November 2011 science
Talk Magazines!!!!! New Yorker, Science, Atlantic, Mad......
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1qebo
The goal: through June 2011 by the end of this year, so April and part or all of May this month.
2qebo
April 2011
The Inflation Debate by Paul Steinhardt
Well, I read this, but I don't understand it. And I'm not interested enough to try very hard. Extrapolate back from what universe is now to a very early state. This state does not match the big bang. There is a gap, from about 10^-35 to 10^-30 seconds. In the early 1980s, Alan Guth proposed that the gap could be filled with cosmic inflation, the consequence of a force that repulsed rather than attracted. This idea has fit with unified theories of physics (e.g. string theory), and also with observations. However, there are issues. Only a small fraction of possible initial conditions, and only precise tuning of possible parameters, would result in the current observed state of the universe. And with "quantum jittering", inflation continues forever in most of space. Wherever it stops, a bubble forms. We live in one bubble among an infinite number of bubbles with an infinite variety of properties; anything that can happen does happen, so predictions cannot be tested. The author and colleagues propose an alternative: cyclic theory, in which the big bang is not the beginning, but a bounce from a previous contraction.
Animation: http://www.scientificamerican.com/article.cfm?id=inflation-creates-infinity-univ...
The Enemy Within by Maryn McKenna
Gram-negative bacteria have a double membrane that is difficult to penetrate, and exchange DNA more easily than gram-positive bacteria. This makes development of new antibiotics more difficult, and resistance to existing antibiotics more easily spread. The gram-negative Klebsiella pneumoniae is a common infection in hospital ICUs. In 1996, a sample was found to be resistant to some carbapenems, a class of antibiotic typically used as a last resort. A gene encodes an enzyme that attacks the carbapenem before it crosses the double membrane. Since then, the resistant gene has been traced from North Carolina to New York to the world at large, and has been found in the gram-negative E. coli also. Antibiotic development takes about a decade, and there is nothing in the pipeline for gram-negative bacteria.
Neuroscience in the Courtroom by Michael Gazzaniga
fMRIs show brain activity, but interpretations are far from definitive. However, as research continues, they may become admissible as supporting evidence in trials, both answering or raising questions about personal responsibility. Not ready for prime time, but the issues should be considered now.
Can the Dead Sea Live? by Eitan Haddock
The Jordan River once contributed 1300 million cubic meters of water per year to the Dead Sea; now the number is 30 million because the water is taken by surrounding countries. Evaporation exceeds replenishment, the sea is receding, and sinkholes are forming around it. A proposed solution is to transfer water from the Red Sea. This is not universally endorsed because of possible side effects.
Photos: http://www.scientificamerican.com/article.cfm?id=haddok-dead-sea-disappearing
Solving the Cocktail Party Problem by Graham Collins
People in a crowd can focus on one conversation or another. Computers can't. The standard computer method for a single strand is to apply statistics to build phonemes into words. With multiple strands, there are too many possibilities. One approach is to alternate standards analysis with separating voices (e.g. one is louder than the other), refining iteratively.
The Orderly Chaos of Proteins by Keith Dunker and Richard Kriwacki
Since the 1890s, it has been supposed that virtually all proteins are rigid 3-D structures that bind with other molecules lock-and-key. But many are more flexible, and can reconfigure to bind with multiple targets. This has been known in a smattering of cases since the early 1900s, but only recently understood to be common. The structure of proteins is determined with a nuclear magnetic resonance (NMR) spectrometer. The protein p27 is an example; it has sections that fold and unfold into temporary structures that bind to and inhibit various kinase enzymes, which attach phosphates to other proteins and set off a cascade of events. p27 regulates cell division, and there is less of it in cancer cells. The protein calcineurin has a lock-and-key mechanism to remove phosphates from other proteins, and an unstructured region that can bind to the structured region; the protein inactivates itself. About 600 partially or totally unstructured proteins have been identified; there are 100,000 or so proteins in the human body. Research indicates that more complex organisms tend to have a higher proportion of flexible proteins, possibly as high as 35 percent in humans. As a general rule, unstructured proteins are better at signalling and regulation, necessary to coordinate activity within and between cells, but this does not mean they evolved later. Proteins composed of hydrophilic amino acids tend to be less structured than proteins composed of hydrophobic amino acids, and the trend of amino acid evolution was hydrophobic to hydrophilic. In the RNA world, a plausible candidate for the origin of life, RNA functions included catalysis (now the responsibility of proteins) and genetic information storage (now the responsibility of DNA). Possibly as proteins became more structured, they were better able to replace RNA in catalysis.
Animation: http://www.scientificamerican.com/article.cfm?id=flexible-proteins-web-extra
Seconds Before the Big One by Richard Allen
An earthquakes consists of two waves: p-wave (primary) and s-wave (shear). Although the timing and location of earthquakes is unpredictable, p-waves, which don't cause much damage, can be detected before s-waves, which do. A 30-second warning, if properly integrated with communication and response systems, is enough for equipment to be shut down, for example. Japan and Mexico have such warning and response systems. The US does not. Seismic detectors in California are concentrated around Los Angeles and San Francisco, but need to be placed about every 15 miles in between; accuracy is improved with data from multiple varied locations.
Animation: http://www.scientificamerican.com/article.cfm?id=quakes-slow-march-big-earthquak...
Food Fight by Brendan Borrell
Interview with Roger Beachy, director of the National Institute of Food and Agriculture (at the time of publication; he departed shortly afterward: http://news.sciencemag.org/scienceinsider/2011/04/beachy-to-leave-key-agricultur.... After childhood on an Amish farm in Ohio, he became a plant biologist specializing in genetically modified crops. This is not a contradiction; plants that are resistant to disease require less pesticide.
Natural-Born Killer by Kenneth Catania
The tentacled snake of southeast Asia is an aquatic snake with, per its name, tentacles. The author set out to determine the function of the tentacles, observed its behavior, and shifted focus. More interesting than the snake, to me, is a diagram of the fish neuron and muscle reflex for rapid escape from most predators. Alas, not escape from the tentacled snake, which triggers the fish to do its thing, and loops around to catch it; experiments have shown this is innate motion, not prediction of fish location. BTW, the tentacles sense presence of fish, as surmised.
Video: http://www.scientificamerican.com/article.cfm?id=catania-tentacled-snake-capture...
The Inflation Debate by Paul Steinhardt
Well, I read this, but I don't understand it. And I'm not interested enough to try very hard. Extrapolate back from what universe is now to a very early state. This state does not match the big bang. There is a gap, from about 10^-35 to 10^-30 seconds. In the early 1980s, Alan Guth proposed that the gap could be filled with cosmic inflation, the consequence of a force that repulsed rather than attracted. This idea has fit with unified theories of physics (e.g. string theory), and also with observations. However, there are issues. Only a small fraction of possible initial conditions, and only precise tuning of possible parameters, would result in the current observed state of the universe. And with "quantum jittering", inflation continues forever in most of space. Wherever it stops, a bubble forms. We live in one bubble among an infinite number of bubbles with an infinite variety of properties; anything that can happen does happen, so predictions cannot be tested. The author and colleagues propose an alternative: cyclic theory, in which the big bang is not the beginning, but a bounce from a previous contraction.
Animation: http://www.scientificamerican.com/article.cfm?id=inflation-creates-infinity-univ...
The Enemy Within by Maryn McKenna
Gram-negative bacteria have a double membrane that is difficult to penetrate, and exchange DNA more easily than gram-positive bacteria. This makes development of new antibiotics more difficult, and resistance to existing antibiotics more easily spread. The gram-negative Klebsiella pneumoniae is a common infection in hospital ICUs. In 1996, a sample was found to be resistant to some carbapenems, a class of antibiotic typically used as a last resort. A gene encodes an enzyme that attacks the carbapenem before it crosses the double membrane. Since then, the resistant gene has been traced from North Carolina to New York to the world at large, and has been found in the gram-negative E. coli also. Antibiotic development takes about a decade, and there is nothing in the pipeline for gram-negative bacteria.
Neuroscience in the Courtroom by Michael Gazzaniga
fMRIs show brain activity, but interpretations are far from definitive. However, as research continues, they may become admissible as supporting evidence in trials, both answering or raising questions about personal responsibility. Not ready for prime time, but the issues should be considered now.
Can the Dead Sea Live? by Eitan Haddock
The Jordan River once contributed 1300 million cubic meters of water per year to the Dead Sea; now the number is 30 million because the water is taken by surrounding countries. Evaporation exceeds replenishment, the sea is receding, and sinkholes are forming around it. A proposed solution is to transfer water from the Red Sea. This is not universally endorsed because of possible side effects.
Photos: http://www.scientificamerican.com/article.cfm?id=haddok-dead-sea-disappearing
Solving the Cocktail Party Problem by Graham Collins
People in a crowd can focus on one conversation or another. Computers can't. The standard computer method for a single strand is to apply statistics to build phonemes into words. With multiple strands, there are too many possibilities. One approach is to alternate standards analysis with separating voices (e.g. one is louder than the other), refining iteratively.
The Orderly Chaos of Proteins by Keith Dunker and Richard Kriwacki
Since the 1890s, it has been supposed that virtually all proteins are rigid 3-D structures that bind with other molecules lock-and-key. But many are more flexible, and can reconfigure to bind with multiple targets. This has been known in a smattering of cases since the early 1900s, but only recently understood to be common. The structure of proteins is determined with a nuclear magnetic resonance (NMR) spectrometer. The protein p27 is an example; it has sections that fold and unfold into temporary structures that bind to and inhibit various kinase enzymes, which attach phosphates to other proteins and set off a cascade of events. p27 regulates cell division, and there is less of it in cancer cells. The protein calcineurin has a lock-and-key mechanism to remove phosphates from other proteins, and an unstructured region that can bind to the structured region; the protein inactivates itself. About 600 partially or totally unstructured proteins have been identified; there are 100,000 or so proteins in the human body. Research indicates that more complex organisms tend to have a higher proportion of flexible proteins, possibly as high as 35 percent in humans. As a general rule, unstructured proteins are better at signalling and regulation, necessary to coordinate activity within and between cells, but this does not mean they evolved later. Proteins composed of hydrophilic amino acids tend to be less structured than proteins composed of hydrophobic amino acids, and the trend of amino acid evolution was hydrophobic to hydrophilic. In the RNA world, a plausible candidate for the origin of life, RNA functions included catalysis (now the responsibility of proteins) and genetic information storage (now the responsibility of DNA). Possibly as proteins became more structured, they were better able to replace RNA in catalysis.
Animation: http://www.scientificamerican.com/article.cfm?id=flexible-proteins-web-extra
Seconds Before the Big One by Richard Allen
An earthquakes consists of two waves: p-wave (primary) and s-wave (shear). Although the timing and location of earthquakes is unpredictable, p-waves, which don't cause much damage, can be detected before s-waves, which do. A 30-second warning, if properly integrated with communication and response systems, is enough for equipment to be shut down, for example. Japan and Mexico have such warning and response systems. The US does not. Seismic detectors in California are concentrated around Los Angeles and San Francisco, but need to be placed about every 15 miles in between; accuracy is improved with data from multiple varied locations.
Animation: http://www.scientificamerican.com/article.cfm?id=quakes-slow-march-big-earthquak...
Food Fight by Brendan Borrell
Interview with Roger Beachy, director of the National Institute of Food and Agriculture (at the time of publication; he departed shortly afterward: http://news.sciencemag.org/scienceinsider/2011/04/beachy-to-leave-key-agricultur.... After childhood on an Amish farm in Ohio, he became a plant biologist specializing in genetically modified crops. This is not a contradiction; plants that are resistant to disease require less pesticide.
Natural-Born Killer by Kenneth Catania
The tentacled snake of southeast Asia is an aquatic snake with, per its name, tentacles. The author set out to determine the function of the tentacles, observed its behavior, and shifted focus. More interesting than the snake, to me, is a diagram of the fish neuron and muscle reflex for rapid escape from most predators. Alas, not escape from the tentacled snake, which triggers the fish to do its thing, and loops around to catch it; experiments have shown this is innate motion, not prediction of fish location. BTW, the tentacles sense presence of fish, as surmised.
Video: http://www.scientificamerican.com/article.cfm?id=catania-tentacled-snake-capture...
3qebo
Following up on various articles about brain connections and gene expression, a TED talk re brain maps: http://www.ted.com/talks/allan_jones_a_map_of_the_brain.html. Brains are sliced and stained, and tissue RNA is tagged, to determine which genes are activated in each of 1000ish samples. Results go into a publicly accessible database: http://www.brain-map.org/, and can be viewed in the downloadable desktop application Brain Explorer: http://human.brain-map.org/explorer.html.
4qebo
May 2011
7 Radical Energy Solutions
Potential for huge impact if successful, but it's a big if. I skimmed; not sufficiently knowledgeable about or interested in mechanics. Each is accompanied by a small diagram.
Video: http://www.scientificamerican.com/article.cfm?id=radical-energy-solutions-intera...
The Lost Galaxies by James Geach
Dark matter and dark energy constitute 96% of the universe. Baryonic matter (w/ neutrons and protons, the stuff we're familiar with) is the remainder, and only 10% of it is accounted for. Working backward from current conditions of the universe, it's possible to determine the amount of matter at different stages since the big bang. 5 billion years after the big bang, baryonic matter had not collapsed into galaxies. In the 9 billion years since, most has gone missing. Maybe it's WHIM (warm-hot intergalactic medium), which is detectable, with difficulty, if conditions are right, and is now being mapped. Galaxies, it seems, are fluid systems more than stable structures.
Animation: http://www.scientificamerican.com/article.cfm?id=geach-galactic-growth-spurt
The Hidden Organ in Our Eyes by Ignacio Provencio
Mice genetically engineered to lack rods and cones cannot see, but can still adjust their circadian clocks to light and dark. If eyes are surgically removed, the mice cannot adjust their circadian clocks. Although it has been known that photoreceptors exist for functions other than vision, discovering them in eyes was a surprise; cells of the retina have been studied for 150 years. Vertebrate retinas have three layers: rods and cones are deepest, and information is transferred through the middle layer to ganglion cells on the surface. The rods and cones detect light with optins, a class of protein pigments. A study of cells in the tails of tadpoles revealed a related protein, melanopsin, which darkens in the presence of light, even when cultured in a dish. This protein is not in rod and cone cells, but it is in ganglion cells. Mice genetically engineered to lack the gene for melanopsin were expected not to have a non-visual response to light, but this turned out to be wrong. The cells that make melanopsin are necessary for circadian clocks, but either melanopsin or rods and cones will do. The article has a useful diagram summarizing the experimental results.
Related: http://www.scientificamerican.com/article.cfm?id=circadian-diseases-and-remedies
The Strangest Numbers in String Theory by John Baez and John Huerta
Complex numbers (a + bi), discovered by Gerolamo Cardano in the 1500s, describe transformations in 2-dimensional space. Quaternions (a + bi + cj + dk), discovered by William Hamilton in 1843, describe transformations in 3-dimensional space. Why four numbers for three dimensions? The numbers correspond to pitch (angle up or down), yaw (angle left or right)), roll (angle of wings), and stretching/shrinking. Octonions were discovered by John Graves, a friend of Hamilton, but also by Arthur Cayley, who published first and got the credit in 1845, and describe transformations in 8-dimensional space. Supersymmetry theory, which is not yet supported by experimental evidence, has it that every matter particle has partner force particle, and that the laws of physics would be unchanged if matter and force particles were interchanged. Quantum mechanics in its standard 3-dimensional version has spinors that describe wave motion of matter particles, and vectors that describe wave motion of force particles, but an inelegant system for describing the interactions of matter and force particles. In a universe with without time, vectors and spinors coincide in 1-, 2-, 4-, 8-dimensional space, and supersymmetry gives a unified description of matter and force. In string theory, a 1-dimensional string traces a 2-dimensional surface over time; if dimensions for the string and time are added, supersymmetry arises in 3, 4, 6, 10 dimensions. In M-theory, a 2-dimensional membrane traces a 3-dimensional volume over time; if dimensions for the membrane and time are added, supersymmetry arises in 4, 5, 7, 11 dimensions. Neither string theory nor M-theory has devised any experimentally testable predictions. But physicists are attracted to the mathematical elegance.
(I should stress that I do not understand this... I am merely extracting assertions from the article.)
Video: http://www.scientificamerican.com/article.cfm?id=octonions-web-exclusive
Fast Track to Vaccines by Alan Aderem
An ideal vaccine evokes a sequence of reactions: dendritic cells absorb antigens and travel to the lymph nodes, where they pass the antigens to T cells. Killer T cells identify and destroy infected cells. Helper T cells interact with B cells to generate antibodies. Memory T cells and memory B cells remain and become active when similar antigens invade. The yellow fever vaccine is ideal. HIV vaccines so far have not been. What's the difference? The field of "systems biology" investigates. The yellow fever vaccine was given to volunteers, and their blood was tested at several points afterward to see which genes were activated and develop a "signature of protection". Since there is no ideal HIV vaccine, tests have been done with various SIV vaccines given to monkeys. The goal is to reduce the effort to create vaccines. Traditionally, rounds of basic research to develop a vaccine formula are followed by a series of formal and expensive clinical trials as the formula is tweaked. In the systems biology approach, the initial formula can be tweaked and analyzed for its match to the signature more easily before it reaches the stage of clinical trials.
Video: http://www.scientificamerican.com/article.cfm?id=systems-video-untagles-old-myst...
The Space Station's Crown Jewel by George Musser
The Alpha Magnetic Spectrometer was delivered to the International Space Station in May. It detects cosmic rays. "Cosmic rays are subatomic particles and atomic nuclei that zip and zap through space, coming from ordinary stars, supernovae explosions, neutron stars, black holes and who knows what -- the last category naturally being of greatest interest and the main impetus for a brand-new instrument."
Video: http://www.scientificamerican.com/article.cfm?id=ams-additional-resources
The Growing Menace from Superweeds by Jerry Adler
The active ingredient in the herbicide Roundup is glyphosate, which inhibits the EPSPS enzyme that builds three amino acids essential to plants and bacteria but not to animals. It must be applied directly to leaves, and it is not selective; it kills all plants. The solution: glyphosate resistant crops, developed in the early 1990s. This worked for awhile, but glyphosate resistance has evolved in the weeds. This is a different mechanism than the Roundup Ready plants; the gene did not jump. The resistance comes in two forms. In one, the gene for EPSPS is replicated, so the amount of ESPS overwhelms the amount of herbicide. In the other, it's not yet clear what is happening; the plant sacrifices its lower leaves but retains its meristem which produces new growth.
Info: http://www.scientificamerican.com/article.cfm?id=superweeds-farming-threat-ragwe...
Masters of Disguise by Peter Forbes
Mimicry is an ideal subject of study for evolutionary biologists because the selection pressure (predation) and the traits under selection (perceivable by others) are clear. One example: Caterpillars of the large blue Maculinea arion butterfly of Europe and Asia emit a chemical that attracts Myrmica sabuleti ants. The ants carry the caterpillars to their nest, where the caterpillars eat ant larvae. The ants don't merely tolerate the caterpillars; they actively kill larvae to feed them. Why? The caterpillars emit an sound that mimics the queen. Another example: The Heliconius butterfly wing pattern, which mimics... (what? the article doesn't say) is also an identifier of potential mates. The gene for wing color is linked to the gene for mate choice (there's a gene for this?). This is a mechanism for speciation, and indeed in Costa Rica two wing patterns are near to becoming two species.
Photos: http://www.scientificamerican.com/article.cfm?id=forbes-animal-disguises-avoid-p...
Inner Sparks by Alicia Anstead
Interview with Charles Limb, ENT surgeon who specializes in cochlear implants, and saxophone player. He specializes in hearing because he loves music, and one focus of research is why people with cochlear implants have trouble with music perception. Another focus is is creativity. He has devised a keyboard that can be played while the head is inside an MRI machine. During improvisation, the prefrontal cortex changes: activity decreases in the lateral prefrontal region involved in conscious self-monitoring and self-inhibition, and activity increases in the medial prefrontal region involved in self-expression.
Video: http://www.scientificamerican.com/article.cfm?id=anstead-limb-your-brain-on-jazz
So it's taken me three hours this morning to summarize several articles that I couldn't manage to deal with quickly when I initially read them. I'm unconvinced this is a worthwhile effort, and yet, it does force me to reread and kind of understand, enough to articulate plausible sentences and retain a mental infrastructure, even if the vast audience of this thread does not care.
7 Radical Energy Solutions
Potential for huge impact if successful, but it's a big if. I skimmed; not sufficiently knowledgeable about or interested in mechanics. Each is accompanied by a small diagram.
Video: http://www.scientificamerican.com/article.cfm?id=radical-energy-solutions-intera...
The Lost Galaxies by James Geach
Dark matter and dark energy constitute 96% of the universe. Baryonic matter (w/ neutrons and protons, the stuff we're familiar with) is the remainder, and only 10% of it is accounted for. Working backward from current conditions of the universe, it's possible to determine the amount of matter at different stages since the big bang. 5 billion years after the big bang, baryonic matter had not collapsed into galaxies. In the 9 billion years since, most has gone missing. Maybe it's WHIM (warm-hot intergalactic medium), which is detectable, with difficulty, if conditions are right, and is now being mapped. Galaxies, it seems, are fluid systems more than stable structures.
Animation: http://www.scientificamerican.com/article.cfm?id=geach-galactic-growth-spurt
The Hidden Organ in Our Eyes by Ignacio Provencio
Mice genetically engineered to lack rods and cones cannot see, but can still adjust their circadian clocks to light and dark. If eyes are surgically removed, the mice cannot adjust their circadian clocks. Although it has been known that photoreceptors exist for functions other than vision, discovering them in eyes was a surprise; cells of the retina have been studied for 150 years. Vertebrate retinas have three layers: rods and cones are deepest, and information is transferred through the middle layer to ganglion cells on the surface. The rods and cones detect light with optins, a class of protein pigments. A study of cells in the tails of tadpoles revealed a related protein, melanopsin, which darkens in the presence of light, even when cultured in a dish. This protein is not in rod and cone cells, but it is in ganglion cells. Mice genetically engineered to lack the gene for melanopsin were expected not to have a non-visual response to light, but this turned out to be wrong. The cells that make melanopsin are necessary for circadian clocks, but either melanopsin or rods and cones will do. The article has a useful diagram summarizing the experimental results.
Related: http://www.scientificamerican.com/article.cfm?id=circadian-diseases-and-remedies
The Strangest Numbers in String Theory by John Baez and John Huerta
Complex numbers (a + bi), discovered by Gerolamo Cardano in the 1500s, describe transformations in 2-dimensional space. Quaternions (a + bi + cj + dk), discovered by William Hamilton in 1843, describe transformations in 3-dimensional space. Why four numbers for three dimensions? The numbers correspond to pitch (angle up or down), yaw (angle left or right)), roll (angle of wings), and stretching/shrinking. Octonions were discovered by John Graves, a friend of Hamilton, but also by Arthur Cayley, who published first and got the credit in 1845, and describe transformations in 8-dimensional space. Supersymmetry theory, which is not yet supported by experimental evidence, has it that every matter particle has partner force particle, and that the laws of physics would be unchanged if matter and force particles were interchanged. Quantum mechanics in its standard 3-dimensional version has spinors that describe wave motion of matter particles, and vectors that describe wave motion of force particles, but an inelegant system for describing the interactions of matter and force particles. In a universe with without time, vectors and spinors coincide in 1-, 2-, 4-, 8-dimensional space, and supersymmetry gives a unified description of matter and force. In string theory, a 1-dimensional string traces a 2-dimensional surface over time; if dimensions for the string and time are added, supersymmetry arises in 3, 4, 6, 10 dimensions. In M-theory, a 2-dimensional membrane traces a 3-dimensional volume over time; if dimensions for the membrane and time are added, supersymmetry arises in 4, 5, 7, 11 dimensions. Neither string theory nor M-theory has devised any experimentally testable predictions. But physicists are attracted to the mathematical elegance.
(I should stress that I do not understand this... I am merely extracting assertions from the article.)
Video: http://www.scientificamerican.com/article.cfm?id=octonions-web-exclusive
Fast Track to Vaccines by Alan Aderem
An ideal vaccine evokes a sequence of reactions: dendritic cells absorb antigens and travel to the lymph nodes, where they pass the antigens to T cells. Killer T cells identify and destroy infected cells. Helper T cells interact with B cells to generate antibodies. Memory T cells and memory B cells remain and become active when similar antigens invade. The yellow fever vaccine is ideal. HIV vaccines so far have not been. What's the difference? The field of "systems biology" investigates. The yellow fever vaccine was given to volunteers, and their blood was tested at several points afterward to see which genes were activated and develop a "signature of protection". Since there is no ideal HIV vaccine, tests have been done with various SIV vaccines given to monkeys. The goal is to reduce the effort to create vaccines. Traditionally, rounds of basic research to develop a vaccine formula are followed by a series of formal and expensive clinical trials as the formula is tweaked. In the systems biology approach, the initial formula can be tweaked and analyzed for its match to the signature more easily before it reaches the stage of clinical trials.
Video: http://www.scientificamerican.com/article.cfm?id=systems-video-untagles-old-myst...
The Space Station's Crown Jewel by George Musser
The Alpha Magnetic Spectrometer was delivered to the International Space Station in May. It detects cosmic rays. "Cosmic rays are subatomic particles and atomic nuclei that zip and zap through space, coming from ordinary stars, supernovae explosions, neutron stars, black holes and who knows what -- the last category naturally being of greatest interest and the main impetus for a brand-new instrument."
Video: http://www.scientificamerican.com/article.cfm?id=ams-additional-resources
The Growing Menace from Superweeds by Jerry Adler
The active ingredient in the herbicide Roundup is glyphosate, which inhibits the EPSPS enzyme that builds three amino acids essential to plants and bacteria but not to animals. It must be applied directly to leaves, and it is not selective; it kills all plants. The solution: glyphosate resistant crops, developed in the early 1990s. This worked for awhile, but glyphosate resistance has evolved in the weeds. This is a different mechanism than the Roundup Ready plants; the gene did not jump. The resistance comes in two forms. In one, the gene for EPSPS is replicated, so the amount of ESPS overwhelms the amount of herbicide. In the other, it's not yet clear what is happening; the plant sacrifices its lower leaves but retains its meristem which produces new growth.
Info: http://www.scientificamerican.com/article.cfm?id=superweeds-farming-threat-ragwe...
Masters of Disguise by Peter Forbes
Mimicry is an ideal subject of study for evolutionary biologists because the selection pressure (predation) and the traits under selection (perceivable by others) are clear. One example: Caterpillars of the large blue Maculinea arion butterfly of Europe and Asia emit a chemical that attracts Myrmica sabuleti ants. The ants carry the caterpillars to their nest, where the caterpillars eat ant larvae. The ants don't merely tolerate the caterpillars; they actively kill larvae to feed them. Why? The caterpillars emit an sound that mimics the queen. Another example: The Heliconius butterfly wing pattern, which mimics... (what? the article doesn't say) is also an identifier of potential mates. The gene for wing color is linked to the gene for mate choice (there's a gene for this?). This is a mechanism for speciation, and indeed in Costa Rica two wing patterns are near to becoming two species.
Photos: http://www.scientificamerican.com/article.cfm?id=forbes-animal-disguises-avoid-p...
Inner Sparks by Alicia Anstead
Interview with Charles Limb, ENT surgeon who specializes in cochlear implants, and saxophone player. He specializes in hearing because he loves music, and one focus of research is why people with cochlear implants have trouble with music perception. Another focus is is creativity. He has devised a keyboard that can be played while the head is inside an MRI machine. During improvisation, the prefrontal cortex changes: activity decreases in the lateral prefrontal region involved in conscious self-monitoring and self-inhibition, and activity increases in the medial prefrontal region involved in self-expression.
Video: http://www.scientificamerican.com/article.cfm?id=anstead-limb-your-brain-on-jazz
So it's taken me three hours this morning to summarize several articles that I couldn't manage to deal with quickly when I initially read them. I'm unconvinced this is a worthwhile effort, and yet, it does force me to reread and kind of understand, enough to articulate plausible sentences and retain a mental infrastructure, even if the vast audience of this thread does not care.
6sibylline
I really appreciate this effort Q -- esp posting the links to the videos. I've forwarded several to the spousal unit.
7qebo
June 2011
Living in a Quantum World by Vlatko Vedral
Quantum physics is supposed to be confined to microscopic scales, but recent experiments are revealing quantum effects in macroscopic systems. Example #1: Atoms in a salt crystal were expected to show quantum effects only at the level of individual molecules, but they line up with a magnetic field more quickly than predicted by classical physics, indicating coordination by quantum entanglement. Example #2: Migrating robins are oblivious to magnetic field direction, but sensitive to its inclination -- unless blindfolded. A theory supported by circumstantial evidence but not yet confirmed is that the eye has a molecule with an entangled pair of electrons, which with enough energy from visible light separate become sensitive to the magnetic field, resulting in different chemical reactions that translate into different neurological impulses. A list of experiments over last dozen years includes an intriguing "octopus-shaped" molecule.
Quantum Entanglement: http://www.scientificamerican.com/article.cfm?id=quantum-entaglement-more-inform...
A Test for Consciousness by Christof Koch and Giulio Tononi
How will we know when a machine is conscious? The authors are neurobiologists focused on the question of "how brains give rise to subjective experience", and have formulated the "integrative information theory": consciousness is highly informative (each state rules out many other possible states), and conscious information is integrated (elements are experienced together, not independently). So consciousness is the capacity for integrated information. So capacity is low in a system with many elements that do the same thing or interact at random. A computer cannot process an image and answer questions about what is there and whether the various components make sense. The authors propose this, rather than the Turing test, as a test for consciousness.
Photo Contest (ended September 1): http://www.scientificamerican.com/article.cfm?id=koch-contest-fool-the-machine-c...
Planning for the Black Swan by Adam Piore
The Fukushima Daiichi nuclear power plant disaster raised questions about designs of proposed nuclear power plants in the US. A major contender is the Westinghouse AP1000, which relies on natural forces to prevent meltdown without need for human intervention, but this design was a response to Three Mile Island, where partial core meltdown was caused by human error, not natural disaster.
Interactive Map: http://www.scientificamerican.com/article.cfm?id=piore-how-close-do-you-live-to-...
A Nobel Celebration
Excerpts from articles of Nobel Prize winners in physiology and medicine that have appeared in Scientific American. George Wald (1967 prize) re the origin of life (1954 article). Francis Crick (1962 prize) re DNA (1954 article). Christian de Duve (1974 prize) re the origin of complex cells (1996 article). F. M. Murnet (1960 prize) re viruses (1951 article). Stanley Prusiner (1997 prize) re prion diseases (1995 article). Carol Greider and Elizabeth Blackburn (2009 prize) re telomeres and cancer (1996 article). N. Tinbergen (1973 prize) re animal courtship (1954 article). Konrad Lorenz (1973 prize) re evolution of animal behavior (1958 article). Bernard Katz (1970 prize) re nerve impulses (1952 article). Eric Kandel (2000 prize) re nerve cells (1970 article). Francis Crick (1962 prize) and Christof Koch re consciousness (1992 article).
More Excerpts: http://www.scientificamerican.com/article.cfm?id=lindau-nobel-laureate-speak-in-...
Inside the Meat Lab by Jeffrey Bartholet
Overlaps with the May 23 NYer about artificial meat, is about the same person, Willem van Eelen, but more sciency, with a diagram of the process and elaboration on the difficulties of getting stem cells to do what they're told.
Interview: http://www.scientificamerican.com/article.cfm?id=meat-future-of-cultured-meat-in...
The Smartest Bacteria on Earth by Anna Kuchment
A short article with a striking image of soil microbe Paenibacillus vortex. Eshel Ben-Jacob studies the genomes of bacteria. He compared genomes of over 500 species, counting genes associated with social function (communication, processing environmental information, synthesizing chemicals useful for competition), and determined P. vortex among the most intelligent. It forms dense swarms that move outward as a unit and leave behind trails that become a communication network.
Image: http://www.scientificamerican.com/article.cfm?id=bacteria-smallest-on-earth-excl...
The Devil's Cancer by Menna Jones and Hamish McCallum
The Tasmanian devil population is threatened by the "facial tumor disease", a contagious cancer. It is contagious because of an unusual configuration of circumstances: it sheds cells, the devils bite each other during sex and fights, and they are genetically similar so the cancer cells are not recognized as alien by immune systems. The devils on the fringes of the population tend to be more resistant, and are being studied, with the hope of replenishment.
Video: http://www.scientificamerican.com/article.cfm?id=cancer-devils-advocates-catchin...
Greater Glory by Edward Larson
In February 2011, Robert Scott's team happened by chance to encounter Roald Amundsen's team preparing to approach the South Pole when they were supposed to be at the North Pole. Scott decided that rather than change plans and enter into a race, he would continue as if he didn't know, and conduct scientific research along the way. Amundsen reached the South Pole a month before Scott. Scott and several others died on the return trip. Edward Wilson died among the fossils he'd collected of Glossopteris, a plant of the Paleozoic, supporting Darwin's theory that it had evolved on a southern land mass somehow connected to other southern continents.
Interview and recording of Scott's journal entries: http://www.scientificamerican.com/article.cfm?id=south-pole-robert-falcon-scott-...
"I Stick to the Science by Michael Lemonick
Interview with Richard Muller, who was skeptical about existing methods for analyzing temperature, so he tried a different method. And results were similar. He continues to think that the politics are exaggerated.
Transcript of Congress hearing: http://www.scientificamerican.com/article.cfm?id=muller-hearing
So... Goal for 2011 achieved. Goal for 2012 is to finish 2011 and catch up w/ current issues. I'll start a new thread soon.
Living in a Quantum World by Vlatko Vedral
Quantum physics is supposed to be confined to microscopic scales, but recent experiments are revealing quantum effects in macroscopic systems. Example #1: Atoms in a salt crystal were expected to show quantum effects only at the level of individual molecules, but they line up with a magnetic field more quickly than predicted by classical physics, indicating coordination by quantum entanglement. Example #2: Migrating robins are oblivious to magnetic field direction, but sensitive to its inclination -- unless blindfolded. A theory supported by circumstantial evidence but not yet confirmed is that the eye has a molecule with an entangled pair of electrons, which with enough energy from visible light separate become sensitive to the magnetic field, resulting in different chemical reactions that translate into different neurological impulses. A list of experiments over last dozen years includes an intriguing "octopus-shaped" molecule.
Quantum Entanglement: http://www.scientificamerican.com/article.cfm?id=quantum-entaglement-more-inform...
A Test for Consciousness by Christof Koch and Giulio Tononi
How will we know when a machine is conscious? The authors are neurobiologists focused on the question of "how brains give rise to subjective experience", and have formulated the "integrative information theory": consciousness is highly informative (each state rules out many other possible states), and conscious information is integrated (elements are experienced together, not independently). So consciousness is the capacity for integrated information. So capacity is low in a system with many elements that do the same thing or interact at random. A computer cannot process an image and answer questions about what is there and whether the various components make sense. The authors propose this, rather than the Turing test, as a test for consciousness.
Photo Contest (ended September 1): http://www.scientificamerican.com/article.cfm?id=koch-contest-fool-the-machine-c...
Planning for the Black Swan by Adam Piore
The Fukushima Daiichi nuclear power plant disaster raised questions about designs of proposed nuclear power plants in the US. A major contender is the Westinghouse AP1000, which relies on natural forces to prevent meltdown without need for human intervention, but this design was a response to Three Mile Island, where partial core meltdown was caused by human error, not natural disaster.
Interactive Map: http://www.scientificamerican.com/article.cfm?id=piore-how-close-do-you-live-to-...
A Nobel Celebration
Excerpts from articles of Nobel Prize winners in physiology and medicine that have appeared in Scientific American. George Wald (1967 prize) re the origin of life (1954 article). Francis Crick (1962 prize) re DNA (1954 article). Christian de Duve (1974 prize) re the origin of complex cells (1996 article). F. M. Murnet (1960 prize) re viruses (1951 article). Stanley Prusiner (1997 prize) re prion diseases (1995 article). Carol Greider and Elizabeth Blackburn (2009 prize) re telomeres and cancer (1996 article). N. Tinbergen (1973 prize) re animal courtship (1954 article). Konrad Lorenz (1973 prize) re evolution of animal behavior (1958 article). Bernard Katz (1970 prize) re nerve impulses (1952 article). Eric Kandel (2000 prize) re nerve cells (1970 article). Francis Crick (1962 prize) and Christof Koch re consciousness (1992 article).
More Excerpts: http://www.scientificamerican.com/article.cfm?id=lindau-nobel-laureate-speak-in-...
Inside the Meat Lab by Jeffrey Bartholet
Overlaps with the May 23 NYer about artificial meat, is about the same person, Willem van Eelen, but more sciency, with a diagram of the process and elaboration on the difficulties of getting stem cells to do what they're told.
Interview: http://www.scientificamerican.com/article.cfm?id=meat-future-of-cultured-meat-in...
The Smartest Bacteria on Earth by Anna Kuchment
A short article with a striking image of soil microbe Paenibacillus vortex. Eshel Ben-Jacob studies the genomes of bacteria. He compared genomes of over 500 species, counting genes associated with social function (communication, processing environmental information, synthesizing chemicals useful for competition), and determined P. vortex among the most intelligent. It forms dense swarms that move outward as a unit and leave behind trails that become a communication network.
Image: http://www.scientificamerican.com/article.cfm?id=bacteria-smallest-on-earth-excl...
The Devil's Cancer by Menna Jones and Hamish McCallum
The Tasmanian devil population is threatened by the "facial tumor disease", a contagious cancer. It is contagious because of an unusual configuration of circumstances: it sheds cells, the devils bite each other during sex and fights, and they are genetically similar so the cancer cells are not recognized as alien by immune systems. The devils on the fringes of the population tend to be more resistant, and are being studied, with the hope of replenishment.
Video: http://www.scientificamerican.com/article.cfm?id=cancer-devils-advocates-catchin...
Greater Glory by Edward Larson
In February 2011, Robert Scott's team happened by chance to encounter Roald Amundsen's team preparing to approach the South Pole when they were supposed to be at the North Pole. Scott decided that rather than change plans and enter into a race, he would continue as if he didn't know, and conduct scientific research along the way. Amundsen reached the South Pole a month before Scott. Scott and several others died on the return trip. Edward Wilson died among the fossils he'd collected of Glossopteris, a plant of the Paleozoic, supporting Darwin's theory that it had evolved on a southern land mass somehow connected to other southern continents.
Interview and recording of Scott's journal entries: http://www.scientificamerican.com/article.cfm?id=south-pole-robert-falcon-scott-...
"I Stick to the Science by Michael Lemonick
Interview with Richard Muller, who was skeptical about existing methods for analyzing temperature, so he tried a different method. And results were similar. He continues to think that the politics are exaggerated.
Transcript of Congress hearing: http://www.scientificamerican.com/article.cfm?id=muller-hearing
So... Goal for 2011 achieved. Goal for 2012 is to finish 2011 and catch up w/ current issues. I'll start a new thread soon.
