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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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#430734 Why XPRIZE Is Asking Writers to Take Us ...

In a world of accelerating change, educating the public about the implications of technological advancements is extremely important. We can continue to write informative articles and speculate about the kind of future that lies ahead. Or instead, we can take readers on an immersive journey by using science fiction to paint vivid images of the future for society.
The XPRIZE Foundation recently announced a science fiction storytelling competition. In recent years, the organization has backed and launched a range of competitions to propel innovation in science and technology. These have been aimed at a variety of challenges, such as transforming the lives of low-literacy adults, tackling climate change, and creating water from thin air.
Their sci-fi writing competition asks participants to envision a groundbreaking future for humanity. The initiative, in partnership with Japanese airline ANA, features 22 sci-fi stories from noteworthy authors that are now live on the website. Each of these stories is from the perspective of a different passenger on a plane that travels 20 years into the future through a wormhole. Contestants will compete to tell the story of the passenger in Seat 14C.
In addition to the competition, XPRIZE has brought together a science fiction advisory council to work with the organization and imagine what the future will look like. According to Peter Diamandis, founder and executive chairman, “As the future becomes harder and harder to predict, we look forward to engaging some of the world’s most visionary storytellers to help us imagine what’s just beyond the horizon and chart a path toward a future of abundance.”
The Importance of Science Fiction
Why is an organization like XPRIZE placing just as much importance on fiction as it does on reality? As Isaac Asimov has pointed out, “Modern science fiction is the only form of literature that consistently considers the nature of the changes that face us.” While the rest of the world reports on a new invention, sci-fi authors examine how these advancements affect the human condition.
True science fiction is distinguished from pure fantasy in that everything that happens is within the bounds of the physical laws of the universe. We’ve already seen how sci-fi can inspire generations and shape the future. 3D printers, wearable technology, and smartphones were first seen in Star Trek. Targeted advertising and air touch technology was first seen in Philip K. Dick’s 1958 story “The Minority Report.” Tanning beds, robot vacuums, and flatscreen TVs were seen in The Jetsons. The internet and a world of global instant communication was predicted by Arthur C. Clarke in his work long before it became reality.
Sci-fi shows like Black Mirror or Star Trek aren’t just entertainment. They allow us to imagine and explore the influence of technology on humanity. For instance, how will artificial intelligence impact human relationships? How will social media affect privacy? What if we encounter alien life? Good sci-fi stories take us on journeys that force us to think critically about the societal impacts of technological advancements.
As sci-fi author Yaasha Moriah points out, the genre is universal because “it tackles hard questions about human nature, morality, and the evolution of society, all through the narrative of speculation about the future. If we continue to do A, will it necessarily lead to problems B and C? What implicit lessons are being taught when we insist on a particular policy? When we elevate the importance of one thing over another—say, security over privacy—what could be the potential benefits and dangers of that mentality? That’s why science fiction has such an enduring appeal. We want to explore deep questions, without being preached at. We want to see the principles in action, and observe their results.”
An Extension of STEAM Education
At its core, this genre is a harmonious symbiosis between two distinct disciplines: science and literature. It is an extension of STEAM education, an educational approach that combines science, technology, engineering, the arts, and mathematics. Story-telling with science fiction allows us to use the arts in order to educate and engage the public about scientific advancements and its implications.
According to the National Science Foundation, research on art-based learning of STEM, including the use of narrative writing, works “beyond expectation.” It has been shown to have a powerful impact on creative thinking, collaborative behavior and application skills.
What does it feel like to travel through a wormhole? What are some ethical challenges of AI? How could we terraform Mars? For decades, science fiction writers and producers have answered these questions through the art of storytelling.
What better way to engage more people with science and technology than through sparking their imaginations? The method makes academic subject areas many traditionally perceived as boring or dry far more inspiring and engaging.
A Form of Time Travel
XPRIZE’s competition theme of traveling 20 years into the future through a wormhole is an appropriate beacon for the genre. In many ways, sci-fi is a precautionary form of time travel. Before we put a certain technology, scientific invention, or policy to use, we can envision and explore what our world would be like if we were to do so.
Sci-fi lets us explore different scenarios for the future of humanity before deciding which ones are more desirable. Some of these scenarios may be radically beyond our comfort zone. Yet when we’re faced with the seemingly impossible, we must remind ourselves that if something is within the domain of the physical laws of the universe, then it’s absolutely possible.
Stock Media provided by NASA_images / Pond5 Continue reading

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#430579 What These Lifelike Androids Can Teach ...

For Dr. Hiroshi Ishiguro, one of the most interesting things about androids is the changing questions they pose us, their creators, as they evolve. Does it, for example, do something to the concept of being human if a human-made creation starts telling you about what kind of boys ‘she’ likes?
If you want to know the answer to the boys question, you need to ask ERICA, one of Dr. Ishiguro’s advanced androids. Beneath her plastic skull and silicone skin, wires connect to AI software systems that bring her to life. Her ability to respond goes far beyond standard inquiries. Spend a little time with her, and the feeling of a distinct personality starts to emerge. From time to time, she works as a receptionist at Dr. Ishiguro and his team’s Osaka University labs. One of her android sisters is an actor who has starred in plays and a film.

ERICA’s ‘brother’ is an android version of Dr. Ishiguro himself, which has represented its creator at various events while the biological Ishiguro can remain in his offices in Japan. Microphones and cameras capture Ishiguro’s voice and face movements, which are relayed to the android. Apart from mimicking its creator, the Geminoid™ android is also capable of lifelike blinking, fidgeting, and breathing movements.
Say hello to relaxation
As technological development continues to accelerate, so do the possibilities for androids. From a position as receptionist, ERICA may well branch out into many other professions in the coming years. Companion for the elderly, comic book storyteller (an ancient profession in Japan), pop star, conversational foreign language partner, and newscaster are some of the roles and responsibilities Dr. Ishiguro sees androids taking on in the near future.
“Androids are not uncanny anymore. Most people adapt to interacting with Erica very quickly. Actually, I think that in interacting with androids, which are still different from us, we get a better appreciation of interacting with other cultures. In both cases, we are talking with someone who is different from us and learn to overcome those differences,” he says.
A lot has been written about how robots will take our jobs. Dr. Ishiguro believes these fears are blown somewhat out of proportion.
“Robots and androids will take over many simple jobs. Initially there might be some job-related issues, but new schemes, like for example a robot tax similar to the one described by Bill Gates, should help,” he says.
“Androids will make it possible for humans to relax and keep evolving. If we compare the time we spend studying now compared to 100 years ago, it has grown a lot. I think it needs to keep growing if we are to keep expanding our scientific and technological knowledge. In the future, we might end up spending 20 percent of our lifetime on work and 80 percent of the time on education and growing our skills.”
Android asks who you are
For Dr. Ishiguro, another aspect of robotics in general, and androids in particular, is how they question what it means to be human.
“Identity is a very difficult concept for humans sometimes. For example, I think clothes are part of our identity, in a way that is similar to our faces and bodies. We don’t change those from one day to the next, and that is why I have ten matching black outfits,” he says.
This link between physical appearance and perceived identity is one of the aspects Dr. Ishiguro is exploring. Another closely linked concept is the connection between body and feeling of self. The Ishiguro avatar was once giving a presentation in Austria. Its creator recalls how he felt distinctly like he was in Austria, even capable of feeling sensation of touch on his own body when people laid their hands on the android. If he was distracted, he felt almost ‘sucked’ back into his body in Japan.
“I am constantly thinking about my life in this way, and I believe that androids are a unique mirror that helps us formulate questions about why we are here and why we have been so successful. I do not necessarily think I have found the answers to these questions, so if you have, please share,” he says with a laugh.
His work and these questions, while extremely interesting on their own, become extra poignant when considering the predicted melding of mind and machine in the near future.
The ability to be present in several locations through avatars—virtual or robotic—raises many questions of both philosophical and practical nature. Then add the hypotheticals, like why send a human out onto the hostile surface of Mars if you could send a remote-controlled android, capable of relaying everything it sees, hears and feels?
The two ways of robotics will meet
Dr. Ishiguro sees the world of AI-human interaction as currently roughly split into two. One is the chat-bot approach that companies like Amazon, Microsoft, Google, and recently Apple, employ using stationary objects like speakers. Androids like ERICA represent another approach.
“It is about more than the form factor. I think that the android approach is generally more story-based. We are integrating new conversation features based on assumptions about the situation and running different scenarios that expand the android’s vocabulary and interactions. Another aspect we are working on is giving androids desire and intention. Like with people, androids should have desires and intentions in order for you to want to interact with them over time,” Dr. Ishiguro explains.
This could be said to be part of a wider trend for Japan, where many companies are developing human-like robots that often have some Internet of Things capabilities, making them able to handle some of the same tasks as an Amazon Echo. The difference in approach could be summed up in the words ‘assistant’ (Apple, Amazon, etc.) and ‘companion’ (Japan).
Dr. Ishiguro sees this as partly linked to how Japanese as a language—and market—is somewhat limited. This has a direct impact on viability and practicality of ‘pure’ voice recognition systems. At the same time, Japanese people have had greater exposure to positive images of robots, and have a different cultural / religious view of objects having a ‘soul’. However, it may also mean Japanese companies and android scientists are both stealing a lap on their western counterparts.
“If you speak to an Amazon Echo, that is not a natural way to interact for humans. This is part of why we are making human-like robot systems. The human brain is set up to recognize and interact with humans. So, it makes sense to focus on developing the body for the AI mind, as well as the AI. I believe that the final goal for both Japanese and other companies and scientists is to create human-like interaction. Technology has to adapt to us, because we cannot adapt fast enough to it, as it develops so quickly,” he says.
Banner image courtesy of Hiroshi Ishiguro Laboratories, ATR all rights reserved.
Dr. Ishiguro’s team has collaborated with partners and developed a number of android systems:
Geminoid™ HI-2 has been developed by Hiroshi Ishiguro Laboratories and Advanced Telecommunications Research Institute International (ATR).
Geminoid™ F has been developed by Osaka University and Hiroshi Ishiguro Laboratories, Advanced Telecommunications Research Institute International (ATR).
ERICA has been developed by ERATO ISHIGURO Symbiotic Human-Robot Interaction Project Continue reading

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#429969 Mimicking the human hand

Tactile robot hands that copy the complexity of the human hand, including “touch” are already here. A bit creepy, if you ask me…

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#428908 The ‘Gentle Bot’ can pick ...

Cornell University researchers have developed a soft, human-like, robotic hand with interior and exterior sensors that “feels” what it touches via stretchy optical waveguides with LEDs.

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