Posts Tagged ‘biochemistry’
“There are more things in heaven and Earth, Horatio, than are dreamt of in your philosophy”*…
And some of them were recently found in the woods near Boston…
Researchers have unearthed a trove of wonders in the soil of a Massachusetts forest: an assortment of giant viruses unlike anything scientists had ever seen. The find suggests this group of relatively massive parasites has an even greater ecological diversity and evolutionary importance than researchers knew.
Giant viruses can exceed 2 micrometers in diameter, on par with some bacteria. They can also harbor immense genomes, which reach 2.5 megabases—larger than the genomes of far more complex organisms. Between the discovery of these impressively sized viruses in algae and the culturing of amoeba-infecting Mimiviruses, most of the research on the group has focused on viruses that inhabit freshwater environments. But DNA sequencing has long indicated that giant viruses are diverse and abundant elsewhere, too—especially in sediments and soils, which are estimated to host some 97% of all the viral particles on Earth. Indeed, genomic sequencing of the soils of Harvard Forest—a roughly 16-square-kilometer area west of Boston—indicated the presence of numerous, novel giant viruses.
Now, electron microscopy has allowed scientists to see what others had only sequenced. The diversity of forms was astounding, they report in a bioRxiv preprint. Not only did the researchers see the 20-sided icosahedral shapes they expected, they spotted ones with myriad modifications—tails, altered points, and multilayered or channeled structures abounded. There were even viruses with long tubular appendages, which the team dubbed “Gorgon” morphology [photo above]. Furthermore, many of these putative viral particles were coated with almost hairlike projections, which varied in length, thickness, density, and shape.
The findings suggest virologists have much to discover about how giant viruses interact with their host cells. That likely means the ecological roles these viruses play in soils—and elsewhere they’re found—are woefully underappreciated…
Microbes come in a variety of shapes, hinting at undiscovered ecological diversity: “Alien-looking viruses discovered in Massachusetts forest,” in @ScienceMagazine.
* Shakespeare, Hamlet
As we marvel at multifariousness (and note that viruses, while generally considered to be non-living and thus not considered microorganisms, are colloquially lumped in with microbes), 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.
“Nature is full for us of seeming inconsistencies and glad surprises”*…
George Musser talks with biologist Michael Levin about his practice of uncovering the incredible, latent abilities of living things…
Michael Levin, a developmental biologist at Tufts University, has a knack for taking an unassuming organism and showing it’s capable of the darnedest things. He and his team once extracted skin cells from a frog embryo and cultivated them on their own. With no other cell types around, they were not “bullied,” as he put it, into forming skin tissue. Instead, they reassembled into a new organism of sorts, a “xenobot,” a coinage based on the Latin name of the frog species, Xenopus laevis. It zipped around like a paramecium in pond water. Sometimes it swept up loose skin cells and piled them until they formed their own xenobot—a type of self-replication. For Levin, it demonstrated how all living things have latent abilities. Having evolved to do one thing, they might do something completely different under the right circumstances.
Not long ago I met Levin at a workshop on science, technology, and Buddhism in Kathmandu. He hates flying but said this event was worth it. Even without the backdrop of the Himalayas, his scientific talk was one of the most captivating I’ve ever heard. Every slide introduced some bizarre new experiment. Butterflies retain memories from when they were caterpillars, even though their brains turned to mush in the chrysalis. Cut off the head and tail of a planarian, or flatworm, and it can grow two new heads; if you amputate again, the worm will regrow both heads. Levin argues the worm stores the new shape in its body as an electrical pattern. In fact, he thinks electrical signaling is pervasive in nature; it is not limited to neurons. Recently, Levin and colleagues found that some diseases might be cured by retraining the gene and protein networks as one might train a neural network. But when I sat down to talk to the audacious biologist on the hotel patio, I mostly wanted to hear about slime mold…
Read on for a fascinating conversation: “The Biologist Blowing Our Minds,” @drmichaellevin and @gmusser in @NautilusMag.
* Margaret E. Barber
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As we’re amazed, we might send tidy birthday greetings to Irwin Rose; he was born on this date in 1926. A biologist and biochemist, he shared the 2004 Nobel Prize in Chemistry for the discovery of ubiquitin-mediated protein degradation.
Ubiquitin is a small protein molecule that attaches to other proteins, tagging them for removal, which are thus recognized by the cell’s proteasomes. These structures are the cell’s waste-disposal units, allowing the proteins to be broken down into tiny pieces for reuse; this ubiquitin-mediated process cleans up unwanted proteins resulting during cell division, and performs quality control on newly synthesized proteins… which matters, as faulty protein-breakdown processes lead to such conditions as cystic fibrosis, several neurodegenerative diseases, and certain types of cancer.
“Real generosity towards the future lies in giving all to the present”*…
Iwan Rhys Morus suggests that we’re enthralled to a Victorian paradigm that haunts us still: the idea that inventors and entrepreneurs hold the keys to the utopian future…
Tech titans like Elon Musk and Jeff Bezos present themselves as men who could single-handedly shape the future. For their supporters, their ruthless drive toward success is their key virtue. And their showmanship — Musk sending a Tesla Roadster into space on a Falcon Heavy rocket, or Bezos sending Captain Kirk into orbit with Blue Origin — is a way of demonstrating that virtue and asserting they are in control.
We owe to the Victorians the idea that there is a firm link between virtue and technological agency. They established a powerful paradigm that continues to haunt us: that the future is (or can be) a utopia, and inventors and entrepreneurs are the ones who know how to get there.
While our notions of virtue have shifted today, we still assume that future-making is the prerogative of very specific sorts of innovators — even as their imagined identities have fractured and transformed. The assumption that innovation is the property of charismatic individuals still underlies the way we think about technology.
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The seductive power of Victorian thinking about the relationship between character, technology, and the future remains pervasive, even if views about just what the proper character of the inventor should be have shifted….
With its focus on individual virtue, the Victorian vision of the future is an exclusive one. When we subscribe to this paradigm about how — and by whom — the future is made, we’re also relinquishing control over that future. We’re acknowledging that tomorrow belongs to them, not to us.
“Back To The Victorian Future,” by @irmorus1 in @NoemaMag. Eminently worth reading in full.
* Albert Camus
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As we ponder power and its purpose, we might send inclusive birthday greetings to Jacques Lucien Monod; he was born on this date in 1910. A biochemist, he shared (with with François Jacob and André Lwoff) the Nobel Prize in Physiology or Medicine in 1965, “for their discoveries concerning genetic control of enzyme and virus synthesis.”
But Monod, who became the director of the Pasteur Institute, also made significant contributions to the philosophy of science– in particular via his 1971 book (based on a series of his lectures) Chance and Necessity, in which he examined the philosophical implications of modern biology. The importance of Monod’s work as a bridge between the chance and necessity of evolution and biochemistry on the one hand, and the human realm of choice and ethics on the other, can be seen in his influence on philosophers, biologists, and computer scientists including Daniel Dennett, Douglas Hofstadter, Marvin Minsky, and Richard Dawkins.
“Oxygen / Everything needs it”*…
As tongues of flame lapped the planet’s largest tract of rain forest over the past few weeks, it has rightfully inspired the world’s horror. The entire Amazon could be nearing the edge of a desiccating feedback loop, one that could end in catastrophic collapse. This collapse would threaten millions of species, from every branch of the tree of life, each of them—its idiosyncratic splendor, its subjective animal perception of the world—irretrievable once it’s gone. This arson has been tacitly encouraged by a Brazilian administration that is determined to develop the rain forest, over the objections of its indigenous inhabitants and the world at large. Losing the Amazon, beyond representing a planetary historic tragedy beyond measure, would also make meeting the ambitious climate goals of the Paris Agreement all but impossible. World leaders need to marshal all their political and diplomatic might to save it.
The Amazon is a vast, ineffable, vital, living wonder. It does not, however, supply the planet with 20 percent of its oxygen.
As the biochemist Nick Lane wrote in his 2003 book Oxygen, “Even the most foolhardy destruction of world forests could hardly dint our oxygen supply, though in other respects such short-sighted idiocy is an unspeakable tragedy.”…
There are very many very good reasons not to burn down the Amazon rain forest. Still, humans could burn every living thing on the planet and still not dent its oxygen supply: “The Amazon Is Not Earth’s Lungs.”
(Again– burning down the rainforest is bad, very very bad. But as long-time environmental reporter Michael Shellenberger argues, if we ground our concerns in the actual details of what’s happening, we’re much likelier to find effective responses.)
* Mary Oliver (from her collection Twist)
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As we take a deep breath, we might recall that it was on this date in 1666 that the Great Fire of London broke out. The conflagration raged for four days, mostly in the City of London, within the old Roman walls; it did not spread to the aristocratic district of Westminster, to Charles II’s Palace of Whitehall, nor to most of the suburban slums. It destroyed 13,200 houses, St. Paul’s Cathedral, and 87 parish churches. Miraculously, fewer than 20 people lost their lives.
“You give me fever”*…
People drew maps of body locations where they feel basic emotions (top row) and more complex ones (bottom row). Hot colors show regions that people say are stimulated during the emotion. Cool colors indicate deactivated areas
When a team of scientists in Finland asked people to map out where they felt different emotions on their bodies, they found that the results were surprisingly consistent, even across cultures.
People reported that happiness and love sparked activity across nearly the entire body, while depression had the opposite effect: It dampened feelings in the arms, legs and head. Danger and fear triggered strong sensations in the chest area, the volunteers said. And anger was one of the few emotions that activated the arms…
Read the whole story at “Mapping Emotions On The Body: Love Makes Us Warm All Over,” and peruse the research paper in the Proceedings of the National Academy of Sciences.
* from “Fever,” written by Eddie Cooley and Otis Blackwell, who used the pseudonym “John Davenport.” It was originally recorded by Little Willie John in 1956, then covered by various artists, notably Peggy Lee, Elvis Presley, Ella Fitzgerald, Usha Uthup, Ray Charles, Nancy Sinatra, The McCoys, The Blues Band, Boney M., Amanda Lear, La Lupe, Madonna, Fishtank Ensemble, The Jam, The Cramps, Wanda Jackson, Bette Midler, Michael Bublé, and Suzi Quatro
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As we as we try to recall whether it’s “mind over body” or “body over mind,” we might send emotional birthday greetings to Karl Sune Detlof Bergström; he was born on this date in 1916. An accomplished biochemist, Bergström shared the 1982 Nobel Prize in Physiology or Medicine with Bengt I. Samuelsson and John R. Vane for the isolation, identification, and analysis of prostaglandins and related biologically active substances. As these biochemical compounds influence such physiological phenomena in mammals as blood pressure and body temperature, they are surely active in the reactions mapped by the Finns, above.
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