Tag Archives: Cornell University

Effective safety strategies for CRISPR (clustered regularly interspaced short palindromic repeats) gene drive experiments

It’s very peculiar being able to understand each word individually in clustered regularly interspaced short palindromic repeats (CRISPR) but not being able to puzzle out much meaning other than the widely known ‘it’s a gene editor’.

Regardless, CRISPR is a powerful gene editing tool and that can lead to trouble. Even before CRISPR, we’ve had some genetic accidents. Perhaps the best known is the ‘killer bee’ or Africanized bee (from its Wikepedia entry),

The Africanized bee, also known as the Africanised honey bee, and known colloquially as “killer bee”, is a hybrid of the western honey bee species (Apis mellifera), produced originally by cross-breeding [emphasis mine] of the East African lowland honey bee (A. m. scutellata) with various European honey bees such as the Italian honey bee A. m. ligustica and the Iberian honey bee A. m. iberiensis.

The Africanized honey bee was first introduced to Brazil in 1956 in an effort to increase honey production, but 26 swarms escaped quarantine in 1957 [emphasis mine]. Since then, the hybrid has spread throughout South America and arrived in North America in 1985. Hives were found in South Texas of the United States in 1990.

Africanized bees are typically much more defensive than other varieties of honey bee, and react to disturbances faster than European honey bees. They can chase a person a quarter of a mile (400 m); they have killed some 1,000 humans, with victims receiving ten times more stings than from European honey bees. They have also killed horses and other animals.

Getting back to how powerful CRISPR is, a group of scientists has developed a set of strategies for safeguarding gene drive experiments (from a January 22, 2019 eLife press release also on EurekAlert),

Researchers have demonstrated for the first time how two molecular strategies can safeguard CRISPR gene drive experiments in the lab, according to a study published today in eLife.

Their findings, first reported on bioRxiv, suggest that scientists can effectively use synthetic target sites and split drives to conduct gene drive research, without the worry of causing an accidental spread throughout a natural population.

Gene drives, such as those trialled in malaria mosquitoes, are genetic packages designed to spread among populations. They do this via a process called ‘drive conversion’, where the Cas9 enzyme and a molecule called guide RNA (gRNA) cut at a certain site in the genome. The drive is then copied in when the DNA break is repaired.

“CRISPR-based gene drives have sparked both enthusiasm and deep concerns due to their potential for genetically altering entire species,” explains first author Jackson Champer, Postdoctoral Fellow in the Department of Biological Statistics and Computational Biology at Cornell University, New York. “This raises the question about our ability to prevent the unintended spread of such drives from the laboratory into the natural world.

“Current strategies for avoiding accidental spread involve physically confining drive-containing organisms. However, it is uncertain whether this sufficiently reduces the likelihood of any accidental escape into the wild, given the possibility of human error.”

Two molecular safeguarding strategies have recently been proposed that go beyond simply confining research organisms. The first is synthetic target site drive, which homes into engineered genomic sites that are absent in wild organisms. The second is split drive, where the drive construct lacks a type of enzyme called the endonuclease and relies instead on one engineered into a distant site.

“The nature of these strategies means that they should prevent an efficient spread outside of their respective laboratory lines,” Champer adds. “We wanted to see if they both had a similar performance to standard homing drives, and if they would therefore be suitable substitutes in early gene-drive research.”

To do this, the team designed and tested three synthetic target site drives in the fruit fly Drosophila melanogaster. Each drive targeted an enhanced green fluorescent protein (EGFP) gene introduced at one of three different sites in the genome. For split drives, they designed a drive construct that targeted the X-linked gene yellow and lacked Cas9.

Their analyses revealed that CRISPR gene drives with synthetic target sites such as EGFP show similar behaviour to standard drives, and can therefore be used for most testing in place of these drives. The split drives demonstrated similar performance, and also allow for natural sequences to be targeted in situations where the use of synthetic targets is difficult. These include population-suppression drives that require the targeting of naturally occurring genes

“Based on our findings, we suggest these safeguarding strategies should be adopted consistently in the development and testing of future gene drives,” says senior author Philipp Messer, Assistant Professor in the Department of Biological Statistics and Computational Biology at Cornell University. “This will be important for large-scale cage experiments aimed at improving our understanding of the expected population dynamics of candidate drives. Ultimately, this understanding will be crucial for discussing the feasibility and risks of releasing successful drives into the wild, for example to reduce malaria and other vector-borne diseases.”

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

Molecular safeguarding of CRISPR gene drive experiments by Jackson Champer, Joan Chung, Yoo Lim Lee, Chen Liu, Emily Yang, Zhaoxin Wen, Andrew G Clark, Philipp W Messer. DOI: 10.7554/eLife.41439 Short Report Jan 22, 2019

This paper is open access. For anyone who doesn’t mind reading an earlier version of a paper you can find it at bioRxiv, at https://www.biorxiv.org/content/early/2018/09/08/411876.

elife, which i’ve mentioned here here before in a February 8, 2018 posting is a (from their About eLife webpage)

… non-profit organisation inspired by research funders and led by scientists. Our mission is to help scientists accelerate discovery by operating a platform for research communication that encourages and recognises the most responsible behaviours in science.

Popcorn-powered robots

A soft robotic device powered by popcorn, constructed by researchers in Cornell’s Collective Embodied Intelligence Lab. Courtesy: Cornell University

What an intriguing idea, popcorn-powered robots, and one I have difficulty imagining even with the help of the image above. A July 26, 2018 Cornell University news release (an edited version is on EurekAlert) by Melanie Lefkowitz describes the concept,

Cornell researchers have discovered how to power simple robots with a novel substance that, when heated, can expand more than 10 times in size, change its viscosity by a factor of 10 and transition from regular to highly irregular granules with surprising force.

You can also eat it with a little butter and salt.

“Popcorn-Driven Robotic Actuators,” a recent paper co-authored by doctoral student Steven Ceron, mechanical engineering, and Kirstin H. Petersen, assistant professor of electrical and computer engineering, examines how popcorn’s unique qualities can power inexpensive robotic devices that grip, expand or change rigidity.

“The goal of our lab is to try to make very minimalistic robots which, when deployed in high numbers, can still accomplish great things,” said Petersen, who runs Cornell’s Collective Embodied Intelligence Lab. “Simple robots are cheap and less prone to failures and wear, so we can have many operating autonomously over a long time. So we are always looking for new and innovative ideas that will permit us to have more functionalities for less, and popcorn is one of those.”

The study is the first to consider powering robots with popcorn, which is inexpensive, readily available, biodegradable and of course, edible. Since kernels can expand rapidly, exerting force and motion when heated, they could potentially power miniature jumping robots. Edible devices could be ingested for medical procedures. The mix of hard, unpopped granules and lighter popped corn could replace fluids in soft robots without the need for air pumps or compressors.

“Pumps and compressors tend to be more expensive, and they add a lot of weight and expense to your robot,” said Ceron, the paper’s lead author. “With popcorn, in some of the demonstrations that we showed, you just need to apply voltage to get the kernels to pop, so it would take all the bulky and expensive parts out of the robots.”

Since kernels can’t shrink once they’ve popped, a popcorn-powered mechanism can generally be used only once, though multiple uses are conceivable because popped kernels can dissolve in water, Ceron said.

The researchers experimented with Amish Country Extra Small popcorn, which they chose because the brand did not use additives. The extra-small variety had the highest expansion ratio of those they tested.

After studying popcorn’s properties using different types of heating, the researchers constructed three simple robotic actuators – devices used to perform a function.

For a jamming actuator, 36 kernels of popcorn heated with nichrome wire were used to stiffen a flexible silicone beam. For an elastomer actuator, they constructed a three-fingered soft gripper, whose silicone fingers were stuffed with popcorn heated by nichrome wire. When the kernels popped, the expansion exerted pressure against the outer walls of the fingers, causing them to curl. For an origami actuator, they folded recycled Newman’s Own organic popcorn bags into origami bellows folds, filled them with kernels and microwaved them. The expansion of the kernels was strong enough to support the weight of a nine-pound kettlebell.

The paper was presented at the IEEE [Institute of Electrical and Electronics Engineers] International Conference on Robotics and Automation in May and co-authored with Aleena Kurumunda ’19, Eashan Garg ’20, Mira Kim ’20 and Tosin Yeku ’20. Petersen said she hopes it inspires researchers to explore the possibilities of other nontraditional materials.

“Robotics is really good at embracing new ideas, and we can be super creative about what we use to generate multifunctional properties,” she said. “In the end we come up with very simple solutions to fairly complex problems. We don’t always have to look for high-tech solutions. Sometimes the answer is right in front of us.”

The work was supported by the Cornell Engineering Learning Initiative, the Cornell Electrical and Computer Engineering Early Career Award and the Cornell Sloan Fellowship.

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

Popcorn-Driven Robotic Actuators by Steven Ceron, Aleena Kurumunda, Eashan Garg, Mira Kim, Tosin Yeku, and Kirstin Petersen. Presented at the IEEE International Conference on Robotics and Automation held in May 21-25, 2018 in Brisbane, Australia.

The researchers have made this video demonstrating the technology,

Ooblek (non-Newtonian goo) and bras from Reebok

I have taken a liberty in the title for this piece, strictly speaking the non-Newtonian goo in the bra isn’t the stuff (ooblek) made of cornstarch and water from your childhood science experiments but it has many of the same qualities. The material in the Reebok bra, PureMove, is called Shear Thickening Fluid and was developed at the University of Delaware in 2005 and subsequently employed by NASA (US National Aeronautics and Space Administration) for use in the suits used by astronauts as noted in an August 6, 2018 article by Elizabeth Secgran for Fast Company who explains how it came be used for the latest sports bra,

While the activewear industry floods the market with hundreds of different sports bras every season, research shows that most female consumers are unsatisfied with their sports bra options, and 1 in 5 women avoid exercise altogether because they don’t have a sports bra that fits them properly.

Reebok wants to make that experience a thing of the past. Today, it launches a new bra, the PureMove, that adapts to your movements, tightening up when you’re moving fast and relaxing when you’re not. …

When I visited Reebok’s Boston headquarters, Witek [Danielle Witek, Reebok designer who spearheaded the R&D making the bra possible] handed me a jar of the fluid with a stick in it. When I moved the stick quickly, it seemed to turn into a solid, and when I moved it slowly, it had the texture of honey. Witek and the scientists have incorporated this fluid into a fabric that Reebok dubs “Motion Sense Technology.” The fluid is woven into the textile, so that on the surface, it looks and feels like the synthetic material you might find in any sports bra. But what you can’t see is that the fabric adapts to the body’s shape, the velocity of the breast tissue in motion, and the type and force of movement. It stretches less with high-impact movements and then stretches more during rest and lower intensity activities.

I tested an early version of the PureMove bra a few months ago, before it had even gone into production. I did a high-intensity workout that involved doing jumping jacks and sprints, followed by a cool-down session. The best thing about the bra was that I didn’t notice it at all. I didn’t feel stifled when I was just strolling around the gym, and I didn’t feel like I was unsupported when I was running around. Ultimately, the best bras are the ones that you don’t have to think about so you can focus on getting on with your life.

Since this technology is so new, Reebok had to do a lot of testing to make sure the bra would actually do what it advertised. The company set up a breast biomechanics testing center with the help of the University of Delaware, with 54 separate motion sensors tracking and measuring various parts of a tester’s chest area. This is a far more rigorous approach than most testing facilities in the industry that typically only use between two to four sensors. Over the course of a year, the facility gathered the data required for the scientists and Reebok product designers to develop the PureMove bra.

… If it’s well-received, the logical next step would be to incorporate the Motion Sense Technology into other products, like running tights or swimsuits, since transitioning between compression and looseness is something that we want in all of our sportswear. ..

According to the Reebok PureMove bra webpage, it was available from August 16, 2018,

Credit: Reebok

It’s $60 (I imagine those are US dollars).

For anyone interested in the science of non-Newtonian goo, shear thickening fluid, and NASA, there’s a November 24, 2015 article by Lydia Chain for Popular Science (Note: Links have been removed),

There’s an experiment you may have done in high school: When you mix cornstarch with water—a concoction colloquially called oobleck—and give it a stir, it acts like a liquid. But scrape it quickly or hit it hard, and it stiffens up into a solid. If you set the right pace, you can even run on top of a pool of the stuff. This phenomenon is called shear force thickening, and scientists have been trying to understand how it happens for decades.

There are two main theories, and figuring out which is right could affect the way we make things like cement, body armor, concussion preventing helmets, and even spacesuits.

The prevailing theory is that it’s all about the fluid dynamics (the nature of how fluids move) of the liquid and the particles in a solution. As the particles are pushed closer and closer together, it becomes harder to squeeze the liquid out from between them. Eventually, it’s too hard to squeeze out any more fluid and the particles lock up into hydrodynamic clusters, still separated by a thin film of fluid. They then move together, thickening the mixture and forming a solid.

The other idea is that contact forces like friction keep the particles locked together. Under this theory, when force is applied, the particles actually touch. The shearing force and friction keep them pressed together, which makes the solution more solid.

“The debate has been raging, and we’ve been wracking our brains to think of a method to conclusively go one way or the other,” says Itai Cohen, a physicist at Cornell University. He and his team recently ran a new experiment that seems to point to friction as the driving cause of shear thickening.

Norman Wagner, a chemical engineer at the University of Delaware, says that research into frictional interactions like this is important, but notes that he isn’t completely convinced as Cohen’s team didn’t measure friction directly (they inferred it was friction from their modeling however they didn’t find the exact measurement of the friction between the particles). He also says that there’s a lot of data in the field already that strongly indicates hydrodynamic clusters as the cause for shear thickening.

Wagner and his team are working on a NASA funded project to improve space suits so that micrometeorites or other debris can’t puncture them. They have also bent their technology to make padding for helmets and shin guards that would do a better job protecting athletes from harmful impacts. They are even making puncture resistant gloves that would give healthcare workers the same dexterity as current ones but with extra protection against accidental needle sticks.

“It’s a very exciting area,” says Wagner. He’s very interested in designing materials that automatically protect someone, without robotics or power. …

I guess that in 2015 Wagner didn’t realize his work would also end up in a 2018 sports bra.

Genetic engineering: an eggplant in Bangladesh and a synthetic biology grant at Concordia University (Canada)

I have two bits of genetic engineering news.

Eggplants in Bangladesh

I always marvel at their beauty,

Bt eggplant is the first genetically engineered food crop to be successfully introduced in South Asia. The crop is helping some of the world’s poorest farmers feed their families and communities while reducing the use of pesticides. Photo by Cornell Alliance for Science.

A July 17, 2018 news item on phys.org describes a genetic engineering application,

Ansar Ali earned just 11,000 taka – about $130 U.S. dollars – from eggplant he grew last year in Bangladesh. This year, after planting Bt eggplant, he brought home more than double that amount, 27,000 taka. It’s a life-changing improvement for a subsistence farmer like Ali.

Bt eggplant, or brinjal as it’s known in Bangladesh, is the first genetically engineered food crop to be successfully introduced in South Asia. Bt brinjal is helping some of the world’s poorest farmers to feed their families and communities, improve profits and dramatically reduce pesticide use. That’s according to Tony Shelton, Cornell professor of entomology and director of the Bt brinjal project funded by the United States Agency for International Development (USAID). Shelton and Jahangir Hossain, the country coordinator for the project in Bangladesh, lead the Cornell initiative to get these seeds into the hands of the small-scale, resource-poor farmers who grow a crop consumed daily by millions of Bangladeshis.

A July 11, 2018 Cornell University news release by Krisy Gashler, which originated the news item, expands on the theme (Note: Links have been removed),

Bt brinjal was first developed by the Indian seed company Mahyco in the early 2000s. Scientists inserted a gene from the bacterium Bacillus thuringiensis (thus the name, Bt) into nine brinjal varieties. The plants were engineered to resist the fruit and shoot borer, a devastating insect whose larvae bore into the stem and fruit of an eggplant. The insects cause up to 80 percent crop loss.

The Bt protein produced by the engineered eggplant causes the fruit and shoot borer larva to stop feeding, but is safe for humans consuming the eggplant, as proven through years of biosafety trials. In fact, Bt is commonly used by organic farmers to control caterpillars but has to be sprayed frequently to be effective. The Bt eggplant produces essentially the same protein as in the spray. More than 80 percent of field corn and cotton grown in the U.S. contains a Bt gene for insect control.

“Farmers growing Bt brinjal in Bangladesh are seeing three times the production of other brinjal varieties, at half the production cost, and are getting better prices at the market,” Hossain said.

A recent survey found 50 percent of farmers in Bangladesh said that they experienced illness due to the intense spraying of insecticides. Most farmers work in bare feet and without eye protection, leading to pesticide exposure that causes skin and eye irritation, and vomiting.

“It’s terrible for these farmers’ health and the health of the environment to spray so much,” said Shelton, who found that pesticide use on Bt eggplant was reduced as much as 92 percent in commercial Bt brinjal plantings. “Bt brinjal is a solution that’s really making a difference in people’s lives.”

Alhaz Uddin, a farmer in the Tangail district, made 6,000 taka growing traditional brinjal, but had to spend 4,000 taka on pesticides to combat fruit and shoot borer.

“I sprayed pesticides several times in a week,” he said. “I got sick many times during the spray.”

Mahyco initially wanted to introduce Bt brinjal in India and underwent years of successful safety testing. But in 2010, due to pressure from anti-biotechnology groups, the Indian minister of the environment placed a moratorium on the seeds. It is still in effect today, leaving brinjal farmers there without the effective and safe method of control available to their neighbors in Bangladesh.

Even before the Indian moratorium, Cornell scientists hosted delegations from Bangladesh that wanted to learn about Bt brinjal and the Agricultural Biotechnology Support Project II (ABSP II), a consortium of public and private institutions in Asia and Africa intended to help with the commercial development, regulatory approval and dissemination of bio-engineered crops, including Bt brinjal.

Cornell worked with USAID, Mahyco and the Bangladesh Agricultural Research Institute to secure regulatory approval, and in 2014 the Bangladeshi government distributed a small number of Bt brinjal plants to 20 farmers in four districts. The next year 108 farmers grew Bt brinjal, and the following year the number of farmers more than doubled to 250. In 2017 the number increased to 6,512 and in 2018 to 27,012. The numbers are likely even higher, according to Shelton, as there are no constraints against farmers saving seeds and replanting.

“Farmers who plant Bt brinjal are required to plant a small perimeter of traditional brinjal around the Bt variety; research has shown that the insects will infest plants in the buffer area, and this will slow their evolutionary development of resistance to the Bt plants,” Shelton said.

In a March 2017 workshop, Bangladeshi Agriculture Minister Begum Matia Chowdhury called Bt brinjal “a success story of local and foreign collaboration.”

“We will be guided by the science-based information, not by the nonscientific whispering of a section of people,” Chowdhury said. “As human beings, it is our moral obligation that all people in our country should get food and not go to bed on an empty stomach. Biotechnology can play an important role in this effect.”

Here’s what an infested eggplant looks like,

Non-Bt eggplant infested with fruit and shoot borer. Photo by Cornell Alliance for Science

It looks more like a fig than an eggplant.

This is part of a more comprehensive project as revealed in a March 29, 2016 Cornell University news release issued on the occasion of a $4.8M, three-year grant from the U.S. Agency for International Development (USAID),

… The award supports USAID’s work under Feed the Future, the U.S. government’s global initiative to fight hunger and improve food security using agricultural science and technology.

In the Feed the Future South Asia Eggplant Improvement Partnership, Cornell will protect eggplant farmers from yield losses and improve their livelihoods in partnership with the Bangladesh Agricultural Research Institute (BARI) and the University of the Philippines at Los Baños. Eggplant, or brinjal, is a staple crop that is an important source of income and nutrition for farmers and consumers in South Asia.

Over the past decade, Cornell has led the Agricultural Biotechnology Support Project II (ABSPII), also funded by USAID, that prompted a consortium of institutions in Asia and Africa to use the tools of modern biotechnology, particularly genetic engineering, to improve crops to address major production constraints for which conventional plant breeding tools have not been effective.

In October 2013, Bangladesh became the first country in South Asia to approve commercial cultivation of a genetically engineered food crop. In February 2014, Matia Chowdhury, the Bangladesh minister of agriculture, released four varieties of Bt brinjal to 20 farmers. With the establishment of the 20 Bt brinjal demonstration plots in 2014 and 104 more in 2015, BARI reported a noticeable decrease in fruit and shoot borer infestation, increased yields, decreased use of pesticide and improved income for farmers.

The Feed the Future South Asia Eggplant Improvement Partnership addresses and integrates all elements of the commercialization process — including technology development, regulation, marketing, seed distribution, and product stewardship. It also provides strong platforms for policy development, capacity building, gender equality, outreach and communication.

Moving on from practical applications …

Canada’s synthetic biology training centre

It seems Concordia University (Montréa) is a major Canadian centre for all things ‘synthetic biological’. (from the History and Vision webpage on Concordia University’s Centre for Applied Synthetic Biology webspace),

History and vision

Emerging in 2012 from a collaboration between the Biology and Electrical and Computer Engineering Departments, the Centre received University-wide status in 2016 growing its membership to include Biochemistry, Journalism, Communication Studies, Mechanical, Industrial and Chemical Engineering.


Timeline

T17-36393-VPRG-Timeline-graphic-promo-v4

You can see the timeline does not yet include 2018 development(s). Also it started as “a collaboration between the Biology and Electrical and Computer Engineering Departments?” This suggests a vastly different approach to genetic engineering that that employed in the “eggplant” research. From a July 16, 2018 posting on the Genome Alberta blog,

The Natural Sciences and Engineering Research Council of Canada (NSERC) has committed $1.65 million dollars over six years to establish a research and training program at Concordia’s Centre for Applied Synthetic Biology.

The funds were awarded after Malcolm Whiteway (…), professor of biology and the Canada Research Chair in Microbial Genomics, and the grant application team submitted a proposal to NSERC’s Collaborative Research and Training Experience (CREATE) program.

The Synthetic Biology Applications CREATE program — or SynBioApps — will help students acquire and develop important professional skills that complement their academic education and improve their job-readiness.

‘Concordia is a natural fit’

“As the Canadian leader in synthetic biology and as the home of the country’s only genome foundry, Concordia is a natural fit for a training program in this growing area of research,” says Christophe Guy, vice-president of Research and Graduate Studies.

“In offering a program like SynBioApps, we are providing our students with both a fundamental education in science and the business skills they’ll need to transition into their professional careers.”

The program’s aims are twofold: First, it will teach students how to design and construct cells and proteins for the development of new products related to human health, green technologies, and fundamental biological investigations. Second, it will provide cross-disciplinary training and internship opportunities through the university’s District 3 Innovation Center.

SynBioApps will be open to students from biology, biochemistry, engineering, computing, and mathematics.

“The ability to apply engineering approaches to biological systems promises to revolutionize both biology and industry,” says Whiteway, who is also a member of the Centre for Applied Synthetic Biology.

“The SynBioApps program at Concordia will provide a training program to develop the students who will both investigate the biology and build these industries.”

You can find out more about Concordia’s Centre for Applied Synthetic Biology here (there are jobs listed on their home page) and you can find information about the Synthetic Biology Applications (SynBioApps) training programme here.

Nanoscale measurements for osteoarthritis biomarker

There’s a new technique for measuring hyaluronic acid (HA), which appears to be associated with osteoarthritis. A March 12, 2018 news item on ScienceDaily makes the announcement,

For the first time, scientists at Wake Forest Baptist Medical Center have been able to measure a specific molecule indicative of osteoarthritis and a number of other inflammatory diseases using a newly developed technology.

This preclinical [emphasis mine] study used a solid-state nanopore sensor as a tool for the analysis of hyaluronic acid (HA).

I looked at the abstract for the paper (citation and link follow at end of this post) and found that it has been tested on ‘equine models’. Presumably they mean horses or, more accurately, members of the horse family. The next step is likely to be testing on humans, i.e., clinical trials.

A March 12, 2018 Wake Forest Baptist Medical Center news release (also on EurekAlert), which originated the news item, provides more details,

HA is a naturally occurring molecule that is involved in tissue hydration, inflammation and joint lubrication in the body. The abundance and size distribution of HA in biological fluids is recognized as an indicator of inflammation, leading to osteoarthritis and other chronic inflammatory diseases. It can also serve as an indicator of how far the disease has progressed.

“Our results established a new, quantitative method for the assessment of a significant molecular biomarker that bridges a gap in the conventional technology,” said lead author Adam R. Hall, Ph.D., assistant professor of biomedical engineering at Wake Forest School of Medicine, part of Wake Forest Baptist.

“The sensitivity, speed and small sample requirements of this approach make it attractive as the basis for a powerful analytic tool with distinct advantages over current assessment technologies.”

The most widely used method is gel electrophoresis, which is slow, messy, semi-quantitative, and requires a lot of starting material, Hall said. Other technologies include mass spectrometry and size-exclusion chromatography, which are expensive and limited in range, and multi-angle light scattering, which is non-quantitative and has limited precision.

The study, which is published in the current issue of Nature Communications, was led by Hall and Elaheh Rahbar, Ph.D., of Wake Forest Baptist, and conducted in collaboration with scientists at Cornell University and the University of Oklahoma.

In the study, Hall, Rahbar and their team first employed synthetic HA polymers to validate the measurement approach. They then used the platform to determine the size distribution of as little as 10 nanograms (one-billionth of a gram) of HA extracted from the synovial fluid of a horse model of osteoarthritis.

The measurement approach consists of a microchip with a single hole or pore in it that is a few nanometers wide – about 5,000 times smaller than a human hair. This is small enough that only individual molecules can pass through the opening, and as they do, each can be detected and analyzed. By applying the approach to HA molecules, the researchers were able to determine their size one-by-one. HA size distribution changes over time in osteoarthritis, so this technology could help better assess disease progression, Hall said.

“By using a minimally invasive procedure to extract a tiny amount of fluid – in this case synovial fluid from the knee – we may be able to identify the disease or determine how far it has progressed, which is valuable information for doctors in determining appropriate treatments,” he said.

Hall, Rahbar and their team hope to conduct their next study in humans, and then extend the technology with other diseases where HA and similar molecules play a role, including traumatic injuries and cancer.

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

Label-free analysis of physiological hyaluronan size distribution with a solid-state nanopore sensor by Felipe Rivas, Osama K. Zahid, Heidi L. Reesink, Bridgette T. Peal, Alan J. Nixon, Paul L. DeAngelis, Aleksander Skardal, Elaheh Rahbar, & Adam R. Hall. Nature Communications volume 9, Article number: 1037 (2018) doi:10.1038/s41467-018-03439-x
Published online: 12 March 2018

This paper is open access.

Ingenuity Lab (a nanotechnology initiative), the University of Alberta, and Carlo Montemagno—what is happening in Canadian universities? (2 of 2)

You can find Part 1 of the latest installment in this sad story here.

Who says Carlo Montemagno is a star nanotechnology researcher?

Unusually and despite his eminent stature, Dr. Montemagno does not rate a Wikipedia entry. Luckily, his CV (curriculum vitae) is online (placed there by SIU) so we can get to know a bit more (the CV is a 63 pp. document) about the man’s accomplishments (Note: There are some formatting differences), Note: Unusually, I will put my comments into the excerpted CV using [] i.e., square brackets to signify my input,

Carlo Montemagno, PhD
University of Alberta
Department of Chemical and Materials Engineering
and
NRC/CNRC National Institute for Nanotechnology
Edmonton, AB T6G 2V4
Canada

 

Educational Background

1995, Ph.D., Department of Civil Engineering and Geological Sciences, College of Earth and Mineral Sciences University of Notre Dame

1990, M.S., Petroleum and Natural Gas Engineering, College of Earth and Mineral Sciences, Pennsylvania State University

1980, B.S., Agricultural and Biological Engineering, College of Engineering, Cornell University

Supplemental Education

1986, Practical Environmental Law, Federal Publications, Washington, DC

1985, Effective Executive Training Program, Wharton Business School, University of Pennsylvannia, Philadelphia, PA

1980, Civil Engineer Corp Officer Project, CECOS & General Management School, Port Hueneme, CA

[He doesn’t seem to have taken any courses in the last 30 years.]

Professional Experience

(Select Achievements)

Over three decades of experience in shepherding complex organizations both inside and outside academia. Working as a builder, I have led organizations in government, industry and higher education during periods of change and challenge to achieved goals that many perceived to be unattainable.

University of Alberta, Edmonton AB 9/12 to present

9/12 to present, Founding Director, Ingenuity Lab [largely defunct as of April 18, 2018], Province of Alberta

8/13 to present, Director Biomaterials Program, NRC/CNRC National Institute for Nanotechnology [It’s not clear if this position still exists.]

10/13 to present, Canada Research Chair, Government of Canada in Intelligent Nanosystems [Canadian universities receive up to $200,000 for an individual Canada research chair. The money can be used to fund the chair in its entirety or it can be added to other monies., e.g., faculty salary. There are two tiers, one for established researchers and one for new researchers. Montemagno would have been a Tier 1 Canada Research Chair. At McGill University {a major Canadian educational institution} for example, total compensation including salary, academic stipend, benefits, X-coded research funds would be a maximum of $200,000 at Montemagno’s Tier 1 level. See: here scroll down about 90% of the way).

3/13 to present, AITF iCORE Strategic Chair, Province of Alberta in BioNanotechnology and Biomimetic Systems [I cannot find this position in the current list of the University of Alberta Faculty of Science’s research chairs.]

9/12 to present, Professor, Faculty of Engineering, Chemical and Materials Engineering

Crafted and currently lead an Institute that bridges multiple organizations named Ingenuity Lab (www.ingenuitylab.ca). This Institute is a truly integrated multidisciplinary organization comprised of dedicated researchers from STEM, medicine, and the social sciences. Ingenuity Lab leverages Alberta’s strengths in medicine, engineering, science and, agriculture that are present in multiple academic enterprises across the province to solve grand challenges in the areas of energy, environment, and health and rapidly translate the solutions to the economy.

The exciting and relevant feature of Ingenuity Lab is that support comes from resources outside the normal academic funding streams. Core funding of approximately $8.6M/yr emerged by working and communicating a compelling vision directly with the Provincial Executive and Legislative branches of government. [In the material I’ve read, the money for the research was part of how Dr. Montemagno was wooed by the University of Alberta. My understanding is that he himself did not obtain the funding, which in CAD was $100M over 10 years. Perhaps the university was able to attract the funding based on Dr. Montemagno’s reputation and it was contingent on his acceptance?] I significantly augmented these base resources by developing Federal Government, and Industry partnership agreements with a suite of multinational corporations and SME’s across varied industry sectors.

Collectively, this effort is generating enhanced resource streams that support innovative academic programming, builds new research infrastructure, and enables high risk/high reward research. Just as important, it established new pathways to interact meaningfully with local and global communities.

Strategic Leadership

•Created the Ingenuity Lab organization including a governing board representing multiple academic institutions, government and industry sectors.

•Developed and executed a strategic plan to achieve near and long-term strategic objectives.

•Recruited~100 researchers representing a wide range disciplnes.[sic] [How hard can it be to attract researchers in this job climate?]

•Built out ~36,000 S.F. of laboratory and administrative space.

•Crafted operational policy and procedures.

•Developed and implemented a unique stakeholder inclusive management strategy focused on the rapid translation of solutions to the economy.

Innovation and Economic Engagement

•Member of the Expert Panel on innovation, commissioned by the Government of Alberta, to assess opportunities, challenges and design and implementation options for Alberta’s multi-billion dollar investment to drive long-term economic growth and diversification. The developed strategy is currently being implemented. [Details?]

•Served as a representive [sic] on multiple Canadian national trade missions to Asia, United States and the Middle East. [Sounds like he got to enjoy some nice trips.]

•Instituted formal development partnerships with several multi-national corporations including Johnson & Johnson, Cenovus and Sabuto Inc. [Details?]

•Launched multiple for-profit joint ventures founded on technologies collaboratively developed with industry with funding from both private and public sources. [Details?]

Branding

•Developed and implement a communication program focused on branding of Ingenuity Lab’s unique mission, both regionally and globally, to the lay public, academia, government, and industry. [Why didn’t the communication specialist do this? ]

This effort employs traditional paper, online, and social media outlets to effectively reach different demographics.

•Awarded “Best Nanotechnology Research Organization–2014” by The New Economy. [What is the New Economy? The Economist, yes. New Economy, no.]

Global Development

•Executed formal research and education partnerships with the Yonsei Institute of Convergence Technology and the Yonsei Bio-IT MicroFab Center in Korea, Mahatma Gandhi University in India. and the Italian Institute of Technology. [{1}The Yonsei Institute of Convergence Technology doesn’t have any news items prior to 2015 or after 2016. The Ingenuity Lab and/or Carlo Montemagno did not feature in them. {2} There are six Mahatma Ghandi Universities in India. {3} The Italian Institute of Technology does not have any news listings on the English language version of its site.]

•Opened Ingenuity Lab, India in May 2015. Focused on translating 21st-century technology to enable solutions appropriate for developing nations in the Energy, Agriculture, and Health economic sectors. [Found this May 9, 2016 notice on the Asia Pacific Foundation of Canada website, noting this: “… opening of the Ingenuity Lab Research Hub at Mahatma Gandhi University in Kottayam, in the Indian state of Kerala.” There’s also this May 6, 2016 news release. I can’t find anything on the Mahatma Ghandi University Kerala website.]

•Established partnership research and development agreements with SME’s in both Israel and India.

•Developed active research collaborations with medical and educational institutions in Nepal, Qatar, India, Israel, India and the United States.

Community Outreach

•Created Young Innovators research experience program to educate, support and nurture tyro undergraduate researchers and entrepreneurs.

•Developed an educational game, “Scopey’s Nano Adventure” for iOS and Android platforms to educate 6yr to 10yr olds about Nanotechnology. [What did the children learn? Was this really part of the mandate?]

•Delivered educational science programs to the lay public at multiple, high profile events. [Which events? The ones on the trade junkets?]

University of Cincinnati, Cincinnati OH 7/06 to 8/12

7/10 to 8/12 Founding Dean, College of Engineering and Applied Science

7/09 to 6/10 Dean, College of Applied Science

7/06 to 6/10 Dean, College of Engineering

7/06 to 8/12 Geier Professor of College of Engineering Engineering Education

7/06 to 8/12, Professor of Bioengineering, College of Engineering & College of Medicine

University of California, Los Angeles 7/01 to 6/06

5/03 to 6/06, Associate Director California Nanosystems Institute

7/02 to 6/06, Co-Director NASA Center for Cell Mimetic Space Exploration

7/02 to 6/06, Founding Department Chair, Department of Bioengineering

7/02 to 6/06, Chair Biomedical Engineering IDP

7/01 to 6/02, Chair of Academic Biomedical Engineering IDP Affairs

7/01 to 6/06, Carol and Roy College of Engineering and Applied Doumani Professor of Sciences Biomedical Engineering

7/01 to 6/06, Professor Mechanical and Aerospace Engineering

Recommending Montemagno

Presumably the folks at Southern Illinois University asked for recommendations from Montemagno’s previous employers. So, how did he get a recommendation from the folks in Alberta when according to Spoerre’s April 10, 2018 article the Ingenuity Lab was undergoing a review as of June 2017 by the province of Alberta’s Alberta Innovates programme? I find it hard to believe that the folks at the University of Alberta were unaware of the review.

When you’re trying to get rid of someone, it’s pretty much standard practice that once they’ve gotten the message, you give a good recommendation to their prospective employer. The question begs to be asked, how many times have employers done this for Montemagno?

Stars in their eyes

Every one exaggerates a bit on their résumé or CV. One of my difficulties with this whole affair lies in how Montemagno can be described as a ‘nanotechnology star’. The accomplishments foregrounded on Montemagno’s CV are administrative and if memory serves, the University of Cincinnati too. Given the situation with the Ingenuity Lab, I’m wondering about these accomplishments.

Was due diligence performed by SIU, the University of the Alberta, or anywhere else that Montemagno worked? I realize that you’re not likely to get much information from calling up the universities where he worked previously, especially if there was a problem and they wanted to get rid of him. Still, did someone check out his degrees, his start-ups,  dig a little deeper into some of his claims?

His credentials and stated accomplishments are quite impressive and I, too,  would have been dazzled. (He also lists positions at the Argonne National Laboratory and at Cornell University.) I’ve picked at some bits but one thing that stands out to me is the move from UCLA to the University of Cincinnati. It’s all big names: UCLA, Cornell, NASA, Argonne and then, not: University of Cincinnati, University of Alberta, Southern Illinois University—what happened?

(If anyone better versed in the world of academe and career has answers, please do add them to the comments.)

It’s tempting to think the Peter Principle (one of them) was at work here. In brief, this principle states that as you keep getting better jobs on based on past performance you reach a point where you can’t manage the new challenges having risen to your level of incompetence.In accepting the offer from the University of Alberta had Dr. Montemagno risen to his level of incompetence? Or, perhaps it was just one big failure. Unfortunately, any excuses don’t hold up under the weight of a series of misjudgments and ethical failures. Still, I’m guessing that Dr. Montemagno was hoping for a big win on a project such as this (from an Oct. 19, 2016 news release on MarketWired),

Ingenuity Lab Carbon Solutions announced today that it has been named as one of the 27 teams advancing in the $20M NRG COSIA Carbon XPRIZE. The competition sees scientists develop technologies to convert carbon dioxide emissions into products with high net value.

The Ingenuity Lab Carbon Solutions team – headquartered in Edmonton of Alberta, Canada – has made it to the second round of competition. Its team of 14 has proposed to convert CO2 waste emitted from a natural gas power plant into usable chemical products.

Ingenuity Lab Carbon Solutions is comprised of a multidisciplinary group of scientists and engineers, and was formed in the winter of 2012 to develop new approaches for the chemical industry. Ingenuity Lab Carbon Solutions is sponsored by CCEMC, and has also partnered with Ensovi for access to intellectual property and know how.

I can’t identify CCEMC with any certainty but Ensovi is one of Montemagno’s six start-up companies, as listed in his CV,

Founder and Chief Technical Officer, Ensovi, LLC., Focused on the production of low-cost bioenergy and high-value added products from sunlight using bionanotechnology, Total Funding; ~$10M, November 2010-present.

Sadly the April 9,2018 NRG COSIA Carbon XPRIZE news release  announcing the finalists in round 3 of the competition includes an Alberta track of five teams from which the Ingenuity Lab is notably absent.

The Montemagno affair seems to be a story of hubris, greed, and good intentions. Finally, the issues associated with Dr. Montemagno give rise to another, broader question.

Is something rotten in Canada’s higher education establishment?

Starting with the University of Alberta:

it would seem pretty obvious that if you’re hiring family member(s) as part of the deal to secure a new member of faculty that you place and follow very stringent rules. No rewriting of the job descriptions, no direct role in hiring or supervising, no extra benefits, no inflated salaries in other words, no special treatment for your family as they know at the University of Alberta since they have policies for this very situation.

Yes, universities do hire spouses (although a daughter, a nephew, and a son-in-law seems truly excessive) and even when the university follows all of the rules, there’s resentment from staff (I know because I worked in a university). There is a caveat to the rule, there’s resentment unless that spouse is a ‘star’ in his or her own right or an exceptionally pleasant person. It’s also very helpful if the spouse is both.

I have to say I loved Fraser Forbes that crazy University of Alberta engineer who thought he’d make things better by telling us that the family’s salaries had been paid out of federal and provincial funds rather than university funds. (sigh) Forbes was the new dean of engineering at the time of his interview in the CBC’s April 10, 2018 online article but that no longer seems to be the case as of April 19, 2018.

Given Montemagno’s misjudgments, it seems cruel that Forbes was removed after one foolish interview. But, perhaps he didn’t want the job after all. Regardless, those people who were afraid to speak out about Dr. Montemagno cannot feel reassured by Forbes’ apparent removal.

Money, money, money

Anyone who has visited a university in Canada (and presumably the US too) has to have noticed the number of ‘sponsored’ buildings and rooms. The hunger for money seems insatiable and any sensible person knows it’s unsupportable over the long term.

The scramble for students

Mel Broitman in a Sept. 22, 2016 article for Higher Education lays out some harsh truths,

Make no mistake. It is a stunning condemnation and a “wakeup call to higher education worldwide”. The recent UNESCO report states that academic institutions are rife with corruption and turning a blind eye to malpractice right under their noses. When UNESCO, a United Nations organization created after the chaos of World War II to focus on moral and intellectual solidarity, makes such an alarming allegation, it’s sobering and not to be dismissed.

So although Canadians typically think of their society and themselves as among the more honest and transparent found anywhere, how many Canadian institutions are engaging in activities that border on dishonest and are not entirely transparent around the world?

It is overwhelmingly evident that in the last two decades we have witnessed first-hand a remarkable and callous disregard for academic ethics and standards in a scramble by Canadian universities and colleges to sign up foreign students, who represent tens of millions of dollars to their bottom lines.

We have been in a school auditorium in China and listened to the school owner tell prospective parents that the Grade 12 marks from the Canadian provincial school board program can be manipulated to secure admission for their children into Canadian universities. This, while the Canadian teachers sat oblivious to the presentation in Chinese.

In hundreds of our own interaction with students who completed the Canadian provincial school board’s curriculum in China and who achieved grades of 70% and higher in their English class have been unable to achieve even a basic level of English literacy in the written tests we have administered.   But when the largest country of origin for incoming international students and revenue is China – the Canadian universities admitting these students salivate over the dollars and focus less on due diligence.

We were once asked by a university on Canada’s west coast to review 200 applications from Saudi Arabia, in order to identify the two or three Saudi students who were actually eligible for conditional admission to that university’s undergraduate engineering program. But the proposal was scuttled by the university’s ESL department that wanted all 200 to enroll in its language courses. It insisted on and managed conditional admissions for all 200. It’s common at Canadian universities for the ESL program “tail” to wag the campus “dog” when it comes to admissions. In fact, recent Canadian government regulations have been proposed to crack down on this practice as it is an affront to academic integrity.

If you have time, do read the rest as it’s eye-opening. As for the report Broitman cites, I was not able to find it. Broitman gives a link to the report in response to one of the later comments and there’s a link in Tony Bates’s July 31, 2016 posting but you will get a “too bad, so sad” message should you follow either link.The closed I can get to it is this Advisory Statement for Effective International Practice; Combatting Corruption and Enhancing Integrity: A Contemporary Challenge for the Quality and Credibility of Higher Education (PDF). The ‘note’ was jointly published by the (US) Council for Higher Education (CHEA) and UNESCO.

What about the professors?

As they scramble for students, the universities appear to be cutting their ‘teaching costs’, from an April 18, 2018 article by Charles Menzies (professor of anthropology and an elected member of the UBC [University of British Columbia] Board)  for THE UBYSSEY (UBC) student newspaper,

For the first time ever at UBC the contributions of student tuition fees exceeded provincial government contributions to UBC’s core budget. This startling fact was the backdrop to a strenuous grilling of UBC’s VP Finance and Provost Peter Smailes by governors at the Friday the 13 meeting of UBC’s Board of Governors’ standing committee for finance.

Given the fact students contribute more to UBC’s budget than the provincial government, governors asked why more wasn’t being done to enhance the student experience. By way of explanation the provost reiterated UBC’s commitment to the student experience. In a back-and-forth with a governor the provost outlined a range of programs that focus on enhancing the student experience. At several points the chair of the Board would intervene and press the provost for more explanations and elaboration. For his part the provost responded in a measured and deliberate tone outlining the programs in play, conceding more could be done, and affirming the importance of students in the overall process.

As a faculty member listening to this, I wondered about the background discourse undergirding the discussion. How is focussing on a student’s experience at UBC related to our core mission: education and research? What is actually being meant by experience? Why is no one questioning the inadequacy of the government’s core contribution? What about our contingent colleagues? Our part-time precarious colleagues pick up a great deal of the teaching responsibilities across our campuses. Is there not something we can do to improve their working conditions? Remember, faculty working conditions are student learning conditions. From my perspective all these questions received short shrift.

I did take the opportunity to ask the provost, given how financially sound our university is, why more funds couldn’t be directed toward improving the living and working conditions of contingent faculty. However, this was never elaborated upon after the fact.

There is much about the university as a total institution that seems driven to cultivate experiences. A lot of Board discussion circles around ideas of reputation and brand. Who pays and how much they pay (be they governments, donors, or students) is also a big deal. Cultivating a good experience for students is central to many of these discussions.

What is this experience that everyone is talking about? I hear about classroom experience, residence experience, and student experience writ large. Very little of it seems to be specifically tied to learning (unless it’s about more engaging, entertaining, learning with technology). While I’m sure some Board colleagues will disagree with this conclusion, it does seem to me that the experience being touted is really the experience of a customer seeking fulfilment through the purchase of a service. What is seen as important is not what is learned, but the grade; not the productive struggle of learning but the validation of self in a great experience as a member of an imagined community. A good student experience very likely leads to a productive alumni relationship — one where the alumni feels good about giving money.

Inside UBC’s Board of Governors

Should anyone be under illusions as to what goes on at the highest levels of university governance, there is the telling description from Professor Jennifer Berdahl about her experience on a ‘search committee for a new university president’ of the shameful treatment of previous president, Arvind Gupta (from Berdahl’s April 25, 2018 posting on her eponymous blog),

If Prof. Chaudhry’s [Canada Research Chair and Professor Ayesha Chaudhry’s resignation was announced in an April 25, 2018 UBYSSEY article by Alex Nguyen and Zak Vescera] experience was anything like mine on the UBC Presidential Search Committee, she quickly realized how alienating it is to be one of only three faculty members on a 21-person corporate-controlled Board. It was likely even worse for Chaudhry as a woman of color. Combining this with the Board’s shenanigans that are designed to manipulate information and process to achieve desired decisions and minimize academic voices, a sense of helpless futility can set in. [emphasis mine]

These shenanigans include [emphasis mine] strategic seating arrangements, sudden breaks during meetings when conversation veers from the desired direction, hand-written notes from the secretary to speaking members, hundreds of pages of documents sent the night before a meeting, private tête-à-têtes arranged between a powerful board member and a junior or more vulnerable one, portals for community input vetted before sharing, and planning op-eds to promote preferred perspectives. These are a few of many tricks employed to sideline unpopular voices, mostly academic ones.

It’s impossible to believe that UBC’s BoG is the site for these shenanigans take place. The question I have is how many BoGs and how much damage are they inflicting?

Finally getting back to my point, simultaneous with cutting back on teaching and other associated costs and manipulative, childish behaviour at BoG meetings, large amounts of money are being spent to attract ‘stars’ such as Dr. Montemagno. The idea is to attract students (and their money) to the institution where they can network with the ‘stars’. What the student actually learns does not seem to be the primary interest.

So, what kind of deals are the universities making with the ‘stars’?

The Montemagno affair provides a few hints but, in the end,I don’t know and I don’t think anyone outside the ‘sacred circle’ does either. UBC, for example,is quite secretive and, seemingly, quite liberal in its use of nondisclosure agreements (NDA). There was the scandal a few years ago when president Arvind Gupta abruptly resigned after one year in his position. As far as I know, no one has ever gotten to the bottom of this mystery although there certainly seems to have been a fair degree skullduggery involved.

After a previous president, Martha Cook Piper took over the reigns in an interim arrangement, Dr. Santa J. Ono (his Wikipedia entry) was hired.  Interestingly, he was previously at the University of Cincinnati, one of Montemagno’s previous employers. That university’s apparent eagerness to treat Montemagno’s extras seems to have led to the University of Alberta’s excesses.  So, what deal did UBC make with Dr. Ono? I’m pretty sure both he and the university are covered by an NDA but there is this about his tenure as president at the University of Cincinnati (from a June 14, 2016 article by Jack Hauen for THE UBYSSEY),

… in exchange for UC not raising undergraduate tuition, he didn’t accept a salary increase or bonus for two years. And once those two years were up, he kept going: his $200,000 bonus in 2015 went to “14 different organizations and scholarships, including a campus LGBTQ centre, a local science and technology-focused high school and a program for first-generation college students,” according to the Vancouver Sun.

In 2013 he toured around the States promoting UC with a hashtag of his own creation — #HottestCollegeInAmerica — while answering anything and everything asked of him during fireside chats.

He describes himself as a “servant leader,” which is a follower of a philosophy of leadership focused primarily on “the growth and well-being of people and the communities to which they belong.”

“I see my job as working on behalf of the entire UBC community. I am working to serve you, and not vice-versa,” he said in his announcement speech this morning.

Thank goodness it’s possible to end this piece on a more or less upbeat note. Ono seems to be what my father would have called ‘a decent human being’. It’s nice to be able to include a ‘happyish’ note.

Plea

There is huge money at stake where these ‘mega’ science and technology projects are concerned. The Ingenuity Lab was $100M investment to be paid out over 10 years and some basic questions don’t seem to have been asked. How does this person manage money? Leaving aside any issues with an individual’s ethics and moral compass, scientists don’t usually take any courses in business and yet they are expected to manage huge budgets. Had Montemagno handled a large budget or any budget? It’s certainly not foregrounded (and I’d like to see dollar amounts) in his CV.

As well, the Ingenuity Lab was funded as a 10 year project. Had Montemagno ever stayed in one job for 10 years? Not according to his CV. His longest stint was approximately eight years when he was in the US Navy in the 1980s. Otherwise, it was five to six years, including the Ingenuity Lab stint.

Meanwhile, our universities don’t appear to be applying the rules and protocols we have in place to ensure fairness. This unseemly rush for money seems to have infected how Canadian universities attract (local, interprovincial, and, especially, international) students to pay for their education. The infection also seems to have spread into the ways ‘star’ researchers and faculty members are recruited to Canadian universities while the bulk of the teaching staff are ‘starved’ under one pretext or another while a BoG may or may not be indulging in shenanigans designed to drive decision-making to a preordained outcome. And, for the most part, this is occurring under terms of secrecy that our intelligence agencies must envy.

In the end, I can’t be the only person wondering how all this affects our science.

An exoskeleton for a cell-sized robot

A January 3, 2018 news item on phys.org announces work on cell-sized robots,

An electricity-conducting, environment-sensing, shape-changing machine the size of a human cell? Is that even possible?

Cornell physicists Paul McEuen and Itai Cohen not only say yes, but they’ve actually built the “muscle” for one.

With postdoctoral researcher Marc Miskin at the helm, the team has made a robot exoskeleton that can rapidly change its shape upon sensing chemical or thermal changes in its environment. And, they claim, these microscale machines – equipped with electronic, photonic and chemical payloads – could become a powerful platform for robotics at the size scale of biological microorganisms.

“You could put the computational power of the spaceship Voyager onto an object the size of a cell,” Cohen said. “Then, where do you go explore?”

“We are trying to build what you might call an ‘exoskeleton’ for electronics,” said McEuen, the John A. Newman Professor of Physical Science and director of the Kavli Institute at Cornell for Nanoscale Science. “Right now, you can make little computer chips that do a lot of information-processing … but they don’t know how to move or cause something to bend.”

Cornell University has produced a video of the researchers discussing their work (about 3 mins. running time)

For those who prefer text or need it to reinforce their understanding, there’s a January 2, 2018 Cornell University news release (also on EurekAlert but dated Jan. 3, 2018) by Tom Fleischman, which originated the news item,

The machines move using a motor called a bimorph. A bimorph is an assembly of two materials – in this case, graphene and glass – that bends when driven by a stimulus like heat, a chemical reaction or an applied voltage. The shape change happens because, in the case of heat, two materials with different thermal responses expand by different amounts over the same temperature change.

As a consequence, the bimorph bends to relieve some of this strain, allowing one layer to stretch out longer than the other. By adding rigid flat panels that cannot be bent by bimorphs, the researchers localize bending to take place only in specific places, creating folds. With this concept, they are able to make a variety of folding structures ranging from tetrahedra (triangular pyramids) to cubes.

In the case of graphene and glass, the bimorphs also fold in response to chemical stimuli by driving large ions into the glass, causing it to expand. Typically this chemical activity only occurs on the very outer edge of glass when submerged in water or some other ionic fluid. Since their bimorph is only a few nanometers thick, the glass is basically all outer edge and very reactive.

“It’s a neat trick,” Miskin said, “because it’s something you can do only with these nanoscale systems.”

The bimorph is built using atomic layer deposition – chemically “painting” atomically thin layers of silicon dioxide onto aluminum over a cover slip – then wet-transferring a single atomic layer of graphene on top of the stack. The result is the thinnest bimorph ever made. One of their machines was described as being “three times larger than a red blood cell and three times smaller than a large neuron” when folded. Folding scaffolds of this size have been built before, but this group’s version has one clear advantage.

“Our devices are compatible with semiconductor manufacturing,” Cohen said. “That’s what’s making this compatible with our future vision for robotics at this scale.”

And due to graphene’s relative strength, Miskin said, it can handle the types of loads necessary for electronics applications. “If you want to build this electronics exoskeleton,” he said, “you need it to be able to produce enough force to carry the electronics. Ours does that.”

For now, these tiniest of tiny machines have no commercial application in electronics, biological sensing or anything else. But the research pushes the science of nanoscale robots forward, McEuen said.

“Right now, there are no ‘muscles’ for small-scale machines,” he said, “so we’re building the small-scale muscles.”

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

Graphene-based bimorphs for micron-sized, autonomous origami machines by Marc Z. Miskin, Kyle J. Dorsey, Baris Bircan, Yimo Han, David A. Muller, Paul L. McEuen, and Itai Cohen. PNAS [Proceedings of the National Academy of Sciences] 2018 doi: 10.1073/pnas.1712889115 published ahead of print January 2, 2018

This paper is behind a paywall.

(Merry Christmas!) Japanese tree frogs inspire hardware for the highest of tech: a swarmalator

First, the frog,

[Japanese Tree Frog] By 池田正樹 (talk)masaki ikeda – Own work, Public Domain, https://commons.wikimedia.org/w/index.php?curid=4593224

I wish they had a recording of the mating calls for Japanese tree frogs since they were the inspiration for mathematicians at Cornell University (New York state, US) according to a November 17, 2017 news item on ScienceDaily,

How does the Japanese tree frog figure into the latest work of noted mathematician Steven Strogatz? As it turns out, quite prominently.

“We had read about these funny frogs that hop around and croak,” said Strogatz, the Jacob Gould Schurman Professor of Applied Mathematics. “They form patterns in space and time. Usually it’s about reproduction. And based on how the other guy or guys are croaking, they don’t want to be around another one that’s croaking at the same time as they are, because they’ll jam each other.”

A November 15, 2017 Cornell University news release (also on EurekAlert but dated November 17, 2017) by Tom Fleischman, which originated the news item, details how the calls led to ‘swarmalators’ (Note: Links have been removed),

Strogatz and Kevin O’Keeffe, Ph.D. ’17, used the curious mating ritual of male Japanese tree frogs as inspiration for their exploration of “swarmalators” – their term for systems in which both synchronization and swarming occur together.

Specifically, they considered oscillators whose phase dynamics and spatial dynamics are coupled. In the instance of the male tree frogs, they attempt to croak in exact anti-phase (one croaks while the other is silent) while moving away from a rival so as to be heard by females.

This opens up “a new class of math problems,” said Strogatz, a Stephen H. Weiss Presidential Fellow. “The question is, what do we expect to see when people start building systems like this or observing them in biology?”

Their paper, “Oscillators That Sync and Swarm,” was published Nov. 13 [2017] in Nature Communications. Strogatz and O’Keeffe – now a postdoctoral researcher with the Senseable City Lab at the Massachusetts Institute of Technology – collaborated with Hyunsuk Hong from Chonbuk National University in Jeonju, South Korea.

Swarming and synchronization both involve large, self-organizing groups of individuals interacting according to simple rules, but rarely have they been studied together, O’Keeffe said.

“No one had connected these two areas, in spite of the fact that there were all these parallels,” he said. “That was the theoretical idea that sort of seduced us, I suppose. And there were also a couple of concrete examples, which we liked – including the tree frogs.”

Studies of swarms focus on how animals move – think of birds flocking or fish schooling – while neglecting the dynamics of their internal states. Studies of synchronization do the opposite: They focus on oscillators’ internal dynamics. Strogatz long has been fascinated by fireflies’ synchrony and other similar phenomena, giving a TED Talk on the topic in 2004, but not on their motion.

“[Swarming and synchronization] are so similar, and yet they were never connected together, and it seems so obvious,” O’Keeffe said. “It’s a whole new landscape of possible behaviors that hadn’t been explored before.”

Using a pair of governing equations that assume swarmalators are free to move about, along with numerical simulations, the group found that a swarmalator system settles into one of five states:

  • Static synchrony – featuring circular symmetry, crystal-like distribution, fully synchronized in phase;
  • Static asynchrony – featuring uniform distribution, meaning that every phase occurs everywhere;
  • Static phase wave – swarmalators settle near others in a phase similar to their own, and phases are frozen at their initial values;
  • Splintered phase wave – nonstationary, disconnected clusters of distinct phases; and
  • Active phase wave – similar to bidirectional states found in biological swarms, where populations split into counter-rotating subgroups; also similar to vortex arrays formed by groups of sperm.

Through the study of simple models, the group found that the coupling of “sync” and “swarm” leads to rich patterns in both time and space, and could lead to further study of systems that exhibit this dual behavior.

“This opens up a lot of questions for many parts of science – there are a lot of things to try that people hadn’t thought of trying,” Strogatz said. “It’s science that opens doors for science. It’s inaugurating science, rather than culminating science.”

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

Oscillators that sync and swarm by Kevin P. O’Keeffe, Hyunsuk Hong, & Steven H. Strogatz. Nature Communications 8, Article number: 1504 (2017) doi:10.1038/s41467-017-01190-3 Published online: 15 November 2017

This paper is open access.

One last thing, these frogs have also inspired WiFi improvements (from the Japanese tree frog Wikipedia entry; Note: Links have been removed),

Journalist Toyohiro Akiyama carried some Japanese tree frogs with him during his trip to the Mir space station in December 1990.[citation needed] Calling behavior of the species was used to create an algorithm for optimizing Wi-Fi networks.[3]

While it’s not clear in the Wikipedia entry, the frogs were part of an experiment. Here’s a link to and a citation for the paper about the experiment, along with an abstract,

The Frog in Space (FRIS) experiment onboard Space Station Mir: final report and follow-on studies by Yamashita, M.; Izumi-Kurotani, A.; Mogami, Y.; Okuno,k M.; Naitoh, T.; Wassersug, R. J. Biol Sci Space. 1997 Dec 11(4):313-20.

Abstract

The “Frog in Space” (FRIS) experiment marked a major step for Japanese space life science, on the occasion of the first space flight of a Japanese cosmonaut. At the core of FRIS were six Japanese tree frogs, Hyla japonica, flown on Space Station Mir for 8 days in 1990. The behavior of these frogs was observed and recorded under microgravity. The frogs took up a “parachuting” posture when drifting in a free volume on Mir. When perched on surfaces, they typically sat with their heads bent backward. Such a peculiar posture, after long exposure to microgravity, is discussed in light of motion sickness in amphibians. Histological examinations and other studies were made on the specimens upon recovery. Some organs, such as the liver and the vertebra, showed changes as a result of space flight; others were unaffected. Studies that followed FRIS have been conducted to prepare for a second FRIS on the International Space Station. Interspecific diversity in the behavioral reactions of anurans to changes in acceleration is the major focus of these investigations. The ultimate goal of this research is to better understand how organisms have adapted to gravity through their evolution on earth.

The paper is open access.

Gecko lets go!

After all these years of writing about geckos and their adhesive properties it seems that geckos sometimes slip or let go, theoretically. (BTW, there’s a Canadian connection’ one of  the researchers is at the University of Calgary in the province of Alberta.) From a July 19, 2017 Cornell University news release (also on EurekAlert),

Geckos climb vertically up trees, walls and even windows, thanks to pads on the digits of their feet that employ a huge number of tiny bristles and hooks.

Scientists have long marveled at the gecko’s adhesive capabilities, which have been described as 100 times more than what is needed to support their body weight or run quickly up a surface.

But a new theoretical study examines for the first time the limits of geckos’ gripping ability in natural contexts. The study, recently published in the Journal of the Royal Society Interface, reports there are circumstances – such as when geckos fear for their lives, leap into the air and are forced to grab on to a leaf below – when they need every bit of that fabled adhesive ability, and sometimes it’s not enough.

“Geckos are notoriously described as having incredible ability to adhere to a surface,” said Karl Niklas, professor of plant evolution at Cornell University and a co-author of the paper. The study’s lead authors, Timothy Higham at the University of California, Riverside, and Anthony Russell at the University of Calgary, Canada, both zoologists, brought Niklas into the project for his expertise on plant biomechanics.

“The paper shows that [adhesive capability] might be exaggerated, because geckos experience falls and a necessity to grip a surface like a leaf that requires a much more tenacious adhesion force; the paper shows that in some cases the adhesive ability can be exceeded,” Niklas said.

In the theoretical study, the researchers developed computer models to understand if there are common-place instances when the geckos’ ability to hold on to surfaces might be challenged, such as when canopy-dwelling geckos are being chased by a predator and are forced to leap from a tree, hoping to land on a leaf below. The researchers incorporated ecological observations, adhesive force measurements, and body size and shape measurements of museum specimens to conduct simulations. They also considered the biomechanics of the leaves, the size of the leaves and the angles on the surface that geckos might land on to determine impact forces. Calculations were also based on worst-case scenarios, where a gecko reaches a maximum speed when it is no longer accelerating, called “terminal settling velocity.”

“Leaves are cantilevered like diving boards and they go through harmonic motion [when struck], so you have to calculate the initial deflection and orientation, and then consider how does that leaf rebound and can the gecko still stay attached,” Niklas said.

The final result showed that in some cases geckos don’t have enough adhesion to save themselves, he added.

Higham and Russell are planning to travel to French Guiana to do empirical adhesive force studies on living geckos in native forests.

The basic research helps people better understand how geckos stick to surfaces, and has the potential for future applications that mimic such biological mechanisms.

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

Leaping lizards landing on leaves: escape-induced jumps in the rainforest canopy challenge the adhesive limits of geckos by Timothy E. Higham, Anthony P. Russell, Karl J. Niklas. Journal of the Royal Society Interface June 2017 Volume 14, issue 131 DOI: 10.1098/rsif.2017.0156 Published 28 June 2017

I think the authors had some fun with that title. In any event, the paper is behind a paywall.