Posts Tagged ‘genetics’
“When you mix science and politics, you get politics:*…
Tina Hesman Saey on a looming threat to the U.S…
Soviet scientists in the 1930s knew what could happen if they bucked the party line: denunciation, firing and banishment from the scientific establishment, even imprisonment and death. Political reprisals against those who opposed the views of dictator Joseph Stalin and his followers — and the dubious science they endorsed — led to the starvation of millions, as well as to decades of lost progress in fields from agriculture to molecular biology.
Now, scientists are warning that history could repeat itself — but in the United States.
A new proposal from the U.S. Office of Management and Budget would put political appointees in charge of funding decisions traditionally overseen by scientists. In recent years, the federal government has funded about 40 percent of basic science research in the United States.
The OMB’s more than 400-page proposed rule change would let political appointees decide how to hand out federal research funds and who can get them. It would cut funding for collaboration with scientists in other countries and restrict scientists’ ability to communicate their findings. What’s more, it could prevent research on matters that President Donald Trump’s administration has deemed “not in the national interest” — such as studies on health disparities, mRNA-based vaccines and research that doesn’t recognize biological sex as a strict binary.
The new rules would also give OMB the power to rescind previously approved research funds. The proposal “poses a sweeping threat to federal grantmaking and the responsible stewardship of American taxpayer dollars,” the science advocacy group Stand Up for Science Foundation said in a report. In addition, it would impact nonscientific grants supporting services for mental health, housing, education, veterans and Tribal nations, affecting the health and well-being of millions.
So far, OMB has received more than 98,000 comments on the proposal. The public comment period closes July 13. It then will be up to OMB to decide whether to keep the rule as is, revise it or scrap it.
These far-reaching measures are already drawing parallels to dark moments in scientific history. Some researchers say the recent mass firings, policy changes and grant cancellations at federal research institutions, including the U.S. National Institutes of Health and Centers for Disease Control and Prevention, closely mirror what happened in the U.S.S.R. under Stalin. “A similar threat now hangs over U.S. science,” the editorial board of The New England Journal of Medicine wrote in June.
Its editorial invoked the example of Trofim Lysenko [see here], an agronomist and astute political operator who rose to power in the 1930s Soviet Union under Stalin.
Until the 1930s, “the Soviet Union was a real powerhouse in the field of genetics,” says Lee Dugatkin, an evolutionary biologist and historian of science at the University of Louisville in Kentucky.
Then, Lysenko came along. “This guy was your sort of classic charlatan,” Dugatkin says. “He had the equivalent of a mail order degree in agriculture, but he was quite good with the press, and he started to basically spread this idea out there that he was capable of dramatically increasing crop yield, particularly wheat.”
Lysenko’s supposed innovation was a process called vernalization and amounted to soaking seeds in freezing water. The resulting plants — and all their offspring — should be resistant to the U.S.S.R.’s famously cold winters, Lysenko reasoned.
His reasoning was based on a disproven idea in evolutionary biology called Lamarckian inheritance. French biologist Jean-Baptiste Lamarck and his followers thought that things an organism experiences in its lifetime can be handed down to the next generation. The classic example is a giraffe that has to stretch to reach leaves producing offspring with long necks.
This idea ran counter to Mendelian genetics, which holds that genes — not environmental influences — control traits and are passed to offspring. Mendelian geneticists thought it would take five years to breed more cold-tolerant crops. Lysenko said he could do it in two to three years.
Stalin didn’t have time to wait. He was trying to get collective farms going and needed to increase crop yields to feed more than 150 million people. Large parts of the country had already suffered from famine in 1932 and 1933 and about 6 million people died. Some resorted to cannibalism.
Stalin embraced Lysenko’s quick-fix approach. That decision, says Michael Gordin, a historian of science at Princeton University, was “something that the majority of people at the time, and everyone since, considers the wrong side of the dispute.”
Lysenko was put in charge of a prestigious genetics institute and forced his scientifically unsound farming practices on the collective farms. His methods were disastrous.
Soaking seeds in freezing water hampered germination, leading to crop losses. Millions starved. Meanwhile, Mendelian genetics was branded a “whore of capitalism,” and geneticists were forced to renounce their views or lose their jobs. Many were jailed, and almost a dozen were executed or died in prison.
The Soviet Union lost its scientific leadership role and sat on the sidelines for important scientific discoveries of the 1950s and beyond. One, Gordin says, was the development of “massively” productive hybrid corn. The country also missed out on the discovery of DNA and the advent of molecular biology, putting Soviet genetics decades behind the rest of the world.
Soviet genetics did not recover from Lysenko’s influence until after the break-up of the Soviet Union in the late 1980s and early 1990s, Gordin says. “I think you’d be hard pressed to find anybody who thinks that … Russia is today, or Ukraine, or any post-Soviet successor state, is a leading molecular biology country.”…
The Soviets did it, and it didn’t end well: “Here’s what happens when you put politicians in charge of science,” from @thsaey.bsky.social in @sciencenews.bsky.social.
See also: Idiocracy
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As we remember the past so as not to repeat it, we might recall that it was on this date in 1834 that the Spanish Inquisition (finally) ended. Authorized by Pope Sixtus IV in 1478, the Inqusition was initially led by inquisitors (Miguel de Morillo and Juan de San Martín) who were appointed by the future Catholic monarchs, King Ferdinand II of Aragon and Queen Isabella I of Castile. It was originally (ostensibly) intended primarily to identify heretics; its aim, to maintain Christian orthodoxy. But it became an effective instrument of state power by replacing the Medieval Inquisition, which was under Papal control.
Over its course, the Inquisition prosecuted an estimated 150,000 people for various offences. An estimated 3,000–5,000 were turned over to the state for execution, particularly in the initial 50 years, mostly by burning at the stake. Other punishments included penance and public flogging, exile, enslavement on galleys, and prison terms ranging from several years to life. In many of these punishments an important motive was the confiscation of all the victims’ property.
As Monty Python observed, “nobody expects the Spanish Inquisition.” And nobody expected it to last 356 years.
“Juggling is sometimes called the art of controlling patterns, controlling patterns in time and space”*…
A skill for our times…
The Library of Juggling is an attempt to list all of the popular (and perhaps not so popular) juggling tricks in one organized place. Despite the growing popularity of juggling, few websites are dedicated to collecting and archiving the various patterns that are being performed. Most jugglers are familiar with iconic tricks such as the Cascade and Shower, but what about Romeo’s Revenge or the 531 Mills Mess? The goal of this website is to guarantee that the tricks currently circulating around the internet and at juggling conventions are found, animated, and catalogued for the world to see. It is a daunting task, but for the sake of jugglers everywhere it must be done.
For every trick found in the Library, there will be an animated representation of the pattern created via JugglingLab, in addition to general information about the trick (siteswap, difficulty level, prerequisite tricks, etc.). If I am able to run the pattern, then I will provide a text-based tutorial for the trick with the help of animations. I will also include links to other tutorials for the trick that can be found online, ranging from YouTube videos to private sites like this one. If I am unable to provide my own tutorial, there will still be a short description of the trick in addition to outside tutorials and demonstrations…
… if you have come to the Library looking to find out how to start juggling, than it would be best to begin with the Three Ball Cascade pattern. If you are a juggler who is already familiar with the basics, then the various tricks included in the Library can be accessed via the navigation tree on the left, or you can click here to view all of the tricks by difficulty…
Enjoy “The Library of Juggling.”
And see also: “The Museum of Juggling History,” the resources at the International Jugglers’ Association, and “The world cannot be governed without juggling.”
* mathematician (and juggler) Ronald Graham
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As we toss ’em up, we might send carefully-calculated birthday greetings to G. H. Hardy; he was born on this date in 1877. A mathematician who made fundamental contributions to number theory and mathematical analysis, Hardy juggled other interests as well– for example his Hardy–Weinberg principle (“allele and genotype frequencies in a population will remain constant from generation to generation in the absence of other evolutionary influences”) is now a basic principle of population genetics.
In Hardy’s own estimation, his greatest contribution was something else altogether: from 1917, Hardy was the mentor of the Indian mathematician Srinivasa Ramanujan, a relationship that has become celebrated. Hardy almost immediately recognised Ramanujan’s extraordinary (albeit untutored brilliance), and the two became close collaborators. When asked by a young Paul Erdős what his greatest contribution to mathematics was, Hardy unhesitatingly replied that it was the discovery of Ramanujan, remarking that on a scale of mathematical ability, his own ability would be 25, Littlewood would be 30, Hilbert would be 80, and Ramanujan would be 100.
“There is no such thing as a dysfunctional organization, because every organization is perfectly aligned to achieve the results it currently gets”*…
… and if we’re not careful, we might not be too pleased with what we get. Sam Altman says the one-person billion-dollar company is coming. Evan Ratliff tells the tale of his attempt to build a completely AI-automated venture…
… If you’ve spent any time consuming any AI news this year—and even if you’ve tried desperately not to—you may have heard that in the industry, 2025 is the “year of the agent.” This year, in other words, is the year when AI systems are evolving from passive chatbots, waiting to field our questions, to active players, out there working on our behalf.
There’s not a well agreed upon definition of AI agents, but generally you can think of them as versions of large language model chatbots that are given autonomy in the world. They are able to take in information, navigate digital space, and take action. There are elementary agents, like customer service assistants that can independently field, triage, and handle inbound calls, or sales bots that can cycle through email lists and spam the good leads. There are programming agents, the foot soldiers of vibe coding. OpenAI and other companies have launched “agentic browsers” that can buy plane tickets and proactively order groceries for you.
In the year of our agent, 2025, the AI hype flywheel has been spinning up ever more grandiose notions of what agents can be and will do. Not just as AI assistants, but as full-fledged AI employees that will work alongside us, or instead of us. “What jobs are going to be made redundant in a world where I am sat here as a CEO with a thousand AI agents?” asked host Steven Bartlett on a recent episode of The Diary of a CEO podcast. (The answer, according to his esteemed panel: nearly all of them). Dario Amodei of Anthropic famously warned in May that AI (and implicitly, AI agents) could wipe out half of all entry-level white-collar jobs in the next one to five years. Heeding that siren call, corporate giants are embracing the AI agent future right now—like Ford’s partnership with an AI sales and service agent named “Jerry,” or Goldman Sachs “hiring” its AI software engineer, “Devin.” OpenAI’s Sam Altman, meanwhile, talks regularly about a possible billion-dollar company with just one human being involved. San Francisco is awash in startup founders with virtual employees, as nearly half of the companies in the spring class of Y Combinator are building their product around AI agents.
Hearing all this, I started to wonder: Was the AI employee age upon us already? And even, could I be the proprietor of Altman’s one-man unicorn? As it happens, I had some experience with agents, having created a bunch of AI agent voice clones of myself for the first season of my podcast, Shell Game.
I also have an entrepreneurial history, having once been the cofounder and CEO of the media and tech startup Atavist, backed by the likes of Andreessen Horowitz, Peter Thiel’s Founders Fund, and Eric Schmidt’s Innovation Endeavors. The eponymous magazine we created is still thriving today. I wasn’t born to be a startup manager, however, and the tech side kind of fizzled out. But I’m told failure is the greatest teacher. So I figured, why not try again? Except this time, I’d take the AI boosters at their word, forgo pesky human hires, and embrace the all-AI employee future…
Eminently worth reading in full: “All of My Employees Are AI Agents, and So Are My Executives,” from @evrat.bsky.social in @wired.com.
Via Caitlin Dewey (@caitlindewey.bsky.social), whose tease/summary puts it plainly:
Ratliff, the undefeated king of tech journalism stunts, is back with another banger: For this piece and the accompanying podcast series, he created a start-up staffed entirely by so-called AI agents. The agents can communicate by email, Slack, text and phone, both with Ratliff and among themselves, and they have free range to complete tasks like writing code and searching the open internet. Despite their capabilities, however, the whole project’s a constant farce. A funny, stupid, telling farce that says quite a lot about the future of work that many technologists envision now…
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As we analyze autonomy, we might we might spare a jaundiced thought for Trofim Denisovich Lysenko; he died on this date in 1976. A Soviet biologist and agronomist, he believed the Mendelian theory of heredity to be wrong, and developed his own, allowing for “soft inheritance”– the heretability of learned behavior. (He believed that in one generation of a hybridized crop, the desired individual could be selected and mated again and continue to produce the same desired product, without worrying about separation/segregation in future breeds–he assumed that after a lifetime of developing (acquiring) the best set of traits to survive, those must be passed down to the next generation.)
In many way Lysenko’s theories recall Lamarck’s “organic evolution” and its concept of “soft evolution” (the passage of learned traits), though Lysenko denied any connection. He followed I. V. Michurin’s fanciful idea that plants could be forced to adapt to any environmental conditions, for example converting summer wheat to winter wheat by storing the seeds in ice. With Stalin’s support for two decades, he actively obstructed the course of Soviet biology, caused the imprisonment and death of many of the country’s eminent biologists who disagreed with him, and imposed conditions that contributed to the disastrous decline of Soviet agriculture and the famines that resulted.
Interestingly, some current research suggests that heritable learning– or a semblance of it– may in fact be happening by virtue of epigenetics… though nothing vaguely resembling Lysenko’s theory.
“The most important factor in survival is neither intelligence nor strength but adaptability”*…
Indeed. Scientists have accepted this precept since Charles Darwin‘s publication of Origin of the Species. But how– and at what pace– does that adaptation happen? From those earliest days, the assumption was that change/adaptation happened slowly, roughly evenly– gradually– over time.
But in 1972, paleontologists Niles Eldredge and Stephen Jay Gould published a landmark paper developing their theory and called it punctuated equilibria. Their paper built upon Ernst Mayr‘s model of geographic speciation, I. M. Lerner‘s theories of developmental and genetic homeostasis, and their own empirical research. Eldredge and Gould proposed that the degree of gradualism commonly attributed to Darwin is virtually nonexistent in the fossil record, and that stasis dominates the history of most fossil species. Rather, they argued, when significant evolutionary change occurs, it is generally restricted to rare and geologically rapid events of branching speciation called cladogenesis (the process by which a species splits into two distinct species, rather than one species gradually transforming into another).
Jake Buhler reports on recent work that confirms the punctuated equilibrium theory and adds more detail…
Over the last half-billion years, squid, octopuses and their kin have evolved much like a fireworks display, with long, anticipatory pauses interspersed with intense, explosive changes. The many-armed diversity of cephalopods is the result of the evolutionary rubber hitting the road right after lineages split into new species, and precious little of their evolution has been the slow accumulation of gradual change.
They aren’t alone. Sudden accelerations spring from the crooks of branches in evolutionary trees, across many scales of life — seemingly wherever there’s a branching system of inherited modifications — in a dynamic not examined in traditional evolutionary models.
That’s the perspective emerging from a new mathematical framework (opens a new tab) published in Proceedings of the Royal Society B that describes the pace of evolutionary change. The new model, part of a roughly 50-year-long reimagining of evolution’s tempo, is rooted in the concept of punctuated equilibrium, which was introduced by the paleontologists Niles Eldredge and Stephen Jay Gould in 1972.
“Species would just sit still in the fossil record for millions of years, and then all of a sudden — bang! — they would turn into something else,” explained Mark Pagel, an evolutionary biologist at the University of Reading in the United Kingdom.
Punctuated equilibrium was initially a controversial proposal. The theory diverged from the dominant, century-long view that evolution adhered to a slow, steady pace of Darwinian gradualism, in which species incrementally and almost imperceptibly developed into new ones. It opened the confounding possibility that there was a discontinuity between the selection processes behind the microevolutionary changes that occur within a population and those driving the long-term, broad-scale changes that take place higher than the species level, known as macroevolution.
In the decades since, researchers have continued to debate these views as they’ve gathered more data: Paleontologists have accumulated fossil datasets tracing macroevolutionary changes in ancient lineages, while molecular biologists have reconstructed microevolution on a more compressed timescale — in DNA and the proteins they encode.
Now there are enough datasets to more fully test the theories of evolutionary change. Recently, a team of scientists blended insights from several evolutionary models with new methods to build a mathematical framework that better captures real evolutionary processes. When the team applied their tools to a selection of evolutionary datasets (including their own data from research into an ancient protein family), they found that evolutionary spikes weren’t just common, but somewhat predictably clustered at the forks in the evolutionary tree.
Their model showed that proteins contort themselves into new iterations more rapidly around the time they diverge from each other. Human languages twist and recast themselves at the bifurcations in their own family tree. Cephalopods’ soft bodies sprout arms and bloom with suckers at these same splits.
The new study adds to previous support for the punctuated equilibrium phenomenon, said Pagel, who wasn’t involved in the project. However, the rapid evolutionary behavior isn’t a unique process separate from natural selection, as Eldredge and Gould suggested, but rather the result of periods of extremely rapid adaptation propelling evolutionary change.
“This is really a rather beautiful story in the philosophy of science,” Pagel said…
Read on for the fascinating story of the updated evolutionary model shows that living systems evolve in a split-and-hit-the-gas dynamic, where new lineages appear in sudden bursts rather than during a long marathon of gradual changes: “The Sudden Surges That Forge Evolutionary Trees,” from @jakebuehler.bsky.social in @quantamagazine.bsky.social.
Given the strains that the Antropocene is putting on our environment, this could be timely…
* Charles Darwin
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As we dissect development, we might spare a thought for Barabara McClintock; she died on this date in 1992. A cytogeneticist, she is regarded as one of the most important figures in the history of genetics. In the 1940s and 50s McClintock’s work on the cytogenetics of maize led her to theorize that genes are transposable – they can move around – on and between chromosomes. McClintock drew this inference by observing changing patterns of coloration in maize kernels over generations of controlled crosses. The idea that genes could move did not seem to fit with what was then known about genes, but improved molecular techniques of the late 1970s and early 1980s allowed other scientists to confirm her discovery. She was awarded the 1983 Nobel Prize in Physiology or Medicine, the first American woman to win an unshared Nobel Prize.
For more on McClintock’s work and its legacy, see here and here.
“An understanding of the natural world, and what’s in it is a source of not only great curiosity but great fulfillment”*…
Ah yes, but in what does that understanding consist? John Long considers the competing frameworks of Linnaeus and Buffon…
The modern science biography must hold back no punches in its mission to represent the subject’s life, equally celebrating their great works while including their personal shortcomings.
Jürgen Neffe’s Einstein: A Biography (2005) and Dava Sobel’s The Elements of Marie Curie (2024) are wonderful examples of this style. Such books succeed in clearly explaining the complex science of their subject’s work for non-scientific readers, enabling a deep appreciation of their achievements and bringing them to life as rounded, flawed humans.
The modern science biography must hold back no punches in its mission to represent the subject’s life, equally celebrating their great works while including their personal shortcomings.
Jürgen Neffe’s Einstein: A Biography (2005) and Dava Sobel’s The Elements of Marie Curie (2024) are wonderful examples of this style. Such books succeed in clearly explaining the complex science of their subject’s work for non-scientific readers, enabling a deep appreciation of their achievements and bringing them to life as rounded, flawed humans.
Jason Roberts’ Every Living Thing – The Great and Deadly Race to Know all Life is another of these rare works. This engrossing, precisely researched book focuses on two central characters born in the same year: Carl Linnaeus (1707-1778), a Swede, and Frenchman Georges-Louis LeClerc, the Compte de Buffon (1707-1788), better known as just Buffon.
Roberts’ book won the 2025 Pulitzer Prize for biography. His writing pulls the reader effortlessly through the story, revealing delightful, unexpected twists and turns in the two men’s complex and disparate lives. Each worked diligently to reach a level of global notoriety for their many published books. Both are revered in the natural history world today.
Linnaeus, a biologist and physician, is known for his system of hierarchical classification: how all living things comprise a genus and species, (we humans are Homo sapiens), which fit into families, orders, classes and so on. (A good many intermediate ranks were added later). While his work has been hugely influential, Linnaeus is portrayed by Roberts at times as being lazy, vain and unethical.
Linnaeus was primarily driven to be the first to name new species. Buffon was working on a grand thesis of how all life’s organisms function and are related to one another. A wealthy count who inherited a vast fortune at the age of ten, Buffon trained as a lawyer but became fascinated by the trees that grew in his large garden.
Buffon is best known today for his extensive books on natural history and works on mathematics and cosmology. He calculated the Earth was much older than the Bible predicted and that life sprung from unorganised matter. He explored the relationships between organisms rather than how they were classified. His core work formed the basis for modern evolutionary theory.
Why was all this important? At the time, the task of classifying plants was vital to the growing economies of nations. Travellers to the far reaches of the globe brought back examples of economically valuable new species, like plant foods, medicinal plants or beautiful ornamental specimens.
The author’s central thesis is Linnaeus was not as brilliant as history paints him and Buffon was a far greater genius for his day.
Where does genius come from, Roberts asks? Is it inherent by birth, grown from an inspiring education, or is it something within that is nurtured by passion?
Both these brilliant men who made a lasting mark on science came from not very inspiring families. Nor did they excel at school or university. This story shows success in academic work is not just about intellect, but intimately tied to the ethics and morality of doing research…
Eminently worth reading in full: “How do we understand life on Earth? A prize-winning biography charts the tension between two types of science ‘genius’” from @theconversation.com.
* David Attenborough, who also observed, “We moved from being a part of nature to being apart from nature.”
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As we noodle on knowing, we might send birthday greetings to Gregor Mendel; he was born on this date in 1822 (though some sources give the date as July 20). A botanist, geneticist, and monk, he pioneered in the study of heredity.
Mendel spent his adult life with the Augustinian monastery in Brunn, where as a plant experimenter, he was the first to lay the mathematical foundation of the science of genetics, in what came to be called Mendelism. Over the period 1856-63, Mendel grew and analyzed over 28,000 pea plants. He carefully studied for each their plant height, pod shape, pod color, flower position, seed color, seed shape and flower color. He made two very important generalizations from his pea experiments, known today as the Laws of Heredity, and coined the genetic terms recessiveness and dominance. He read a paper on his studies in 1865 to the Brünn Society for Natural Sciences in Moravia– but it lay unappreciated until 1900.
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