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  • feedwordpress 08:01:11 on 2018/03/24 Permalink
    Tags: biology, , eFLOWER, first flower, flower, , , , , ,   

    “The earth laughs in flowers”*… 

     

    The first flower?

    With the incredible diversity of flowers that exist today—from pinprick-sized duckweed to the meters-high blooms of a corpse flower—it’s hard to imagine that they all descend from just a single species. Charles Darwin himself wrung his hands over how flowering plants exploded in diversity early in their evolution. Now, researchers have figured out what the ancestral flower might have looked like. The study may help them uncover how flowers took over the world.

    Fossils are the surest way to learn about organisms that lived in the past, but these are hard to come by for early flowers: The earliest preserved blossoms date back some 130 million years—at least 10 million years after the time when researchers think the ancestor of all flowering plants was alive. But there is another way to learn about species that are long gone: by taking a careful look at the forms of their modern descendants, and tracing the history of those forms back to the trunk of their family tree.

    To that end, dozens of researchers participating in the eFLOWER project amassed data from scientific papers to create the largest database of the structures of modern flowers, like their sexual organs and the layouts of their petals. The analysis included more than 13,000 data points spanning back to a 1783 description by famous evolutionary biologist Jean-Baptiste Lamarck. Combining those data with a DNA-based family tree and information about fossils, the scientists tested millions of configurations of how flowers may have changed through time to determine the most likely structure and shape for the earliest flowers.

    Though the team’s reconstructed ancestral flower [pictured above] doesn’t look radically different than many modern flowers, it does have a combination of traits not found today…

    Pick (up) the tale in toto at: “The world’s first flower may have looked like this.”

    * Ralph Waldo Emerson

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    As we cultivate our gardens, we might send fecund birthday greetings to Sidney Walter Fox; he was born on this date in 1912.  A biochemist interested in the biological origin of life, he studied the synthesis of amino acids from inorganic molecules.  He gave the name proteinoid to the protein-like polymer that results from a mixture of amino acids subjected to such considerable heating as would be present during the volcanic primordial earth (in the “primordial soup” as it’s colloquially known).  Fox observed that when proteinoids or “thermal proteins,” are placed in water, they self-organize into microspheres or protocells, possible precursors of the contemporary living cell.  Fox argued that RNA or DNA need not date back to the origin of life; and he showed that proteinoid “microspheres,” as he called them, exhibit growth, metabolism, reproduction (by budding), and responsiveness to stimuli – all properties of life – though without a genetic system.

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  • feedwordpress 09:01:59 on 2017/11/20 Permalink
    Tags: biology, , , , , mass, matter, , , ,   

    “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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  • feedwordpress 08:01:47 on 2017/10/15 Permalink
    Tags: biology, , , cook pines, Herbert Faulkner Copeland, , leaning trees, , ,   

    “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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  • feedwordpress 08:01:40 on 2017/08/16 Permalink
    Tags: biology, Chang, Eng, , , gliding, , , siamese twins,   

    “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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  • feedwordpress 08:01:52 on 2017/08/10 Permalink
    Tags: abiogenesis, biology, , , , , , , teleporter,   

    “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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  • feedwordpress 08:01:54 on 2017/07/28 Permalink
    Tags: biology, , , , , , , , ,   

    “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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  • feedwordpress 08:01:24 on 2017/05/07 Permalink
    Tags: biology, Bloody Tuesday, , , , , , San Franscisco, , strike,   

    “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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  • feedwordpress 09:01:12 on 2017/03/03 Permalink
    Tags: biology, , genetic drift, , , , , , Sewall Wright, ,   

    “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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  • feedwordpress 09:01:16 on 2016/12/12 Permalink
    Tags: , biology, , , , , , Midlands Enlightenment, public domain, ,   

    “Widespread public access to knowledge, like public education, is one of the pillars of our democracy, a guarantee that we can maintain a well-informed citizenry”*… 

     

    Top Row (left to right): André Breton; Buster Keaton; László Moholy-Nagy   Middle Row (left to right): Gertrude Stein; H. G. Wells; Frank O’Hara; Alfred Stieglitz   Bottom Row (left to right): Evelyn Waugh; D. T. Suzuki; Paul Nash; Mina Loy

    Via Public Domain Review

    Pictured above is our top pick of those whose works will, on 1st January 2017, enter the public domain in many countries around the world. Of the eleven featured, five will be entering the public domain in countries with a “life plus 70 years” copyright term (e.g. most European Union members, Brazil, Israel, Nigeria, Russia, Turkey, etc.) and six in countries with a “life plus 50 years” copyright term (e.g. Canada, New Zealand, and many countries in Asia and Africa) — those that died in the year 1946 and 1966 respectively. As always it’s a varied gaggle who’ve assembled for our graduation photo, including the founder of the Surrealist movement, a star of the silent film era, the Japanese author behind the popularisation of Buddhism in the West, two female writers at the heart of the Modernist scene, and one of the “fathers of science fiction”…

    More on each of the “graduates” at Class of 2017.

    * Scott Turow, attorney, author, President of the Author’s Guild

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    As we share and share alike, we might send foresightful birthday greetings to Erasmus Darwin; he was born on this date in 1731.  Erasmus was an accomplished doctor (he declined an offer to be personal physician to Charles III).  He was also a restless inventor, devising both a copying machine and a speaking machine to impress his friends (inventions he shared rather than patenting). But he is better remembered as a key thinker in the “Midlands Enlightenment”– a founder of the Lunar Society of Birmingham and author of (among other works) The Botanic Garden, a poem that anticipates the Big Bang theory in its description of an explosion, a “mass” which “starts into a million suns,” and Zoonomia, or, The Laws of Organic Life, which contained one of the first formal theories of evolution… one that foreshadowed the theories of Erasmus’ reader– and grandson– Charles… all of which are in the public domain.

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  • feedwordpress 08:01:13 on 2016/09/04 Permalink
    Tags: , artificial life, biology, Chinese Room, , John McCarthy, John Searle, , , ,   

    “God help us — for art is long, and life so short”*… 

     

    The creation of a homunculus, an artificially made miniature human, from an 1899 edition of Goethe’s Faust

    Making life artificially wasn’t as big a deal for the ancients as it is for us. Anyone was supposed to be able to do it with the right recipe, just like baking bread. The Roman poet Virgil described a method for making synthetic bees, a practice known as bougonia, which involved beating a poor calf to death, blocking its nose and mouth, and leaving the carcass on a bed of thyme and cinnamon sticks. “Creatures fashioned wonderfully appear,” he wrote, “first void of limbs, but soon awhir with wings.”

    This was, of course, simply an expression of the general belief in spontaneous generation: the idea that living things might arise from nothing within a fertile matrix of decaying matter. Roughly 300 years earlier, Aristotle, in his book On the Generation of Animals, explained how this process yielded vermin, such as insects and mice. No one doubted it was possible, and no one feared it either (apart from the inconvenience); one wasn’t “playing God” by making new life this way.

    The furor that has sometimes accompanied the new science of synthetic biology—the attempt to reengineer living organisms as if they were machines for us to tinker with, or even to build them from scratch from the component parts—stems from a decidedly modern construct, a “reverence for life.” In the past, fears about this kind of technological hubris were reserved mostly for proposals to make humans by artificial means—or as the Greeks would have said, by techne, art…

    Philip Ball digs into myth, history, and science to untangle the roots of our fears of artificial life: “Man Made: A History of Synthetic Life.”

    * Johann Wolfgang von Goethe, Faust: Part One

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    As we marvel that “it’s alive!,” we might send carefully-coded birthday greetings to John McCarthy; he was born on this date in 1927.  An eminent computer and cognitive scientist– he was awarded both the Turning Prize and the National Medal of Science– McCarthy coined the phrase “artificial Intelligence” to describe the field of which he was a founder.

    It was McCarthy’s 1979 article, “Ascribing Mental Qualities to Machines” (in which he wrote, “Machines as simple as thermostats can be said to have beliefs, and having beliefs seems to be a characteristic of most machines capable of problem solving performance”) that provoked John Searle‘s 1980 disagreement in the form of his famous Chinese Room Argument… provoking a broad debate that continues to this day.

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