More on this book
Community
Kindle Notes & Highlights
Read between
February 11 - March 7, 2019
anomalous form of creature, a whole category of life, previously unsuspected and now known as the archaea.
horizontal gene transfer. The third is a revelation, or anyway a strong likelihood, about our own deepest ancestry. We ourselves—we humans—probably come from creatures that, as recently as forty years ago, were unknown to exist.
Genes don’t move just vertically. They can also pass laterally across species boundaries, across wider gaps, even between different kingdoms of life, and some have come sideways into our own lineage—the primate lineage—from unsuspected, nonprimate sources.
antibiotic-resistant bacteria, a quiet crisis destined to become noisier. Dangerous bugs such as MRSA (methicillin-resistant Staphylococcus aureus, which kills more than eleven thousand people annually in the United States and many more thousands around the world) can abruptly acquire whole kits of drug-resistance genes, from entirely different kinds of bacteria, by horizontal gene transfer.
Woese and his colleagues had discovered “a separate form of life” constituting a “third kingdom” of biological forms in addition to the recognized two, ran on November 3, 1977. It was front page, above the fold, shouldering aside
Oswald Avery, at the Rockefeller Institute in New York, identified the substance, the “transforming principle,” that can cause such sudden change from one bacterial identity to another. It was deoxyribonucleic acid.
corn geneticist Barbara McClintock, discovering genes that bounce from one point to another on the chromosomes of her favorite plant, worked with very little support or recognition through the prime years of her career—and then accepted a Nobel Prize at age eighty-one.
Lynn Margulis, a Chicago-educated microbiologist unique in almost every way, shared at least one thing with McClintock: the frustrations of being dismissed by some colleagues as an eccentric and obdurate woman.
Charles Darwin kept a small notebook, which he labeled “B,” devoted to the wildest idea he ever had.
He read widely, scribbling facts and phrases into various notebooks. The “A” notebook was devoted to geology. The B notebook was first of a series on what, to himself only, he called “transmutation.” You can guess what that meant. Darwin had begun thinking his way toward a theory of evolution.
“The tree of life should perhaps be called the coral of life, base of branches dead,” ancestral forms gone.
In Aristotle’s History of Animals, written during the fourth century BCE, the tree of life is not yet a tree. It’s more like a ladder of nature or—as later Latinized from his Greek—a scala naturae. According to Aristotle, the diversity of the natural world “proceeds” from lifeless things such as earth and fire to living creatures such as animals “little by little,” in a progression so incremental that it’s impossible to draw absolute lines between one form and another.
We all know Leeuwenhoek’s name from our reading in high school of Paul de Kruif’s Microbe Hunters (a terrible book full of concocted dialogue and bogus detail, but an influential doorway to the subject) or other storybook histories of science, though we might not remember that Leeuwenhoek was a draper in Delft who started making his own magnifying lenses in order to better inspect the thread-count of textiles.
Lamarck had probably helped his standing among the revolutionaries back in 1790 while employed at what was then the Jardin du Roi, when he urged dropping the royal label and renaming that institution the Jardin des Plantes.
Lamarck nowadays is commonly associated with what his name came to represent: Lamarckism, an easy but imprecise label for the idea of the inheritance of acquired characteristics.
But that single tenet was never Lamarck in totality. He had other ideas, some even worse. He believed in spontaneous generation. He disbelieved in extinction, at least as a natural process. He argued that “subtle fluids,” surging through the bodies of living creatures, helped reshape them adaptively.
With his free time, especially rainy days and evenings, young Edward studied science and the classics. Ambitious and hungry, he thought he was preparing himself for Harvard.
Darwin published On the Origin of Species. That 1859 book, not the 1858 paper or excerpts, launched the Darwinian revolution.
“As buds give rise by growth to fresh buds,” Darwin wrote, and those buds grow to be twigs, and those twigs grow to be branches, some vigorous, some feeble, some thriving, some dying, “so by generation I believe it has been with the great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever branching and beautiful ramifications.” There’s a nice word: ramifications.
Eleven major lineages began the ascent. Eight of those came to dead ends—meaning, they went extinct. Trilobites, ammonites, ichthyosaurs, and plesiosaurs had all suffered such ends, leaving no descendants of any sort. One lineage rose through the eons without splitting, without tilting, like a beanstalk—meaning that it persisted through time, unchanged. That’s much the way horseshoe crabs, sometimes called living fossils, have survived relatively unchanged (at least externally, so far as fossilization can show) over 450 million years. The other two lineages, dominating the diagram, branched
...more
Crick himself had also started thinking beyond that problem, to the question of how proteins are physically assembled from the coded information, with one amino acid brought into line after another.
Sometime in 1957 Crick gathered his thoughts and his informed guesses on this problem—about how DNA gets translated into proteins—and in September he addressed the annual symposium of the
Carl Woese came to the University of Illinois, in Urbana, in 1964,
Woese was thirty-six years old and was hired with immediate tenure, which gave him some latitude to undertake risky, laborious research projects without need to worry about quick publications. His professorship was in the Department of Microbiology, though he had trained as a biophysicist, not a microbiologist, and had spent little time if any peering through microscopes at bacteria and other tiny bugs.
Woese confided, was to “unravel the course of events” leading to the origin of the simplest cells—the cells that microbiologists called prokaryotes, by which they meant bacteria. Eukaryotes constituted the other big category, the other domain, and all forms of cellular life (that is, not including viruses)
But those didn’t satisfy Woese. He wanted something more basic, more universal—something that went all the way back, or nearly all the way, to the beginnings of life. “The obvious choice of molecules here lies in the components of the translation apparatus,” he told Crick. “What more ancient lineages are there?” By “translation apparatus,” Woese meant the decoding mechanism, the system that turns DNA information into proteins—the same system that Crick had groped toward understanding in his 1958 paper “On Protein Synthesis.”
Every living cell, including bacteria, including the cells of our own bodies, including those of plants and of fungi and of every other cellular organism, contains many ribosomes. They function as assembly mechanisms, taking in genetic information, plus raw material in the form of amino acids, and producing those larger physical products: proteins. In plainer words: ribosomes turn genes into living bodies. Because the proteins they produce become three-dimensional molecules, a better metaphor than Brenner’s tape-reader, for our own day, might be this: the ribosome is a 3-D printer.
Transient in space (through the cell) and transient in time (used and discarded). But that’s only one kind of RNA, messenger RNA, performing one function. There’s more. RNA can serve as a building block as well as a message. Ribosomes, for instance, are composed of structural RNA molecules and proteins, just as an espresso machine might be made of both steel and plastic.
Woese saw the secret truth that RNA—not just a molecule, but a family of versatile, complex, underappreciated molecules—is really more interesting and dynamic than its famed counterpart, DNA.
Fred Sanger’s pioneering work was the standard at that time for efforts at sequencing RNA.
Woese himself was not an experimentalist. He was a theorist, a thinker, like Francis Crick. “He never used any of the equipment in his own lab,” Sogin said. None of it—unless
Woese had quit medical school two days into his third-year rotation in pediatrics.
After his death in December 2012, Woese’s files of scientific correspondence, manuscripts, journal articles, and other materials went to the University of Illinois Archives to be indexed, curated, and preserved.
Pauling’s sidekick, had helped articulate the very premise that Carl Woese was now putting dramatically to use: that the branching of lineages “should in principle be definable in terms of molecular information alone.”
Fox continued, in flashes, to show his value to Woese as a thinker. Gradually he proved himself, not just sufficiently to work on sequence comparisons but well enough to become Woese’s trusted partner, as well as the sole coauthor on the culminating paper in 1977, with its announcement of a third kingdom of life.
three Germans cared—not just Otto Kandler, who became a great pal to Woese, but also Wolfram Zillig, an eminent biologist who directed the Max Planck Institute for Biochemistry, in Munich, and his younger associate, Karl Stetter, formerly a student of Kandler’s.
Ralph Wolfe came. So did Ford Doolittle, George Fox, and Bill Balch. Woese not only traveled to Munich again but also delivered the welcoming address—and he made that a substantive lecture, rich with ideas and provocations, not just a ceremonial greeting.
Later, she would call Sagan “unbelievably self-centered,” a neglectful father, and a husband more needy of adoration than she could bear. The marriage, she would say, was like “a torture chamber shared with children.”
She divorced him in 1964.
Does this drawing reveal Ernst Haeckel as a throwback anthropocentrist in the guise of a Darwinian, as some scholars have argued? Was his great oak just another ladder of nature, of the sort Aristotle proposed and Charles Bonnet had been designing back in 1745? Does it show that Haeckel took humans as the crown of creation, the end point toward which a teleological evolutionary process was directed? Not necessarily.
Alfred S. Romer, a paleontologist at Harvard, was one of the great tree makers of the midcentury, and his reached a broad audience of young scientists-in-training through his influential textbooks, most notably Vertebrate Paleontology.
separated Monera (bacteria) from Protista (simple creatures with cell nuclei). So for Copeland, using the formal names, it was Monera, Protista, Plantae, and Animalia. He argued his case more fully in a 1956 book, which is full
The Rockefeller Institute Hospital, where Avery had his lab, was America’s leading center of research on pneumococcal pneumonia, which Avery studied for much of the following two decades. But after the Griffith paper in 1928, and with some tugging by his junior colleagues, his focus
