Synthetic Biology: Engineering Life To Examine It

Synthetic biology is an area of science devoted to engineering novel biological circuits, devices, systems, genomes or even whole organisms. This rather broad description of what "synthetic biology" encompasses reflects the multidisciplinary nature of this field which integrates ideas derived from biology, engineering, chemistry and mathematical modeling as well as a vast arsenal of experimental tools developed in each of these disciplines. Specific examples of "synthetic biology" include the engineering of microbial organisms that are able to mass produce fuels or other valuable raw materials, synthesizing large chunks of DNA to replace whole chromosomes or even the complete genome in certain cells, assembling synthetic cells or introducing groups of genes into cells so that these genes can form functional circuits by interacting with each other. Synthesis in the context of synthetic biology can signify the engineering of artificial genes or biological systems that do not exist in nature (i.e. synthetic = artificial or unnatural), but synthesis can also stand for integration and composition, a meaning which is closer to the Greek origin of the word. It is this latter aspect of synthetic biology which makes it an attractive area for basic scientists who are trying to understand the complexity of biological organisms. Instead of the traditional molecular biology focus on studying just one single gene and its function, synthetic biology is engineering biological composites that consist of multiple genes and regulatory elements of each gene. This enables scientists to interrogate the interactions of these genes, their regulatory elements and the proteins encoded by the genes with each other. Synthesis serves as a path to analysis.

One goal of synthetic biologists is to create complex circuits in cells to facilitate biocomputing, building biological computers that are as powerful or even more powerful that traditional computers. While such gene circuits and cells that have been engineered have some degree of memory and computing power, they are no match for the comparatively gigantic computing power of even small digital computers. Nevertheless, we have to keep in mind that the field is very young and advances are progressing at a rapid pace.

One of the major recent advances in synthetic biology occurred in 2013 when an MIT research team led by Rahul Sarpeshkar and Timothy Lu at MIT created analog computing circuits in cells. Most synthetic biology groups that engineer gene circuits in cells to create biological computers have taken their cues from contemporary computer technology. Nearly all of the computers we use are digital computers, which process data using discrete values such as 0's and 1's. Analog data processing on the other hand uses a continuous range of values instead of 0's and 1's. Digital computers have supplanted analog computing in nearly all areas of life because they are easy to program, highly efficient and process analog signals by converting them into digital data. Nature, on the other hand, processes data and information using both analog and digital approaches. Some biological states are indeed discrete, such as heart cells which are electrically depolarized and then repolarized in periodical intervals in order to keep the heart beating. Such discrete states of cells (polarized / depolarized) can be modeled using the ON and OFF states in the biological circuit described earlier. However, many biological processes, such as inflammation, occur on a continuous scale. Cells do not just exist in uninflamed and inflamed states; instead there is a continuum of inflammation from minimal inflammatory activation of cells to massive inflammation. Environmental signals that are critical for cell behavior such as temperature, tension or shear stress occur on a continuous scale and there is little evidence to indicate that cells convert these analog signals into digital data.

Most of the attempts to create synthetic gene circuits and study information processing in cells have been based on a digital computing paradigm. Sarpeshkar and Lu instead wondered whether one could construct analog computation circuits and take advantage of the analog information processing systems that may be intrinsic to cells.

by Jalees Rehman, 3Quarks Daily | Read more:

Image: uncredited

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Lykke Li

A Lonely Quest for Facts on Genetically Modified Crops

[ed. See also: The GMO Apple the Industry Hates.]

Kona, Hawaii - From the moment the bill to ban genetically engineered crops on the island of Hawaii was introduced in May 2013, it garnered more vocal support than any the County Council here had ever considered, even the perennially popular bids to decriminalize marijuana.

Public hearings were dominated by recitations of the ills often attributed to genetically modified organisms, or G.M.O.s: cancer in rats, a rise in childhood allergies, out-of-control superweeds, genetic contamination, overuse of pesticides, the disappearance of butterflies and bees.

Like some others on the nine-member Council, Greggor Ilagan was not even sure at the outset of the debate exactly what genetically modified organisms were: living things whose DNA has been altered, often with the addition of a gene from a distant species, to produce a desired trait. But he could see why almost all of his colleagues had been persuaded of the virtue of turning the island into what the bill’s proponents called a “G.M.O.-free oasis.”

“You just type ‘G.M.O.’ and everything you see is negative,” he told his staff. Opposing the ban also seemed likely to ruin anyone’s re-election prospects.

Yet doubts nagged at the councilman, who was serving his first two-year term. The island’s papaya farmers said that an engineered variety had saved their fruit from a devastating disease. A study reporting that a diet of G.M.O. corn caused tumors in rats, mentioned often by the ban’s supporters, turned out to have been thoroughly debunked.

And University of Hawaii biologists urged the Council to consider the global scientific consensus, which holds that existing genetically engineered crops are no riskier than others, and have provided some tangible benefits.

“Are we going to just ignore them?” Mr. Ilagan wondered.

Urged on by Margaret Wille, the ban’s sponsor, who spoke passionately of the need to “act before it’s too late,” the Council declined to form a task force to look into such questions before its November vote. But Mr. Ilagan, 27, sought answers on his own. In the process, he found himself, like so many public and business leaders worldwide, wrestling with a subject in which popular beliefs often do not reflect scientific evidence.

At stake is how to grow healthful food most efficiently, at a time when a warming world and a growing population make that goal all the more urgent.

Scientists, who have come to rely on liberals in political battles over stem-cell research, climate change and the teaching of evolution, have been dismayed to find themselves at odds with their traditional allies on this issue. Some compare the hostility to G.M.O.s to the rejection of climate-change science, except with liberal opponents instead of conservative ones. (...)

Like three-quarters of the voters on Hawaii Island, known as the Big Island, Mr. Ilagan supported President Obama in the 2012 election. When he took office himself a month later, after six years in the Air National Guard, he planned to focus on squatters, crime prevention and the inauguration of a bus line in his district on the island’s eastern rim.

He had also promised himself that he would take a stance on all topics, never registering a “kanalua” vote — the Hawaiian term for “with reservation.”

But with the G.M.O. bill, he often despaired of assembling the information he needed to definitively decide. Every time he answered one question, it seemed, new ones arose. Popular opinion masqueraded convincingly as science, and the science itself was hard to grasp. People who spoke as experts lacked credentials, and G.M.O. critics discounted those with credentials as being pawns of biotechnology companies.

“It takes so much time to find out what’s true,” he complained.

So many emails arrived in support of the ban that, as a matter of environmental responsibility, the Council clerks suspended the custom of printing them out for each Council member. But Mr. Ilagan had only to consult his inbox to be reminded of the prevailing opinion.

“Do the right thing,” one Chicago woman wrote, “or no one will want to take a toxic tour of your poisoned paradise.”

by Amy Harmon, NY Times |  Read more:

Image: Jim Wilson 

How to Stay Dry Forever

I hate being rained on. I especially hate it when it's cold. You'd have thought that with all our 21st-century Google-Glass exploring-Mars engineering marvellousness, we would have made more progress on the problem of rain. But no. The umbrella is a few thousand years old and is nowhere near an optimal solution, especially in blustery windy weather. Wet-weather clothing works if you wear it, but most people don't because it looks so awful.

From a materials-science perspective, the best solution for the British weather would be an invisible waterproof coating that you can spray on the clothes you actually do want to wear. Excitingly such materials have now been invented; they borrow tricks from nature, and they may yet get us singing in the rain.

Traditional waterproofing involves materials that are hydrophobic – in other words molecules that repel water. Waxes and other oily materials fall into this category because of the way they share their electrons at an atomic scale. Water molecules are polar, which means they have plus and minus charged ends. Waxes and oils prefer their electrons more equally distributed and so find it hard to conform to the polarity of water, and in the stand-off they repel each other. Hence oil and water don't mix. This hydrophobic behaviour is bad for vinaigrettes but good for waterproofing.

Nature uses this trick too but is much better at it. Go into a garden during a rain shower and have a look at how many leaves repel water so effectively that water droplets sit like jewels glistening on their surface. Lotus leaves have long been known to have this superhydrophobic property, but no one knew why until electron microscopes revealed something very odd about the surface of the lotus leaf. There is a waxy material there, yes, but it is arranged on the surface in the form of billions of tiny microscopic bumps. When a drop of water sits on a hydrophobic surface it tries to minimise its area of contact, because it wants to minimise its interaction with the non-polar waxy material.

The bumps on the lotus leaf drastically increase this area of waxiness, forcing the droplet to sit up precariously on the tips of the bumps. In this, the Cassie-Baxter state, the droplet becomes very mobile and quickly slides off the leaf. So by manipulating just the bumpiness of its surface, lotus leaves are far better at repelling water.

The mobility of the droplets has another effect. By zooming around the surface of the leaf rather than sticking, the droplets of water collect small particles of dust, hoovering them up. This cleaning mechanism of these superhydrophobic surfaces is called the lotus effect.

by Mark Miodownik, Guardian | Read more:
Image: Alarmy

Ice Bowl II

[ed. The '67 Championship was one of the best NFL games in history (and I watched it on tv in Honolulu. Yea!). Here's a short six-minute video.]

The Green Bay Packers' playoff game Sunday against the San Francisco 49ers could be one of the coldest in NFL history, rivaling the subzero temperatures of the 1967 Ice Bowl.

Temperatures at Lambeau Field are expected to be -2F (-19C) at kick off, and by the fourth quarter may reach -7F (-21C), with wind chills approaching -30F (-34 C), according to the National Weather Service. The so-called Ice Bowl, the 1967 NFL championship game in which the Packers beat the Dallas Cowboys to advance to Super Bowl II, saw cold as severe as -13F (-25C), with a wind chill of -46F (-43C).

In these temperatures, exposed skin can become frostbitten in minutes and hypothermia can equally quickly. Players can huddle around giant heaters on the sidelines, but fans will have to take extra safety measures, such as dressing in layers and sipping warm drinks. The Packers plan to pass free coffee, hot chocolate, and 70,000 hand warmers, which fans can slip into gloves and jackets to provide warmth for up to 10 hours. (...)

Lambeau Field has a heating system buried beneath the turf to keep the field from freezing, but it failed during the Ice Bowl, leaving the sod feeling as though "someone had taken a stucco wall and laid it on the ground", according to journalist David Maraniss. The system was upgraded in 1997 to include 30 miles of heating pipes, so players on Sunday can expect softer landings.

The field should be relatively clear Sunday, with no snow in the forecast. The stands had been filled with snow during the week, but the team, continuing a popular tradition, invited members of the public to help shovel it for $10 per hour. Though Packers' tickets sell notoriously quickly, the severe forecast scared off many from buying seats to the playoff game, and the NFL threatened not to air the game on local TV if the team failed to sell out. Corporate partners of the Packers stepped in to assist, however, and helped the team avert disaster for Wisconsin. (...)

The 1967 game took a major toll on players, said Ed Gruver, the author of a book called The Ice Bowl: The Cold Truth. Packers coach Vince Lombardi didn't let most of his players wear gloves, so several, including Hall of Fame quarterback Bart Starr, suffered varying degrees of frostbite, Gruver said. One Cowboys player had respiratory problems due to breathing in so much frigid air, he added, and Dallas quarterback Don Meredith's calls were inarticulate because his lips were frozen.

by Alan Yuhas, Guardian |  Read more:

Image: Wesley Hitt/Getty Images

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Duane Michals, Madame Schroedinger’s Cat, 1998
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The Hard-Won Lessons of the Solitary Years

When my then-boyfriend Mark lost the lease on his Brooklyn apartment, moving in together made good sense. We were in our 40s, both battle-scarred from decades of romantic unhappiness, and had finally found the relationship we had longed for our entire lives. So even though the timing was bad (we had been dating for only six months), we knew where this was headed. Why wait?

“I’m ready to take it to the next level,” said Mark, while cooking chicken paprikash in his soon-to-expire apartment.

I watched this sweet, handsome man sauté onions, and my heart turned upside down. After two decades of dating guys who could barely commit to next week, here was a wonderful man who wanted to be with me, plain and simple.

I was thrilled — and terrified. Sure, Mark and I were having a glorious time: weekends picking apples in the Pennsylvania countryside, brunches at his favorite Mexican diner. But living together was different. Or at least I thought it would be. I couldn’t know for sure. Because, to my deep embarrassment, I was nearly 40 and had never shared a home with a boyfriend.

For most of my adult life, I was unattached. I spent my 30s with a slowly escalating fear that I would never find a partner. My anxiety wasn’t merely about getting older and supposedly less desirable in our youth-obsessed culture. I also worried that my single years were shaping me, hardening me into a woman too finicky and insular for a lifetime partnership.

I had noticed that friends going through breakups often took solace in the fact that they had learned from those failed romances. They had acquired important skills such as how to be vulnerable, how to set boundaries, how to listen and how to speak up. They had learned the art of compromise and forgiveness and how to love someone even when you don’t always like them. Through practice and repetition, they were mastering this exquisite, complicated dance, cultivating wisdom and muscle memory that could be successfully applied to future relationships.

I was glad my friends had found an upside to their heartache, but statements like those also made me nervous. If one learned how to have a happy partnership by trial and error, then I was missing crucial on-the-job training.

Even so, when it came to the particular question of whether Mark and I should move in together, I knew my concerns were valid. “It’s too soon, and for the wrong reason,” I told my friend Paul at a bar one night.

He shook his head, looked at the ceiling and said, “No wonder you’re single.”

by Sara Eckel, NY Times |  Read more:

Image: Brian Rea

h/t YMFY

The Big Year

[ed. See also: Audubon Christmas Bird Count.]

Homer, Alaska - A wayward Siberian bird seen last month not only caught the attention of local and Alaska birders, it brought another visitor thousands of miles just to tag it.

That sighting of a rustic bunting by Massachusetts birder Neil Hayward helped him tie the record of 748 bird species seen in one year set in 1998 by Sandy Komito.

Last Saturday, Hayward broke Komito’s record — if three provisional species sightings stand — when he spotted a great skua in the Atlantic Ocean off Cape Hatteras, N.C.

The rustic bunting came as a 40th birthday present for Hayward, who flew all the way from Fort Lauderdale, Fla., to spot the rare bird. With the help of Homer bird guide Aaron Lang of Wilderness Birding, Hayward easily saw the rustic bunting flying with a group of juncos at a bird feeder on Hohe Street.

“That was a nice way to spend my birthday,” Hayward said last week in a phone interview from his home in Cambridge, Mass., near Boston. “It was kind of fitting that happened in Alaska. Alaska has been such a big part of my Big Year.”

Non-birders might be familiar with the idea of a Big Year from the book, “The Big Year: A Tale of Man, Nature, and Fowl Obsession” by Mark Obmascik, or the movie based on it, “The Big Year,” starring Jack Black, Owen Wilson and Steve Martin. Wilson played Kenny Bostick, the character based on Sandy Komito.

In a Big Year, birders attempt to see as many species of birds as possible in North America in one year. Sometimes birders are in ruthless competition, as shown in the movie, but in 2013, Hayward was way ahead of any other birder.

by Michael Armstrong, Homer News |  Read more:

Image: Neil Hayward

[ed. Nice hat. I've never understood why hipsters went for a porkpie when a fedora is so much classier]
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Civilian Photography, Now Rising to New Level

Five years ago, the DJI Phantom 2 Vision would have seemed like a science fiction film prop or a piece of surveillance hardware flown only by the sexiest of superspies. But it is the first camera-carrying drone you may want to own — and you could do that without spending thousands of dollars.

This drone is an intelligent, remote-controlled air vehicle that can fly far out of direct line of sight of its operator. It can record great video and photo stills from a thousand feet in the air over whatever “target” you can imagine. If it loses the connection to its remote control, it can even use GPS to fly automatically back to its launching point and land by itself. It is just like what you see on the news, only smaller, with about 20 to 25 minutes of flying time and less aggressive missions.

I’m not exaggerating here: From the moment I opened the (huge) box containing this four-bladed flying machine and its remote control, I felt a degree of wariness that I imagine you’d feel if a bit of a stealth bomber fell off and landed in your backyard.

But once that wariness wore off, and I’d gotten over the complexity of the hardware, the one word to sum up the Phantom 2 Vision is fun. Oh, my goodness, this thing is fun.

The Vision is the latest quadrocopter from DJI, which has been in the business for a relatively short while. It’s not a toy by any means — and at $1,200, it is certainly not cheap. But it’s a world away from those tiny $20 remote-control helicopters that probably filled many a stocking this Christmas. The Vision is serious hardware.

by Kit Eaton, NY Times |  Read more:

Image: Kit Eaton

A Speck in the Sea

Looking back, John Aldridge knew it was a stupid move. When you’re alone on the deck of a lobster boat in the middle of the night, 40 miles off the tip of Long Island, you don’t take chances. But he had work to do: He needed to start pumping water into the Anna Mary’s holding tanks to chill, so that when he and his partner, Anthony Sosinski, reached their first string of traps a few miles farther south, the water would be cold enough to keep the lobsters alive for the return trip. In order to get to the tanks, he had to open a metal hatch on the deck. And the hatch was covered by two 35-gallon Coleman coolers, giant plastic insulated ice chests that he and Sosinski filled before leaving the dock in Montauk harbor seven hours earlier. The coolers, full, weighed about 200 pounds, and the only way for Aldridge to move them alone was to snag a box hook onto the plastic handle of the bottom one, brace his legs, lean back and pull with all his might.

And then the handle snapped.

Suddenly Aldridge was flying backward, tumbling across the deck toward the back of the boat, which was wide open, just a flat, slick ramp leading straight into the black ocean a few inches below. Aldridge grabbed for the side of the boat as it went past, his fingertips missing it by inches. The water hit him like a slap. He went under, took in a mouthful of Atlantic Ocean and then surfaced, sputtering. He yelled as loud as he could, hoping to wake Sosinski, who was asleep on a bunk below the front deck. But the diesel engine was too loud, and the Anna Mary, on autopilot, moving due south at six and a half knots, was already out of reach, its navigation lights receding into the night. Aldridge shouted once more, panic rising in his throat, and then silence descended. He was alone in the darkness. A single thought gripped his mind: This is how I’m going to die. (...)

The first thing you’re supposed to do, if you’re a fisherman and you fall in the ocean, is to kick off your boots. They’re dead weight that will pull you down. But as Aldridge treaded water, he realized that his boots were not pulling him down; in fact, they were lifting him up, weirdly elevating his feet and tipping him backward. Aldridge’s boots were an oddity among the members of Montauk’s commercial fishing fleet: thick green rubber monstrosities that were guaranteed to keep your feet warm down to minus 58 degrees Fahrenheit, a temperature Montauk had not experienced since the ice age. Sosinski made fun of the boots, but Aldridge liked them: they were comfortable and sturdy and easy to slip on and off. And now, as he bobbed in the Atlantic, he had an idea of how they might save his life.

Treading water awkwardly, Aldridge reached down and pulled off his left boot. Straining, he turned it upside down, raised it up until it cleared the waves, then plunged it back into the water, trapping a boot-size bubble of air inside. He tucked the inverted boot under his left armpit. Then he did the same thing with the right boot. It worked; they were like twin pontoons, and treading water with his feet alone was now enough to keep him stable and afloat.

The boots gave Aldridge a chance to think. He wasn’t going to sink — not right away, anyway. But he was still in a very bad situation. He tried to take stock: It was about 3:30 a.m. on July 24, a clear, starry night lit by a full moon. The wind was calm, but there was a five-foot swell, a remnant of a storm that blew through a couple of days earlier. The North Atlantic water was chilly — 72 degrees — but bearable, for now. Dawn was still two hours away. Aldridge set a goal, the first of many he would assign himself that day: Just stay afloat till sunrise.

by Paul Tough, NY Times |  Read more:

Image: Daniel Shea

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Fiona Apple

Silver Ball Revival

For $13, you can play pinball until your arms fall off at Seattle's working pinball museum.

The two-story storefront in Seattle's International District is filled with games from every era from the 1960s to today.

The museum, which houses about 50 or so machines, started in 2010 as one couple's obsession and grew to be something they wanted to share with others, or as Cindy Martin puts it: a good solution when they ran out of space in their garage.

"Any serious collector will tell you collecting these machines is an incurable disease," said Charlie Martin, her husband and business partner.

They keep the equipment fixed up — with some help from other collectors — offer brief historical information and "fun" ratings on small cards above the games and sell snacks, beer and soda to visitors from around the world.

The Seattle museum is one of a handful around the country celebrating a pastime that seems to be in the midst of revival.

by Donna Gordon Blankenship, AP |  Read more:

Image: Jim Young, Reuters

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Why Didn't the Creator of Hashtag Patent the Concept?

[ed. See also: How did the idea for hashtags originate on Twitter?]

For two reasons, primarily:

1. claiming a government-granted monopoly on the use of hashtags would have likely inhibited their adoption, which was the antithesis of what I was hoping for, which was broad-based adoption and support — across networks and mediums.
2. I had no interest in making money (directly) off hashtags. They are born of the Internet, and should be owned by no one. The value and satisfaction I derive from seeing my funny little hack used as widely as it is today is valuable enough for me to be relieved that I had the foresight not to try to lock down this stupidly simple but effective idea.

Chris Messina, Creator of the hastag via: Quora

Image via The Guardian

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