Drosophila

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Longevity: To the Limits and Beyond (Research and Perspectives in Longevity) by Jean-Marie Robine, James W. Vaupel, Bernard Jeune, Michel Allard

computer age, conceptual framework, demographic transition, Drosophila, epigenetics, life extension, longitudinal study, phenotype, stem cell, stochastic process

Proc Natl Acad Sci USA 92:7540-7544 Luckinbill LS, Clare MJ (1985) Selection for life span in Drosophila melanogaster. Heredity 58:9-18 Masoro EJ (1992) Retardation of aging processes by nutritional means. Ann NY Acad Sci 673:29-35 Medawar PB (1952) An unsolved problem of biology. London, H K Lewis. Orr WC, Sohal RS (1994) Extension of life-span by overexpression of superoxide dismutase and catalase in Drosophila melanogaster. Science 263:1128-1130 Partridge L, Barton NH (1993) Optimality, mutation and the evolution of ageing. Nature 362:305-311 Rose MR (1984) Laboratory evolution of postponed senescence in Drosophila melanogaster. Evolution 38:1004-1010 Schachter F, Cohen D, Kirkwood TBL (1993) Prospects for the genetics of human longevity. Human Genet 91:519-526 Service PM (1987) Physiological mechanisms of increased stress resistance in Drosophila melanogaster selected for postponed senescence.

Rev. 65:375-398 Noy N, Schwartz H, Gafni A (1985) Age-related changes in the redox status ofrat muscle cells and their role in enzyme aging. Mech. Ageing Dev. 29:63-69 Orr WC, Sohal RS (1992) The effects of catalase gene overexpression on life span and resistance to oxidative stress in transgenic Drosophila melanogaster. Arch. Biochem. Biophys. 297:35-41 Orr WC, Sohal RS (1993) The effects of Cu-Zn superoxide dismutase gene overexpression on life span and resistance to oxidative stress in transgenic Drosophila melanogaster. Arch. Biochem. Biophys. 301 :34-40 Oxidative Stress May Be a Causal Factor in Senescence of Animals 153 Orr WC, Sohal RS (1994) Extension of life-span by overexpression of superoxide dismutase and catalase in Drosophila melanogaster. Science 263:1128-1130 Pearl R (1928) The rate of living. Alfred A. Knopf, Inc., New York Radi R, Turrens JF, Chang LY, Bush KM, Crapo JD, Freeman BA (1991) Detection of catalase in rat heart mitochondria.

In light of the importance of mitochondrial prooxidant generation, current efforts are directed at bolstering intramitochondrial antioxidant levels, thereby lowering the rate of ROS release to all other parts of the cell. Transgenic lines overexpressing MnSOD have been generated and are currently being characterized. Glutathione peroxidase, which acts in tandem with MnSOD in mitochondria in some systems, has proven refractory in Drosophila. The flies do not contain detectable levels of endogenous glutathione peroxidase activity, and attempts to express the human enzyme were thwarted by the inability of Drosophila to translate the unique selenocysteine codon at the active site. Recent reports of intramitochondrial catalase activity in rat heart (Radi et al. 1991) raise the possibility that catalase could be modified to enter mitochondria and substitute for glutathione peroxidase in these experiments. In summary, experiments conducted in this laboratory suggest that oxidative stress may be a fundamental causal factor in aging in representative species of at least two phyla.


pages: 608 words: 150,324

Life's Greatest Secret: The Race to Crack the Genetic Code by Matthew Cobb

a long time ago in a galaxy far, far away, anti-communist, Asilomar, Asilomar Conference on Recombinant DNA, Benoit Mandelbrot, Berlin Wall, bioinformatics, Claude Shannon: information theory, conceptual framework, Copley Medal, dark matter, discovery of DNA, double helix, Drosophila, epigenetics, factory automation, From Mathematics to the Technologies of Life and Death, James Watt: steam engine, John von Neumann, Kickstarter, New Journalism, Norbert Wiener, phenotype, post-materialism, Stephen Hawking

A concerted attack in which the full resources of the world state of science are exploited can hardly fail.33 * In the 1930s, most geneticists were not particularly concerned with finding out what genes are made of; they were more interested in discovering what genes actually do. There was a potential link between these two approaches. As the Drosophila geneticist Jack Schultz put it in 1935, by studying the effects of genes it should be possible ‘to find out something about the nature of the gene’.34 One of the scientists who took Schultz’s suggestion very seriously was George Beadle, who had studied the genetics of eye colour in Drosophila in Morgan’s laboratory, alongside the Franco-Russian geneticist Boris Ephrussi. When Ephrussi returned to Paris, Beadle followed him to continue their work. Their objective was to establish the biochemical basis of the mutations that changed the eye-colour of Drosophila flies. Beadle and Ephrussi’s experiments failed: the biochemistry of their system was too complicated, and they were unable to extract the relevant chemicals from the fly’s tiny eyes.

The first animal genome to be completed, in 1998, was that of the nematode worm, Caenorhabditis elegans, closely followed by that of the tiny vinegar fly, Drosophila melanogaster, in 2000. These projects provided vital information about two widely used laboratory organisms and were testing-grounds for different technical and commercial approaches to genome sequencing. The C. elegans genome project, led by John Sulston, was entirely funded by public money, whereas the Drosophila genome was a joint effort between publicly funded researchers and a company called Celera Genomics, led by Craig Venter, a molecular biologist turned entrepreneur. Despite the very different motivations of the public and private researchers, the Drosophila genome project was a success. In contrast, the Human Genome Project, which took place in parallel, was the focus of clashes of scientific and commercial outlook as well as of personality.40 The human genome contains around 3 billion base pairs, far more than that of C. elegans (100 million base pairs) or Drosophila (140 million base pairs).

To resolve this problem, Venter and his Celera colleagues enlisted computer scientists to develop algorithms for assembling the sequence, and they were able to prove the validity of their approach with the Drosophila genome. Despite hostility from many scientists around the world, Venter was probably right to argue that this method would make it possible to complete the project. Nevertheless, problems remained – even with the cleverest algorithms in the world, it is not possible to join up all of the bits of sequences. To get over this problem, recalcitrant parts of the genome were amplified in bacteria to try and bridge the gap. This does not always work – some sections of the human and the Drosophila genomes have still not been joined up, fifteen years after the sequences were published. Despite the continuing clashes, the completion of the draft human genome was announced by President Bill Clinton in 2000, even though it was in fact nowhere near finished.


She Has Her Mother's Laugh by Carl Zimmer

23andMe, agricultural Revolution, clean water, clockwatching, cloud computing, dark matter, discovery of DNA, double helix, Drosophila, Elon Musk, epigenetics, Fellow of the Royal Society, Flynn Effect, friendly fire, Gary Taubes, germ theory of disease, Isaac Newton, longitudinal study, medical bankruptcy, meta analysis, meta-analysis, microbiome, moral panic, mouse model, New Journalism, out of africa, phenotype, Ralph Waldo Emerson, Scientific racism, statistical model, stem cell, twin studies

At the time, he was getting his PhD at the University of California, San Diego, studying genes in Drosophila and related flies. He tinkered with their genes and observed whether he could change how their embryos developed. But the best tools he could use were clumsy and crude. In 2013, Gantz heard that researchers had figured out how to use CRISPR to alter a gene in Drosophila with easy precision. “It was one of the things I was waiting for,” Gantz told me when I visited him at his laboratory on a eucalyptus-covered hillside by the Pacific. After hearing the news, he had immediately ordered CRISPR molecules of his own and started trying them out. He had no idea he was about to discover a way to use CRISPR to alter heredity on a species-wide scale. Gantz decided to try out CRISPR by altering a Drosophila gene called yellow. It was, in a sense, an inherited choice.

These molecular hackers first came to light in the 1920s with the discovery of flies with too many daughters. A Russian biologist named Sergey Gershenson went into a forest to trap a species of fly called Drosophila obscura. When he brought the flies back to the Institute of Experimental Biology in Moscow, he figured out how to keep them alive on a diet of fermented raisins, potatoes, and water. Some of the female flies he trapped were carrying fertilized eggs, which they then laid by the thousands. Gershenson picked some of their offspring to breed new lines he could study for inherited traits. There was something peculiar about two of the lines, Gershenson noticed. Typically, a batch of eggs produced by Drosophila obscura contains an even balance of males and females. But in two of Gershenson’s lines, the mothers tended to produce far more daughters than sons.

He would never set foot in the Soviet Union again. In 1928, Morgan headed west to the California Institute of Technology, and Dobzhansky went with him to the orange-scented hills of Pasadena. Once Dobzhansky had settled into his new Western home, he drew up a plan to study how genetic variations were spread out over the range of a wild species. He knew he couldn’t study Morgan’s favorite, Drosophila melanogaster. It was a garbage-feeding camp follower. Instead, Dobzhansky picked Drosophila pseuodoobscura, a truly wild animal that lived across a range stretching from Guatemala to British Columbia. Dobzhansky bought a Model A Ford and started driving into remote mountain ranges to catch flies from isolated populations. Back in Pasadena, he bred the flies and inspected their chromosomes under a microscope. Comparing one fly to another, Dobzhansky sometimes spotted a section of a chromosome that was flipped.


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The Ancestor's Tale: A Pilgrimage to the Dawn of Evolution by Richard Dawkins

agricultural Revolution, Alfred Russel Wallace, complexity theory, delayed gratification, double helix, Drosophila, Haight Ashbury, invention of writing, lateral thinking, Louis Pasteur, mass immigration, nuclear winter, out of africa, Peter Singer: altruism, phenotype, Richard Feynman, Ronald Reagan, Spread Networks laid a new fibre optics cable between New York and Chicago, Steven Pinker, the High Line, urban sprawl

Blood vessels, nerves, muscle blocks, cartilage discs and ribs, where present, all follow the repetitive, modular plan. As with Drosophila the modules, though following the same general plan as each other, are different in detail. And like the insect division into head, thorax and abdomen, vertebrae are grouped into cervical (neck), thoracic (upper back vertebrae with ribs), lumbar (lower back vertebrae without ribs) and caudal (tail). As in Drosophila, the cells, whether they are bone cells, muscle cells, cartilage cells or anything else, need to know which segment they are in. And as in Drosophila, they know because of Hox genes -- Hox genes that recognisably correspond to particular Drosophila Hox genes -- although, unsurprisingly, given the immensity of time since Concestor 26, they are far from identical. Again as in Drosophila, the Hox genes are arranged in the right order on the chromosome.

When two, three or four versions of a Hox gene impinge upon one segment, their effects are combined. And, as with Drosophila, all mouse Hox genes exert their strongest effect in the first (most anterior) segment in their domain of influence, with a gradient of decreasing expression downstream in more posterior segments. It gets better. With minor exceptions, each gene from the Drosophila array of eight Hox genes resembles its opposite number in the mouse series more than it resembles the other seven genes in the Drosophila series. And they are in the same order along their respective chromosomes. Every one of the eight Drosophila genes has at least one representative in the mouse series of 13. The detailed gene-for-gene coincidence between Drosophila and mouse can only indicate shared inheritance -- from Concestor 26, the grand progenitor of all the protostomes and all the deuterostomes.

A particularly notable member of this family is Pax6, which corresponds to the gene known as ey in Drosophila. I've already mentioned that Pax6 is responsible for telling cells to make eyes. The same gene makes eyes in animals as different as Drosophila and mouse, even though the eyes produced are radically different in the two animals. In a similar way to Hox genes, Pax6 doesn't tell cells how to make an eye. It only tells them that here is the place to make an eye. A rather parallel example is the small family of genes called tinman. Again tinman genes are present in both Drosophila and mice. In Drosophila, tinman genes are responsible for telling cells to make a heart, and they normally express themselves in just the right place to make a Drosophila heart. As we have by now come to expect, tinman genes are also involved in telling mouse cells to make a heart in the right place for a mouse's heart.


pages: 309 words: 101,190

Climbing Mount Improbable by Richard Dawkins, Lalla Ward

Buckminster Fuller, computer age, Drosophila, Fellow of the Royal Society, industrial robot, invention of radio, John von Neumann, Menlo Park, phenotype, Robert X Cringely, stem cell, trade route

A collection of arthromorphs bred by artificial selection with an eye to their resemblance, however vague, to real arthropods. Figure 7.15 Homeotic mutations: (a) four-winged Drosophila. In normal Drosophila the second pair of wings is replaced by halteres, as in Figure 7.11; (b) normal (upper) and mutant (lower) silkworm caterpillars. Normally there are proper insect legs only on the three thoracic segments. The mutant has nine ‘thoracic’ segments. Figure 7.15 shows examples of so-called homeotic mutations in the fruitfly Drosophila and in the silkworm caterpillar. The normal Drosophila, like all flies, has only a single pair of wings. The second pair of wings is replaced by halteres as explained above. The picture shows a mutant Drosophila in which not only is there a second pair of wings instead of halteres, the entire second thoracic segment is reduplicated in substitution for the third thoracic segment.

Rebecca Quiring and Uwe Waldorf, working in the same Swiss laboratory, found that these particular mammal genes are almost identical, in their DNA sequences, to the ey gene in Drosophila. This means that the same, gene has come down from remote ancestors to modern animals as distant from each other as mammals and insects. Moreover, in both these major branches of the animal kingdom the gene seems to have a lot to do with eyes. Remarkable fact number three is almost too startling. Halder, Callaerts and Gehring succeeded in introducing the mouse gene into Drosophila embryos. Mirabile dictu, the mouse gene induced ectopic eyes in Drosophila. Figure 5.29 (bottom) shows a small compound eye induced on the leg of a fruitfly by the mouse equivalent of ey. Notice, by the way, that it is an insect compound eye that has been induced, not a mouse eye. The mouse gene has simply switched on the eyemaking developmental machinery of Drosophila. Genes with pretty much the same DNA sequence as ey have been found also in molluscs, marine worms called nemertines, and sea-squirts.

Now, it is a general fact that although all of an animal’s genes are present in all its cells, only a minority of those genes are actually turned on or ‘expressed’ in any given part of the body. This is why livers are different from kidneys, even though both contain the same complete set of genes. In the adult Drosophila, ey usually expresses itself only in the head, which is why the eyes develop there. George Halder, Patrick Callaerts and Walter Gehring discovered an experimental manipulation that led to ey’s being expressed in other parts of the body. By doctoring Drosophila larvae in cunning ways, they succeeded in making ey express itself in the antennae, the wings and the legs. Amazingly, the treated adult flies grew up with fully formed compound eyes on their wings, legs, antennae and elsewhere (Figure 5.29). Though slightly smaller than ordinary eyes, these ‘ectopic’ eyes are proper compound eyes with plenty of properly formed ommatidia.


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More Than You Know: Finding Financial Wisdom in Unconventional Places (Updated and Expanded) by Michael J. Mauboussin

Albert Einstein, Andrei Shleifer, Atul Gawande, availability heuristic, beat the dealer, Benoit Mandelbrot, Black Swan, Brownian motion, butter production in bangladesh, buy and hold, capital asset pricing model, Clayton Christensen, clockwork universe, complexity theory, corporate governance, creative destruction, Daniel Kahneman / Amos Tversky, deliberate practice, demographic transition, discounted cash flows, disruptive innovation, diversification, diversified portfolio, dogs of the Dow, Drosophila, Edward Thorp, en.wikipedia.org, equity premium, Eugene Fama: efficient market hypothesis, fixed income, framing effect, functional fixedness, hindsight bias, hiring and firing, Howard Rheingold, index fund, information asymmetry, intangible asset, invisible hand, Isaac Newton, Jeff Bezos, Kenneth Arrow, Laplace demon, Long Term Capital Management, loss aversion, mandelbrot fractal, margin call, market bubble, Menlo Park, mental accounting, Milgram experiment, Murray Gell-Mann, Nash equilibrium, new economy, Paul Samuelson, Pierre-Simon Laplace, quantitative trading / quantitative finance, random walk, Richard Florida, Richard Thaler, Robert Shiller, Robert Shiller, shareholder value, statistical model, Steven Pinker, stocks for the long run, survivorship bias, The Wisdom of Crowds, transaction costs, traveling salesman, value at risk, wealth creators, women in the workforce, zero-sum game

—Bill Gates, Fortune, 1998 Fruit Flies and Futility Geneticists and biologists love to work with Drosophila melanogaster, a common fruit fly, and have made it a staple of biological study. Indeed, insights from Drosophila research helped a trio of scientists win the 1995 Nobel prize in medicine. Thousands of researchers continue to study the Drosophila to better understand various genetic and developmental issues. Drosophila is attractive to scientists because they understand its features and it is easy to handle. But the fly has another essential feature that scientists covet: its life cycle. Drosophila go from embryo to death in about two weeks. This rapid rate of reproduction allows scientists to study hundreds of generations of the fly’s development and mutations in a relatively short time. Drosophila’s fast evolution provides scientists with important clues about evolution in other species, which generally evolve at a relatively glacial pace.1 Why should businesspeople care about Drosophila?

Drosophila’s fast evolution provides scientists with important clues about evolution in other species, which generally evolve at a relatively glacial pace.1 Why should businesspeople care about Drosophila? A sound body of evidence now suggests that the average speed of evolution is accelerating in the business world. Just as scientists have learned a great deal about evolutionary change from fruit flies, investors can benefit from understanding the sources and implications of accelerated business evolution. The most direct consequence of more rapid business evolution is that the time an average company can sustain a competitive advantage—that is, generate an economic return in excess of its cost of capital—is shorter than it was in the past. This trend has potentially important implications for investors in areas such as valuation, portfolio turnover, and diversification.

The data show evidence for this increased diversification. Finally, the rate of change in the business world demands that investors spend more time understanding the dynamics of organizational change. Success and failure at fast-changing companies may provide investors with some useful mental models for appreciating change at the slower evolving companies. The business world is going the way of Drosophila. 22 All the Right Moves How to Balance the Long Term with the Short Term Strategy in complex systems must resemble strategy in board games. You develop a small and useful tree of options that is continuously revised based on the arrangement of pieces and the actions of your opponent. It is critical to keep the number of options open. It is important to develop a theory of what kinds of options you want to have open.


pages: 283 words: 85,906

The Clock Mirage: Our Myth of Measured Time by Joseph Mazur

Albert Einstein, Alfred Russel Wallace, Arthur Eddington, computer age, Credit Default Swap, Danny Hillis, Drosophila, Eratosthenes, Henri Poincaré, Intergovernmental Panel on Climate Change (IPCC), invention of movable type, Isaac Newton, Jeff Bezos, job automation, Mark Zuckerberg, mass immigration, Pepto Bismol, self-driving car, Stephen Hawking, twin studies

In effect, it is the fruit fly’s molecular clock hand encapsulated in a single cell; moreover, it has since been discovered that the biological clock in most mammals works by the same feedback loop, though in mammals it takes a whole group of per genes for the process to continue. It could be that this Drosophila melanogaster per gene model is the result of organic evolutionary adaptation of the earth’s circadian environment to maximize survival and well-being on a planet where life existence is governed by the alternation of light and darkness. Molecular instructions of clock genes and proteins during Drosophila circadian rhythms: (a) late evening, (b) nighttime, (c) morning, (d) daytime Here is how the circadian oscillator of Drosophila melanogaster works. The per gene in the nucleus of the cell transcribes mRNA molecules that migrate to the cytoplasm to give information and a green light for ribosomes (the protein workshop) to build both stable and unstable protein molecules.

Perhaps that is why fruit flies hatch in highest numbers at dawn.14 And also perhaps, this is why human sleep patterns tend to conform to ordered sleep times and why any disruption of the order creates confusion in subsequent sleep periods.15 Many living organisms, from snow fleas to Mimosa pudica, have evolved internal clock mechanisms that synchronize behavior, metabolism, and physiology with circadian rhythms. Humans, too, have specific cells that work as clock mechanisms tuned to circadian rhythms, but their oscillators are far more complex.16 Here is what is known. First, the Drosophila model is now acknowledged to parallel molecular mechanisms in humans, and since Drosophila and humans have functional homologues of most parts of human disease genes, the Drosophila model is enormously effective for research into human diseases and drug discovery. It tells how the cell is attached to the night-day cycle of sleep, melatonin and endocrine activity, cardiovascular changes, body temperatures, blood pressures, immune differences, and renal functions. Humans are programmed to be diurnal, active in the daytime and inactive (or less active) at night.

Early fruit fly molecular research at Cal Tech is documented in Ronald Konopka’s and Seymour Benzer’s landmark 1971 publication, which reports success in generating mutant genes that became arrhythmic.11 Leading chronologists claim that the work of Konopka and Benzer had an influence on the field of chronobiology that cannot be overstated, and their conclusions “were prescient for the entire circadian field and all of its subsequent molecular sophistication.”12 The simpler story, told here, is sure to be considered raw to the biochemists and entomologists that call the fruit fly a Drosophila melanogaster, though I expect it is the best that can be done within these few pages. So, without getting into the full description of the differences between protein functions of humans and flies, we can interpret the Drosophila model of the circadian clock as simply a feedback loop that operates by a specific gene expression with a relatively short half-life. In essence and in generality, the loop simply behaves like this: the quantity of A molecules increases, reaching a threshold that creates B molecules (with a relatively short half-life), which in turn shut down production of the A molecules.


Raw Data Is an Oxymoron by Lisa Gitelman

23andMe, collateralized debt obligation, computer age, continuous integration, crowdsourcing, disruptive innovation, Drosophila, Edmond Halley, Filter Bubble, Firefox, fixed income, Google Earth, Howard Rheingold, index card, informal economy, Isaac Newton, Johann Wolfgang von Goethe, knowledge worker, liberal capitalism, lifelogging, longitudinal study, Louis Daguerre, Menlo Park, optical character recognition, Panopticon Jeremy Bentham, peer-to-peer, RFID, Richard Thaler, Silicon Valley, social graph, software studies, statistical model, Stephen Hawking, Steven Pinker, text mining, time value of money, trade route, Turing machine, urban renewal, Vannevar Bush, WikiLeaks

Only months later Morgan declared himself, none too happily, to be “head Data Bite Man over ears in my flies.”8 The problem was not only the reproductive rate of fruit flies, but also their propensity to mutate in response to environmental change—the precise feature that made Drosophila so valuable to the geneticist interested in hereditary features and mutations across generations. Mendel’s peas had been docile and well behaved by comparison: they were smooth or shriveled, and followed comparatively clear patterns of generational inheritance—a far cry from the seemingly endless variety of eye colors, wing shapes, and body sizes that emerged in the Drosophila “breeder reactor.” In the face of this nineteenth-century data deluge, geneticists “had no choice but to adopt a fundamentally new system of naming and classifying factors.”9 In the lab, Drosophila became a new creature, one that could not exist outside that institution. But, it also reconfigured the lab itself, giving rise to new kinds of scientific places and persons, including “a new variety of experimental biologist, with distinctive repertoires of work and a distinctive culture of production”10 In Kohler’s striking language, experimental biologists became “lords of the fly,” and the flies returned the favor.

Once inside the lab, the fruit fly took on a new life of its own and came to drive research at paces never before seen in genetics—eventually demanding novel data management and classification strategies. Scientists first began to use the fruit fly for genetic research in 1901 at Harvard and since then it has become a dominant species in this new ecosystem: the lab. While capable of sleepily surviving the outdoor winter, Drosophila took to the warmth and security of labs with perennial reproduction. Defining an entirely new criterion of fitness, its productivity in this new ecological niche pushed down the traditional species inhabiting the genetic lab: the rat and mouse, the pea and primrose. One of the foremost early Drosophila scientists, Thomas Morgan, writing of the relentless reproductive productivity of Melanogaster, enthused: “It is wonderful material. They breed all the year round and give a new generation every sixteen days.” As time passed, however, he became “overwhelmed with work”: “who could have foreseen such a deluge.

This is in some ways the ambition of contemporary “big science” investments: a more complex, dynamic, and commensurable world in which data really can flow freely like corn, leaving new systems, processes, and discoveries in their wake. To do this, we must domesticate data: establishing rituals and routines of collection, creating safe pathways for samples to travel, and setting metadata standards to render them comprehensible by others. And in doing so, data increasingly domesticate us. Flies Dissatisfied with Information System As historian of science Robert Kohler describes, the fruit fly Drosophila (and its most common lab species, D. Melanogaster) was not born as a laboratory animal per se.7 Already “cosmopolitan,” it has cohabited with us in cities for millennia; it is the fruit fly most likely to appear if you were to put a banana out on your window sill and then wait for the larvae to mature. Breeding ferociously in autumn, it is most plentiful at the beginning of the academic year—just in time for a fresh crop of undergraduate, graduate, and faculty experiments.


pages: 518 words: 107,836

How Not to Network a Nation: The Uneasy History of the Soviet Internet (Information Policy) by Benjamin Peters

Albert Einstein, American ideology, Andrei Shleifer, Benoit Mandelbrot, bitcoin, Brownian motion, Claude Shannon: information theory, cloud computing, cognitive dissonance, computer age, conceptual framework, continuation of politics by other means, crony capitalism, crowdsourcing, cuban missile crisis, Daniel Kahneman / Amos Tversky, David Graeber, Dissolution of the Soviet Union, Donald Davies, double helix, Drosophila, Francis Fukuyama: the end of history, From Mathematics to the Technologies of Life and Death, hive mind, index card, informal economy, information asymmetry, invisible hand, Jacquard loom, John von Neumann, Kevin Kelly, knowledge economy, knowledge worker, linear programming, mandelbrot fractal, Marshall McLuhan, means of production, Menlo Park, Mikhail Gorbachev, mutually assured destruction, Network effects, Norbert Wiener, packet switching, Pareto efficiency, pattern recognition, Paul Erdős, Peter Thiel, Philip Mirowski, RAND corporation, rent-seeking, road to serfdom, Ronald Coase, scientific mainstream, Steve Jobs, Stewart Brand, stochastic process, technoutopianism, The Structural Transformation of the Public Sphere, transaction costs, Turing machine

Boris Stillman, Linguistic Geometry (New York: Springer, 2000), xi. 41. Bruce Abramson, Digital Phoenix: Why the Information Economy Collapsed and How It Will Rise Again (Cambridge: MIT Press), 89–90. 42. Johnson, White King and Red Queen, chap. 6. 43. Nathan Engsmenger, “Is Chess the Drosophila of Artificial Intelligence?,” Social Studies of Science 42 (1) (2011): 5–30. See also John McCarthy, “Chess as the Drosophila of AI,” accessed April 15, 2015, http://jmc.stanford.edu/articles/drosophila/drosophila.pdf. 44. E. M. Landis and I. M. Yaglom, “About Aleksandr Semenovich Kronrod,” Uspekhi Matematicheskikh Nauk 56 (5) (2001): 191–201, accessed April 15, 2015, http://www.mathnet.ru/links/1e483992e9f2c42fda4390d0116737a3/rm448.pdf. 45. Wiener, God and Golem, Inc., 15–25. 46. Jad Abumrad and Robert Krulwich (hosts), “The Rules Can Set You Free,” RadioLab, National Public Radio, April 9, 2013. 47.

Masani, Pesi R. Nobert Wiener, 1894–1964. Boston: Birkhäuser Verlag, 1990. Maturana, Humberto, and Francisco Valera, Autopoiesis and Cognition: The Realization of the Living. Boston: Reidel, 1980. Mayr, Otto. Authority, Liberty, and Automatic Machinery in Early Modern Europe. Baltimore: Johns Hopkins University Press, 1989. McCarthy, John. “Chess as the Drosophila of AI.” Accessed April 15, 2015, http://jmc.stanford.edu/articles/drosophila/drosophila.pdf. McCulloch, Warren S. “A Heterarchy of Values Determined by the Topology of Nervous Nets.” Bulletin of Mathematical Biophysics 7 (1945): 89–93. McCulloch, Warren S., and Walter Pitts. “A Logical Calculus of Ideas Immanent in Nervous Activity,” Bulletin of Mathematical Biophysics 5 (1943):115–133. McDonald, Christopher Felix. “Building the Information Society: A History of Computing as a Mass Medium.”

In the early 1990s, shaken by the collapse of the Soviet Union and years from death, Botvinnik reached out one last time with strategic advice for Yeltsin’s government but to no avail.42 There is a truism in the history of science that science serves many specific social purposes but basic research need not begin with any single goal in mind. Biologists, for example, run test on fruit flies—or Drosophila—not because they are particularly devoted to improving the life of fruit flies; they do so because fruit flies are convenient test subjects that reproduce quickly and cheaply. Computer chess has been called “the drosophila of artificial intelligence” (Alexander Kronrod’s phrase, popularized by American computer scientist John McCarthy) because it is thought to stand in as an affordable test case for larger strategic programming projects, which include both artificial intelligence as well as planning the Soviet command economy.43 Kronrod, himself a distinguished Soviet mathematician and computer scientist, also collaborated with Kantorovich on the computer planning of the economy and with Botvinnik on the algorithm that defeated the Kotok-McCarthy American chess program in 1966 and 1967.44 The unexpected joy of computer programming lay in finding new applications for old techniques, which in many ways was the same allure that fascinated general-purpose computer programmers since Turing.


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Testosterone Rex: Myths of Sex, Science, and Society by Cordelia Fine

assortative mating, Cass Sunstein, credit crunch, Donald Trump, Downton Abbey, Drosophila, epigenetics, experimental economics, gender pay gap, George Akerlof, glass ceiling, helicopter parent, longitudinal study, meta analysis, meta-analysis, phenotype, publication bias, risk tolerance

If, as Darwin suggested, sexual selection acts more strongly on males, then this implies greater variation in the reproductive success of males than in females—that is, a wider range between the least, and the most, reproductively successful individuals. Bateman put this assumption to the test for the very first time.4 To do this, he ran six series of experiments in which male and female fruit flies (Drosophila melanogaster) were trapped together in glass containers for three to four days. At the end of this period, Bateman worked out as best he could how many offspring each male and female had produced, and from how many different mates. He needed considerable ingenuity to do this, since the discipline of molecular biology, that today brings paternity-testing kits to supermarket shelves, did not exist in the 1940s.

Considered together with the bias toward counting fathers’ offspring, they concluded “that there is no serious statistical basis in Bateman’s data for his conclusion that the reproductive success of females does not increase with the numbers of mates females have.”16 It probably goes without saying that it is something of a setback that Bateman’s principles are contradicted by Bateman’s data. Of course, evolutionary biologists interested in sexual selection weren’t idly lolling around for decades on the grounds that good old Bateman had discovered everything they needed to know back in 1948. They were busy doing experiments, and contemporary research has identified many species to which Bateman’s principles do appear to apply.17 However, Drosophila melanogaster turn out to be just the beginning of a more complicated empirical story. By 2012, a lengthy table in an academic behavioral ecology journal listed thirty-nine species, from across the animal kingdom, in which research had established that female promiscuity brings about greater reproductive success.18 And while in many of these species this link is nonetheless stronger for males, sometimes it’s equal (for instance, in the yellow-pine chipmunk and the wild eastern salamander).19 This helps to explain why, contrary to the historical understanding that promiscuity is generally the preserve of males, it’s now clear that female promiscuity is abundant across the animal kingdom—from fruitflies20 to humpback whales21—and is “widespread” among primates.22 This revelation owes a large debt to the DNA paternity-testing techniques that have enabled researchers to part the veils of discretion that previously obscured rampant female promiscuity (most particularly in many supposedly monogamous female birds).23 Consider the lek: a mating arrangement in which males compete with each other in a specific territory or arena in a winner-takes-all conflict for sexual access to females.

In Elgar’s lab, male stick insects (Macleay’s Spectre) are offered a mating opportunity every week. Despite apparently having nothing more demanding to do all day than resemble a stick, they only rouse themselves to take up this mating opportunity 30–40 percent of the time.47 Male mealworm beetles, Mormon crickets, and European starlings are similarly indifferent to female charms on a regular basis.48 Indeed, it turns out that even male Drosophila, the original poster boys for the benefits of a philandering lifestyle, sometimes refuse the advances of willing females, presumably on the grounds that they’re saving their sperm for the right partner.49 Given all the complications of the original Bateman story, it’s unsurprising that there turns out to be no straightforward relation between parental investment and parental care either. For many years, people were so carried away by the dizzying reproductive possibilities of males that they forgot to ask where all the females-to-be-fertilized were to come from.50 Overlooked was the fact that most of the females might already be busy with existing offspring.


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Endless Forms Most Beautiful: The New Science of Evo Devo by Sean B. Carroll

Albert Einstein, Alfred Russel Wallace, Brownian motion, dark matter, Drosophila, Johann Wolfgang von Goethe, the scientific method

ROBERT HILL, MRC HUMAN GENETICS UNIT, EDINBURGH, SCOTLAND; FROM PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCE, USA 99 (2002): 7548 Frankenflies In order to make further progress into what monsters could teach us about the rules of development, a continual supply of abnormal types was needed, monsters that would breed true in the laboratory such that their offspring and subsequent generations would exhibit the same characteristics. In 1915, geneticist Calvin Bridges obtained the first true breeding homeotic mutant in the fruit fly Drosophila melanogaster , which was then just beginning to become a leading species for genetic investigations. Bridges isolated a spontaneous mutation that caused the tiny hindwings of the fruit fly to resemble the large forewings. He dubbed this mutant bithorax . Subsequently, several more homeotic mutants were identified in Drosophila . For example, a rather spectacular mutant Antennapedia causes the development of legs in place of the antennae on the head (figure 2.9). It is remarkable how these homeotic mutants can so completely transform one structure into another.

It is not that development is stunted or fails, but that the fate of an entire structure is altered, such that a part is put in the wrong place or the wrong number of parts form. Crucially, the transformation is of one serial homolog into the likeness of another (antenna to leg, hindwing to forewing). They are also so intriguing because each transformation is due to a mutation at a single gene. In Drosophila , only a small number of “homeotic” genes give homeotic forms when they are mutated, indicating that a small number of “master” genes govern the differentiation of serially homologous body parts in the fly. F IG . 2.9 Homeotic mutant fruit fly. Left, a normal fly head with antennae; right, an Antennapedia mutant fly in which the antennae are transformed into legs.

As much as I would like to tell you how the leopard gets his pattern, there is even less hard data to go on for these patterns, in mammals at least, than for striped patterns. More is known, however, in insects about how complex patterns of black spots and stripes are made, and this has been a particular interest in my laboratory. The bodies and parts of the many species of fruit flies, for example, display a great variety of black patterns. The black pigment in these bugs is also melanin. In Drosophila melanogaster the abdomen and thorax are patterned, the bristles on the body are very dark, but the wings are generally clear and pale. In other species, large amounts of black pigment may be distributed throughout the body, or restricted to specific places. In one species, D. biarmipes , the wings of male flies bear a conspicuous black spot toward their tips (figure 9.9).


pages: 331 words: 104,366

Deep Thinking: Where Machine Intelligence Ends and Human Creativity Begins by Garry Kasparov

3D printing, Ada Lovelace, AI winter, Albert Einstein, AltaVista, barriers to entry, Berlin Wall, business process, call centre, Charles Lindbergh, clean water, computer age, Daniel Kahneman / Amos Tversky, David Brooks, Donald Trump, Douglas Hofstadter, Drosophila, Elon Musk, Erik Brynjolfsson, factory automation, Freestyle chess, Gödel, Escher, Bach, job automation, Leonard Kleinrock, low earth orbit, Mikhail Gorbachev, Nate Silver, Norbert Wiener, packet switching, pattern recognition, Ray Kurzweil, Richard Feynman, rising living standards, rolodex, Second Machine Age, self-driving car, Silicon Valley, Silicon Valley startup, Skype, speech recognition, stem cell, Stephen Hawking, Steven Pinker, technological singularity, The Coming Technological Singularity, The Signal and the Noise by Nate Silver, Turing test, Vernor Vinge, Watson beat the top human players on Jeopardy!, zero-sum game

In 1946, Binet’s work was advanced by the Dutch psychologist Adriaan de Groot, whose extensive testing of chess players revealed the importance of pattern recognition and peeled away at the mysteries of human intuition in decision making. John McCarthy, the American computer scientist who coined the term “artificial intelligence” in 1956, called chess the “Drosophila of AI,” referring to how the humble fruit fly was the ideal subject for countless seminal scientific experiments in biology, especially genetics. By the end of the 1980s, the computer chess community had largely resigned this great experiment. In 1990, Ken Thompson of Belle was openly recommending the game Go as a more promising target for real advances in machine cognition. In the same year, the compendium Computers, Chess, and Cognition included an entire section on Go, titled “A New Drosophila for AI?” The nineteen-by-nineteen Go board with its 361 black and white stones is too big of a matrix to crack by brute force, too subtle to be decided by the tactical blunders that define human losses to computers at chess.

Our increasingly powerful machines give us the security to be more ambitious and better prepared, but we still have to make the choice to do it. Technology has lowered the barrier to entry in dozens of business sectors, which should prompt more experimentation and investment. Powerful models allow us to simulate the impact of change better than ever, lowering risk. Once again using chess machines as our favorite Drosophila fruit-fly test subject and metaphor, Grandmasters have used the ability to prepare with engines and databases to play riskier, more experimental opening variations. Many members of the chess community were afraid that super-strong machines would damage professional chess irreparably by reducing Grandmasters to the role of puppets doing little more than relaying the moves their engines told them were the best.

The young stars the Kasparov Chess Foundation brings together also represent California, Wisconsin, Utah, Florida, Alabama, and Texas. For the last two decades, especially with the proliferation of the Internet and cell phones, a dominant topic has been how technology will enable people from all over the world to become entrepreneurs, or scientists, or anything they want despite where they live. Here, again, our little chess Drosophila has already shown the way. The talent is out there; people only need the tools to express it. Chess sneaks through the cracks of cultural, geographic, technological, and economic barriers, disguised as an innocuous pastime. Again and again, it serves as a model for everything from artificial intelligence to online gaming to problem solving and gamification in education. The boom in young Grandmasters and how they think should serve as an example for traditional education as well, with similar cautions.


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The Gene: An Intimate History by Siddhartha Mukherjee

Albert Einstein, Alfred Russel Wallace, All science is either physics or stamp collecting, Any sufficiently advanced technology is indistinguishable from magic, Asilomar, Asilomar Conference on Recombinant DNA, Benoit Mandelbrot, butterfly effect, dark matter, discovery of DNA, double helix, Drosophila, epigenetics, Ernest Rutherford, experimental subject, Internet Archive, invisible hand, Isaac Newton, longitudinal study, medical residency, moral hazard, mouse model, New Journalism, out of africa, phenotype, Pierre-Simon Laplace, Ponzi scheme, Ralph Waldo Emerson, Scientific racism, stem cell, The Bell Curve by Richard Herrnstein and Charles Murray, Thomas Malthus, twin studies

Darbishire (Chicago: Open Court, 1909). In the 1930s, Theodosius Dobzhansky: Robert E. Kohler, Lords of the Fly: Drosophila Genetics and the Experimental Life (Chicago: University of Chicago Press, 1994), “From Laboratory to Field: Evolutionary Genetics.” In September 1943, Dobzhansky: Th. Dobzhansky, “Genetics of natural populations IX. Temporal changes in the composition of populations of Drosophila pseudoobscura,” Genetics 28, no. 2 (1943): 162. Dobzhansky could demonstrate it experimentally: Details of Dobzhansky’s experiments are sourced from Theodosius Dobzhansky, “Genetics of natural populations XIV. A response of certain gene arrangements in the third chromosome of Drosophila pseudoobscura to natural selection,” Genetics 32, no. 2 (1947): 142; and S. Wright and T. Dobzhansky, “Genetics of natural populations; experimental reproduction of some of the changes caused by natural selection in certain populations of Drosophila pseudoobscura,” Genetics 31 (March 1946): 125–56.

its one-billionth human base pair: David Dickson and Colin Macilwain, “ ‘It’s a G’: The one-billionth nucleotide,” Nature 402, no. 6760 (1999): 331. it had sequenced the genome of the fruit fly: Declan Butler, “Venter’s Drosophila ‘success’ set to boost human genome efforts,” Nature 401, no. 6755 (1999): 729–30. In March 2000, Science published: “The Drosophila genome,” Science 287, no. 5461 (2000): 2105–364. Of the 289 human genes known to be: David N. Cooper, Human Gene Evolution (Oxford: BIOS Scientific Publishers, 1999), 21. 177 genes: William K. Purves, Life: The Science of Biology (Sunderland, MA: Sinauer Associates, 2001), 262. “a man like me”: Marsh, William Blake, 56. “The lesson is that the complexity”: Quote from the director of the Berkeley Drosophila Genome Project, Gerry Rubin, in Robert Sanders, “UC Berkeley collaboration with Celera Genomics concludes with publication of nearly complete sequence of the genome of the fruit fly,” press release, UC Berkeley, March 24, 2000, http://www.berkeley.edu/news/media/releases/2000/03/03-24-2000.html.

On a winter evening in 1911, Sturtevant, then a twenty-year-old undergraduate student in Morgan’s lab, brought the available experimental data on the linkage of Drosophila (fruit fly) genes to his room and—neglecting his mathematics homework—spent the night constructing the first map of genes in flies. If A was tightly linked to B, and very loosely linked to C, Sturtevant reasoned, then the three genes must be positioned on the chromosome in that order and with proportional distance from each other: A . B . . . . . . . . . . C . If an allele that created notched wings (N) tended to be co-inherited with an allele that made short bristles (SB), then the two genes, N and SB, must be on the same chromosome, while the unlinked gene for eye color must be on a different chromosome. By the end of the evening, Sturtevant had sketched the first linear genetic map of half a dozen genes along a Drosophila chromosome. Sturtevant’s rudimentary genetic map would foreshadow the vast and elaborate efforts to map genes along the human genome in the 1990s.


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The Extended Phenotype: The Long Reach of the Gene by Richard Dawkins

Alfred Russel Wallace, assortative mating, Douglas Hofstadter, Drosophila, epigenetics, Gödel, Escher, Bach, impulse control, Menlo Park, Necker cube, p-value, phenotype, quantitative trading / quantitative finance, selection bias, stem cell

Some may balk at treating ‘a genetic contribution to variation in X’ as equivalent to ‘a gene or genes for X’. But this is a routine genetic practice, and one which close examination shows to be almost inevitable. Other than at the molecular level, where one gene is seen directly to produce one protein chain, geneticists never deal with units of phenotype as such. Rather, they always deal with differences. When a geneticist speaks of a gene ‘for’ red eyes in Drosophila, he is not speaking of the cistron which acts as template for the synthesis of the red pigment molecule. He is implicitly saying: there is variation in eye colour in the population; other things being equal, a fly with this gene is more likely to have red eyes than a fly without the gene. That is all that we ever mean by a gene ‘for’ red eyes. This happens to be a morphological rather than a behavioural example, but exactly the same applies to behaviour.

In a society with harem defence by dominant males, a male who is known to be homosexual is more likely to be tolerated by a dominant male than a known heterosexual male, and an otherwise subordinate male may be able, by virtue of this, to obtain clandestine copulations with females. But I raise the ‘sneaky male’ hypothesis not as a plausible possibility so much as a way of dramatizing how easy and inconclusive it is to dream up explanations of this kind (Lewontin, 1979b, used the same didactic trick in discussing apparent homosexuality in Drosophila). The main point I wish to make is quite different and much more important. It is again the point about how we characterize the phenotypic feature that we are trying to explain. Homosexuality is, of course, a problem for Darwinians only if there is a genetic component to the difference between homosexual and heterosexual individuals. While the evidence is controversial (Weinrich 1976), let us assume for the sake of argument that this is the case.

It is in constant danger, however, of being upset by genes that subvert the meiotic process to their own advantage … There are many refinements of meiosis and sperm formation whose purpose is apparently to render such cheating unlikely. And yet some genes have managed to beat the system.’ Crow suggests that segregation distorters may be much more common than we ordinarily realize, for the methods of geneticists are not well geared to detecting them, especially if they produce only slight, quantitative effects. The SD genes in Drosophila are particularly well studied, and here there is some indication as to the actual mechanism of distortion. ‘While the homologous chromosomes are still paired up during meiosis, the SD chromosome might do something to its normal partner (and rival) that later causes a dysfunction of the sperm receiving the normal chromosome … SD might actually break the other chromosome’ (Crow 1979, my macabre emphasis).


pages: 220 words: 66,518

The Biology of Belief: Unleashing the Power of Consciousness, Matter & Miracles by Bruce H. Lipton

Albert Einstein, Benoit Mandelbrot, correlation does not imply causation, discovery of DNA, double helix, Drosophila, epigenetics, Isaac Newton, Mahatma Gandhi, mandelbrot fractal, Mars Rover, On the Revolutions of the Heavenly Spheres, phenotype, placebo effect, randomized controlled trial, selective serotonin reuptake inhibitor (SSRI), stem cell

Notice that proteins within one functional group, such as those concerned with sex determination (arrow), also influence proteins with a completely different function, like RNA synthesis (i.e., RNA helicase). Newtonian research scientists have not fully appreciated the extensive interconnectivity among the cell’s biological information networks. Map of interactions among a very small set of the cellular proteins (shaded and numbered circles) found in a Drosophila (fruit fly) cell. Most of the proteins are associated with the synthesis and metabolism of RNA molecules. Proteins enclosed within ovals are grouped according to specific pathway functions. Connecting lines indicate protein-protein interactions. Protein interconnections among the different pathways reveal how interfering with one Protein may produce profound “side effects” upon other related pathways.

Nature 409: 814-816. Baylin, S. B. (1997). “DNA METHYLATION: Tying It All Together: Epigenetics, Genetics, Cell Cycle, and Cancer.” Science 277(5334): 1948-1949. Blaxter, M. (2003). “Two worms are better than one.” Nature 426: 395-396. Bray, D. (2003). “Molecular Prodigality.” Science 299: 1189-1190. Celniker, S. E., D. A. Wheeler, et al. (2002). “Finishing a whole-genome shotgun: Release 3 of the Drosophila melanogaster euchromatic genome sequence.” Genome Biology 3(12): 0079.1-0079.14. Chakravarti, A. and P. Little (2003). “Nature, nurture and human disease.” Nature 421: 412-414. Darwin, F., Ed. (1888). Charles Darwin: Life and Letters. London, Murray. Dennis, C. (2003). “Altered states.” Nature 421: 686-688. Goodman, L. (2003). “Making a Genesweep: It’s Official!” Bio-IT World. Jablonka, E. and M.

“A Low Number Wins the GeneSweep Pool.” Science 300: 1484. Pennisi, E. (2003b). “Gene Counters Struggle to Get the Right Answer.” Science 301: 1040-1041. Pray, L. A. (2004). “Epigenetics: Genome, Meet Your Environment.” The Scientist 14-20. Reik, W. and J. Walter (2001). “Genomic Imprinting: Parental Influence on the Genome.” Nature Reviews Genetics 2: 21+. Schmucker, D., J. C. Clemens, et al. (2000). “Drosophila Dscam Is an Axon Guidance Receptor Exhibiting Extraordinary Molecular Diversity.” Cell 101: 671-684. Seppa, N. (2000). “Silencing the BRCA1 gene spells trouble.” Science News 157: 247. Silverman, P. H. (2004). “Rethinking Genetic Determinism: With only 30,000 genes, what is it that makes humans human?” The Scientist 32-33. Surani, M. A. (2001). “Reprogramming of genome function through epigenetic inheritance.”


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Power, Sex, Suicide: Mitochondria and the Meaning of Life by Nick Lane

Benoit Mandelbrot, clockwork universe, double helix, Drosophila, Geoffrey West, Santa Fe Institute, Louis Pasteur, mandelbrot fractal, out of africa, phenotype, random walk, Richard Feynman, stem cell, unbiased observer

., and de Paepe, R. The nucleo-mitochondrial conflict in cytoplasmic male sterilities revisited. Genetica 117: 3–16; 2003. Sabar, M., Gagliardi, D., Balk, J., and Leaver, C. J. ORFB is a subunit of F1F(O)-ATP synthase: Insight into the basis of cytoplasmic male sterility in sunflower. EMBO (European Molecular Biology Organization) Reports 4: 381–386; 2003. Drosophila giant sperm Pitnick, S., and Karr, T. L. Paternal products and by-products in Drosophila development. Proceedings of the Royal Society of London B: Biological Sciences 265: 821–826; 1998. Heteroplasmy in angiosperms Zhang, Q., Liu, Y., and Sodmergen. Examination of the cytoplasmic DNA in male reproductive cells to determine the potential for cytoplasmic inheritance in 295 angiosperm species. Plant Cell Physiology 44: 941–951; 2003. Ooplasmic transfer Barritt, J.

The situation is not helped by the retention of historical names for the same gene in different organisms. I am reminded of Celtic music, in which the same tune goes by several names, and the same title refers to several different tunes: an endless stream of lovely variation, but scarcely conducive to a straightforward understanding. Just to give a genetic example, the gene ced-3 in nematode worms is known as nedd-2 in mice, dcp-1 in Drosophila, and ICE, or interleukin-1 betaconverting enzyme, in humans (as at the time it was known to be involved in the production of the immune messenger, interleukin 1-beta). After discovering its importance in nematode worms, ICE turned out to be the prototype caspase Conflict in the Body 207 in humans too, and it is now known as caspase-1, although it seems to play a lesser role in human apoptosis.

In mice and humans, for example, the male mitochondria are tagged with a protein called ubiquitin, which marks them up for destruction in the egg. In most cases, the male mitochondria are degraded within a few days of entry to the egg. In other species the male mitochondria are excluded from the egg altogether, or even from the sperm, as in crayfish and some plants. Perhaps the most bizarre method of excluding the male mitochondria is found in the giant sperm of some species of fruit fly (Drosophila), which can be more than ten times longer than the total male body length when uncoiled. The testes required to produce such mammoth sperm comprise more than 10 per cent of the total adult body mass, and retard male development markedly. Their evolutionary purpose is unknown. Such extraordinary sperm add far more cytoplasm to the egg than normal. What’s more, the sperm tail persists in the egg, raising the question of its fate.


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The Cancer Chronicles: Unlocking Medicine's Deepest Mystery by George Johnson

Atul Gawande, Cepheid variable, Columbine, dark matter, discovery of DNA, double helix, Drosophila, epigenetics, Gary Taubes, Harvard Computers: women astronomers, Isaac Newton, Magellanic Cloud, meta analysis, meta-analysis, microbiome, mouse model, Murray Gell-Mann, phenotype, profit motive, stem cell

., “Novel Transcription Factor Involved in Neurogenesis,” Developmental Biology 344, no. 1 (2010): 493. [http://www.researchgate.net/publication/47383131_Novel_transcription_factor_involved_in_neurogenesis] 24. so many new scraps of information: Venugopala Reddy Bommireddy Venkata, Cordelia Rauskolb, and Kenneth D. Irvine, “Fat-Hippo Signaling Regulates the Proliferation and Differentiation of Drosophila Optic Neuroepithelia,” Developmental Biology 344, no. 1 (2010): 506 [http://www.researchgate.net/publication/47383178_Fat-Hippo_signaling_regulates_the_proliferation_and_differentiation_of_Drosophila_optic_neuroepithelia]; and Thomas L. Gallagher and Joshua Arribere, “Fox1 and Fox4 Regulate Muscle-specific Splicing in Zebrafish and Are Required for Cardiac and Skeletal Muscle Functions,” Developmental Biology 344, no. 1 (2010): 491–92. [http://www.researchgate.net/publication/47383123_Fox1_and_Fox4_regulate_muscle-specific_splicing_in_zebrafish_and_are_required_for_cardiac_and_skeletal_muscle_functions] 25. a whimsical turn: Cristina L.

Starting at the upper left-hand corner, she explained how a molecule, Dmrt5, equipped with a molecular digit called a zinc finger, might help control the genetic switches during the maturation of the brain. The experiments were with mice and chickens. I followed as best I could as she periodically glanced at my face for signs of comprehension. At what level should she calibrate her explanation? “What animal do you work on?” she finally asked. Drosophila, Xenopus, C. elegans…so many possibilities. I told her I was a science writer. She ratcheted down the level a couple of notches until I got the gist. Grateful for her patience, I walked to the lobby, sat down with my laptop, and googled “zinc fingers,” “Dmrt5,” and “Emma Farley,” seeing that she had received a prize for an earlier version of her poster. Piece by piece I was putting together a map.

As I walked by more posters, terms that only hours ago were unfamiliar leapt at me again and again. We won’t understand cancer without understanding development, and it was astonishing how, in the year that had passed since the previous meeting, so many new scraps of information had accumulated, the titles laden with that curious terminology: “Fat-Hippo Signaling Regulates the Proliferation and Differentiation of Drosophila Optic Neuroepithelia.” (During development Hippo genes help determine the size of organs and have been implicated in certain cancers.) “Fox1 and Fox4 Regulate Muscle-Specific Splicing in Zebrafish and are Required for Cardiac and Skeletal Muscle Functions.” (When mutated, they too can propel the growth of malignant tumors.) To draw attention to the findings, a poster would occasionally take a whimsical turn. “1 + 1 = 3” explored the synergistic relationship between two hormones in plant growth.


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Energy: A Human History by Richard Rhodes

Albert Einstein, animal electricity, California gold rush, Cesare Marchetti: Marchetti’s constant, Copley Medal, dark matter, David Ricardo: comparative advantage, decarbonisation, demographic transition, Dmitri Mendeleev, Drosophila, Edmond Halley, energy transition, Ernest Rutherford, Fellow of the Royal Society, flex fuel, income inequality, Intergovernmental Panel on Climate Change (IPCC), invention of the steam engine, invisible hand, Isaac Newton, James Watt: steam engine, joint-stock company, Menlo Park, Mikhail Gorbachev, new economy, nuclear winter, oil rush, oil shale / tar sands, oil shock, peak oil, Ralph Nader, Richard Feynman, Ronald Reagan, selection bias, Simon Kuznets, The Rise and Fall of American Growth, Thomas Malthus, Thorstein Veblen, uranium enrichment, urban renewal, Vanguard fund, working poor, young professional

The son of a university mathematician who had given up teaching for farming in southern Alabama, Sturtevant discovered gene mapping while still a Columbia University undergraduate. That work, begun in 1911 and published in 1913, won him a desk in the famous “fly room” at Columbia where fruit flies—Drosophila melanogaster—served as model organisms for genetic research. Sturtevant moved to Caltech in 1928 and taught and did research there for the rest of his career, studying the genetics of Drosophila, horses, fowl, mice, moths, snails, iris, and evening primrose.30 He issued his challenge to the AEC chairman in Washington in June 1954 during his annual address as president of the Pacific Division of the American Association for the Advancement of Science. Sturtevant was disturbed, he said, that a figure of authority such as Chairman Strauss should have claimed that low levels of radiation were harmless.

A key figure in this debate was a geneticist named Hermann Muller, a small dynamo of a man, five feet two inches tall, born in Manhattan in 1890 and another denizen of the fly room as a Columbia undergraduate and graduate student. In 1926, now a professor of zoology at the University of Texas in Austin, Muller reported discovering artificial mutation—demonstrating for the first time that irradiating Drosophila with X-rays increased its mutation rate. That discovery, giving researchers an artificial method of inducing mutation, made it possible to shape experiments to study the genetic basis of life. Muller received the 1946 Nobel Prize in Physiology or Medicine for his discovery. An iconoclastic socialist, Muller had a deep interest in eugenics. Since he believed eugenic improvement would be ethical only in a classless society—he denounced the American eugenics movement for its racism and elitism—he moved to the Soviet Union from 1933 to 1937 to do genetics research.

New York: Houghton Mifflin, 1962. Carter, Jimmy. Why Not the Best? Jimmy Carter: The First Fifty Years. Fayetteville: University of Arkansas Press, 1996. First published 1975. Casey, Robert. The Model T: A Centennial History. Baltimore: Johns Hopkins University Press, 2008. Caspari, Ernest, and Curt Stern. “The Influence of Chronic Irradiation with Gamma-Rays at Low Dosages on the Mutation Rate in Drosophila Melanogaster.” Genetics 33, no. 1 (1948): 75–95. Castaneda, Christopher J. Invisible Fuel: Manufactured and Natural Gas in America, 1800–2000. New York: Twayne, 1999. ———. Regulated Enterprise: Natural Gas Pipelines and Northeastern Markets, 1938–1954. Columbus: Ohio State University Press, 1993. ———. “The Texas-Northeast Connection: The Rise of the Post–World War II Gas Pipeline Industry,” Houston Review 12, no. 2 (1990).


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Inferior: How Science Got Women Wrong-And the New Research That's Rewriting the Story by Angela Saini

Albert Einstein, demographic transition, Drosophila, feminist movement, gender pay gap, meta analysis, meta-analysis, mouse model, out of africa, place-making, scientific mainstream, Steven Pinker, the scientific method, women in the workforce

“Gender Differences and Similarities in Receptivity to Sexual Invitations: Effects of Location and Risk Perception.” Archives of Sexual Behavior 44, no. 8 (2015): 2257–65. Gowaty, Patricia Adair, Rebecca Steinichen, and Wyatt W. Anderson. “Mutual Interest Between the Sexes and Reproductive Success in Drosophila pseudoobscura.” Evolution 56, no. 12 (2002): 2537–40. Gowaty, Patricia Adair, Yong-Kyu Kim, and Wyatt W. Anderson. “No Evidence of Sexual Selection in a Repetition of Bateman’s Classic Study of Drosophila melanogaster.” Proceedings of the National Academy of Sciences of the United States of America 109, no. 29 (2012): 11740–45. Trivers, Robert L. “Sexual Selection and Resource-Accruing Abilities in Anolis garmani.” Evolution 30, no. 2 (1976): 253–69. Janicke, Tim, et al. “Darwinian Sex Roles Confirmed Across the Animal Kingdom.”

The Evolving Female: A Life History Perspective. Princeton, NJ: Princeton University Press, 1997. Chapter 6: Choosy, Not Chaste Clark, Russell D., and Elaine Hatfield. “Gender Differences in Receptivity to Sexual Offers.” Journal of Psychology and Human Sexuality 2, no. 1 (1989): 39–55. ——. “Love in the Afternoon.” Psychological Inquiry 14, nos. 3 and 4 (2003): 227–31. Bateman, Angus J. “Intra-Sexual Selection in Drosophila.” Heredity 2 (1948): 349–68. Trivers, Robert L., “Parental Investment and Sexual Selection.” In Sexual Selection and the Descent of Man, edited by Bernard Campbell, 136–79. Chicago: Aldine, 1972. Symons, Donald. The Evolution of Human Sexuality. New York: Oxford University Press, 1979. Geertz, Clifford. “Sociosexology.” New York Review of Books, January 24, 1980. https://www.nybooks.com/articles/1980/01/24/sociosexology/.


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Junk DNA: A Journey Through the Dark Matter of the Genome by Nessa Carey

dark matter, discovery of DNA, double helix, Downton Abbey, Drosophila, epigenetics, Kickstarter, mouse model, phenotype, placebo effect, stem cell, Stephen Hawking, Steve Jobs

Requirement of Mis6 centromere connector for localizing a CENP-A-like protein in fission yeast. Science. 2000 Jun 23;288(5474):2215–9 6. Blower MD, Karpen GH. The role of Drosophila CID in kinetochore formation, cell-cycle progression and heterochromatin interactions. Nat Cell Biol. 2001 Aug;3(8):730–9 7. Hori T, Amano M, Suzuki A, Backer CB, Welburn JP, Dong Y, McEwen BF, Shang WH, Suzuki E, Okawa K, Cheeseman IM, Fukagawa T. CCAN makes multiple contacts with centromeric DNA to provide distinct pathways to the outer kinetochore. Cell. 2008 Dec 12;135(6):1039–52 8. Heun P, Erhardt S, Blower MD, Weiss S, Skora AD, Karpen GH. Mislocalization of the Drosophila centromere-specific histone CID promotes formation of functional ectopic kinetochores. Dev Cell. 2006 Mar;10(3):303–15. 9. Van Hooser AA, Ouspenski II, Gregson HC, Starr DA, Yen TJ, Goldberg ML, Yokomori K, Earnshaw WC, Sullivan KF, Brinkley BR.

Next-generation sequencing identifies the Danforth’s short tail mouse mutation as a retrotransposon insertion affecting Ptf1a expression. PLoS Genet. 2013;9(2):e1003205 3. Bogdanik LP, Chapman HD, Miers KE, Serreze DV, Burgess RW. A MusD retrotransposon insertion in the mouse Slc6a5 gene causes alterations in neuromuscular junction maturation and behavioral phenotypes. PLoS One. 2012;7(1):e30217 4. Schneuwly S, Klemenz R, Gehring WJ. Redesigning the body plan of Drosophila by ectopic expression of the homoeotic gene Antennapedia. Nature. 1987 Feb 26–Mar 4;325(6107):816–8 5. Mortlock DP, Post LC, Innis JW. The molecular basis of hypodactyly (Hd): a deletion in Hoxa 13 leads to arrest of digital arch formation. Nat Genet. 1996 Jul;13(3):284–9 6. Rowe HM, Jakobsson J, Mesnard D, Rougemont J, Reynard S, Aktas T, Maillard PV, Layard-Liesching H, Verp S, Marquis J, Spitz F, Constam DB, Trono D.


pages: 400 words: 99,489

The Sirens of Mars: Searching for Life on Another World by Sarah Stewart Johnson

Albert Einstein, Alfred Russel Wallace, Astronomia nova, back-to-the-land, cuban missile crisis, dark matter, Drosophila, Elon Musk, invention of the printing press, Isaac Newton, Johannes Kepler, low earth orbit, Mars Rover, Mercator projection, Pierre-Simon Laplace, Ronald Reagan, scientific mainstream, sensible shoes

“WOULD NOT BE CURRENT” Ibid. HUNDREDS OF YEARS The mini-DVD is expected to last approximately five hundred years. Bruce Betts, “We Make It Happen,” The Planetary Report. THE OLDEST PIECES INCLUDED “Visions of Mars: The Stories,” The Planetary Society. VOLTAIRE’S “MICROMÉGAS” Voltaire, “Micromégas,” Blake Linton Wilfong, ed., Free Sci-Fi Classics. STUDY DROSOPHILA Jeffrey R. Powell, Progress and Prospects in Evolutionary Biology: The Drosophila Model (Oxford University Press, 1997). DUTCH BOOK Kees Boeke, Cosmic View: The Universe in 40 Jumps (New York: John Day Company, 1957). This book was also the inspiration for a famous short film, Powers of Ten, produced by Ray and Charles Eames in 1977. Chapter 10: Sweet Water POOLED AND FORMED LAKES “Mars Science Laboratory Landing Site: Gale Crater,” NASA Mars Exploration Program (July 22, 2011).

What kind of magnifying glass would have seen ancient cells slumbering so deep in the permafrost, barely respiring, so easily extinguished? Like the giant, I’d spent a lot of time trying to peer into worlds too small to see. Once, in one of my teaching labs at Oxford, I’d spent hours observing a tiny fruit-fly larva. Students of developmental biology and genetics, almost without exception, study Drosophila as a model organism—the hovering black dots of the adults as well as the eggs, larva, and pupa. The organisms grow quickly, and by playing with their genes, scientists can manipulate them rather mercilessly, causing them to grow eyes on their legs or extra sets of wings and learning a great deal in the process. In that particular lab, I’d been told to familiarize myself with the larva’s functioning under a dissecting scope, then to mount its brain on a glass slide, to study normal cell division, along with its testes, to study germ cell division into gametes.


pages: 592 words: 152,445

The Woman Who Smashed Codes: A True Story of Love, Spies, and the Unlikely Heroine Who Outwitted America's Enemies by Jason Fagone

Albert Einstein, Charles Lindbergh, Columbine, cuban missile crisis, Drosophila, Edward Snowden, en.wikipedia.org, Fellow of the Royal Society, index card, Internet Archive, pattern recognition, Robert Gordon, Ronald Reagan, side project, Silicon Valley, X Prize

She saw that the ground floor contained some microscopes and work shelves. An interior door led to the greenhouse that William managed, which is where Fabyan had him breeding new strains of crops and flowers, violets and wheat, and a type of corn with no cob. Upstairs, he said, was his sleeping quarters, and down here was a little laboratory where he ran genetics experiments with living fruit flies, Drosophila melanogaster. Elizebeth could see his bottles full of the teensy-weensy flies. Each bottle was about the size of a coffee mug, only thinner, and was smeared with some overripe banana that the flies ate. William explained that geneticists like to use fruit flies in experiments because they reproduce very quickly, then die. If you marry a normal fruit fly with a fly that has yellow eyes, say—a genetic mutation, an alteration in the biological code—they will produce children in three weeks, and you can look at the children to see if they have yellow eyes, showing they inherited the yellow-eye gene.

At twenty-five WFF was born September 24, 1891, so he would have been just shy of twenty-five; they were a little more than one year apart in age. old, creaky structure Transcript of ESF interview with Marshall Research Library staff members Tony Crawford and Lynn Biribauer, Tape #5, June 6, 1974, 5. teensy-weensy flies Ibid. quickly, then die Ibid. 50 one bottle of flies into another I am relying on my memory of performing this exact type of Drosophila experiment in high school. Thanks to my AP Biology teacher, Mr. Anderson. 150 workers Norman Klein, “Building Supermen at Fabyan’s Colony,” Chicago Daily News, April 22, 1921. Susumu Kobayashi Kopec, The Sabines at Riverbank, 27. Jack “the Sailor” Ibid. Belle Cumming Ibid., 50. Silvio Silvestri Ibid., 4, 26. “Achieve success!” ESF interview with Valaki, November 11, 1976, transcribed January 12, 2012, 10.

See also codebreakers defined, xvi cryptograms defined, xvi frequencies of letters, 69–70, 83–84 “The Gold-Bug” (Poe), 60–61 cryptographers, defined, xvi Cryptography Engineering (Schneier, Ferguson, and Kohno), 119 Cryptolog (journal), 340 “cryptologic schizophrenia,” 237–38 cryptology, defined, xvi Crypto-Set Headquarters Army Game, 155 Cuba, 180 Cuban Missile Crisis, 339 Cumming, Belle, 50, 159 Cunningham, Walter McCook, 322 Curie, Marie, 142 Czechoslovakia, 180, 308 Dachau concentration camp, 143, 178, 302 Dahl, Roald, 214–15 Darwin, Charles, 39 De Augmentis Scientarium (Bacon), 40 De Furtivis Literarum Notis (della Porta), 155–56 Delegacia de Ordem Politica e Social (DOPS), 245–46 Della Porta, Giambattista, 155–56 DeMille, Cecil B., 172 Detective Fiction Weekly, 169 Dickinson, Velvalee, 292–96 digital ciphers, 124 Dinieus, Edna Smith, 7, 170, 311 death of mother, 64–65 Mexican vacation, 207 William and, 60 disappearing ink, 184 DNA, 24 Doe, Harry, 144 Doll Lady. See Dickinson, Velvalee Donovan, William, 240–41, 316 Dove, Billie, 51 Driscoll, Agnes Meyer, 131 Drosophila melanogaster, 49–50, 58 Dunninger, Joseph “Amazing Dunninger,” 321 Duquesne, Frederick Joubert, 232–34, 300 Eagle’s Nest (Kehlsteinhaus), 306, 310–11 Ecuador, 180–81 Edison, Thomas, 24 Einsatzgruppen, 178 Einstein, Albert, 24, 79, 308, 355n Eisenhour, Bert, 30, 44, 48–49 electroshock therapy, 151, 219 Elizabeth I of England, 11–12, 38–39, 43, 57 Engels, Albrecht “Alfredo,” 227–29, 241–42, 243, 245, 247 Engledew Cottage, 46, 84, 97 Enigma, 125–26, 194–202, 263–64, 283 British codebreakers, 124, 196–97, 221 Circuit 3-N, 249, 260–61, 266–69, 272–75, 278–79, 285 Elizebeth’s work, 194, 197–202, 260–61, 267, 283, 284–86 Polish breakthroughs, 196–97, 200 William’s curiosity about, 125–26 Enola Gay, 313–14 Erasmus, 8, 9 Ezra, Isaac, 166–67, 331 Ezra, Judah, 166–67, 331 Fabyan, George appearance of, 52–53 declining health and death of, 158–59, 322 Elizebeth and, 46, 51–52, 53, 156 departure and return from Riverbank, 113–15 first meeting and job offer, 5–6, 15–19 family background of, 23–24, 89–90 personality of, 51–53, 95 Riverbank Laboratories.


Global Catastrophic Risks by Nick Bostrom, Milan M. Cirkovic

affirmative action, agricultural Revolution, Albert Einstein, American Society of Civil Engineers: Report Card, anthropic principle, artificial general intelligence, Asilomar, availability heuristic, Bill Joy: nanobots, Black Swan, carbon-based life, cognitive bias, complexity theory, computer age, coronavirus, corporate governance, cosmic microwave background, cosmological constant, cosmological principle, cuban missile crisis, dark matter, death of newspapers, demographic transition, Deng Xiaoping, distributed generation, Doomsday Clock, Drosophila, endogenous growth, Ernest Rutherford, failed state, feminist movement, framing effect, friendly AI, Georg Cantor, global pandemic, global village, Gödel, Escher, Bach, hindsight bias, Intergovernmental Panel on Climate Change (IPCC), invention of agriculture, Kevin Kelly, Kuiper Belt, Law of Accelerating Returns, life extension, means of production, meta analysis, meta-analysis, Mikhail Gorbachev, millennium bug, mutually assured destruction, nuclear winter, P = NP, peak oil, phenotype, planetary scale, Ponzi scheme, prediction markets, RAND corporation, Ray Kurzweil, reversible computing, Richard Feynman, Ronald Reagan, scientific worldview, Singularitarianism, social intelligence, South China Sea, strong AI, superintelligent machines, supervolcano, technological singularity, technoutopianism, The Coming Technological Singularity, Tunguska event, twin studies, uranium enrichment, Vernor Vinge, War on Poverty, Westphalian system, Y2K

Ifwe suppose that alleles influencing many behaviours or skills in the human population provide an advantage when they are rare, but lose that advantage when they are common, there will be a tendency for the population to accumulate these alleles at such intermediate frequencies. And, as noted earlier, if these genes are maintained by frequency dependence, the cost to the population of maintaining this diversity can be low. Numerous examples of frequency-dependent balancing selection have been found in populations. One that influences behaviours has been found in Drosophila melanogaster. Natural populations of this fly are polymorphic for two alleles at a locus (for, standing for forager) that codes for a protein kinase. A recessive allele at this locus, sitter, causes larvae to sit in the same spot while feeding. The dominant allele, rover, causes its carriers to move about while feeding. Neither allele can take over (reach fixation) in the population. Rover has an advantage when food is scarce, because rover larvae can find more food and grow more quickly than sitter larvae.

Genetic evidence for complex speciation of humans and chimpanzees. Nature, 441 , 1 1 03-1 108. Silver, L. (1998) . Remaking Eden (New York: Harper). Singh-Manoux, A., Marmot, M.G., and Adler, N . E . (2005) . Does subjective social status predict health and change in health status better than objective status? Psychosomatic Medicine, 67, 855-86 1 . Sokolowski, M . B . , Pereira, H . S . , and Hughes, K . ( 1 997). Evolution offoraging behavior in Drosophila by density-dependent selection. Proc. Nat!. Acad. Sci. ( USA), 94, 7373-7377. Spira, A. and Multigner, L. ( 1 998). Environmental factors and male infertility. Human Reprod., 13, 2041-2042. Surovell, T., Waguespack, N . , and Brantingham, P . J . (2005). Global archaeo­ logical evidence for proboscidean overkill. Proc. Nat!. Acad. Sci. ( USA), 1 02, 623 1-6236. Tagliatela, J . P . , Savage-Rumbaugh, S., and Baker, L.A. (2003).

105, 106 deterministic systems, probability estimates 6 developing countries, vulnerability to biological attack 473-4 developmental period, artificial intelligence 322 diagnosis, infectious disease 469-70 Diamond, ) . 66, 357 Dick, S.). 1 3 3 die rolling, conjunction fallacy 96-7 diffusion of responsibility 1 1 0 dinosaurs, extinction 5 1 disaster policy 372-5 disconfirmation bias (motivated scepticism) 99, 100 discount rates, global warming 192-3, 198, 200 disjunctive probability estimation 98 dispensationalism 74 disruptive technologies 432 distribution of disaster 367-9 distribution tails 1 5 6-7 DNA synthesis technology 458-60 increasing availability 450 outsourcing 465 risk management 463-4 dollar-loss power of disasters 368-9 Doomsday Argument 129-3 1 doomsday clock, Bulletin of Atomic Scientists vii, viii Index dotcom bubble burst, insurance costs 1 7 3 Drake equation 2 14-1 5 Drexler, K . E . 3 3 1 , 485, 486, 488, 495 Engines ofCreation 499-500 Nanosystems: Molecular Machinery, Manufacturing and Computation 501-2 Drosophila melanogaster, frequency-dependent balancing selection 63 dual-use challenge, biotechnolo gy 45 1-2, 455-8 Dubos, R., Man Adapting 304 duration, totalitarianism 506-10 537 education, role in nuclear disarmament 440-1 The Effects ofNuclear War, Office of Technolo gy Assessment ( 1 979) 389, 401 Elbaradei, M. 401 El Chich6n eruption ( 1982) effect on climate 270 effects on ocean productivity 2 1 1 electroweak theory 354-5 El Nino Southern Oscillation 278 emer gin g diseases 16, 82 emissions targets 277 dust showers, cosmic 2 3 1-3 emissions taxes 194-6, 197, 198 DWI M (Do-What-1-Mean) instruction emotions, artificial intelli gence 320-1 empty space transitions 355-7 322-3 Dynamics of Populations of Planetary Systems, Kneevic, Z. and Milani, A. 2 3 5 dys genic pressures 6 2 Dyson, F , scaling hypothesis 43-4, 4 5 early warnin g systems nuclear attack 384 terrorist-initiated false alarms 426-7 Earth ejection from solar system 35-6 end of complex life 8 fate of 34-5, 44 magnetic field reversals 250 variation in eccentricity 239 Earth-crossin g bodies, search for 226 earthquake insurance, California 173 earthquakes 7 risk mitigation 372 energy power 368 Earth's axis, wobbles 268 Earth system models of intermediate complexity (EM !


A Brief History of Everyone Who Ever Lived by Adam Rutherford

23andMe, agricultural Revolution, Albert Einstein, Alfred Russel Wallace, bioinformatics, British Empire, colonial rule, dark matter, delayed gratification, demographic transition, double helix, Drosophila, epigenetics, Google Earth, Isaac Newton, Kickstarter, longitudinal study, meta analysis, meta-analysis, out of africa, phenotype, sceptred isle, theory of mind, Thomas Malthus, twin studies

However, this is almost certainly a twentieth-century post hoc analysis, and is rejected by most academic folklorists. 10 Drosophila researchers have no such formal nomenclature compunction. Many genes are initially discovered in these flies because we can manipulate and mutate them so much more easily than in bigger animals, and with fewer ethical barriers than necessarily exist for humans. Often, though, mammalian geneticists would then look for a similar or equivalent gene in mice or humans and, more often than not, the name for the human equivalent would be derived from the original – and often descriptive or just plain fun – moniker given to the fly. The stellar Nobel-prize winning embryologist Christiane Nüsslein-Volhard discovered the Toll family of genes in drosophila in the 1980s, and the name was given after she was heard to exclaim, ‘Das ist ja toll!’

We modern humans weren’t the only ones in the Human Genome Project. Somewhat counterintuitively, there were six species included in the project’s primary aims. A genome is much more useful if it can be compared to another, and that includes genomes from other species. So, the original mission of the first creatures to join the genome club aside from us included the most commonly used model organisms – the fly Drosophila melanogaster; the rat and the mouse; our closest ape relative, the chimp; and an oddity, the honey bee, for it is a social beast, and almost all members don’t get to reproduce at all, but serve their queen with whom they share exactly half their DNA. All of these were due to have their entire genomes read, deciphered and interrogated over the cusp of the twentieth century. In 1997, using precisely the same techniques being developed for living humans, a Swedish researcher working in Leipzig quietly laid the foundation stones for a new, utterly revolutionary field – palaeogenetics.


pages: 846 words: 232,630

Darwin's Dangerous Idea: Evolution and the Meanings of Life by Daniel C. Dennett

Albert Einstein, Alfred Russel Wallace, anthropic principle, assortative mating, buy low sell high, cellular automata, combinatorial explosion, complexity theory, computer age, conceptual framework, Conway's Game of Life, Danny Hillis, double helix, Douglas Hofstadter, Drosophila, finite state, Gödel, Escher, Bach, In Cold Blood by Truman Capote, invention of writing, Isaac Newton, Johann Wolfgang von Goethe, John von Neumann, Murray Gell-Mann, New Journalism, non-fiction novel, Peter Singer: altruism, phenotype, price mechanism, prisoner's dilemma, QWERTY keyboard, random walk, Richard Feynman, Rodney Brooks, Schrödinger's Cat, selection bias, Stephen Hawking, Steven Pinker, strong AI, the scientific method, theory of mind, Thomas Malthus, Turing machine, Turing test

Recent discoveries suggest otherwise — though only time will tell; no Dogma ever rolled over and died without a fight. For instance, Marilyn Houck (Houck et al. 1991.) has found evidence that, about forty years ago, in either Florida or Central America, a tiny mite that feeds on fruit flies happened to {142} puncture the egg of a fly of the Drosophila willistoni species, and in the process picked up some of that species' characteristic DNA, which it then inadvertently transmitted to the egg of a (wild) Drosophila melanogaster fly! This could explain the sudden explosion in the wild of a particular DNA element common in D. willistoni but previously unheard of in D. melanogaster populations. She might add: What else could explain it? It sure looks like species plagiarism. Other researchers are looking at other possible vehicles for speedy design travel in the world of natural (as opposed to artificial) genetics.

The orthodox theory mustn't presuppose any process of directed mutation — that would be a skyhook for sure — but it can leave open the possibility of somebody's discovering nonmiraculous mechanisms that can bias the distribution of mutations in speed-up directions. Eigen's ideas about quasi-species in chapter 8 are a case in point. In earlier chapters, I have drawn attention to various other possible cranes that are currently being investigated: trans-species "plagiarism" of nucleotide sequences (Houck's Drosophila), the crossovers made possible by the innovation of sex (Holland's genetic algorithms), the exploration of multiple variations by small teams (Wright's "demes") that return to the parent population (Schull's "intelligent species"), and Gould's "higher level species sorting," to name four. Since these debates all fit comfortably within the commodious walls of contemporary Darwinism, they don't need further scrutiny from us, fascinating though they are.

Geneticists have recently identified a chromosomal structure they call the homeobox; in spite of differences, this structure is identifiable in widely separated species of animals — perhaps in them all — so it is very ancient, and it plays a central role in embryological development. We may be startled at first to learn that a gene identified as playing a major role in eye development in the homeobox of mice has almost the same codon spelling as a gene dubbed (for its phenotypic effect) eyeless when it was identified in the homeobox of the fruitfly, Drosophila. But we would be even more flabbergasted were we to discover that the brain-cell complex that stored the original meme for bifocals in Benjamin Franklin's brain was the same as, or very similar to, the brain-cell complex that is called upon today to store the meme for bifocals whenever any child in Asia, Africa, or Europe first learns about them — by reading about them, seeing them on television, or noticing them on a parent's nose.


pages: 476 words: 120,892

Life on the Edge: The Coming of Age of Quantum Biology by Johnjoe McFadden, Jim Al-Khalili

agricultural Revolution, Albert Einstein, Alfred Russel Wallace, bioinformatics, complexity theory, dematerialisation, double helix, Douglas Hofstadter, Drosophila, Ernest Rutherford, Gödel, Escher, Bach, invention of the printing press, Isaac Newton, James Watt: steam engine, Louis Pasteur, New Journalism, phenotype, Richard Feynman, Schrödinger's Cat, theory of mind, traveling salesman, uranium enrichment, Zeno's paradox

Turin, A. Mershin and E. M. Skoulakis, “Molecular vibration-sensing component in Drosophila melanogaster olfaction,” Proceedings of the National Academy of Sciences, vol. 108: 9 (2011), pp. 3797–802. 12 J. C. Brookes, F. Hartoutsiou, A. P. Horsfield and A. M. Stoneham, “Could humans recognize odor by phonon assisted tunneling?,” Physical Review Letters, vol. 98: 3 (2007), p. 038101. Chapter 6: The butterfly, the fruit fly and the quantum robin 1 F. A. Urquhart, “Found at last: the monarch’s winter home,” National Geographic, Aug. 1976. 2 R. Stanewsky, M. Kaneko, P. Emery, B. Beretta, K. Wager-Smith, S. A. Kay, M. Rosbash and J. C. Hall, “The cryb mutation identifies cryptochrome as a circadian photoreceptor in Drosophila,” Cell, vol. 95: 5 (1998), pp. 681–92. 3 H. Zhu, I. Sauman, Q. Yuan, A. Casselman, M.

The monarch butterfly’s sun compass works by comparing the height of the sun with the time of day—a relationship that varies with both latitude and longitude. It must also have a body clock that, like our own, is similarly automatically entrained by light, to compensate for the changing times of sunrise and sunset during its long migration. But where does the monarch house its circadian sense? As the Urquharts discovered, butterflies are not the easiest animals to work with; the fruit fly, Drosophila, which we encountered in the last chapter sniffing its way through a maze, is a much more convenient laboratory insect as it breeds very rapidly and can easily mutate. Like us, fruit flies adjust their circadian rhythms to the cycles of light and dark. In 1998, geneticists found a fruit-fly mutant whose circadian rhythm could not be affected by exposure to light.2 They discovered that the mutation was in a gene encoding an eye protein called cryptochrome.


pages: 265 words: 74,000

The Numerati by Stephen Baker

Berlin Wall, Black Swan, business process, call centre, correlation does not imply causation, Drosophila, full employment, illegal immigration, index card, Isaac Newton, job automation, job satisfaction, McMansion, Myron Scholes, natural language processing, PageRank, personalized medicine, recommendation engine, RFID, Silicon Valley, Skype, statistical model, Watson beat the top human players on Jeopardy!

Up to now, we've seen how employers can track our procrastination and our e-mails, and how they'll be able, increasingly, to optimize us as workers. We've seen how advertisers attempt to turn our mouse clicks and movements into mathematical models that anticipate our every urge. In what we've seen so far, it's others who have their way with our growing mountain of data. They grab it, they analyze it, they use it. Whether we're shopping or taking out a loan, we're laboring for the Numerati in much the way a drosophila fly works for a white-coated lab technician. Sometimes we get discounts and prizes. Sometimes we can say no. But once we agree to an offer, we're specimens. And yet, in the world of blogs and YouTube and social networking sites like MySpace, millions of people broadcast their lives voluntarily. They pile up details by the shovel load. Privacy often looks like an afterthought, if it's considered at all.

And if those whose paths we cross share these of these interests, our profile will pop up on their phones, and we presumably won't mind at all when one of them touches our elbow and says, "I had a coq au vin to die for at this little bistro..." In the workplace, a similar system could alert us to colleagues in the cafeteria who have mastered the Linux operating system or are knee-deep in the genetics of drosophila flies. But take this a step further. Our movements with a cell phone can paint an in-depth profile for each of us, each one endlessly more detailed than those forms my wife and I filled out for Chemistry.com. If we give them permission to examine us the way Dan Andresen and his team study their cows, they can scrutinize our movements and social networks. They can map the DNA of our behavior.


A Natural History of Beer by Rob DeSalle

agricultural Revolution, British Empire, double helix, Drosophila, Louis Pasteur, microbiome, NP-complete, phenotype, placebo effect, wikimedia commons

“Ferment in the Family Tree: Does a Frugivorous Dietary Heritage Influence Contemporary Patterns of Human Ethanol Use?” Integrative and Comparative Biology 44: 304–314. Schoon, H. A., M. Fehr, and A. Schoon. 1992. “Case Report: Acute Alcohol Intoxication in a Hedgehog (Erinaceus europaeus).” Kleintierpraxis 37: 329–332. Shohat-Ophir, G., K. R. Kaun, R. Azanchi, H. Mohammed, and U. Heberlein. 2012. “Sexual Deprivation Increases Ethanol Intake in Drosophila.” Science 335: 1351–1355. Starmer, W. T., W. B. Heed, and E. S. Rockwood-Sluss. 1977. “Extension of Longevity in Drosophila mojavensis by Environmental Ethanol: Differences between Subraces.” Proceedings of the National Academy of Sciences of the United States of America 74, no. 1: 387–391. Tyson, N. deG. 1995. “The Milky Way Bar.” Natural History 103: 16–18. Wiens, F., A. Zitzmann, M.-A. Lachance, M. Yegles, et al. 2008. “Chronic Intake of Fermented Floral Nectar by Wild Treeshrews.”


pages: 404 words: 131,034

Cosmos by Carl Sagan

Albert Einstein, Alfred Russel Wallace, Arthur Eddington, clockwork universe, dematerialisation, double helix, Drosophila, Edmond Halley, Eratosthenes, Ernest Rutherford, germ theory of disease, global pandemic, invention of movable type, invention of the telescope, Isaac Newton, Johannes Kepler, Lao Tzu, Louis Pasteur, Magellanic Cloud, Mars Rover, Menlo Park, music of the spheres, pattern recognition, planetary scale, Search for Extraterrestrial Intelligence, spice trade, Thales and the olive presses, Thales of Miletus, Tunguska event

To learn the practical side of genetics, I spent many months working with fruit flies, Drosophila melanogaster (which means the black-bodied dew-lover)—tiny benign beings with two wings and big eyes. We kept them in pint milk bottles. We would cross two varieties to see what new forms emerged from the rearrangement of the parental genes, and from natural and induced mutations. The females would deposit their eggs on a kind of molasses the technicians placed inside the bottles; the bottles were stoppered; and we would wait two weeks for the fertilized eggs to become larvae, the larvae pupae, and the pupae to emerge as new adult fruit flies. One day I was looking through a low-power binocular microscope at a newly arrived batch of adult Drosophila immobilized with a little ether, and was busily separating the different varieties with a camel’s-hair brush.

I was sure it had emerged from one of the pupae in the molasses. I didn’t mean to disturb Muller but … “Does it look more like Lepidoptera than Diptera?” he asked, his face illuminated from below. I didn’t know what this meant, so he had to explain: “Does it have big wings? Does it have feathery antennae?” I glumly nodded assent. Muller switched on the overhead light and smiled benignly. It was an old story. There was a kind of moth that had adapted to Drosophila genetics laboratories. It was nothing like a fruit fly and wanted nothing to do with fruit flies. What it wanted was the fruit flies’ molasses. In the brief time that the laboratory technician took to unstopper and stopper the milk bottle—for example, to add fruit flies—the mother moth made a dive-bombing pass, dropping her eggs on the run into the tasty molasses. I had not discovered a macro-mutation.


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Where Good Ideas Come from: The Natural History of Innovation by Steven Johnson

Ada Lovelace, Albert Einstein, Alfred Russel Wallace, carbon-based life, Cass Sunstein, cleantech, complexity theory, conceptual framework, cosmic microwave background, creative destruction, crowdsourcing, data acquisition, digital Maoism, digital map, discovery of DNA, Dmitri Mendeleev, double entry bookkeeping, double helix, Douglas Engelbart, Douglas Engelbart, Drosophila, Edmond Halley, Edward Lloyd's coffeehouse, Ernest Rutherford, Geoffrey West, Santa Fe Institute, greed is good, Hans Lippershey, Henri Poincaré, hive mind, Howard Rheingold, hypertext link, invention of air conditioning, invention of movable type, invention of the printing press, invention of the telephone, Isaac Newton, Islamic Golden Age, James Hargreaves, James Watt: steam engine, Jane Jacobs, Jaron Lanier, Johannes Kepler, John Snow's cholera map, Joseph Schumpeter, Joseph-Marie Jacquard, Kevin Kelly, lone genius, Louis Daguerre, Louis Pasteur, Mason jar, mass immigration, Mercator projection, On the Revolutions of the Heavenly Spheres, online collectivism, packet switching, PageRank, patent troll, pattern recognition, price mechanism, profit motive, Ray Oldenburg, Richard Florida, Richard Thaler, Ronald Reagan, side project, Silicon Valley, silicon-based life, six sigma, Solar eclipse in 1919, spinning jenny, Steve Jobs, Steve Wozniak, Stewart Brand, The Death and Life of Great American Cities, The Great Good Place, The Wisdom of Crowds, Thomas Kuhn: the structure of scientific revolutions, transaction costs, urban planning

Cajal’s theory that the nervous system was composed of billions of tiny nerve centers—to become known as neurons—led the discovery of neurotransmitters, chemicals that relay messages across synapses. WASHING MACHINE (1908) American engineer Alva John Fisher pioneered the first electric washing machine by attaching a motor to the traditional model of a hand-cranked washer. The Chicago-based Hurley Machine Company introduced the product in 1908. GENES ON CHROMOSOMES (1910) American embryologist Thomas Hunt Morgan’s experiments with genetic mutations and the fruit fly Drosophila melanogaster led him and his team of students at Columbia University to discover how heredity was in part governed by genes transported by chromosomes. SUPERCONDUCTIVITY (1911) In 1911, Dutch physicist Heike Kamerlingh Onnes tested the behavior and properties of metals such as lead, tin, and mercury when placed at liquid helium temperatures, and discovered that they lost all resistance when cooled to cryogenic levels.

De Forest, Lee Delaware Department of Natural Resources and Environmental Control Dennett, Daniel Denucé, Jean-Louis-Paul Deoxyribonucleic acid, see DNA Descartes, René Design that Matters DEVONthink Dickens, Charles Difference Engine Digital Equipment Corporation Din, Taqi al- Dinosaurs, extinction of Diodorus Siculus Djerassi, Carl DNA complementary replication system of double-helix structure of forensic use of natural selection and repair system in Doppler effect Dorian scale Dorsey, Jack Double-entry accounting Drais, Karl von Dreams Drosophila melanogaster Duchamp, Marcel Dujardin, Edouard Dunbar, Kevin DuPont Corporation DVD players Dylan, Bob Earthquakes Eccles, John Carew Edison, Thomas Alva Einstein, Albert EKG Electrical batteries Electric motors Electroencephalogram (EEG) Electromagnetic spectrum Electrons Elevators Elizabeth I, Queen of England Elliptical orbits Encyclopaedia Britannica Endorphins Engelbart, Doug Engels, Friedrich England commons of Enlightenment in Industrial Revolution in Victorian ENIAC Enlightenment Eno, Brian Enquire software application Enzymes Erdapfel Error inventions generated by noise and paradigm shifts and Ether Evans, Oliver Evolution adjacent possible in Darwin’s theory of of facial expressions mutation in see also Natural selection Exaptation in coffeehouse model in evolutionary theory in subcultures in shared media Exposition Universelle (Paris) Eyeglasses bifocal concave lens Fabricius, Johannes and David Facebook Fahrenheit, Daniel Gabriel Falcon, Jean Falling bodies, law of Faraday, Michael Farnsworth, Philo Federal Bureau of Investigation (FBI) Automated Case Support system Counterterrorism Radical Fundamentalist Unit (RFU) Federal Communications Commission (FCC) Ferdinand III, Holy Roman Emperor Fermi, Enrico Ferraris, Galileo Ferro, Scipione del Fick, Adolf Eugen Finley, James Fiore, Antonio Firearms Fischer, Claude Fisher, Alva John Fitch, John FitzRoy, Vice Admiral James Flaubert, Gustave Fleming, Alexander Flemming, Walther Fletcher, William Flintlock firing mechanism Flush toilets Flying shuttle Ford Motor Company Forensics, DNA Foursquare France, medical establishment in Franklin, Benjamin Franklin, Rosalind Frasca, David Fraunhofer, Joseph von Freud, Sigmund Fuchsian functions Fulton, Robert GABA Galápagos Islands Galileo Galilei Galvani, Luigi Gamma ray bursts Gates, Bill Gatling gun General Electric Geological uniformitarianism Geometry Gerhardt, Charles Germany technology companies in viticulture in in World War I, Germ theory Getting, Ivan Gilbert, William Ginsburg, Charles Paulson Gladwell, Malcolm Global Positioning System (GPS) Global warming Goddard, Robert H.


pages: 291 words: 81,703

Average Is Over: Powering America Beyond the Age of the Great Stagnation by Tyler Cowen

Amazon Mechanical Turk, Black Swan, brain emulation, Brownian motion, business cycle, Cass Sunstein, choice architecture, complexity theory, computer age, computer vision, computerized trading, cosmological constant, crowdsourcing, dark matter, David Brooks, David Ricardo: comparative advantage, deliberate practice, Drosophila, en.wikipedia.org, endowment effect, epigenetics, Erik Brynjolfsson, eurozone crisis, experimental economics, Flynn Effect, Freestyle chess, full employment, future of work, game design, income inequality, industrial robot, informal economy, Isaac Newton, Johannes Kepler, John Markoff, Khan Academy, labor-force participation, Loebner Prize, low skilled workers, manufacturing employment, Mark Zuckerberg, meta analysis, meta-analysis, microcredit, Myron Scholes, Narrative Science, Netflix Prize, Nicholas Carr, P = NP, pattern recognition, Peter Thiel, randomized controlled trial, Ray Kurzweil, reshoring, Richard Florida, Richard Thaler, Ronald Reagan, Silicon Valley, Skype, statistical model, stem cell, Steve Jobs, Turing test, Tyler Cowen: Great Stagnation, upwardly mobile, Yogi Berra

It is a critical development for the future of our labor markets and global economy. The way humans are playing chess with computers now is, I propose, a model that high earners will be emulating in years and decades to come. To understand intelligent machines and their future influence, we would do well to note Alexander Kronrod’s idea that “chess is the Drosophila of artificial intelligence.” In other words, looking at chess is one way to make sense of the broader picture, just as the fruit fly (the Drosophila) has helped us decipher human genetics. After World War II, computer science pioneers Alan Turing and Claude Shannon both saw that computers would one day play chess, and wrote seminal articles on how it might happen; Turing was brilliant enough to figure out how computers would play chess even before other scientists had figured out computers.


pages: 281 words: 79,958

Denialism: How Irrational Thinking Hinders Scientific Progress, Harms the Planet, and Threatens Our Lives by Michael Specter

23andMe, agricultural Revolution, Anne Wojcicki, Any sufficiently advanced technology is indistinguishable from magic, Asilomar, carbon footprint, Cass Sunstein, clean water, Drosophila, food miles, invention of gunpowder, out of africa, personalized medicine, placebo effect, profit motive, randomized controlled trial, Richard Feynman, Richard Feynman: Challenger O-ring, Ronald Reagan, Simon Singh, Skype, stem cell, Ted Kaczynski, the scientific method, Thomas Malthus, twin studies, Upton Sinclair, X Prize

But there is much more we don’t understand—including how some genes work to protect us from illnesses that other genes cause. Meanwhile, that 99 percent figure has been published everywhere and is used as the basis of a propaganda war by both sides in the race debate. There is no disputing our homogeneity. It is also true, however, that we share 98.4 percent of our genes with chimpanzees. Few people would argue that makes us nearly identical to them. Even drosophila—the common fruit fly—has a genetic structure that shares almost two-thirds of its DNA with humans. Does that mean we are mostly like fruit flies? The simple and largely unanswered question remains: what can we learn from the other 1 percent (or less) of our genome that sets us apart from everyone else? “WHAT WE ARE going to find is precisely that the other percent plays a role in determining why one person gets schizophrenia or diabetes while another doesn’t, why one person responds well to a drug while another can’t tolerate it,” Neil Risch said.

HHS common ancestor complementary and alternative medicine (CAM), see alternative medicines Complete Genomics Condit, Celeste conspiracy: assumptions of confusion among theorists of Continental Army, vaccination of cordyceps corporate greed cowpox cox-2 inhibitors (coxibs)- Creation Museum Crick, Francis Crohn’s disease crystal meth Cuba, agriculture in Cuyahoga River, afire cyclooxygenase-2 DALYs (disability-adjusted life years) Darwin, Charles deCODE genetics Defense Advanced Research Projects Agency (DARPA) denialism: arguments used in and conspiracy theories distortion of facts in forms of and loss of control use of term DES (diethylstilbestrol) diphtheria disability-adjusted life years (DALYs) disease, see illness disposable biological systems, creation of DNA: capacity of tools for study of comparisons of components of cost of processing decoding sequences of do-i t-yourself research on and genome studies Internet sales of open-source biology of personal analysis of and polio virus research recombinant technology resurrecting self-re plicating structure of synthetic Dole, Bob Dostoyevsky, Fyodor Drazen, Jeffrey drosophila Drug Enforcement Administration (DEA) drug metabolizing enzymes drug resistance Duesberg, Peter DuPont Corporation Dyson, Freeman echinacea education Ehrlich, Paul, The Population Bomb Einstein, Albert eleuthero (Siberian ginseng) Elizabeth I, queen of England Emanuel, Ezekiel encephalopathy Endy, Drew energy, new sources of energy drinks Enlightenment Enriquez, Juan environmental issues: and agriculture and genetics pollution solutions to ephedra ETC Group eugenics Every Child by Two evolution common ancestor in and genetic modification and human genome intelligent design as alternative to of machines manipulation of natural selection rejection of the idea of and survival theory of extinct animals, bringing back to life falciparum parasite Falk, Gary W.


pages: 287 words: 87,204

Erwin Schrodinger and the Quantum Revolution by John Gribbin

Albert Einstein, Albert Michelson, All science is either physics or stamp collecting, Arthur Eddington, British Empire, Brownian motion, double helix, Drosophila, Edmond Halley, Ernest Rutherford, Fellow of the Royal Society, Henri Poincaré, Isaac Newton, Johannes Kepler, John von Neumann, lateral thinking, Richard Feynman, Schrödinger's Cat, Solar eclipse in 1919, The Present Situation in Quantum Mechanics, the scientific method, trade route, upwardly mobile

Genes are sections of chromosomes, and it is a change in a gene (sometimes called a mutation) that produces changes in individual members of a species on which evolution can act. But how big does a change in the molecule of life (whatever it may be) have to be in order to produce a significant change in the individual? In the 1935 paper that so intrigued Schrödinger, Delbrück and his colleagues, using data from experiments in which mutations were caused in fruit flies (drosophila) by X-rays, suggested that a mutation can be caused by a single change at one place in a molecule—in modern terminology, a change as simple as changing an A to a G in a DNA helix. The scientific paper that conveyed this dramatic information became known, from the colour of the cover on the reprints that circulated (increasingly after Schrödinger drew attention to it), as “the green pamphlet.” But just as Schrödinger’s What Is Life?

He had also read Schrödinger’s book, in 1946 while still an undergraduate, and it was instrumental in determining his future career path. He said in 1984, in a talk given at Indiana University: “From the moment I read Schrödinger’s What Is Life? I became polarised towards finding out the secret of the gene.” With typical chutzpah, he also said: “It was clear in those days that physicists were brighter than biologists.” Although he started working for a PhD on drosophila at Indiana University, in Bloomington, he soon switched to X-ray studies of a type of virus known as a bacteriophage. Armed with a fresh PhD and still only twenty-two, in 1950 Watson travelled to Copenhagen, where he carried out more work on bacteriophage, and then, in 1951, to Cambridge, where he met up with Crick at the Cavendish—through the pure chance of their happening to share a room at the laboratory.


pages: 357 words: 98,854

Epigenetics Revolution: How Modern Biology Is Rewriting Our Understanding of Genetics, Disease and Inheritance by Nessa Carey

Albert Einstein, British Empire, Build a better mousetrap, conceptual framework, discovery of penicillin, double helix, Drosophila, epigenetics, Fellow of the Royal Society, life extension, mouse model, phenotype, selective serotonin reuptake inhibitor (SSRI), stem cell, stochastic process, Thomas Kuhn: the structure of scientific revolutions, twin studies

It seemed that they bind to the region from which they are transcribed, and repress gene expression on that same chromosome. But if we go back to our analogy from the start of this chapter, we’d have to say that it’s now becoming clear we have built a pretty small shed and already cemented quite a bit of rubble to the roof. There’s an amazing family of genes, called HOX genes. When they’re mutated in fruit flies (Drosophila melanogaster) the results are incredible phenotypes, such as legs growing out of the head14. There’s a long ncRNA known as HOTAIR, which regulates a region of genes called the HOX-D cluster. Just like the long ncRNAs investigated by Jeannie Lee, HOTAIR binds the PRC2 complex and creates a chromatin region which is marked with repressive histone modifications. But HOTAIR is not transcribed from the HOX-D position on chromosome 12.

Honeybees also expressed proteins that were able to bind to methylated DNA. Together, these data showed that honeybee cells could both ‘write’ and ‘read’ an epigenetic code. Until these data were published, nobody had really wanted to take a guess as to whether or not honeybees would possess a DNA methylation system. This was because the most widely used experimental system in insects, the fruit fly Drosophila melanogaster, whom we met earlier in this book, doesn’t methylate its DNA. It’s interesting to discover that honeybees have an intact DNA methylation system. But this doesn’t prove that DNA methylation is involved in the responses to royal jelly, or the persistent effects of this foodstuff on the physical form and behaviour of mature bees. This issue was addressed by some elegant work from the laboratory of Dr Ryszard Maleszka at the Australian National University in Canberra.


pages: 474 words: 136,787

The Red Queen: Sex and the Evolution of Human Nature by Matt Ridley

affirmative action, Alfred Russel Wallace, assortative mating, Atahualpa, Bonfire of the Vanities, demographic transition, double helix, Drosophila, feminist movement, invention of agriculture, Menlo Park, phenotype, rent control, theory of mind, twin studies, University of East Anglia, women in the workforce, zero-sum game

., 1987, ‘The Biological Role of Consciousness’, Mindwaves, ed. C. Blakemore and S. Greenfield, Blackwell, Oxford, pp. 361–74 —1990, ‘The Mechanical Mind’, Annual Review of Neuroscience, 13:15–24 —(unpublished) ‘The Inevitability of Consciousness’, Chapter draft Basolo, A. L., 1990, ‘Female Preference Predates the Evolution of the Sword in Swordtail Fish’, Science, 250:808–10 Bateman, A. J., 1948, ‘Intrasexual Selection in Drosophila’, Heredity, 2:349–68 Beeman, R. W., Friesen, K. S. and Denell, R. E., 1992, ‘Maternal-effect Selfish Genes in Flour Beetles’, Science, 256:89–92 Bell, G., 1982, The Masterpiece of Nature, Croom Helm, London —1987, ‘Two Theories of Sex and Variation’, The Evolution of Sex and Its Consequences, ed. S. C. Stearns, Birkhauser, Basel, pp. 117–33 —1988, Sex and Death in Protozoa: The History of an Obsession, Cambridge University Press, Cambridge —and Burt, A., 1990, ‘B-chromosomes: Germ-line Parasites Which Induce Changes in Host Recombination’, Parasitology, 100:S19–S26 —and Maynard Smith, J., 1987, ‘Short-term Selection for Recombination among Mutually Antagonistic Species’, Nature, 328:66–8 Bell, Q., 1976, On Human Finery (second edition), Hogarth Press, London Bellis, M.

., eds, 1979, Evolutionary Biology and Human Social Behavior: An Anthropological Perspective, Duxbury, North Scituate, Massachusetts Chao, L., 1992, ‘Evolution of Sex in RNA Viruses’, Trends in Ecology and Evolution, 7:147–51 —Tran, T., and Matthews, C., 1992, ‘Müller’s Ratchet and the Advantage of Sex in the Virus phi-6’, Evolution, 46:289–99 Charlesworth, B. and Hartl, D. L., 1978, ‘Population Dynamics of the Segregation Distorter Polymorphism of Drosophila melanogaster’, Genetics, 89:171–92 Charnov, E. L., 1982, The Theory of Sex Allocation, Princeton University Press, Princeton Cherfas, J. and Gribbin, J., 1984, The Redundant Male, Pantheon, New York Cherry, M. I., 1990, ‘Tail Length and Female Choice’, Trends in Ecology and Evolution, 5:349–50 Chomsky, N., 1957, Syntactic Structures, Mouton, The Hague Clarke, B. C., 1979, ‘The Evolution of Genetic Diversity’, Proceedings of the Royal Society of London B, 205:453–74 Clay, K., 1991, ‘Parasitic Castration of Plants by Fungi’, Trends in Ecology and Evolution, 6: 162–6 Clutton-Brock, T.


Sorting Things Out: Classification and Its Consequences (Inside Technology) by Geoffrey C. Bowker

affirmative action, business process, corporate governance, Drosophila, information retrieval, loose coupling, Menlo Park, Mitch Kapor, natural language processing, Occam's razor, QWERTY keyboard, Scientific racism, scientific worldview, sexual politics, statistical model, Stephen Hawking, Stewart Brand, the built environment, the medium is the message, transaction costs, William of Occam

Scientific inversions of infrastructure were the theme of a path­ breaking edited volume, The Right Tools for the Job: At Work in Twenti­ eth-Century Life Sciences (Clarke and Fujimura 1 992). The purpose of this volume was to tell the history of biology in a new way-from the point of view of the materials that constrain and enable biological researchers. Rats, petri dishes, taxidermy, planaria, drosophila, and test tubes take center stage in this narrative. The standardization of genetic research on a few specially bred organisms (notably drosophila) has constrained the pacing of research and the ways the questions may be framed, and it has given biological supply houses an important, invisible role in research horizons. While elephants or whales might answer different kinds of biological questions, they are obviously un­ wieldy lab animals. While pregnant cow's urine played a critical role in the discovery and isolation of reproductive hormones, no historian of biology had thought it important to describe the task of obtaining gallons of it on a regular basis.


Epigenetics: How Environment Shapes Our Genes by Richard C. Francis

agricultural Revolution, cellular automata, double helix, Drosophila, epigenetics, experimental subject, longitudinal study, Machine translation of "The spirit is willing, but the flesh is weak." to Russian and back, meta analysis, meta-analysis, phenotype, stem cell, twin studies

Curr Opin Genet Dev 17(2): 139–144. Carrell, D. T., and S. S. Hammoud (2010). “The human sperm epigenome and its potential role in embryonic development.” Mol Hum Reprod 16(1): 37–47. Cassidy, S. B., and D. H. Ledbetter (1989). “Prader-Willi syndrome.” Neurol Clin 7(1): 37–54. Castle, W. E., F. W. Carpenter, et al. (1906). “The effects of inbreeding, cross-breeding, and selection upon fertility and variability of Drosophila.” Proc Am Acad Arts Sci 41. Castle, W. E., and S. Wright (1916). “Studies of inheritance in guinea pigs and rats.” Carnegie Inst Wash Publ 241: 163–190. Cattanach, B. M., C. V. Beechey, et al. (2006). “Interactions between imprinting effects: Summary and review.” Cytogenet Genome Res 113(1–4): 17–23. Champagne, F. A., and J. P. Curley (2009). “Epigenetic mechanisms mediating the long-term effects of maternal care on development.”


How Emotions Are Made: The Secret Life of the Brain by Lisa Feldman Barrett

airport security, Albert Einstein, Albert Michelson, Drosophila, en.wikipedia.org, epigenetics, framing effect, Google Glasses, Isaac Newton, longitudinal study, luminiferous ether, meta analysis, meta-analysis, phenotype, placebo effect, randomized controlled trial, Shai Danziger, Skype, Steven Pinker, the scientific method, theory of mind, Thomas Kuhn: the structure of scientific revolutions

Boston Globe, June 30. http://clbb.mgh.harvard.edu/will-we-ever-know-why-dzhokhar-tsarnaev-spoke-after-it-was-too-late. Gibson, William T., Carlos R. Gonzalez, Conchi Fernandez, Lakshminarayanan Ramasamy, Tanya Tabachnik, Rebecca R. Du, Panna D. Felsen, Michael R. Maire, Pietro Perona, and David J. Anderson. 2015. “Behavioral Responses to a Repetitive Visual Threat Stimulus Express a Persistent State of Defensive Arousal in Drosophila.” Current Biology 25 (11): 1401–1415. Gilbert, Charles D., and Wu Li. 2013. “Top-Down Influences on Visual Processing.” Nature Reviews Neuroscience 14 (5): 350–363. Gilbert, D. T. 1998. “Ordinary Personology.” In The Handbook of Social Psychology, edited by S. T. Fiske and L. Gardner, 89–150. New York: McGraw-Hill. Giuliano, Ryan J., Elizabeth A. Skowron, and Elliot T. Berkman. 2015. “Growth Models of Dyadic Synchrony and Mother-Child Vagal Tone in the Context of Parenting At-Risk.”

Madrick, Jeff. 2014. Seven Bad Ideas: How Mainstream Economists Have Damaged America and the World. New York: Vintage. Maihöfner, Christian, Clemens Forster, Frank Birklein, Bernhard Neundörfer, and Hermann O. Handwerker. 2005. “Brain Processing During Mechanical Hyperalgesia in Complex Regional Pain Syndrome: A Functional MRI Study.” Pain 114 (1): 93–103. Malik, Bilal R., and James J. L. Hodge. 2014. “Drosophila Adult Olfactory Shock Learning.” Journal of Visualized Experiments (90): 1–5. doi:10.3791/50107. Malt, Barbara, and Phillip Wolff. 2010. Words and the Mind: How Words Capture Human Experience. New York: Oxford University Press. Marder, E., and A. L. Taylor. 2011. “Multiple Models to Capture the Variability in Biological Neurons and Networks.” Nature Neuroscience 14: 133–138. Marder, Eve. 2012.


pages: 266 words: 76,299

Ever Since Darwin: Reflections in Natural History by Stephen Jay Gould

Alfred Russel Wallace, British Empire, correlation coefficient, Drosophila, European colonialism, invisible hand, Isaac Newton, Monroe Doctrine, Paul Samuelson, Scientific racism, sexual politics, the scientific method, twin studies

If genes only specify that we are large enough to live in a world of gravitational forces, need to rest our bodies by sleeping, and do not photosynthesize, then the realm of genetic determinism will be relatively uninspiring. What is the direct evidence for genetic control of specific human social behavior? At the moment, the answer is none whatever. (It would not be impossible, in theory, to gain such evidence by standard, controlled experiments in breeding, but we do not raise people in Drosophila bottles, establish pure lines, or control environments for invariant nurturing.) Sociobiologists must therefore advance indirect arguments based on plausibility. Wilson uses three major strategies: universality, continuity, and adaptiveness. 1.Universality: If certain behaviors are invariably found in our closest primate relatives and among humans themselves, a circumstantial case for common, inherited genetic control may be advanced.


pages: 312 words: 78,053

Generation A by Douglas Coupland

Burning Man, call centre, Drosophila, hive mind, index card, Live Aid, Magellanic Cloud, McJob, new economy, post-work, Ronald Reagan, Silicon Valley, stem cell, Stephen Hawking

I wanted to tell them that their religion was invented thousands of years ago as a way of explaining to those people lucky enough (or unlucky enough) to live past the age of twenty-one the fact that life is too short. These crones, I wanted to tell them that what I would look for in a religion is an explanation of why life is so long. I’m still looking. Forget religion, I want to mutate. I want so badly to mutate. I was sitting in the sun in the Bois de Vincennes, willing my body to mutate into whatever it is human beings are slated to turn into next. Do we get giant drosophila fly eyes? Wings? Elephantine snouts? I dream of the day we mutate into something better than the hyped-up chimps we are, chimps who eat Knorr Swiss cream of cauliflower soup while pretending not to notice that half the planet’s at war, fighting over . . . what? Over the right to eat packaged soup without having to emotionally accept our species’ darkness. We are one fucked-up claque of monkeys.


pages: 654 words: 204,260

A Short History of Nearly Everything by Bill Bryson

Albert Einstein, Albert Michelson, Alfred Russel Wallace, All science is either physics or stamp collecting, Arthur Eddington, Barry Marshall: ulcers, Brownian motion, California gold rush, Cepheid variable, clean water, Copley Medal, cosmological constant, dark matter, Dava Sobel, David Attenborough, double helix, Drosophila, Edmond Halley, Ernest Rutherford, Fellow of the Royal Society, Harvard Computers: women astronomers, Isaac Newton, James Watt: steam engine, John Harrison: Longitude, Kevin Kelly, Kuiper Belt, Louis Pasteur, luminiferous ether, Magellanic Cloud, Menlo Park, Murray Gell-Mann, out of africa, Richard Feynman, Stephen Hawking, supervolcano, Thomas Malthus, Wilhelm Olbers

Chromosomes had been discovered by chance in 1888 and were so called because they readily absorbed dye and thus were easy to see under the microscope. By the turn of the twentieth century it was strongly suspected that they were involved in the passing on of traits, but no one knew how, or even really whether, they did this. Morgan chose as his subject of study a tiny, delicate fly formally called Drosophila melanogaster, but more commonly known as the fruit fly (or vinegar fly, banana fly, or garbage fly). Drosophila is familiar to most of us as that frail, colorless insect that seems to have a compulsive urge to drown in our drinks. As laboratory specimens fruit flies had certain very attractive advantages: they cost almost nothing to house and feed, could be bred by the millions in milk bottles, went from egg to productive parenthood in ten days or less, and had just four chromosomes, which kept things conveniently simple.


pages: 448 words: 84,462

Testing Extreme Programming by Lisa Crispin, Tip House

c2.com, continuous integration, data acquisition, database schema, Donner party, Drosophila, hypertext link, index card, job automation, web application

Alistair Cockburn, "Characterizing People as Non-Linear, First-Order Components in Software Development," http://alistair.cockburn.us. Martin Fowler, Refactoring: Improving the Design of Existing Code, Addison-Wesley, 1999; 0201485672. Garth House, More Litanies for All Occasions, Judson Press, 2000; 0817013547. Marilyn G. House, Ice Skating Fundamentals, Kendall/Hunt, 1996; 0787209945. Verl Lee House, "The Interaction of Three Mutants Affecting the Vein Pattern in Drosophila melanogaster," Ph.D. diss., University of California at Berkeley, 1950. Ron Jeffries, Ann Anderson, and Chet Hendrickson, Extreme Programming Installed, Addison-Wesley, 2001; 0201708426. Andrew Hunt and David Thomas, The Practical Programmer: From Journeyman to Master, Addison-Wesley, 2000; 020161622X. Cem Kaner, James Bach, and Bret Pettichord, Lessons Learned in Software Testing, John Wiley & Sons, 2001; 0471081124.


pages: 319 words: 90,965

The End of College: Creating the Future of Learning and the University of Everywhere by Kevin Carey

Albert Einstein, barriers to entry, Bayesian statistics, Berlin Wall, business cycle, business intelligence, carbon-based life, Claude Shannon: information theory, complexity theory, David Heinemeier Hansson, declining real wages, deliberate practice, discrete time, disruptive innovation, double helix, Douglas Engelbart, Douglas Engelbart, Downton Abbey, Drosophila, Firefox, Frank Gehry, Google X / Alphabet X, informal economy, invention of the printing press, inventory management, John Markoff, Khan Academy, Kickstarter, low skilled workers, Lyft, Marc Andreessen, Mark Zuckerberg, meta analysis, meta-analysis, natural language processing, Network effects, open borders, pattern recognition, Peter Thiel, pez dispenser, ride hailing / ride sharing, Ronald Reagan, Ruby on Rails, Sand Hill Road, self-driving car, Silicon Valley, Silicon Valley startup, social web, South of Market, San Francisco, speech recognition, Steve Jobs, technoutopianism, transcontinental railway, uber lyft, Vannevar Bush

The p-sets in this part of the course used another computer program, called the “Integrative Genome Viewer,” which allowed me to see what happens when mutations alter single base pairs in a DNA sequence that can run hundreds of millions of pairs long, resulting in a new set of instructions for protein creation and sometimes disastrous consequences for the organism in question. In another p-set, we had to breed multiple generations of fruit flies in a computer simulator and submit “cages” containing, say, 1,000 virtual drosophila showing a particular statistical distribution of characteristics—this many wings of this shape, this many eyes of that color—as evidence of the underlying genetic inheritance patterns. It was taxing work. As one of the MIT students taking the course later told me, “Learning science is about spending hours banging away at something until you get it right.” The p-sets were designed for the 9 percent of top high school applicants who are accepted by MIT.


A Crack in Creation: Gene Editing and the Unthinkable Power to Control Evolution by Jennifer A. Doudna, Samuel H. Sternberg

3D printing, Asilomar, Asilomar Conference on Recombinant DNA, carbon footprint, Chuck Templeton: OpenTable:, double helix, Drosophila, Mark Zuckerberg, microbiome, mouse model, phenotype, Ralph Waldo Emerson, Richard Feynman, Silicon Valley, Skype, stem cell, Steven Pinker

Chandrasegaran, “Hybrid Restriction Enzymes: Zinc Finger Fusions to Fok I Cleavage Domain,” Proceedings of the National Academy of Sciences of the United States of America 93 (1996): 1156–60. also worked in frog eggs: M. Bibikova et al., “Stimulation of Homologous Recombination Through Targeted Cleavage by Chimeric Nucleases,” Molecular and Cellular Biology 21 (2001): 289–97. produce a precise genetic alteration in a whole organism: M. Bibikova et al., “Targeted Chromosomal Cleavage and Mutagenesis in Drosophila Using Zinc-Finger Nucle­ases,” Genetics 161 (2002): 1169–75. Matthew Porteus and David Baltimore were the first: M. H. Porteus and D. Baltimore, “Chimeric Nucleases Stimulate Gene Targeting in Human Cells,”Science 300 (2003): 763. Fyodor Urnov and colleagues corrected a mutation: F. D. Urnov et al., “Highly Efficient Endogenous Human Gene Correction Using Designed Zinc-Finger Nucleases,” Nature 435 (2005): 646–51.


pages: 336 words: 93,672

The Future of the Brain: Essays by the World's Leading Neuroscientists by Gary Marcus, Jeremy Freeman

23andMe, Albert Einstein, bioinformatics, bitcoin, brain emulation, cloud computing, complexity theory, computer age, computer vision, conceptual framework, correlation does not imply causation, crowdsourcing, dark matter, data acquisition, Drosophila, epigenetics, global pandemic, Google Glasses, iterative process, linked data, mouse model, optical character recognition, pattern recognition, personalized medicine, phenotype, race to the bottom, Richard Feynman, Ronald Reagan, semantic web, speech recognition, stem cell, Steven Pinker, supply-chain management, Turing machine, twin studies, web application

“The brain has a body: Adaptive behavior emerges from interactions of nervous system, body and environment.” Trends in Neurosciences 20 (12): 553–57. Harvey, C. D., F. Collman, D. A. Dombeck, and D. W. Tank. 2009. “Intracellular dynamics of hippocampal place cells during virtual navigation.” Nature 461 (7266): 941–46. doi:10.1038/nature08499. Seelig, J. D., M. E. Chiappe, G. K. Lott, A. Dutta, J. E. Osborne,M. B. Reiser, and V. Jayaraman. 2010. “Two-photon calcium imaging from head-fixed Drosophila during optomotor walking behavior. Nature Methods 7 (7): 535–40: doi:10.1038/nmeth.1468. PROJECT MINDSCOPE Christof Koch With Clay Reid, Hongkui Zeng, Stefan Mihalas, Mike Hawrylycz, John Philips, Chinh Dang, and Allan Jones The human brain, with its eighty-six billion nerve cells, is the most complex piece of organized matter in the known universe. It is the organ responsible for behavior, memory, and perception, including that most mysterious of all phenomena, consciousness.


pages: 322 words: 88,197

Wonderland: How Play Made the Modern World by Steven Johnson

Ada Lovelace, Alfred Russel Wallace, Antoine Gombaud: Chevalier de Méré, Berlin Wall, bitcoin, Book of Ingenious Devices, Buckminster Fuller, Claude Shannon: information theory, Clayton Christensen, colonial exploitation, computer age, conceptual framework, crowdsourcing, cuban missile crisis, Drosophila, Edward Thorp, Fellow of the Royal Society, game design, global village, Hedy Lamarr / George Antheil, HyperCard, invention of air conditioning, invention of the printing press, invention of the telegraph, Islamic Golden Age, Jacquard loom, Jacques de Vaucanson, James Watt: steam engine, Jane Jacobs, John von Neumann, joint-stock company, Joseph-Marie Jacquard, land value tax, Landlord’s Game, lone genius, mass immigration, megacity, Minecraft, moral panic, Murano, Venice glass, music of the spheres, Necker cube, New Urbanism, Oculus Rift, On the Economy of Machinery and Manufactures, pattern recognition, peer-to-peer, pets.com, placebo effect, probability theory / Blaise Pascal / Pierre de Fermat, profit motive, QWERTY keyboard, Ray Oldenburg, spice trade, spinning jenny, statistical model, Steve Jobs, Steven Pinker, Stewart Brand, supply-chain management, talking drums, the built environment, The Great Good Place, the scientific method, The Structural Transformation of the Public Sphere, trade route, Turing machine, Turing test, Upton Sinclair, urban planning, Victor Gruen, Watson beat the top human players on Jeopardy!, white flight, white picket fence, Whole Earth Catalog, working poor, Wunderkammern

In cognitive science, the litany of insights that derived from the study of chess could almost fill an entire textbook, insights that have helped us understand the human capacity for problem solving, pattern recognition, visual memory, and the crucial skill that scientists call, somewhat awkwardly, chunking, which involves grouping a collection of ideas or facts into a single “chunk” so that they can be processed and remembered as a unit. (A chess player’s ability to recognize and often name a familiar sequence of moves is a classic example of mental chunking.) Some cognitive scientists compared the impact of chess on their field to Drosophila, the fruit fly that played such a central role in early genetics research. But the prominence of chess in the first fifty years of both cognitive and computer science also produced a distorted vision of intelligence itself. It helped cement the brain-as-computer metaphor: a machine driven by logic and pattern recognition, governed by elemental rules that could be decoded with enough scrutiny.


pages: 346 words: 92,984

The Lucky Years: How to Thrive in the Brave New World of Health by David B. Agus

active transport: walking or cycling, Affordable Care Act / Obamacare, Albert Einstein, butterfly effect, clean water, cognitive dissonance, crowdsourcing, Danny Hillis, Drosophila, Edward Lorenz: Chaos theory, en.wikipedia.org, epigenetics, Kickstarter, longitudinal study, medical residency, meta analysis, meta-analysis, microbiome, microcredit, mouse model, Murray Gell-Mann, New Journalism, pattern recognition, personalized medicine, phenotype, placebo effect, publish or perish, randomized controlled trial, risk tolerance, statistical model, stem cell, Steve Jobs, Thomas Malthus, wikimedia commons

Katherine Hobson, “Many Kids Who Are Obese or Overweight Don’t Know It,” NPR Health, July 23, 2014, www.npr.org: http://www.npr.org/sections/health-shots/2014/07/23/334091461/many-kids-who-are-obese-and-overweight-dont-know-it. 7. G. G. Kuhnle et al., “Association Between Sucrose Intake and Risk of Overweight and Obesity in a Prospective Sub-Cohort of the European Prospective Investigation into Cancer in Norfolk (EPIC-Norfolk),” Public Health Nutrition (February 23, 2015): 1–10 (Epub ahead of print). 8. S. Gill et al., “Time-Restricted Feeding Attenuates Age-Related Cardiac Decline in Drosophila,” Science 347, no. 6227 (March 13, 2015): 1265–69, doi:10.1126/science.1256682. Also see Michael Price, “You Are When You Eat,” San Diego State University News Center, March 12, 2015, http://universe.sdsu.edu/sdsu_newscenter/news_story.aspx?sid=75480. 9. Ellie Zolfagharifard, “400,000-Year-Old Teeth Reveal First Evidence of Man-Made Pollution—and Show the ‘Caveman Diet’ Really Was Balanced,” DailyMail.com (UK), June 17, 2015, www.dailymail.co.uk/sciencetech/article-3128818/400-000-year-old-teeth-reveal-evidence-man-pollution-shows-caveman-diet-really-balanced.html, accessed August 8, 2015. 10.


pages: 487 words: 95,085

JPod by Douglas Coupland

Asperger Syndrome, Drosophila, finite state, G4S, game design, Maui Hawaii, McMansion, neurotypical, pez dispenser, pre–internet, QWERTY keyboard, Ronald Reagan, special economic zone, wage slave, Y2K

You're a depressing assemblage of pop culture influences and cancelled emotions, driven by the sputtering engine of only the most banal form of capitalism. You spend your life feeling as if you're perpetually on the brink of being obsolete—whether it's labour market obsolescence or cultural unhipness. And it's all catching up with you. You live and die by the development cycle. You're glamorized drosophila flies, with the company regulating your life cycles at whim. If it isn't a budget-driven eighteen-month game production schedule, it's a five-year hardware obsolescence schedule. Every five years you have to throw away everything you know and learn a whole new set of hardware and software specs, relegating what was once critical to our lives to the cosmic slag heap." Cowboy considered this. "So, then, what's wrong with that?"


pages: 798 words: 240,182

The Transhumanist Reader by Max More, Natasha Vita-More

23andMe, Any sufficiently advanced technology is indistinguishable from magic, artificial general intelligence, augmented reality, Bill Joy: nanobots, bioinformatics, brain emulation, Buckminster Fuller, cellular automata, clean water, cloud computing, cognitive bias, cognitive dissonance, combinatorial explosion, conceptual framework, Conway's Game of Life, cosmological principle, data acquisition, discovery of DNA, Douglas Engelbart, Drosophila, en.wikipedia.org, endogenous growth, experimental subject, Extropian, fault tolerance, Flynn Effect, Francis Fukuyama: the end of history, Frank Gehry, friendly AI, game design, germ theory of disease, hypertext link, impulse control, index fund, John von Neumann, joint-stock company, Kevin Kelly, Law of Accelerating Returns, life extension, lifelogging, Louis Pasteur, Menlo Park, meta analysis, meta-analysis, moral hazard, Network effects, Norbert Wiener, pattern recognition, Pepto Bismol, phenotype, positional goods, prediction markets, presumed consent, Ray Kurzweil, reversible computing, RFID, Ronald Reagan, scientific worldview, silicon-based life, Singularitarianism, social intelligence, stem cell, stochastic process, superintelligent machines, supply-chain management, supply-chain management software, technological singularity, Ted Nelson, telepresence, telepresence robot, telerobotics, the built environment, The Coming Technological Singularity, the scientific method, The Wisdom of Crowds, transaction costs, Turing machine, Turing test, Upton Sinclair, Vernor Vinge, Von Neumann architecture, Whole Earth Review, women in the workforce, zero-sum game

They have the money, power, and prestige. All the evolutionists have is scientific truth. I think many of you know how this is going to play out. References Arrison, Sonia (2011) 100 Plus: How the Coming Age of Longevity Will Change Everything, from Careers and Relationships to Family and Faith. New York: Basic Books. Burke, Molly K., et al. (2010) “Genome-Wide Analysis of a Long-Term Evolution Experiment with Drosophila.” Nature 467, pp. 587–590. Comfort, Alex (1979) The Biology of Senescence, 3rd edn. New York: Elsevier North Holland, Inc. Cordain, Loren. (2002) The Paleo Diet. New York: Wiley. de Grey, Aubrey and Rae, M. (2007) Ending Aging. New York: St. Martin’s Griffin. de Vany, Arthur (2011) The New Evolution Diet. New York: Rodale. Garland, Theodore Jr. and Michael R., eds. (2009) Experimental Evolution.

Lindeberg, Staffan E. (2010) Food and Western Disease: Health and Nutrition from an Evolutionary Perspective. New York: Wiley-Blackwell. Magary, Drew (2011) The Postmortal. London: Penguin Books. Martinez, Daniel E. (1998) “Mortality Patterns Suggest a Lack of Senescence in Hydra.” Experimental Gerontology 33, pp. 217–225. Matsagas, Kennedy, et al. (2009) “Long-Term Functional Side-Effects of Stimulants and Sedatives in Drosophila melanogaster.” PLoS One 4(8), e6578. Mueller, Laurence D., Rauser, Casandra L., and Michael R. (2011) Does Aging Stop? New York: Oxford University Press. Passanati, Hardip B., Rose, Michael R., and Matos, Margarida (2005) Methuselah Flies: A Case Study in the Evolution of Aging. Singapore: World Scientific Publishing. Rose, Michael R. (1984) “The Evolutionary Route to Methuselah,” New Scientist, July 26.


Beautiful Visualization by Julie Steele

barriers to entry, correlation does not imply causation, data acquisition, database schema, Drosophila, en.wikipedia.org, epigenetics, global pandemic, Hans Rosling, index card, information retrieval, iterative process, linked data, Mercator projection, meta analysis, meta-analysis, natural language processing, Netflix Prize, pattern recognition, peer-to-peer, performance metric, QR code, recommendation engine, semantic web, social graph, sorting algorithm, Steve Jobs, web application, wikimedia commons

Sören Auer, Christian Bizer, and Kingsley Idehen, admins. Leipzig: Universität Leipizig; Berlin: Freie Universität Berlin; Burlington, MA: OpenLink Software. http://dbpedia.org. Doreian, P., V. Batagelj, and A. Ferligoj. 2005. Generalized Blockmodeling (Structural Analysis in the Social Sciences). Cambridge: Cambridge University Press. Flybase. 2008. Rachel Drysdale and the FlyBase Consortium. FlyBase. Drosophila: 45–59. doi: 10.1007/978-1-59745-583-1_3. See also http://flybase.org/static_pages/docs/release_notes.html. Freebase. 2009. Freebase. San Francisco, CA: Metaweb Technologies. http://www.freebase.com. For data dumps, see http://download.freebase.com/datadumps/. Garner, Ralph. 1963. “A computer-oriented graph theoretic analysis of citation index structures.” In Three Drexel Information Science Research Studies, ed.


pages: 311 words: 94,732

The Rapture of the Nerds by Cory Doctorow, Charles Stross

3D printing, Ayatollah Khomeini, butterfly effect, cognitive dissonance, combinatorial explosion, complexity theory, Credit Default Swap, dematerialisation, Drosophila, epigenetics, Extropian, gravity well, greed is good, haute couture, hive mind, margin call, negative equity, phenotype, plutocrats, Plutocrats, rent-seeking, Richard Feynman, telepresence, Turing machine, Turing test, union organizing

asks Doc Dagbjört, looking rather more cheerful than the situation warrants. “From inside the containment? No.” The Vulture looks thoughtful. “But from traces of carapace scraped off the walls of the Bey residence nursery, we have obtained a partial genotype. Tell your guidebooks or familiars or whatever to download Exhibit B for you. As you can see, the genome of the said item is chimeric and shows signs of crude tampering, but it’s largely derived from Drosophila, Mus musculus, and a twenty-first-century situationist artist or politician called Sarah Palin. Large chunks of its genome appear to be wholly artificial, though, written entirely in Arabic, and there’s an aqueous-phase Turing machine partially derived from octopus ribosomes to interpret them. It looks as if something has been trying to use the sharia code as a platform for implementing a legal virtual machine.


pages: 367 words: 102,188

Sleepyhead: Narcolepsy, Neuroscience and the Search for a Good Night by Henry Nicholls

A. Roger Ekirch, Donald Trump, double helix, Drosophila, global pandemic, Kickstarter, longitudinal study, meta analysis, meta-analysis, mouse model, placebo effect, Saturday Night Live, stem cell, web application, Yom Kippur War

p. 15 on a surfboard Narcolepsy in the UK, ‘What’s the Strangest Place You’ve Fallen Asleep?’, 1 June 2017. 2 Let there be light p. 17 to sense the Sun without ever seeing it André Klarsfeld, ‘At the Dawn of Chronobiology’, 2013 <https://docs.google.com/viewer?a=v&pid=sites&srcid=ZGVmYXVsdGRvbWFpbnxrbGFyc2ZlbGRhbmRyZXxneDo0OTIyYzUwY2IyYWVjMjg2> [accessed 16 August 2017]. p. 18 they called it Period Ronald J. Konopka and Seymour Benzer, ‘Clock Mutants of Drosophila melanogaster’, Proceedings of the National Academy of Sciences, 68.9 (1971), 2112–16. p. 19 the circadian rhythm within each cell ‘The 2017 Nobel Prize in Physiology or Medicine - Press Release’, nobelprize.org, 10 February 2017, <http://www.nobelprize.org/nobel_prizes/medicine/laureates/2017/press.html> [accessed 29 October 2017]. p. 20 near-24-hour period Martin R. Ralph and Michael Menaker, ‘A Mutation of the Circadian System in Golden Hamsters’, Science, 241.4870 (1988), 1225–27.


pages: 297 words: 96,509

Time Paradox by Philip G. Zimbardo, John Boyd

Albert Einstein, cognitive dissonance, Drosophila, endowment effect, hedonic treadmill, impulse control, indoor plumbing, loss aversion, mental accounting, meta analysis, meta-analysis, Necker cube, Ronald Reagan, science of happiness, The Wealth of Nations by Adam Smith, twin studies

But they do associate their best and worst experiences with the circumstances that accompanied and preceded them, which allows them to seek or avoid those circumstances in the future. Expose a fruit fly to the odor of tennis shoes, give it a very tiny electric shock, and for the rest of its very tiny life it will avoid places that smell tennis-shoey. The ability to associate pleasure or pain with its circumstances is so vitally important that nature has installed that ability in every one of her creatures, from Drosophila melanogaster to Ivan Pavlov. But if that ability is necessary for creatures like us, it certainly isn’t sufficient, because the kind of learning it enables is far too limited. If an organism can do no more than associate particular experiences with particular circumstances, then it can learn only a very small lesson, namely, to seek or avoid those particular circumstances in the future. A well-timed shock may teach a fruit fly to avoid the tennis-shoe smell, but it won’t teach it to avoid the smell of snowshoes, ballet slippers, Manolo Blahniks, or a scientist armed with a miniature stun gun.


pages: 321 words: 85,893

The Vegetarian Myth: Food, Justice, and Sustainability by Lierre Keith

British Empire, car-free, clean water, cognitive dissonance, correlation does not imply causation, Drosophila, dumpster diving, en.wikipedia.org, Gary Taubes, Haber-Bosch Process, longitudinal study, McMansion, meta analysis, meta-analysis, out of africa, peak oil, placebo effect, Rosa Parks, the built environment

More than 10,000 alkaloids, 20,000 terpenes, and 8000 polyphenols are known … Through complex feedback loops, plants constantly sense what is happening in the world around them and, in response, vary the numbers, combinations, and amounts of the phytochemicals they make.118 These chemicals are used for obvious tasks like fighting off insects, fungi, or bacteria. Susan Allport dubs phyto-chemicals “plants’ armed services. Plants cannot flee from hungry predators, of course, so they became experts in chemical warfare instead.”119 They also use chemicals to call pollinators and protectors with a specificity that is exquisite enough to stop your breath. Saguaro cacti need a unique species of Drosophila fly. The cacti release a volatile steroidal compound that the flies must have to reach sexual maturity and reproduce. In return, the flies and their larva eat the decaying parts of the cacti, keeping the plants healthy. The volatiles are so precise that for 6,803 larvae on the average saguaro cactus, only one is not the correct species.120 Each of the world’s seven hundred plus species of figs has its own specific fig wasp, wasps who hand pollinate that fig’s seeds.


The Deep Learning Revolution (The MIT Press) by Terrence J. Sejnowski

AI winter, Albert Einstein, algorithmic trading, Amazon Web Services, Any sufficiently advanced technology is indistinguishable from magic, augmented reality, autonomous vehicles, Baxter: Rethink Robotics, bioinformatics, cellular automata, Claude Shannon: information theory, cloud computing, complexity theory, computer vision, conceptual framework, constrained optimization, Conway's Game of Life, correlation does not imply causation, crowdsourcing, Danny Hillis, delayed gratification, discovery of DNA, Donald Trump, Douglas Engelbart, Drosophila, Elon Musk, en.wikipedia.org, epigenetics, Flynn Effect, Frank Gehry, future of work, Google Glasses, Google X / Alphabet X, Guggenheim Bilbao, Gödel, Escher, Bach, haute couture, Henri Poincaré, I think there is a world market for maybe five computers, industrial robot, informal economy, Internet of things, Isaac Newton, John Conway, John Markoff, John von Neumann, Mark Zuckerberg, Minecraft, natural language processing, Netflix Prize, Norbert Wiener, orbital mechanics / astrodynamics, PageRank, pattern recognition, prediction markets, randomized controlled trial, recommendation engine, Renaissance Technologies, Rodney Brooks, self-driving car, Silicon Valley, Silicon Valley startup, Socratic dialogue, speech recognition, statistical model, Stephen Hawking, theory of mind, Thomas Bayes, Thomas Kuhn: the structure of scientific revolutions, traveling salesman, Turing machine, Von Neumann architecture, Watson beat the top human players on Jeopardy!, X Prize, Yogi Berra

program=Reading+the+Human+Genome+with +Sydney+Brenner. 3. Imaginal discs are the developmental primordia of legs and antennae in flies. 4. Sydney Brenner has published his original story in S. Brenner, “Francisco Crick in Paradiso,” Current Biology. 6, no. 9 (1996): 1202: “I shared an office with Francis Crick for twenty years in Cambridge. At one time he was interested in embryology and spent a lot of time thinking about imaginal discs in Drosophila. One day, he threw the book he was reading down onto his desk with an exasperated cry. ‘God knows how these imaginal discs work!’ In a flash I saw the whole story of Francis arriving in heaven and Peter welcoming him with ‘Oh, Dr. Crick, you must be tired after your long journey. Do sit down, have a drink and relax.’ ‘No,’ says Francis, ‘I must see this fellow, God; I have to ask him a question.’


pages: 380 words: 104,841

The Human Age: The World Shaped by Us by Diane Ackerman

23andMe, 3D printing, additive manufacturing, airport security, Albert Einstein, augmented reality, back-to-the-land, carbon footprint, clean water, dark matter, dematerialisation, double helix, Drosophila, epigenetics, Google Earth, Google Glasses, haute cuisine, Internet of things, Loebner Prize, Louis Pasteur, Masdar, mass immigration, megacity, microbiome, nuclear winter, personalized medicine, phenotype, Ray Kurzweil, refrigerator car, Search for Extraterrestrial Intelligence, SETI@home, skunkworks, Skype, stem cell, Stewart Brand, the High Line, theory of mind, urban planning, urban renewal, Whole Earth Catalog

As a Cornell grad student, I often stopped by the fetid biology lab to admire the eggplant-blackness of the bellies, the spiky hairs, the gaudy prisms of the eyes—some apricot, some teal, some brick red, some yellow, some the blue of ships on Delft pottery. I still recall the tiny haunting eyes of the fruit flies, like the captive souls of past lab assistants, and the swooping melody of their Latin name: Drosophila melanogaster, which translates poetically as “dark-bellied dew sipper.” Because fruit flies thrive in sultry weather (82°F), the lab offered students a warm den during those numbing upstate winters when ice clotted in beards and mittens, coeds exhaled stark white clouds, and the walkways looked like a toboggan run. A favorite of biologists hoping to peer into the dark corners of human nature, fruit flies have it all—they’re prowling for mates eight to twelve hours after birth, easy to raise, and able to lay a hundred eggs a day.


pages: 382 words: 115,172

The Diet Myth: The Real Science Behind What We Eat by Tim Spector

biofilm, British Empire, Colonization of Mars, cuban missile crisis, David Strachan, double helix, Drosophila, epigenetics, hygiene hypothesis, Kickstarter, life extension, longitudinal study, Mahatma Gandhi, meta analysis, meta-analysis, microbiome, phenotype, randomized controlled trial, Steve Jobs, twin studies

Structural changes of gut microbiota during berberine-mediated prevention of obesity and insulin resistance in high-fat diet-fed rats. 33 http://www.sciencemag.org/content/342/6162/1035 34 Alcock, J., Bioessays (8 Aug 2014); doi: 10.1002/bies.201400071. Is eating behavior manipulated by the gastrointestinal microbiota? Evolutionary pressures and potential mechanisms. 35 Vijay-Kumar, M., Science (9 Apr 2010); 328(5975): 228–31. Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5. 36 Shin, S.C., Science (2011); 334 (6056): 670–4. Drosophila microbiome modulates host developmental and metabolic homeostasis via insulin signalling. 37 Tremaroli, V., Nature (13 Sep 2012); 489(7415): 242–9. Functional interactions between the gut microbiota and host metabolism. 7 Protein: Animal 1 Diamond, J., Guns, Germs and Steel (Norton, 1997) 2 Atkins, R., The Diet Revolution (Bantam Books, 1981) 3 Bueno, N.B., Br J Nutr (Oct 2013); 110(7): 1178–87.


pages: 372 words: 111,573

10% Human: How Your Body's Microbes Hold the Key to Health and Happiness by Alanna Collen

Asperger Syndrome, Barry Marshall: ulcers, Berlin Wall, biofilm, clean water, correlation does not imply causation, David Strachan, discovery of penicillin, Drosophila, Fall of the Berlin Wall, friendly fire, germ theory of disease, global pandemic, hygiene hypothesis, Ignaz Semmelweis: hand washing, illegal immigration, John Snow's cholera map, Kickstarter, Louis Pasteur, Maui Hawaii, meta analysis, meta-analysis, microbiome, phenotype, placebo effect, the scientific method

The intestinal microbiota affect central levels of brain-derived neurotropic factor and behavior in mice. Gastroenterology 141: 599–609. 15. Voigt, C.C., Caspers, B. and Speck, S. (2005). Bats, bacteria and bat smell: Sex-specific diversity of microbes in a sexually-selected scent organ. Journal of Mammalogy 86: 745–749. 16. Sharon, G. et al. (2010). Commensal bacteria play a role in mating preference of Drosophila melanogaster. Proceedings of the National Academy of Sciences 107: 20051–20056. 17. Wedekind, C. et al. (1995). MHC-dependent mate preferences in humans. Proceedings of the Royal Society B 260: 245–249. 18. Montiel-Castro, A.J. et al. (2013). The microbiota–gut–brain axis: neurobehavioral correlates, health and sociality. Frontiers in Integrative Neuroscience 7: 1–16. 19. Dinan, T.G. and Cryan, J.F. (2013).


pages: 379 words: 113,656

Six Degrees: The Science of a Connected Age by Duncan J. Watts

Berlin Wall, Bretton Woods, business process, corporate governance, Drosophila, Erdős number, experimental subject, fixed income, Frank Gehry, Geoffrey West, Santa Fe Institute, industrial cluster, invisible hand, Long Term Capital Management, market bubble, Milgram experiment, MITM: man-in-the-middle, Murray Gell-Mann, Network effects, new economy, Norbert Wiener, Paul Erdős, peer-to-peer, rolodex, Ronald Coase, scientific worldview, Silicon Valley, supply-chain management, The Nature of the Firm, The Wealth of Nations by Adam Smith, Toyota Production System, transaction costs, transcontinental railway, Vilfredo Pareto, Y2K

It was, he told me, one of the model organisms that biologists have picked out for extensive study, and possibly someone had looked at its neural network. Possibly! After only a cursory amount of research, and helped out by a biologist friend of Steve’s who happened to be an expert on C. elegans, I quickly discovered that C. elegans is no bit player in the world of biomedical research. Alongside the fruit fly Drosophila, the bacterium E. coli, and possibly yeast, the tiny earth-dwelling nematode C. elegans is the most studied and, at least among worm biologists, the most celebrated of organisms. First proposed as a model organism in 1965 by Sydney Brenner, a contemporary of Watson and Crick, and thirty years later a pivotal player in the human genome project, C. elegans has spent over three decades under the microscope.


pages: 228 words: 119,593

Practical Manual of Thyroid and Parathyroid Disease by Asit Arora, Neil Tolley, R. Michael Tuttle

Drosophila, epigenetics, longitudinal study, meta analysis, meta-analysis, mouse model, phenotype, randomized controlled trial, selection bias

A National Cancer Data Base report on 53,856 cases of thyroid carcinoma treated in the U.S., 1985–1995. Cancer 1998;83:2638–48. 188. Jones RL, Judson IR. The development and application of imatinib. Expert Opin Drug Saf 2005;4:183–91. 189. Carlomagno F, et al. ZD6474, an orally available inhibitor of KDR tyrosine kinase activity, efficiently blocks oncogenic RET kinases. Cancer Res 2002;62:7284–90. 190. Vidal M, et al. ZD6474 suppresses oncogenic RET isoforms in a Drosophila model for type 2 multiple endocrine neoplasia syndromes and papillary thyroid carcinoma. Cancer Res 2005;65:3538–41. 191. Hoffmann S, et al. Targeting the EGF/VEGF-R system by tyrosine-kinase inhibitors—a novel antiproliferative/ antiangiogenic strategy in thyroid cancer. Langenbecks Arch Surg 2006;391:589–96. 192. Tamura T, et al. A phase I dose-escalation study of ZD6474 in Japanese patients with solid, malignant tumors.


pages: 1,261 words: 294,715

Behave: The Biology of Humans at Our Best and Worst by Robert M. Sapolsky

autonomous vehicles, Bernie Madoff, biofilm, blood diamonds, British Empire, Broken windows theory, Brownian motion, car-free, clean water, cognitive dissonance, corporate personhood, corporate social responsibility, Daniel Kahneman / Amos Tversky, delayed gratification, desegregation, different worldview, double helix, Drosophila, Edward Snowden, en.wikipedia.org, epigenetics, Flynn Effect, framing effect, fudge factor, George Santayana, global pandemic, hiring and firing, illegal immigration, impulse control, income inequality, John von Neumann, Loma Prieta earthquake, long peace, longitudinal study, loss aversion, Mahatma Gandhi, meta analysis, meta-analysis, Mohammed Bouazizi, Monkeys Reject Unequal Pay, mouse model, mutually assured destruction, Nelson Mandela, Network effects, out of africa, Peter Singer: altruism, phenotype, placebo effect, publication bias, RAND corporation, risk tolerance, Rosa Parks, selective serotonin reuptake inhibitor (SSRI), self-driving car, Silicon Valley, social intelligence, Stanford marshmallow experiment, Stanford prison experiment, stem cell, Steven Pinker, strikebreaker, theory of mind, transatlantic slave trade, traveling salesman, trickle-down economics, twin studies, ultimatum game, Walter Mischel, wikimedia commons, zero-sum game

., “Alternative Isoform Regulation in Human Tissue Transcriptomes,” Nat 456 (2008): 470; Q. Pan et al., “Deep Surveying of Alternative Splicing Complexity in the Human Transcriptome by High-Throughput Sequencing,” Nat Gen, 40 (2008): 1413. 11. A. Muotri et al., “Somatic Mosaicism in Neuronal Precursor Cells Mediated by L1 Retrotransposition,” Nat 435 (2005): 903; P. Perrat et al., “Transposition-Driven Genomic Heterogeneity in the Drosophila Brain,” Sci 340 (2013): 91; G. Vogel, “Do Jumping Genes Spawn Diversity?” Sci 332 (2011): 300; J. Baillie et al., “Somatic Retrotransposition Alters the Genetic Landscape of the Human Brain,” Nat 479 (2011): 534. 12. A. Eldar and M. Elowitz, “Functional Roles for Noise in Genetic Circuits,” Nat 467 (2010): 167; C. Finch and T. Kirkwood, Chance, Development, and Aging (Oxford: Oxford University Press, 2000). 13.

Packer, “Non-offspring Nursing in Social Carnivores: Minimizing the Costs,” Behav Ecology 5 (1994): 362. 21. Footnote: G. Alvarez et al., “The Role of Inbreeding in the Extinction of a Europrean Royal Dynasty,” PLoS ONE 4 (2009): e5174. 22. Theoretical model: B. Bengtsson, “Avoiding Inbreeding: At What Cost?” J Theoretical Biol 73 (1978): 439. 23. Insects: S. Robinson et al., “Preference for Related Mates in the Fruit Fly, Drosophila melanogaster,” Animal Behav 84 (2012): 1169. Lizards: M. Richard et al., “Optimal Level of Inbreeding in the Common Lizard,” Proc Royal Soc of London B 276 (2009): 2779. Fish, and related parents invested more in rearing: T. Thünken et al., “Active Inbreeding in a Cichlid Fish and Its Adaptive Significance,” Curr Biol 17 (2007): 225. Numerous birds: P. Bateson, “Preferences for Cousins in Japanese Quail,” Nat 295 (1982): 236; L.


pages: 436 words: 140,256

The Rise and Fall of the Third Chimpanzee by Jared Diamond

agricultural Revolution, assortative mating, Atahualpa, Columbian Exchange, correlation coefficient, double helix, Drosophila, European colonialism, invention of gunpowder, invention of the wheel, invention of writing, longitudinal study, out of africa, phenotype, Scientific racism, Search for Extraterrestrial Intelligence, the scientific method, trade route

Bell, 'Evolutionary and non-evolutionary theories of senescence', American Naturalist 124, pp. 600-3 (1984); E. Beutler, 'Planned obsolescence in humans and in other biosystems', Perspectives in Biology and Medicine 29, pp. 175-79 (1986); R.J. Goss, 'Why mammals don't regenerate—or do they? , News in Physiological Sciences 2, 112-15 (1987); L.D. Mueller, 'Evolution of accelerated senescence in laboratory populations of Drosophila, Proceedings of the National Academy of Sciences 84, pp. 1974-77 (1987); and T.B. Kirkwood, The nature and causes of ageing', pp. 193–206 in a book edited by D. Evered and J. Whelan, Research and the Ageing Population (John Wiley, Chichester, 1988). Two books exemplifying the physiological (proximate-cause) approach to aging are by R.L. Walford, The Immunologic Theory of Aging (Munksgaard, Copenhagen, 1969), and MacFarlane Burnett, Intrinsic Mutagenesis: A Genetic Approach to Ageing (John Wiley, New York, 1974).


Rainbows End by Vernor Vinge

Drosophila, failed state, MITM: man-in-the-middle, technological singularity, Vernor Vinge

The Stranger gave out one of its dismissive laughs, and Robert noticed Miri’s face jerk up. She might do better with this manipulator than Robert. After all, she wasn’t desperate for his help. “Ah, Miri, you read but you don’t understand. If you had access just now to the wider net — and a few hundred hours of research — perhaps you’d understand that molecular biology depends more on data depth and analysis than it does on the particular class of organism. In his Drosophila melanogaster alfredü — is that what you call them, Alfred? — we have the metabolic pathways that are the basis for all animal cognition.” Minus the editorial comments, this did look like some of the pdf. They rounded a corner and saw the source of the sounds. ” Viola, Alfred’s three hundred thousand fruit flies, now being folded into convenient shipping cartridges.” The Stranger’s face and body bore less and less resemblance to the original Sharif.


pages: 420 words: 130,714

Science in the Soul: Selected Writings of a Passionate Rationalist by Richard Dawkins

agricultural Revolution, Alfred Russel Wallace, anthropic principle, Any sufficiently advanced technology is indistinguishable from magic, Boris Johnson, David Attenborough, Donald Trump, double helix, Drosophila, epigenetics, Fellow of the Royal Society, Google Earth, John Harrison: Longitude, Kickstarter, lone genius, Mahatma Gandhi, mental accounting, Necker cube, nuclear winter, out of africa, p-value, phenotype, place-making, placebo effect, random walk, Ray Kurzweil, Richard Feynman, Search for Extraterrestrial Intelligence, stem cell, Stephen Hawking, Steve Wozniak, Steven Pinker, the scientific method, twin studies

After all, DC-8 saltations, such as the proposed macro-mutational elongation of the giraffe’s neck, may appear very complex: muscle blocks, vertebrae, nerves, blood vessels, all have to elongate together. Why does this not make it a 747 saltation, and therefore rule it out? We know that single mutations can orchestrate changes in growth rates of many diverse parts of organs, and, when we think about developmental processes, it is not in the least surprising that this should be so. When a single mutation causes a Drosophila to grow a leg where an antenna ought to be, the leg grows in all its formidable complexity. But this is not mysterious or surprising, not a 747 saltation, because the organization of a leg is already present in the body before the mutation. Wherever, as in embryogenesis, we have a hierarchically branching tree of causal relationships, a small alteration at a senior node of the tree can have large and complex ramified effects on the tips of the twigs.


The Science of Language by Noam Chomsky

Alan Turing: On Computable Numbers, with an Application to the Entscheidungsproblem, Alfred Russel Wallace, British Empire, Brownian motion, dark matter, Drosophila, epigenetics, finite state, Howard Zinn, phenotype, statistical model, stem cell, Steven Pinker, theory of mind

‘Canalization’ captures the remarkable fact that despite genetic variation and mutation within a genome and considerable environmental variation, plus a lot of variation in specific ‘input,’ the result of development is a stable and clearly distinct phenotype. It is generally agreed that canalization depends on fixed pathways of development. Waddington invented the term “chreodes” for these. Developmental biologists have not adopted his term, nor his related term “homeorhesis,” for biologically expressed processes that constitute such pathways of development. A lot has happened since Waddington's early (1940, 1942) work on canalization with drosophila wings and a ‘heat stress’ gene; the field draws a lot of attention now, and research continues. For a fairly recent review of developments and issues, see Salazar-Ciudad (2007). The contemporary research program known as “evo-devo” indicates clearly that development and growth are due to more than the genetic instructions contained in what are called “master” genes, the genes that specify that a creature will have, say, vision, or that some pattern will appear on butterfly wings, etc.


pages: 475 words: 134,707

The Hype Machine: How Social Media Disrupts Our Elections, Our Economy, and Our Health--And How We Must Adapt by Sinan Aral

Airbnb, Albert Einstein, Any sufficiently advanced technology is indistinguishable from magic, augmented reality, Bernie Sanders, bitcoin, carbon footprint, Cass Sunstein, computer vision, coronavirus, correlation does not imply causation, COVID-19, Covid-19, crowdsourcing, cryptocurrency, death of newspapers, disintermediation, Donald Trump, Drosophila, Edward Snowden, Elon Musk, en.wikipedia.org, Erik Brynjolfsson, experimental subject, facts on the ground, Filter Bubble, global pandemic, hive mind, illegal immigration, income inequality, Kickstarter, knowledge worker, longitudinal study, low skilled workers, Lyft, Mahatma Gandhi, Mark Zuckerberg, Menlo Park, meta analysis, meta-analysis, Metcalfe’s law, mobile money, move fast and break things, move fast and break things, multi-sided market, Nate Silver, natural language processing, Network effects, performance metric, phenotype, recommendation engine, Robert Bork, Robert Shiller, Robert Shiller, Second Machine Age, sentiment analysis, shareholder value, skunkworks, Snapchat, social graph, social intelligence, social software, social web, statistical model, stem cell, Stephen Hawking, Steve Jobs, Telecommunications Act of 1996, The Chicago School, The Wisdom of Crowds, theory of mind, Tim Cook: Apple, Uber and Lyft, uber lyft, WikiLeaks, Yogi Berra

., “Dorsal Raphe Dopamine Neurons Represent the Experience of Social Isolation,” Cell 164, no. 4 (2016): 617–31. Isolation is aversive and unsafe for social species: John T. Cacioppo, Stephanie Cacioppo, and Dorret I. Boomsma, “Evolutionary Mechanisms for Loneliness,” Cognition and Emotion 28, no. 1 (2014): 3–21. It decreases the life span of fruit flies: Hongyu Ruan and Chun-Fang Wu, “Social Interaction–Mediated Lifespan Extension of Drosophila Cu/Zn Superoxide Dismutase Mutants,” Proceedings of the National Academy of Sciences 105, no. 21 (2008): 7506–10. It promotes obesity and Type II diabetes: Katsunori Nonogaki, Kana Nozue, and Yoshitomo Oka, “Social Isolation Affects the Development of Obesity and Type 2 Diabetes in Mice,” Endocrinology 148, no. 10 (2007): 4658–66. It increases stress responses: Alexis M. Stranahan, David Khalil, and Elizabeth Gould, “Social Isolation Delays the Positive Effects of Running on Adult Neurogenesis,” Nature Neuroscience 9, no. 4 (2006): 526–33.


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Cooked: A Natural History of Transformation by Michael Pollan

biofilm, bioinformatics, Columbian Exchange, correlation does not imply causation, creative destruction, dematerialisation, Drosophila, energy security, Gary Taubes, Hernando de Soto, hygiene hypothesis, Kickstarter, Louis Pasteur, Mason jar, microbiome, peak oil, Ralph Waldo Emerson, Steven Pinker, women in the workforce

And they bare [it].When the ruler of the feast had tasted the water that was made wine, and knew not whence it was: (but the servants which drew the water knew) the governor of the feast called the bridegroom, And saith unto him, Every man at the beginning doth set forth good wine; and when men have well drunk, then that which is worse: [but] thou hast kept the good wine until now. “This beginning of miracles did Jesus in Cana of Galilee, and manifested forth his glory; and his disciples believed on him.” (John 2:7–11) * One species of fruit fly—Drosophila melanogaster—consumes alcohol as a way to medicate itself; the alcohol poisons a tiny parasitic wasp in its gut that otherwise would kill the fly. The alcohol kills the wasp by causing its internal organs to shoot out of its anus. Milan, Neil F., et al., “Alcohol Consumption as Self-Medication Against Blood-Borne Parasites in the Fruit Fly,” Current Biology 22 No. 6 (2012): 488–93


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The Precipice: Existential Risk and the Future of Humanity by Toby Ord

3D printing, agricultural Revolution, Albert Einstein, artificial general intelligence, Asilomar, Asilomar Conference on Recombinant DNA, availability heuristic, Columbian Exchange, computer vision, cosmological constant, cuban missile crisis, decarbonisation, defense in depth, delayed gratification, demographic transition, Doomsday Clock, Drosophila, effective altruism, Elon Musk, Ernest Rutherford, global pandemic, Intergovernmental Panel on Climate Change (IPCC), Isaac Newton, James Watt: steam engine, Mark Zuckerberg, mass immigration, meta analysis, meta-analysis, Mikhail Gorbachev, mutually assured destruction, Nash equilibrium, Norbert Wiener, nuclear winter, p-value, Peter Singer: altruism, planetary scale, race to the bottom, RAND corporation, Ronald Reagan, self-driving car, Stanislav Petrov, Stephen Hawking, Steven Pinker, Stewart Brand, supervolcano, survivorship bias, the scientific method, uranium enrichment

J. (1974). “The History of the Human Population.” Scientific American, 231(3), 40–51. Cohen, G. A. (2011). “Rescuing Conservatism: A Defense of Existing Value,” in Reasons and Recognition: Essays on the Philosophy of T. M. Scanlon (pp. 203–26). Oxford University Press. Cohen, M. N. (1989). Health and the Rise of Civilization. Yale University Press. Coles, L. S. (1994). “Computer Chess: The Drosophila of AI.” AI Expert, 9(4). Collingridge, D. (1982). The Social Control of Technology. St. Martin’s Press. Collins, G. S., Melosh, H. J., and Marcus, R. A. (2005). “Earth Impact Effects Program: A Web-Based Computer Program for Calculating the Regional Environmental Consequences of a Meteoroid Impact on Earth.” Meteoritics and Planetary Science, 40(6), 817–40. Collins, M., et al. (2013). “Long-Term Climate Change: Projections, Commitments and Irreversibility,” in T.


pages: 574 words: 164,509

Superintelligence: Paths, Dangers, Strategies by Nick Bostrom

agricultural Revolution, AI winter, Albert Einstein, algorithmic trading, anthropic principle, anti-communist, artificial general intelligence, autonomous vehicles, barriers to entry, Bayesian statistics, bioinformatics, brain emulation, cloud computing, combinatorial explosion, computer vision, cosmological constant, dark matter, DARPA: Urban Challenge, data acquisition, delayed gratification, demographic transition, different worldview, Donald Knuth, Douglas Hofstadter, Drosophila, Elon Musk, en.wikipedia.org, endogenous growth, epigenetics, fear of failure, Flash crash, Flynn Effect, friendly AI, Gödel, Escher, Bach, income inequality, industrial robot, informal economy, information retrieval, interchangeable parts, iterative process, job automation, John Markoff, John von Neumann, knowledge worker, longitudinal study, Menlo Park, meta analysis, meta-analysis, mutually assured destruction, Nash equilibrium, Netflix Prize, new economy, Norbert Wiener, NP-complete, nuclear winter, optical character recognition, pattern recognition, performance metric, phenotype, prediction markets, price stability, principal–agent problem, race to the bottom, random walk, Ray Kurzweil, recommendation engine, reversible computing, social graph, speech recognition, Stanislav Petrov, statistical model, stem cell, Stephen Hawking, strong AI, superintelligent machines, supervolcano, technological singularity, technoutopianism, The Coming Technological Singularity, The Nature of the Firm, Thomas Kuhn: the structure of scientific revolutions, transaction costs, Turing machine, Vernor Vinge, Watson beat the top human players on Jeopardy!, World Values Survey, zero-sum game

., Welker, E., and Svoboda, K. 2002. “Long-Term In Vivo Imaging of Experience-Dependent Synaptic Plasticity in Adult Cortex.” Nature 420 (6917): 788–94. Traub, Wesley A. 2012. “Terrestrial, Habitable-Zone Exoplanet Frequency from Kepler.” Astrophysical Journal 745 (1): 1–10. Truman, James W., Taylor, Barbara J., and Awad, Timothy A. 1993. “Formation of the Adult Nervous System.” In The Development of Drosophila Melanogaster, edited by Michael Bate and Alfonso Martinez Arias. Plainview, NY: Cold Spring Harbor Laboratory. Tuomi, Ilkka. 2002. “The Lives and the Death of Moore’s Law.” First Monday 7 (11). Turing, A. M. 1950. “Computing Machinery and Intelligence.” Mind 59 (236): 433–60. Turkheimer, Eric, Haley, Andreana, Waldron, Mary, D’Onofrio, Brian, and Gottesman, Irving I. 2003. “Socioeconomic Status Modifies Heritability of IQ in Young Children.”


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The Language Instinct: How the Mind Creates Language by Steven Pinker

Albert Einstein, cloud computing, David Attenborough, double helix, Drosophila, elephant in my pajamas, finite state, illegal immigration, Joan Didion, Loebner Prize, mass immigration, Maui Hawaii, meta analysis, meta-analysis, MITM: man-in-the-middle, natural language processing, out of africa, phenotype, rolodex, Ronald Reagan, Sapir-Whorf hypothesis, Saturday Night Live, speech recognition, Steven Pinker, theory of mind, transatlantic slave trade, Turing machine, Turing test, twin studies, Yogi Berra

The rule nicely interfaces with the mental dictionary: dog would be listed as a noun stem meaning “dog,” and -s would be listed as a noun inflection meaning “plural of.” This rule is the simplest, most stripped-down example of anything we would want to call a rule of grammar. In my laboratory we use it as an easily studied instance of mental grammar, allowing us to document in great detail the psychology of linguistic rules from infancy to old age in both normal and neurologically impaired people, in much the same way that biologists focus on the fruit fly Drosophila to study the machinery of genes. Though simple, the rule that glues an inflection to a stem is a surprisingly powerful computational operation. That is because it recognizes an abstract mental symbol, like “noun stem,” instead of being associated with a particular list of words or a particular list of sounds or a particular list of meanings. We can use the rule to inflect any item in the mental dictionary that lists “noun stem” in its entry, without caring what the word means; we can convert not only dog to dogs but also hour to hours and justification to justifications.


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Human Diversity: The Biology of Gender, Race, and Class by Charles Murray

23andMe, affirmative action, Albert Einstein, Alfred Russel Wallace, Asperger Syndrome, assortative mating, basic income, bioinformatics, Cass Sunstein, correlation coefficient, Daniel Kahneman / Amos Tversky, double helix, Drosophila, epigenetics, equal pay for equal work, European colonialism, feminist movement, glass ceiling, Gunnar Myrdal, income inequality, Kenneth Arrow, labor-force participation, longitudinal study, meta analysis, meta-analysis, out of africa, p-value, phenotype, publication bias, quantitative hedge fund, randomized controlled trial, replication crisis, Richard Thaler, risk tolerance, school vouchers, Scientific racism, selective serotonin reuptake inhibitor (SSRI), Silicon Valley, social intelligence, statistical model, Steven Pinker, The Bell Curve by Richard Herrnstein and Charles Murray, the scientific method, The Wealth of Nations by Adam Smith, theory of mind, Thomas Kuhn: the structure of scientific revolutions, twin studies, universal basic income, working-age population

Psychological Medicine 39 (2): 255–65. Bartels, M., C. E. M. van Beijsterveldt, and D. I. Boomsma. 2009. “Breastfeeding, Maternal Education and Cognitive Function: A Prospective Study in Twins.” Behavior Genetics 39: 616–22. Bartz, J. A., J. Zaki, N. Bolger et al. 2011. “Social Effects of Oxytocin in Humans: Context and Person Matter.” Trends in Cognitive Sciences 15 (7): 301–9. Bateman, A. J. 1948. “Intra-sexual Selection in Drosophila.” Heredity 2: 349. Bates, Timothy C., Narelle K. Hansell, Nicholas G. Martin et al. 2016. “When Does Socioeconomic Status (SES) Moderate the Heritability of IQ? No Evidence for G × SES Interaction for IQ in a Representative Sample of 1176 Australian Adolescent Twin Pairs.” Intelligence 56: 10–15. Bates, Timothy C., Gary J. Lewis, and Alexander Weiss. 2013. “Childhood Socioeconomic Status Amplifies Genetic Effects on Adult Intelligence.”


pages: 936 words: 252,313

Good Calories, Bad Calories: Challenging the Conventional Wisdom on Diet, Weight Control, and Disease by Gary Taubes

Albert Einstein, California gold rush, cognitive dissonance, collaborative editing, Drosophila, Everything should be made as simple as possible, experimental subject, Gary Taubes, invention of agriculture, John Snow's cholera map, longitudinal study, meta analysis, meta-analysis, phenotype, placebo effect, Ralph Nader, randomized controlled trial, Richard Feynman, Robert Gordon, selection bias, the scientific method, Thomas Kuhn: the structure of scientific revolutions, twin studies, unbiased observer, Upton Sinclair

American Journal of Public Health and the Nation’s Health. Feb.; 56(2):299–314. Christlieb, A. R., A. S. Krolweski, and J. H. Warram. 1994. “Hypertension.” In Kahn and Weir, eds., 1994, 817–35. Cioffi, L. A., W. P. James, and T. B. Van Itallie, eds. 1981. The Body Weight Regulatory System: Normal and Disturbed Mechanisms. New York: Raven Press. Clancy, D. J., D. Gems, L. G. Harshman, et al. 2001. “Extension of Life-Span by Loss of CHICO, a Drosophila Insulin Receptor Substrate Protein.” Science. April 6; 292(5514):104–6. Clarke, H. T. 1941. “Rudolf Schoenheimer.” Science. Dec. 12; 94(2450):553–54. Cleave, T. L. 1975. The Saccharine Disease: The Master Disease of Our Time. New Canaan, Conn.: Keats Publishing. ———. 1962. Peptic Ulcer. Bristol: John Wright & Sons. ———. 1956. “The Neglect of Natural Principles in Current Medical Practice.”


Hawaii by Jeff Campbell

airport security, big-box store, California gold rush, carbon footprint, centre right, Charles Lindbergh, commoditize, creative destruction, Drosophila, G4S, haute couture, land reform, lateral thinking, low-wage service sector, Maui Hawaii, polynesian navigation, risk/return, sustainable-tourism, upwardly mobile, urban sprawl, wage slave, white picket fence

These creepy-crawlies evolved from a mere 350 to 400 colonizing species; on average, every bug that was tossed into the jet stream and crash-landed successfully became two dozen new bugs uniquely adapted to various niches in Hawaii’s diverse island ecosystems. What puzzles scientists, though, is that there is no average rate. Some species hardly evolved at all, while others are off-the-charts: Drosophila flies evolved into over 600 species; Hyposmocoma moths evolved into over 350 species. Eight other insects account for over 100 species, some particular to only an acre or two. One of the most common adaptations was losing wings, or flightlessness. Most of Hawaii’s insects arrived by air – mainly beetles, small flies, wasps, moths, bugs and leafhoppers. Hawaii has no native ants, termites or cockroaches (or mayflies or bumble bees, or 85% of the world’s insect families).


Betrayal of Trust: The Collapse of Global Public Health by Laurie Garrett

accounting loophole / creative accounting, airport security, Albert Einstein, anti-communist, Ayatollah Khomeini, Berlin Wall, biofilm, clean water, collective bargaining, desegregation, discovery of DNA, discovery of penicillin, Drosophila, employer provided health coverage, Fall of the Berlin Wall, germ theory of disease, global pandemic, illegal immigration, indoor plumbing, Induced demand, John Snow's cholera map, Jones Act, Louis Pasteur, Mahatma Gandhi, mass incarceration, Maui Hawaii, means of production, Menlo Park, Mikhail Gorbachev, mouse model, Nelson Mandela, new economy, nuclear winter, phenotype, profit motive, Project Plowshare, RAND corporation, randomized controlled trial, Right to Buy, Ronald Reagan, sexual politics, Silicon Valley, stem cell, the scientific method, urban decay, urban renewal, War on Poverty, working poor, Works Progress Administration, yellow journalism

Cancer death rates first began a downward dip in 1992, largely due to lower tobacco smoking rates in the United States and associated declines in lung cancer deaths. In 1998 about half a million Americans died of cancers, primarily of the lung (160,000); colon (55,000); breast (44,000); and prostate (39,000). 59. Service, R. F. “Borrowing from biology to power the petite.” Science 283 (1999): 27–28. 60. See, for example, Dickson, D. “Ventner’s Drosophila ‘success’ set to boost human genome efforts.” Nature 401 (1999): 729; “Genome prospecting.” Special issue. Science 286 (1999): 443–31; Normille, D., and Pennisi, E. “Team wrapping up sequence of first human chromosome.” Science 285 (1999): 2038–39; “Special issue: The future of medicine.” Time (January 11, 1999); and Tang, Y. P., Shimizu, É., Dube, G. R., et al. “Genetic enhancement of learning and memory in mice.”


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Rationality: From AI to Zombies by Eliezer Yudkowsky

Albert Einstein, Alfred Russel Wallace, anthropic principle, anti-pattern, anti-work, Arthur Eddington, artificial general intelligence, availability heuristic, Bayesian statistics, Berlin Wall, Build a better mousetrap, Cass Sunstein, cellular automata, cognitive bias, cognitive dissonance, correlation does not imply causation, cosmological constant, creative destruction, Daniel Kahneman / Amos Tversky, dematerialisation, different worldview, discovery of DNA, Douglas Hofstadter, Drosophila, effective altruism, experimental subject, Extropian, friendly AI, fundamental attribution error, Gödel, Escher, Bach, hindsight bias, index card, index fund, Isaac Newton, John Conway, John von Neumann, Long Term Capital Management, Louis Pasteur, mental accounting, meta analysis, meta-analysis, money market fund, Nash equilibrium, Necker cube, NP-complete, P = NP, pattern recognition, Paul Graham, Peter Thiel, Pierre-Simon Laplace, placebo effect, planetary scale, prediction markets, random walk, Ray Kurzweil, reversible computing, Richard Feynman, risk tolerance, Rubik’s Cube, Saturday Night Live, Schrödinger's Cat, scientific mainstream, scientific worldview, sensible shoes, Silicon Valley, Silicon Valley startup, Singularitarianism, Solar eclipse in 1919, speech recognition, statistical model, Steven Pinker, strong AI, technological singularity, The Bell Curve by Richard Herrnstein and Charles Murray, the map is not the territory, the scientific method, Turing complete, Turing machine, ultimatum game, X Prize, Y Combinator, zero-sum game

In which case, if mice were to evolve the ability to fly and migrate for the winter, they would probably form a single reproductive population, and would evolve to extinction as the segregation-distorter evolved to fixation. Around 50% of the total genome of maize consists of transposons, DNA elements whose primary function is to copy themselves into other locations of DNA. A class of transposons called “P elements” seem to have first appeared in Drosophila only in the middle of the twentieth century, and spread to every population of the species within 50 years. The “Alu sequence” in humans, a 300-base transposon, is repeated between 300,000 and a million times in the human genome. This may not extinguish a species, but it doesn’t help it; transposons cause more mutations which are as always mostly harmful, decrease the effective copying fidelity of DNA.