Daily Science Clips
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Daily Science Clips
A mish-mash of interesting pop science articles that catch my eye
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Your Coding Style Is Like a Digital Fingerprint

Your Coding Style Is Like a Digital Fingerprint | Daily Science Clips | Scoop.it
If you think that good code is a plain, expressionless and elegant string of characters that is, at its best, utterly anonymous, think again. New research suggests that programmers have ways of writing code, which can be used as a digital fingerprints.

Whether it's how they space out code using spaces and tabs, naming conventions with capitals and underscores, or quirks in commenting, a team from Drexel University, the University of Maryland, the University of Goettingen, and Princeton can spot who wrote a piece of code—with alarming accuracy. Using natural language processing and machine learning to work out who wrote anonymous pieces of source code based on coding style alone, the team can identify the person behind the script with 95 percent accuracy.

Via Ashish Umre
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'Geography of Hate' maps racism and homophobia on Twitter

'Geography of Hate' maps racism and homophobia on Twitter | Daily Science Clips | Scoop.it

Twitter, even more than many other social media tools, can feel disconnected from the real world. But a group of students and professors at research site Floating Sheep have built a comprehensive map of some of Twitter's most distasteful content: the racist, homophobic, or ableist slurs that can proliferate online. Called Geography of Hate, the interactive map charts ten relatively common slurs across the continental US, either by general category or individually. Looking at the whole country, you'll often see a mass of red or what the map's creators call a "blue smog of hate." Zooming in, however, patches appear over individual regions or cities; some may be predictable, while others are not.


Via Complexity Digest
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Designing interlocking building blocks to create complex biological tissues

Designing interlocking building blocks to create complex biological tissues | Daily Science Clips | Scoop.it

Researchers at Columbia Engineering have developed a new "plug-and-play" method to assemble complex cell microenvironments that is a scalable, highly precise way to fabricate tissues with any spatial organization or interest -- such as those found in the heart or skeleton or vasculature. The study reveals new ways to better mimic the enormous complexity of tissue development, regeneration, and disease.

 

"George Eng, an MD/PhD student in my lab who just received his doctoral degree, designed a lock-and-key technique to build cellular assemblies using a variety of shapes that lock into templates much the way you would use LEGO building blocks," says Gordana Vunjak-Novakovic, who led the study and is the Mikati Foundation Professor of Biomedical Engineering at Columbia Engineering and professor of medical sciences. "What is really important about this technique is that these shapes are tiny -- just a fraction of millimeter, the thickness of a human hair -- and that their precise arrangements are made using cell-friendly hydrogels."

 

Tissue cells in the human body form specific architectures that are critical for the function of each tissue. Cardiac cells, for example, are aligned to create maximum force acting in one direction. Cells without specific spatial organization may never become fully functional if they do not recapitulate their intrinsic organization found in the body. The Columbia Engineering technique enables researchers to construct unique and controlled cell patterns that allow precise studies of cell function, so that, Vunjak-Novakovic adds, "we can now ask some of the more complex questions about how the cells respond to the entire context of their environment. This will help us explore cellular behavior during the progression of disease and test the effects of drugs, stem cells, and various other therapeutic measures."

 

"We used a LEGO-like lock-and-key docking system to spatially localize different cell populations with high specificity and precision," Eng explains. "And, since each shape is docking independent of each other, large tissues can be organized simultaneously, instead of having to create a sequential, brick-by-brick type of organization. With this method, we can design and create better tissues for potential organ replacement."

 

"The beauty of this method is that complex configurations of living cellular material -- many different types of cells, molecules, and extracellular materials -- emerge in the lab in precise three-dimensional geometries in a way that can be used by anyone, as no special equipment is involved," Vunjak-Novakovic adds.

 

Eng is excited about leveraging the microtechnologies used to make computer chips with biomedical engineering techniques to make cells to fabricate new organs. "We develop new ideas and methods to try and alleviate disease by assembling tiny subunits of cells into larger, more functional organs," he says. "It's really like a scene from science fiction! To be on the frontier of scientific discovery, developing new methods and products that we hope will have therapeutic benefit for people is quite fulfilling and motivating. And there's such an exciting element of discovery in designing new cellular microenvironments, studying the rules that define cell communication and organization."

 

Next steps in the application of this new technique include fabrication of different types of functional tissues, such as well-organized cardiac muscle, a tissue whose function critically depends on its architecture and cell alignment, incorporating blood vessel networks along with organized cardiac cells. The method will also be extended to the design of pathological microenvironments of interest, such as tumor models.

 

"Our lab has worked for many years in building 'human-on-a-chip' systems that will allow us to see cellular responses representative of those of whole body physiology," says Vunjak-Novakovic. "We're also very interested in developing technologies that can advance biological experimentation and allow us to ask more complex questions. This study, which was conducted over the last four years, is contributing to both of these areas and helping us advance our methods for screening of therapeutic cells and factors."

 


Via Dr. Stefan Gruenwald
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A protein ‘passport’ that helps nanoparticles get past immune system

A protein ‘passport’ that helps nanoparticles get past immune system | Daily Science Clips | Scoop.it

Macrophages — literally, "big eaters" — are a main part of the body's innate immune system . These cells find and engulf invaders, like bacteria, viruses, splinters and dirt. Unfortunately, macrophages also eat helpful foreigners, including nanoparticles that deliver drugs or help image tumors.


Along with members of his lab, Dennis Discher, professor of chemical and biomolecular engineering in the School of Engineering and Applied Science, has developed a "passport" that could be attached to therapeutic particles and devices, tricking macrophages into leaving them alone. 

Taking a cue from a membrane protein that the body's own cells use to tell macrophages not to eat them, the researchers engineered a the simplest functional version of that protein and attached it to plastic nanoparticles. These passport-carrying nanoparticles remained in circulation significantly longer than ones without the peptide, when tested in a mouse model.

 

In 2008, Discher’s group showed that the human protein CD47, found on almost all mammalian cell membranes, binds to a macrophage receptor known as SIRPa in humans. Like a patrolling border guard inspecting a passport, if a macrophage’s SIRPa binds to a cell’s CD47, it tells the macrophage that the cell isn’t an invader and should be allowed to proceed on.

 

“There may be other molecules that help quell the macrophage response,” Discher said. “But human CD47 is clearly one that says, ‘Don’t eat me’.” Since the publication of that study, other researchers determined the combined structure of CD47 and SIRPa together. Using this information, Discher’s group was able to computationally design the smallest sequence of amino acids that would act like CD47. This “minimal peptide” would have to fold and fit well enough into the receptor of SIRPa to serve as a valid passport. After chemically synthesizing this minimal peptide, Discher’s team attached it to conventional nanoparticles that could be used in a variety of experiments. “Now, anyone can make the peptide and put it on whatever they want,” Rodriguez said.

 

The research team’s experiments used a mouse model to demonstrate better imaging of tumors and as well as improved efficacy of an anti-cancer drug-delivery particle.

 

As this minimal peptide might one day be attached to a wide range of drug-delivery vehicles, the researchers also attached antibodies of the type that could be used in targeting cancer cells or other kinds of diseased tissue. Beyond a proof of concept for therapeutics, these antibodies also served to attract the macrophages’ attention and ensure the minimal peptide’s passport was being checked and approved.

 

Video is here: http://tinyurl.com/b6dthgb


Via Dr. Stefan Gruenwald
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Empathy found in rats: Rats preferred freeing caged rats rather than eating food placed in the cage

Empathy found in rats: Rats preferred freeing caged rats rather than eating food placed in the cage | Daily Science Clips | Scoop.it

At the very least, the new experiment reported in Science is going to make people think differently about what it means to be a “rat.” Eventually, though, it may tell us interesting things about what it means to be a human being.

In a simple experiment, researchers at the University of Chicago sought to find out whether a rat would release a fellow rat from an unpleasantly restrictive cage if it could. The answer was yes.

 

The free rat, occasionally hearing distress calls from its compatriot, learned to open the cage and did so with greater efficiency over time. It would release the other animal even if there wasn’t the payoff of a reunion with it. Astonishingly, if given access to a small hoard of chocolate chips, the free rat would usually save at least one treat for the captive — which is a lot to expect of a rat.

 

The researchers came to the unavoidable conclusion that what they were seeing was empathy — and apparently selfless behavior driven by that mental state.


Via Dr. Stefan Gruenwald
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Cloud of atoms goes beyond absolute zero - physics-math - 03 January 2013 - New Scientist

Cloud of atoms goes beyond absolute zero - physics-math - 03 January 2013 - New Scientist | Daily Science Clips | Scoop.it
The existence of negative temperatures on the Kelvin scale could help us understand dark energy as well as revise the thinking about what temperature
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Computer scientists find vulnerabilities in Cisco VoIP phones

Computer scientists find vulnerabilities in Cisco VoIP phones | Daily Science Clips | Scoop.it
Researchers have found vulnerabilities in Cisco VoIP telephones, recently demonstrating how they can insert malicious code into a Cisco VoIP phone (any of the 14 Cisco Unified IP Phone models) and start eavesdropping on private conversations—not...
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Musicology :: Cymascope Research

Musicology :: Cymascope Research | Daily Science Clips | Scoop.it

Shannon Novak, a New Zealand-born fine artist, commissioned us to image 12 piano notes as inspiration for a series of 12 musical canvases. We decided to image the notes in video mode because when we observed the 'A1' note we discovered, surprisingly, that the energy envelope changes over time as the string's harmonics mix in the piano's wooden bridge. Instead of the envelope being fairly stable, as we had imagined, the harmonics actually cause the CymaGlyphs to be wonderfully dynamic. Our ears can easily detect the changes in the harmonics and the CymaScope now reveals them--probably a first in acoustic physics.

Capturing the dynamics was only possible with HD video but taming the dynamics of the piano's first strike, followed by the short plateau and long decay phase, was tricky. We achieved the result with the help of a professional audio compressor operating in real time.

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Chinese medicine yields secrets: Atomic mechanism of two-headed molecule derived from Chang Shan, a traditional chinese herb

Chinese medicine yields secrets: Atomic mechanism of two-headed molecule derived from Chang Shan, a traditional chinese herb | Daily Science Clips | Scoop.it
The mysterious inner workings of Chang Shan -- a Chinese herbal medicine used for thousands of years to treat fevers associated with malaria -- have been uncovered thanks to a high-resolution structure solved by scientists.
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Rapid Folding of DNA into Nanoscale Shapes at Constant Temperature

We demonstrate that, at constant temperature, hundreds of DNA strands can cooperatively fold a long template DNA strand within minutes into complex nanoscale objects. Folding occurred out of equilibrium along nucleation-driven pathways at temperatures that could be influenced by the choice of sequences, strand lengths, and chain topology. Unfolding occurred in apparent equilibrium at higher temperatures than those for folding. Folding at optimized constant temperatures enabled the rapid production of three-dimensional DNA objects with yields that approached 100%. The results point to similarities with protein folding in spite of chemical and structural differences. The possibility for rapid and high-yield assembly will enable DNA nanotechnology for practical applications.
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Turing Pattern Fingered for Digit Formation

Sixty years ago, noted mathematician Alan Turing described how two interacting chemicals diffusing through space could form interacting wave patterns. Recently, experiments have suggested that Turing's mechanisms play a role in the growth of feathers, hair follicles, the branching pattern of lungs, and even the left-right asymmetry that puts the heart on the left side of the chest. In this issue of Science, a team of biologists offer fresh evidence that this theory guides how some parts of the body develop, as Turing's model also appears to describe the pattern that leads to digit formation in the developing mouse paw.
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Surgeons implant first brain ‘pacemaker’ for Alzheimer’s disease in US

Surgeons implant first brain ‘pacemaker’ for Alzheimer’s disease in US | Daily Science Clips | Scoop.it
Researchers at Johns Hopkins Medicine have surgically implanted a pacemaker-like device into the brain of a patient in the early stages of Alzheimer’s disease, the first such operation in the United States.

The device, which provides deep brain stimulation and has been used in thousands of people with Parkinson’s disease, is seen as a possible means of boosting memory and reversing cognitive decline. Instead of focusing on drug treatments, many of which have failed in recent clinical trials, the research focuses on the use of the low-voltage electrical charges delivered directly to the brain. There is no cure for Alzheimer’s disease yet.

 

The surgery is part of a federally funded, multicenter clinical trial marking a new direction in clinical research designed to slow or halt the ravages of the disease, which slowly robs its mostly elderly victims of a lifetime of memories and the ability to perform the simplest of daily tasks, researchers at Johns Hopkins say. Some 40 patients are expected to receive the deep brain stimulation implant over the next year or so at Johns Hopkins and four other institutions in North America as part of the Advance Study led by Constantine G. Lyketsos, M.D., M.H.S., a professor of psychiatry and behavioral sciences at the Johns Hopkins University School of Medicine, and Andres Lozano, M.D., Ph.D., chairman of the neurology department at the University of Toronto. Only patients whose cognitive impairment is mild enough that they can decide on their own to participate will be included in the trial. Other sites performing the operation, supported by the National Institutes of Health’s National Institute on Aging (R01AG042165), are the University of Toronto, the University of Pennsylvania, the University of Florida, and Banner Health System in Phoenix, Ariz. The medical device company, Functional Neuromodulation Ltd., is also supporting the trial.

 

While experimental for Alzheimer’s patients, more than 80,000 people with the neurodegenerative disorder Parkinson’s disease have undergone the procedure over the past 15 years, with many reporting fewer tremors and requiring lower doses of medication afterward, Lyketsos says. Other researchers are testing deep brain stimulation to control depression and obsessive-compulsive disorder resistant to other therapies. The surgery involves drilling holes into the skull to implant wires into the fornix on either side of the brain. The fornix is a brain pathway instrumental in bringing information to the hippocampus, the portion of the brain where learning begins and memories are made, and where the earliest symptoms of Alzheimer’s appear to arise. The wires are attached to a pacemaker-like device, the “stimulator,” which generates tiny electrical impulses into the brain 130 times a second. The patients don’t feel the current, Rosenberg says. “Deep brain stimulation might prove to be a useful mechanism for treating Alzheimer’s disease, or it might help us develop less invasive treatments based on the same mechanism,” Rosenberg says. By 2050, the number of people age 65 and older with Alzheimer’s disease may triple, experts say, from 5.2 million to a projected 11 million to 16 million, unless effective treatments are found.


Via Dr. Stefan Gruenwald
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Why Too Much Data Disables Your Decision Making

Why Too Much Data Disables Your Decision Making | Daily Science Clips | Scoop.it

 

Quick, think back to a major decision. You know, the kind that compelled you to read everything on a topic and lead you to spend hours devouring every last scrap of data.

 

How'd that work out for you?

We like to think that more information drives smarter decisions; that the more details we absorb, the better off we'll be. It's why we subscribe to Google Alerts, cling to our iPhone, and fire up our TweetDeck. Knowledge, we're told, is power. But what if our thirst for data is actually holding us back? What if obsessing over information actually reduces the quality of our decisions?

That's the question raised by Princeton and Stanford University psychologists in a fascinating study titled On the Pursuit and Misuse of Useless Information. Their experiment was simple. Participants were divided into two groups. Group 1 read the following: Imagine that you are a loan officer at a bank reviewing the mortgage application of a recent college graduate with a stable, well-paying job and a solid credit history. The applicant seems qualified, but during the routine credit check you discover that for the last three months the applicant has not paid a $5,000 debt to his charge card account......


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How Google "Translates" Pictures into Words Using Vector Space Mathematics | MIT Technology Review

How Google "Translates" Pictures into Words Using Vector Space Mathematics | MIT Technology Review | Daily Science Clips | Scoop.it
Google engineers have trained a machine-learning algorithm to write picture captions using the same techniques it developed for language translation.
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A Boy And His Atom: The World's Smallest Movie

A Boy And His Atom: The World's Smallest Movie | Daily Science Clips | Scoop.it
Scientists at IBM Research have made the world's smallest movie by moving individual atoms with a scanning tunneling microscope.
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World's first 3D-printed car will move from 3D printer to road soon

World's first 3D-printed car will move from 3D printer to road soon | Daily Science Clips | Scoop.it

An engineer named Jim Kor is printing, as in building, a car. The Winnipeg, Manitoba, car visionary is responsible for the Urbee 2, being readied for the road, intended eventually as an about-town car, with three wheels, and built for two passengers. It looks like a big, shiny red bug cruising down the road. Interest grows in its means of production and implications for car manufacturing in the future.

If printing cars develop, conventional manufacturing plants might operate aside very small "cottage" plants deploying lights-out manufacturing. Kor's company, Kor Ecologic, is responsible for the Urbee 2, described as strong as steel yet lightweight. (The motto for the company is "Reasonable Design.") By using 3-D printing, there is a special focus on lightness but strength; he is creating large pieces with varied thicknesses. The Urbee's car body will be assembled from about 50 separate parts. The team's practice is to take small part from a big car and make them into single large pieces. The less pieces, the less car weight. The lighter the car, the more miles per gallon. The less spaces between parts and the Urbee becomes the more aerodynamic. The teardrop-shaped car has a curb weight of 1,200 pounds. The bumper, which is made in two pieces, required 300 hours to finish. The entire car takes about 2,500 hours.

The printing process to make the car is called Fused Deposition Modeling. (FDM), where one lays down thin layers (0.04 mm) of melted plastic filament. The FDM approach enables tight control by the designer, who is able to add thickness and rigidity to special sections. Kor likes to compare the fender of a future Urbee with a bird bone. As shown in a cross section of a bird bone, he said there is bone only where the bird needs strength, and the FDM process can replicate a bird bone.

 

Kor has been printing the body pieces at RedEye, a business unit of Stratasys, which uses 3-D printers to produce on-demand parts and prototypes. Kor Ecologic has drawn up specific design ideals that are applied to the Urbee car project..A few of them are highlighted here. "Use the least amount of energy possible for every kilometer traveled. Cause as little pollution as possible during manufacturing, operation and recycling of the car. Use materials available as close as possible to where the car is built. Use materials that can be recycled again and again….

 

Be simple to understand, build, and repair. Be as safe as possible to drive. Be affordable." Kor does not have a high-priced toy in mind but rather an economy car. He has received orders for 14 cars. Most of the orders are from those involved in designing the car. Kor is presently planning to make one car and to drive it, when it is ready, with a partner, from San Francisco to New York City. They hope to do it on ten gallons of gas; Kor would prefer to use pure ethanol. They will try to prove without argument that they did the drive with existing traffic.


Via Dr. Stefan Gruenwald
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U.S./China team determines structure of virus with Blue Waters

U.S./China team determines structure of virus with Blue Waters | Daily Science Clips | Scoop.it
Simulations carried out using the Blue Waters petascale supercomputer have determined the structure of the rabbit hemorrhagic disease virus (RHDV), which causes a highly infectious and often fatal illness in domestic and wild rabbits.
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How to Create a Vision for Your Career | Monster

How to Create a Vision for Your Career | Monster | Daily Science Clips | Scoop.it
Do you find it difficult to see where you’ll be in the coming years? Create a vision for the professional and personal life you desire by asking yourself these 10 questions.

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Anita's curator insight, February 2, 2013 3:32 PM

It's not a one-time, winner take all proposition. It can be done in steps.

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Computational research in the era of open access: Standards and best practices | The Curious Wavefunction, Scientific American Blog Network

Computational research in the era of open access: Standards and best practices | The Curious Wavefunction, Scientific American Blog Network | Daily Science Clips | Scoop.it
This is an opinion piece I wrote for a new planned journal on open computational research that for one reason or another failed to take off. ...
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Fructose has different effect than glucose on brain regions that regulate appetite

In a study examining possible factors regarding the associations between fructose consumption and weight gain, brain magnetic resonance imaging of study participants indicated that ingestion of glucose but not fructose reduced cerebral blood flow...
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X-ray imaging detectors | Print Edition - Physics Today

X-ray imaging detectors | Print Edition - Physics Today | Daily Science Clips | Scoop.it

Advances in detector technology, in concert with new synchrotron sources, x-ray optics, and computational methods, are opening new ways to probe the structure and dynamics of matter.

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MIT discovers a new state of matter, a new kind of magnetism | ExtremeTech

MIT discovers a new state of matter, a new kind of magnetism | ExtremeTech | Daily Science Clips | Scoop.it
Researchers at MIT have discovered a new state of matter with a new kind of magnetism. This new state, called a quantum spin liquid (QSL), could lead to significant advances in data storage.
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NIH Offers to Help Universities Improve Training, Boost Diversity

Although some social scientists and biomedical researchers have complained that U.S. universities are training far more graduate students and postdocs than will ever find jobs in academic research, and others argue that any potential oversupply will find jobs in industry or other sectors, almost everyone agrees: The current training system takes too long and isn't designed to prepare young biomedical scientists for nonacademic jobs. So last week, the National Institutes of Health announced a plan to prepare scientists for a range of careers, move students through their Ph.D.s faster, and bolster the pay of postdocs. Officials say the changes are not aimed at reducing or even stabilizing the number of graduates but are intended to improve the training experience.
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Hacking the Human Brain: The Next Domain of Warfare

Hacking the Human Brain: The Next Domain of Warfare | Daily Science Clips | Scoop.it
t’s been fashionable in military circles to talk about cyberspace as a “fifth domain” for warfare, along with land, space, air and sea. But there’s a sixth and arguably more important warfighting domain emerging: the human brain.

This new battlespace is not just about influencing hearts and minds with people seeking information. It’s about involuntarily penetrating, shaping, and coercing the mind in the ultimate realization of Clausewitz’s definition of war: compelling an adversary to submit to one’s will. And the most powerful tool in this war is brain-computer interface (BCI) technologies, which connect the human brain to devices.

Current BCI work ranges from researchers compiling and interfacing neural data such as in the Human Conectome Project to work by scientists hardening the human brain against rubber hose cryptanalysis to technologists connecting the brain to robotic systems. While these groups are streamlining the BCI for either security or humanitarian purposes, the reality is that misapplication of such research and technology has significant implications for the future of warfare.

Where BCIs can provide opportunities for injured or disabled soldiers to remain on active duty post-injury, enable paralyzed individuals to use their brain to type, or allow amputees to feel using bionic limbs, they can also be exploited if hacked. BCIs can be used to manipulate … or kill.
Via Daniel House, Dr. Stefan Gruenwald
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mdashf's curator insight, December 14, 2012 3:44 PM

Ethical Paradigms of science

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How Large Is Your Network? The Power of 2nd and 3rd Degree Connections

How Large Is Your Network? The Power of 2nd and 3rd Degree Connections | Daily Science Clips | Scoop.it

Imagine you receive a digital camera with a built-in memory card for your birthday. You bring it on a six-month trip to Africa where you won’t have access to a computer—so all the photos you want to keep must fit on that one memory card. When you first arrive you snap photos freely, and maybe even record some short videos. But after a month or so, the memory card starts filling up. Now you’re forced to be more judicious in deciding how to use that storage. You might take fewer pictures. You might decide to reduce the quality/resolution of the photos you do take in order to fit more. You’ll probably cut back on videos. Still, inevitably, you’ll hit capacity, at which point if you wish to take new photos you’ll have to delete old ones.

 

The maximum number of relationships we can realistically manage—the number that can fit on the memory card, as it were—is described as Dunbar’s Number, after evolutionary psychologist Robin Dunbar. But maybe it shouldn’t be. In the early nineties, Dunbar studied the social connections within groups of monkeys and apes. He theorized that the maximum size of their overall social group was limited by the small size of their neocortex. It requires brainpower to socialize with other animals, so it follows that the smaller the primate’s brain, the less efficient it is at socializing, and the fewer other primates it can befriend. He then extrapolated that humans have an especially large neocortex and so should be able to more efficiently socialize with a great number of humans. Based on our neocortex size, Dunbar calculated that humans should be able to maintain relationships with no more than roughly 150 people at a time. To cross-check the theory, he studied anthropological field reports and other clues from villages and tribes in the hunter-gatherer era. Sure enough, he found the size of surviving tribes tended to be about 150. And when he observed modern human societies, he found that many businesses and military groups organize their people into cliques of about 150. To wit: Dunbar’s Number of 150.


Via Ashish Umre
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