Friday, October 30, 2015

now e. coli has benefits?? gut biome very impressive little universe

ScienceThe benefits of Escherichia coli
Infection and intestinal damage can trigger severe muscle wasting and loss of fat in mice. How this happens is poorly understood. Palaferri Schieber et al. discovered a protective Escherichia coli strain in their mouse colony. Mice intestinally colonized with the E. coli and infected with the food-poisoning bug Salmonella or with the lung pathogen Burkholderia did not waste away. Without the E. coli, similarly infected mice became fatally ill. The protective E. coli stimulated an innate immune mechanism that ensured that muscle-signaling pathways were not damaged by infection. Thus, the friendly E. coli allowed its host to tolerate and survive the pathogens.

epigenetics: stressed dads == offspring with neuropsychiatric disorders

ars technicaPaternal stress given to offspring via RNA packed into sperm
The idea that parents can transmit environmentally acquired traits to their offspring has been intuitively attractive ever since Lamarck proposed it in 1801. It had to go underground as evidence continuously piled up supporting Darwin's theory of natural selection, but it seems to be enjoying a popular resurgence with the discovery of epigenetics. Epigenetics explains how information can be transmitted between generations without the involvement of DNA sequences.
A number of recent studies have suggested that stress levels and the nutritional status of parents (and even grandparents) can influence the health of their offspring. But these studies have been somewhat murky on the details on how this transmission could occur. Now scientists who had previously shown that paternal stress impacts the next generation of mice have zeroed in on how it happens: males pack their sperm with RNA that influences gene activity in their offspring.
Through the uterine environment, mothers can pass their environmental exposures on to the fetuses they are nurturing. Thus, studies looking at mechanisms of epigenetic inheritance tend to focus on fathers—pretty much all they give to the fetus is genetic material. And male mice don't need to help in rearing the young, so this genetic material can be their only contribution to the next generation.
In earlier work, these scientists exposed male mice to six weeks of alternating stressors like 36 hours of constant light, a 15-minute exposure to fox odor, exposure to a novel object (marbles) overnight, 15 minutes of restraint in a 50 mL conical tube, multiple cage changes, white noise all night long, or saturated bedding.
Poor little guys.
Then the scientists allowed the mice to breed. Adult offspring of these chronically stressed dads had reduced hypothalamic-pituitary-adrenal stress axis reactivity; when they themselves were restrained for 15 minutes, they did not make as much corticosterone as mice sired by relaxed dads. This is relevant, and problematic, because blunted stress responses in humans are associated with neuropsychiatric disorders like depression, schizophrenia, and autism.

if life came early to the universe, then it would seem to be part of the universe's purpose

phys.orgMost earth-like worlds have yet to be born, according to theoretical study

Earth came early to the party in the evolving universe. According to a new theoretical study, when our solar system was born 4.6 billion years ago only eight percent of the potentially habitable planets that will ever form in the universe existed. And, the party won't be over when the sun burns out in another 6 billion years. The bulk of those planets—92 percent—have yet to be born.

chromatin target for epigenetic changes

Science |

Epigenetic mechanisms control the combination of genes that are switched on and off in any given cell. In turn, this combination, called the transcriptional program, determines the identity and the fate of cells, which are deregulated in diseases such as cancer, inflammation, or neurological disorders. Chemical modifications (such as methylation or acetylation) of chromatin—an ensemble of nuclear factors, especially histone proteins around which DNA is wrapped—act as epigenetic signals. Enzymes that write or erase these chemical “marks,” and proteins that bind and interpret them, represent an important target class for drugs (1). On page 291 of this issue, Jiao and Liu (2) report the crystal structure of one prominent such enzyme called enhancer of zeste homolog 2 (Ezh2) in complex with obligatory protein binding partners. This structure, which has been largely elusive, provides clarity on the regulation of EZH2 catalytic activity and is an important step toward rational drug design.

specialized intelligences more effective at specific problems

phys.orgSystem that replaces human intuition with algorithms outperforms human teams

Big-data analysis consists of searching for buried patterns that have some kind of predictive power. But choosing which "features" of the data to analyze usually requires some human intuition. In a database containing, say, the beginning and end dates of various sales promotions and weekly profits, the crucial data may not be the dates themselves but the spans between them, or not the total profits but the averages across those spans.

MIT researchers aim to take the human element out of big-data analysis, with a new system that not only searches for patterns but designs the feature set, too. To test the first prototype of their system, they enrolled it in three data science competitions, in which it competed against human teams to find predictive patterns in unfamiliar data sets. Of the 906 teams participating in the three competitions, the researchers' "Data Science Machine" finished ahead of 615.
In two of the three competitions, the predictions made by the Data Science Machine were 94 percent and 96 percent as accurate as the winning submissions. In the third, the figure was a more modest 87 percent. But where the teams of humans typically labored over their prediction algorithms for months, the Data Science Machine took somewhere between two and 12 hours to produce each of its entries.
"We view the Data Science Machine as a natural complement to human intelligence," says Max Kanter, whose MIT master's thesis in computer science is the basis of the Data Science Machine. "There's so much data out there to be analyzed. And right now it's just sitting there not doing anything. So maybe we can come up with a solution that will at least get us started on it, at least get us moving."

alternative living arrangements

sfistStep Inside Oakland's Illegal Dystopian Shipping Container Community, Containertopia
"It's pretty much my dream post-apocalyptic cyberpunk setup," says Luke Iseman near his 160-square-foot box home. With a camp stove and a fridge "that's a really simple hack," his miniature shipping container nightmare chamber sits alongside 11 others in a warehouse at an undisclosed location in Oakland. File under: Apartment Sadness?
Bloomberg reports that the 31-year-old cool guy Wharton graduate has been chased from two other locations by the authorities. But, like an idiot, Iseman has no plans to give up. “I’d rather ask forgiveness than ask permission,” the entrepreneur says in high Silicon Valley fashion.
Iseman rakes in $1,000 a month for each of the 11 structures docked in the 17,000-square-foot warehouse he rents for $9,100. His tenants include a Facebook engineer, a SolarCity programmer, and a bicycle messenger. This, as Iseman calls it, is "Containertopia."

fountain of youth, or where's the d*** off button!

Tech TimesSwitching Off Over 200 Genes Linked To Aging Extends Lifespan By 60 Percent
A 10-year research conducted by scientists at the University of Washington and Buck Institute for Research on Aging in the United States may have found a partial chunk of the so-called Fountain of Youth. The team has identified around 238 genes which, when removed, can extend lifespan by 60 percent.
The study was conducted on 4,698 yeast strains. The research team said the results can be replicated in humans after a series of tests conducted on roundworms. By counting yeast cells and monitoring the consequences that followed when a single gene is blocked or removed, the team was able to identify the number of 'daughter cells' that a 'mother cell' can produce before it stops dividing

Wednesday, October 14, 2015

speaking of dyson, here's some of dyson's recent speaking...

The Register | Interview The life of physicist Freeman Dyson spans advising bomber command in World War II, working at Princeton University in the States as a contemporary of Einstein, and providing advice to the US government on a wide range of scientific and technical issues.
He is a rare public intellectual who writes prolifically for a wide audience. He has also campaigned against nuclear weapons proliferation.
At America's Oak Ridge National Laboratory, Dyson was looking at the climate system before it became a hot political issue, over 25 years ago. He provides a robust foreword to a report written by Intergovernmental Panel on Climate Change cofounder Indur Goklany on CO2 – a report published[PDF] today by the Global Warming Policy Foundation (GWPF).
An Obama supporter who describes himself as "100 per cent Democrat," Dyson says he is disappointed that the President "chose the wrong side." Increasing CO2 in the atmosphere does more good than harm, he argues, but it is not an insurmountable crisis. Climate change, he tells us, "is not a scientific mystery but a human mystery. How does it happen that a whole generation of scientific experts is blind to obvious facts?"
We invited Dyson to talk about climate change and other matters, including a question from your correspondent's kids – how will we do interstellar travel?

a dyson sphere?

The Atlantic | In the Northern hemisphere’s sky, hovering above the Milky Way, there are two constellations—Cygnus the swan, her wings outstretched in full flight, and Lyra, the harp that accompanied poetry in ancient Greece, from which we take our word “lyric.”

Between these constellations sits an unusual star, invisible to the naked eye, but visible to the Kepler Space Telescope, which stared at it for more than four years, beginning in 2009.

“We’d never seen anything like this star,” says Tabetha Boyajian, a postdoc at Yale. “It was really weird. We thought it might be bad data or movement on the spacecraft, but everything checked out.”

Kepler was looking for tiny dips in the light emitted by this star. Indeed, it was looking for these dips in more than 150,000 stars, simultaneously, because these dips are often shadows cast by transiting planets. Especially when they repeat, periodically, as you’d expect if they were caused by orbiting objects.

The Kepler Space Telescope collected a great deal of light from all of those stars it watched. So much light that Kepler’s science team couldn’t process it all with algorithms. They needed the human eye, and human cognition, which remains unsurpassed in certain sorts of pattern recognition. Kepler’s astronomers decided to found Planet Hunters, a program that asked “citizen scientists” to examine light patterns emitted by the stars, from the comfort of their own homes.

In 2011, several citizen scientists flagged one particular star as “interesting” and “bizarre.” The star was emitting a light pattern that looked stranger than any of the others Kepler was watching.

The light pattern suggests there is a big mess of matter circling the star, in tight formation. That would be expected if the star were young. When our solar system first formed, four and a half billion years ago, a messy disk of dust and debris surrounded the sun, before gravity organized it into planets, and rings of rock and ice.

But this unusual star isn’t young. If it were young, it would be surrounded by dust that would give off extra infrared light. There doesn’t seem to be an excess of infrared light around this star.

It appears to be mature.
And yet, there is this mess of objects circling it. A mess big enough to block a substantial number of photons that would have otherwise beamed into the tube of the Kepler Space Telescope. If blind nature deposited this mess around the star, it must have done so recently. Otherwise, it would be gone by now. Gravity would have consolidated it, or it would have been sucked into the star and swallowed, after a brief fiery splash.

Wednesday, October 7, 2015

runner's high is also like smoking dope + endorphins

ACS | After a nice long bout of aerobic exercise, some people experience what’s known as a “runner’s high”: a feeling of euphoria coupled with reduced anxiety and a lessened ability to feel pain. For decades, scientists have associated this phenomenon with an increased level in the blood of β-endorphins, opioid peptides thought to elevate mood.
Now, German researchers have shown the brain’s endocannabinoid system—the same one affected by marijuana’s Δ9-tetrahydrocannabinol (THC)—may also play a role in producing runner’s high, at least in mice

cyanobacteria produce 100s of millions of tons of hydrocarbons a year

PNAS | A number of organisms synthesize hydrocarbons, but the scale at which this occurs in the environment is unknown. Here, we provide the first global estimates of hydrocarbon production by the two most abundant cyanobacteria on Earth, Prochlorococcus and Synechococcus. We suggest that these organisms represent a significant and widespread source of hydrocarbons to the world’s oceans, which in turn may sustain populations of obligate hydrocarbon-degrading bacteria known to be important in consuming anthropogenic oil spills. Our study demonstrates the role cyanobacteria play in the ocean ‟hydrocarbon cycle” and reveals the massive scale of this process. The widespread distribution of cyanobacteria and hydrocarbon-degrading bacteria in freshwater, marine, and terrestrial environments suggests the hydrocarbon cycle is pervasive in many natural ecosystems.

Russia's Syrian moves a counterattack on OPEC?

Oilprice | President Putin’s recent moves in the Middle East—to shore up Bashar al-Assad’s regime in Syria through deployment of combat aircraft, equipment, and manpower and build-out of air-, naval-, and ground-force bases, and the agreement in the last week with Iran, Iraq, and Syria on intelligence and security cooperation—could contribute to Russian efforts to combat the myriad negative pressures on Russia’s vital energy industry.
Live by Energy…
Energy is the foundation of Russia, its economy, its government, and its political system. Putin has highlighted on various occasions the contribution Russia’s mineral wealth, in particular oil and natural gas, must make for Russia to be able to sustain economic growth, promote industrial development, catch up with the developed economies, and modernize Russia’s military and military industry.

$1 beellion dollars

CNN | In the arid plains of the southern New Mexico desert, between the site of the first atomic bomb test and the U.S.-Mexico border, a new city is rising from the sand.
Planned for a population of 35,000, the city will showcase a modern business district downtown, and neat rows of terraced housing in the suburbs. It will be supplied with pristine streets, parks, malls and a church.
But no one will ever call it home.

Confederacy mythos hoodwinks poor whites

Raw Story | Nobody can accuse Frank Hyman of not being a true Southerner.
The Beaufort County, South Carolina native attended segregated schools as a child. At 18, he campaigned against the late Sen. Strom Thurmond and served on the Durham, North Carolina, City Council where he wrote the first Living Wage Ordinance in the South. But he also says that his favorite uncle, AJ, was a KKK Wizard who kept a machine gun in the trunk of his car.
Hyman’s a stone mason, a carpenter and an avid gardener who writes the “Coop Builder” column for Chickens Magazine. You can have him build you a custom chicken coop if you’d like.
And he wants people to know that for a significant share of white Southerners, the Confederacy — and the slave economy it defended — was a huge scam. And in an essay that ran last month in a number of newspapers across the South, he argued that the mythology surrounding the Confederacy still hoodwinks many of his white working-class Southerners to this day.
Hyman appeared on Politics and Reality Radio last week to lay out his argument. Below is  a transcript of our discussion that’s been edited for length and clarity.

Friday, October 2, 2015

applying science to human behavior

Science | Computational psychophysiology is an interdisciplinary field that employs methods from the disciplines of psychology, physiology, neuroscience, computer science, mathematics, and physics to investigate human behavior. Modern technologies, such as positron emission tomography and functional magnetic resonance imaging, now enable researchers to look inside the brain with unprecedented clarity and are facilitating a better understanding of neurological disorders and neurodegenerative diseases. By combining the power of computational techniques with psychophysiology studies, researchers can generate far more in-depth data analyses and a greater understanding of the processes underlying behavior.

crystal-like patterns in neuronal firing

Science | [...] Imagine my renewed excitement when, as a budding neuroscientist at university, I learned that there was crystal-like neural activity in the brain. There is a group of neurons in the parahippocampal formation named “grid cells” that fire in hexagonal symmetry (3) (see the figure, panel A, left). Grid neurons themselves are not necessarily arranged in a crystal-like pattern in the brain [although some argue this could be the case (4)]. Rather, each cell acts as a crystal “generator,” where the fundamental blocks are fields of neural activity.
Grid cell firing appears to be invariant to properties of the enclosure (e.g., size, shape), as well as an animal's behavior (e.g., running speed, grooming), which prompts the suggestion that they represent an internally generated path integration system for navigation (3). The universal metric of space had been found (356)!

every cell in your body has a potentially (likely?) unique genome

Science | Every cell of your body was generated by cell division, forming a lineage tree that goes back to the fertilized egg. Mutations are introduced by errors in DNA replication at every cell division, as well as by mutational processes that operate continuously, such as exposure to ultraviolet light. As a consequence, every cell may have its own unique genome, with potentially distinct gains and losses of function. Furthermore, these mutations create a record of the developmental ancestry of each cell, which can be used to reconstruct their lineage tree.

Homologous structures in fractally uncompressing terraforming machines

Science | Live birth has evolved repeatedly across the major taxonomic groups, but in the vast majority it is the female that does the brooding. The most developed case of gender reversal in brooding occurs among seahorses. In some seahorse species, males not only incubate the eggs internally but develop a pouch structure that is strikingly similar to a uterus in terms of form and function. Whittington et al. produced a detailed transcriptome of the genes up-regulated during pregnancy in male Hippocampus abdominalis and found that those involved in embryo growth and support functions, such as nutrient transport and waste removal, were generally homologous to those seen in pregnant female mammals and reptiles. Thus, it seems that the pregnancy pathway is much the same whether fish or mammal, female or male

culture of competence

Turn the volume off for this one. The music makes NO sense.

China and Russia launching payment clearinghouse to route around SWIFT

Aviso | Control of how payments are processed – and in what currency – carries a lot of weight. Most recently the likes of President Assad in Syria and Russia’s Vladimir Putin have been on the receiving end of payment-related sanctions. This is why there is an ongoing global political power play as Russia and China explore payment processing possibilities to challenge ‘Western’ – and dollar – dominance in this sphere.
In March 2014 Western governments used Visa and MasterCard to cut off prominent Russian businessmen and  political aides of Russian President Vladimir Putin from their accounts. The sanctions also targeted Russian financial institutions (including Bank Rossiya which was also included in a U.S. Government blacklist), a move that infuriated Russia. The businessmen and institutions were placed on this blacklist after Putin’s annexation of Crimea. 
The Society for Worldwide Interbank Financial Telecommunication (SWIFTdeclined to add its name to those imposing sanctions, allowing Russia to maintain access to the global payments system. They did, however, get involved in 2012 when expelling Iranian banks from their system.

IT workers allege discrimination from H1-B workers

Network World | Some U.S. IT workers who have been replaced with H-1B contractors are alleging discrimination and are going to court. They are doing so in increasing numbers.

There are at least seven IT workers at Disney who are pursuing, or plan to pursue, federal and state discrimination administrative complaints over their layoffs. Another Disney worker, still employed by the firm, has filed a state administrative discrimination complaint in California. These complaints are a first step to litigation.

Separately, there are ongoing court cases alleging discrimination against two of the largest India-based IT services firms, Infosys and Tata Consultancy Services. The federal judges in each of cases have given a green light for the plaintiffs to proceed after rejecting dismissal efforts.

There may be federal interest in examining this issue. The U.S. Department of Justice's Office of Special Counsel for Immigration-Related Unfair Employment Practices was asked by 10 U.S. senators in April to examine the IT layoffs at Southern California Edison (SCE) and to determine whether SCE or its contractors were "engaged in prohibited citizenship status discrimination."

What's being challenged, in sum, is the job replacement system created by the H-1B program. U.S. IT workers, as a condition for their severance, are being made to train H-1B visa-holding contractor replacements to take over their jobs.

The contractors often work for IT services firms that employ large numbers of H-1B workers. Most of these workers are from India and regional countries. This practice of replacing U.S. workers with foreign workers constitutes national origin discrimination, say its critics.