(Roughly) Daily

Posts Tagged ‘scientific method

“Brains exist because the distribution of resources necessary for survival and the hazards that threaten survival vary in space and time”*…

And, it seems, they not only evolve, but in ways and with a frequency we’ve only just begun to appreciate. It’s long been noted that evolution seems to have a thing for “carcinization”– crabs have evolved separately at least five times. (Oh, and apparently also for anteaters…) Recent findings hint that evolution might have the same sort of jones for the brain. Amy Maxmen reports…

Our brains, perched atop a network of nerve cells that ascend the length of our bodies, are thought to have arisen once in an animal hundreds of millions of years ago and then evolved over time. However, new findings suggest instead that brains and nervous systems originated multiple times from scratch.

The findings, published today in Nature, highlight an ancient and gelatinous marine predator called a comb jelly [pictured at top]. Unlike pulsating jellyfish, comb jellies swim by “rowing” their many hair-like cilia, which are arranged in rows called combs. They possess rudimentary brains and sophisticated nervous systems replete with elongated cells that communicate through synapses much like our own. Some comb jellies show mirror-like bilateral symmetry, as do we. And like most animals, their muscles derive from a middle tissue layer, which does not exist in jellyfish or sponges, another ancient type of aquatic creature. 

So it’s little wonder that biologists have long placed the comb jelly group close to worms, flies, and humans on the evolutionary tree of life; sponges emerge at the base, meaning that this group appeared first. In this traditional view, complex body parts like the brain and muscles arose gradually, and only once, since those parts look similar across related animals, and the chances of that same evolutionary process being repeated seems slim.

But this scenario was shaken by a report in Science last year, which suggested that the comb jelly group emerged before jellyfish and even the brainless, muscle-less sponges, more than 550 million years ago.

Some biologists doubted the rearrangement because it implied two equally uncomfortable possibilities: that the ancestor of all living animals had true muscles and a rudimentary brain, and then sponges and jellyfish lost those parts without a trace; or that the great animal ancestor was simple, and comb jellies evolved separately from all the other animals, yet ended up with rather similar nervous systems, muscles, and bilateral symmetry. When paleontologist Graham Budd heard the news last year, he said, “It is effectively saying animals evolved twice. Frankly, I’m not ready to believe it.”  

Without a time machine, it’s impossible to know what our great ancestor looked like. However, today’s report adds more support to the notion that she was simple and comb jellies independently evolved their complex body parts. Leonid Moroz, a neurobiologist at the University of Florida’s Whitney Laboratory for Marine Bioscience, and his colleagues confirm comb jellies’ position below sponges at the base of the evolutionary tree with an analysis of genetic sequences from 11 comb jelly species…

… In an essay for Nautilus called “Evolution, You’re Drunk,” I described how hypotheses entrenched in the notion that evolution leads toward increasing complexity have recently begun to teeter. Now Moroz’s study adds another shove. It seconds the finding that simple sponges, long placed at the base of the evolutionary tree, actually evolved after the sophisticated comb jelly group arose. The story of how complexity evolves is more complex than scientists realized.

Furthermore, the brain—the epitome of complexity—seems to have sprouted up at least twice over evolutionary time. This clashes with the traditional notion that complex, multifaceted features come about in a very specific way, and each emerges just one time. “What everyone has said about complexity is wrong,” Moroz says. “It can happen more than once.” 

Finding that comb jellies independently arrived at similar ends as other animals might also have surprised the late paleontologist Stephen Jay Gould, who famously doubted that animals would look the same today if the world were to begin again—if we could replay “the tape of life.”

Is such convergence in design a coincidence? Probably not, guesses Andreas Hejnol, an evolutionary developmental biologist at the Sars International Centre for Marine Molecular Biology in Norway. “If you need a fast communication system, it helps to have extended cells that communicate through chemicals,” he says. In other words, the structure of the nervous system reflects its function. So if intelligent life exists elsewhere in the universe, it’s not too far a stretch to think it could possess a brain comprised of trillions of neurons. Hejnol asks, “How else could it be?”…

The mysterious mechanism of evolution: “Evolution May Be Drunk, But It’s Serious About Making Brains,” from @amymaxmen.bsky.social‬ in @nautil.us‬.

* John M. Allman, Evolving Brains

###

As we contemplate the changing comprehension of cerebra, we might send thoughtful birthday greetings to Sir Karl Raimund Popper; he was born on this date in 1902.  One of the greatest philosophers of science of the 20th century, Popper is best known for his rejection of the classical inductivist views on the scientific method, in favor of empirical falsification: a theory in the empirical sciences can never be proven, but it can be falsified, meaning that it can and should be scrutinized by decisive experiments.  (Or more simply put, whereas classical inductive approaches considered hypotheses false until proven true, Popper reversed the logic: conclusions drawn from an empirical finding are true until proven false.)

Popper was also a powerful critic of historicism in political thought, and (in books like The Open Society and Its Enemies and The Poverty of Historicism) an enemy of authoritarianism and totalitarianism (in which role he was a mentor to George Soros).

A black and white portrait of Sir Karl Raimund Popper, a prominent philosopher of science, displaying a thoughtful expression.

 source

And sadly: RIP, Tom Lehrer.

Portrait of singer-songwriter Tom Lehrer, during a rare interview at his home near Santa Cruz, California, USA in early 2000. (source)

“The street finds its own uses for things”*…

Your correspondent is off again, this time across borders and for a little longer that my last few absences; regauler service should resume around April 19…

The estimable Matt Webb on an approach to thnking more comprhensively and creatively about the ultimate impacts of and given innovation…

… I recently learnt about twig, which is a biotech startup manufacturing industrial chemicals using custom bacteria.

The two examples they cite: palm oil which is used in lipstick but displaces rainforests; isoprene which is used to make tyres but comes from fossil fuels.

What if instead you could engineer a strain of bacteria to bulk produce these chemicals sustainably?

The capabilities are present in the metabolic pathways. So that’s what twig does. At scale, is the promise.

  1. I hadn’t realised this kind of biotech had gotten to commercialisation! And in London too. Good stuff.
  2. What Are The Civilian Applications?

What Are The Civilian Applications? is of course a Culture ship name, a GSV (General Systems Vehicle) from The Use of Weapons by Iain M. Banks.

It is also an oblique strategy we deployed regularly in design workshops back in the day at BERG, introduced (I think? Gang please correct me if I’m wrong) by long-time design leader and friend Matt Jones. That’s his project history. Go have a read.

Let me unpack.

Oblique Strategies (a history) by Brian Eno and Peter Schmidt, 1975: a deck of approx 100 cards, each of which is a prompt to bump you out of a creative hole.

For example:

Honor thy error as a hidden intention

Or:

Discard an axiom

And so on.

In product invention, which is kinda what we did at BERG and kinda what I do now, it’s handy to carry your own toolkit of prompts. So I adopted What Are The Civilian Applications? into my personal deck of oblique strategies.

Therefore.

What would do you with engineered bacteria that can make palm oil or whatever, if it were cheap enough to play with, if the future were sufficiently distributed, if we all had it at home?

Like, it’s a good question to ask. What would civilians do with engineered bacteria?

Tomato soup.

Instead of buying tomato soup at the store, I’d have a little starter living in a jar. A bioreactor all of my own, and I’d fill it with intelligently designed bacteria that eat slop and excrete ersatz Heinz tomato soup.

I’m not 100% sure what “slop” is in this context. The food I mean. Maybe the bacteria just get energy from sunlight, fix carbon from the air, and I drop in a handful of vitamin gummies or fish flakes every Monday?

A second oblique strategy adopted into my personal deck over the years:

A good science fiction story should be able to predict not the automobile but the traffic jam,” by Frederik Pohl. As previously discussed re a national drone network.

Let’s say I can go to the store and buy a can of Perpetual Heinz, or however they brand it. A can with a sunroof on the top and a tap on the side that I keep in the garden and I can juice it for soup once a week for a year, or until the bacterial population diverges enough that I’m at risk of brewing neurotoxins or psychedelics or strange and wonderful new flavours or something.

Heinz is not going to like that, economically. They’ll require me to enrol in some kind of printer and printer ink business model where I have to subscribe to the special vitamin pills to keep (a) the soup colony alive and (b) their shareholders happy.

Which will end up being pricey, like the monthly cash we all pay out to mutually incompatible streaming services. Demand will arise for black market FMCGs on the dark web. Jars of illegal Infinite Coca Cola that only requires the cheap generic slop and it tastes just the same.

So I love to play with these strategies and imagine what the world might be like. Each step makes a sort of sense yet you end up somewhere fantastical – that’s the journey I want to take you on in text, too. Then the game, in product invention, is to take those second order possibilities and bring them back to today. (I’m giving away all my secrets now.)

But I prefer cosier, more everyday futures:

Grandma’s secret cake recipe, passed down generation to generation, could be literally passed down: a flat slab of beige ooze kept in a battered pan, DNA-spliced and perfected by guided evolution by her own deft and ancient hands, a roiling wet mass of engineered microbes that slowly scabs over with delicious sponge cake, a delectable crust to be sliced once a week and enjoyed still warm with cream and spoons of pirated jam.

A small jar of precious, proprietary cake ooze handed down parent to child, parent to child, together with a rack filled with the other family starter recipes, a special coming of age moment, a ceremony…

Thinking broadly and deeply about the implications of innovations: “What Are The Civilian Applications?” from @genmon.fyi.

(Image above: source)

* William Gibson

###

As we ponder the particulars of progress, we might spare a thought for Francis Bacon– the English Renaissance philosopher, lawyer, linguist, composer, mathematician, geometer, musician, poet, painter, astronomer, classicist, philosopher, historian, theologian, architect, father of modern empirical science (The Baconian– aka The Scientific– Method), and patron of modern democracy, whom some allege was the illegitimate son of Queen Elizabeth I of England (and other’s, the actual author of Shakespeare’s plays). He died on this date in 1561… after (about a month earlier) he had stuffed a dressed chicken with snow to see how long the flesh could be preserved by the extreme cold. He caught a cold and perished from its complications.

source

Written by (Roughly) Daily

April 9, 2025 at 1:00 am

“Every great advance in science has issued from a new audacity of the imagination”*…

Itai Yanai and Martin Lercher on the importance of interdisciplinarity and creativity in science…

The hypothesis-testing mode of science, which François Jacob called “day science,” operates within the confines of a particular scientific field. As highly specialized experts, we confidently and safely follow the protocols of our paradigms and research programs . But there is another side of science, which Jacob called “night science”: the much less structured process by which new ideas arise and questions and hypotheses are generated. While day science is compartmentalized, night science is truly interdisciplinary. You may bring an answer from your home field to another discipline, or conversely, venturing into another field may let you discover a route towards answering a research question in your
main discipline. To be most creative, we may be best off cultivating interests in many areas, much like Renaissance thinkers such as Leonardo da Vinci or Galileo Galilei. But this creativity-enhancing interdisciplinarity comes at a price we may call “expert’s dilemma”: with your loss of status as a highly focused expert comes a loss of credibility, making it harder to get your work accepted by your peers. To resolve the dilemma, we must find our own balance between disciplinary day science expertise and interdisciplinary night science creativity…

Eminently worth reading in full: “Renaissance minds in 21st century science,” from @ItaiYanai and @MartinJLercher.

See also: “Night Science

And for more: see their project’s home page and listen to their podcast.

Apposite: “8 lessons on lifelong learning from an astrophysicist,” from Ethan Siegel.

* John Dewey

###

As we find a balance, we might send easily-reproducible birthday greetings to a man who was moved by necessity to cross disciplinary boundaries, Alois Senefelder; he was born on this date in 1771. A playwright and actor, was having trouble getting his plays printed;  he needed a less expensive and more efficient printing alternative to relief printed hand set type or etched plates. So he invented the technique we call lithography– the biggest revolution in the printing industry since Gutenberg’s movable type.

 The principle is simple: oil-based printing ink and water repel each other. The image is drawn on a stone (Bavarian limestone for Senefelder) with greasy crayon, after which the stone is soaked in water, which is absorbed into the part of the stone not covered in greasy paint. The ink is rolled onto the stone. The image areas of the stone accept ink and undrawn areas reject it. Finally, a piece of paper is pressed onto the stone, and the ink transfers onto the paper from the stone.

Senefelder called the technique “stone printing” or “chemical printing,” but the French name “lithography” became more widely adopted. Today photo lithography is used to print magazines and books, but the original process of drawing by hand on litho stones still exists in the fine art world.

Lithograph of Senefelder (source)

“The spirit of inquiry and the courage to challenge the status quo are at the heart of scientific progress”*…

Adam Mastroianni on the challenges– and opportunities– facing science…

Randomized-controlled trials only caught on about 80 years ago, and whenever I think about that, I have to sit down and catch my breath for a while. The thing everybody agrees is the “gold standard” of evidence, the thing the FDA requires before it will legally allow you to sell a drug—that thing is younger than my grandparents.

There are a few records of things that kind of look like randomized-controlled trials throughout history, but people didn’t really appreciate the importance of RCTs until 1948, when the British Medical Research Council published a trial on streptomycin for tuberculosis. Humans have possessed the methods of randomization for thousands of years—dice, coins, the casting of lots—and we’ve been trying to cure diseases for as long as we’ve been human. Why did it take us so long to put them together?

I think the answer is: first, we had to stop trusting Zeus.

To us, coin flips are random (“Heads: I go first. Tails: you go first.”). But to an ancient human, coin flips aren’t random at all—they reveal the will of the gods (“Heads: Zeus wants me to go first. Tails: Zeus wants you to go first”). In the Bible, for instance, people are always casting lots to figure out what God wants them to do: which goat to kill, who should get each tract of land, when to start a genocide, etc.

This is, of course, a big problem for running RCTs. If you think that the outcome of a coin flip is meaningful rather than meaningless, you can’t use it to produce two equivalent groups, and you can’t study the impact of doing something to one group and not the other. You can only run a ZCT—a Zeus controlled trial.

It’s easy to see how technology can lead to scientific discoveries. Make microscope -> discover mitochondria.

Clearly, though, sometimes those technologies get invented entirely inside our heads. Stop trusting Zeus -> develop RCTs.

Which raises the question: what mental technologies haven’t we invented yet? What brain switches are just waiting to be flipped?…

On reinvigorating science: “Declining trust in Zeus is a technology,” from @a_m_mastroianni.

Apposite to an issue he raises: “Citation cartels help some mathematicians—and their universities—climb the rankings,” from @ScienceMagazine.

[Image above: source]

Elizabeth Blackwell

###

As we deliberate on discovery, we might send micro-biological birthday greetings to a woman who modeled the attitude and behavior that Mastroianni suggests: Ruth Sager; she was born on this date in 1918. A pioneering geneticist, she had, in effect, two careers.

In the 1950s and 1960s, she pioneered the field of cytoplasmic genetics by discovering transmission of genetic traits through chloroplast DNA, the first known example of genetics not involving the cell nucleus. She identified a second set of genes were found outside of the cell’s nucleus, which, even though they were nonchrosomomal, also influenced inherited characteristics. The academic community did not acknowledge the significance of her contribution until after the second wave of feminism in the 1970s.

Then, in the early 1970s, she moved into cancer genetics (with a specific focus on breast cancer); she proposed and investigated the roles of tumor suppressor genes. She identified over 100 potential tumor suppressor genes, developed cell culture methods to study normal and cancerous human and other mammalian cells in the laboratory, and pioneered the research into “expression genetics,” the study of altered gene expression.

source

“Oh dark, dark, dark, amid the blaze of noon, irrevocably dark, total eclipse without all hope of day”*…

Today is the occasion of an annular eclipse, which will pass through eight U.S. states before crossing the Gulf of Mexico and to transit Mexico, Guatemala, Belize, Honduras, Nicaragua, Costa Rica, Panama, Colombia, and Brazil. While some people in the Western Hemisphere will witness a “ring of fire” during the eclipse, many more will experience the phenomenon of crescent sunlight. Rebecca Boyle has advice on how we might approach it…

… This Saturday, for some people in the Western Hemisphere, the Sun will disappear for a few minutes and appear to leave a flaming hole in the sky. Instead of a ball of fire, the Sun will transform into a ring of fire, a strange and wondrous sight. This is an annular solar eclipse, and it happens because the Moon is right smack in front of the Sun.

A solar eclipse only happens during new Moon phases, when we otherwise wouldn’t be able to see our nearest celestial companion. Though we get a new Moon every month, we do not get solar eclipses as often because of our satellite’s oddball path around the planet. Sometimes the Moon casts a shadow just above Earth, and sometimes just below. This weekend, the Moon’s shadow will fall onto Earth, just right for people in parts of the Western Hemisphere to see it.

The annular eclipse is a preview of a more incredible, rarer event next April, when a total solar eclipse will cross the continental United States. There is no experience on Earth like a total eclipse; make plans to see it, if you can. But this weekend’s “ring of fire” eclipse is an event you should try to see first (safely, with eclipse glasses), if you can get yourself into the western U.S. or parts of Central and South America. Here’s a map showing the eclipse path; if you can’t travel to see it in person, you can watch the eclipse online.

Eclipses happen because the Sun and Moon appear to be roughly the same diameter. The Sun is actually about 400 times larger than the Moon, but it is also about 400 times more distant, so they seem like the same size in our sky.

The Moon’s shadow forms two concentric cones, composed of an inner shadow called the umbra, where the sun is completely obscured, and an outer, broader cone called a penumbra, where sunlight still shines but it is partially blocked. The umbra can be seen in a narrow geographic ribbon across the Americas, and it’s where you will see a full eclipse; under the penumbra, which covers much of the western U.S., Central and South America, you will see a partial eclipse.

Like the gears of a clock, a combination of precise positions and movements initiate an eclipse of the Sun. As Earth spins, day breaks. The Sun and Moon appear to trace a path across the sky. The Sun is not moving (at least not perceptibly); Earth’s rotation makes the star’s position change. The Moon is moving around us while the Earth rotates, so it seems to move too, but it appears to go slower than our star. The partial solar eclipse begins as the Sun catches up to the Moon’s position in our sky. On Saturday morning around 8:06 a.m. Pacific time, people in Eugene, Oregon, will be the first to see the Moon appear to take a bite out of the Sun. The bite will get progressively bigger until the full annular eclipse begins at 9:16 a.m. Pacific time.

The annular eclipse only lasts about four minutes (depending on your precise location under the Moon’s shadow) but the partial eclipse, which will be visible over a much wider geographic area, lasts about an hour and 15 minutes before and afterward. During this phase, shadows cast by objects on Earth will change in unusual ways. One lovely place to be during a partial solar eclipse is underneath a tree, if you can find an evergreen or a deciduous tree that has not dropped its leaves yet. Look at the ground. In the dappled light, you will see crescents everywhere: the crescent Sun.

Sunlight is the heavens reaching down to touch us right where we stand; I think about this when I step into the light. But crescent sunlight is the Moon joining this experience. Its darkness, rather than its light, reaches out to touch us, too…

An informative and lyrical guide to today’s eclipse: “During an Annular Eclipse, Look to the Shadows,” from @rboyle31 in @atlasobscura.

* John Milton, Samson Agonistes

###

As we don’t look directly, we might recall that on this date in 1609, Galileo (who has claim to the titles Father of observational astronomy, modern-era classical physics, the scientific method, and modern science) put the telescope to use in his astronomical work. Upon hearing (at age 40) that a Dutch optician had invented a glass that made distant objects appear larger, Galileo crafted his telescope. He continued to improve his device, ultimately achieving 30X magnification, and recorded his observations of the Moon, the moons of Jupiter, the Phases of Venus, Sunspots, The Milky Way, and more. He published his initial telescopic astronomical observations in March 1610 in a brief treatise entitled Sidereus Nuncius (Starry Messenger).

Telescopes were also a profitable sideline for Galileo, who sold them to merchants who found them useful both at sea and as items of trade.

Galileo’s “cannocchiali” telescopes at the Museo Galileo, Florence (source)

Written by (Roughly) Daily

October 14, 2023 at 1:00 am