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#434823 The Tangled Web of Turning Spider Silk ...

Spider-Man is one of the most popular superheroes of all time. It’s a bit surprising given that one of the more common phobias is arachnophobia—a debilitating fear of spiders.

Perhaps more fantastical is that young Peter Parker, a brainy high school science nerd, seemingly developed overnight the famous web-shooters and the synthetic spider silk that he uses to swing across the cityscape like Tarzan through the jungle.

That’s because scientists have been trying for decades to replicate spider silk, a material that is five times stronger than steel, among its many superpowers. In recent years, researchers have been untangling the protein-based fiber’s structure down to the molecular level, leading to new insights and new potential for eventual commercial uses.

The applications for such a material seem near endless. There’s the more futuristic visions, like enabling robotic “muscles” for human-like movement or ensnaring real-life villains with a Spider-Man-like web. Near-term applications could include the biomedical industry, such as bandages and adhesives, and as a replacement textile for everything from rope to seat belts to parachutes.

Spinning Synthetic Spider Silk
Randy Lewis has been studying the properties of spider silk and developing methods for producing it synthetically for more than three decades. In the 1990s, his research team was behind cloning the first spider silk gene, as well as the first to identify and sequence the proteins that make up the six different silks that web slingers make. Each has different mechanical properties.

“So our thought process was that you could take that information and begin to to understand what made them strong and what makes them stretchy, and why some are are very stretchy and some are not stretchy at all, and some are stronger and some are weaker,” explained Lewis, a biology professor at Utah State University and director of the Synthetic Spider Silk Lab, in an interview with Singularity Hub.

Spiders are naturally territorial and cannibalistic, so any intention to farm silk naturally would likely end in an orgy of arachnid violence. Instead, Lewis and company have genetically modified different organisms to produce spider silk synthetically, including inserting a couple of web-making genes into the genetic code of goats. The goats’ milk contains spider silk proteins.

The lab also produces synthetic spider silk through a fermentation process not entirely dissimilar to brewing beer, but using genetically modified bacteria to make the desired spider silk proteins. A similar technique has been used for years to make a key enzyme in cheese production. More recently, companies are using transgenic bacteria to make meat and milk proteins, entirely bypassing animals in the process.

The same fermentation technology is used by a chic startup called Bolt Threads outside of San Francisco that has raised more than $200 million for fashionable fibers made out of synthetic spider silk it calls Microsilk. (The company is also developing a second leather-like material, Mylo, using the underground root structure of mushrooms known as mycelium.)

Lewis’ lab also uses transgenic silkworms to produce a kind of composite material made up of the domesticated insect’s own silk proteins and those of spider silk. “Those have some fairly impressive properties,” Lewis said.

The researchers are even experimenting with genetically modified alfalfa. One of the big advantages there is that once the spider silk protein has been extracted, the remaining protein could be sold as livestock feed. “That would bring the cost of spider silk protein production down significantly,” Lewis said.

Building a Better Web
Producing synthetic spider silk isn’t the problem, according to Lewis, but the ability to do it at scale commercially remains a sticking point.

Another challenge is “weaving” the synthetic spider silk into usable products that can take advantage of the material’s marvelous properties.

“It is possible to make silk proteins synthetically, but it is very hard to assemble the individual proteins into a fiber or other material forms,” said Markus Buehler, head of the Department of Civil and Environmental Engineering at MIT, in an email to Singularity Hub. “The spider has a complex spinning duct in which silk proteins are exposed to physical forces, chemical gradients, the combination of which generates the assembly of molecules that leads to silk fibers.”

Buehler recently co-authored a paper in the journal Science Advances that found dragline spider silk exhibits different properties in response to changes in humidity that could eventually have applications in robotics.

Specifically, spider silk suddenly contracts and twists above a certain level of relative humidity, exerting enough force to “potentially be competitive with other materials being explored as actuators—devices that move to perform some activity such as controlling a valve,” according to a press release.

Studying Spider Silk Up Close
Recent studies at the molecular level are helping scientists learn more about the unique properties of spider silk, which may help researchers develop materials with extraordinary capabilities.

For example, scientists at Arizona State University used magnetic resonance tools and other instruments to image the abdomen of a black widow spider. They produced what they called the first molecular-level model of spider silk protein fiber formation, providing insights on the nanoparticle structure. The research was published last October in Proceedings of the National Academy of Sciences.

A cross section of the abdomen of a black widow (Latrodectus Hesperus) spider used in this study at Arizona State University. Image Credit: Samrat Amin.
Also in 2018, a study presented in Nature Communications described a sort of molecular clamp that binds the silk protein building blocks, which are called spidroins. The researchers observed for the first time that the clamp self-assembles in a two-step process, contributing to the extensibility, or stretchiness, of spider silk.

Another team put the spider silk of a brown recluse under an atomic force microscope, discovering that each strand, already 1,000 times thinner than a human hair, is made up of thousands of nanostrands. That helps explain its extraordinary tensile strength, though technique is also a factor, as the brown recluse uses a special looping method to reinforce its silk strands. The study also appeared last year in the journal ACS Macro Letters.

Making Spider Silk Stick
Buehler said his team is now trying to develop better and faster predictive methods to design silk proteins using artificial intelligence.

“These new methods allow us to generate new protein designs that do not naturally exist and which can be explored to optimize certain desirable properties like torsional actuation, strength, bioactivity—for example, tissue engineering—and others,” he said.

Meanwhile, Lewis’ lab has discovered a method that allows it to solubilize spider silk protein in what is essentially a water-based solution, eschewing acids or other toxic compounds that are normally used in the process.

That enables the researchers to develop materials beyond fiber, including adhesives that “are better than an awful lot of the current commercial adhesives,” Lewis said, as well as coatings that could be used to dampen vibrations, for example.

“We’re making gels for various kinds of of tissue regeneration, as well as drug delivery, and things like that,” he added. “So we’ve expanded the use profile from something beyond fibers to something that is a much more extensive portfolio of possible kinds of materials.”

And, yes, there’s even designs at the Synthetic Spider Silk Lab for developing a Spider-Man web-slinger material. The US Navy is interested in non-destructive ways of disabling an enemy vessel, such as fouling its propeller. The project also includes producing synthetic proteins from the hagfish, an eel-like critter that exudes a gelatinous slime when threatened.

Lewis said that while the potential for spider silk is certainly headline-grabbing, he cautioned that much of the hype is not focused on the unique mechanical properties that could lead to advances in healthcare and other industries.

“We want to see spider silk out there because it’s a unique material, not because it’s got marketing appeal,” he said.

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#433895 Sci-Fi Movies Are the Secret Weapon That ...

If there’s one line that stands the test of time in Steven Spielberg’s 1993 classic Jurassic Park, it’s probably Jeff Goldblum’s exclamation, “Your scientists were so preoccupied with whether or not they could, they didn’t stop to think if they should.”

Goldblum’s character, Dr. Ian Malcolm, was warning against the hubris of naively tinkering with dinosaur DNA in an effort to bring these extinct creatures back to life. Twenty-five years on, his words are taking on new relevance as a growing number of scientists and companies are grappling with how to tread the line between “could” and “should” in areas ranging from gene editing and real-world “de-extinction” to human augmentation, artificial intelligence and many others.

Despite growing concerns that powerful emerging technologies could lead to unexpected and wide-ranging consequences, innovators are struggling with how to develop beneficial new products while being socially responsible. Part of the answer could lie in watching more science fiction movies like Jurassic Park.

Hollywood Lessons in Societal Risks
I’ve long been interested in how innovators and others can better understand the increasingly complex landscape around the social risks and benefits associated with emerging technologies. Growing concerns over the impacts of tech on jobs, privacy, security and even the ability of people to live their lives without undue interference highlight the need for new thinking around how to innovate responsibly.

New ideas require creativity and imagination, and a willingness to see the world differently. And this is where science fiction movies can help.

Sci-fi flicks are, of course, notoriously unreliable when it comes to accurately depicting science and technology. But because their plots are often driven by the intertwined relationships between people and technology, they can be remarkably insightful in revealing social factors that affect successful and responsible innovation.

This is clearly seen in Jurassic Park. The movie provides a surprisingly good starting point for thinking about the pros and cons of modern-day genetic engineering and the growing interest in bringing extinct species back from the dead. But it also opens up conversations around the nature of complex systems that involve both people and technology, and the potential dangers of “permissionless” innovation that’s driven by power, wealth and a lack of accountability.

Similar insights emerge from a number of other movies, including Spielberg’s 2002 film “Minority Report”—which presaged a growing capacity for AI-enabled crime prediction and the ethical conundrums it’s raising—as well as the 2014 film Ex Machina.

As with Jurassic Park, Ex Machina centers around a wealthy and unaccountable entrepreneur who is supremely confident in his own abilities. In this case, the technology in question is artificial intelligence.

The movie tells a tale of an egotistical genius who creates a remarkable intelligent machine—but he lacks the awareness to recognize his limitations and the risks of what he’s doing. It also provides a chilling insight into potential dangers of creating machines that know us better than we know ourselves, while not being bound by human norms or values.

The result is a sobering reminder of how, without humility and a good dose of humanity, our innovations can come back to bite us.

The technologies in Jurassic Park, Minority Report, and Ex Machina lie beyond what is currently possible. Yet these films are often close enough to emerging trends that they help reveal the dangers of irresponsible, or simply naive, innovation. This is where these and other science fiction movies can help innovators better understand the social challenges they face and how to navigate them.

Real-World Problems Worked Out On-Screen
In a recent op-ed in the New York Times, journalist Kara Swisher asked, “Who will teach Silicon Valley to be ethical?” Prompted by a growing litany of socially questionable decisions amongst tech companies, Swisher suggests that many of them need to grow up and get serious about ethics. But ethics alone are rarely enough. It’s easy for good intentions to get swamped by fiscal pressures and mired in social realities.

Elon Musk has shown that brilliant tech innovators can take ethical missteps along the way. Image Credit:AP Photo/Chris Carlson
Technology companies increasingly need to find some way to break from business as usual if they are to become more responsible. High-profile cases involving companies like Facebook and Uber as well as Tesla’s Elon Musk have highlighted the social as well as the business dangers of operating without fully understanding the consequences of people-oriented actions.

Many more companies are struggling to create socially beneficial technologies and discovering that, without the necessary insights and tools, they risk blundering about in the dark.

For instance, earlier this year, researchers from Google and DeepMind published details of an artificial intelligence-enabled system that can lip-read far better than people. According to the paper’s authors, the technology has enormous potential to improve the lives of people who have trouble speaking aloud. Yet it doesn’t take much to imagine how this same technology could threaten the privacy and security of millions—especially when coupled with long-range surveillance cameras.

Developing technologies like this in socially responsible ways requires more than good intentions or simply establishing an ethics board. People need a sophisticated understanding of the often complex dynamic between technology and society. And while, as Mozilla’s Mitchell Baker suggests, scientists and technologists engaging with the humanities can be helpful, it’s not enough.

An Easy Way into a Serious Discipline
The “new formulation” of complementary skills Baker says innovators desperately need already exists in a thriving interdisciplinary community focused on socially responsible innovation. My home institution, the School for the Future of Innovation in Society at Arizona State University, is just one part of this.

Experts within this global community are actively exploring ways to translate good ideas into responsible practices. And this includes the need for creative insights into the social landscape around technology innovation, and the imagination to develop novel ways to navigate it.

People love to come together as a movie audience.Image credit: The National Archives UK, CC BY 4.0
Here is where science fiction movies become a powerful tool for guiding innovators, technology leaders and the companies where they work. Their fictional scenarios can reveal potential pitfalls and opportunities that can help steer real-world decisions toward socially beneficial and responsible outcomes, while avoiding unnecessary risks.

And science fiction movies bring people together. By their very nature, these films are social and educational levelers. Look at who’s watching and discussing the latest sci-fi blockbuster, and you’ll often find a diverse cross-section of society. The genre can help build bridges between people who know how science and technology work, and those who know what’s needed to ensure they work for the good of society.

This is the underlying theme in my new book Films from the Future: The Technology and Morality of Sci-Fi Movies. It’s written for anyone who’s curious about emerging trends in technology innovation and how they might potentially affect society. But it’s also written for innovators who want to do the right thing and just don’t know where to start.

Of course, science fiction films alone aren’t enough to ensure socially responsible innovation. But they can help reveal some profound societal challenges facing technology innovators and possible ways to navigate them. And what better way to learn how to innovate responsibly than to invite some friends round, open the popcorn and put on a movie?

It certainly beats being blindsided by risks that, with hindsight, could have been avoided.

Andrew Maynard, Director, Risk Innovation Lab, Arizona State University

This article is republished from The Conversation under a Creative Commons license. Read the original article.

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#432878 Chinese Port Goes Full Robot With ...

By the end of 2018, something will be very different about the harbor area in the northern Chinese city of Caofeidian. If you were to visit, the whirring cranes and tractors driving containers to and fro would be the only things in sight.

Caofeidian is set to become the world’s first fully autonomous harbor by the end of the year. The US-Chinese startup TuSimple, a specialist in developing self-driving trucks, will replace human-driven terminal tractor-trucks with 20 self-driving models. A separate company handles crane automation, and a central control system will coordinate the movements of both.

According to Robert Brown, Director of Public Affairs at TuSimple, the project could quickly transform into a much wider trend. “The potential for automating systems in harbors and ports is staggering when considering the number of deep-water and inland ports around the world. At the same time, the closed, controlled nature of a port environment makes it a perfect proving ground for autonomous truck technology,” he said.

Going Global
The autonomous cranes and trucks have a big task ahead of them. Caofeidian currently processes around 300,000 TEU containers a year. Even if you were dealing with Lego bricks, that number of units would get you a decent-sized cathedral or a 22-foot-long aircraft carrier. For any maritime fans—or people who enjoy the moving of heavy objects—TEU stands for twenty-foot equivalent unit. It is the industry standard for containers. A TEU equals an 8-foot (2.43 meter) wide, 8.5-foot (2.59 meter) high, and 20-foot (6.06 meter) long container.

While impressive, the Caofeidian number pales in comparison with the biggest global ports like Shanghai, Singapore, Busan, or Rotterdam. For example, 2017 saw more than 40 million TEU moved through Shanghai port facilities.

Self-driving container vehicles have been trialled elsewhere, including in Yangshan, close to Shanghai, and Rotterdam. Qingdao New Qianwan Container Terminal in China recently laid claim to being the first fully automated terminal in Asia.

The potential for efficiencies has many ports interested in automation. Qingdao said its systems allow the terminal to operate in complete darkness and have reduced labor costs by 70 percent while increasing efficiency by 30 percent. In some cases, the number of workers needed to unload a cargo ship has gone from 60 to 9.

TuSimple says it is in negotiations with several other ports and also sees potential in related logistics-heavy fields.

Stable Testing Ground
For autonomous vehicles, ports seem like a perfect testing ground. They are restricted, confined areas with few to no pedestrians where operating speeds are limited. The predictability makes it unlike, say, city driving.

Robert Brown describes it as an ideal setting for the first adaptation of TuSimple’s technology. The company, which, amongst others, is backed by chipmaker Nvidia, have been retrofitting existing vehicles from Shaanxi Automobile Group with sensors and technology.

At the same time, it is running open road tests in Arizona and China of its Class 8 Level 4 autonomous trucks.

The Camera Approach
Dozens of autonomous truck startups are reported to have launched in China over the past two years. In other countries the situation is much the same, as the race for the future of goods transportation heats up. Startup companies like Embark, Einride, Starsky Robotics, and Drive.ai are just a few of the names in the space. They are facing competition from the likes of Tesla, Daimler, VW, Uber’s Otto subsidiary, and in March, Waymo announced it too was getting into the truck race.

Compared to many of its competitors, TuSimple’s autonomous driving system is based on a different approach. Instead of laser-based radar (LIDAR), TuSimple primarily uses cameras to gather data about its surroundings. Currently, the company uses ten cameras, including forward-facing, backward-facing, and wide-lens. Together, they produce the 360-degree “God View” of the vehicle’s surroundings, which is interpreted by the onboard autonomous driving systems.

Each camera gathers information at 30 frames a second. Millimeter wave radar is used as a secondary sensor. In total, the vehicles generate what Robert Brown describes with a laugh as “almost too much” data about its surroundings and is accurate beyond 300 meters in locating and identifying objects. This includes objects that have given LIDAR problems, such as black vehicles.

Another advantage is price. Companies often loathe revealing exact amounts, but Tesla has gone as far as to say that the ‘expected’ price of its autonomous truck will be from $150,0000 and upwards. While unconfirmed, TuSimple’s retrofitted, camera-based solution is thought to cost around $20,000.

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#430830 Biocomputers Made From Cells Can Now ...

When it comes to biomolecules, RNA doesn’t get a lot of love.
Maybe you haven’t even heard of the silent workhorse. RNA is the cell’s de facto translator: like a game of telephone, RNA takes DNA’s genetic code to a cellular factory called ribosomes. There, the cell makes proteins based on RNA’s message.
But RNA isn’t just a middleman. It controls what proteins are formed. Because proteins wiz around the cell completing all sorts of important processes, you can say that RNA is the gatekeeper: no RNA message, no proteins, no life.
In a new study published in Nature, RNA finally took center stage. By adding bits of genetic material to the E. Coli bacteria, a team of biohackers at the Wyss Institute hijacked the organism’s RNA messengers so that they only spring into action following certain inputs.
The result? A bacterial biocomputer capable of performing 12-input logic operations—AND, OR, and NOT—following specific inputs. Rather than outputting 0s and 1s, these biocircuits produce results based on the presence or absence of proteins and other molecules.
“It’s the greatest number of inputs in a circuit that a cell has been able to process,” says study author Dr. Alexander Green at Arizona State University. “To be able to analyze those signals and make a decision is the big advance here.”
When given a specific set of inputs, the bacteria spit out a protein that made them glow neon green under fluorescent light.
But synthetic biology promises far more than just a party trick—by tinkering with a cell’s RNA repertoire, scientists may one day coax them to photosynthesize, produce expensive drugs on the fly, or diagnose and hunt down rogue tumor cells.
Illustration of an RNA-based ‘ribocomputing’ device that makes logic-based decisions in living cells. The long gate RNA (blue) detects the binding of an input RNA (red). The ribosome (purple/mauve) reads the gate RNA to produce an output protein. Image Credit: Alexander Green / Arizona State University
The software of life
This isn’t the first time that scientists hijacked life’s algorithms to reprogram cells into nanocomputing systems. Previous work has already introduced to the world yeast cells that can make anti-malaria drugs from sugar or mammalian cells that can perform Boolean logic.
Yet circuits with multiple inputs and outputs remain hard to program. The reason is this: synthetic biologists have traditionally focused on snipping, fusing, or otherwise arranging a cell’s DNA to produce the outcomes they want.
But DNA is two steps removed from proteins, and tinkering with life’s code often leads to unexpected consequences. For one, the cell may not even accept and produce the extra bits of DNA code. For another, the added code, when transformed into proteins, may not act accordingly in the crowded and ever-changing environment of the cell.
What’s more, tinkering with one gene is often not enough to program an entirely new circuit. Scientists often need to amp up or shut down the activity of multiple genes, or multiple biological “modules” each made up of tens or hundreds of genes.
It’s like trying to fit new Lego pieces in a specific order into a room full of Lego constructions. Each new piece has the potential to wander off track and click onto something it’s not supposed to touch.
Getting every moving component to work in sync—as you might have guessed—is a giant headache.
The RNA way
With “ribocomputing,” Green and colleagues set off to tackle a main problem in synthetic biology: predictability.
Named after the “R (ribo)” in “RNA,” the method grew out of an idea that first struck Green back in 2012.
“The synthetic biological circuits to date have relied heavily on protein-based regulators that are difficult to scale up,” Green wrote at the time. We only have a limited handful of “designable parts” that work well, and these circuits require significant resources to encode and operate, he explains.
RNA, in comparison, is a lot more predictable. Like its more famous sibling DNA, RNA is composed of units that come in four different flavors: A, G, C, and U. Although RNA is only single-stranded, rather than the double helix for which DNA is known for, it can bind short DNA-like sequences in a very predictable manner: Gs always match up with Cs and As always with Us.
Because of this predictability, it’s possible to design RNA components that bind together perfectly. In other words, it reduces the chance that added RNA bits might go rogue in an unsuspecting cell.
Normally, once RNA is produced it immediately rushes to the ribosome—the cell’s protein-building factory. Think of it as a constantly “on” system.
However, Green and his team found a clever mechanism to slow them down. Dubbed the “toehold switch,” it works like this: the artificial RNA component is first incorporated into a chain of A, G, C, and U folded into a paperclip-like structure.
This blocks the RNA from accessing the ribosome. Because one RNA strand generally maps to one protein, the switch prevents that protein from ever getting made.
In this way, the switch is set to “off” by default—a “NOT” gate, in Boolean logic.
To activate the switch, the cell needs another component: a “trigger RNA,” which binds to the RNA toehold switch. This flips it on: the RNA grabs onto the ribosome, and bam—proteins.
BioLogic gates
String a few RNA switches together, with the activity of each one relying on the one before, and it forms an “AND” gate. Alternatively, if the activity of each switch is independent, that’s an “OR” gate.
“Basically, the toehold switches performed so well that we wanted to find a way to best exploit them for cellular applications,” says Green. They’re “kind of the equivalent of your first transistors,” he adds.
Once the team optimized the designs for different logic gates, they carefully condensed the switches into “gate RNA” molecules. These gate RNAs contain both codes for proteins and the logic operations needed to kickstart the process—a molecular logic circuit, so to speak.
If you’ve ever played around with an Arduino-controlled electrical circuit, you probably know the easiest way to test its function is with a light bulb.
That’s what the team did here, though with a biological bulb: green fluorescent protein, a light-sensing protein not normally present in bacteria that—when turned on—makes the microbugs glow neon green.
In a series of experiments, Green and his team genetically inserted gate RNAs into bacteria. Then, depending on the type of logical function, they added different combinations of trigger RNAs—the inputs.
When the input RNA matched up with its corresponding gate RNA, it flipped on the switch, causing the cell to light up.

Their most complex circuit contained five AND gates, five OR gates, and two NOTs—a 12-input ribocomputer that functioned exactly as designed.
That’s quite the achievement. “Everything is interacting with everything else and there are a million ways those interactions could flip the switch on accident,” says RNA researcher Dr. Julies Lucks at Northwestern University.
The specificity is thanks to RNA, the authors explain. Because RNAs bind to others so predictably, we can now design massive libraries of gate and trigger units to mix-and-match into all types of nano-biocomputers.
RNA BioNanobots
Although the technology doesn’t have any immediate applications, the team has high hopes.
For the first time, it’s now possible to massively scale up the process of programming new circuits into living cells. We’ve expanded the library of available biocomponents that can be used to reprogram life’s basic code, the authors say.
What’s more, when freeze-dried onto a piece of tissue paper, RNA keeps very well. We could potentially print RNA toehold switches onto paper that respond to viruses or to tumor cells, the authors say, essentially transforming the technology into highly accurate diagnostic platforms.
But Green’s hopes are even wilder for his RNA-based circuits.
“Because we’re using RNA, a universal molecule of life, we know these interactions can also work in other cells, so our method provides a general strategy that could be ported to other organisms,” he says.
Ultimately, the hope is to program neural network-like capabilities into the body’s other cells.
Imagine cells endowed with circuits capable of performing the kinds of computation the brain does, the authors say.
Perhaps one day, synthetic biology will transform our own cells into fully programmable entities, turning us all into biological cyborgs from the inside. How wild would that be?
Image Credit: Wyss Institute at Harvard University Continue reading

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