine Harmon Courage writes in Quanta:

Once-powerful antibiotics are losing their efficacy at a disconcerting pace as bacteria evolve immunity to our drugs. At least 700,000 people around the world now die each year from infections that could formerly be treated with antibiotics. A report last year from the United Nations Interagency Coordination Group on Antimicrobial Resistance warned that if no new major advances are made by 2050, mortality could leap to 10 million deaths a year.

What makes this prognosis all the more dire is that the antibiotic pipeline has slowed to a trickle. In the past two decades, only a few new antibiotics have been found that kill bacteria in novel ways, and rising resistance is a problem for all of them. Meanwhile, traditional methods of identifying antibiotics by screening natural compounds continue to come up short. Because of this, some researchers are now turning from the wet lab to silicon power in hopes of finding an answer.

In the February 20 issue of Cell, one team of scientists announced that they — and a powerful deep learning algorithm — had found a totally new antibiotic, one with an unconventional mechanism of action that allows it to fight infections that are resistant to multiple drugs. The compound was hiding in plain sight (as a possible diabetes treatment) because humans didn’t know what to look for. But the computer did.

Using computers and machine learning to make sense of mountains of biomedical data is nothing new. But the team at the Massachusetts Institute of Technology, led by James Collins, who studies applications of systems biology to antibiotic resistance, and Regina Barzilay, an artificial intelligence researcher, achieved success by developing a neural network that avoids scientists’ potentially limiting preconceptions about what to look for. Instead, the computer develops its own expertise.

With this discovery platform, which has been made freely available, “you’re going to identify molecules that don’t look like antibiotics you’re used to seeing,” Collins said. “It really shows how you can use the emerging technology of deep learning in an innovative manner to discover new chemistries.”

Nature’s Dry Well

Ever since Alexander Fleming derived the first antibiotic from fungus, nature has been the font for our antibacterial drugs. But isolating, screening and synthesizing thousands of natural compounds for laboratory tests is extremely expensive and time-consuming.

To narrow the search, researchers have sought to understand how bacteria live and multiply, and then pursued compounds that attack those processes (such as by damaging bacteria’s cell walls, blocking their reproduction, or inhibiting their protein production). “You start with the mechanisms, and then you reverse-engineer the molecule,” Barzilay said.

Even with the introduction of computer-assisted, high-throughput screening methods in the 1980s, however, progress in antibiotic development was virtually nonexistent in the decades that followed. Screening occasionally turned up drug candidates that were toxic to bacteria, but they were too similar to existing antibiotics to be effective against resistant bacteria. Pharmaceutical companies have since largely abandoned antibiotic development, despite the need, in favor of more lucrative drugs for chronic conditions. [Emphasis added. A surprising number of chronic conditions can (in many but not all) cases be effectively treated by lifestyle changes (such as changes in diet and level of exercise). I’ll point out How Not to Die as a useful guide. However, pharmaceutical companies derive no income from patient changes in diet and exercise, only from selling drugs, and thus pharmaceutical companies spend an enormous amount pushing drugs and encouraging a de-emphasis of lifestyle changes. – LG]

The new work by Barzilay, Collins and their colleagues, however, takes a radically fresh, almost paradoxical approach to drug discovery: It ignores how the medicine works. It’s an approach that can succeed only with the support of extremely powerful computing.

Agnostic Learning

Behind the new antibiotic finding is a deep neural network, in which the nodes and connections of its learning architecture are inspired by the interconnected neurons in the brain. Neural networks, which are adept at recognizing patterns, are deployed across various industries and consumer technologies for uses such as image and speech recognition. Conventional computer programs might screen a library of molecules to find certain defined chemical structures, but neural networks can be trained to learn for themselves which structural signatures might be useful — and then find them.

Collins, Barzilay and their team trained their network to look for any compound that would inhibit the growth of the bacterium Escherichia coli. They did so by  . . .

Continue reading.

Written by LeisureGuy

9 March 2020 at 6:46 pm

The parrots that understand probabilities

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Written by LeisureGuy

9 March 2020 at 12:15 pm

Seven Moral Rules Found All Around the World

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The Eldest referred to this on Facebook, and it stimulated my interest. Oliver Scott Curry writes at the Evolution Institute:

What is morality? And are there any universal moral values? Scholars have debated these questions for millennia. But now, thanks to science, we have the answers.

Converging lines of evidence – from game theory, ethology, psychology, and anthropology – suggest that morality is a collection of tools for promoting cooperation1.

For 50 million years humans and their ancestors have lived in social groups. During this time natural selection equipped them with a range of adaptations for realizing the enormous benefits of cooperation that social life affords. More recently, humans have built on these benevolent biological foundations with cultural innovations – norms, rules, institutions – that further bolster cooperation. Together, these biological and cultural mechanisms provide the motivation for social, cooperative and altruistic behavior; and they provide the criteria by which we evaluate the behavior of others. And, according to the theory of ‘morality as cooperation’, it is precisely this collection of cooperative traits that constitute human morality.

What’s more, the theory leads us to expect that, because there are many types of cooperation, there will be many types of morality. Kin selection explains why we feel a special duty of care for our families, and why we abhor incest. Mutualism explains why we form groups and coalitions (there is strength and safety in numbers), and hence why we value unity, solidarity, and loyalty. Social exchange explains why we trust others, reciprocate favors, feel guilt and gratitude, make amends, and forgive. And conflict resolution explains: why we engage in costly displays of prowess such as bravery and generosity; why we defer to our superiors; why we divide disputed resources fairly; and why we recognize prior possession.

And, as predicted by the theory, these seven moral rules appear to be universal across cultures:

  1. love your family
  2. help your group
  3. return favors
  4. be brave
  5. defer to authority
  6. be fair
  7. respect others’ property

My colleagues and I analyzed ethnographic accounts of ethics from 60 societies (comprising over 600,000 words from over 600 sources)2. We found that these seven cooperative behaviors were always considered morally good. We found examples of most of these morals in most societies. Crucially, there were no counter-examples – no societies in which any of these behaviors were considered morally bad. And we observed these morals with equal frequency across continents; they were not the exclusive preserve of ‘the West’ or any other region.

For example, among the Amhara, . . .

Continue reading. There’s more. Emphasis added.

ScienceAlert has an article with a slightly different statement of the seven principles:

These cooperative behaviours and rules – the proposed universal moral code – are the following:

  1. helping family,
  2. helping your group,
  3. reciprocating,
  4. being brave,
  5. deferring to superiors (respect),
  6. dividing disputed resources (fairness), and
  7. respecting prior possession (property rights).

I added the numbering.

Written by LeisureGuy

6 March 2020 at 10:26 am

Posted in Daily life, Evolution

Disease: The revenge of domesticated animals — Michael Greger

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This is a fascinating video from seven years ago, when Dr. Greger was seriously overweight. It’s particularly interesting right now as we face an incipient pandemic of coronavirus. Thanks to JvR for pointing it out (again):

 

Be sure to watch this, and take note of the resources he mentions — for example, the CDC site on pandemic flu preparation.

Candidly, I don’t think any serious steps will be taken. We will treat it much as we treat climate: we now what the problem is, but we take no serious steps to address it because that would require substantive change.

Note that this talk was deliver seven years ago. And nothing really has been done — and we now have the coronavirus moving toward pandemic status.

Written by LeisureGuy

24 February 2020 at 7:08 pm

You’re Likely to Get the Coronavirus

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Perhaps it’s a good time to read The Great Influenza: The Epic Story of the Deadliest Plague in History, by John Barry—wonderful book. (Link is to inexpensive secondhand copies. I do recommend hardcover.)

James Hamblin writes in the Atlantic:

In May 1997, a 3-year-old boy developed what at first seemed like the common cold. When his symptoms—sore throat, fever, and cough—persisted for six days, he was taken to the Queen Elizabeth Hospital in Hong Kong. There his cough worsened, and he began gasping for air. Despite intensive care, the boy died.

Puzzled by his rapid deterioration, doctors sent a sample of the boy’s sputum to China’s Department of Health. But the standard testing protocol couldn’t fully identify the virus that had caused the disease. The chief virologist decided to ship some of the sample to colleagues in other countries.

At the U.S. Centers for Disease Control and Prevention in Atlanta, the boy’s sputum sat for a month, waiting for its turn in a slow process of antibody-matching analysis. The results eventually confirmed that this was a variant of influenza, the virus that has killed more people than any in history. But this type had never before been seen in humans. It was H5N1, or “avian flu,” discovered two decades prior, but known only to infect birds.

By then, it was August. Scientists sent distress signals around the world. The Chinese government swiftly killed 1.5 million chickens (over the protests of chicken farmers). Further cases were closely monitored and isolated. By the end of the year there were 18 known cases in humans. Six people died.

This was seen as a successful global response, and the virus was not seen again for years. In part, containment was possible because the disease was so severe: Those who got it became manifestly, extremely ill. H5N1 has a fatality rate of around 60 percent—if you get it, you’re likely to die. Yet since 2003, the virus has killed only 455 people. The much “milder” flu viruses, by contrast, kill fewer than 0.1 percent of people they infect, on average, but are responsible for hundreds of thousands of deaths every year.

Severe illness caused by viruses such as H5N1 also means that infected people can be identified and isolated, or that they died quickly. They do not walk around feeling just a little under the weather, seeding the virus. The new coronavirus (known technically as SARS-CoV-2) that has been spreading around the world can cause a respiratory illness that can be severe. The disease (known as COVID-19) seems to have a fatality rate of less than 2 percent—exponentially lower than most outbreaks that make global news. The virus has raised alarm not despite that low fatality rate, but because of it.

Coronaviruses are similar to influenza viruses in that they are both single strands of RNA. Four coronaviruses commonly infect humans, causing colds. These are believed to have evolved in humans to maximize their own spread—which means sickening, but not killing, people. By contrast, the two prior novel coronavirus outbreaks—SARS (severe acute respiratory syndrome) and MERS (Middle East respiratory syndrome, named for where the first outbreak occurred)—were picked up from animals, as was H5N1. These diseases were highly fatal to humans. If there were mild or asymptomatic cases, they were extremely few. Had there been more of them, the disease would have spread widely. Ultimately, SARS and MERS each killed fewer than 1,000 people.

COVID-19 is already reported to have killed more than twice that number. With its potent mix of characteristics, this virus is unlike most that capture popular attention: It is deadly, but not too deadly. It makes people sick, but not in predictable, uniquely identifiable ways. Last week, 14 Americans tested positive on a cruise ship in Japan despite feeling fine—the new virus may be most dangerous because, it seems, it may sometimes cause no symptoms at all.

The world has responded with unprecedented speed and mobilization of resources. The new virus was identified extremely quickly. Its genome was sequenced by Chinese scientists and shared around the world within weeks. The global scientific community has shared genomic and clinical data at unprecedented rates. Work on a vaccine is well under way. The Chinese government enacted dramatic containment measures, and the World Health Organization declared an emergency of international concern. All of this happened in a fraction of the time it took to even identify H5N1 in 1997. And yet the outbreak continues to spread.


The Harvard epidemiology professor Marc Lipsitch is exacting in his diction, even for an epidemiologist. Twice in our conversation he started to say something, then paused and said, “Actually, let me start again.” So it’s striking when one of the points he wanted to get exactly right was this: “I think the likely outcome is that it will ultimately not be containable.”

Containment is the first step in responding to any outbreak. In the case of COVID-19, the possibility (however implausible) of preventing a pandemic seemed to play out in a matter of days. Starting in January, China began cordoning off progressively larger areas, radiating outward from Wuhan City and eventually encapsulating some 100 million people. People were barred from leaving home, and lectured by drones if they were caught outside. Nonetheless, the virus has now been found in 24 countries.

Despite the apparent ineffectiveness of such measures—relative to their inordinate social and economic cost, at least—the crackdown continues to escalate. Under political pressure to “stop” the virus, last Thursday the Chinese government announced that officials in the Hubei province would be going door to door, testing people for fevers and looking for signs of illness, then sending all potential cases to quarantine camps. But even with the ideal containment, the virus’s spread may have been inevitable. Testing people who are already extremely sick is an imperfect strategy if people can spread the virus without even feeling bad enough to stay home from work.

Lipsitch predicts that, within the coming year, some 40 to 70 percent of people around the world will be infected with the virus that causes COVID-19. But, he clarifies emphatically, this does not mean that all will have severe illnesses. “It’s likely that many will have mild disease, or may be asymptomatic,” he said. As with influenza, which is often life-threatening to people with chronic health conditions and of older age, most cases pass without medical care. (Overall, around 14 percent of people with influenza have no symptoms.)

Lipsitch is far from alone in his belief that this virus will continue to spread widely. The emerging consensus among epidemiologists is that the most likely outcome of this outbreak is a new seasonal disease—a fifth “endemic” coronavirus. With the other four, people are not known to develop long-lasting immunity. If this one follows suit, and if the disease continues to be as severe as it is now, “cold and flu season” could become “cold and flu and COVID-19 season.”

At this point, it is not even known . . .

Continue reading.

Written by LeisureGuy

24 February 2020 at 6:15 pm

Yuval Noah Harari’s History of Everyone, Ever

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Yuval Harari’s book Sapiens is one of the books on the list of books I find myself repeatedly recommending. To my eyes, it is a history of memetic evolution. Highly readable and very interesting.

Ian Parker writes in the New Yorker:

In 2008, Yuval Noah Harari, a young historian at the Hebrew University of Jerusalem, began to write a book derived from an undergraduate world-history class that he was teaching. Twenty lectures became twenty chapters. Harari, who had previously written about aspects of medieval and early-modern warfare—but whose intellectual appetite, since childhood, had been for all-encompassing accounts of the world—wrote in plain, short sentences that displayed no anxiety about the academic decorum of a study spanning hundreds of thousands of years. It was a history of everyone, ever. The book, published in Hebrew as “A Brief History of Humankind,” became an Israeli best-seller; then, as “Sapiens,” it became an international one. Readers were offered the vertiginous pleasure of acquiring apparent mastery of all human affairs—evolution, agriculture, economics—while watching their personal narratives, even their national narratives, shrink to a point of invisibility. President Barack Obama, speaking to CNN in 2016, compared the book to a visit he’d made to the pyramids of Giza.

“Sapiens” has sold more than twelve million copies. “Three important revolutions shaped the course of history,” the book proposes. “The Cognitive Revolution kick-started history about 70,000 years ago. The Agricultural Revolution sped it up about 12,000 years ago. The Scientific Revolution, which got under way only 500 years ago, may well end history and start something completely different.” Harari’s account, though broadly chronological, is built out of assured generalization and comparison rather than dense historical detail. “Sapiens” feels like a study-guide summary of an immense, unwritten text—or, less congenially, like a ride on a tour bus that never stops for a poke around the ruins. (“As in Rome, so also in ancient China: most generals and philosophers did not think it their duty to develop new weapons.”) Harari did not invent Big History, but he updated it with hints of self-help and futurology, as well as a high-altitude, almost nihilistic composure about human suffering. He attached the time frame of aeons to the time frame of punditry—of now, and soon. His narrative of flux, of revolution after revolution, ended urgently, and perhaps conveniently, with a cliffhanger. “Sapiens,” while acknowledging that “history teaches us that what seems to be just around the corner may never materialise,” suggests that our species is on the verge of a radical redesign. Thanks to advances in computing, cyborg engineering, and biological engineering, “we may be fast approaching a new singularity, when all the concepts that give meaning to our world—me, you, men, women, love and hate—will become irrelevant.”

Harari, who is slim, soft-spoken, and relentless in his search for an audience, has spent the years since the publication of “Sapiens” in conversations about this cliffhanger. His two subsequent best-sellers—“Homo Deus” (2017) and “21 Lessons for the 21st Century” (2018)—focus on the present and the near future. Harari now defines himself as both a historian and a philosopher. He dwells particularly on the possibility that biometric monitoring, coupled with advanced computing, will give corporations and governments access to more complete data about people—about their desires and liabilities—than people have about themselves. A life under such scrutiny, he said recently, is liable to become “one long, stressing job interview.”

If Harari weren’t always out in public, one might mistake him for a recluse. He is shyly oracular. He spends part of almost every appearance denying that he is a guru. But, when speaking at conferences where C.E.O.s meet public intellectuals, or visiting Mark Zuckerberg’s Palo Alto house, or the Élysée Palace, in Paris, he’ll put a long finger to his chin and quietly answer questions about Neanderthals, self-driving cars, and the series finale of “Game of Thrones.” Harari’s publishing and speaking interests now occupy a staff of twelve, who work out of a sunny office in Tel Aviv, where an employee from Peru cooks everyone vegan lunches. Here, one can learn details of a scheduled graphic novel of “Sapiens”—a cartoon version of Harari, wearing wire-framed glasses and looking a little balder than in life, pops up here and there, across time and space. There are also plans for a “Sapiens” children’s book, and a multi-season “Sapiens”-inspired TV drama, covering sixty thousand years, with a script by the co-writer of Mel Gibson’s “Apocalypto.”

Harari seldom goes to this office. He works at the home he shares with Itzik Yahav, his husband, who is also his agent and manager. They live in a village of expensive modern houses, half an hour inland from Tel Aviv, at a spot where Israel’s coastal plain is first interrupted by hills. The location gives a view of half the country and, hazily, the Mediterranean beyond. Below the house are the ruins of the once mighty Canaanite city of Gezer; Harari and Yahav walk their dog there. Their swimming pool is blob-shaped and, at night, lit a vivid mauve.

At lunchtime one day in September, Yahav drove me to the house from Tel Aviv, in a Porsche S.U.V. with a rainbow-flag sticker on its windshield. “Yuval’s unhappy with my choice of car,” Yahav said, laughing. “He thinks it’s unacceptable that a historian should have money.” While Yahav drove, he had a few conversations with colleagues, on speakerphone, about the fittings for a new Harari headquarters, in a brutalist tower block above the Dizengoff Center mall. He said, “I can’t tell you how much I need a P.A.”—a personal assistant—“but I’m not an easy person.” Asked to consider his husband’s current place in world affairs, Yahav estimated that Harari was “between Madonna and Steven Pinker.”

Harari and Yahav, both in their mid-forties, grew up near each other, but unknown to each other, in Kiryat Ata, an industrial town outside Haifa. (Yahav jokingly called it “the Israeli Chernobyl.”) Yahav’s background is less solidly middle class than his husband’s. When the two men met, nearly twenty years ago, Harari had just finished his graduate studies, and Yahav teased him: “You’ve never worked? You’ve never had to pick up a plate for your living? I was a waiter from age fifteen!” He thought of Harari as a “genius geek.” Yahav, who was then a producer in nonprofit theatre, is now known for making bold, and sometimes outlandish, demands on behalf of his husband. “Because I have only one author, I can go crazy,” he had told me. In the car, he noted that he had declined an invitation to have Harari participate in the World Economic Forum, at Davos, in 2017, because the proposed panels were “not good enough.” A year later, when Harari was offered the main stage, in a slot between Angela Merkel and Emmanuel Macron, Yahav accepted. His recollections of such negotiations are delivered with self-mocking charm and a low, conspiratorial laugh. He likes to say, “You don’t understand—Yuval works for me! ”

We left the highway and drove into the village. He said of Harari, “When I meet my friends, he’s usually not invited, because my friends are crazy and loud. It’s too much for him. He shuts down.” When planning receptions and dinners for Harari, Yahav follows a firm rule: “Not more than eight people.”

For more than a decade, Harari has spent several weeks each year on a silent-meditation retreat, usually in India. At home, he starts his day with an hour of meditation; in the summer, he also swims for half an hour while listening to nonfiction audiobooks aimed at the general reader. (Around the time of my visit, he was listening to a history of the Cuban Revolution, and to a study of the culture of software engineering.) He swims the breaststroke, wearing a mask, a snorkel, and “bone conduction” headphones that press against his temples, bypassing the ears.

When Yahav and I arrived at the house, Harari was working at the kitchen table, reading news stories from Ukraine, printed for him by an assistant. He had an upcoming speaking engagement in Kyiv, at an oligarch-funded conference. He was also planning a visit to the United Arab Emirates, which required some delicacy—the country has no diplomatic ties with Israel.

The house was open and airy, and featured a piano. (Yahav plays.) Harari was wearing shorts and Velcro-fastened sandals, and, as Yahav fondly observed, his swimming headphones had left imprints on his head. Harari explained to me that the device “beams sound into the skull.” Later, with my encouragement, he put on his cyborgian getup, including the snorkel, and laughed as I took a photograph, saying, “Just don’t put that in the paper, because Itzik will kill both me and you.”

Unusually for a public intellectual, Harari has drawn up a mission statement. It’s pinned on a bulletin board in the Tel Aviv office, and begins, “Keep your eyes on the ball. Focus on the main global problems facing humanity.” It also says, “Learn to distinguish reality from illusion,” and “Care about suffering.” The statement used to include “Embrace ambiguity.” This was cut, according to one of Harari’s colleagues, because it was too ambiguous.

One recent afternoon, Naama Avital, the operation’s C.E.O., and Naama Wartenburg, Harari’s chief marketing officer, were sitting with Yahav, wondering if Harari would accept a hypothetical invitation to appear on a panel with President Donald Trump.

“I think that whenever Yuval is free to say exactly what he thinks, then it’s O.K.,” Avital said.

Yahav, surprised, said that he could perhaps imagine a private meeting, “but to film it—to film Yuval with Trump?”

“You’d have a captive audience,” Wartenburg said.

Avital agreed, noting, “There’s a politician, but then there are his supporters—and you’re talking about tens of millions of people.”

“A panel with Trump?” Yahav asked. He later said that he had never accepted any speaking invitations from Israeli settlers in the West Bank, adding that Harari, although not a supporter of settlements, might have been inclined to say yes.

Harari has acquired a large audience in a short time, and—like the Silicon Valley leaders who admire his work—he can seem uncertain about what to do with his influence. Last summer, he was criticized when readers noticed that the Russian translation of “21 Lessons for the 21st Century” had been edited to make it more palatable to Vladimir Putin’s government. Harari had approved some of these edits, and had replaced a discussion of Russian misinformation about its 2014 annexation of Crimea with a passage about false statements made by President Trump.

Harari’s office is still largely a boutique agency serving the writing and speaking interests of one client. But, last fall, it began to brand part of its work under the heading of “Sapienship.” The office remains a for-profit enterprise, but it has taken on some of the ambitions and attributes of a think tank, or the foundation of a high-minded industrialist. Sapienship’s activities are driven by what Harari’s colleagues call his “vision.” Avital explained that some projects she was working on, such as “Sapiens”-related school workshops, didn’t rely on “everyday contact with Yuval.”

Harari’s vision takes the form of a list. “That’s something I have from students,” he told me. “They like short lists.” His proposition, often repeated, is that humanity faces three primary threats: nuclear war, ecological collapse, and technological disruption. Other issues that politicians commonly talk about—terrorism, migration, inequality, poverty—are lesser worries, if not distractions. In part because there’s little disagreement, at least in a Harari audience, about the seriousness of the nuclear and climate threats, and about how to respond to them, Harari highlights the technological one. Last September, while appearing onstage with Reuven Rivlin, Israel’s President, at an “influencers’ summit” in Tel Aviv, Harari said, in Hebrew, “Think about a situation where somebody in Beijing or San Francisco knows what every citizen in Israel is doing at every moment—all the most intimate details about every mayor, member of the Knesset, and officer in the Army, from the age of zero.” He added, “Those who will control the world in the twenty-first century are those who will control data.”

He also said that Homo sapiens would likely disappear, in a tech-driven upgrade. Harari often disputes the notion that he makes prophecies or predictions—indeed, he has claimed to do “the opposite”—but a prediction acknowledging uncertainty is still a prediction. Talking to Rivlin, Harari said, “In two hundred years, I can pretty much assure you that there will not be any more Israelis, and no Homo sapiens—there will be something else.”

“What a world,” Rivlin said. The event ended in a hug.

Afterward, Harari said of Rivlin, “He took my message to be kind of pessimistic.” Although the two men had largely spoken past each other, they were in some ways aligned. . .

Continue reading.

Written by LeisureGuy

13 February 2020 at 12:41 pm

East to Eden: The Apple’s Origin

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Roger Deakin, with Robert Macfarlane, writes in Emergence magazine:

Introduction & Postscript

by Robert Macfarlane

In the summer of 2006, my friend the writer, forester, and naturalist Roger Deakin died of cancer, too fast and too young. A woodsman to the last, his pine coffin was decorated with a wreath of oak leaves, and his ashes were given to the earth in view of mature stands of cherry, oak, and silver birch. I was new to death then, but even had I not been, the loss of Roger would still have struck hard to my heart. “I want my friends to come up unstoppably, like weeds,” Roger wrote once in a journal entry, and our friendship, though only a handful of years old, was a weedy one, flourishing out of all proportion to its calendar.

Roger’s abrupt death felt most cruel to me in its lopping of future growth. We had made such plans! To stake out the badger setts in a wood near Roger’s Suffolk home at Walnut Tree Farm, with some infra-red goggles that Roger was confident he could source. To construct a coracle (birchwood frame, cowhide hull), and then paddle it across a meaningful stretch of ocean—or, failing that, across a good-sized pond. There were books to write together, conservation battles to fight, television programmes to make, jokes to tell, and all those unfinished—no, unstarted—conversations that, in the manner of conversations with Roger, would rapidly branch outwards, ending very far from where they had first taken root.

Roger was many things—a filmmaker, environmentalist, campaigner, poet, teacher—but he became best known for his trilogy of extraordinary non-fiction books about nature, people, and place: Waterlog (1999), his classic account of swimming through Britain’s rivers, lakes, estuaries, and lochs; Wildwood: A Journey Through Trees (2007), which describes his years spent travelling through forests and woodland cultures in Britain, Australia, Europe, and Central Asia, as well as chronicling his long family history of radical and community involvement with trees and forestry (“I am a woodlander,” he wrote in the opening pages of that book, “I have sap in my veins”); and Notes from Walnut Tree Farm (2008), which gathers decades of his writing about his home landscape in Suffolk. Roger travelled widely but always returned to that timber-framed farmhouse and the twelve acres of meadow, hedgerow, and copse that surrounded it. This was his fixed point, where one foot of his compass was planted, while the other roved and circled.

What follows here is a chapter from Roger’s Wildwood, to which I have written a short postscript essay that tells—by means of the story of a seed and a tree—how Roger continues to root and branch through my life and the lives of many others, long after his death.

East to Eden

Iam travelling to Kazakhstan, propelled by a story told to me by Barrie Juniper that is something between the Book of Genesis and the Just So Stories: How the Apple Began. Beside a black mulberry tree he planted thirty years ago outside the porters’ lodge at St Catherine’s College Oxford, I met Barrie, a don of the college, luminary of the Oxford Plant Sciences Department and apple guru. Ruby stains of the fallen mulberries smudged the paving stones. I had heard of Juniper’s pioneering work in tracking down the origins of the domestic apple to the Tien Shan Mountains of Kazakhstan and had come to sit at his feet and learn more. Over lunch, he outlined the long journey of the domestic apple from the wild fruit forests of the Tien Shan along the so-called Silk Road to the west. In the course of that journey, Juniper has discovered, the wild apple of the Tien Shan, Malus sieversus, evolved into the domestic apple, Malus domesticus, and eventually found its way to Britain with the Romans.

Barrie Juniper spent years searching for the ancestors of the domestic apple. He reckoned there were now some 20,000 varieties in the world including over 6,000 recorded in Britain. Many of the old varieties that haven’t died out altogether have become rarities, so Juniper realized that mapping out their genetic identities through DNA samples was a matter of urgency. In 1998 he travelled to Central Asia with some Oxford colleagues in search of the ur-apple. They went to Kazakhstan, to Alma-Ata, now known as Almaty. Alma-Ata is usually translated as ‘Father of all Apples’, although there is a school of thought in Kazakhstan that believes it is more accurately rendered as ‘Where the Apples Are’. It had taken Juniper over a year’s struggle with Kazakh official protocol to get permission to visit the outlying regions of the Tien Shan Mountains in search of wild apples, but eventually he and his companions set out from Almaty in the summer of 1998 under military escort to the remote mountain slopes known as the Djunguarian Alatau. Here they found forests of wild fruit: wild pears, plums, apricots, hawthorns, rowans and apples. The apples were all Malus sieversii, and their fruits varied enormously in size, shape and flavour, from the hard and the tart to apples that tasted and looked remarkably like our own familiar cultivated apples.

They collected apple specimens and took them home to Oxford, where they analysed their DNA and discovered that Malus sieversii shows a far closer affinity with the domestic apple than with any other wild species. But how could all the thousands of varieties of the domestic apple have descended from the wild fruit forests of the Tien Shan? To add to the mystery, Malus sieversii is reluctant to hybridize with other species. So how did all these variations on the theme of the eating apple arise? What makes the apple such a chameleon? The answer, in a word, is that apple trees are heterozygous. Plant the pips of a hundred apples from the same tree and the new generation of trees can differ, often dramatically, from their parents and from each other. This is how new kinds of apples have arisen by chance over the centuries: people taking a fancy to this or that new fruit, then propagating from that particular tree by taking cuttings from the shoots and grafting them on to other trees. All Bramley seedlings are descended from a single tree in someone’s back garden in Northampton. And so on, down thousands of years, so every single kind of eating apple in the world is a direct descendant of the apples that evolved in the forests of the Tien Shan.

After lunch, Barrie Juniper and I sat down in the fellows’ common room over coffee and the Times Atlas, which we opened at Central Asia. He began to explain how he thinks the domestic apple evolved; a story that ranged from the Yangtze Valley, to Neolithic Mesopotamia, to the orchards of Oxford. According to Juniper, Malus, the botanical family to which all apples belong, first evolved about twelve million years ago. To judge from the twenty-odd wild species that still exist in central and southern China, it probably bore a small fruit with hard but edible seeds not unlike those of its close relation, the rowan tree. The seeds would have been spread by birds. A small group of species penetrated north-west through the fertile country that is now Gansu Province into the area that was to become the Tien Shan Mountains as they arose in the same geological upheaval that created the Himalayas. Juniper believed that just one or possibly two of these ‘bird apple’ seeds was lifted over the rising hills to the Tien Shan and the valley of the Ili River, most likely in the crop or faeces of a migrating bird. The spread of the inhospitable Gobi Desert then prevented any migration of apple seed back to the east, and although they were walled in by glaciation to the west, the ice never reached these mountains.

In the foothills and valleys of the Tien Shan range, the new apple found itself in a genuine paradise. Bears, deer and wild pigs lived in the spreading woodlands, eating the wild fruit in autumn and selecting the sweeter, juicier apples while bees laboured in the pollination department of the same evolutionary project. The bears, living in the abundant caves of the Tien Shan, were avid fruit-eaters, and pips could pass through their guts unharmed to germinate in the dung. As Juniper pointed out, the baseball-glove claws of bears are perfectly suited to the grasping of apples. He had seen how enthusiastically they will vandalize a tree bearing a favourite sweet apple, dragging off whole branches in a kind of rough pruning. Out on the steppe, huge herds of wild horses and donkeys also browsed on the ripe apples and helped them spread westwards and south along the range towards what is now Almaty. Like the bears, they kept on selecting the larger, juicier, sweeter apples, so that as it spread west, the apple gradually became larger. At the same time this evolutionary pressure changed it from a ‘bird’ fruit with edible seeds to a ‘mammal’ fruit with poisonous seeds. The bitter taste of apple pips is cyanide, and the smooth, hard, teardrop seed coat evolved as the perfect streamlined vehicle to pass intact through an animal’s guts.

Juniper believed that by the time the ‘new’ apple had populated the northern slopes of the eastern Tien Shan and reached near Almaty, it had evolved into something like its present size and culinary appeal. Later, as human populations began to travel back and forth along the old animal migration routes between east and west, they helped to spread the new fruit. People call these routes ‘The Silk Roads’, but they were in use five or six thousand years before the discovery of silk, which lent its name to the route only during the period from ad 0 to 400. In the early days, said Juniper, camels would have been the means of transport along the routes, but, although they are as fond of apples as any other herbivore, their digestive system is so efficient that not even apple pips will survive it. Then, around 7,000 years ago, something momentous happened on the plains of Kazakhstan. The horse was domesticated, and soon started to travel the trading routes. The more direct northern trade routes led from Shanghai and Xian via Urumchi in north-west China to Almaty, Tashkent and Bokhara, then through Anatolia all the way to the Mediterranean coast. During winter the Tien Shan Mountains were impassable in the snow, so traders took the long way round to the south. But when the snows melted in July, the caravans turned north and until the first snows in November travelled through the Ili Valley and the Tien Shan range via Almaty, passing through fruit forests on the way. . .

Continue reading. There’s much, much more.

The story of the domestication of the horse (and of the invention of the wheel) is recounted in the fascinating book by David Anthony, The Horse, the Wheel, and Language: How Bronze-Age Riders from the Eurasian Steppes Shaped the Modern World. All domesticated horses are descended from the same stallion.

Written by LeisureGuy

7 February 2020 at 2:55 pm

The very sociable hermit crab

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Katherine Rundell writes in the London Review of Books (and hermit crabs, apparently):

It​ was, perhaps, a hermit crab that ate Amelia Earhart. For five nights after Earhart disappeared from the sky in 1937, the US navy picked up distress signals from Nikumaroro, an uninhabited island in the Western Pacific. When a rescue team reached the island a week later – it took time, since planes had to be loaded onto battleships – it was deserted. But researchers on the island have since discovered human bones matching Earhart’s size: another, later team discovered the shattered glass of a woman’s compact mirror and a few flakes of rouge. The bones were sent to be tested, but were lost on the way, and unless they are found we won’t ever be sure whether they belonged to the valiant, hell-for-leather aviatrix with the face of a lion. But, if the bones were Earhart’s, only 13 were found, and the human body has 206: where were the other 193?

Crunched, perhaps, to fragments. Nikumaroro is home to a colony of coconut hermit crabs: the world’s largest land crab, so called because of its ability to crack open a coconut, manoeuvring a claw into one of the nut’s three eyeholes and prying it open. The oldest live to more than a hundred, and grow to be wider than three feet across: too large to fit in a bathtub, exactly the right size for a nightmare. In 2007, researchers decided to test the Earhart theory. The carcass of a small pig was offered to the crabs on the island, to see what they might have done to Earhart’s dead or dying body. Following their remarkable sense of smell, they found the pig and tore it apart, making off with its bones to their burrows under the roots of the trees. Their strength is monumental: their claw grip can produce up to 3300 newtons of force (the bite force of a tiger is 1500 newtons). Darwin called them ‘monstrous’: he meant it as a compliment.

Even monsters, though, start small. Some hermit crabs inhabit the land and others the sea, but they all begin microscopic and underwater. They’re released as eggs into the ocean, hatch as unprepossessing larvae (though what larvae are prepossessing?) and it’s only after several months that they are large enough to inhabit the smallest empty shell they can find. As they grow, they graduate from one scavenged shell to another, most frequently the delicately sworled shell of a sea snail, grasping its columella with claspers at the tip of their abdomen. They shed their exoskeletons, releasing into the sea a semi- transparent floating crab – a ghost. The coconut crab eventually outgrows all other shells, and begins to live uncovered on the land, but the majority of the 1100-odd species of hermit crabs live in borrowed homes all their lives.

Hermit crabs are not, in fact, hermitical: they’re sociable, often climbing on top of one another to sleep in great piles, and their group behaviour is so intricately ordered that they make the politics of Renaissance courts look simplistic. When a crab comes across a new shell, it will climb into it and try it on for size. If the shell is of good quality but too big, it waits nearby for another crab to come and inspect it. If that crab also finds it too large, it joins the first crab, holding onto its claw until a queue develops – it can stretch to twenty crabs, arranged in order of size from smallest to largest, each holding onto the next: a hermit crab chorus line. When at last a crab arrives who can fit the vacant shell, the first crab in line claims the new crab’s former shell, and there is a flurry of crabs climbing into their neighbour’s home. The crab’s abdomen is soft and vulnerable to attack while exposed, so the whole process takes place with astonishing rapidity.

They’re not only foragers for homes: some are renovators. The anemone hermit crab . . .

Continue reading.

Written by LeisureGuy

3 February 2020 at 4:30 pm

Life without design

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Chiara Marletto, a postdoctoral research associate and junior research fellow at Wolfson College at the University of Oxford, writes in Aeon:

Living things have puzzled and challenged us since the dawn of our species. Even in the light of our modern scientific understanding, they seem remarkable. A merlin falcon hunting its prey, a hummingbird suspended in the air beside a flower, the self-reproduction of a bacterial cell: all are instances of stunning control and precision. How could anything so complex have originated from inert matter?

For millennia, some of the most brilliant thinkers have attempted to answer this question. Most of them concluded that living things must have been produced by an intentional design process. They were wrong, of course: the theory of evolution by variation and natural selection – Charles Darwin’s momentous leap – shows how those stupendously intricate mechanisms can come about without one. Yet the task of showing how life itself can arise without design is surprisingly vexed.

The very problem Darwin’s theory addresses is ultimately rooted in physics: living things have certain properties that seem to set them apart from other aggregations of inert matter. They have many different subparts – instantiating biological adaptations – all coordinating to some function. That’s the key property: they closely resemble objects that have literally been designed, such as factories and robots. For example, the ciliary muscles and the lens in the eye coordinate exquisitely to permit vision, just like the optical components of a sophisticated camera. In modern biology, this is called the appearance of design – a property described by Socrates and given canonical expression in 1802 by William Paley in his ‘watchmaker’ argument for the existence of God.

More generally, living things, again just like factories and robots, have the ability to perform physical transformations with a very high degree of precision, and to do so repeatedly and reliably. A goat’s jaws and heart just keep on chewing and beating for its whole lifetime. If you got the goat to graze your lawn, it would mow it to high accuracy and be just as capable of doing the same when presented with another lawn. It just keeps going: the goat is, among other things, a lawnmowing machine.

Unlike factories, all living things rely on a rather peculiar contrivance: the living cell. Cells can self-reproduce, manufacturing new instances of themselves in a process involving, at its heart, the faithful replication of the genetic information contained in the cell’s DNA. We find this capacity nowhere in the rest of nature. Even among human technologies, there are only dim foreshadowings of it, such as 3D printers that print some of their own spare parts.

Why should such features of living things constitute a problem for physics? Crucially, what can and cannot be made to happen in the physical world is determined by physical laws. For example, a perpetual motion machine cannot be constructed, no matter what resources are devoted to the task, as it is forbidden by those laws. Conversely, given the presence of life in our universe, physics must be such as to allow for it.

But our laws of physics provide only certain elementary objects, such as simple chemicals, in great numbers. These objects do not, in themselves, have the ability to repeatedly cause highly accurate transformations. Neither do they seem adapted to do anything in particular. If they do cause transformations, it is neither very accurately nor reliably: they wear out and make errors, their resources get depleted, and so on. In other words, the laws of physics contain no built-in facility for accurate transformations; nor, in particular, for biological adaptations that can bring such transformations about. They are no-design, in this special sense. Thus the problem with living things, expressed within physics, is that they are highly adapted to effect all sorts of transformations to high accuracy, whereas the laws of physics aren’t.

Given that life isn’t the output of an intentional design process, but evolved, how could living things have evolved given these design-free laws of physics? Darwin’s theory addresses this problem, explaining that variation and natural selection bring about the appearance of design. But this in itself doesn’t close the explanatory gap, as we can see especially clearly in the modern version of Darwin’s theory – neo-Darwinism. At its heart are the replicators, or genes – bits of DNA that are transmitted, by replication, to the next generation. Moreover, for replication to be as accurate as it is in living things, accurate self-reproduction of the cell is also required. In short, the theory presupposes the possibility of certain accurate physical transformations, and these are just what no-design laws of physics fail to provide in their starter kit.

Here’s where the puzzle arises. Biological replication and self‑reproduction are in fact such stupendously well‑orchestrated physical transformations that one must explain how they are possible under the simple, no‑design laws of physics such as ours. This additional explanation, which was not included in the theory of evolution, is essential for that theory to properly explain how living things arise without intentional design – to close the explanatory gap.

Now, it turns out that an explanation of this sort is peculiarly difficult to formulate using the prevailing methods of physics. The latter can predict only what a physical system will do (or will probably do) at a later time, given certain initial conditions and laws of motion. But applying laws of motion to particles is an intractably laborious way to express the appearance of design, replication, self‑reproduction and natural selection. Those processes are highly emergent, involving the collective motion of countless interacting particles.

There is more. Even if one could predict that – given certain dynamical laws and initial conditions – particles would aggregate so as to form a goat at a certain time, this would not at all explain whether a goat could have come about without design. The design of the goat, for all we know, could be encoded in the initial conditions or in the laws of motion. In general, one must explain whether and how a goat is possible (ie, permitted) under no‑design laws of physics; not just predict that it will (or will probably) happen, given some version of the actual laws and initial conditions.

Thinking within the prevailing conception has led some physicists – including the 1963 Nobel Prize-winner Eugene Wigner and the late US-born quantum physicist David Bohm – to conclude that the laws of physics must be tailored to produce biological adaptations in general. This is amazingly erroneous. If it were true, physical theories would have to be patched up with ‘design-bearing’ additions, in the initial conditions or the laws of motion, or both, and the whole explanatory content of Darwinian evolution would be lost.

So, how can we explain physically how replication and self reproduction are possible, given laws that contain no hidden designs, if the prevailing conception’s tools are inadequate?

By applying a new fundamental theory of physics: constructor theory.

Constructor theory is a mode of explanation proposed by David Deutsch, visiting professor of physics at the University of Oxford, who pioneered the theory of the universal quantum computer. With constructor theory, Deutsch generalises some of the insights that led to that earlier idea, applying them now to the whole of physics.

In constructor theory, physical laws are formulated only in terms of which tasks are possible (with arbitrarily high accuracy, reliability, and repeatability), and which are impossible, and why – as opposed to what happens, and what does not happen, given dynamical laws and initial conditions. A task is impossible if there is a law of physics that forbids it. Otherwise, it is possible – which means that a constructor for that task – an object that causes the task to occur and retains the ability to cause it again – can be approximated arbitrarily well in reality. Car factories, robots and living cells are all accurate approximations to constructors.

This radical change of perspective is consistent with current explanations in terms of initial conditions and laws of motion, but permits . . .

Continue reading.

Written by LeisureGuy

21 January 2020 at 4:16 am

Posted in Daily life, Evolution, Memes

A doctor talks about his switch from low-carb/keto diet to whole-food plant-based diet

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And as blog readers know, I also was able to discontinue all my medications (for diabetes, for high blood pressure, and for cholesterol control) 10 weeks after switching from a low-carb diet to a whole-food plant-based diet.

Written by LeisureGuy

20 January 2020 at 9:17 pm

A Year Inside a Growing American Terrorist Movement

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In New York, Photo Portfolio By Mark Peterson, Introduction By Claudia Rankine, and Reporting by James D. Walsh:

When Dylann Storm Roof walked into the Emanuel African Methodist Episcopal Church in Charleston, South Carolina, he joined the Bible-study class before gunning down nine African-Americans as they prayed.

Roof still communicates with his admirers on the outside. In jail, he began exchanging letters with a man in Arkansas named Billy Roper. A former schoolteacher and the son and grandson of Klansmen, Roper leads the Shield Wall Network, a group of several dozen white nationalists who organize rallies and conferences — often collaborating with neighboring hate groups — with the goal of building a white ethno-state. “I have a lot of empathy for him. I’m 47, and he’s young enough to be my son,” Roper said of Roof when interviewed recently for this project. “These millennials and now, I guess, Gen-Zers that are coming up, they are not stupid about the demographic trends and what they portend for the future. That angst, that anxiety that plagues them, drives them to do rash things — whether it’s that rash or not — I can empathize with.” I would humbly suggest we believe that Roper is being sincere, and that he speaks for many.

Roper and Roof are only two of those affiliated with the 148 white-nationalist hate groups in this country. Though it is impossible to calculate their exact membership numbers (as individual groups either conceal or inflate them), their violence is indisputable. White supremacists were responsible for the deaths of at least 39 people in 2018 alone. And the activity has not slowed this year: not in January, as neo-Nazis plastered flyers outside newspaper offices and homes in Washington State and the Carolinas and an army veteran pleaded guilty to killing a black man in New York to “ignite a racial war”; in February, as Vermont synagogues and LGBT centers were vandalized and a self-described white-nationalist Coast Guard lieutenant was arrested for plotting a domestic terror attack; in March, as WELCOME TO GERMANY and GAS THE JEWS were spray-painted outside Oklahoma City Democratic Party and Chickasaw Nation offices and, on the Upper East Side, classmates handed their school’s only black ninth-grader a note reading “n—–s don’t have rights”; in April, as a shooting at a synagogue left one dead and three injured and FBI Director Christopher Wray called white supremacy a “persistent, pervasive” threat to the country; in May, as swastikas fell from the sky — on flyers dropped by drones outside an Ariana Grande concert — and were scrawled on public spaces in at least three states; in June, as far-right groups rallied in Portland, Oregon, for the first time that summer; in July, as a man promoted a white-power manifesto on Instagram before killing three and wounding 17 others at the Gilroy Garlic Festival in California; in August, as another angry young man — this one 1,000 miles away in El Paso, Texas — posted an anti-immigrant manifesto online then committed this year’s most deadly mass shooting, killing 22 and injuring 24 at a Walmart; in September, as the Department of Homeland Security added white-supremacist extremism to its list of priority threats, the same month a swastika appeared on its walls; in October, as swastikas also appeared on Cape Cod and invitations to a white-supremacist gathering were mailed to Maine residents; in November, as a white-supremacist group filmed a video outside Mississippi’s Emmett Till Memorial; nor this month, as students flashed possible white-power signs at an Army-Navy football game.

The photojournalist Mark Peterson has documented this year, traveling the country to surface the extent of the activity and catalogue the most dangerous ideologies. His quotidian look at contemporary American Confederacy and white nationalism shows us our neighbors in other robes. The people portrayed are living among us in every region of the country, in our workplaces, in our government, on social media, and, for some, in our homes. Their culture is made up of both public rallies and private rituals. We see their homes and their streets and their schools, and that these are also our streets and our schools and our neighbors. “These pictures weren’t just taken in the South,” says Peterson, who covers the right wing and began documenting the rise of white nationalism after the 2016 election. “They were taken in New York, in New Jersey, in California, in Portland. The idea of quarantining it or ignoring it: That didn’t work in the past when they tried to do that, and it won’t now.”

The barrage of daily headlines makes it easy to see this year’s incidents as isolated, as white noise in the background of our relentless political moment. But as disturbing as they are, these images portray the American story. It is our inheritance, institutionalized since the Civil War by a government that only recently, and tentatively, began to address domestic terrorism for what it is. White nationalism, legitimized by our president’s support of “very fine people,” has flourished in part because of this refusal to look it squarely in its face and acknowledge it as homegrown. Without a full accounting of the reality, there can be no remedy. To look away is a form of collaboration. —Claudia Rankine

HATE ON THE RISE

After a white supremacist killed 51 people in two New Zealand mosques in March, President Trump was asked if he thought the threat of white nationalism was on the rise. “I don’t, really,” he responded. “I think it’s a small group of people that have very, very serious problems.”

Hate-crime statistics are notoriously difficult to calculate. Local and state law-enforcement agencies are not required to submit numbers to the FBI, laws defining hate crimes vary from state to state, and experts estimate that more than half of all hate crimes go unreported. According to the FBI, hate-crime violence hit a 16-year high in 2018 with the black, Jewish, Latino, and transgender communities being targeted more than ever and the nation’s largest cities seeing the most activity. The FBI’s 2019 numbers won’t be available until next November, but indications suggest they will continue to trend upward. The most deadly mass shooting of 2019 was committed by a xenophobic extremist in El Paso, Texas. “Lone wolf” killers have found their pack.

Continue reading. There’s much more. Photos at the link showing a meme that, unlike Christianity, is gaining ground in the US.

Written by LeisureGuy

19 December 2019 at 3:30 pm

Posted in Daily life, Evolution, Memes

Christianity meme fading in 21st century America

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The above chart is from a Wall Street Journal article. Meme evolution in action.

Written by LeisureGuy

19 December 2019 at 3:20 pm

Posted in Daily life, Evolution, Memes

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