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Posts Tagged ‘biology

“Energy is liberated matter, matter is energy waiting to happen”*…

 

We’ve certainly come a long way since the ancient Greek atomists speculated about the nature of material substance, 2,500 years ago. But for much of this time we’ve held to the conviction that matter is a fundamental part of our physical universe. We’ve been convinced that it is matter that has energy. And, although matter may be reducible to microscopic constituents, for a long time we believed that these would still be recognizable as matter—they would still possess the primary quality of mass.

Modern physics teaches us something rather different, and deeply counter-intuitive. As we worked our way ever inward—matter into atoms, atoms into sub-atomic particles, sub-atomic particles into quantum fields and forces—we lost sight of matter completely. Matter lost its tangibility. It lost its primacy as mass became a secondary quality, the result of interactions between intangible quantum fields. What we recognize as mass is a behavior of these quantum fields; it is not a property that belongs or is necessarily intrinsic to them.

Despite the fact that our physical world is filled with hard and heavy things, it is instead the energy of quantum fields that reigns supreme. Mass becomes simply a physical manifestation of that energy, rather than the other way around…

Modern physics has taught us that mass is not an intrinsic property: “Physics Has Demoted Mass.”

* Bill Bryson, A Short History of Nearly Everything

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As we watch all that is solid melt into air, 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 and caused the imprisonment and death of many of the country’s eminent biologists who disagreed with him.

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.

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Written by LW

November 20, 2017 at 1:01 am

“We can learn a lot from trees: they’re always grounded but never stop reaching heavenward”*…

 

Cook pines at U.C. Irvine

… or reaching in some direction, anyway:

California’s Cook pines have a weird characteristic. The towering trees lean conspicuously to one side, always toward the south, as though buffeted by years of strong winds.

But no one really understands why.

So a few years ago, botanists from Cal Poly San Luis Obispo took up the mystery. They collected data from 100 or so trees in California. Every one leaned south.

Then came an “aha” moment.

The scientists reached out to a colleague in Australia and asked him to check the Cook pines there. What he told them was “crazy,” said Jason Johns, who was the lead author of a study drawn from the research.

“The pattern was there,” he said, “just in the opposite direction.” The trees appeared to be leaning toward the Equator, a trait never before documented in the plant kingdom.

Cook pines are native to New Caledonia, an archipelago in the South Pacific, but they’ve spread the globe, including thousands in California. The Cal Poly researchers found that the leaning pattern held with measurements from Cook pines taken on five Continents.

According to their calculations, the odds that it resulted from chance, said Mr. Johns, “were point zero, zero, with like 14 zeros in front of it. It was pretty clear.”

The why, however, remains an open question.

Mr. Johns was reluctant to venture a theory. Pressed, he talked about a cell process called “signaling cascade” and the interplay between growth, sunlight and gravity.

The Cook pine discovery, he offered, was an example of how far science has to go in understanding the way the world works.

“As you know with anything,” he said, “the more you uncover, the more you realize how little you know.”

The biological compass.

* Everett Mamor

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As we orient to due south, we might spare a thought for Herbert Faulkner Copeland; he died on this date in 1968.  An biologist, he delineated four biological kingdoms, instead of the (then-canonical) two for plants and animals.  A decade after Darwin’s Origin of Species, Ernst Haekel had proposed (1866) adding a kingdom, Protista, for microorganisms, but it was never adopted.  Copeland further discriminated among the microorganisms in a paper in 1938, splitting them into two kingdoms: Monera and Protista.  Copeland identified Monera as organisms without nuclei, and Protista as being largely unicellular, with nuclei.  By 1956, he published a book, The Classification of Lower Organisms, still trying “to persuade the community of biologists” to adopt these four kingdoms.  Change came slowly, but continues now beyond Copeland’s ideas to five or six.  He was the son of botanist Edwin B. Copeland, from whom he learned the principles of classification.

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Written by LW

October 15, 2017 at 1:01 am

“The knack lies in learning how to throw yourself at the ground and miss”*…

 

The oldest gliding mammals ever discovered are strengthening the case for taking to the skies.

Well, they couldn’t exactly soar like the eagles, but the two new species, discovered in China, at least sampled the aerial life. Both date to around 160 million years ago during the Jurassic Period, when mammals as a lineage were first getting off the ground — both metaphorically and literally. They’re not directly related to the gliders of today, however. Gliding instead seems to be advantageous enough that it has appeared several times throughout our evolutionary history…

Both fossils belong to a group of ancestral mammals that have long been extinct. As such, there is no line connecting them to gliding mammals today, indicating that mammalian aerial skills disappeared and re-emerged at least once throughout history. Using birds as an obvious example, flight is a powerful advantage to have. Even as a (temporarily) airborne creature you expend less energy, move faster and evade potential predators — all benefits that make the evolutionary trade-offs worthwhile. It’s not just mammals either, many frog species and even some fish have gained the ability to glide, with evidence that the trait has appeared more than once in those species as well…

The full story at: “Oldest Gliding Mammals Shed Light on the History of Flight.”

* Douglas Adams on flying, in Life, the Universe and Everything

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As we take to the air, we might recall that it was on this date in 1829 that Chang and Eng Bunker, arrived in Boston aboard the ship Sachem to be exhibited to the Western world.  The original “Siamese Twins,” they were  joined at the waist by a band of cartilage, about 8 in. circumference and 4 in. long.  In 1828 British merchant Robert Hunter “discovered” them and paid their family to let them be exhibited as a curiosity during a world tour; at the end of that engagement, the brothers went into business for themselves.  In 1839, they visited Wilkesboro, N.C. with P. T. Barnum; they found the town appealing, settled there, took the surname “Bunker,” became United States citizens, and in 1843 married two sisters with whom they raised 10 children. Only after their death was it discovered that the cartilage that connected them could have been easily and safely removed.

Click here for Mark Twain’s short story, “The Siamese Twins,” based on Chang and Eng.

Chang and Eng Bunker

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Written by LW

August 16, 2017 at 1:01 am

“All of today’s DNA, strung through all the cells of the earth, is simply an extension and elaboration of [the] first molecule”*…

 

The first biological teleporter sits in a lab on the lower level of the San Diego building that houses Synthetic Genomics Inc. (SGI), looking something like a super-sized equipment cart.

The device is actually conglomeration of small machines and lab robots, linked to each other to form one big machine. But this one can do something unprecedented: it can use transmitted digital code to print viruses.

In a series of experiments culminating last year, SGI scientists used genetic instructions sent to the device from elsewhere in the building to automatically manufacture the DNA of the common flu virus. They also produced a functional bacteriophage, a virus that infects bacterial cells.

Although that wasn’t the first time anyone had made a virus from DNA parts, it was the first time it was done automatically, without human hands.

The device, called a “digital-to-biological converter” was unveiled in May. Though still a prototype, instruments like it could one day broadcast biological information from sites of a disease outbreak to vaccine manufacturers, or print out on-demand personalized medicines at patients’ bedsides…

… or project life-as-we-know it into outer space. More at “Biological Teleporter Could Seed Life Through Galaxy.”

* Lewis Thomas, The Medusa and the Snail

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As we beam up, we might spare a thought for Sidney Walter Fox; he died on this date in 1998.  A biochemist, he was responsible for a series of discoveries about the origin of life.  Fox believed in the process of abiogenesis, by which life spontaneously organized itself from the colloquially known “primordial soup,” poolings of various simple organic molecules that existed during the time before life on Earth.  In his experiments (which possessed, he believed, conditions like those of primordial Earth), he demonstrated that it is possible to create protein-like structures from inorganic molecules and thermal energy.  Dr. Fox went on to create microspheres that he said closely resembled bacterial cells and concluded that they could be similar to the earliest forms of life or protocells.

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Written by LW

August 10, 2017 at 1:01 am

“To imagine a language is to imagine a form of life”*…

 

Jeremy England is concerned about words—about what they mean, about the universes they contain. He avoids ones like “consciousness” and “information”; too loaded, he says. Too treacherous. When he’s searching for the right thing to say, his voice breaks a little, scattering across an octave or two before resuming a fluid sonority.

His caution is understandable. The 34-year-old assistant professor of physics at the Massachusetts Institute of Technology is the architect of a new theory called “dissipative adaptation,” which has helped to explain how complex, life-like function can self-organize and emerge from simpler things, including inanimate matter. This proposition has earned England a somewhat unwelcome nickname: the next Charles Darwin. But England’s story is just as much about language as it is about biology…

A new theory on the emergence of life’s complexity: “How Do You Say ‘Life’ in Physics?

* Ludwig Wittgenstein, Philosophical Investigations

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As we resist the urge to simplify, we might send carefully-constructed 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.

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Written by LW

July 28, 2017 at 1:01 am

“There are people in the world so hungry, that God cannot appear to them except in the form of bread”*…

 

We stand at the precipice if we don’t re-evaluate our understanding of poverty and inequality. The narrative in the neo-liberal west is that if you work hard, things work out. If things don’t work out, we have the tendency to blame the victim, leaving them without any choices. Brexit, Le Pen, and the defeat of Hillary Clinton are examples of the cracks that result from inequality and poverty, symptoms of my childhood experience writ large. The Piketty pitchforks are out, and the march to global disorder can only be arrested by adopting measures that begin to price in the stacked deck that I and anyone else born into deep poverty sees, and resents.

I believe we will see the Italian Five Star Movement submit a referendum to leave the EU this year, and that Marine Le Pen has better than even odds of winning the French election. The EU is in danger of buckling under a globalist defeat and may exist in name only two years from now.

These trends are being accelerated by the blind belief that the poor have failed to seize the opportunities that the market or globalization has created. This myth deserves to be taken off life support—and the emerging, empirical, and carefully observed science of poverty can help us do so if we pay it the attention it deserves…

A powerful plea for a fundamental re-understanding of the economic inequality that vexes our society, and of the myth of meritocracy that has helped sustain it: “Why Poverty Is Like a Disease.”

* Mahatma Gandhi

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As we agree with FDR that “the test of our progress is not whether we add more to the abundance of those who have much; it is whether we provide enough for those who have too little,” we might recall that this date in 1907 was “Bloody Tuesday.”  The San Francisco streetcar strike, which had begun two days earlier, erupted into violence when armed strikebreakers fired into an angry crowd of strike supporters.  Soon armed strike sympathizers returned fire.  2 died; 20 were injured.

Armed strike breaker, left, shoots into the crowd on Bloody Tuesday, May 7, 1907. The original caption in The San Francisco Examiner said that “Photographer Coleman” took the picture “the moment before the man running beside him was fatally shot.”

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Written by LW

May 7, 2017 at 1:01 am

“When you have mastered numbers, you will in fact no longer be reading numbers, any more than you read words when reading books. You will be reading meanings.”*…

Errors of judgment about large numbers can have a big impact on the way you view policies and government decisions. The rationale goes like this: The National Science Foundation received $7.463 billion for fiscal year 2016 through the Consolidated Appropriations Act. The total United States budget outlay for 2016 was $3.54 trillion. If you’re someone who perceives the difference between a billion and a trillion as relatively small, you’d think the US is spending a lot of money on the National Science Foundation—in fact, depending on your politics, you might applaud the federal government’s investment or even think it wasteful. But, if you understand that a billion is a thousand times less than a trillion, you can calculate that the Foundation got a paltry 0.2 percent of the budget outlay last year. (It may be more straightforward to think of the budget as roughly one-half to one-third of reported costs for the proposed US-Mexico border wall, and let your values guide you from there.)…

On the significance of scale: “How to Understand Extreme Numbers.

[The image above is, of course, from the ever-wonderful xkcd.]

* W.E.B. Du Bois

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As we nudge ourselves toward numeracy, we might spare a thought for Sewall Wright; he died on this date in 1988.  A geneticist, he was known for his influential work on evolutionary theory and also for his work on path analysis. He was a founder (with Ronald Fisher and J.B.S. Haldane) of population genetics– a major step in the development of the modern evolutionary synthesis combining genetics with evolution.   He is perhaps best remembered for his concept of genetic drift (called the Sewall Wright effect): when small populations of a species are isolated, the few individuals who carry certain relatively rare genes may fail, out of pure chance, to transmit them. The genes may therefore disappear and their loss may lead to the emergence of new species– although natural selection has played no part in the process.

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Written by LW

March 3, 2017 at 1:01 am

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