Functioning ‘mechanical gears’ seen in nature for the first time (2013)

The gear teeth on the opposing hind-legs lock together like those in a car gear-box, ensuring almost complete synchronicity in leg movement - the legs always move within 30 ‘microseconds’ of each other, with one microsecond equal to a millionth of a second.

Previously believed to be only man-made, a natural example of a functioning gear mechanism has been discovered in a common insect - showing that evolution developed interlocking cogs long before we did.

"In Issus, the skeleton is used to solve a complex problem that the brain and nervous system can’t " 
Malcolm Burrows

The juvenile Issus - a plant-hopping insect found in gardens across Europe - has hind-leg joints with curved cog-like strips of opposing ‘teeth’ that intermesh, rotating like mechanical gears to synchronise the animal’s legs when it launches into a jump.

The finding demonstrates that gear mechanisms previously thought to be solely man-made have an evolutionary precedent. Scientists say this is the “first observation of mechanical gearing in a biological structure”.

Through a combination of anatomical analysis and high-speed video capture of normal Issus movements, scientists from the University of Cambridge have been able to reveal these functioning natural gears for the first time. The findings are reported in the latest issue of the journal Science.

The gears in the Issus hind-leg bear remarkable engineering resemblance to those found on every bicycle and inside every car gear-box.

Each gear tooth has a rounded corner at the point it connects to the gear strip; a feature identical to man-made gears such as bike gears – essentially a shock-absorbing mechanism to stop teeth from shearing off.

Image: Cog wheels connecting the hind legs
of the plant hopper, Issus.
Credit: Burrows/Sutton

This is critical for the powerful jumps that are this insect’s primary mode of transport, as even miniscule discrepancies in synchronisation between the velocities of its legs at the point of propulsion would result in “yaw rotation” - causing the Issus to spin hopelessly out of control.

The juvenile Issus - a plant-hopping insect found in gardens across Europe - has hind-leg joints with curved cog-like strips of opposing ‘teeth’ that intermesh, rotating like mechanical gears to synchronise the animal’s legs when it launches into a jump.

The finding demonstrates that gear mechanisms previously thought to be solely man-made have an evolutionary precedent. Scientists say this is the “first observation of mechanical gearing in a biological structure”.

Through a combination of anatomical analysis and high-speed video capture of normal Issus movements, scientists from the University of Cambridge have been able to reveal these functioning natural gears for the first time. The findings are reported in the latest issue of the journal Science.

The gears in the Issus hind-leg bear remarkable engineering resemblance to those found on every bicycle and inside every car gear-box.

Each gear tooth has a rounded corner at the point it connects to the gear strip; a feature identical to man-made gears such as bike gears – essentially a shock-absorbing mechanism to stop teeth from shearing off.

Image: Cog wheels connecting the hind legs
of the plant hopper, Issus.
Credit: Burrows/Sutton

This is critical for the powerful jumps that are this insect’s primary mode of transport, as even miniscule discrepancies in synchronisation between the velocities of its legs at the point of propulsion would result in “yaw rotation” - causing the Issus to spin hopelessly out of control.

“This precise synchronisation would be impossible to achieve through a nervous system, as neural impulses would take far too long for the extraordinarily tight coordination required,” said lead author Professor Malcolm Burrows, from Cambridge’s Department of Zoology.

“By developing mechanical gears, the Issus can just send nerve signals to its muscles to produce roughly the same amount of force - then if one leg starts to propel the jump the gears will interlock, creating absolute synchronicity.

“In Issus, the skeleton is used to solve a complex problem that the brain and nervous system can’t,” said Burrows. “This emphasises the importance of considering the properties of the skeleton in how movement is produced.”

"We usually think of gears as something that we see in human designed machinery, but we've found that that is only because we didn't look hard enough,” added co-author Gregory Sutton, now at the University of Bristol.</ 1px #666; font-size: large; margin: 10px; padding: 10px; position: center; width: 450px;">

"In Issus, the skeleton is used to solve a complex problem that the brain and nervous system can’t "

Malcolm Burrows

The juvenile Issus - a plant-hopping insect found in gardens across Europe - has hind-leg joints with curved cog-like strips of opposing ‘teeth’ that intermesh, rotating like mechanical gears to synchronise the animal’s legs when it launches into a jump.

The finding demonstrates that gear mechanisms previously thought to be solely man-made have an evolutionary precedent. Scientists say this is the “first observation of mechanical gearing in a biological structure”.

Through a combination of anatomical analysis and high-speed video capture of normal Issus movements, scientists from the University of Cambridge have been able to reveal these functioning natural gears for the first time. The findings are reported in the latest issue of the journal Science.

The gears in the Issus hind-leg bear remarkable engineering resemblance to those found on every bicycle and inside every car gear-box.

Each gear tooth has a rounded corner at the point it connects to the gear strip; a feature identical to man-made gears such as bike gears – essentially a shock-absorbing mechanism to stop teeth from shearing off.

Image: Cog wheels connecting the hind legs
of the plant hopper, Issus.
Credit: Burrows/Sutton

This is critical for the powerful jumps that are this insect’s primary mode of transport, as even miniscule discrepancies in synchronisation between the velocities of its legs at the point of propulsion would result in “yaw rotation” - causing the Issus to spin hopelessly out of control.

“This precise synchronisation would be impossible to achieve through a nervous system, as neural impulses would take far too long for the extraordinarily tight coordination required,” said lead author Professor Malcolm Burrows, from Cambridge’s Department of Zoology.

“By developing mechanical gears, the Issus can just send nerve signals to its muscles to produce roughly the same amount of force - then if one leg starts to propel the jump the gears will interlock, creating absolute synchronicity.

“In Issus, the skeleton is used to solve a complex problem that the brain and nervous system can’t,” said Burrows. “This emphasises the importance of considering the properties of the skeleton in how movement is produced.”

"We usually think of gears as something that we see in human designed machinery, but we've found that that is only because we didn't look hard enough,” added co-author Gregory Sutton, now at the University of Bristol.

Image: Cog wheels connecting the hind legs of the plant hopper, Issus.
Credit: Burrows/Sutton

“These gears are not designed; they are evolved - representing high speed and precision machinery evolved for synchronisation in the animal world.”

Interestingly, the mechanistic gears are only found in the insect’s juvenile – or ‘nymph’ – stages, and are lost in the final transition to adulthood. These transitions, called ‘molts’, are when animals cast off rigid skin at key points in their development in order to grow.

It’s not yet known why the Issus loses its hind-leg gears on reaching adulthood. The scientists point out that a problem with any gear system is that if one tooth on the gear breaks, the effectiveness of the whole mechanism is damaged. While gear-teeth breakage in nymphs could be repaired in the next molt, any damage in adulthood remains permanent.

It may also be down to the larger size of adults and consequently their ‘trochantera’ – the insect equivalent of the femur or thigh bones. The bigger adult trochantera might allow them to create enough friction to power the enormous leaps from leaf to leaf without the need for intermeshing gear teeth to drive it, say the scientists.

Inset image: an Issus nymph

Each gear strip in the juvenile Issus was around 400 micrometres long and had between 10 to 12 teeth, with both sides of the gear in each leg containing the same number – giving a gearing ratio of 1:1.

Unlike man-made gears, each gear tooth is asymmetrical and curved towards the point where the cogs interlock – as man-made gears need a symmetric shape to work in both rotational directions, whereas the Issus gears are only powering one way to launch the animal forward.

While there are examples of apparently ornamental cogs in the animal kingdom - such as on the shell of the cog wheel turtle or the back of the wheel bug - gears with a functional role either remain elusive or have been rendered defunct by evolution.

The Issus is the first example of a natural cog mechanism with an observable function, say the scientists.

For more information, please contact fred.lewsey@admin.cam.ac.uk

ORIGINAL: Cambridge University

Malcolm Burrows†, Gregory Sutton*

12 Sep 2013

div>

Image: Cog wheels connecting the hind legs of the plant hopper, Issus.
Credit: Burrows/Sutton

“These gears are not designed; they are evolved - representing high speed and precision machinery evolved for synchronisation in the animal world.”

Interestingly, the mechanistic gears are only found in the insect’s juvenile – or ‘nymph’ – stages, and are lost in the final transition to adulthood. These transitions, called ‘molts’, are when animals cast off rigid skin at key points in their development in order to grow.

It’s not yet known why the Issus loses its hind-leg gears on reaching adulthood. The scientists point out that a problem with any gear system is that if one tooth on the gear breaks, the effectiveness of the whole mechanism is damaged. While gear-teeth breakage in nymphs could be repaired in the next molt, any damage in adulthood remains permanent.

It may also be down to the larger size of adults and consequently their ‘trochantera’ – the insect equivalent of the femur or thigh bones. The bigger adult trochantera might allow them to create enough friction to power the enormous leaps from leaf to leaf without the need for intermeshing gear teeth to drive it, say the scientists.

Inset image: an Issus nymph

Each gear strip in the juvenile Issus was around 400 micrometres long and had between 10 to 12 teeth, with both sides of the gear in each leg containing the same number – giving a gearing ratio of 1:1.

Unlike man-made gears, each gear tooth is asymmetrical and curved towards the point where the cogs interlock – as man-made gears need a symmetric shape to work in both rotational directions, whereas the Issus gears are only powering one way to launch the animal forward.

While there are examples of apparently ornamental cogs in the animal kingdom - such as on the shell of the cog wheel turtle or the back of the wheel bug - gears with a functional role either remain elusive or have been rendered defunct by evolution.

The Issus is the first example of a natural cog mechanism with an observable function, say the scientists.

For more information, please contact fred.lewsey@admin.cam.ac.uk

ORIGINAL: Cambridge University

Malcolm Burrows†, Gregory Sutton*

12 Sep 2013

text-align: justify;"> “This precise synchronisation would be impossible to achieve through a nervous system, as neural impulses would take far too long for the extraordinarily tight coordination required,” said lead author Professor Malcolm Burrows, from Cambridge’s Department of Zoology.

“By developing mechanical gears, the Issus can just send nerve signals to its muscles to produce roughly the same amount of force - then if one leg starts to propel the jump the gears will interlock, creating absolute synchronicity.

“In Issus, the skeleton is used to solve a complex problem that the brain and nervous system can’t,” said Burrows. “This emphasises the importance of considering the properties of the skeleton in how movement is produced.”

"We usually think of gears as something that we see in human designed machinery, but we've found that that is only because we didn't look hard enough,” added co-author Gregory Sutton, now at the University of Bristol.</ 1px #666; font-size: large; margin: 10px; padding: 10px; position: center; width: 450px;">

"In Issus, the skeleton is used to solve a complex problem that the brain and nervous system can’t "

Malcolm Burrows

The juvenile Issus - a plant-hopping insect found in gardens across Europe - has hind-leg joints with curved cog-like strips of opposing ‘teeth’ that intermesh, rotating like mechanical gears to synchronise the animal’s legs when it launches into a jump.

The finding demonstrates that gear mechanisms previously thought to be solely man-made have an evolutionary precedent. Scientists say this is the “first observation of mechanical gearing in a biological structure”.

Through a combination of anatomical analysis and high-speed video capture of normal Issus movements, scientists from the University of Cambridge have been able to reveal these functioning natural gears for the first time. The findings are reported in the latest issue of the journal Science.

The gears in the Issus hind-leg bear remarkable engineering resemblance to those found on every bicycle and inside every car gear-box.

Each gear tooth has a rounded corner at the point it connects to the gear strip; a feature identical to man-made gears such as bike gears – essentially a shock-absorbing mechanism to stop teeth from shearing off.

Image: Cog wheels connecting the hind legs
of the plant hopper, Issus.
Credit: Burrows/Sutton

This is critical for the powerful jumps that are this insect’s primary mode of transport, as even miniscule discrepancies in synchronisation between the velocities of its legs at the point of propulsion would result in “yaw rotation” - causing the Issus to spin hopelessly out of control.

“This precise synchronisation would be impossible to achieve through a nervous system, as neural impulses would take far too long for the extraordinarily tight coordination required,” said lead author Professor Malcolm Burrows, from Cambridge’s Department of Zoology.

“By developing mechanical gears, the Issus can just send nerve signals to its muscles to produce roughly the same amount of force - then if one leg starts to propel the jump the gears will interlock, creating absolute synchronicity.

“In Issus, the skeleton is used to solve a complex problem that the brain and nervous system can’t,” said Burrows. “This emphasises the importance of considering the properties of the skeleton in how movement is produced.”

"We usually think of gears as something that we see in human designed machinery, but we've found that that is only because we didn't look hard enough,” added co-author Gregory Sutton, now at the University of Bristol.

Image: Cog wheels connecting the hind legs of the plant hopper, Issus.
Credit: Burrows/Sutton

“These gears are not designed; they are evolved - representing high speed and precision machinery evolved for synchronisation in the animal world.”

Interestingly, the mechanistic gears are only found in the insect’s juvenile – or ‘nymph’ – stages, and are lost in the final transition to adulthood. These transitions, called ‘molts’, are when animals cast off rigid skin at key points in their development in order to grow.

It’s not yet known why the Issus loses its hind-leg gears on reaching adulthood. The scientists point out that a problem with any gear system is that if one tooth on the gear breaks, the effectiveness of the whole mechanism is damaged. While gear-teeth breakage in nymphs could be repaired in the next molt, any damage in adulthood remains permanent.

It may also be down to the larger size of adults and consequently their ‘trochantera’ – the insect equivalent of the femur or thigh bones. The bigger adult trochantera might allow them to create enough friction to power the enormous leaps from leaf to leaf without the need for intermeshing gear teeth to drive it, say the scientists.

Inset image: an Issus nymph

Each gear strip in the juvenile Issus was around 400 micrometres long and had between 10 to 12 teeth, with both sides of the gear in each leg containing the same number – giving a gearing ratio of 1:1.

Unlike man-made gears, each gear tooth is asymmetrical and curved towards the point where the cogs interlock – as man-made gears need a symmetric shape to work in both rotational directions, whereas the Issus gears are only powering one way to launch the animal forward.

While there are examples of apparently ornamental cogs in the animal kingdom - such as on the shell of the cog wheel turtle or the back of the wheel bug - gears with a functional role either remain elusive or have been rendered defunct by evolution.

The Issus is the first example of a natural cog mechanism with an observable function, say the scientists.

For more information, please contact fred.lewsey@admin.cam.ac.uk

ORIGINAL: Cambridge University

Malcolm Burrows†, Gregory Sutton*

12 Sep 2013

div>

Image: Cog wheels connecting the hind legs of the plant hopper, Issus.
Credit: Burrows/Sutton

“These gears are not designed; they are evolved - representing high speed and precision machinery evolved for synchronisation in the animal world.”

Interestingly, the mechanistic gears are only found in the insect’s juvenile – or ‘nymph’ – stages, and are lost in the final transition to adulthood. These transitions, called ‘molts’, are when animals cast off rigid skin at key points in their development in order to grow.

It’s not yet known why the Issus loses its hind-leg gears on reaching adulthood. The scientists point out that a problem with any gear system is that if one tooth on the gear breaks, the effectiveness of the whole mechanism is damaged. While gear-teeth breakage in nymphs could be repaired in the next molt, any damage in adulthood remains permanent.

It may also be down to the larger size of adults and consequently their ‘trochantera’ – the insect equivalent of the femur or thigh bones. The bigger adult trochantera might allow them to create enough friction to power the enormous leaps from leaf to leaf without the need for intermeshing gear teeth to drive it, say the scientists.

Inset image: an Issus nymph

Each gear strip in the juvenile Issus was around 400 micrometres long and had between 10 to 12 teeth, with both sides of the gear in each leg containing the same number – giving a gearing ratio of 1:1.

Unlike man-made gears, each gear tooth is asymmetrical and curved towards the point where the cogs interlock – as man-made gears need a symmetric shape to work in both rotational directions, whereas the Issus gears are only powering one way to launch the animal forward.

While there are examples of apparently ornamental cogs in the animal kingdom - such as on the shell of the cog wheel turtle or the back of the wheel bug - gears with a functional role either remain elusive or have been rendered defunct by evolution.

The Issus is the first example of a natural cog mechanism with an observable function, say the scientists.

For more information, please contact fred.lewsey@admin.cam.ac.uk

ORIGINAL: Cambridge University

Malcolm Burrows†, Gregory Sutton*

12 Sep 2013

The Future of Printing is Bigger, Smaller and Living!

The pace of change in the printing industry has never been swifter. The future is arriving in record time, and it is both diverse and very exciting.

Every sector of the printing industry including macro printing is experiencing incremental, micro trends. This overview instead looks at macro trends...in micro printing and other sectors.

Large Format 3D Printing

A new wave of big format 3D printers is being introduced for use in:

• Branding with mascots and three-dimensional logos
• Integration of 2D and 3D designs for advertising and signage
• Prototyping when a full-size model is essential
• Sculpture and other art forms
• Furniture fabrication
• Parts fabrication
• Promotional applications where being large and being unique are the two keys

The Massivit 1800 is one example of a large-format printer. Layer after additive layer is laid down to create 3D products as large as 180cm high, 150cm wide and 120cm deep.

Nano Printing – Smaller, Thinner and Less Costly

Perhaps no other sector in the industry is generating as much excitement as the integration of Nano technology with three-dimensional printing. To be fair, this printing isn't quite yet dealing in Nano size, as one nanometre is one billionth of a metre. Nanography – the intersection of printing and Nano technology – is using materials measured in micrometres (microns) which are one-millionth of a metre. That's still impressively small.

Nano printing in a three-dimensional format is becoming the fabrication method of choice for a diverse and growing range of products in use now or coming soon including:

• Lithium-ion microbatteries for implants and tiny robots
• Tunable acoustic arrays
• Efficient energy scavengers
• Diagnostic devices
• Compact sensors
• Nanowalls for various applications

Nano technology is allowing for small printing, but there is a similar application worth considering: thin printing.

The key is ink that becomes dry polymeric film just 500nm (nanometres) thick. It bonds instantly and permanently to the substrate without colour penetration. Its advantages are many:

• Colors are amazingly vivid
• Nearly any substrate is suitable including low-cost papers
• Waste is minimized
• There are no emissions
• Energy use is very low
• Water-based inks are less costly than solvent and UV-based inks

It turns out that the Nano world is a cheaper world. Tiny three-dimensional printing and thin/nanographic printing are both money savers. Thin ink means less ink and less cost. Three-dimensional printing uses less material than when molds are built first.

Printing that Lives

This is where 3D printing sounds more science fiction than reality, but as noted, the future is arriving faster than most would have estimated. The process is called bioprinting, and it is a natural extension of the advances made in 3D print technology.

According to the Australian Academy of Science's Nova site, "Biofabrication can be defined as the production of complex living and non-living biological products from raw materials such as living cells, molecules, extracellular matrices, and biomaterials."

While still in the early stages of development, biofabrication might well be used to produce living tissue such as skin, bone, blood vessels and entire organs for use in replacement rather than transplant.

While advances here are slow due to the immense complexity of cellular organisms, current technology offers hope of customised solutions not only for each medical problem but for each patient.

Similarly, three-dimensional printing will increasingly be used to produce personalized implants such as titanium bone replacements and orthodontic devices with a "perfect" fit for each recipient.

Better New World

Doomsayers abound who say we're headed for a "Brave New World" of technology run amok. These advances in printing remind us that, instead, a better new world is coming into view right now. Gutenberg's printing press revolutionized the world starting in the mid-15th Century. An evolution in printing methods soon started that has continued unabated, and the world is reaping its benefits.

ORIGINAL: Engadget

Kerry Blake , @KerryBlake16

2016/10/27

TetraPOT uses mangroves to grow a greener sea defense system

Tetrapods, those curious concrete structures that resemble oversized toy jacks, protect shores across the world from life-threatening waves—but they’re not environmentally friendly or sustainable. Inspired to create a “stronger yet greener sea defense” system, Taiwanese designer Sheng-Hung Lee designed the TetraPOT, a fusion between the concrete tetrapod and natural mangroves. The innovative design uses the iconic four-pronged tetrapod shape with the insertion of a biodegradable pre-seeded pot to grow mangrove trees that filter water pollution, protect the shores, and beautify coastlines. 

Lee envisions the TetraPOT as a hybrid between artificial sea defense and natural sea defense, an idea encapsulated in his design slogan: “It is not only a defense, but also an ecosystem. A home for other living [things].” The TetraPOT is an opportunity to restore the world’s mangrove forests, 35% of which has been destroyed. Unlike the common tetrapod, the TetraPOT is partly hollowed out to create room for a biodegradable pot insert, soil, and space for roots to grow. When rising tides water the pre-seeded layers, the organic layers will begin to decompose and allow the mangrove trees to expand its root system through three lower openings.

Related: Are Mangroves The Solution to Urban Sustainability in Asia?

Over time, roots from one TetraPOT will connect with its neighbors as well as the shoreline to reinforce the sea defense system, reducing the risk of dislodgment. The mangroves will also attract greater biodiversity to the region and help clean the air and water. Lee, who currently works with IDEO in Shanghai, plans to work with the local government to test out TetraPOT prototypes on Chongming Island. The TetraPOT has received several prestigious awards, including the James Dyson Award and red dot Design Award.

+ TetraPOT

ORIGINAL: Inhabitat

by Lucy Wang

2016/10/24

Google's AI can now learn from its own memory independently

An artist's impression of the DNC. Credit: DeepMind

The DeepMind artificial intelligence (AI) being developed by Google's parent company, Alphabet, can now intelligently build on what's already inside its memory, the system's programmers have announced.

Their new hybrid system – called a Differential Neural Computer (DNC) – pairs a neural network with the vast data storage of conventional computers, and the AI is smart enough to navigate and learn from this external data bank. 

What the DNC is doing is effectively combining external memory (like the external hard drive where all your photos get stored) with the neural network approach of AI, where a massive number of interconnected nodes work dynamically to simulate a brain.

"These models... can learn from examples like neural networks, but they can also store complex data like computers," write DeepMind researchers Alexander Graves and Greg Wayne in a blog post.

At the heart of the DNC is a controller that constantly optimises its responses, comparing its results with the desired and correct ones. Over time, it's able to get more and more accurate, figuring out how to use its memory data banks at the same time.

Take a family tree: after being told about certain relationships, the DNC was able to figure out other family connections on its own – writing, rewriting, and optimising its memory along the way to pull out the correct information at the right time.

Another example the researchers give is a public transit system, like the London Underground. Once it's learned the basics, the DNC can figure out more complex relationships and routes without any extra help, relying on what it's already got in its memory banks.

In other words, it's functioning like a human brain, taking data from memory (like tube station positions) and figuring out new information (like how many stops to stay on for).

Of course, any smartphone mapping app can tell you the quickest way from one tube station to another, but the difference is that the DNC isn't pulling this information out of a pre-programmed timetable – it's working out the information on its own, and juggling a lot of data in its memory all at once.

The approach means a DNC system could take what it learned about the London Underground and apply parts of its knowledge to another transport network, like the New York subway.

The system points to a future where artificial intelligence could answer questions on new topics, by deducing responses from prior experiences, without needing to have learned every possible answer beforehand.

Credit: DeepMind

Of course, that's how DeepMind was able to beat human champions at Go – by studying millions of Go moves. But by adding external memory, DNCs are able to take on much more complex tasks and work out better overall strategies, its creators say.

"Like a conventional computer, [a DNC] can use its memory to represent and manipulate complex data structures, but, like a neural network, it can learn to do so from data," the researchers explain in Nature.

In another test, the DNC was given two bits of information: "John is in the playground," and "John picked up the football." With those known facts, when asked "Where is the football?", it was able to answer correctly by combining memory with deep learning. (The football is in the playground, if you're stuck.)

Making those connections might seem like a simple task for our powerful human brains, but until now, it's been a lot harder for virtual assistants, such as Siri, to figure out.

With the advances DeepMind is making, the researchers say we're another step forward to producing a computer that can reason independently.

And then we can all start enjoying our robot-driven utopia – or technological dystopia – depending on your point of view.

ORIGINAL: ScienceAlert
By DAVID NIELD

14 OCT 2016

Google's Deep Mind Gives AI a Memory Boost That Lets It Navigate London's Underground

Photo: iStockphoto

Google’s DeepMind artificial intelligence lab does more than just develop computer programs capable of beating the world’s best human players in the ancient game of Go. The DeepMind unit has also been working on the next generation of deep learning software that combines the ability to recognize data patterns with the memory required to decipher more complex relationships within the data.

Deep learning is the latest buzz word for artificial intelligence algorithms called neural networks that can learn over time by filtering huge amounts of relevant data through many “deep” layers. The brain-inspired neural network layers consist of nodes (also known as neurons). Tech giants such as Google, Facebook, Amazon, and Microsoft have been training neural networks to learn how to better handle tasks such as recognizing images of dogs or making better Chinese-to-English translations. These AI capabilities have already benefited millions of people using Google Translate and other online services.

But neural networks face huge challenges when they try to rely solely on pattern recognition without having the external memory to store and retrieve information. To improve deep learning’s capabilities, Google DeepMind created a “differentiable neural computer” (DNC) that gives neural networks an external memory for storing information for later use.

“Neural networks are like the human brain; we humans cannot assimilate massive amounts of data and we must rely on external read-write memory all the time,” says Jay McClelland, director of the Center for Mind, Brain and Computation at Stanford University. “We once relied on our physical address books and Rolodexes; now of course we rely on the read-write storage capabilities of regular computers.”

McClelland is a cognitive scientist who served as one of several independent peer reviewers for the Google DeepMind paper that describes development of this improved deep learning system. The full paper is presented in the 12 Oct 2016 issue of the journal Nature.

The DeepMind team found that the DNC system’s combination of the neural network and external memory did much better than a neural network alone in tackling the complex relationships between data points in so-called “graph tasks.” For example, they asked their system to either simply take any path between points A and B or to find the shortest travel routes based on a symbolic map of the London Underground subway.

An unaided neural network could not even finish the first level of training, based on traveling between two subway stations without trying to find the shortest route. It achieved an average accuracy of just 37 percent after going through almost two million training examples. By comparison, the neural network with access to external memory in the DNC system successfully completed the entire training curriculum and reached an average of 98.8 percent accuracy on the final lesson.

The external memory of the DNC system also proved critical to success in performing logical planning tasks such as solving simple block puzzle challenges. Again, a neural network by itself could not even finish the first lesson of the training curriculum for the block puzzle challenge. The DNC system was able to use its memory to store information about the challenge’s goals and to effectively plan ahead by writing its decisions to memory before acting upon them.

In 2014, DeepMind’s researchers developed another system, called the neural Turing machine, that also combined neural networks with external memory. But the neural Turing machine was limited in the way it could access “memories” (information) because such memories were effectively stored and retrieved in fixed blocks or arrays. The latest DNC system can access memories in any arbitrary location, McClelland explains.

The DNC system’s memory architecture even bears a certain resemblance to how the hippocampus region of the brain supports new brain cell growth and new connections in order to store new memories. Just as the DNC system uses the equivalent of time stamps to organize the storage and retrieval of memories, human “free recall” experiments have shown that people are more likely to recall certain items in the same order as first presented.

Despite these similarities, the DNC’s design was driven by computational considerations rather than taking direct inspiration from biological brains, DeepMind’s researchers write in their paper. But McClelland says that he prefers not to think of the similarities as being purely coincidental.

“The design decisions that motivated the architects of the DNC were the same as those that structured the human memory system, although the latter (in my opinion) was designed by a gradual evolutionary process, rather than by a group of brilliant AI researchers,” McClelland says.

Human brains still have significant advantages over any brain-inspired deep learning software. For example, human memory seems much better at storing information so that it is accessible by both context or content, McClelland says. He expressed hope that future deep learning and AI research could better capture the memory advantages of biological brains.

DeepMind’s DNC system and similar neural learning systems may represent crucial steps for the ongoing development of AI. But the DNC system still falls well short of what McClelland considers the most important parts of human intelligence.

The DNC is a sophisticated form of external memory, but ultimately it is like the papyrus on which Euclid wrote the elements. The insights of mathematicians that Euclid codified relied (in my view) on a gradual learning process that structured the neural circuits in their brains so that they came to be able to see relationships that others had not seen, and that structured the neural circuits in Euclid’s brain so that he could formulate what to write. We have a long way to go before we understand fully the algorithms the human brain uses to support these processes. 

It’s unclear when or how Google might take advantage of the capabilities offered by the DNC system to boost its commercial products and services. The DeepMind team was “heads down in research” or too busy with travel to entertain media questions at this time, according to a Google spokesperson.

But Herbert Jaeger, professor for computational science at Jacobs University Bremen in Germany, sees the DeepMind team’s work as a “passing snapshot in a fast evolution sequence of novel neural learning architectures.” In fact, he’s confident that the DeepMind team already has something better than the DNC system described in the Nature paper. (Keep in mind that the paper was submitted back in January 2016.)

DeepMind’s work is also part of a bigger trend in deep learning, Jaeger says. The leading deep learning teams at Google and other companies are racing to build new AI architectures with many different functional modules—among them, attentional control or working memory; they then train the systems through deep learning. 

“The DNC is just one among dozens of novel, highly potent, and cleverly-thought-out neural learning systems that are popping up all over the place,” Jaeger says.

ORIGINAL: IEEE Spectrum

By Jeremy Hsu

12 Oct 2016

IChemE Global Awards 2016 Finalist - 'Light-activated synthetic tissues', University of Oxford, UK

The University of Oxford has engineered new high-value synthetic tissues, controllable with an external stimulus. ‘Bottom-up’ approaches in synthetic biology have been used to construct synthetic cells from simple biological components. By using a droplet-based 3D printer synthetic tissues are created, comprising hundreds of communicating synthetic cells, which can perform sophisticated functions such as protein synthesis. In addition, it has shown that 3D-printed synthetic tissues can be controlled externally by light and demonstrate electrical communication, similar to neuronal transmission. Printed synthetic tissues might be used in medicine and could even interface directly with living tissues.

University of Oxford is an IChemE Global Awards finalist for the Biotechnology Award. 

“We are delighted that our project has been chosen as a finalist for the IChemE Global Biotechnology Award. These synthetic tissues, namely materials analogous to biological tissues, can be remotely activated by light and demonstrate rapid electrical signalling through defined pathways, precisely the role of neurons. Our goal is to use these completely new and high value 3D-printed materials in medicinal applications, including drug delivery and tissue replacement.” 

- Michael Booth, Junior Research Fellow, University of Oxford

ORIGINAL: IChemE

Oct 10, 2016

Launched: A Synthetic Biology Factory for Making Weird New Organisms

Photo: Eliza Strickland
The automated lab at Ginkgo Bioworks enables a design-build-test cycle for creating novel organisms.

Raising glasses of genetically modified beer, the synthetic biologists at Ginkgo Bioworks celebrated the launch of a new automated lab last month. By applying engineering principles to biology, and with the help of some nifty robotic equipment, Ginkgo has created a factory for churning out exotic lifeforms, the likes of which have never before been seen on this planet. 

The home brew was an example of the potential applications of synthetic biology, a new field that builds on recent progress in genetic assembly methods. Scientists can now manufacture snippets of synthetic DNA and slip them into organisms, giving those critters strange new capabilities.

Photo: Ana-Maria Murphy-Teixidor
Guests at the launch party sampled
Ginkgo Bioworks's home brew.

For example, the brewer’s yeast used to make beer for the launch party had genes from an orange tree added to its own DNA. During the fermentation stage of the brewing process, those genes caused the yeast to produce valencene, an organic compound with a citrusy flavor. Speaking scientifically, it was delicious.

Ginkgo Bioworks, a hip young company based in South Boston, recently raised $100 million on the promise of finding many such useful applications for synthetic biology. And it used some of that cash to build Bioworks2, the company’s vast new lab that uses robotic systems to make an assembly line for organisms.

Ginkgo needs to make microbes on a grand scale in order to find those that can function as tiny biological factories. When a client comes in with a request for a custom-made organism, Gingko begins its bulk experimentation. Many of the altered organisms will be duds, but through cycles of iteration the bioengineers eventually devise a microbe that turns out the desirable product. The company is messing around with organisms that produce chemical ingredients for perfumes, beverages, pesticides, and laundry detergent. 

Ginkgo Bioworks’ business model centers on the microbes themselves, not the end products. “We’re not in the business of manufacturing chemicals, flavors, or fragrances,” explains Ginkgo creative director Christina Agapakis. “We specialize in the organsims, and we partner with our customers who will make the product.” Ginkgo licenses organisms to its customers, she says, and gets royalties if they’re used.

But building an organism to spec is no easy task. Genetics still isn’t well understood; there’s no universal catalog listing of genes that details what they all do. And biology is messy. Even if researchers know what a particular gene does in an orange tree, for example, when they add it to a yeast cell, it might interact with the native DNA in unexpected ways. If they’re adding several genes from different species to that yeast cell, things get even more complicated.

That’s why Ginkgo takes an engineering approach to biology, hewing to a rigorous design-build-test cycle. In this case, they’re designing, building, and testing living organisms.

Photo: Eliza StricklandAt the new Bioworks2 lab, Ginkgo's synthetic biologists can test out thousands of variants for a new organism.

The new lab’s extreme automation is critical to this approach, says Patrick Boyle, Ginkgo’s head of organism design. “In grad school, I might have taken my five best ideas and tried them out,” Boyle says. “Here we take our 1000 best ideas, try them all out, and see which works best.” 

So how does that design, build, and test cycle work in practice? Take Ginkgo’s first efforts in the perfume business as an example. Ginkgo is working with the French perfumier Robertet on a yeast that spits out rose oil. There’s a business case for making this microbe: Extracting traditional rose oil from rose petals is expensive, and high-end perfumiers look down on chemical substitutes. But adding the right genes from a rose plant to a yeast cell could make it produce the real oil, just in an untraditional way. 

Design: A yeast serves as the biological “chassis,” the base for the customized creature. Ginkgo designers then search the scientific literature, looking for genes that would cause a cell to produce useful enzymes. They’re looking for enzymes that can work within the yeast cell’s metabolic process; when they feed sugar to the yeast it should carry out chemical reactions that ultimately result in rose oil. 

They hunt for genes all across the biological kingdoms: “We ask, ‘How have different biological niches solved this biochemistry problem, and how can we adapt them to our purposes?’” says Boyle. They can combine genes from different organisms into metabolic pathways, but this requires scaled-up science. “If you have 100 possible enzymes that can serve as a step in a four-step pathway, that’s a lot of design space to explore,” Boyle says.

Build: Ginkgo outsources the actual manufacturing of synthetic DNA, ordering up batches from companies like Twist Bioscience and Gen9. Boyle says the company will receive 700 million base-pairs of synthetic DNA in the next year and a half, which represents half the world’s current market for synthetic DNA. A company like Ginkgo can only exist because the cost of manufacturing DNA has recently come down dramatically. 

When a batch of manufactured DNA arrives at Ginkgo, liquid-handling robots add the various snippets to yeast cells and let the cells grow and multiply. Creative director Agapakis says these robots are getting better and better. “During my PhD, I spent a lot of time moving tiny amounts of fluid around,” she says. “When we started Ginkgo, a lot of the robots looked like eight-armed grad students—there were a lot of pipettes.”

Image: Labcyte

A high-tech liquid-handling robot 

moves samples via sound waves.

Now Ginkgo has liquid-handling robots like the Echo 525, which moves nanoliters of liquid using targeted pulses of sound. The machine sends ultrasonic waves upward at a sample plate, focusing on just one of the plate’s 1536 tiny wells, and propels the droplet of liquid upward to a new vessel. It can move the contents of a plate in about 20 minutes. 

Test: Once Ginkgo has 1000 yeast variants containing different mashups of genes, it’s time to see if the cells are making their product: for example, rose oil. The researchers use mass spectrometry machines to break apart the cells and examine all the molecules inside. They check whether the yeast is producing the oil, of course, but also whether the yeast is healthy. Using some of the cell’s metabolic energy to produce rose oil could interfere with other processes and “change the total picture,” says Agapakis. 

Even when they’ve found a few yeast variants that seem to do a good job of cranking out oil, Ginkgo’s job isn’t done. The bioengineers still need to see whether the organism can make a product that’s truly useful to the customer. 

Boyle says that in the case of rose oil, they study each yeast to determine its overall “fragrance profile.” While a cell may be making certain useful fragrance molecules, it may be making other molecules that are distinctly not useful. “I like the fresh-baked bread smell, but it’s not great when you’re trying to sell a perfume,” Boyle says. “So how do we cut down on background fragrances?” The perfume, which could currently be called eau de baguette, is still a work in progress.

Perfume is just the beginning for this ambitious company. Agapakis sees biological manufacturing as the way of the future, and she doesn’t mind sounding like “a college student in a dorm room” when she talks about it. “Biology makes things that grow themselves,” she says. “A tree grows itself from sunlight and water, that’s amazing.” At Bioworks2, she hopes to create experimental lifeforms that will really blow college students’ minds. 

ORIGINAL: IEEE Spectrum

By Eliza Strickland

10 Oct 2016