Tag Archives: University of Chicago

Touchy robots and prosthetics

I have briefly speculated about the importance of touch elsewhere (see my July 19, 2019 posting regarding BlocKit and blockchain; scroll down about 50% of the way) but this upcoming news bit and the one following it put a different spin on the importance of touch.

Exceptional sense of touch

Robots need a sense of touch to perform their tasks and a July 18, 2019 National University of Singapore press release (also on EurekAlert) announces work on an improved sense of touch,

Robots and prosthetic devices may soon have a sense of touch equivalent to, or better than, the human skin with the Asynchronous Coded Electronic Skin (ACES), an artificial nervous system developed by a team of researchers at the National University of Singapore (NUS).

The new electronic skin system achieved ultra-high responsiveness and robustness to damage, and can be paired with any kind of sensor skin layers to function effectively as an electronic skin.

The innovation, achieved by Assistant Professor Benjamin Tee and his team from the Department of Materials Science and Engineering at the NUS Faculty of Engineering, was first reported in prestigious scientific journal Science Robotics on 18 July 2019.

Faster than the human sensory nervous system

“Humans use our sense of touch to accomplish almost every daily task, such as picking up a cup of coffee or making a handshake. Without it, we will even lose our sense of balance when walking. Similarly, robots need to have a sense of touch in order to interact better with humans, but robots today still cannot feel objects very well,” explained Asst Prof Tee, who has been working on electronic skin technologies for over a decade in hope of giving robots and prosthetic devices a better sense of touch.

Drawing inspiration from the human sensory nervous system, the NUS team spent a year and a half developing a sensor system that could potentially perform better. While the ACES electronic nervous system detects signals like the human sensor nervous system, it is made up of a network of sensors connected via a single electrical conductor, unlike the nerve bundles in the human skin. It is also unlike existing electronic skins which have interlinked wiring systems that can make them sensitive to damage and difficult to scale up.

Elaborating on the inspiration, Asst Prof Tee, who also holds appointments in the NUS Department of Electrical and Computer Engineering, NUS Institute for Health Innovation & Technology (iHealthTech), N.1 Institute for Health and the Hybrid Integrated Flexible Electronic Systems (HiFES) programme, said, “The human sensory nervous system is extremely efficient, and it works all the time to the extent that we often take it for granted. It is also very robust to damage. Our sense of touch, for example, does not get affected when we suffer a cut. If we can mimic how our biological system works and make it even better, we can bring about tremendous advancements in the field of robotics where electronic skins are predominantly applied.”

ACES can detect touches more than 1,000 times faster than the human sensory nervous system. For example, it is capable of differentiating physical contacts between different sensors in less than 60 nanoseconds – the fastest ever achieved for an electronic skin technology – even with large numbers of sensors. ACES-enabled skin can also accurately identify the shape, texture and hardness of objects within 10 milliseconds, ten times faster than the blinking of an eye. This is enabled by the high fidelity and capture speed of the ACES system.

The ACES platform can also be designed to achieve high robustness to physical damage, an important property for electronic skins because they come into the frequent physical contact with the environment. Unlike the current system used to interconnect sensors in existing electronic skins, all the sensors in ACES can be connected to a common electrical conductor with each sensor operating independently. This allows ACES-enabled electronic skins to continue functioning as long as there is one connection between the sensor and the conductor, making them less vulnerable to damage.

Smart electronic skins for robots and prosthetics

ACES’ simple wiring system and remarkable responsiveness even with increasing numbers of sensors are key characteristics that will facilitate the scale-up of intelligent electronic skins for Artificial Intelligence (AI) applications in robots, prosthetic devices and other human machine interfaces.

“Scalability is a critical consideration as big pieces of high performing electronic skins are required to cover the relatively large surface areas of robots and prosthetic devices,” explained Asst Prof Tee. “ACES can be easily paired with any kind of sensor skin layers, for example, those designed to sense temperatures and humidity, to create high performance ACES-enabled electronic skin with an exceptional sense of touch that can be used for a wide range of purposes,” he added.

For instance, pairing ACES with the transparent, self-healing and water-resistant sensor skin layer also recently developed by Asst Prof Tee’s team, creates an electronic skin that can self-repair, like the human skin. This type of electronic skin can be used to develop more realistic prosthetic limbs that will help disabled individuals restore their sense of touch.

Other potential applications include developing more intelligent robots that can perform disaster recovery tasks or take over mundane operations such as packing of items in warehouses. The NUS team is therefore looking to further apply the ACES platform on advanced robots and prosthetic devices in the next phase of their research.

For those who like videos, the researchers have prepared this,

Here’s a link to and a citation for the paper,

A neuro-inspired artificial peripheral nervous system for scalable electronic skins by Wang Wei Lee, Yu Jun Tan, Haicheng Yao, Si Li, Hian Hian See, Matthew Hon, Kian Ann Ng, Betty Xiong, John S. Ho and Benjamin C. K. Tee. Science Robotics Vol 4, Issue 32 31 July 2019 eaax2198 DOI: 10.1126/scirobotics.aax2198 Published online first: 17 Jul 2019:

This paper is behind a paywall.

Picking up a grape and holding his wife’s hand

This story comes from the Canadian Broadcasting Corporation (CBC) Radio with a six minute story embedded in the text, from a July 25, 2019 CBC Radio ‘As It Happens’ article by Sheena Goodyear,

The West Valley City, Utah, real estate agent [Keven Walgamott] lost his left hand in an electrical accident 17 years ago. Since then, he’s tried out a few different prosthetic limbs, but always found them too clunky and uncomfortable.

Then he decided to work with the University of Utah in 2016 to test out new prosthetic technology that mimics the sensation of human touch, allowing Walgamott to perform delicate tasks with precision — including shaking his wife’s hand. 

“I extended my left hand, she came and extended hers, and we were able to feel each other with the left hand for the first time in 13 years, and it was just a marvellous and wonderful experience,” Walgamott told As It Happens guest host Megan Williams. 

Walgamott, one of seven participants in the University of Utah study, was able to use an advanced prosthetic hand called the LUKE Arm to pick up an egg without cracking it, pluck a single grape from a bunch, hammer a nail, take a ring on and off his finger, fit a pillowcase over a pillow and more. 

While performing the tasks, Walgamott was able to actually feel the items he was holding and correctly gauge the amount of pressure he needed to exert — mimicking a process the human brain does automatically.

“I was able to feel something in each of my fingers,” he said. “What I feel, I guess the easiest way to explain it, is little electrical shocks.”

Those shocks — which he describes as a kind of a tingling sensation — intensify as he tightens his grip.

“Different variations of the intensity of the electricity as I move my fingers around and as I touch things,” he said. 

To make that [sense of touch] happen, the researchers implanted electrodes into the nerves on Walgamott’s forearm, allowing his brain to communicate with his prosthetic through a computer outside his body. That means he can move the hand just by thinking about it.

But those signals also work in reverse.

The team attached sensors to the hand of a LUKE Arm. Those sensors detect touch and positioning, and send that information to the electrodes so it can be interpreted by the brain.

For Walgamott, performing a series of menial tasks as a team of scientists recorded his progress was “fun to do.”

“I’d forgotten how well two hands work,” he said. “That was pretty cool.”

But it was also a huge relief from the phantom limb pain he has experienced since the accident, which he describes as a “burning sensation” in the place where his hand used to be.

A July 24, 2019 University of Utah news release (also on EurekAlert) provides more detail about the research,

Keven Walgamott had a good “feeling” about picking up the egg without crushing it.

What seems simple for nearly everyone else can be more of a Herculean task for Walgamott, who lost his left hand and part of his arm in an electrical accident 17 years ago. But he was testing out the prototype of a high-tech prosthetic arm with fingers that not only can move, they can move with his thoughts. And thanks to a biomedical engineering team at the University of Utah, he “felt” the egg well enough so his brain could tell the prosthetic hand not to squeeze too hard.

That’s because the team, led by U biomedical engineering associate professor Gregory Clark, has developed a way for the “LUKE Arm” (so named after the robotic hand that Luke Skywalker got in “The Empire Strikes Back”) to mimic the way a human hand feels objects by sending the appropriate signals to the brain. Their findings were published in a new paper co-authored by U biomedical engineering doctoral student Jacob George, former doctoral student David Kluger, Clark and other colleagues in the latest edition of the journal Science Robotics. A copy of the paper may be obtained by emailing robopak@aaas.org.

“We changed the way we are sending that information to the brain so that it matches the human body. And by matching the human body, we were able to see improved benefits,” George says. “We’re making more biologically realistic signals.”

That means an amputee wearing the prosthetic arm can sense the touch of something soft or hard, understand better how to pick it up and perform delicate tasks that would otherwise be impossible with a standard prosthetic with metal hooks or claws for hands.

“It almost put me to tears,” Walgamott says about using the LUKE Arm for the first time during clinical tests in 2017. “It was really amazing. I never thought I would be able to feel in that hand again.”

Walgamott, a real estate agent from West Valley City, Utah, and one of seven test subjects at the U, was able to pluck grapes without crushing them, pick up an egg without cracking it and hold his wife’s hand with a sensation in the fingers similar to that of an able-bodied person.

“One of the first things he wanted to do was put on his wedding ring. That’s hard to do with one hand,” says Clark. “It was very moving.”

Those things are accomplished through a complex series of mathematical calculations and modeling.

The LUKE Arm

The LUKE Arm has been in development for some 15 years. The arm itself is made of mostly metal motors and parts with a clear silicon “skin” over the hand. It is powered by an external battery and wired to a computer. It was developed by DEKA Research & Development Corp., a New Hampshire-based company founded by Segway inventor Dean Kamen.

Meanwhile, the U’s team has been developing a system that allows the prosthetic arm to tap into the wearer’s nerves, which are like biological wires that send signals to the arm to move. It does that thanks to an invention by U biomedical engineering Emeritus Distinguished Professor Richard A. Normann called the Utah Slanted Electrode Array. The array is a bundle of 100 microelectrodes and wires that are implanted into the amputee’s nerves in the forearm and connected to a computer outside the body. The array interprets the signals from the still-remaining arm nerves, and the computer translates them to digital signals that tell the arm to move.

But it also works the other way. To perform tasks such as picking up objects requires more than just the brain telling the hand to move. The prosthetic hand must also learn how to “feel” the object in order to know how much pressure to exert because you can’t figure that out just by looking at it.

First, the prosthetic arm has sensors in its hand that send signals to the nerves via the array to mimic the feeling the hand gets upon grabbing something. But equally important is how those signals are sent. It involves understanding how your brain deals with transitions in information when it first touches something. Upon first contact of an object, a burst of impulses runs up the nerves to the brain and then tapers off. Recreating this was a big step.

“Just providing sensation is a big deal, but the way you send that information is also critically important, and if you make it more biologically realistic, the brain will understand it better and the performance of this sensation will also be better,” says Clark.

To achieve that, Clark’s team used mathematical calculations along with recorded impulses from a primate’s arm to create an approximate model of how humans receive these different signal patterns. That model was then implemented into the LUKE Arm system.

Future research

In addition to creating a prototype of the LUKE Arm with a sense of touch, the overall team is already developing a version that is completely portable and does not need to be wired to a computer outside the body. Instead, everything would be connected wirelessly, giving the wearer complete freedom.

Clark says the Utah Slanted Electrode Array is also capable of sending signals to the brain for more than just the sense of touch, such as pain and temperature, though the paper primarily addresses touch. And while their work currently has only involved amputees who lost their extremities below the elbow, where the muscles to move the hand are located, Clark says their research could also be applied to those who lost their arms above the elbow.

Clark hopes that in 2020 or 2021, three test subjects will be able to take the arm home to use, pending federal regulatory approval.

The research involves a number of institutions including the U’s Department of Neurosurgery, Department of Physical Medicine and Rehabilitation and Department of Orthopedics, the University of Chicago’s Department of Organismal Biology and Anatomy, the Cleveland Clinic’s Department of Biomedical Engineering and Utah neurotechnology companies Ripple Neuro LLC and Blackrock Microsystems. The project is funded by the Defense Advanced Research Projects Agency and the National Science Foundation.

“This is an incredible interdisciplinary effort,” says Clark. “We could not have done this without the substantial efforts of everybody on that team.”

Here’s a link to and a citation for the paper,

Biomimetic sensory feedback through peripheral nerve stimulation improves dexterous use of a bionic hand by J. A. George, D. T. Kluger, T. S. Davis, S. M. Wendelken, E. V. Okorokova, Q. He, C. C. Duncan, D. T. Hutchinson, Z. C. Thumser, D. T. Beckler, P. D. Marasco, S. J. Bensmaia and G. A. Clark. Science Robotics Vol. 4, Issue 32, eaax2352 31 July 2019 DOI: 10.1126/scirobotics.aax2352 Published online first: 24 Jul 2019

This paper is definitely behind a paywall.

The University of Utah researchers have produced a video highlighting their work,

The roles mathematics and light play in cellular communication

These are two entirely different types of research but taken together they help build a picture about how the cells in our bodies function.

Cells and light

An April 30, 2018 news item on phys.org describes work on controlling biology with light,

Over the past five years, University of Chicago chemist Bozhi Tian has been figuring out how to control biology with light.

A longterm science goal is devices to serve as the interface between researcher and body—both as a way to understand how cells talk among each other and within themselves, and eventually, as a treatment for brain or nervous system disorders [emphasis mine] by stimulating nerves to fire or limbs to move. Silicon—a versatile, biocompatible material used in both solar panels and surgical implants—is a natural choice.

In a paper published April 30 in Nature Biomedical Engineering, Tian’s team laid out a system of design principles for working with silicon to control biology at three levels—from individual organelles inside cells to tissues to entire limbs. The group has demonstrated each in cells or mice models, including the first time anyone has used light to control behavior without genetic modification.

“We want this to serve as a map, where you can decide which problem you would like to study and immediately find the right material and method to address it,” said Tian, an assistant professor in the Department of Chemistry.

Researchers built this thin layer of silicon lace to modulate neural signals when activated by light. Courtesy of Yuanwen Jiang and Bozhi Tian

An April 30, 2018 University of Chicago news release by Louise Lerner, which originated the news item, describes the work in greater detail,

The scientists’ map lays out best methods to craft silicon devices depending on both the intended task and the scale—ranging from inside a cell to a whole animal.

For example, to affect individual brain cells, silicon can be crafted to respond to light by emitting a tiny ionic current, which encourages neurons to fire. But in order to stimulate limbs, scientists need a system whose signals can travel farther and are stronger—such as a gold-coated silicon material in which light triggers a chemical reaction.

The mechanical properties of the implant are important, too. Say researchers would like to work with a larger piece of the brain, like the cortex, to control motor movement. The brain is a soft, squishy substance, so they’ll need a material that’s similarly soft and flexible, but can bind tightly against the surface. They’d want thin and lacy silicon, say the design principles.

The team favors this method because it doesn’t require genetic modification or a power supply wired in, since the silicon can be fashioned into what are essentially tiny solar panels. (Many other forms of monitoring or interacting with the brain need to have a power supply, and keeping a wire running into a patient is an infection risk.)

They tested the concept in mice and found they could stimulate limb movements by shining light on brain implants. Previous research tested the concept in neurons.

“We don’t have answers to a number of intrinsic questions about biology, such as whether individual mitochondria communicate remotely through bioelectric signals,” said Yuanwen Jiang, the first author on the paper, then a graduate student at UChicago and now a postdoctoral researcher at Stanford. “This set of tools could address such questions as well as pointing the way to potential solutions for nervous system disorders.”

Other UChicago authors were Assoc. Profs. Chin-Tu Chen and Chien-Min Kao, Asst. Prof Xiaoyang, postdoctoral researchers Jaeseok Yi, Yin Fang, Xiang Gao, Jiping Yue, Hsiu-Ming Tsai, Bing Liu and Yin Fang, graduate students Kelliann Koehler, Vishnu Nair, and Edward Sudzilovsky, and undergraduate student George Freyermuth.

Other researchers on the paper hailed from Northwestern University, the University of Illinois at Chicago and Hong Kong Polytechnic University.

The researchers have also made this video illustrating their work,

via Gfycat Tiny silicon nanowires (in blue), activated by light, trigger activity in neurons. (Courtesy Yuanwen Jiang and Bozhi Tian)

Here’s a link to and a citation for the paper,

Rational design of silicon structures for optically controlled multiscale biointerfaces by Yuanwen Jiang, Xiaojian Li, Bing Liu, Jaeseok Yi, Yin Fang, Fengyuan Shi, Xiang Gao, Edward Sudzilovsky, Ramya Parameswaran, Kelliann Koehler, Vishnu Nair, Jiping Yue, KuangHua Guo, Yin Fang, Hsiu-Ming Tsai, George Freyermuth, Raymond C. S. Wong, Chien-Min Kao, Chin-Tu Chen, Alan W. Nicholls, Xiaoyang Wu, Gordon M. G. Shepherd, & Bozhi Tian. Nature Biomedical Engineering (2018) doi:10.1038/s41551-018-0230-1 Published: 30 April 2018

This paper is behind a paywall.

Mathematics and how living cells ‘think’

This May 2, 2018 Queensland University of Technology (QUT; Australia) press release is also on EurekAlert,

How does the ‘brain’ of a living cell work, allowing an organism to function and thrive in changing and unfavourable environments?

Queensland University of Technology (QUT) researcher Dr Robyn Araujo has developed new mathematics to solve a longstanding mystery of how the incredibly complex biological networks within cells can adapt and reset themselves after exposure to a new stimulus.

Her findings, published in Nature Communications, provide a new level of understanding of cellular communication and cellular ‘cognition’, and have potential application in a variety of areas, including new targeted cancer therapies and drug resistance.

Dr Araujo, a lecturer in applied and computational mathematics in QUT’s Science and Engineering Faculty, said that while we know a great deal about gene sequences, we have had extremely limited insight into how the proteins encoded by these genes work together as an integrated network – until now.

“Proteins form unfathomably complex networks of chemical reactions that allow cells to communicate and to ‘think’ – essentially giving the cell a ‘cognitive’ ability, or a ‘brain’,” she said. “It has been a longstanding mystery in science how this cellular ‘brain’ works.

“We could never hope to measure the full complexity of cellular networks – the networks are simply too large and interconnected and their component proteins are too variable.

“But mathematics provides a tool that allows us to explore how these networks might be constructed in order to perform as they do.

“My research is giving us a new way to look at unravelling network complexity in nature.”

Dr Araujo’s work has focused on the widely observed function called perfect adaptation – the ability of a network to reset itself after it has been exposed to a new stimulus.

“An example of perfect adaptation is our sense of smell,” she said. “When exposed to an odour we will smell it initially but after a while it seems to us that the odour has disappeared, even though the chemical, the stimulus, is still present.

“Our sense of smell has exhibited perfect adaptation. This process allows it to remain sensitive to further changes in our environment so that we can detect both very feint and very strong odours.

“This kind of adaptation is essentially what takes place inside living cells all the time. Cells are exposed to signals – hormones, growth factors, and other chemicals – and their proteins will tend to react and respond initially, but then settle down to pre-stimulus levels of activity even though the stimulus is still there.

“I studied all the possible ways a network can be constructed and found that to be capable of this perfect adaptation in a robust way, a network has to satisfy an extremely rigid set of mathematical principles. There are a surprisingly limited number of ways a network could be constructed to perform perfect adaptation.

“Essentially we are now discovering the needles in the haystack in terms of the network constructions that can actually exist in nature.

“It is early days, but this opens the door to being able to modify cell networks with drugs and do it in a more robust and rigorous way. Cancer therapy is a potential area of application, and insights into how proteins work at a cellular level is key.”

Dr Araujo said the published study was the result of more than “five years of relentless effort to solve this incredibly deep mathematical problem”. She began research in this field while at George Mason University in Virginia in the US.

Her mentor at the university’s College of Science and co-author of the Nature Communications paper, Professor Lance Liotta, said the “amazing and surprising” outcome of Dr Araujo’s study is applicable to any living organism or biochemical network of any size.

“The study is a wonderful example of how mathematics can have a profound impact on society and Dr Araujo’s results will provide a set of completely fresh approaches for scientists in a variety of fields,” he said.

“For example, in strategies to overcome cancer drug resistance – why do tumours frequently adapt and grow back after treatment?

“It could also help understanding of how our hormone system, our immune defences, perfectly adapt to frequent challenges and keep us well, and it has future implications for creating new hypotheses about drug addiction and brain neuron signalling adaptation.”

Hre’s a link to and a citation for the paper,

The topological requirements for robust perfect adaptation in networks of any size by Robyn P. Araujo & Lance A. Liotta. Nature Communicationsvolume 9, Article number: 1757 (2018) doi:10.1038/s41467-018-04151-6 Published: 01 May 2018

This paper is open access.

Quantum entanglement in near-macroscopic objects

Researchers at Finland’s Aalto University seem excited in an April 25, 2018 news item on phys.org,

Perhaps the strangest prediction of quantum theory is entanglement, a phenomenon whereby two distant objects become intertwined in a manner that defies both classical physics and a common-sense understanding of reality. In 1935, Albert Einstein expressed his concern over this concept, referring to it as “spooky action at a distance.”

Today, entanglement is considered a cornerstone of quantum mechanics, and it is the key resource for a host of potentially transformative quantum technologies. Entanglement is, however, extremely fragile, and it has previously been observed only in microscopic systems such as light or atoms, and recently in superconducting electric circuits.

In work recently published in Nature, a team led by Prof. Mika Sillanpää at Aalto University in Finland has shown that entanglement of massive objects can be generated and detected.

The researchers managed to bring the motions of two individual vibrating drumheads—fabricated from metallic aluminium on a silicon chip—into an entangled quantum state. The macroscopic objects in the experiment are truly massive compared to the atomic scale—the circular drumheads have a diametre similar to the width of a thin human hair.

An April 20,2018 Aalto University press release (also on EurekAlert), which originated the news item, provides more detail,

‘The vibrating bodies are made to interact via a superconducting microwave circuit. The electromagnetic fields in the circuit carry away any thermal disturbances, leaving behind only the quantum mechanical vibrations’, says Professor Sillanpää, describing the experimental setup.

Eliminating all forms of external noise is crucial for the experiments, which is why they have to be conducted at extremely low temperatures near absolute zero, at –273 °C. Remarkably, the experimental approach allows the unusual state of entanglement to persist for long periods of time, in this case up to half an hour. In comparison, measurements on elementary particles have witnessed entanglement to last only tiny fractions of a second.

‘These measurements are challenging but extremely fascinating. In the future, we will attempt to teleport the mechanical vibrations. In quantum teleportation, properties of physical bodies can be transmitted across arbitrary distances using the channel of “spooky action at a distance”. We are still pretty far from Star Trek, though,’ says Dr. Caspar Ockeloen-Korppi, the lead author on the work, who also performed the measurements.

The results demonstrate that it is now possible to have control over the most delicate properties of objects whose size approaches the scale of our daily lives. The achievement opens doors for new kinds of quantum technologies, where the entangled drumheads could be used as routers or sensors. The finding also enables new studies of fundamental physics in, for example, the poorly understood interplay of gravity and quantum mechanics.

The team also included scientists from the University of New South Wales in Australia, the University of Chicago in the USA, and the University of Jyväskylä in Finland, whose theoretical innovations paved the way for the laboratory experiment.

An illustration has been made available,

An illustration of the 15-micrometre-wide drumheads prepared on silicon chips used in the experiment. The drumheads vibrate at a high ultrasound frequency, and the peculiar quantum state predicted by Einstein was created from the vibrations. Image: Aalto University / Petja Hyttinen & Olli Hanhirova, ARKH Architects.

Here’s a link to and a citation for the paper,

Stabilized entanglement of massive mechanical oscillators by C. F. Ockeloen-Korppi, E. Damskägg, J.-M. Pirkkalainen, M. Asjad, A. A. Clerk, F. Massel, M. J. Woolley & M. A. Sillanpää. Nature volume 556, pages478–482 (2018) doi:10.1038/s41586-018-0038-x Published online: 25 April 2018

This paper is behind a paywall.

Why don’t you CRISPR yourself?

It must have been quite the conference. Josiah Zayner plunged a needle into himself and claimed to have changed his DNA (deoxyribonucleic acid) while giving his talk. (*Segue: There is some Canadian content if you keep reading.*) From an Oct. 10, 2017 article by Adele Peters for Fast Company (Note: A link has been removed),

“What we’ve got here is some DNA, and this is a syringe,” Josiah Zayner tells a room full of synthetic biologists and other researchers. He fills the needle and plunges it into his skin. “This will modify my muscle genes and give me bigger muscles.”

Zayner, a biohacker–basically meaning he experiments with biology in a DIY lab rather than a traditional one–was giving a talk called “A Step-by-Step Guide to Genetically Modifying Yourself With CRISPR” at the SynBioBeta conference in San Francisco, where other presentations featured academics in suits and the young CEOs of typical biotech startups. Unlike the others, he started his workshop by handing out shots of scotch and a booklet explaining the basics of DIY [do-it-yourwelf] genome engineering.

If you want to genetically modify yourself, it turns out, it’s not necessarily complicated. As he offered samples in small baggies to the crowd, Zayner explained that it took him about five minutes to make the DNA that he brought to the presentation. The vial held Cas9, an enzyme that snips DNA at a particular location targeted by guide RNA, in the gene-editing system known as CRISPR. In this case, it was designed to knock out the myostatin gene, which produces a hormone that limits muscle growth and lets muscles atrophy. In a study in China, dogs with the edited gene had double the muscle mass of normal dogs. If anyone in the audience wanted to try it, they could take a vial home and inject it later. Even rubbing it on skin, Zayner said, would have some effect on cells, albeit limited.

Peters goes on to note that Zayner has a PhD in molecular biology and biophysics and worked for NASA (US National Aeronautics and Space Administration). Zayner’s Wikipedia entry fills in a few more details (Note: Links have been removed),

Zayner graduated from the University of Chicago with a Ph.D. in biophysics in 2013. He then spent two years as a researcher at NASA’s Ames Research Center,[2] where he worked on Martian colony habitat design. While at the agency, Zayner also analyzed speech patterns in online chat, Twitter, and books, and found that language on Twitter and online chat is closer to how people talk than to how they write.[3] Zayner found NASA’s scientific work less innovative than he expected, and upon leaving in January 2016, he launched a crowdfunding campaign to provide CRISPR kits to let the general public experiment with editing bacterial DNA. He also continued his grad school business, The ODIN, which sells kits to let the general public experiment at home. As of May 2016, The ODIN had four employees and operates out of Zayner’s garage.[2]

He refers to himself as a biohacker and believes in the importance in letting the general public participate in scientific experimentation, rather than leaving it segregated to labs.[2][4][1] Zayner found the biohacking community exclusive and hierarchical, particularly in the types of people who decide what is “safe”. He hopes that his projects can let even more people experiment in their homes. Other scientists responded that biohacking is inherently privileged, as it requires leisure time and money, and that deviance from the safety rules of concern would lead to even harsher regulations for all.[5] Zayner’s public CRISPR kit campaign coincided with wider scrutiny over genetic modification. Zayner maintained that these fears were based on misunderstandings of the product, as genetic experiments on yeast and bacteria cannot produce a viral epidemic.[6][7] In April 2015, Zayner ran a hoax on Craigslist to raise awareness about the future potential of forgery in forensics genetics testing.[8]

In February 2016, Zayner performed a full body microbiome transplant on himself, including a fecal transplant, to experiment with microbiome engineering and see if he could cure himself from gastrointestinal and other health issues. The microbiome from the donors feces successfully transplanted in Zayner’s gut according to DNA sequencing done on samples.[2] This experiment was documented by filmmakers Kate McLean and Mario Furloni and turned into the short documentary film Gut Hack.[9]

In December 2016, Zayner created a fluorescent beer by engineering yeast to contain the green fluorescent protein from jellyfish. Zayner’s company, The ODIN, released kits to allow people to create their own engineered fluorescent yeast and this was met with some controversy as the FDA declared the green fluorescent protein can be seen as a color additive.[10] Zayner, views the kit as a way that individual can use genetic engineering to create things in their everyday life.[11]

I found the video for Zayner’s now completed crowdfunding campaign,

I also found The ODIN website (mentioned in the Wikipedia essay) where they claim to be selling various gene editing and gene engineering kits including the CRISPR editing kits mentioned in Peters’ article,

In 2016, he [Zayner] sold $200,000 worth of products, including a kit for yeast that can be used to brew glowing bioluminescent beer, a kit to discover antibiotics at home, and a full home lab that’s roughly the cost of a MacBook Pro. In 2017, he expects to double sales. Many kits are simple, and most buyers probably aren’t using the supplies to attempt to engineer themselves (many kits go to classrooms). But Zayner also hopes that as people using the kits gain genetic literacy, they experiment in wilder ways.

Zayner sells a full home biohacking lab that’s roughly the cost of a MacBook Pro. [Photo: The ODIN]

He questions whether traditional research methods, like randomized controlled trials, are the only way to make discoveries, pointing out that in newer personalized medicine (such as immunotherapy for cancer, which is personalized for each patient), a sample size of one person makes sense. At his workshop, he argued that people should have the choice to self-experiment if they want to; we also change our DNA when we drink alcohol or smoke cigarettes or breathe in dirty city air. Other society-sanctioned activities are more dangerous. “We sacrifice maybe a million people a year to the car gods,” he said. “If you ask someone, ‘Would you get rid of cars?’–no.” …

US researchers both conventional and DIY types such as Zayner are not the only ones who are editing genes. The Chinese study mentioned in Peters’ article was written up in an Oct. 19, 2015 article by Antonio Regalado for the MIT [Massachusetts Institute of Technology] Technology Review (Note: Links have been removed),

Scientists in China say they are the first to use gene editing to produce customized dogs. They created a beagle with double the amount of muscle mass by deleting a gene called myostatin.

The dogs have “more muscles and are expected to have stronger running ability, which is good for hunting, police (military) applications,” Liangxue Lai, a researcher with the Key Laboratory of Regenerative Biology at the Guangzhou Institutes of Biomedicine and Health, said in an e-mail.

Lai and 28 colleagues reported their results last week in the Journal of Molecular Cell Biology, saying they intend to create dogs with other DNA mutations, including ones that mimic human diseases such as Parkinson’s and muscular dystrophy. “The goal of the research is to explore an approach to the generation of new disease dog models for biomedical research,” says Lai. “Dogs are very close to humans in terms of metabolic, physiological, and anatomical characteristics.”

Lai said his group had no plans breed to breed the extra-muscular beagles as pets. Other teams, however, could move quickly to commercialize gene-altered dogs, potentially editing their DNA to change their size, enhance their intelligence, or correct genetic illnesses. A different Chinese Institute, BGI, said in September it had begun selling miniature pigs, created via gene editing, for $1,600 each as novelty pets.

People have been influencing the genetics of dogs for millennia. By at least 36,000 years ago, early humans had already started to tame wolves and shape the companions we have today. Charles Darwin frequently cited dog breeding in The Origin of Species to demonstrate how evolution gradually occurs by a process of selection. With CRISPR, however, evolution is no longer gradual or subject to chance. It is immediate and under human control.

It is precisely that power that is stirring wide debate and concern over CRISPR. Yet at least some researchers think that gene-edited dogs could put a furry, friendly face on the technology. In an interview this month, George Church, a professor at Harvard University who leads a large effort to employ CRISPR editing, said he thinks it will be possible to augment dogs by using DNA edits to make them live longer or simply make them smarter.

Church said he also believed the alteration of dogs and other large animals could open a path to eventual gene editing of people. “Germline editing of pigs or dogs offers a line into it,” he said. “People might say, ‘Hey, it works.’ ”

In the meantime, Zayner’s ideas are certainly thought provoking. I’m not endorsing either his products or his ideas but it should be noted that early science pioneers such as Humphrey Davy and others experimented on themselves. For anyone unfamiliar with Davy, (from the Humphrey Davy Wikipedia entry; Note: Links have been removed),

Sir Humphry Davy, 1st Baronet PRS MRIA FGS (17 December 1778 – 29 May 1829) was a Cornish chemist and inventor,[1] who is best remembered today for isolating a series of substances for the first time: potassium and sodium in 1807 and calcium, strontium, barium, magnesium and boron the following year, as well as discovering the elemental nature of chlorine and iodine. He also studied the forces involved in these separations, inventing the new field of electrochemistry. Berzelius called Davy’s 1806 Bakerian Lecture On Some Chemical Agencies of Electricity[2] “one of the best memoirs which has ever enriched the theory of chemistry.”[3] He was a Baronet, President of the Royal Society (PRS), Member of the Royal Irish Academy (MRIA), and Fellow of the Geological Society (FGS). He also invented the Davy lamp and a very early form of incandescent light bulb.

Canadian content*

A Nov. 11, 2017 posting on the Canadian Broadcasting Corporation’s (CBC) Quirks and Quarks blog notes that self-experimentation has a long history and goes on to describe Zayner’s and others biohacking exploits before describing the legality of biohacking in Canada,

With biohackers entering into the space traditionally held by scientists and clinicians, it begs questions. Professor Timothy Caulfield, a Canada research chair in health, law and policy at the University of Alberta, says when he hears of somebody giving themselves biohacked gene therapy, he wonders: “Is this legal? Is this safe? And if it’s not safe, is there anything that we can do about regulating it? And to be honest with you that’s a tough question and I think it’s an open question.”

In Canada, Caulfield says, Health Canada focuses on products. “You have to have something that you are going to regulate or you have to have something that’s making health claims. So if there is a product that is saying I can cure X, Y, or Z, Health Canada can say, ‘Well let’s make sure the science really backs up that claim.’ The problem with these do-it-yourself approaches is there isn’t really a product. You know these people are experimenting on themselves with something that may or may not be designed for health purposes.”

According to Caufield, if you could buy a gene therapy kit that was being marketed to you to biohack yourself, that would be different. “Health Canada could jump in. But right here that’s not the case,” he says.

There are places in the world that do regulate biohacking, says Caulfield. “Germany, for example, they have specific laws for it. And here in Canada we do have a regulatory framework that says that you cannot do gene therapy that will alter the germ line. In other words, you can’t do gene therapy or any kind of genetic editing that will create a change that you will pass on to your offspring. So that would be illegal, but that’s not what’s happening here. And I don’t think there’s a regulatory framework that adequately captures it.”

Infectious disease and policy experts aren’t that concerned yet about the possibility of a biohacker unleashing a genetically modified super germ into the population.

“I think in the future that could be a problem,”says Caulfield, “but this isn’t something that would be easy to do in your garage. I think it’s complicated science. But having said that, the science is moving quickly. We need to think about how we are going to control the potential harms.”

You can find out more about the ‘wild’ people (mostly men) of early science in Richard Holmes’ 2008 book, The Age of Wonder: How the Romantic Generation Discovered the Beauty and Terror of Science.

Finally, should you be interested in connecting with synthetic biology enthusiasts, entrepreneurs, and others, SynBioBeta is more than a conference; it’s also an activity hub.

ETA January 25, 2018 (five minutes later): There are some CRISPR/CAS9 events taking place in Toronto, Canada on January 24 and 25, 2018. One is a workshop with Portuguese artist, Marta de Menezes, and the other is a panel discussion. See my January 10, 2018 posting for more details.

*’Segue: There is some Canadian content if you keep reading.’ and ‘Canadian content’ added January 25, 2018 six minutes after first publication.

ETA February 20, 2018: Sarah Zhang’s Feb. 20, 2018 article for The Atlantic revisits Josiah Zayner’s decision to inject himself with CRISPR,

When Josiah Zayner watched a biotech CEO drop his pants at a biohacking conference and inject himself with an untested herpes treatment, he realized things had gone off the rails.

Zayner is no stranger to stunts in biohacking—loosely defined as experiments, often on the self, that take place outside of traditional lab spaces. You might say he invented their latest incarnation: He’s sterilized his body to “transplant” his entire microbiome in front of a reporter. He’s squabbled with the FDA about selling a kit to make glow-in-the-dark beer. He’s extensively documented attempts to genetically engineer the color of his skin. And most notoriously, he injected his arm with DNA encoding for CRISPR that could theoretically enhance his muscles—in between taking swigs of Scotch at a live-streamed event during an October conference. (Experts say—and even Zayner himself in the live-stream conceded—it’s unlikely to work.)

So when Zayner saw Ascendance Biomedical’s CEO injecting himself on a live-stream earlier this month, you might say there was an uneasy flicker of recognition.

“Honestly, I kind of blame myself,” Zayner told me recently. He’s been in a soul-searching mood; he recently had a kid and the backlash to the CRISPR stunt in October [2017] had been getting to him. “There’s no doubt in my mind that somebody is going to end up hurt eventually,” he said.

Yup, it’s one of the reasons for rules; people take things too far. The trick is figuring out how to achieve balance between risk taking and recklessness.

Machine learning programs learn bias

The notion of bias in artificial intelligence (AI)/algorithms/robots is gaining prominence (links to other posts featuring algorithms and bias are at the end of this post). The latest research concerns machine learning where an artificial intelligence system trains itself with ordinary human language from the internet. From an April 13, 2017 American Association for the Advancement of Science (AAAS) news release on EurekAlert,

As artificial intelligence systems “learn” language from existing texts, they exhibit the same biases that humans do, a new study reveals. The results not only provide a tool for studying prejudicial attitudes and behavior in humans, but also emphasize how language is intimately intertwined with historical biases and cultural stereotypes. A common way to measure biases in humans is the Implicit Association Test (IAT), where subjects are asked to pair two concepts they find similar, in contrast to two concepts they find different; their response times can vary greatly, indicating how well they associated one word with another (for example, people are more likely to associate “flowers” with “pleasant,” and “insects” with “unpleasant”). Here, Aylin Caliskan and colleagues developed a similar way to measure biases in AI systems that acquire language from human texts; rather than measuring lag time, however, they used the statistical number of associations between words, analyzing roughly 2.2 million words in total. Their results demonstrate that AI systems retain biases seen in humans. For example, studies of human behavior show that the exact same resume is 50% more likely to result in an opportunity for an interview if the candidate’s name is European American rather than African-American. Indeed, the AI system was more likely to associate European American names with “pleasant” stimuli (e.g. “gift,” or “happy”). In terms of gender, the AI system also reflected human biases, where female words (e.g., “woman” and “girl”) were more associated than male words with the arts, compared to mathematics. In a related Perspective, Anthony G. Greenwald discusses these findings and how they could be used to further analyze biases in the real world.

There are more details about the research in this April 13, 2017 Princeton University news release on EurekAlert (also on ScienceDaily),

In debates over the future of artificial intelligence, many experts think of the new systems as coldly logical and objectively rational. But in a new study, researchers have demonstrated how machines can be reflections of us, their creators, in potentially problematic ways. Common machine learning programs, when trained with ordinary human language available online, can acquire cultural biases embedded in the patterns of wording, the researchers found. These biases range from the morally neutral, like a preference for flowers over insects, to the objectionable views of race and gender.

Identifying and addressing possible bias in machine learning will be critically important as we increasingly turn to computers for processing the natural language humans use to communicate, for instance in doing online text searches, image categorization and automated translations.

“Questions about fairness and bias in machine learning are tremendously important for our society,” said researcher Arvind Narayanan, an assistant professor of computer science and an affiliated faculty member at the Center for Information Technology Policy (CITP) at Princeton University, as well as an affiliate scholar at Stanford Law School’s Center for Internet and Society. “We have a situation where these artificial intelligence systems may be perpetuating historical patterns of bias that we might find socially unacceptable and which we might be trying to move away from.”

The paper, “Semantics derived automatically from language corpora contain human-like biases,” published April 14  [2017] in Science. Its lead author is Aylin Caliskan, a postdoctoral research associate and a CITP fellow at Princeton; Joanna Bryson, a reader at University of Bath, and CITP affiliate, is a coauthor.

As a touchstone for documented human biases, the study turned to the Implicit Association Test, used in numerous social psychology studies since its development at the University of Washington in the late 1990s. The test measures response times (in milliseconds) by human subjects asked to pair word concepts displayed on a computer screen. Response times are far shorter, the Implicit Association Test has repeatedly shown, when subjects are asked to pair two concepts they find similar, versus two concepts they find dissimilar.

Take flower types, like “rose” and “daisy,” and insects like “ant” and “moth.” These words can be paired with pleasant concepts, like “caress” and “love,” or unpleasant notions, like “filth” and “ugly.” People more quickly associate the flower words with pleasant concepts, and the insect terms with unpleasant ideas.

The Princeton team devised an experiment with a program where it essentially functioned like a machine learning version of the Implicit Association Test. Called GloVe, and developed by Stanford University researchers, the popular, open-source program is of the sort that a startup machine learning company might use at the heart of its product. The GloVe algorithm can represent the co-occurrence statistics of words in, say, a 10-word window of text. Words that often appear near one another have a stronger association than those words that seldom do.

The Stanford researchers turned GloVe loose on a huge trawl of contents from the World Wide Web, containing 840 billion words. Within this large sample of written human culture, Narayanan and colleagues then examined sets of so-called target words, like “programmer, engineer, scientist” and “nurse, teacher, librarian” alongside two sets of attribute words, such as “man, male” and “woman, female,” looking for evidence of the kinds of biases humans can unwittingly possess.

In the results, innocent, inoffensive biases, like for flowers over bugs, showed up, but so did examples along lines of gender and race. As it turned out, the Princeton machine learning experiment managed to replicate the broad substantiations of bias found in select Implicit Association Test studies over the years that have relied on live, human subjects.

For instance, the machine learning program associated female names more with familial attribute words, like “parents” and “wedding,” than male names. In turn, male names had stronger associations with career attributes, like “professional” and “salary.” Of course, results such as these are often just objective reflections of the true, unequal distributions of occupation types with respect to gender–like how 77 percent of computer programmers are male, according to the U.S. Bureau of Labor Statistics.

Yet this correctly distinguished bias about occupations can end up having pernicious, sexist effects. An example: when foreign languages are naively processed by machine learning programs, leading to gender-stereotyped sentences. The Turkish language uses a gender-neutral, third person pronoun, “o.” Plugged into the well-known, online translation service Google Translate, however, the Turkish sentences “o bir doktor” and “o bir hem?ire” with this gender-neutral pronoun are translated into English as “he is a doctor” and “she is a nurse.”

“This paper reiterates the important point that machine learning methods are not ‘objective’ or ‘unbiased’ just because they rely on mathematics and algorithms,” said Hanna Wallach, a senior researcher at Microsoft Research New York City, who was not involved in the study. “Rather, as long as they are trained using data from society and as long as society exhibits biases, these methods will likely reproduce these biases.”

Another objectionable example harkens back to a well-known 2004 paper by Marianne Bertrand of the University of Chicago Booth School of Business and Sendhil Mullainathan of Harvard University. The economists sent out close to 5,000 identical resumes to 1,300 job advertisements, changing only the applicants’ names to be either traditionally European American or African American. The former group was 50 percent more likely to be offered an interview than the latter. In an apparent corroboration of this bias, the new Princeton study demonstrated that a set of African American names had more unpleasantness associations than a European American set.

Computer programmers might hope to prevent cultural stereotype perpetuation through the development of explicit, mathematics-based instructions for the machine learning programs underlying AI systems. Not unlike how parents and mentors try to instill concepts of fairness and equality in children and students, coders could endeavor to make machines reflect the better angels of human nature.

“The biases that we studied in the paper are easy to overlook when designers are creating systems,” said Narayanan. “The biases and stereotypes in our society reflected in our language are complex and longstanding. Rather than trying to sanitize or eliminate them, we should treat biases as part of the language and establish an explicit way in machine learning of determining what we consider acceptable and unacceptable.”

Here’s a link to and a citation for the Princeton paper,

Semantics derived automatically from language corpora contain human-like biases by Aylin Caliskan, Joanna J. Bryson, Arvind Narayanan. Science  14 Apr 2017: Vol. 356, Issue 6334, pp. 183-186 DOI: 10.1126/science.aal4230

This paper appears to be open access.

Links to more cautionary posts about AI,

Aug 5, 2009: Autonomous algorithms; intelligent windows; pretty nano pictures

June 14, 2016:  Accountability for artificial intelligence decision-making

Oct. 25, 2016 Removing gender-based stereotypes from algorithms

March 1, 2017: Algorithms in decision-making: a government inquiry in the UK

There’s also a book which makes some of the current use of AI programmes and big data quite accessible reading: Cathy O’Neil’s ‘Weapons of Math Destruction: How Big Data Increases Inequality and Threatens Democracy’.

Regrowing bone

The ability to grow bone or bone-like material could change life substantially for people with certain kinds of injuries. Scientists at Northwestern University and the University of Chicago have been able to regrow bone in a skull (according to a March 8, 2017 Northwestern University news release (also on EurekAlert),

A team of researchers repaired a hole in a mouse’s skull by regrowing “quality bone,” a breakthrough that could drastically improve the care of people who suffer severe trauma to the skull or face.

The work by a joint team of Northwestern Engineering and University of Chicago researchers was a resounding success, showing that a potent combination of technologies was able to regenerate the skull bone with supporting blood vessels in just the discrete area needed without developing scar tissue — and more rapidly than with previous methods.

“The results are very exciting,” said Guillermo Ameer, professor of biomedical engineering at Northwestern’s McCormick School of Engineering, and professor of surgery at Feinberg School of Medicine.

Supported by the China Scholarship Council, National Institute of Dental and Craniofacial Research, Chicago Community Trust, and National Center for Advancing Translational Sciences, the research was published last week in the journal PLOS One. Russell Reid, associate professor of surgery at the University of Chicago Medical Center, is the article’s corresponding author. Reid, his long-time collaborator Dr. Tong-Chuan He, and colleagues in Hyde Park brought the surgical and biological knowledge and skills. Zari P. Dumanian, affiliated with the medical center’s surgery department, was the paper’s first author.

“This project was a true collaborative team effort in which our Regenerative Engineering Laboratory provided the biomaterials expertise,” Ameer said.

Injuries or defects in the skull or facial bones are very challenging to treat, often requiring the surgeon to graft bone from the patient’s pelvis, ribs, or elsewhere, a painful procedure in itself. Difficulties increase if the injury area is large or if the graft needs to be contoured to the angle of the jaw or the cranial curve.

But if all goes well with this new approach, it may make painful bone grafting obsolete.

In the experiment, the researchers harvested skull cells from the mouse and engineered them to produce a potent protein to promote bone growth. They then used Ameer’s hydrogel, which acted like a temporary scaffolding, to deliver and contain these cells to the affected area. It was the combination of all three technologies that proved so successful, Ameer said.

Using calvaria or skull cells from the subject meant the body didn’t reject those cells.

The protein, BMP9, has been shown to promote bone cell growth more rapidly than other types of BMPs. Importantly, BMP9 also appeared to improve the creation of blood vessels in the area. Being able to safely deliver skull cells that are capable of rapidly regrowing bone in the affected site, in vivo as opposed to using them to grow bone in the laboratory, which would take a very long time, promises a therapy that might be more “surgeon friendly, if you will, and not too complicated to scale up for the patients,” Ameer said.

The scaffolding developed in Ameer’s laboratory, which is a material based on citric acid and called PPCN-g, is a liquid that when warmed to body temperature becomes a gel-like elastic material. “When applied, the liquid, which contains cells capable of producing bone, will conform to the shape of the bone defect to make a perfect fit,” Ameer said. “It then stays in place as a gel, localizing the cells to the site for the duration of the repair.” As the bone regrows, the PPCN-g is reabsorbed by the body.

“What we found is that these cells make natural-looking bone in the presence of the PPCN-g,” Ameer said. “The new bone is very similar to normal bone in that location.”

In fact, the three-part method was successful on a number of fronts: The regenerated bone was better quality, the bone growth was contained to the area defined by the scaffolding, the area healed much more quickly, and the new and old bone were continuous with no scar tissue.

The potential, if the procedure can be adapted to treat people that suffered trauma from car accidents or aggressive cancers that have affected the skull or face, would be huge, and give surgeons a much-sought-after option.

“The reconstruction procedure is a lot easier when you can harvest a few cells, make them produce the BMP9 protein, mix them in the PPCN-g solution, and apply it to the bone defect site to jump-start the new bone growth process where you want it.” Ameer said.

Ameer cautioned that the technology is years away to being used in humans, but added, “We did show proof of concept that we can heal large defects in the skull that would normally not heal on their own using a protein, cells and a new material that come together in a completely new way. Our team is very excited about these findings and the future of reconstructive surgery.”

Here’s a link and a citation for the paper,

Repair of critical sized cranial defects with BMP9-transduced calvarial cells delivered in a thermoresponsive scaffold by Zari P. Dumanian, Viktor Tollemar, Jixing Ye, Minpeng Lu, Yunxiao Zhu, Junyi Liao, Guillermo A. Ameer, Tong-Chuan He, Russell R. Reid. PLOS http://dx.doi.org/10.1371/journal.pone.0172327 Published: March 1, 2017

This is an open access paper.

Nanotechnology and Pakistan

I don’t often get information about nanotechnology in Pakistan so this March 6, 2017 news article by Mrya Imran on the TheNews.com website provides some welcome insight,

Pakistan has the right level of expert human resource and scientific activity in the field of nanotechnology. A focused national strategy and sustainable funding can make Pakistan one of the leaders in this sector.

These views were expressed by Professor of Physics in University of Illinois and Founder and President of NanoSi Advanced Technology, Inc. Dr Munir H. Nayfeh.  Dr Nayfeh, along with Executive Director, Centre for Nanoscale Science and Technology, and Research Faculty, Department of Agricultural and Biological Engineering, University of Illinois, Dr. Irfan Ahmad and Associate Professor and Director of Medical Physics Programme, Pritzker School of Medicine, University of Chicago, Dr. Bulent Aydogan were invited by COMSATS Institute of Information Technology (CIIT) to deliver lectures on nanotechnology research and entrepreneurship with special focus on cancer nanomedicine.

The objective of the visit was to motivate and mentor faculty and students at COMSATS and also to provide feedback to campus administration and the Federal Ministry of Science and Technology on strategic initiatives to help develop the next generation of science and engineering workforce in Pakistan.

A story of success for the Muslim youth from areas affected by conflict and war, Dr Nayfeh, a Palestinian by origin, was brought up in a conflict area by a mother who did not know how to read and write. For him, the environment was actually a motivator to work hard and study. “My mother was uneducated but she always wanted her children to get the highest degree possible and both my parents supported us in whatever way possible to achieve our dreams,” he recalled.

Comparing Pakistan with other developing countries in scientific research enterprise, he said that despite lack of resources, he has observed some decent amount of research outcome from the existing setups. About their visits to different labs, he said that they found faculty members and researchers in need of for more and more funds. “I don’t blame them as I am also looking for more and more fund even in America. This is a positive sign which shows that these set ups are alive and want to do more.”

Dr. Nayfeh is greatly impressed with the number of women researchers and students in Pakistan. “In Tunisia and Algeria, there were decent number of women in this field but Pakistan has the most and there are more publications coming out of Pakistan as compared to other developing countries.”

If you have the time, I suggest you read the article in its entirety.

Would you like to invest in the Argonne National Laboratory’s reusable oil spill sponge?

A March 7, 2017 news item on phys.org describes some of the US Argonne National Laboratory’s research into oil spill cleanup technology,

When the Deepwater Horizon drilling pipe blew out seven years ago, beginning the worst oil spill [BP oil spill in the Gulf of Mexico] in U.S. history, those in charge of the recovery discovered a new wrinkle: the millions of gallons of oil bubbling from the sea floor weren’t all collecting on the surface where it could be skimmed or burned. Some of it was forming a plume and drifting through the ocean under the surface.

Now, scientists at the U.S. Department of Energy’s (DOE) Argonne National Laboratory have invented a new foam, called Oleo Sponge, that addresses this problem. The material not only easily adsorbs oil from water, but is also reusable and can pull dispersed oil from the entire water column—not just the surface.

A March 6, 2017 Argonne National Laboratory news release (also on EurekAlert) by Louise Lerner, which originated the news item, provides more information about the work,

“The Oleo Sponge offers a set of possibilities that, as far as we know, are unprecedented,” said co-inventor Seth Darling, a scientist with Argonne’s Center for Nanoscale Materials and a fellow of the University of Chicago’s Institute for Molecular Engineering.

We already have a library of molecules that can grab oil, but the problem is how to get them into a useful structure and bind them there permanently.

The scientists started out with common polyurethane foam, used in everything from furniture cushions to home insulation. This foam has lots of nooks and crannies, like an English muffin, which could provide ample surface area to grab oil; but they needed to give the foam a new surface chemistry in order to firmly attach the oil-loving molecules.

Previously, Darling and fellow Argonne chemist Jeff Elam had developed a technique called sequential infiltration synthesis, or SIS, which can be used to infuse hard metal oxide atoms within complicated nanostructures.

After some trial and error, they found a way to adapt the technique to grow an extremely thin layer of metal oxide “primer” near the foam’s interior surfaces. This serves as the perfect glue for attaching the oil-loving molecules, which are deposited in a second step; they hold onto the metal oxide layer with one end and reach out to grab oil molecules with the other.

The result is Oleo Sponge, a block of foam that easily adsorbs oil from the water. The material, which looks a bit like an outdoor seat cushion, can be wrung out to be reused—and the oil itself recovered.

Oleo Sponge

At tests at a giant seawater tank in New Jersey called Ohmsett, the National Oil Spill Response Research & Renewable Energy Test Facility, the Oleo Sponge successfully collected diesel and crude oil from both below and on the water surface.

“The material is extremely sturdy. We’ve run dozens to hundreds of tests, wringing it out each time, and we have yet to see it break down at all,” Darling said.

Oleo Sponge could potentially also be used routinely to clean harbors and ports, where diesel and oil tend to accumulate from ship traffic, said John Harvey, a business development executive with Argonne’s Technology Development and Commercialization division.

Elam, Darling and the rest of the team are continuing to develop the technology.

“The technique offers enormous flexibility, and can be adapted to other types of cleanup besides oil in seawater. You could attach a different molecule to grab any specific substance you need,” Elam said.

The team is actively looking to commercialize [emphasis mine] the material, Harvey said; those interested in licensing the technology or collaborating with the laboratory on further development may contact partners@anl.gov.

Here’s a link to and a citation for the paper,

Advanced oil sorbents using sequential infiltration synthesis by Edward Barry, Anil U. Mane, Joseph A. Libera, Jeffrey W. Elam, and Seth B. Darling. J. Mater. Chem. A, 2017,5, 2929-2935 DOI: 10.1039/C6TA09014A First published online 11 Jan 2017

This paper is behind a paywall.

The two most recent posts here featuring oil spill technology are my Nov. 3, 2016 piece titled: Oil spill cleanup nanotechnology-enabled solution from A*STAR and my Sept. 15, 2016 piece titled: Canada’s Ingenuity Lab receives a $1.7M grant to develop oil recovery system for oil spills. I hope that one of these days someone manages to commercialize at least one of the new oil spill technologies. It seems that there hasn’t been much progress since the BP (Deepwater Horizon) oil spill. If someone has better information than I do about the current state of oil spill cleanup technologies, please do leave a comment.

Phagocytosis for a bioelectronic future

The process by which a cell engulfs matter is known as phagocytosis. One of the best known examples of failed phagocytosis is that of asbestos fibres in the lungs where lung cells have attempted to engulf a fibre that’s just too big and ends up piercing the cell. When enough of the cells are pierced, the person is diagnosed with mesothelioma.

This particular example of phagocytosis is a happier one according to a Dec. 16, 2016 article by Meghan Rosen for ScienceNews,

Human cells can snack on silicon.

Cells grown in the lab devour nano-sized wires of silicon through an engulfing process known as phagocytosis, scientists report December 16 in Science Advances.

Silicon-infused cells could merge electronics with biology, says John Zimmerman, a biophysicist now at Harvard University. “It’s still very early days,” he adds, but “the idea is to get traditional electronic devices working inside of cells.” Such hybrid devices could one day help control cellular behavior, or even replace electronics used for deep brain stimulation, he says.

Scientists have been trying to load electronic parts inside cells for years. One way is to zap holes in cells with electricity, which lets big stuff, like silicon nanowires linked to bulky materials, slip in. Zimmerman, then at the University of Chicago, and colleagues were looking for a simpler technique, something that would let tiny nanowires in easily and could potentially allow them to travel through a person’s bloodstream — like a drug.

A Dec. 22, 2016 University of Chicago news release by Matt Wood provides more detail,

“You can treat it as a non-genetic, synthetic biology platform,” said Bozhi Tian, PhD, assistant professor of chemistry and senior author of the new study. “Traditionally in biology we use genetic engineering and modify genetic parts. Now we can use silicon parts, and silicon can be internalized. You can target those silicon parts to specific parts of the cell and modulate that behavior with light.”

In the new study, Tian and his team show how cells consume or internalize the nanowires through phagocytosis, the same process they use to engulf and ingest nutrients and other particles in their environment. The nanowires are simply added to cell media, the liquid solution the cells live in, the same way you might administer a drug, and the cells take it from there. Eventually, the goal would be to inject them into the bloodstream or package them into a pill.

Once inside, the nanowires can interact directly with individual parts of the cell, organelles like the mitochondria, nucleus and cytoskeletal filaments. Researchers can then stimulate the nanowires with light to see how individual components of the cell respond, or even change the behavior of the cell. They can last up to two weeks inside the cell before biodegrading.

Seeing how individual parts of a cell respond to stimulation could give researchers insight into how medical treatments that use electrical stimulation work at a more detailed level. For instance, deep brain stimulation helps treat tremors from movement disorders like Parkinson’s disease by sending electrical signals to areas of the brain. Doctors know it works at the level of tissues and brain structures, but seeing how individual components of nerve cells react to these signals could help fine tune and improve the treatment.

The experiments in the study used umbilical vascular endothelial cells, which make up blood vessel linings in the umbilical cord. These cells readily took up the nanowires, but others, like cardiac muscle cells, did not. Knowing that some cells consume the wires and some don’t could also prove useful in experimental settings and give researchers more ways to target specific cell types.

Tian and his team manufactures the nanowires in their lab with a chemical vapor deposition system that grows the silicon structures to different specifications. They can adjust size, shape, and electrical properties as needed, or even add defects on purpose for testing. They can also make wires with porous surfaces that could deliver drugs or genetic material to the cells. The process gives them a variety of ways to manipulate the properties of the nanowires for research.

Seeing how individual parts of a cell respond to stimulation could give researchers insight into how medical treatments that use electrical stimulation work at a more detailed level. For instance, deep brain stimulation helps treat tremors from movement disorders like Parkinson’s disease by sending electrical signals to areas of the brain. Doctors know it works at the level of tissues and brain structures, but seeing how individual components of nerve cells react to these signals could help fine tune and improve the treatment.

The experiments in the study used umbilical vascular endothelial cells, which make up blood vessel linings in the umbilical cord. These cells readily took up the nanowires, but others, like cardiac muscle cells, did not. Knowing that some cells consume the wires and some don’t could also prove useful in experimental settings and give researchers more ways to target specific cell types.

Tian and his team manufactures the nanowires in their lab with a chemical vapor deposition system that grows the silicon structures to different specifications. They can adjust size, shape, and electrical properties as needed, or even add defects on purpose for testing. They can also make wires with porous surfaces that could deliver drugs or genetic material to the cells. The process gives them a variety of ways to manipulate the properties of the nanowires for research.

Here’s a link to and a citation for the paper,

Cellular uptake and dynamics of unlabeled freestanding silicon nanowires by John F. Zimmerman, Ramya Parameswaran, Graeme Murray, Yucai Wang, Michael Burke, and Bozhi Tian. Science Advances  16 Dec 2016: Vol. 2, no. 12, e1601039 DOI: 10.1126/sciadv.1601039

This paper appears to be open access.

Innovation and two Canadian universities

I have two news bits and both concern the Canadian universities, the University of British Columbia (UBC) and the University of Toronto (UofT).

Creative Destruction Lab – West

First, the Creative Destruction Lab, a technology commercialization effort based at UofT’s Rotman School of Management, is opening an office in the west according to a Sept. 28, 2016 UBC media release (received via email; Note: Links have been removed; this is a long media release which interestingly does not mention Joseph Schumpeter the man who developed the economic theory which he called: creative destruction),

The UBC Sauder School of Business is launching the Western Canadian version of the Creative Destruction Lab, a successful seed-stage program based at UofT’s Rotman School of Management, to help high-technology ventures driven by university research maximize their commercial impact and benefit to society.

“Creative Destruction Lab – West will provide a much-needed support system to ensure innovations formulated on British Columbia campuses can access the funding they need to scale up and grow in-province,” said Robert Helsley, Dean of the UBC Sauder School of Business. “The success our partners at Rotman have had in helping commercialize the scientific breakthroughs of Canadian talent is remarkable and is exactly what we plan to replicate at UBC Sauder.”

Between 2012 and 2016, companies from CDL’s first four years generated over $800 million in equity value. It has supported a long line of emerging startups, including computer-human interface company Thalmic Labs, which announced nearly USD $120 million in funding on September 19, one of the largest Series B financings in Canadian history.

Focusing on massively scalable high-tech startups, CDL-West will provide coaching from world-leading entrepreneurs, support from dedicated business and science faculty, and access to venture capital. While some of the ventures will originate at UBC, CDL-West will also serve the entire province and extended western region by welcoming ventures from other universities. The program will closely align with existing entrepreneurship programs across UBC, including, e@UBC and HATCH, and actively work with the BC Tech Association [also known as the BC Technology Industry Association] and other partners to offer a critical next step in the venture creation process.

“We created a model for tech venture creation that keeps startups focused on their essential business challenges and dedicated to solving them with world-class support,” said CDL Founder Ajay Agrawal, a professor at the Rotman School of Management and UBC PhD alumnus.

“By partnering with UBC Sauder, we will magnify the impact of CDL by drawing in ventures from one of the country’s other leading research universities and B.C.’s burgeoning startup scene to further build the country’s tech sector and the opportunities for job creation it provides,” said CDL Director, Rachel Harris.

CDL uses a goal-setting model to push ventures along a path toward success. Over nine months, a collective of leading entrepreneurs with experience building and scaling technology companies – called the G7 – sets targets for ventures to hit every eight weeks, with the goal of maximizing their equity-value. Along the way ventures turn to business and technology experts for strategic guidance on how to reach goals, and draw on dedicated UBC Sauder students who apply state-of the-art business skills to help companies decide which market to enter first and how.

Ventures that fail to achieve milestones – approximately 50 per cent in past cohorts – are cut from the process. Those that reach their objectives and graduate from the program attract investment from the G7, as well as other leading venture-capital firms.

Currently being assembled, the CDL-West G7 will be comprised of entrepreneurial luminaries, including Jeff Mallett, the founding President, COO and Director of Yahoo! Inc. from 1995-2002 – a company he led to $4 billion in revenues and grew from a startup to a publicly traded company whose value reached $135 billion. He is now Managing Director of Iconica Partners and Managing Partner of Mallett Sports & Entertainment, with ventures including the San Francisco Giants, AT&T Park and Mission Rock Development, Comcast Bay Area Sports Network, the San Jose Giants, Major League Soccer, Vancouver Whitecaps FC, and a variety of other sports and online ventures.

Already bearing fruit, the Creative Destruction Lab partnership will see several UBC ventures accepted into a Machine Learning Specialist Track run by Rotman’s CDL this fall. This track is designed to create a support network for enterprises focused on artificial intelligence, a research strength at UofT and Canada more generally, which has traditionally migrated to the United States for funding and commercialization. In its second year, CDL-West will launch its own specialist track in an area of strength at UBC that will draw eastern ventures west.

“This new partnership creates the kind of high impact innovation network the Government of Canada wants to encourage,” said Brandon Lee, Canada’s Consul General in San Francisco, who works to connect Canadian innovation to customers and growth capital opportunities in Silicon Valley. “By collaborating across our universities to enhance our capacity to turn the scientific discoveries into businesses in Canada, we can further advance our nation’s global competitiveness in the knowledge-based industries.”

The Creative Destruction Lab is guided by an Advisory Board, co-chaired by Vancouver-based Haig Farris, a pioneer of the Canadian venture capitalist industry, and Bill Graham, Chancellor of Trinity College at UofT and former Canadian cabinet minister.

“By partnering with Rotman, UBC Sauder will be able to scale up its support for high-tech ventures extremely quickly and with tremendous impact,” said Paul Cubbon, Leader of CDL-West and a faculty member at UBC Sauder. “CDL-West will act as a turbo booster for ventures with great ideas, but which lack the strategic roadmap and funding to make them a reality.”

CDL-West launched its competitive application process for the first round of ventures that will begin in January 2017. Interested ventures are encouraged to submit applications via the CDL website at: www.creativedestructionlab.com

Background

UBC Technology ventures represented at media availability

Awake Labs is a wearable technology startup whose products measure and track anxiety in people with Autism Spectrum Disorder to better understand behaviour. Their first device, Reveal, monitors a wearer’s heart-rate, body temperature and sweat levels using high-tech sensors to provide insight into care and promote long term independence.

Acuva Technologies is a Vancouver-based clean technology venture focused on commercializing breakthrough UltraViolet Light Emitting Diode technology for water purification systems. Initially focused on point of use systems for boats, RVs and off grid homes in North American market, where they already have early sales, the company’s goal is to enable water purification in households in developing countries by 2018 and deploy large scale systems by 2021.

Other members of the CDL-West G7 include:

Boris Wertz: One of the top tech early-stage investors in North America and the founding partner of Version One, Wertz is also a board partner with Andreessen Horowitz. Before becoming an investor, Wertz was the Chief Operating Officer of AbeBooks.com, which sold to Amazon in 2008. He was responsible for marketing, business development, product, customer service and international operations. His deep operational experience helps him guide other entrepreneurs to start, build and scale companies.

Lisa Shields: Founder of Hyperwallet Systems Inc., Shields guided Hyperwallet from a technology startup to the leading international payments processor for business to consumer mass payouts. Prior to founding Hyperwallet, Lisa managed payments acceptance and risk management technology teams for high-volume online merchants. She was the founding director of the Wireless Innovation Society of British Columbia and is driven by the social and economic imperatives that shape global payment technologies.

Jeff Booth: Co-founder, President and CEO of Build Direct, a rapidly growing online supplier of home improvement products. Through custom and proprietary web analytics and forecasting tools, BuildDirect is reinventing and redefining how consumers can receive the best prices. BuildDirect has 12 warehouse locations across North America and is headquartered in Vancouver, BC. In 2015, Booth was awarded the BC Technology ‘Person of the Year’ Award by the BC Technology Industry Association.

Education:

CDL-west will provide a transformational experience for MBA and senior undergraduate students at UBC Sauder who will act as venture advisors. Replacing traditional classes, students learn by doing during the process of rapid equity-value creation.

Supporting venture development at UBC:

CDL-west will work closely with venture creation programs across UBC to complete the continuum of support aimed at maximizing venture value and investment. It will draw in ventures that are being or have been supported and developed in programs that span campus, including:

University Industry Liaison Office which works to enable research and innovation partnerships with industry, entrepreneurs, government and non-profit organizations.

e@UBC which provides a combination of mentorship, education, venture creation, and seed funding to support UBC students, alumni, faculty and staff.

HATCH, a UBC technology incubator which leverages the expertise of the UBC Sauder School of Business and entrepreneurship@UBC and a seasoned team of domain-specific experts to provide real-world, hands-on guidance in moving from innovative concept to successful venture.

Coast Capital Savings Innovation Hub, a program base at the UBC Sauder Centre for Social Innovation & Impact Investing focused on developing ventures with the goal of creating positive social and environmental impact.

About the Creative Destruction Lab in Toronto:

The Creative Destruction Lab leverages the Rotman School’s leading faculty and industry network as well as its location in the heart of Canada’s business capital to accelerate massively scalable, technology-based ventures that have the potential to transform our social, industrial, and economic landscape. The Lab has had a material impact on many nascent startups, including Deep Genomics, Greenlid, Atomwise, Bridgit, Kepler Communications, Nymi, NVBots, OTI Lumionics, PUSH, Thalmic Labs, Vertical.ai, Revlo, Validere, Growsumo, and VoteCompass, among others. For more information, visit www.creativedestructionlab.com

About the UBC Sauder School of Business

The UBC Sauder School of Business is committed to developing transformational and responsible business leaders for British Columbia and the world. Located in Vancouver, Canada’s gateway to the Pacific Rim, the school is distinguished for its long history of partnership and engagement in Asia, the excellence of its graduates, and the impact of its research which ranks in the top 20 globally. For more information, visit www.sauder.ubc.ca

About the Rotman School of Management

The Rotman School of Management is located in the heart of Canada’s commercial and cultural capital and is part of the University of Toronto, one of the world’s top 20 research universities. The Rotman School fosters a new way to think that enables graduates to tackle today’s global business and societal challenges. For more information, visit www.rotman.utoronto.ca.

It’s good to see a couple of successful (according to the news release) local entrepreneurs on the board although I’m somewhat puzzled by Mallett’s presence since, if memory serves, Yahoo! was not doing that well when he left in 2002. The company was an early success but utterly dwarfed by Google at some point in the early 2000s and these days, its stock (both financial and social) has continued to drift downwards. As for Mallett’s current successes, there is no mention of them.

Reuters Top 100 of the world’s most innovative universities

After reading or skimming through the CDL-West news you might think that the University of Toronto ranked higher than UBC on the Reuters list of the world’s most innovative universities. Before breaking the news about the Canadian rankings, here’s more about the list from a Sept, 28, 2016 Reuters news release (receive via email),

Stanford University, the Massachusetts Institute of Technology and Harvard University top the second annual Reuters Top 100 ranking of the world’s most innovative universities. The Reuters Top 100 ranking aims to identify the institutions doing the most to advance science, invent new technologies and help drive the global economy. Unlike other rankings that often rely entirely or in part on subjective surveys, the ranking uses proprietary data and analysis tools from the Intellectual Property & Science division of Thomson Reuters to examine a series of patent and research-related metrics, and get to the essence of what it means to be truly innovative.

In the fast-changing world of science and technology, if you’re not innovating, you’re falling behind. That’s one of the key findings of this year’s Reuters 100. The 2016 results show that big breakthroughs – even just one highly influential paper or patent – can drive a university way up the list, but when that discovery fades into the past, so does its ranking. Consistency is key, with truly innovative institutions putting out groundbreaking work year after year.

Stanford held fast to its first place ranking by consistently producing new patents and papers that influence researchers elsewhere in academia and in private industry. Researchers at the Massachusetts Institute of Technology (ranked #2) were behind some of the most important innovations of the past century, including the development of digital computers and the completion of the Human Genome Project. Harvard University (ranked #3), is the oldest institution of higher education in the United States, and has produced 47 Nobel laureates over the course of its 380-year history.

Some universities saw significant movement up the list, including, most notably, the University of Chicago, which jumped from #71 last year to #47 in 2016. Other list-climbers include the Netherlands’ Delft University of Technology (#73 to #44) and South Korea’s Sungkyunkwan University (#66 to #46).

The United States continues to dominate the list, with 46 universities in the top 100; Japan is once again the second best performing country, with nine universities. France and South Korea are tied in third, each with eight. Germany has seven ranked universities; the United Kingdom has five; Switzerland, Belgium and Israel have three; Denmark, China and Canada have two; and the Netherlands and Singapore each have one.

You can find the rankings here (scroll down about 75% of the way) and for the impatient, the University of British Columbia ranked 50th and the University of Toronto 57th.

The biggest surprise for me was that China, like Canada, had two universities on the list. I imagine that will change as China continues its quest for science and innovation dominance. Given how they tout their innovation prowess, I had one other surprise, the University of Waterloo’s absence.