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Posts Tagged ‘history of science

“To achieve style, begin by affecting none”*…

The first issue of the Philosophical Transactions of the Royal Society

From Roger’s Bacon, in New Science, a brief history of scientific writing…

Since the founding of the first scientific journal in 1665, there have been calls to do away with stylistic elements in favor of clarity, concision, and precision.

In 1667, Thomas Sprat urged members of the Royal Society to “reject all the amplifications, digressions, and swellings of style; to return back to the primitive purity, and shortness, when men delivered so many things, almost in an equal number of words.” Some 200 years later, Charles Darwin said much the same: “I think too much pains cannot be taken in making the style transparently clear and throwing eloquence to the dogs” (Aaronson, 1977).

Darwin and Sprat eventually got their way. Modern scientific writing is homogenous, cookie-cutter, devoid of style. But scientific papers weren’t always like this.

Writing in The Last Word On Nothing blog, science journalist Roberta Kwok explains how old articles differ from their modern counterparts:

Scientists used to admit when they don’t know what the hell is going on.

When philosopher Pierre Gassendi tried to capture observations of Mercury passing in front of the Sun in 1631, he was beset by doubts:

“[T]hrown into confusion, I began to think that an ordinary spot would hardly pass over that full distance in an entire day. And I was undecided indeed… I wondered if perhaps I could not have been wrong in some way about the distance measured earlier.”

They get excited and use italics.

In 1892, a gentleman named William Brewster observed a bird called a northern shrike attacking a meadow mouse in Massachusetts. After tussling with its prey, he wrote, “[t]he Shrike now looked up and seeing me jumped on the mouse with both feet and flew off bearing it in its claws.”

They write charming descriptions.

Here’s French scientist Jean-Henri Fabre rhapsodizing about the emperor moth in his book, The Life of the Caterpillar (1916):

Who does not know the magnificent Moth, the largest in Europe, clad in maroon velvet with a necktie of white fur? The wings, with their sprinkling of grey and brown, crossed by a faint zig-zag and edged with smoky white, have in the centre a round patch, a great eye with a black pupil and a variegated iris containing successive black, white, chestnut and purple arcs.

All this to say: Scientists in the pre-modern era wrote freely, despite calls to do away with that freedom. At some point, narrative and literary styles vanished and were replaced with rigid formats and impoverished prose.  The question now is: Have we gone too far in removing artistry from scientific writing?

For a well-argued case that we have– “the way that we write is inseparable from the way that we think, and restrictions in one necessarily lead to restrictions in the other”– read on: “Research Papers Used to Have Style. What Happened?,” from @RogersBacon1 and @newscienceorg.

* E. B. White, The Elements of Style

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As we ponder purposive prose, we might spare a thought for Johann Adam Schall von Bell; he died on this date in 1666. An expressive writer in both German and Chinese, he was an astronomer and Jesuit missionary to China who revised the Chinese calendar, translated Western astronomical books, and was head of Imperial Board of Astronomy (1644-64). Given the Chinese name “Tang Ruowang,” he became a trusted adviser (1644-61) to Emperor Shun-chih, first emperor of the Ch’ing dynasty (1644-1911/12), who made him a mandarin.

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“Can’t have dirty garbage!”*…

Rebecca Alter, with a paean to an unexpected TikTok delight…

At some point earlier this year, my For You Page changed for the better. Between cute boys making sandwiches, Brian Jordan Alvarez videos, and American Girl Doll memes, I started getting the occasional video from @nycsanitation. I don’t think I’ve ever watched through a full video on TikTok from any government department, local or federal, but @nycsanitation has clawed its way through algorithms and attention spans to be that rarest of finds: an official organization or company account that’s actually good. The Department comes across in its TikToks as a bunch of genuine, hardworking salt-of-the-earth folks. I mean that literally; @nycsanitation TikTok reminds us that they’re the ones in charge of salting the streets in winter…

Read on for wondrous examples featuring googly-eyed snowplow trucks and earnest charm: “The Department of Sanitation Has an Oddly Excellent TikTok,” from @ralter in @Curbed.

* Spongebob

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As we keep it clean, we might might recall that it was on this date in 1865 that Joseph Lister, a student of Pasteur’s germ theory, performed the first successful antiseptic surgery (using carbolic acid to disinfect a compound fracture suffered by an 11-year-old boy). After four days, he discovered that no infection had developed, and after a total of six weeks he was amazed to discover that the boy’s bones had fused back together, without suppuration. He subsequently published his results in The Lancet in a series of six articles, running from March through July 1867.

Lister developed his approach to extend to Lister instructing surgeons under his responsibility to wear clean gloves and wash their hands before and after operations with five per cent carbolic acid solutions. Instruments were also washed in the same solution, and assistants sprayed the solution in the operating room.

At first, his suggestions were criticized: germ theory was in its infancy and his techniques were deemed too taxing. But his results– sharp reduction in post-op infection and death– ultimately carried the day. Indeed, he so revolutionized his field that he is known as “father of modern surgery.”

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“Why, sometimes I’ve believed as many as six impossible things before breakfast”*…

Imaginary numbers were long dismissed as mathematical “bookkeeping.” But now, as Karmela Padavic-Callaghan explains, physicists are proving that they describe the hidden shape of nature…

Many science students may imagine a ball rolling down a hill or a car skidding because of friction as prototypical examples of the systems physicists care about. But much of modern physics consists of searching for objects and phenomena that are virtually invisible: the tiny electrons of quantum physics and the particles hidden within strange metals of materials science along with their highly energetic counterparts that only exist briefly within giant particle colliders.

In their quest to grasp these hidden building blocks of reality scientists have looked to mathematical theories and formalism. Ideally, an unexpected experimental observation leads a physicist to a new mathematical theory, and then mathematical work on said theory leads them to new experiments and new observations. Some part of this process inevitably happens in the physicist’s mind, where symbols and numbers help make invisible theoretical ideas visible in the tangible, measurable physical world.

Sometimes, however, as in the case of imaginary numbers – that is, numbers with negative square values – mathematics manages to stay ahead of experiments for a long time. Though imaginary numbers have been integral to quantum theory since its very beginnings in the 1920s, scientists have only recently been able to find their physical signatures in experiments and empirically prove their necessity…

Learn more at “Imaginary numbers are real,” from @Ironmely in @aeonmag.

* The Red Queen, in Lewis Carroll’s Through the Looking Glass

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As we get real, we might spare a thought for two great mathematicians…

Georg Friedrich Bernhard Riemann died on this date in 1866. A mathematician who made contributions to analysis, number theory, and differential geometry, he is remembered (among other things) for his 1859 paper on the prime-counting function, containing the original statement of the Riemann hypothesis, regarded as one of the most influential papers in analytic number theory.

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Andrey (Andrei) Andreyevich Markov died on this date in 1922.  A Russian mathematician, he helped to develop the theory of stochastic processes, especially those now called Markov chains: sequences of random variables in which the future variable is determined by the present variable but is independent of the way in which the present state arose from its predecessors.  (For example, the probability of winning at the game of Monopoly can be determined using Markov chains.)  His work on the study of the probability of mutually-dependent events has been developed and widely applied to the biological, physical, and social sciences, and is widely used in Monte Carlo simulations and Bayesian analyses.

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“Over the long term, symbiosis is more useful than parasitism. More fun, too.”*…

Blue-green formations of malachite form in copper deposits near the surface as they weather. But they could only arise after life raised atmospheric oxygen levels, starting about 2.5 billion years ago.

There are many more varieties of minerals on earth than previously believed– and about half of them formed as parts or byproducts of living things…

The impact of Earth’s geology on life is easy to see, with organisms adapting to environments as different as deserts, mountains, forests, and oceans. The full impact of life on geology, however, can be easy to miss.

A comprehensive new survey of our planet’s minerals now corrects that omission. Among its findings is evidence that about half of all mineral diversity is the direct or indirect result of living things and their byproducts. It’s a discovery that could provide valuable insights to scientists piecing together Earth’s complex geological history—and also to those searching for evidence of life beyond this world.

In a pair of papers published on July 1, 2022 in American Mineralogist, researchers Robert HazenShaunna Morrison and their collaborators outline a new taxonomic system for classifying minerals, one that places importance on precisely how minerals form, not just how they look. In so doing, their system acknowledges how Earth’s geological development and the evolution of life influence each other.

Their new taxonomy, based on an algorithmic analysis of thousands of scientific papers, recognizes more than 10,500 different types of minerals. That’s almost twice as many as the roughly 5,800 mineral “species” in the classic taxonomy of the International Mineralogical Association, which focuses strictly on a mineral’s crystalline structure and chemical makeup.

Morrison and Hazen also identified 57 processes that individually or in combination created all known minerals. These processes included various types of weathering, chemical precipitations, metamorphic transformation inside the mantle, lightning strikes, radiation, oxidation, massive impacts during Earth’s formation, and even condensations in interstellar space before the planet formed. They confirmed that the biggest single factor in mineral diversity on Earth is water, which through a variety of chemical and physical processes helps to generate more than 80 percent of minerals.

But they also found that life is a key player: One-third of all mineral kinds form exclusively as parts or byproducts of living things—such as bits of bones, teeth, coral, and kidney stones (which are all rich in mineral content) or feces, wood, microbial mats, and other organic materials that over geologic time can absorb elements from their surroundings and transform into something more like rock. Thousands of minerals are shaped by life’s activity in other ways, such as germanium compounds that form in industrial coal fires. Including substances created through interactions with byproducts of life, such as the oxygen produced in photosynthesis, life’s fingerprints are on about half of all minerals.

But they also found that life is a key player: One-third of all mineral kinds form exclusively as parts or byproducts of living things—such as bits of bones, teeth, coral, and kidney stones (which are all rich in mineral content) or feces, wood, microbial mats, and other organic materials that over geologic time can absorb elements from their surroundings and transform into something more like rock. Thousands of minerals are shaped by life’s activity in other ways, such as germanium compounds that form in industrial coal fires. Including substances created through interactions with byproducts of life, such as the oxygen produced in photosynthesis, life’s fingerprints are on about half of all minerals.

Historically, scientists “have artificially drawn a line between what is geochemistry and what is biochemistry,” said Nita Sahai, a biomineralization specialist at the University of Akron in Ohio who was not involved in the new research. In reality, the boundary between animal, vegetable, and mineral is much more fluid.

A new origins-based system for classifying minerals reveals the huge geochemical imprint that life has left on Earth. It could help us identify other worlds with life too: “Life Helps Make Almost Half of All Minerals on Earth,” from @jojofoshosho0 in @QuantaMagazine.

Larry Wall

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As we muse on minerals, we might send systemic birthday greetings to Thomas Samuel Kuhn; he was born on this date in 1922.  A physicist, historian, and philosopher of science, Kuhn believed that scientific knowledge didn’t advance in a linear, continuous way, but via periodic “paradigm shifts.”  Karl Popper had approached the same territory in his development of the principle of “falsification” (to paraphrase, a theory isn’t false until it’s proven true; it’s true until it’s proven false).  But while Popper worked as a logician, Kuhn worked as a historian.  His 1962 book The Structure of Scientific Revolutions made his case; and while he had– and has— his detractors, Kuhn’s work has been deeply influential in both academic and popular circles (indeed, the phrase “paradigm shift” has become an English-language staple).

“What man sees depends both upon what he looks at and also upon what his previous visual-conception experience has taught him to see.”

Thomas S. Kuhn, The Structure of Scientific Revolutions

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“I have all these great genes, but they’re recessive. That’s the problem here.”*…

DNA Sequence chromatograms produced by automated sequencing machines

When the Human Genome Initiative published its first findings in 2002, the world was shocked. Genetic biologists, however, had long ago come to realize that DNA sequences are only part of the story of how organisms develop…

Fueled by the expectation that knowing the sequence of our DNA would tell us who we are, US funding agencies launched one of the most ambitious scientific efforts of all time in 1990. I refer, of course, to the Human Genome Initiative. Since then, the pace of that effort has been furious:even before the decade was over, the finishing line was clearly in view. When in February 2001, two rival teams announced the results of their first analysis of this invaluable information, their report made front-page headlines around the world. Humans, it seems, have far fewer genes than had been expected — in fact, only a third more than the lowly roundworm. How can this be? And what does it mean? Are we really so similar to, and so little more than, mere worms? News of the extent of our commonality with all living species is as stunning as it is humbling. But at the same time, it invites a certain incredulity — and that not merely because of human pride. Simple observation of the manifest diversity of life also makes us resist, for it is impossible not to wonder: what is it, if not the number (and in many cases, even the structure) of the ‘genes’ encoded in our DNA that accounts for the extraordinary differences among living organisms? For the answer to this question, it seems that we will have to look to the regulatory dynamics that determine how the sequence information of the DNA is to be used by the cell. Here, in the complex regulation of genetic transcription, of translation, of protein structure and function, is where we will find what makes us human beings rather than worms, flies or mice. Knowledge of the sequence of our DNA can tell us an enormous amount, but it can almost certainly not tell us who we are.

But not everyone was taken aback by this news. While readers of the popular press may have been stunned, few biologists working at the frontiers of research in molecular genetics were astonished. True, they had expected a larger number of human ‘genes’, but they had long ago come to realise that DNA sequences are only part of the story of how organisms develop, and even of what we mean by a ‘gene’. They recognise, for example, that the spatial and temporal patterns of expression of a gene are even more crucial to the specification of an organism than the structure of that ‘gene’ is. They also know that no single definition of this word ‘gene’ can suffice. Of the many different definitions that are required to make sense of current usage, two stand out with particular clarity: one referring to a particular region of the DNA, and another to the unit of messenger RNA that is used in the synthesis of a particular protein. The number of genes of the second kind is in fact very much larger than that of the first kind (current estimates suggest more than ten times as many), for the fact is that many different ‘genes’ can be constructed out of a single specified region of the DNA. Because the particular context in which they use the word makes its meaning quite clear, ambiguities in usage rarely create problems for practising biologists. Not so, however, for most readers. Outside the laboratory, such linguistic uncertainties can lead to both confusion and misunderstanding — not only around the question of how many genes we have, but also of what genes are made of, where they reside, what they do and, perhaps most important, what genes are for.

The good news is that research in genetics has never been more exciting, and over the last few decades both the depth and the breadth of our understanding of the nature of genetic activity have grown spectacularly. With each advance, the picture of the role of genes in development that biologists learn to draw grows ever more complex and sophisticated, and in ever more conspicuous defiance of the simple mantra with which they began. The word ‘gene’ does not begin to do justice to the ingenuity of the mechanisms required to put biological organisms together — no more than the concept of the neuron does to the ingenuity and dynamic complexity of neural organisation, and no more than talk of individual minds to the complexities of language and cognition…

Unpacking the genome hasn’t turned out to be the master key to understanding life that many thought it would be– but that’s no reason not to celebrate what it does illuminate: “The century of the gene,” from Evelyn Fox Keller in @EngelsbergIdeas.

* Calvin, in Calvin and Hobbes (Bill Watterson)

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As we investigate inheritance, we might spare a thought for D’Arcy Wentworth Thompson; he died on this date in 1948.  A classics scholar who was also an accomplished biologist and mathematician, Thompson is best remembered for On Growth and Form (1917, new ed. 1942), a profound consideration of the shapes of living things, starting from the simple premise that “everything is the way it is because it got that way.”  Thus one must study not only finished forms, but also the forces that molded them: “the form of an object is a ‘diagram of forces’, in this sense, at least, that from it we can judge of or deduce the forces that are acting or have acted upon it.”

The book paved the way for the scientific explanation of morphogenesis, the process by which patterns are formed in plants and animals.  Thompson’s description of the mathematical beauty of nature inspired thinkers as diverse as Alan Turing and Claude Levi-Strauss, and artists including Henry Moore, Salvador Dali, and Jackson Pollock.  Peter Medawar, the 1960 Nobel Laureate in Medicine, called On Growth and Form “the finest work of literature in all the annals of science that have been recorded in the English tongue.”

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Written by (Roughly) Daily

June 21, 2022 at 1:00 am

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