(Roughly) Daily

Posts Tagged ‘Visualization’

“In the beginning there is the stem cell; it is the origin of an organism’s life”*…

Illustration depicting a fluctuating surface with wavy lines and a small sphere resting on top, representing concepts of energy or surface tension.
Waddington’s classic drawing of the epigenetic landscape. A ball, representing a pluripotent cell or population, is poised to roll downhill into valleys, each of which represent a specialized cell type, such as a blood cell, liver cell, or brain cell. From The Strategy of the Genes by C.H. Waddington

C.H. Waddington’s powerful image of embryonic stem cells specializing on a rolling landscape has captivated biologists since the 1950s. As Philip Ball reports, experimental data is finally confirming– and complicating– his visionary ideas…

By the middle of the 20th century, it had begun to seem that biology was almost solved. Charles Darwin’s theory of evolution by natural selection explained how organisms change and adapt. The modern science of genetics showed how it works at the molecular scale. Genes governing the traits of organisms get passed down from parent to offspring, and random mutations create the variations from which natural selection picks the “fittest.” Natural selection and genetics fitted together in what the biologist Julian Huxley christened “the modern synthesis” in his 1942 book). Once it was shown in 1953 that the genes are encoded by DNA, the rest of biology looked like little more than piecing together details.

But not everyone was satisfied. The British biologist Conrad Hal Waddington), known to his friends and colleagues as Wad, thought this focus on genes was all very well. But it wasn’t clear to him, or anyone else, exactly how genes shape the forms and features of organisms — how they reliably generate all the different tissues of the body, in all the right places, during embryonic development. Around the same time that Huxley unveiled the modern synthesis, Waddington presented a novel picture of how this might unfold.

He visualized the developmental process as a landscape with hills and valleys that split every so often like those in a river network. At the very top of the highest hill he imagined a ball, which represented a population of cells in their earliest embryonic form — what we now call stem or pluripotent cells, which have the potential to become any cell type. The progression of the cells towards their fates — to become, say, skin cells, muscle cells, or nerve cells — is like the ball rolling downhill through the landscape.

When the ball reaches a branching point (bifurcation), the model’s “gravity” pulls it to one track or the other: In scientific terms, it must differentiate. Through a particular sequence of such branching decisions, Waddington argued, cells specialize into their mature types, or fates, each expressing a particular set of genes. The cells are restricted to a small number of well-defined states because they are “canalized,” in Waddington’s lexicon: trapped and channeled by the sides of the valley. In this way, a limited number of cell types reliably arise from the activity of an army of genes.

Waddington’s landscape has been “remarkably useful as a conceptual scaffold,” said James Briscoe, a developmental biologist at the Francis Crick Institute in London. “The core ideas — that development is progressive, that cell states are distinct, that bifurcations represent [cell] fate decisions, that canalization implies robustness — all survive.”

“There’s so much richness to some of the concepts Waddington was trying to share,” said Susanne Rafelski, a biochemist at the Institute for Stem Cell and Regenerative Medicine in Seattle.

But the concept was more of a visual metaphor than a representation of an actual biological process. Or so it seemed. In the past several years, researchers have mapped out the real topography of cell-state spaces — in effect, Waddington’s landscapes — from experimental data collected from many thousands of cells over the course of embryonic development. Those analyses are revealing that development is not a mere readout of a genetic program, but rather a dynamic process in which communities of cells build themselves, and the very landscape they navigate, by mutual negotiation and interaction, into an organism.

This cartography of development is now helping researchers understand how identical cells in the early embryo develop into the distinct tissues and cell types of a complex organism. This matters enormously for regenerative medicine and stem-cell engineering, Briscoe said: “If you understand the landscape topology and know where the bifurcations lie, you can in principle design methods that steer cell populations to desired states with precision, rather than by trial and error.”

Waddington’s metaphor, then, could be the key to understanding and reshaping possibilities for what cells, tissues, and embryos can be…

Read on: “How Does Life Unfold? A Landscape Metaphor Comes Into Its Own.” from @philipcball.bsky.social in @quantamagazine.org.

* Stewart Sell

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As we appreciate adaptability, we might send healing birthday greetings to Robert Peter Gale; he was born on this date in 1945. A physician and medical researcher, he conducted important research into leukemia and other bone marrow disorders (e.g., aplastic anemia). Gale was a a pioneer in bone marrow transplantation and co-founded the International Bone Marrow Registry. But he is perhaps most widely known for his assistance to foreign governments in treating radiation victims – to the Soviet Union (1986) after the Chernobyl disaster and to Brazil (1987) following an accident in Goiania. As a specialist in bone marrow transplants, he volunteered to treat Chernobyl victims and was invited by Mikhail Gorbachev to travel with a group to Moscow immediately after the April 1986 accident. He performed bone marrow transplants on 13 Chernobyl victims (though many of the highly exposed Chernobyl survivors have since died from latent radiation effects).

A speaker presenting at a conference, standing behind a podium with a logo, while a display screen shows distances from the Earth to the Moon and the Sun.

source

“Now I will tell the captains of the ships, and all the ships together”*…

3D model of a Kynos Galley ship from 1200 BC, illustrating the Cephallenians with numbered markers highlighting different parts of the ship, set against a tranquil ocean backdrop.

Ethan Mollick has created a new site that’s fascinating in two different ways. First and most overtly, it’s a beautiful (and thorough) visualization and explanation of the ships used by the protagonists of The Iliad.

But at the same time, it is a powerful demonstration of (at least one of) the ways that AI might be useful in scholarship and education: Mollick spun up the site last month, using Claude…

In the second book of the Iliad the poet pauses on the brink of the first battle, calls on the Muses, and counts the fleet: twenty-nine contingents, forty-six captains, some 178 place-names, 1,186 ships [and by Thucydides’ reckoning, around 100,000 men]. This site puts every entry on the map, rebuilds the ships from the archaeological evidence [pictured on this site], and lets you read the lines beside the ruins they describe…

“The Catalogue of Ships” from @emollick.bsky.social.

* Homer/The Poet, The Iliad, Book 2, lines 492-3

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As we set sail, we might recall that it was on this date in 331 BCE (long, long ago– but hundreds of years after the action described in The Iliad) that Alexander the Great and the Army of Macedon defeated King Darius III and his Persian Army in the Battle of Gaugamela, effectively the final blow to the Achaemenid Empire, resulting in its complete conquest by Alexander.

A chaotic battle scene with knights on horseback, soldiers on foot, and colorful flags amidst a mountainous landscape.
The Battle of Gaugamela, Jan Brueghel the Elder, 1602 (source)

Written by (Roughly) Daily

October 1, 2026 at 1:00 am

“Nothing can better cure the anthropocentrism that is the author of all our ills than to cast ourselves into the physics of the infinitely large (or the infinitely small)”*…

And very eye-opening it can be. Jason Kottke reports on an article in the most recent issue of the American Journal of Physics with the understated title of “All objects and some questions.”

You just have to admire a chart that casually purports to show every single thing in the Universe in one simple 2D plot. [As the article’s author explain:]

In Fig. 2 [above], we plot all the composite objects in the Universe: protons, atoms, life forms, asteroids, moons, planets, stars, galaxies, galaxy clusters, giant voids, and the Universe itself. Humans are represented by a mass of 70 kg and a radius of 50 cm (we assume sphericity), while whales are represented by a mass of 10^5 kg and a radius of 7 m.

The “sub-Planckian unknown” and “forbidden by gravity” sections of the chart makes the “quantum uncertainty” section seem downright normal — the paper collectively calls these “unphysical regions.” Lovely turns of phrase all.

But what does it all mean? My physics is too rusty to say, but I thought one of the authors’ conjectures was particularly intriguing: “Our plot of all objects also seems to suggest that the Universe is a black hole.”…

Is the universe a black hole? (and other provocative propositions): @kottke on a recent scientific paper: “The Plot of All Objects in the Universe.”

* Julio Cortázar, Around the Day in Eighty Worlds

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As we size up scale, we might recall that it was on this date in 451 that a different kind of attempt to reconcile the finite and the infinite began: the first session of the Council of Chalcedon (in modern-day Turkey) was opened. The fourth ecumenical council of the Christian church, it was attended by over 520 bishops or their representatives (making it the largest and best documented of the first seven ecumenical councils). It was convened by the Roman emperor Marcian to re-assert the teachings of the ecumenical Council of Ephesus against the heresies of Eutyches and Nestorius— whose teachings attempted to dismantle and separate Christ’s divine nature from his humanity (Nestorianism) and further, to limit Christ as solely divine in nature (Monophysitism).

The Council succeeded in that task. As Jaroslav Pelikan characterized their findings:

We all teach harmoniously [that he is] the same perfect in godhead, the same perfect in manhood, truly God and truly man, the same of a reasonable soul and body; homoousios with the Father in godhead, and the same homoousios with us in manhood … acknowledged in two natures without confusion, without change, without division, without separation.

… which marked a turning point in the Christological debates. But it also generated heated disagreements between the council and the Oriental Orthodox Church, which saw things differently– a contention that informed the separation of the Oriental Orthodox Churches from the rest of Christianity… and led to the Council being remembered as “Chalcedon, the Ominous.”

Fourth Ecumenical Council of Chalcedon, 1876 painting by Vasily Surikov (source)

“It is better to have your head in the clouds, and know where you are… than to breathe the clearer atmosphere below them, and think that you are in paradise”*…

Take a ride from the earth’s surface to the Kármán line (the conventionally-acknowledged boundary between Earth’s atmosphere and outer space) on Neal Agarwal‘s (@nealagarwal) Space Elevator.

* Henry David Thoreau

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As we get high, we might recall that this date in 1970 was the first Earth Day.  First suggested by John McConnell for March 21 (the Equinox in the Northern Hemisphere, a day of natural equipoise), Secretary General U Thant signed a UN Proclamation to that effect.  But Earth Day as we know it was founded by U.S. Senator Gaylord Nelson (who was later awarded the Presidential Medal of Freedom Award for his work) as an environmental teach-in to be held on on this date.  The first Earth Day had participants and celebrants in two thousand colleges and universities, roughly ten thousand primary and secondary schools, and hundreds of communities across the United States.  Later that year, President Nixon signed the Environmental Protection Agency into being.  Earth Day is now observed in 192 countries, coordinated by the nonprofit Earth Day Network, chaired by the first Earth Day 1970 organizer Denis Hayes– according to whom Earth Day is now “the largest secular holiday in the world, celebrated by more than a billion people every year.”

Earth Day Flag created by John McConnell

 source

“Look up at the stars and not down at your feet. Try to make sense of what you see, and wonder about what makes the universe exist.”*…

Our environment…

This map shows a slice of our Universe. It was created from astronomical data taken night after night over a period of 15 years using a telescope in New Mexico, USA. We are located at the bottom. At the top is the actual edge of the observable Universe. In between, we see about 200,000 galaxies.

Each tiny dot is a galaxy. About 200,000 are shown with their actual position and color. Each galaxy contains billions of stars and planets. We are located at the bottom. Our galaxy, the Milky Way, is just a dot. Looking up, we see that space is filled with galaxies forming a global filamentary structure. Far away from us (higher up in the map), the filaments become harder to see…

For a (much crisper, more vivid, and interactive) version: “The Map of the Observable Universe.”

* Stephen Hawking

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As we explore, we might recall that it was on this date in 1616 that The Minutes of the Roman Inquisition recorded the conclusion that Galileo’s writings in support of Copernicus’ heliocentric view of the solar system were “foolish and absurd in philosophy, and formally heretical since it explicitly contradicts in many places the sense of Holy Scripture.” The next day, Galileo was called before Cardinal Bellarmine, who (on Pope Paul V’s instruction) ordered Galileo to abandon the teaching. Shortly thereafter, Copernicus’s De Revolutionibus and other heliocentric works were banned (entered onto the Index Librorum Prohibitorum) “until correction.”

Sixteen years later, Galileo “published” Dialogue Concerning the Two Chief World Systems (Dialogo sopra i due massimi sistemi del mondo)– that’s to say, he presented the first copy to his patron, Ferdinando II de’ Medici, Grand Duke of Tuscany.  Dialogue, which compared the heliocentric Copernican and the traditional geo-centric Ptolemaic systems, was an immediate best-seller.

While there was no copyright available to Galileo, his book was printed and distributed under a license from the Inquisition.  Still, the following year it was deemed heretical– and he joined Copernicus on the Index Librorum Prohibitorum: the publication of anything else Galileo had written or ever might write was also banned… a ban that remained in effect until 1835.

Domenico Tintoretto‘s portrait of Galileo (source)

Written by (Roughly) Daily

February 25, 2023 at 1:00 am