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pages: 734 words: 244,010

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

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agricultural Revolution, Alfred Russel Wallace, complexity theory, delayed gratification, double helix, Drosophila, Haight Ashbury, invention of writing, Louis Pasteur, nuclear winter, out of africa, Peter Singer: altruism, phenotype, Richard Feynman, 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

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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.


Raw Data Is an Oxymoron by Lisa Gitelman

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collateralized debt obligation, computer age, continuous integration, crowdsourcing, Drosophila, Edmond Halley, Filter Bubble, Firefox, Google Earth, Howard Rheingold, index card, informal economy, Isaac Newton, Johann Wolfgang von Goethe, knowledge worker, Louis Daguerre, Menlo Park, optical character recognition, 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

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

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Albert Einstein, Andrei Shleifer, Benoit Mandelbrot, bitcoin, Brownian motion, Claude Shannon: information theory, cloud computing, cognitive dissonance, computer age, conceptual framework, crony capitalism, crowdsourcing, cuban missile crisis, Daniel Kahneman / Amos Tversky, David Graeber, Dissolution of the Soviet Union, double helix, Drosophila, Francis Fukuyama: the end of history, From Mathematics to the Technologies of Life and Death, hive mind, index card, informal economy, invisible hand, Jacquard loom, 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, pattern recognition, Paul Erdős, Peter Thiel, 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.


pages: 312 words: 86,770

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

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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: 506 words: 152,049

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

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Alfred Russel Wallace, Douglas Hofstadter, Drosophila, epigenetics, Gödel, Escher, Bach, impulse control, Menlo Park, Necker cube, p-value, phenotype, quantitative trading / quantitative finance, 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: 369 words: 153,018

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

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


pages: 465 words: 103,303

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

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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.


pages: 220 words: 66,518

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

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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, 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.”


pages: 357 words: 98,853

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

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dark matter, discovery of DNA, double helix, Downton Abbey, Drosophila, epigenetics, 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: 846 words: 232,630

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

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Albert Einstein, Alfred Russel Wallace, anthropic principle, 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, Richard Feynman, Rodney Brooks, Schrödinger's Cat, 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: 298 words: 81,200

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

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Ada Lovelace, Albert Einstein, Alfred Russel Wallace, carbon-based life, Cass Sunstein, cleantech, complexity theory, conceptual framework, cosmic microwave background, crowdsourcing, data acquisition, digital Maoism, discovery of DNA, Dmitri Mendeleev, double entry bookkeeping, double helix, 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, Jacquard loom, James Hargreaves, James Watt: steam engine, Jane Jacobs, Jaron Lanier, John Snow's cholera map, Joseph Schumpeter, Joseph-Marie Jacquard, Kevin Kelly, lone genius, Louis Daguerre, Louis Pasteur, Mason jar, 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: 265 words: 74,000

The Numerati by Stephen Baker

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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, 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.


pages: 291 words: 81,703

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

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Amazon Mechanical Turk, Black Swan, brain emulation, Brownian motion, Cass Sunstein, choice architecture, complexity theory, computer age, computer vision, 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, Khan Academy, labor-force participation, Loebner Prize, low skilled workers, manufacturing employment, Mark Zuckerberg, meta analysis, meta-analysis, microcredit, Narrative Science, Netflix Prize, Nicholas Carr, 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

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agricultural Revolution, Anne Wojcicki, Any sufficiently advanced technology is indistinguishable from magic, 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, Richard Feynman: Challenger O-ring, Ronald Reagan, Simon Singh, Skype, stem cell, Ted Kaczynski, the scientific method, Thomas Malthus, 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: 404 words: 131,034

Cosmos by Carl Sagan

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


pages: 476 words: 120,892

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

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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, 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: 357 words: 98,854

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

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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, stem cell, stochastic process, Thomas Kuhn: the structure of scientific revolutions

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: 287 words: 87,204

Erwin Schrodinger and the Quantum Revolution by John Gribbin

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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, John von Neumann, Richard Feynman, 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: 474 words: 136,787

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

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

., 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.


pages: 654 words: 204,260

A Short History of Nearly Everything by Bill Bryson

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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, 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: 798 words: 240,182

The Transhumanist Reader by Max More, Natasha Vita-More

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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, Drosophila, en.wikipedia.org, 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, Louis Pasteur, Menlo Park, meta analysis, meta-analysis, moral hazard, Network effects, Norbert Wiener, P = NP, pattern recognition, phenotype, positional goods, prediction markets, presumed consent, Ray Kurzweil, reversible computing, RFID, Richard Feynman, Ronald Reagan, silicon-based life, Singularitarianism, 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

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.


pages: 321 words: 85,893

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

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

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.


pages: 448 words: 84,462

Testing Extreme Programming by Lisa Crispin, Tip House

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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: 311 words: 94,732

The Rapture of the Nerds by Cory Doctorow, Charles Stross

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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, phenotype, Plutocrats, plutocrats, rent-seeking, Richard Feynman, 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: 336 words: 93,672

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

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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, Google Glasses, iterative process, linked data, mouse model, optical character recognition, pattern recognition, personalized medicine, phenotype, race to the bottom, Richard Feynman, Richard Feynman, Ronald Reagan, semantic web, speech recognition, stem cell, Steven Pinker, supply-chain management, Turing machine, 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: 380 words: 104,841

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

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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, 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: 322 words: 88,197

Wonderland: How Play Made the Modern World by Steven Johnson

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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, 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, Jacquard loom, Jacques de Vaucanson, James Watt: steam engine, Jane Jacobs, John von Neumann, joint-stock company, Joseph-Marie Jacquard, Landlord's Game, lone genius, megacity, Minecraft, Murano, Venice glass, music of the spheres, Necker cube, New Urbanism, Oculus Rift, On the Economy of Machinery and Manufactures, pattern recognition, 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, 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: 379 words: 113,656

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

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Berlin Wall, Bretton Woods, business process, corporate governance, Drosophila, Erdős number, experimental subject, Frank Gehry, Geoffrey West, Santa Fe Institute, invisible hand, Long Term Capital Management, market bubble, Milgram experiment, Murray Gell-Mann, Network effects, new economy, Norbert Wiener, Paul Erdős, rolodex, Ronald Coase, Silicon Valley, supply-chain management, The Nature of the Firm, The Wealth of Nations by Adam Smith, Toyota Production System, transaction costs, transcontinental railway, 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: 297 words: 96,509

Stumbling on Happiness by Daniel Gilbert

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Albert Einstein, cognitive dissonance, Drosophila, endowment effect, 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

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: 297 words: 96,509

Time Paradox by Philip, John Boyd Zimbardo

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Albert Einstein, cognitive dissonance, Drosophila, endowment effect, 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

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: 319 words: 90,965

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

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Albert Einstein, barriers to entry, Berlin Wall, business intelligence, carbon-based life, Claude Shannon: information theory, complexity theory, declining real wages, deliberate practice, discrete time, double helix, Douglas Engelbart, Downton Abbey, Drosophila, Firefox, Frank Gehry, Google X / Alphabet X, informal economy, invention of the printing press, inventory management, Khan Academy, Kickstarter, low skilled workers, Lyft, 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, 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, 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.


pages: 346 words: 92,984

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

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3D printing, 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, 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: 436 words: 140,256

The Rise and Fall of the Third Chimpanzee by Jared Diamond

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agricultural Revolution, Atahualpa, Columbian Exchange, correlation coefficient, double helix, Drosophila, European colonialism, invention of gunpowder, invention of the wheel, invention of writing, out of africa, phenotype, Scientific racism, Search for Extraterrestrial Intelligence, the scientific method, trade route, V2 rocket

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).


pages: 574 words: 164,509

Superintelligence: Paths, Dangers, Strategies by Nick Bostrom

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agricultural Revolution, AI winter, Albert Einstein, algorithmic trading, anthropic principle, anti-communist, artificial general intelligence, autonomous vehicles, barriers to entry, bioinformatics, brain emulation, cloud computing, combinatorial explosion, computer vision, cosmological constant, dark matter, DARPA: Urban Challenge, data acquisition, delayed gratification, demographic transition, Douglas Hofstadter, Drosophila, Elon Musk, en.wikipedia.org, 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 von Neumann, knowledge worker, 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

., 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.”


pages: 372 words: 111,573

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

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Asperger Syndrome, Barry Marshall: ulcers, Berlin Wall, biofilm, clean water, correlation does not imply causation, discovery of penicillin, Drosophila, Fall of the Berlin Wall, friendly fire, germ theory of disease, Ignaz Semmelweis: hand washing, illegal immigration, John Snow's cholera map, 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: 476 words: 148,895

Cooked: A Natural History of Transformation by Michael Pollan

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biofilm, bioinformatics, Columbian Exchange, correlation does not imply causation, dematerialisation, Drosophila, energy security, Gary Taubes, Hernando de Soto, 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


The Science of Language by Noam Chomsky

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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: 382 words: 115,172

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

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biofilm, British Empire, Colonization of Mars, cuban missile crisis, double helix, Drosophila, epigenetics, life extension, Mahatma Gandhi, meta analysis, meta-analysis, microbiome, phenotype, randomized controlled trial, Steve Jobs

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: 936 words: 252,313

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

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Albert Einstein, California gold rush, cognitive dissonance, collaborative editing, Drosophila, experimental subject, Gary Taubes, invention of agriculture, John Snow's cholera map, meta analysis, meta-analysis, phenotype, placebo effect, Ralph Nader, randomized controlled trial, Richard Feynman, Richard Feynman, Robert Gordon, the scientific method, Thomas Kuhn: the structure of scientific revolutions, 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.”


pages: 661 words: 187,613

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

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Albert Einstein, cloud computing, David Attenborough, double helix, Drosophila, elephant in my pajamas, finite state, illegal immigration, Loebner Prize, Maui Hawaii, meta analysis, meta-analysis, natural language processing, out of africa, P = NP, phenotype, rolodex, Ronald Reagan, Saturday Night Live, speech recognition, Steven Pinker, theory of mind, transatlantic slave trade, Turing machine, Turing test, 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.