Tag Archives: COVID-19

D-Wave’s new Advantage quantum computer

Thanks to Bob Yirka’s September 30, 2020 article for phys.org there’s an announcement about D-Wave Systems’ latest quantum computer and an explanation of how D-Wave’s quantum computer differs from other quantum computers. Here’s the explanation (Note: Links have been removed),

Over the past several years, several companies have dedicated resources to the development of a true quantum computer that can tackle problems conventional computers cannot handle. Progress on developing such computers has been slow, however, especially when compared with the early development of the conventional computer. As part of the research effort, companies have taken different approaches. Google and IBM, for example, are working on gate-model quantum computer technology, in which qubits are modified as an algorithm is executed. D-Wave, in sharp contrast, has been focused on developing so-called annealer technology, in which qubits are cooled during execution of an algorithm, which allows for passively changing their value.

Comparing the two is next to impossible because of their functional differences. Thus, using 5,000 qubits in the Advantage system does not necessarily mean that it is any more useful than the 100-qubit systems currently being tested by IBM or Google. Still, the announcement suggests that businesses are ready to start taking advantage of the increased capabilities of quantum systems. D-Wave notes that several customers are already using their system for a wide range of applications. Menten AI, for example, has used the system to design new proteins; grocery chain Save-On-Foods has been using it to optimize business operations; Accenture has been using it to develop business applications; Volkswagen has used the system to develop a more efficient car painting system.

Here’s the company’s Sept. 29, 2020 video announcement,

For those who might like some text, there’s a Sept. 29, 2020 D-Wave Systems press release (Note: Links have been removed; this is long),

D-Wave Systems Inc., the leader in quantum computing systems, software, and services, today [Sept. 29, 2020] announced the general availability of its next-generation quantum computing platform, incorporating new hardware, software, and tools to enable and accelerate the delivery of in-production quantum computing applications. Available today in the Leap™ quantum cloud service, the platform includes the Advantage™ quantum system, with more than 5000 qubits and 15-way qubit connectivity, in addition to an expanded hybrid solver service that can run problems with up to one million variables. The combination of the computing power of Advantage and the scale to address real-world problems with the hybrid solver service in Leap enables businesses to run performant, real-time, hybrid quantum applications for the first time.

As part of its commitment to enabling businesses to build in-production quantum applications, the company announced D-Wave Launch™, a jump-start program for businesses who want to get started building hybrid quantum applications today but may need additional support. Bringing together a team of applications experts and a robust partner community, the D-Wave Launch program provides support to help identify the best applications and to translate businesses’ problems into hybrid quantum applications. The extra support helps customers accelerate designing, building, and running their most important and complex applications, while delivering quantum acceleration and performance.

The company also announced a new hybrid solver. The discrete quadratic model (DQM) solver gives developers and businesses the ability to apply the benefits of hybrid quantum computing to new problem classes. Instead of accepting problems with only binary variables (0 or 1), the DQM solver uses other variable sets (e.g. integers from 1 to 500, or red, yellow, and blue), expanding the types of problems that can run on the quantum computer. The DQM solver will be generally available on October 8 [2020].

With support for new solvers and larger problem sizes backed by the Advantage system, customers and partners like Menten AI, Save-On-Foods, Accenture, and Volkswagen are building and running hybrid quantum applications that create solutions with business value today.

  • Protein design pioneer Menten AI has developed the first process using hybrid quantum programs to determine protein structure for de novo protein design with very encouraging results often outperforming classical solvers. Menten AI’s unique protein designs have been computationally validated, chemically synthesized, and are being advanced to live-virus testing against COVID-19.
  • Western Canadian grocery retailer Save-On-Foods is using hybrid quantum algorithms to bring grocery optimization solutions to their business, with pilot tests underway in-store. The company has been able to reduce the time an important optimization task takes from 25 hours to a mere 2 minutes of calculations each week. Even more important than the reduction in time is the ability to optimize performance across and between a significant number of business parameters in a way that is challenging using traditional methods.
  • Accenture, a leading global professional services company, is exploring quantum, quantum-inspired, and hybrid solutions to develop applications across industries. Accenture recently conducted a series of business experiments with a banking client to pilot quantum applications for currency arbitrage, credit scoring, and trading optimization, successfully mapping computationally challenging business problems to quantum formulations, enabling quantum readiness.
  • Volkswagen, an early adopter of D-Wave’s annealing quantum computer, has expanded its quantum use cases with the hybrid solver service to build a paint shop scheduling application. The algorithm is designed to optimize the order in which cars are being painted. By using the hybrid solver service, the number of color switches will be reduced significantly, leading to performance improvements.

The Advantage quantum computer and the Leap quantum cloud service include:

  • New Topology: The topology in Advantage makes it the most connected of any commercial quantum system in the world. In the D-Wave 2000Q™ system, qubits may connect to 6 other qubits. In the new Advantage system, each qubit may connect to 15 other qubits. With two-and-a-half times more connectivity, Advantage enables the embedding of larger problems with fewer physical qubits compared to using the D-Wave 2000Q system. The D-Wave Ocean™ software development kit (SDK) includes tools for using the new topology. Information on the topology in Advantage can be found in this white paper, and a getting started video on how to use the new topology can be found here.
  • Increased Qubit Count: With more than 5000 qubits, Advantage more than doubles the qubit count of the D-Wave 2000Q system. More qubits and richer connectivity provide quantum programmers access to a larger, denser, and more powerful graph for building commercial quantum applications.
  • Greater Performance & Problem Size: With up to one million variables, the hybrid solver service in Leap allows businesses to run large-scale, business-critical problems. This, coupled with the new topology and more than 5000 qubits in the Advantage system, expands the complexity and more than doubles the size of problems that can run directly on the quantum processing unit (QPU). In fact, the hybrid solver outperformed or matched the best of 27 classical optimization solvers on 87% of 45 application-relevant inputs tested in MQLib. Additionally, greater connectivity of the QPU allows for more compact embeddings of complex problems. Advantage can find optimal solutions 10 to 30 times faster in some cases, and can find better quality solutions up to 64% percent of the time, when compared to the D-Wave 2000Q LN QPU.
  • Expansion of Hybrid Software & Tools in Leap: Further investments in the hybrid solver service, new solver classes, ease-of-use, automation, and new tools provide an even more powerful hybrid rapid development environment in Python for business-scale problems.
  • Flexible Access: Advantage, the expanded hybrid solver service, and the upcoming DQM solver are available in the Leap quantum cloud service. All current Leap customers get immediate access with no additional charge, and new customers will benefit from all the new and existing capabilities in Leap. This means that developers and businesses can get started today building in-production hybrid quantum applications. Flexible purchase plans allow developers and forward-thinking businesses to access the D-Wave quantum system in the way that works for them and their business. 
  • Ongoing Releases: D-Wave continues to bring innovations to market with additional hybrid solvers, QPUs, and software updates through the cloud. Interested users and customers can get started today with Advantage and the hybrid solver service, and will benefit from new components of the platform through Leap as they become available.

“Today’s general availability of Advantage delivers the first quantum system built specifically for business, and marks the expansion into production scale commercial applications and new problem types with our hybrid solver services. In combination with our new jump-start program to get customers started, this launch continues what we’ve known at D-Wave for a long time: it’s not about hype, it’s about scaling, and delivering systems that provide real business value on real business applications,” said Alan Baratz, CEO, D-Wave. “We also continue to invest in the science of building quantum systems. Advantage was completely re-engineered from the ground up. We’ll take what we’ve learned about connectivity and scale and continue to push the limits of innovation for the next generations of our quantum computers. I’m incredibly proud of the team that has brought us here and the customers and partners who have collaborated with us to build hundreds of early applications and who now are putting applications into production.”

“We are using quantum to design proteins today. Using hybrid quantum applications, we’re able to solve astronomical protein design problems that help us create new protein structures,” said Hans Melo, Co-founder and CEO, Menten AI. “We’ve seen extremely encouraging results with hybrid quantum procedures often finding better solutions than competing classical solvers for de novo protein design. This means we can create better proteins and ultimately enable new drug discoveries.”

“At Save-On-Foods, we have been committed to bringing innovation to our customers for more than 105 years. To that end, we are always looking for new and creative ways to solve problems, especially in an environment that has gotten increasingly complex,” said Andrew Donaher, Vice President, Digital & Analytics at Save-On-Foods. “We’re new to quantum computing, and in a short period of time, we have seen excellent early results. In fact, the early results we see with Advantage and the hybrid solver service from D-Wave are encouraging enough that our goal is to turn our pilot into an in-production business application. Quantum is emerging as a potential competitive edge for our business.“

“Accenture is committed to helping our clients prepare for the arrival of mainstream quantum computing by exploring relevant use cases and conducting business experiments now,” said Marc Carrel-Billiard, Senior Managing Director and Technology Innovation Lead at Accenture. “We’ve been collaborating with D-Wave for several years and with early access to the Advantage system and hybrid solver service we’ve seen performance improvements and advancements in the platform that are important steps for helping to make quantum a reality for clients across industries, creating new sources of competitive advantage.”

“Embracing quantum computing is nothing new for Volkswagen. We were the first to run a hybrid quantum application in production in Lisbon last November with our bus routing application,” said Florian Neukart, Director of Advanced Technologies at Volkswagen Group of America. “At Volkswagen, we are focusing on building up a deep understanding of meaningful applications of quantum computing in a corporate context. The D-Wave system gives us the opportunity to address optimization tasks with a large number of variables at an impressive speed. With this we are taking a step further towards quantum applications that will be suitable for everyday business use.”

I found the description of D-Wave’s customers and how they’re using quantum computing to be quite interesting. For anyone curious about D-Wave Systems, you can find out more here. BTW, the company is located in metro Vancouver (Canada).

Gold nanoparticles make a new promise: a non-invasive COVID-19 breathalyser

I believe that swab they stick up your nose to test for COVDI-19 is 10 inches long so it seems to me that discomfort or unpleasant are not the words that best describe the testing experience .

Hopefully, no one will have to find inadequate vocabulary for this new COVID-19 testing assuming that future trials are successful and they are able to put the technology into production. From an August 19, 2020 news item on Nanowerk,

Few people who have undergone nasopharyngeal swabs for coronavirus testing would describe it as a pleasant experience. The procedure involves sticking a long swab up the nose to collect a sample from the back of the nose and throat, which is then analyzed for SARS-CoV-2 RNA [ribonucleic acid] by the reverse-transcription polymerase chain reaction (RT-PCR).

Now, researchers reporting in [American Chemical Society] ACS Nano (“Multiplexed Nanomaterial-Based Sensor Array for Detection of COVID-19 in Exhaled Breath”) have developed a prototype device that non-invasively detected COVID-19 in the exhaled breath of infected patients.

An August 19, 2020 ACS news release (also received via email and on EurekAlert), which originated the news item, provides more technical details,

In addition to being uncomfortable, the current gold standard for COVID-19 testing requires RT-PCR, a time-consuming laboratory procedure. Because of backlogs, obtaining a result can take several days. To reduce transmission and mortality rates, healthcare systems need quick, inexpensive and easy-to-use tests. Hossam Haick, Hu Liu, Yueyin Pan and colleagues wanted to develop a nanomaterial-based sensor that could detect COVID-19 in exhaled breath, similar to a breathalyzer test for alcohol intoxication. Previous studies have shown that viruses and the cells they infect emit volatile organic compounds (VOCs) that can be exhaled in the breath.

The researchers made an array of gold nanoparticles linked to molecules that are sensitive to various VOCs. When VOCs interact with the molecules on a nanoparticle, the electrical resistance changes. The researchers trained the sensor to detect COVID-19 by using machine learning to compare the pattern of electrical resistance signals obtained from the breath of 49 confirmed COVID-19 patients with those from 58 healthy controls and 33 non-COVID lung infection patients in Wuhan, China. Each study participant blew into the device for 2-3 seconds from a distance of 1¬-2 cm. Once machine learning identified a potential COVID-19 signature, the team tested the accuracy of the device on a subset of participants. In the test set, the device showed 76% accuracy in distinguishing COVID-19 cases from controls and 95% accuracy in discriminating COVID-19 cases from lung infections. The sensor could also distinguish, with 88% accuracy, between sick and recovered COVID-19 patients. Although the test needs to be validated in more patients, it could be useful for screening large populations to determine which individuals need further testing, the researchers say.

The authors acknowledge funding from the Technion-Israel Institute of Technology.

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

Multiplexed Nanomaterial-Based Sensor Array for Detection of COVID-19 in Exhaled Breath by Benjie Shan, Yoav Y Broza, Wenjuan Li, Yong Wang, Sihan Wu, Zhengzheng Liu, Jiong Wang, Shuyu Gui, Lin Wang, Zhihong Zhang, Wei Liu, Shoubing Zhou, Wei Jin, Qianyu Zhang, Dandan Hu, Lin Lin, Qiujun Zhang, Wenyu Li, Jinquan Wang, Hu Liu, Yueyin Pan, and Hossam Haick. ACS Nano 2020, XXXX, XXX, XXX-XXX DOI: https://doi.org/10.1021/acsnano.0c05657 Publication Date:August 18, 2020 Copyright © 2020 American Chemical Society

This paper is behind a paywall.

Science fiction, interconnectedness (globality), and pandemics

Mayurika Chakravorty at Carleton University (Department of English) in Ottawa, (Ontario, Canada) points out that the latest pandemic (COVID-19) is an example of how everything is connected (interconnectedness or globality) by way of science fiction in her July 19, 2020 essay on The Conversation (h/t July 20, 2020 item on phys.org), Note: Links have been removed,

In the early days of the coronavirus outbreak, a theory widely shared on social media suggested that a science fiction text, Dean Koontz’s 1981 science fiction novel, The Eyes of Darkness, had predicted the coronavirus pandemic with uncanny precision. COVID-19 has held the entire world hostage, producing a resemblance to the post-apocalyptic world depicted in many science fiction texts. Canadian author Margaret Atwood’s classic 2003 novel Oryx and Crake refers to a time when “there was a lot of dismay out there, and not enough ambulances” — a prediction of our current predicament.

However, the connection between science fiction and pandemics runs deeper. They are linked by a perception of globality, what sociologist Roland Robertson defines as “the consciousness of the world as a whole.”

Chakravorty goes on to make a compelling case (from her July 19, 2020 essay Note: Links have been removed),

In his 1992 survey of the history of telecommunications, How the World Was One, Arthur C. Clarke alludes to the famed historian Alfred Toynbee’s lecture entitled “The Unification of the World.” Delivered at the University of London in 1947, Toynbee envisions a “single planetary society” and notes how “despite all the linguistic, religious and cultural barriers that still sunder nations and divide them into yet smaller tribes, the unification of the world has passed the point of no return.”

Science fiction writers have, indeed, always embraced globality. In interplanetary texts, humans of all nations, races and genders have to come together as one people in the face of alien invasions. Facing an interplanetary encounter, bellicose nations have to reluctantly eschew political rivalries and collaborate on a global scale, as in Denis Villeneuve’s 2018 film, Arrival.

Globality is central to science fiction. To be identified as an Earthling, one has to transcend the local and the national, and sometimes, even the global, by embracing a larger planetary consciousness.

In The Left Hand of Darkness, Ursula K. Le Guin conceptualizes the Ekumen, which comprises 83 habitable planets. The idea of the Ekumen was borrowed from Le Guin’s father, the noted cultural anthropologist Arthur L. Kroeber. Kroeber had, in a 1945 paper, introduced the concept (from Greek oikoumene) to represent a “historic culture aggregate.” Originally, Kroeber used oikoumene to refer to the “entire inhabited world,” as he traced back human culture to one single people. Le Guin then adopted this idea of a common origin of shared humanity in her novel.

..,

Regarding Canada’s response to the crisis [COVID-19], researchers have noted both the immorality and futility of a nationalistic “Canada First” approach.

If you have time, I recommend reading Chakravorty’s July 19, 2020 essay in its entirety.

Gold nanoparticles could help detect the presence of COVID-19 in ten minutes

If this works out, it would make testing for COVID-19 an infinitely easier task. From a May 29, 2020 news item on phys.org,

Scientists from the University of Maryland School of Medicine (UMSOM) developed an experimental diagnostic test for COVID-19 that can visually detect the presence of the virus in 10 minutes. It uses a simple assay containing plasmonic gold nanoparticles to detect a color change when the virus is present. The test does not require the use of any advanced laboratory techniques, such as those commonly used to amplify DNA, for analysis. The authors published their work last week [May 21, 2020] in the American Chemical Society’s nanotechnology journal ACS Nano.

“Based on our preliminary results, we believe this promising new test may detect RNA [ribonucleic acid] material from the virus as early as the first day of infection. Additional studies are needed, however, to confirm whether this is indeed the case,” said study leader Dipanjan Pan, PhD, Professor of Diagnostic Radiology and Nuclear Medicine and Pediatrics at the UMSOM.

Caption: A nasal swab containing a test sample is mixed with a simple lab test. It contains a liquid mixed with gold nanoparticles attached to a molecule that binds to the novel coronavirus. If the virus is present, the gold nanoparticles turns the solution a deep blue color (bottom of the tube) and a precipitation is noticed. If it is not present, the solution retains its original purple color. Credit: University of Maryland School of Medicine

A May 28, 2020 University of Maryland news release (also on EurekAlert), which originated the news item, provides more detail,

Once a nasal swab or saliva sample is obtained from a patient, the RNA is extracted from the sample via a simple process that takes about 10 minutes. The test uses a highly specific molecule attached to the gold nanoparticles to detect a particular protein. This protein is part of the genetic sequence that is unique to the novel coronavirus. When the biosensor binds to the virus’s gene sequence, the gold nanoparticles respond by turning the liquid reagent from purple to blue.

“The accuracy of any COVID-19 test is based on being able to reliably detect any virus. This means it does not give a false negative result if the virus actually is present, nor a false positive result if the virus is not present,” said Dr. Pan. “Many of the diagnostic tests currently on the market cannot detect the virus until several days after infection. For this reason, they have a significant rate of false negative results.”

Dr. Pan created a company called VitruVian Bio to develop the test for commercial application. He plans to have a pre-submission meeting with the U.S. Food and Drug Administration (FDA) within the next month to discuss requirements for getting an emergency use authorization for the test. New FDA policy allows for the marketing of COVID-19 tests without requiring them to go through the usual approval or clearance process. These tests do, however, need to meet certain validation testing requirements to ensure that they provide reliable results.

“This RNA-based test appears to be very promising in terms of detecting the virus. The innovative approach provides results without the need for a sophisticated laboratory facility,” said study co-author Matthew Frieman, PhD, Associate Professor of Microbiology and Immunology at UMSOM.

Although more clinical studies are warranted, this test could be far less expensive to produce and process than a standard COVID-19 lab test; it does not require laboratory equipment or trained personnel to run the test and analyze the results. If this new test meets FDA expectations, it could potentially be used in daycare centers, nursing homes, college campuses, and work places as a surveillance technique to monitor any resurgence of infections.

In Dr. Pan’s laboratory, research scientist Parikshit Moitra, PhD, and UMSOM research fellow Maha Alafeef conducted the studies along with research fellow Ketan Dighe from UMBC.

Dr. Pan holds a joint appointment with the College of Engineering at the University of Maryland Baltimore County and is also a faculty member of the Center for Blood Oxygen Transport and Hemostasis (CBOTH).

“This is another example of how our faculty is driving innovation to fulfill a vital need to expand the capacity of COVID-19 testing,” said Dean E. Albert Reece, MD, PhD, MBA, who is also Executive Vice President for Medical Affairs, UM Baltimore, and the John Z. and Akiko K. Bowers Distinguished Professor, University of Maryland School of Medicine. “Our nation will be relying on inexpensive, rapid tests that can be dispersed widely and used often until we have effective vaccines against this pandemic.”

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

Selective Naked-Eye Detection of SARS-CoV-2 Mediated by N Gene Targeted Antisense Oligonucleotide Capped Plasmonic Nanoparticles by Parikshit Moitra, Maha Alafeef, Ketan Dighe, Matthew B. Frieman, and Dipanjan Pan. ACS Nano 2020, XXXX, XXX, XXX-XXX DOI: https://doi.org/10.1021/acsnano.0c03822 Publication Date:May 21, 2020 Copyright © 2020 American Chemical Society

This paper appears to be open access.

I tried to find Dr. Pan’s company, VitruVian Bio and found a business with an almost identical name, Vitruvian Biomedical, which does not include Dr. Pan on its management team list and this company’s focus is on Alzheimer’s Disease. Finally, there is no mention of the COVID-19 test anywhere on the Vitruvian Biomedical website.

US Food and Drug Administration (FDA) gives first authorization for CRISPR (clustered regularly interspersed short palindromic repeats) use in COVID-19 crisis

Clustered regularly interspersed short palindromic repeats (CRISPR) gene editing has been largely confined to laboratory use or tested in agricultural trials. I believe that is true worldwide excepting the CRISPR twin scandal. (There are numerous postings about the CRISPR twins here including a Nov. 28, 2018 post, a May 17, 2019 post, and a June 20, 2019 post. Update: It was reported (3rd. para.) in December 2019 that He had been sentenced to three years jail time.)

Connie Lin in a May 7, 2020 article for Fast Company reports on this surprising decision by the US Food and Drug Administration (FDA), Note: A link has been removed),

The U.S. Food and Drug Administration has granted Emergency Use Authorization to a COVID-19 test that uses controversial gene-editing technology CRISPR.

This marks the first time CRISPR has been authorized by the FDA, although only for the purpose of detecting the coronavirus, and not for its far more contentious applications. The new test kit, developed by Cambridge, Massachusetts-based Sherlock Biosciences, will be deployed in laboratories certified to carry out high-complexity procedures and is “rapid,” returning results in about an hour as opposed to those that rely on the standard polymerase chain reaction method, which typically requires six hours.

The announcement was made in the FDA’s Coronavirus (COVID-19) Update: May 7, 2020 Daily Roundup (4th item in the bulleted list), Or, you can read the May 6, 2020 letter (PDF) sent to John Vozella of Sherlock Biosciences by the FDA.

As well, there’s the May 7, 2020 Sherlock BioSciences news release (the most informative of the lot),

Sherlock Biosciences, an Engineering Biology company dedicated to making diagnostic testing better, faster and more affordable, today announced the company has received Emergency Use Authorization (EUA) from the U.S. Food and Drug Administration (FDA) for its Sherlock™ CRISPR SARS-CoV-2 kit for the detection of the virus that causes COVID-19, providing results in approximately one hour.

“While it has only been a little over a year since the launch of Sherlock Biosciences, today we have made history with the very first FDA-authorized use of CRISPR technology, which will be used to rapidly identify the virus that causes COVID-19,” said Rahul Dhanda, co-founder, president and CEO of Sherlock Biosciences. “We are committed to providing this initial wave of testing kits to physicians, laboratory experts and researchers worldwide to enable them to assist frontline workers leading the charge against this pandemic.”

The Sherlock™ CRISPR SARS-CoV-2 test kit is designed for use in laboratories certified under the Clinical Laboratory Improvement Amendments of 1988 (CLIA), 42 U.S.C. §263a, to perform high complexity tests. Based on the SHERLOCK method, which stands for Specific High-sensitivity Enzymatic Reporter unLOCKing, the kit works by programming a CRISPR molecule to detect the presence of a specific genetic signature – in this case, the genetic signature for SARS-CoV-2 – in a nasal swab, nasopharyngeal swab, oropharyngeal swab or bronchoalveolar lavage (BAL) specimen. When the signature is found, the CRISPR enzyme is activated and releases a detectable signal. In addition to SHERLOCK, the company is also developing its INSPECTR™ platform to create an instrument-free, handheld test – similar to that of an at-home pregnancy test – that utilizes Sherlock Biosciences’ Synthetic Biology platform to provide rapid detection of a genetic match of the SARS-CoV-2 virus.

“When our lab collaborated with Dr. Feng Zhang’s team to develop SHERLOCK, we believed that this CRISPR-based diagnostic method would have a significant impact on global health,” said James J. Collins, co-founder and board member of Sherlock Biosciences and Termeer Professor of Medical Engineering and Science for MIT’s Institute for Medical Engineering and Science (IMES) and Department of Biological Engineering. “During what is a major healthcare crisis across the globe, we are heartened that the first FDA-authorized use of CRISPR will aid in the fight against this global COVID-19 pandemic.”

Access to rapid diagnostics is critical for combating this pandemic and is a primary focus for Sherlock Biosciences co-founder and board member, David R. Walt, Ph.D., who co-leads the Mass [Massachusetts] General Brigham Center for COVID Innovation.

“SHERLOCK enables rapid identification of a single alteration in a DNA or RNA sequence in a single molecule,” said Dr. Walt. “That precision, coupled with its capability to be deployed to multiplex over 100 targets or as a simple point-of-care system, will make it a critical addition to the arsenal of rapid diagnostics already being used to detect COVID-19.”

This development is particularly interesting since there was a major intellectual property dispute over CRISPR between the Broad Institute (a Harvard University and Massachusetts Institute of Technology [MIT] joint initiative), and the University of California at Berkeley (UC Berkeley). The Broad Institute mostly won in the first round of the patent fight, as I noted in a March 15, 2017 post but, as far as I’m aware, UC Berkeley is still disputing that decision.

In the period before receiving authorization, it appears that Sherlock Biosciences was doing a little public relations and ‘consciousness raising’ work. Here’s a sample from a May 5, 2020 article by Sharon Begley for STAT (Note: Links have been removed),

The revolutionary genetic technique better known for its potential to cure thousands of inherited diseases could also solve the challenge of Covid-19 diagnostic testing, scientists announced on Tuesday. A team headed by biologist Feng Zhang of the McGovern Institute at MIT and the Broad Institute has repurposed the genome-editing tool CRISPR into a test able to quickly detect as few as 100 coronavirus particles in a swab or saliva sample.

Crucially, the technique, dubbed a “one pot” protocol, works in a single test tube and does not require the many specialty chemicals, or reagents, whose shortage has hampered the rollout of widespread Covid-19 testing in the U.S. It takes about an hour to get results, requires minimal handling, and in preliminary studies has been highly accurate, Zhang told STAT. He and his colleagues, led by the McGovern’s Jonathan Gootenberg and Omar Abudayyeh, released the protocol on their STOPCovid.science website.

Because the test has not been approved by the Food and Drug Administration, it is only for research purposes for now. But minutes before speaking to STAT on Monday, Zhang and his colleagues were on a conference call with FDA officials about what they needed to do to receive an “emergency use authorization” that would allow clinical use of the test. The FDA has used EUAs to fast-track Covid-19 diagnostics as well as experimental therapies, including remdesivir, after less extensive testing than usually required.

For an EUA, the agency will require the scientists to validate the test, which they call STOPCovid, on dozens to hundreds of samples. Although “it is still early in the process,” Zhang said, he and his colleagues are confident enough in its accuracy that they are conferring with potential commercial partners who could turn the test into a cartridge-like device, similar to a pregnancy test, enabling Covid-19 testing at doctor offices and other point-of-care sites.

“It could potentially even be used at home or at workplaces,” Zhang said. “It’s inexpensive, does not require a lab, and can return results within an hour using a paper strip, not unlike a pregnancy test. This helps address the urgent need for widespread, accurate, inexpensive, and accessible Covid-19 testing.” Public health experts say the availability of such a test is one of the keys to safely reopening society, which will require widespread testing, and then tracing and possibly isolating the contacts of those who test positive.

If you have time, do read Begley’s in full.

COVID-19 editorial (in response to Canadian Science Policy Centre call for submissions)

I successfully submitted an editorial to the Canadian Science Policy Centre (CSPC). You can find it and a host of others on the CSPC Editorial Series: Response to COVID-19 Pandemic and its Impacts webpage (scroll down under Policy Development) or in the CSPC Featured Editorial Series Volume 1, Issue 2, May 2020 PDF on pp. 31-2.

What I’ve posted here is the piece followed by attribution for the artwork used to illustrate my op-ed in the PDF version of essays and by links to all of my reference materials.

It can become overwhelming as one looks at the images of coffins laid out in various venues, listens to exhausted health care professionals, and sees body bags being loaded onto vans while reading stories about the people who have been hospitalized and/or have died.

In this sea of information, it’s easy to forget that COVID-19 is one in a long history of pandemics. For the sake of brevity, here’s a mostly complete roundup of the last 100 years. The H1N1 pandemic of 1918/19 resulted in either 17 million, 50 million, or 100 million deaths depending on the source of information. The H2N2 pandemic of 1958/59 resulted in approximately 1.1. million deaths; the H3N2 pandemic of 1968/69 resulted in somewhere from 1 to 4 million deaths; and the H1N1pdm09 pandemic of 2009 resulted in roughly 150,000 -575,000 deaths. The HIV/AIDS global pandemic or, depending on the agency, epidemic is ongoing. The estimate for HIVAIDS-related deaths in 2018 alone was between 500,000 – 1.1 million.

It’s now clear that the 2019/20 pandemic will take upwards of 350,000 lives and, quite possibly, many more lives before it has run its course.

On the face of it, the numbers for COVID-19 would not seem to occasion the current massive attempt at physical isolation which ranges across the globe and within entire countries. There is no record of any such previous, more or less global effort. In the past, physical isolation seems to have been practiced on a more localized level.

We are told the current policy ‘flattening the curve’ is an attempt to constrain the numbers so as to lighten the burden on the health care system, i.e. the primary focus being to lessen the number of people needing care at any one time and also lessening the number of deaths and hospitalizations

It’s an idea that can be traced back in more recent times to the 1918/19 pandemic (and stretches back to at least the 17th century when as a student Isaac Newton was sent home from Cambridge to self-isolate from the Great Plague of London).

During the 1918/19 pandemic, Philadelphia and St. Louis, in the US had vastly different experiences. Ignoring advice from infectious disease experts, Philadelphia held a large public parade. Within two or three days, people sickened and, ultimately, 16,000 died in six months. By contrast, St. Louis adopted social and physical isolation measures suffering 2,000 deaths and flattening the curve. (That city too suffered greatly but more slowly.)

In 2019/20, many governments were slow to respond and many have been harshly criticized for their tardiness. Government leaders seem to have been following an older script, something more laissez-faire, something similar to the one we have followed with past pandemics.

We are breaking new ground by following a policy that is untested at this scale.

Viewed positively, the policy hints at a shift in how we view disease and death and hopes are that this heralds a more cohesive and integrated approach to all life on this planet. Viewed more negatively, it suggests an agenda of social control being enacted and promoted to varying degrees across the planet.

Regardless of your perspective, ‘flattening the curve’ seems to have been employed without any substantive consideration of collateral damages and unintended consequences

We are beginning to understand some of the consequences. On April 5, 2020, UN Secretary-General Antonio Guterres expressed grave concern about a global surge in domestic violence. King’s College London and the Australian National University released a report on April 9, 2020 estimating that half a billion people around the world may be pushed into poverty because of these measures.

As well, access to water, which many of us take for granted, can be highly problematic. Homeless people, incarcerated people, indigenous peoples and others note that washing with water and soap, the recommended practice for killing the virus should it land on you, is not a simple matter for them.

More crises such as pandemics, climate change as seen in extreme weather events and water shortages along with rising sea levels around the world, and economic downturns either singly or connected together in ways we have difficulty fully appreciating can be anticipated.

In addition to engaging experts as we navigate our way into the future, we can look to artists, writers, citizen scientists, elders, indigenous communities, rural and urban communities, politicians, philosophers, ethicists, religious leaders, and bureaucrats of all stripes for more insight into the potential for collateral and unintended consequences.

We have the tools what remains is the will and the wit to use them. Brute force analysis has its uses but it’s also important to pay attention to the outliers. “We cannot solve our problems with the same thinking we used when we created them.” (Albert Einstein)

PDF of essays (Response to COVID-19 Pandemic and its Impacts, volume 1, issue 2, May 20202)

Low-resolution detail of an art work by Samuel Monnier. Inspired by the w:Fibonacci word fractal. Orginal owned by Alexis Monnerot-Dumaine. CC BY-SA 3.0

This image of an art piece derived from a Fibonacci word fractal was used to illustrate my essay (pp. 31-2) as reproduced in the PDF only.

For anyone unfamiliar with Fibonacci words (from its Wikipedia entry), Note: Links have been removed,

A Fibonacci word is a specific sequence of binary digits (or symbols from any two-letter alphabet). The Fibonacci word is formed by repeated concatenation in the same way that the Fibonacci numbers are formed by repeated addition.

It is a paradigmatic example of a Sturmian word and specifically, a morphic word.

The name “Fibonacci word” has also been used to refer to the members of a formal language L consisting of strings of zeros and ones with no two repeated ones. Any prefix of the specific Fibonacci word belongs to L, but so do many other strings. L has a Fibonacci number of members of each possible length.

References used for op-ed

That opinion piece was roughly 787 words and as such fit into the 600-800 words submission guideline. It’s been a long time since I’ve written something without links and supporting information. What follows are the supporting sources I used for my statements. (Note: i have also included a few pieces that were published after my op-ed was submitted on April 20, 2020 as they lend further support for some of my contentions.)

Statistics for previous pandemics

https://en.wikipedia.org/wiki/Spanish_flu For 1918/19 numbers see: Mortality; Around the globe, 2nd. para

https://en.wikipedia.org/wiki/2009_swine_flu_pandemic

https://www.mphonline.org/worst-pandemics-in-history/

https://en.wikipedia.org/wiki/List_of_epidemics

https://www.who.int/gho/hiv/epidemic_status/deaths_text/en/

https://www.avert.org/global-hiv-and-aids-statistics

https://vancouversun.com/news/local-news/how-long-is-covid-19-pandemic-going-to-last-what-will-spread-look-like/ The print version of this article by Gordon Hoekstra featured a sidebar with statistics from the Imperial College of London, US Centers for Disease Control, and The Canadian Encyclopedia. Sadly, it has not been reproduced for the online version.

Statistics supporting my projections

https://www.covid-19canada.com/ This is a Canadian site relying on information from the Canadian federal government, Johns Hopkins University (US) and the World Health Organization (WHO) as well as others.

https://www.worldometers.info/coronavirus/ The focus is international with information being supplied by WHO and by various nations.

History of physical and social isolation and ‘flattening the curve’

https://www.washingtonpost.com/history/2020/03/12/during-pandemic-isaac-newton-had-work-home-too-he-used-time-wisely/

https://history.com/news/spanish-flu-pandemic-response-cities

https://www.livescience.com/coronavirus-flatten-the-curve.html What does flattening the curve mean? The writer provides an answer.

Slow response and harsh criticism (e.g., Canada)

https://www.cbc.ca/news/politics/covid-19-government-documents-1.5528726

https://www.cbc.ca/news/politics/coronavirus-pandemic-covid-canadian-military-intelligence-wuhan-1.5528381

https://vancouversun.com/opinion/columnists/douglas-todd-weighing-deaths-from-covid-19-against-deaths-from-despair/

Laissez-faire script

https://slate.com/news-and-politics/2020/04/sweden-coronavirus-response-death-social-distancing.html Essay by ex-pat Swede returning home. Ranges from pointed criticism to strong doubt mixed with hope (at the end) about laissez-faire.

Positive and negative views of the ‘flatten the curve’ policy

https://phys.org/news/2020-04-french-philosopher-virus-exploitation.html A French philosopher, Bernard-Henri Levy, suggests the policy reflects two views “life has become sacred” and the [information system] “helps to bring hysteria to the perception of things … . “

https://business.financialpost.com/diane-francis/diane-francis-to-beat-this-coronavirus-we-must-sacrifice-our-freedoms “To beat this coronavirus, we must sacrifice our freedoms” presents arguments for more control over what people do and don’t do. I find it unpleasantly extreme but Diane Francis supports her contentions with some valid points.

Unintended consequences (the good and the bad)

https://www.voanews.com/covid-19-pandemic/cleaner-air-covid-19-lockdowns-may-save-lives Cleaner air.

https://news.itu.int/sharing-best-practices-on-digital-cooperation-during-covid19-and-beyond/ “I think what COVID has done, is actually to put the will to get the world connected right in front of us – and we rallied around that will,” said Doreen Bogdan-Martin, Director of ITU’s Telecommunication Development Bureau. “We have come together in these very difficult circumstances and we have come up with innovative practices to actually better connect people who actually weren’t connected before.”

https://en.unesco.org/news/unesco-mobilizes-122-countries-promote-open-science-and-reinforced-cooperation-face-covid-19 Open science and more cooperation

https://www.aljazeera.com/news/2020/04/global-surge-domestic-violence-coronavirus-lockdowns-200406065737864.html International rise in domestic violence

https://news.un.org/en/story/2020/04/1061052 International rise in domestic violence

https://www.anu.edu.au/news/all-news/covid-19-to-push-half-a-billion-people-into-poverty Increase in poverty worldwide Australian National University press release

https://www.kcl.ac.uk/news/half-a-billion-people-could-be-pushed-into-poverty-by-covid-19 Increase in poverty worldwide Kings College London press release

https://www.wider.unu.edu/publication/estimates-impact-covid-19-global-poverty Rise in poverty worldwide UN working paper

https://www.techdirt.com/articles/20200422/11395644353/unesco-suggests-covid-19-is-reason-to-create-eternal-copyright.shtml Taking advantage of the situation

https://phys.org/news/2020-04-climate-scientists-world-response-coronavirus.html COVID-19 might prove helpful with climate change

ETC.

You might not want to keep getting advice from your usual (expert) crew only

https://www.frogheart.ca/?p=638 Kevin Dunbar’s research into how problem-solving is improved when you get a more diverse set of experts than usual

https://www.theatlantic.com/magazine/archive/2020/04/the-perks-of-being-a-weirdo/606778/?utm_source=pocket-newtab How loners and weirdos (often found amongst writers, artists, etc.) can promote more creative problem-solving

Brute force analysis and tools for broader consultation

I came up with the term ‘brute force analysis’ after an experience in local participatory budgeting. (For those who don’t know, there’s a movement afoot for a government body [in this case, it was the City of Vancouver] to dedicate a portion of their budget to a community [in this case, it was the West End neighbourhood] for citizens to decide on how the allocation should be sent.)

In our case, volunteers had gone out out and solicited ideas for how neighbourhood residents would like to see the money spent. The ideas were categorized and a call for volunteers to work on committees went out. I ended up on the ‘arts and culture’ committee and we were tasked with taking some 300 – 400 suggestions and establishing a list of 10 – 12 possibilities for more discussion and research after which we were to present three or four to city staff who would select a maximum of two suggestions for a community vote.

Our deadlines, many of which seemed artificially imposed, were tight and we had to be quite ruthless as we winnowed away the suggestions. It became an exercise in determining which were the most frequently made suggestions, hence, ‘brute force analysis’. (This a condensed description of the process.)

As for tools to encourage wider participation, I was thinking of something like ‘Foldit‘ (scroll down to ‘Folding …’.). Both a research project (University of Washington) and a video puzzle game for participants who want to try protein-folding, it’s a remarkable effort first described in my August 6, 2010 posting when the researchers had their work published in Nature with an astonishing 50,000 co-authors.

Albert Einstein

The quote, “We cannot solve our problems with the same thinking we used when we created them,” is attributed to Albert Einstein in many places but I have not been able to find any supporting references or documentation.

The decade that was (2010-19) and the decade to come (2020-29): Science culture in Canada (5 of 5)

At long last, the end is in sight! This last part is mostly a collection of items that don’t fit elsewhere or could have fit elsewhere but that particular part was already overstuffed.

Podcasting science for the people

March 2009 was the birth date for a podcast, then called Skeptically Speaking and now known as Science for the People (Wikipedia entry). Here’s more from the Science for the People About webpage,

Science for the People is a long-format interview podcast that explores the connections between science, popular culture, history, and public policy, to help listeners understand the evidence and arguments behind what’s in the news and on the shelves.

Every week, our hosts sit down with science researchers, writers, authors, journalists, and experts to discuss science from the past, the science that affects our lives today, and how science might change our future.

THE TEAM

Rachelle Saunders: Producer & Host

I love to learn new things, and say the word “fascinating” way too much. I like to talk about intersections and how science and critical thinking intersect with everyday life, politics, history, and culture. By day I’m a web developer, and I definitely listen to way too many podcasts.

….

H/t to GeekWrapped’s 20 Best Science Podcasts.

Science: human contexts and cosmopolitanism

situating science: Science in Human Contexts was a seven-year project ending in 2014 and funded by the Social Sciences and Humanities Research Council of Canada (SSHRC). Here’s more from their Project Summary webpage,

Created in 2007 with the generous funding of the Social Sciences and Humanities Research Council of Canada Strategic Knowledge Cluster grant, Situating Science is a seven-year project promoting communication and collaboration among humanists and social scientists that are engaged in the study of science and technology.

You can find out more about Situating Science’s final days in my August 16, 2013 posting where I included a lot of information about one of their last events titled, “Science and Society 2013 Symposium; Emerging Agendas for Citizens and the Sciences.”

The “think-tank” will dovetail nicely with a special symposium in Ottawa on Science and Society Oct. 21-23. For this symposium, the Cluster is partnering with the Institute for Science, Society and Policy to bring together scholars from various disciplines, public servants and policy workers to discuss key issues at the intersection of science and society. [emphasis mine]  The discussions will be compiled in a document to be shared with stakeholders and the wider public.

The team will continue to seek support and partnerships for projects within the scope of its objectives. Among our top priorities are a partnership to explore sciences, technologies and their publics as well as new partnerships to build upon exchanges between scholars and institutions in India, Singapore and Canada.

The Situating Science folks did attempt to carry on the organization’s work by rebranding the organization to call it the Canadian Consortium for Situating Science and Technology (CCSST). It seems to have been a short-lived volunteer effort.

Meanwhile, the special symposium held in October 2013 appears to have been the springboard for another SSHRC funded multi-year initiative, this time focused on science collaborations between Canada, India, and Singapore, Cosmopolitanism and the Local in Science and Nature from 2014 – 2017. Despite their sunset year having been in 2017, their homepage boasts news about a 2020 Congress and their Twitter feed is still active. Harking back, here’s what the project was designed to do, from the About Us page,

Welcome to our three year project that will establish a research network on “Cosmopolitanism” in science. It closely examines the actual types of negotiations that go into the making of science and its culture within an increasingly globalized landscape. This partnership is both about “cosmopolitanism and the local” and is, at the same time, cosmopolitan and local.

Anyone who reads this blog with any frequency will know that I often comment on the fact that when organizations such as the Council of Canadian Academies bring in experts from other parts of the world, they are almost always from the US or Europe. So, I was delighted to discover the Cosmopolitanism project and featured it in a February 19, 2015 posting.

Here’s more from Cosmopolitanism’s About Us page

Specifically, the project will:

  1. Expose a hitherto largely Eurocentric scholarly community in Canada to widening international perspectives and methods,
  2. Build on past successes at border-crossings and exchanges between the participants,
  3. Facilitate a much needed nation-wide organization and exchange amongst Indian and South East Asian scholars, in concert with their Canadian counterparts, by integrating into an international network,
  4. Open up new perspectives on the genesis and place of globalized science, and thereby
  5. Offer alternative ways to conceptualize and engage globalization itself, and especially the globalization of knowledge and science.
  6. Bring the managerial team together for joint discussion, research exchange, leveraging and planning – all in the aid of laying the grounds of a sustainable partnership

Eco Art (also known as ecological art or environmental art)

I’m of two minds as to whether I should have tried to stuff this into the art/sci subsection in part 2. On balance, I decided that this merited its own section and that part 2 was already overstuffed.

Let’s start in Newfoundland and Labrador with Marlene Creates (pronounced Kreets), here’s more about her from her website’s bio webpage,

Marlene Creates (pronounced “Kreets”) is an environmental artist and poet who works with photography, video, scientific and vernacular knowledge, walking and collaborative site-specific performance in the six-acre patch of boreal forest in Portugal Cove, Newfoundland and Labrador, Canada, where she lives.

For almost 40 years her work has been an exploration of the relationship between human experience, memory, language and the land, and the impact they have on each other. …

Currently her work is focused on the six acres of boreal forest where she lives in a ‘relational aesthetic’ to the land. This oeuvre includes Water Flowing to the Sea Captured at the Speed of Light, Blast Hole Pond River, Newfoundland 2002–2003, and several ongoing projects:

Marlene Creates received a Governor General’s Award in Visual and Media Arts for “Lifetime Artistic Achievement” in 2019. …

As mentioned in her bio, Creates has a ‘forest’ project. The Boreal Poetry Garden,
Portugal Cove, Newfoundland 2005– (ongoing)
. If you are interested in exploring it, she has created a virtual walk here. Just click on one of the index items on the right side of the screen to activate a video.

An October 1, 2018 article by Yasmin Nurming-Por for Canadian Art magazine features 10 artists who focus on environmental and/or land art themes,

As part of her 2016 master’s thesis exhibition, Fredericton [New Brunswick] artist Gillian Dykeman presented the video Dispatches from the Feminist Utopian Future within a larger installation that imagined various canonical earthworks from the perspective of the future. It’s a project that addresses the inherent sense of timelessness in these massive interventions on the natural landscape from the perspective of contemporary land politics. … she proposes a kind of interaction with the invasive and often colonial gestures of modernist Land art, one that imagines a different future for these earthworks, where they are treated as alien in a landscape and as beacons from a feminist future.

A video trailer featuring “DISPATCHES FROM THE FEMINIST UTOPIAN FUTURE” (from Dykeman’s website archive page featuring the show,

If you have the time, I recommend reading the article in its entirety.

Oddly, I did not expect Vancouver to have such an active eco arts focus. The City of Vancouver Parks Board maintains an Environmental Art webpage on its site listing a number of current and past projects.

I cannot find the date for when this Parks Board initiative started but I did find a document produced prior to a Spring 2006 Arts & Ecology think tank held in Vancouver under the auspices of the Canada Council for the Arts, the Canadian Commission for UNESCO, the Vancouver Foundation, and the Royal Society for the Encouragement of the Arts, Manufactures and Commerce (London UK).

In all likelihood, Vancouver Park Board’s Environmental Art webpage was produced after 2006.

I imagine the document and the think tank session helped to anchor any then current eco art projects and encouraged more projects.

The document (MAPPING THE TERRAIN OF CONTEMPORARY ECOART PRACTICE AND COLLABORATION) while almost 14 years old offers a fascinating overview of what was happening internationally and in Canada.

While its early days were in 2008, EartHand Gleaners (Vancouver-based) wasn’t formally founded as an arts non-for-profit organization until 2013. You can find out more about them and their projects here.

Eco Art has been around for decades according to the eco art think tank document but it does seemed to have gained momentum here in Canada over the last decade.

Photography and the Natural Sciences and Engineering Research Council of Canada (NSERC)

Exploring the jack pine tight knit family tree. Credit: Dana Harris Brock University (2018)

Pictured are developing phloem, cambial, and xylem cells (blue), and mature xylem cells (red), in the outermost portion of a jack pine tree. This research aims to identify the influences of climate on the cellular development of the species at its northern limit in Yellowknife, NT. The differences in these cell formations is what creates the annual tree ring boundary.

Science Exposed is a photography contest for scientists which has been run since 2016 (assuming the Past Winners archive is a good indicator for the programme’s starting year).

The 2020 competition recently closed but public voting should start soon. It’s nice to see that NSERC is now making efforts to engage members of the general public rather than focusing its efforts solely on children. The UK’s ASPIRES project seems to support the idea that adults need to be more fully engaged with STEM (science, technology, engineering, and mathematics) efforts as it found that children’s attitudes toward science are strongly influenced by their parents’ and relatives’ attitudes.(See my January 31, 2012 posting.)

Ingenious, the book and Ingenium, the science museums

To celebrate Canada’s 150th anniversary in 2017, then Governor General David Johnston and Tom Jenkins (Chair of the board for Open Text and former Chair of the federal committee overseeing the ‘Review of Federal Support to R&’D [see my October 21, 2011 posting about the resulting report]) wrote a boo about Canada’s inventors and inventions.

Johnston and Jenkins jaunted around the country launching their book (I have more about their June 1, 2017 Vancouver visit in a May 30, 2017 posting; scroll down about 60% of the way]).

The book’s full title, “Ingenious: How Canadian Innovators Made the World Smarter, Smaller, Kinder, Safer, Healthier, Wealthier and Happier ” outlines their thesis neatly.

Not all that long after the book was launched, there was a name change (thankfully) for the Canada Science and Technology Museums Corporation (CSTMC). It is now known as Ingenium (covered in my August 10, 2017 posting).

The reason that name change was such a relief (for those who don’t know) is that the corporation included three national science museums: Canada Aviation and Space Museum, Canada Agriculture and Food Museum, and (wait for it) Canada Science and Technology Museum. On the list of confusing names, this ranks very high for me. Again, I give thanks for the change from CSTMC to Ingenium, leaving the name for the museum alone.

2017 was also the year that the newly refurbished Canada Science and Technology Museum was reopened after more than three years (see my June 23, 2017 posting about the November 2017 reopening and my June 12, 2015 posting for more information about the situation that led to the closure).

A Saskatchewan lab, Convergence, Order of Canada, Year of Science, Animated Mathematics, a graphic novel, and new media

Since this section is jampacked, I’m using subheads.

Saskatchewan

Dr. Brian Eames hosts an artist-in-residence, Jean-Sebastien (JS) Gauthier at the University of Saskatchewan’s College of Medicine Eames Lab. A February 16, 2018 posting here featured their first collaboration together. It covered evolutionary biology, the synchrotron (Canadian Light Source [CLS]) in Saskatoon, and the ‘ins and outs’ of a collaboration between a scientist an artist. Presumably the art-in-residence position indicates that first collaboration went very well.

In January 2020, Brian kindly gave me an update on their current projects. Jean-Sebastin successfully coded an interactive piece for an exhibit at the 2019 Nuit Blanche Saskatoon event using Connect (Xbox). More recently, he got a VR [virtual reality] helmet for an upcoming project or two.

After much clicking on the Nuit Blanche Saskatoon 2019 interactive map, I found this,

Our Glass is a work of interactive SciArt co-created by artist JS Gauthier and biologist Dr Brian F. Eames. It uses cutting-edge 3D microscopic images produced for artistic purposes at the Canadian Light Source, Canada’s only synchrotron facility. Our Glass engages viewers of all ages to peer within an hourglass showing how embryonic development compares among animals with whom we share a close genetic heritage.

Eames also mentioned they were hoping to hold an international SciArt Symposium at the University of Saskatchewan in 2021.

Convergence

Dr. Cristian Zaelzer-Perez, an instructor at Concordia University (Montreal; read this November 20, 2019 Concordia news release by Kelsey Rolfe for more about his work and awards), in 2016 founded the Convergence Initiative, a not-for-profit organization that encourages interdisciplinary neuroscience and art collaborations.

Cat Lau’s December 23, 2019 posting for the Science Borealis blog provides insight into Zaelzer-Perez’s relationship to science and art,

Cristian: I have had a relationship with art and science ever since I have had memory. As a child, I loved to do classifications, from grouping different flowers to collecting leaves by their shapes. At the same time, I really loved to draw them and for me, both things never looked different; they (art and science) have always worked together.

I started as a graphic designer, but the pursuit to learn about nature was never dead. At some point, I knew I wanted to go back to school to do research, to explore and learn new things. I started studying medical technologies, then molecular biology and then jumped into a PhD. At that point, my life as a graphic designer slipped down, because of the focus you have to give to the discipline. It seemed like every time I tried to dedicate myself to one thing, I would find myself doing the other thing a couple years later.

I came to Montreal to do my post-doc, but I had trouble publishing, which became problematic in getting a career. I was still loving what I was doing, but not seeing a future in that. Once again, art came back into my life and at the same time I saw that science was becoming really hard to understand and scientists were not doing much to bridge the gap.

The Convergence Initiative has an impressive array of programmes. Do check it out.

Order of Canada and ‘The Science Lady’

For a writer of children’s science books, an appointment to the Order of Canada is a singular honour. I cannot recall a children’s science book writer previous to Shar Levine being appointed as a Member of the Order of Canada. Known as ‘The Science Lady‘, Levine was appointed in 2016. Here’s more from her Wikipedia entry, Note: Links have been removed,

Shar Levine (born 1953) is an award-winning, best selling Canadian children’s author, and designer.

Shar has written over 70 books and book/kits, primarily on hands-on science for children. For her work in Science literacy and Science promotion, Shar has been appointed to the 2016 Order of Canada. In 2015, she was recognized by the University of Alberta and received their Alumni Honour Award. Levine, and her co-author, Leslie Johnstone, were co-recipients of the Eve Savory Award for Science Communication from the BC Innovation Council (2006) and their book, Backyard Science, was a finalist for the Subaru Award, (hands on activity) from the American Association for the Advancement of Science, Science Books and Films (2005). The Ultimate Guide to Your Microscope was a finalist-2008 American Association for the Advancement of Science/Subaru Science Books and Films Prize Hands -On Science/Activity Books.

To get a sense of what an appointment to the Order of Canada means, here’s a description from the government of Canada website,

The Order of Canada is how our country honours people who make extraordinary contributions to the nation.

Since its creation in 1967—Canada’s centennial year—more than 7 000 people from all sectors of society have been invested into the Order. The contributions of these trailblazers are varied, yet they have all enriched the lives of others and made a difference to this country. Their grit and passion inspire us, teach us and show us the way forward. They exemplify the Order’s motto: DESIDERANTES MELIOREM PATRIAM (“They desire a better country”).

Year of Science in British Columbia

In the Fall of 2010, the British Columbia provincial government announced a Year of Science (coinciding with the school year) . Originally, it was supposed to be a provincial government-wide initiative but the idea percolated through any number of processes and emerged as a year dedicated to science education for youth (according to the idea’s originator, Moira Stilwell who was then a Member of the Legislative Assembly [MLA]’ I spoke with her sometime in 2010 or 2011).

As the ‘year’ drew to a close, there was a finale ($1.1M in funding), which was featured here in a July 6, 2011 posting.

The larger portion of the money ($1M) was awarded to Science World while $100,000 ($0.1 M) was given to the Pacific Institute of Mathematical Sciences To my knowledge there have been no followup announcements about how the money was used.

Animation and mathematics

In Toronto, mathematician Dr. Karan Singh enjoyed a flurry of interest due to his association with animator Chris Landreth and their Academy Award (Oscar) Winning 2004 animated film, Ryan. They have continued to work together as members of the Dynamic Graphics Project (DGP) Lab at the University of Toronto. Theirs is not the only Oscar winning work to emerge from one or more of the members of the lab. Jos Stam, DGP graduate and adjunct professor won his third in 2019.

A graphic novel and medical promise

An academic at Simon Fraser University since 2015, Coleman Nye worked with three other women to produce a graphic novel about medical dilemmas in a genre described as’ ethno-fiction’.

Lissa: A Story about Medical Promise, Friendship, and Revolution (2017) by Sherine Hamdy and Coleman Nye, two anthropologists and Art by Sarula Bao and Caroline Brewer, two artists.

Here’s a description of the book from the University of Toronto Press website,

As young girls in Cairo, Anna and Layla strike up an unlikely friendship that crosses class, cultural, and religious divides. Years later, Anna learns that she may carry the hereditary cancer gene responsible for her mother’s death. Meanwhile, Layla’s family is faced with a difficult decision about kidney transplantation. Their friendship is put to the test when these medical crises reveal stark differences in their perspectives…until revolutionary unrest in Egypt changes their lives forever.

The first book in a new series [ethnoGRAPIC; a series of graphic novels from the University of Toronto Press], Lissa brings anthropological research to life in comic form, combining scholarly insights and accessible, visually-rich storytelling to foster greater understanding of global politics, inequalities, and solidarity.

I hope to write more about this graphic novel in a future posting.

New Media

I don’t know if this could be described as a movement yet but it’s certainly an interesting minor development. Two new media centres have hosted, in the last four years, art/sci projects and/or workshops. It’s unexpected given this definition from the Wikipedia entry for New Media (Note: Links have been removed),

New media are forms of media that are computational and rely on computers for redistribution. Some examples of new media are computer animations, computer games, human-computer interfaces, interactive computer installations, websites, and virtual worlds.[1][2]

In Manitoba, the Video Pool Media Arts Centre hosted a February 2016 workshop Biology as a New Art Medium: Workshop with Marta De Menezes. De Menezes, an artist from Portugal, gave workshops and talks in both Winnipeg (Manitoba) and Toronto (Ontario). Here’s a description for the one in Winnipeg,

This workshop aims to explore the multiple possibilities of artistic approaches that can be developed in relation to Art and Microbiology in a DIY situation. A special emphasis will be placed on the development of collaborative art and microbiology projects where the artist has to learn some biological research skills in order to create the artwork. The course will consist of a series of intense experimental sessions that will give raise to discussions on the artistic, aesthetic and ethical issues raised by the art and the science involved. Handling these materials and organisms will provoke a reflection on the theoretical issues involved and the course will provide background information on the current diversity of artistic discourses centred on biological sciences, as well a forum for debate.

VIVO Media Arts Centre in Vancouver hosted the Invasive Systems in 2019. From the exhibition page,

Picture this – a world where AI invades human creativity, bacteria invade our brains, and invisible technological signals penetrate all natural environments. Where invasive species from plants to humans transform spaces where they don’t belong, technology infiltrates every aspect of our daily lives, and the waste of human inventions ravages our natural environments.

This weekend festival includes an art-science exhibition [emphasis mine], a hands-on workshop (Sat, separate registration required), and guided discussions and tours by the curator (Sat/Sun). It will showcase collaborative works by three artist/scientist pairs, and independent works by six artists. Opening reception will be on Friday, November 8 starting at 7pm; curator’s remarks and performance by Edzi’u at 7:30pm and 9pm. 

New Westminster’s (British Columbia) New Media Gallery recently hosted an exhibition, ‘winds‘ from June 20 – September 29, 2019 that could be described as an art/sci exhibition,

Landscape and weather have long shared an intimate connection with the arts.  Each of the works here is a landscape: captured, interpreted and presented through a range of technologies. The four artists in this exhibition have taken, as their material process, the movement of wind through physical space & time. They explore how our perception and understanding of landscape can be interpreted through technology. 

These works have been created by what might be understood as a sort of scientific method or process that involves collecting data, acute observation, controlled experiments and the incorporation of measurements and technologies that control or collect motion, pressure, sound, pattern and the like. …

Council of Canadian Academies, Publishing, and Open Access

Established in 2005, the Council of Canadian Academies (CCA) (Wikipedia entry) is tasked by various departments and agencies to answer their queries about science issues that could affect the populace and/or the government. In 2014, the CCA published a report titled, Science Culture: Where Canada Stands. It was in response to the Canada Science and Technology Museums Corporation (now called Ingenium), Industry Canada, and Natural Resources Canada and their joint request that the CCA conduct an in-depth, independent assessment to investigate the state of Canada’s science culture.

I gave a pretty extensive analysis of the report, which I delivered in four parts: Part 1, Part 2 (a), Part 2 (b), and Part 3. In brief, the term ‘science culture’ seems to be specifically, i.e., it’s not used elsewhere in the world (that we know of), Canadian. We have lots to be proud of. I was a little disappointed by the lack of culture (arts) producers on the expert panel and, as usual, I bemoaned the fact that the international community included as reviewers, members of the panel, and as points for comparison were drawn from the usual suspects (US, UK, or somewhere in northern Europe).

Science publishing in Canada took a bit of a turn in 2010, when the country’s largest science publisher, NRC (National Research Council) Research Publisher was cut loose from the government and spun out into the private, *not-for-profit publisher*, Canadian Science Publishing (CSP). From the CSP Wikipedia entry,

Since 2010, Canadian Science Publishing has acquired five new journals:

Since 2010, Canadian Science Publishing has also launched four new journals

Canadian Science Publishing offers researchers options to make their published papers freely available (open access) in their standard journals and in their open access journal, (from the CSP Wikipedia entry)

Arctic Science aims to provide a collaborative approach to Arctic research for a diverse group of users including government, policy makers, the general public, and researchers across all scientific fields

FACETS is Canada’s first open access multidisciplinary science journal, aiming to advance science by publishing research that the multi-faceted global community of research. FACETS is the official journal of the Royal Society of Canada’s Academy of Science.

Anthropocene Coasts aims to understand and predict the effects of human activity, including climate change, on coastal regions.

In addition, Canadian Science Publishing strives to make their content accessible through the CSP blog that includes plain language summaries of featured research. The open-access journal FACETS similarly publishes plain language summaries.

*comment removed*

CSP announced (on Twitter) a new annual contest in 2016,

Canadian Science Publishing@cdnsciencepub

New CONTEST! Announcing Visualizing Science! Share your science images & win great prizes! Full details on the blog http://cdnsciencepub.com/blog/2016-csp-image-contest-visualizing-science.aspx1:45 PM · Sep 19, 2016·TweetDeck

The 2016 blog posting is no longer accessible. Oddly for a contest of this type, I can’t find an image archive for previous contests. Regardless, a 2020 competition has been announced for Summer 2020. There are some details on the VISUALIZING SCIENCE 2020 webpage but some are missing, e.g., no opening date, no deadline. They are encouraging you to sign up for notices.

Back to open access, in a January 22, 2016 posting I featured news about Montreal Neuro (Montreal Neurological Institute [MNI] in Québec, Canada) and its then new policy giving researchers world wide access to its research and made a pledge that it would not seek patents for its work.

Fish, Newfoundland & Labrador, and Prince Edward Island

AquAdvantage’s genetically modified salmon was approved for consumption in Canada according to my May 20, 2016 posting. The salmon are produced/farmed by a US company (AquaBounty) but the the work of genetically modifying Atlantic salmon with genetic material from the Chinook (a Pacific ocean salmon) was mostly undertaken at Memorial University in Newfoundland & Labrador.

The process by which work done in Newfoundland & Labrador becomes the property of a US company is one that’s well known here in Canada. The preliminary work and technology is developed here and then purchased by a US company, which files patents, markets, and profits from it. Interestingly, the fish farms for the AquAdvantage salmon are mostly (two out of three) located on Prince Edward Island.

Intriguingly, 4.5 tonnes of the modified fish were sold for consumption in Canada without consumers being informed (see my Sept. 13, 2017 posting, scroll down about 45% of the way).

It’s not all sunshine and roses where science culture in Canada is concerned. Incidents where Canadians are not informed let alone consulted about major changes in the food supply and other areas are not unusual. Too many times, scientists, politicians, and government policy experts want to spread news about science without any response from the recipients who are in effect viewed as a ‘tabula rasa’ or a blank page.

Tying it all up

This series has been my best attempt to document in some fashion or another the extraordinary range of science culture in Canada from roughly 2010-19. Thank you! This series represents a huge amount of work and effort to develop science culture in Canada and I am deeply thankful that people give so much to this effort.

I have inevitably missed people and organizations and events. For that I am very sorry. (There is an addendum to the series as it’s been hard to stop but I don’t expect to add anything or anyone more.)

I want to mention but can’t expand upon,the Pan-Canadian Artificial Intelligence Strategy, which was established in the 2017 federal budget (see a March 31, 2017 posting about the Vector Institute and Canada’s artificial intelligence sector).

Science Borealis, the Canadian science blog aggregator, owes its existence to Canadian Science Publishing for the support (programming and financial) needed to establish itself and, I believe, that support is still ongoing. I think thanks are also due to Jenny Ryan who was working for CSP and championed the initiative. Jenny now works for Canadian Blood Services. Interestingly, that agency added a new programme, a ‘Lay Science Writing Competition’ in 2018. It’s offered n partnership with two other groups, the Centre for Blood Research at the University of British Columbia and Science Borealis

While the Royal Astronomical Society of Canada does not fit into my time frame as it lists as its founding date December 1, 1868 (18 months after confederation), the organization did celebrate its 150th anniversary in 2018.

Vancouver’s Electric Company often produces theatrical experiences that cover science topics such as the one featured in my June 7, 2013 posting, You are very star—an immersive transmedia experience.

Let’s Talk Science (Wikipedia entry) has been heavily involved with offering STEM (science, technology, engineering, and mathematics) programming both as part of curricular and extra-curricular across Canada since 1993.

This organization predates confederation having been founded in 1849 by Sir Sandford Fleming and Kivas Tully in Toronto. for surveyors, civil engineers, and architects. It is the Royal Canadian Institute of Science (Wikipedia entry)_. With almost no interruption, they have been delivering a regular series of lectures on the University of Toronto campus since 1913.

The Perimeter Institute for Theoretical Physics is a more recent beast. In 1999 Mike Lazirides, founder of Research In Motion (now known as Blackberry Limited), acted as both founder and major benefactor for this institute in Waterloo, Ontario. They offer a substantive and imaginative outreach programmes such as Arts and Culture: “Event Horizons is a series of unique and extraordinary events that aim to stimulate and enthral. It is a showcase of innovative work of the highest international standard, an emotional, intellectual, and creative experience. And perhaps most importantly, it is a social space, where ideas collide and curious minds meet.”

While gene-editing hasn’t seemed to be top-of-mind for anyone other than those in the art/sci community that may change. My April 26, 2019 posting focused on what appears to be a campaign to reverse Canada’s criminal ban on human gene-editing of inheritable cells (germline). With less potential for controversy, there is a discussion about somatic gene therapies and engineered cell therapies. A report from the Council of Canadian is due in the Fall of 2020. (The therapies being discussed do not involve germline editing.)

French language science media and podcasting

Agence Science-Presse is unique as it is the only press agency in Canada devoted to science news. Founded in 1978, it has been active in print, radio, television, online blogs, and podcasts (Baladodiffusion). You can find their Twitter feed here.

I recently stumbled across ‘un balados’ (podcast), titled, 20%. Started in January 2019 by the magazine, Québec Science, the podcast is devoted to women in science and technology. 20%, the podcast’s name, is the statistic representing the number of women in those fields. “Dans les domaines de la science et de la technologie, les femmes ne forment que 20% de la main-d’oeuvre.” (from the podcast webpage) The podcast is a co-production between “Québec Science [founded in 1962] et l’Acfas [formerly, l’Association Canadienne-Française pour l’Avancement des Sciences, now, Association francophone pour le savoir], en collaboration avec la Commission canadienne pour l’UNESCO, L’Oréal Canada et la radio Choq.ca.” (also from the podcast webpage)

Does it mean anything?

There have been many developments since I started writing this series in late December 2019. In January 2020, Iran shot down one of its own planes. That error killed some 176 people , many of them (136 Canadians and students) bound for Canada. The number of people who were involved in the sciences, technology, and medicine was striking.

It was a shocking loss and will reverberate for quite some time. There is a memorial posting here (January 13, 2020), which includes links to another memorial posting and an essay.

As I write this we are dealing with a pandemic, COVID-19, which has us all practicing physical and social distancing. Congregations of large numbers are expressly forbidden. All of this is being done in a bid to lessen the passage of the virus, SARS-CoV-2 which causes COVID-19.

In the short term at least, it seems that much of what I’ve described in these five parts (and the addendum) will undergo significant changes or simply fade away.

As for the long term, with this last 10 years having hosted the most lively science culture scene I can ever recall, I’m hopeful that science culture in Canada will do more than survive but thrive.

For anyone who missed them:

Part 1 covers science communication, science media (mainstream and others such as blogging) and arts as exemplified by music and dance: The decade that was (2010-19) and the decade to come (2020-29): Science culture in Canada (1 of 5).

Part 2 covers art/science (or art/sci or sciart) efforts, science festivals both national and local, international art and technology conferences held in Canada, and various bar/pub/café events: The decade that was (2010-19) and the decade to come (2020-29): Science culture in Canada (2 of 5).

Part 3 covers comedy, do-it-yourself (DIY) biology, chief science advisor, science policy, mathematicians, and more: The decade that was (2010-19) and the decade to come (2020-29): Science culture in Canada (3 of 5)

Part 4 covers citizen science, birds, climate change, indigenous knowledge (science), and the IISD Experimental Lakes Area: The decade that was (2010-19) and the decade to come (2020-29): Science culture in Canada (4 of 5)

*”for-profit publisher, Canadian Science Publishing (CSP)” corrected to “not-for-profit publisher, Canadian Science Publishing (CSP)” and this comment “Not bad for a for-profit business, eh?” removed on April 29, 2020 as per Twitter comments,

Canadian Science Publishing @cdnsciencepub

Hi Maryse, thank you for alerting us to your blog. To clarify, Canadian Science Publishing is a not-for-profit publisher. Thank you as well for sharing our image contest. We’ve updated the contest page to indicate that the contest opens July 2020!

10:01am · 29 Apr 2020 · Twitter Web App

Some amusements in the time of COVID-19

Gold stars for everyone who recognized the loose paraphrasing of the title, Love in the Time of Cholera, for Gabrial Garcia Marquez’s 1985 novel.

I wrote my headline and first paragraph yesterday and found this in my email box this morning, from a March 25, 2020 University of British Columbia news release, which compares times, diseases, and scares of the past with today’s COVID-19 (Perhaps politicians and others could read this piece and stop using the word ‘unprecedented’ when discussing COVID-19?),

How globalization stoked fear of disease during the Romantic era

In the late 18th and early 19th centuries, the word “communication” had several meanings. People used it to talk about both media and the spread of disease, as we do today, but also to describe transport—via carriages, canals and shipping.

Miranda Burgess, an associate professor in UBC’s English department, is working on a book called Romantic Transport that covers these forms of communication in the Romantic era and invites some interesting comparisons to what the world is going through today.

We spoke with her about the project.

What is your book about?

It’s about global infrastructure at the dawn of globalization—in particular the extension of ocean navigation through man-made inland waterways like canals and ship’s canals. These canals of the late 18th and early 19th century were like today’s airline routes, in that they brought together places that were formerly understood as far apart, and shrunk time because they made it faster to get from one place to another.

This book is about that history, about the fears that ordinary people felt in response to these modernizations, and about the way early 19th-century poets and novelists expressed and responded to those fears.

What connections did those writers make between transportation and disease?

In the 1810s, they don’t have germ theory yet, so there’s all kinds of speculation about how disease happens. Works of tropical medicine, which is rising as a discipline, liken the human body to the surface of the earth. They talk about nerves as canals that convey information from the surface to the depths, and the idea that somehow disease spreads along those pathways.

When the canals were being built, some writers opposed them on the grounds that they could bring “strangers” through the heart of the city, and that standing water would become a breeding ground for disease. Now we worry about people bringing disease on airplanes. It’s very similar to that.

What was the COVID-19 of that time?

Probably epidemic cholera [emphasis mine], from about the 1820s onward. The Quarterly Review, a journal that novelist Walter Scott was involved in editing, ran long articles that sought to trace the map of cholera along rivers from South Asia, to Southeast Asia, across Europe and finally to Britain. And in the way that its spread is described, many of the same fears that people are evincing now about COVID-19 were visible then, like the fear of clothes. Is it in your clothes? Do we have to burn our clothes? People were concerned.

What other comparisons can be drawn between those times and what is going on now?

Now we worry about the internet and “fake news.” In the 19th century, they worried about what William Wordsworth called “the rapid communication of intelligence,” which was the daily newspaper. Not everybody had access to newspapers, but each newspaper was read by multiple families and newspapers were available in taverns and coffee shops. So if you were male and literate, you had access to a newspaper, and quite a lot of women did, too.

Paper was made out of rags—discarded underwear. Because of the French Revolution and Napoleonic Wars that followed, France blockaded Britain’s coast and there was a desperate shortage of rags to make paper, which had formerly come from Europe. And so Britain started to import rags from the Caribbean that had been worn by enslaved people.

Papers of the time are full of descriptions of the high cost of rags, how they’re getting their rags from prisons, from prisoners’ underwear, and fear about the kinds of sweat and germs that would have been harboured in those rags—and also discussions of scarcity, as people stole and hoarded those rags. It rings very well with what the internet is telling us now about a bunch of things around COVID-19.

Plus ça change, n’est-ce pas?

And now for something completely different

Kudos to all who recognized the Monty Python reference. Now, onto the frogfish,

Thank you to the Monterey Bay Aquarium (in California, US).

A March 22, 2020 University of Washington (state) news release features an interview with the author of a new book on frogfishes,

Any old fish can swim. But what fish can walk, scoot, clamber over rocks, change color or pattern and even fight? That would be the frogfish.

The latest book by Ted Pietsch, UW professor emeritus of aquatic and fishery sciences, explores the lives and habits of these unusual marine shorefishes. “Frogfishes: Biodiversity, Zoogeography, and Behavioral Ecology” was published in March [2020] by Johns Hopkins University Press.

Pietsch, who is also curator emeritus of fishes at the Burke Museum of Natural History and Culture, has published over 200 articles and a dozen books on the biology and behavior of marine fishes. He wrote this book with Rachel J. Arnold, a faculty member at Northwest Indian College in Bellingham and its Salish Sea Research Center.

These walking fishes have stepped into the spotlight lately, with interest growing in recent decades. And though these predatory fishes “will almost certainly devour anything else that moves in a home aquarium,” Pietsch writes, “a cadre of frogfish aficionados around the world has grown within the dive community and among aquarists.” In fact, Pietsch said, there are three frogfish public groups on Facebook, with more than 6,000 members.

First, what is a frogfish?

Ted Pietsch: A member of a family of bony fishes, containing 52 species, all of which are highly camouflaged and whose feeding strategy consists of mimicking the immobile, inert, and benign appearance of a sponge or an algae-encrusted rock, while wiggling a highly conspicuous lure to attract prey.

This is a fish that “walks” and “hops” across the sea bottom, and clambers about over rocks and coral like a four-legged terrestrial animal but, at the same time, can jet-propel itself through open water. Some lay their eggs encapsulated in a complex, floating, mucus mass, called an “egg raft,” while some employ elaborate forms of parental care, carrying their eggs around until they hatch.

They are among the most colorful of nature’s productions, existing in nearly every imaginable color and color pattern, with an ability to completely alter their color and pattern in a matter of days or seconds. All these attributes combined make them one of the most intriguing groups of aquatic vertebrates for the aquarist, diver, and underwater photographer as well as the professional zoologist.

I couldn’t resist the ‘frog’ reference and I’m glad since this is a good read with a number of fascinating photographs and illustrations.,

An illustration of the frogfish Antennarius pictus, published by George Shaw in 1794. From a new book by Ted Pietsch, UW professor of emeritus of aquatic and fishery sciences. Courtesy: University of Washington (state)

h/t phys.org March 24, 2020 news item

Building with bacteria

A block of sand particles held together by living cells. Credit: The University of Colorado Boulder College of Engineering and Applied Science

A March 24, 2020 news item on phys.org features the future of building construction as perceived by synthetic biologists,

Buildings are not unlike a human body. They have bones and skin; they breathe. Electrified, they consume energy, regulate temperature and generate waste. Buildings are organisms—albeit inanimate ones.

But what if buildings—walls, roofs, floors, windows—were actually alive—grown, maintained and healed by living materials? Imagine architects using genetic tools that encode the architecture of a building right into the DNA of organisms, which then grow buildings that self-repair, interact with their inhabitants and adapt to the environment.

A March 23, 2020 essay by Wil Srubar (Professor of Architectural Engineering and Materials Science, University of Colorado Boulder), which originated the news item, provides more insight,

Living architecture is moving from the realm of science fiction into the laboratory as interdisciplinary teams of researchers turn living cells into microscopic factories. At the University of Colorado Boulder, I lead the Living Materials Laboratory. Together with collaborators in biochemistry, microbiology, materials science and structural engineering, we use synthetic biology toolkits to engineer bacteria to create useful minerals and polymers and form them into living building blocks that could, one day, bring buildings to life.

In one study published in Scientific Reports, my colleagues and I genetically programmed E. coli to create limestone particles with different shapes, sizes, stiffnesses and toughness. In another study, we showed that E. coli can be genetically programmed to produce styrene – the chemical used to make polystyrene foam, commonly known as Styrofoam.

Green cells for green building

In our most recent work, published in Matter, we used photosynthetic cyanobacteria to help us grow a structural building material – and we kept it alive. Similar to algae, cyanobacteria are green microorganisms found throughout the environment but best known for growing on the walls in your fish tank. Instead of emitting CO2, cyanobacteria use CO2 and sunlight to grow and, in the right conditions, create a biocement, which we used to help us bind sand particles together to make a living brick.

By keeping the cyanobacteria alive, we were able to manufacture building materials exponentially. We took one living brick, split it in half and grew two full bricks from the halves. The two full bricks grew into four, and four grew into eight. Instead of creating one brick at a time, we harnessed the exponential growth of bacteria to grow many bricks at once – demonstrating a brand new method of manufacturing materials.

Researchers have only scratched the surface of the potential of engineered living materials. Other organisms could impart other living functions to material building blocks. For example, different bacteria could produce materials that heal themselves, sense and respond to external stimuli like pressure and temperature, or even light up. If nature can do it, living materials can be engineered to do it, too.

It also take less energy to produce living buildings than standard ones. Making and transporting today’s building materials uses a lot of energy and emits a lot of CO2. For example, limestone is burned to make cement for concrete. Metals and sand are mined and melted to make steel and glass. The manufacture, transport and assembly of building materials account for 11% of global CO2 emissions. Cement production alone accounts for 8%. In contrast, some living materials, like our cyanobacteria bricks, could actually sequester CO2.

The field of engineered living materials is in its infancy, and further research and development is needed to bridge the gap between laboratory research and commercial availability. Challenges include cost, testing, certification and scaling up production. Consumer acceptance is another issue. For example, the construction industry has a negative perception of living organisms. Think mold, mildew, spiders, ants and termites. We’re hoping to shift that perception. Researchers working on living materials also need to address concerns about safety and biocontamination.

The [US] National Science Foundation recently named engineered living materials one of the country’s key research priorities. Synthetic biology and engineered living materials will play a critical role in tackling the challenges humans will face in the 2020s and beyond: climate change, disaster resilience, aging and overburdened infrastructure, and space exploration.

If you have time and interest, this is fascinating. Strubar is a little exuberant and, at this point, I welcome it.

Fitness

The Lithuanians are here for us. Scientists from the Kaunas University of Technology have just published a paper on better exercises for lower back pain in our increasingly sedentary times, from a March 23, 2020 Kaunas University of Technology press release (also on EurekAlert) Note: There are a few minor grammatical issues,

With the significant part of the global population forced to work from home, the occurrence of lower back pain may increase. Lithuanian scientists have devised a spinal stabilisation exercise programme for managing lower back pain for people who perform a sedentary job. After testing the programme with 70 volunteers, the researchers have found that the exercises are not only efficient in diminishing the non-specific lower back pain, but their effect lasts 3 times longer than that of a usual muscle strengthening exercise programme.

According to the World Health Organisation, lower back pain is among the top 10 diseases and injuries that are decreasing the quality of life across the global population. It is estimated that non-specific low back pain is experienced by 60% to 70% of people in industrialised societies. Moreover, it is the leading cause of activity limitation and work absence throughout much of the world. For example, in the United Kingdom, low back pain causes more than 100 million workdays lost per year, in the United States – an estimated 149 million.

Chronic lower back pain, which starts from long-term irritation or nerve injury affects the emotions of the afflicted. Anxiety, bad mood and even depression, also the malfunctioning of the other bodily systems – nausea, tachycardia, elevated arterial blood pressure – are among the conditions, which may be caused by lower back pain.

During the coronavirus disease (COVID-19) outbreak, with a significant part of the global population working from home and not always having a properly designed office space, the occurrence of lower back pain may increase.

“Lower back pain is reaching epidemic proportions. Although it is usually clear what is causing the pain and its chronic nature, people tend to ignore these circumstances and are not willing to change their lifestyle. Lower back pain usually comes away itself, however, the chances of the recurring pain are very high”, says Dr Irina Klizienė, a researcher at Kaunas University of Technology (KTU) Faculty of Social Sciences, Humanities and Arts.

Dr Klizienė, together with colleagues from KTU and from Lithuanian Sports University has designed a set of stabilisation exercises aimed at strengthening the muscles which support the spine at the lower back, i.e. lumbar area. The exercise programme is based on Pilates methodology.

According to Dr Klizienė, the stability of lumbar segments is an essential element of body biomechanics. Previous research evidence shows that in order to avoid the lower back pain it is crucial to strengthen the deep muscles, which are stabilising the lumbar area of the spine. One of these muscles is multifidus muscle.

“Human central nervous system is using several strategies, such as preparing for keeping the posture, preliminary adjustment to the posture, correcting the mistakes of the posture, which need to be rectified by specific stabilising exercises. Our aim was to design a set of exercises for this purpose”, explains Dr Klizienė.

The programme, designed by Dr Klizienė and her colleagues is comprised of static and dynamic exercises, which train the muscle strength and endurance. The static positions are to be held from 6 to 20 seconds; each exercise to be repeated 8 to 16 times.

Caption: The static positions are to be held from 6 to 20 seconds; each exercise to be repeated 8 to 16 times. Credit: KTU

The previous set is a little puzzling but perhaps you’ll find these ones below easier to follow,

Caption: The exercises are aimed at strengthening the muscles which support the spine at the lower back. Credit: KTU

I think more pictures of intervening moves would have been useful. Now. getting back to the press release,

In order to check the efficiency of the programme, 70 female volunteers were randomly enrolled either to the lumbar stabilisation exercise programme or to a usual muscle strengthening exercise programme. Both groups were exercising twice a week for 45 minutes for 20 weeks. During the experiment, ultrasound scanning of the muscles was carried out.

As soon as 4 weeks in lumbar stabilisation programme, it was observed that the cross-section area of the multifidus muscle of the subjects of the stabilisation group has increased; after completing the programme, this increase was statistically significant (p < 0,05). This change was not observed in the strengthening group.

Moreover, although both sets of exercises were efficient in eliminating lower back pain and strengthening the muscles of the lower back area, the effect of stabilisation exercises lasted 3 times longer – 12 weeks after the completion of the stabilisation programme against 4 weeks after the completion of the muscle strengthening programme.

“There are only a handful of studies, which have directly compared the efficiency of stabilisation exercises against other exercises in eliminating lower back pain”, says Dr Klizienė, “however, there are studies proving that after a year, lower back pain returned only to 30% of people who have completed a stabilisation exercise programme, and to 84% of people who haven’t taken these exercises. After three years these proportions are 35% and 75%.”

According to her, research shows that the spine stabilisation exercises are more efficient than medical intervention or usual physical activities in curing the lower back pain and avoiding the recurrence of the symptoms in the future.

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

Effect of different exercise programs on non-specific chronic low back pain and disability in people who perform sedentary work by Saule Sipavicienea, Irina Klizieneb. Clinical Biomechanics March 2020 Volume 73, Pages 17–27 DOI: https://doi.org/10.1016/j.clinbiomech.2019.12.028

This paper is behind a paywall.

COVID-19: caution and concern not panic

There’s a lot of information being pumped out about COVID-19 and not all of it is as helpful as it might be. In fact, the sheer volume can seem overwhelming despite one’s best efforts to be calm.

Here are a few things I’ve used to help relieve some fo the pressure as numbers in Canada keep rising.

Inspiration from the Italians

I was thrilled to find Emily Rumball’s March 18 ,2020 article titled, “Italians making the most of quarantine is just what the world needs right now (VIDEOS),” on the Daily Hive website. The couple dancing on the balcony while Ginger Rogers and Fred Astaire are shown dancing on the wall above is my favourite.

As the Italians practice social distancing and exercise caution, they are also demonstrating that “life goes on” even while struggling as one of the countries hit hardest by COVID-19.

Investigating viruses and the 1918/19 pandemic vs. COVID-19

There has been some mention of and comparison to the 1918/19 pandemic (also known as the Spanish flu) in articles by people who don’t seem to be particularly well informed about that earlier pandemic. Susan Baxter offers a concise and scathing explanation for why the 1918/19 situation deteriorated as much as it did in her February 8, 2010 posting. As for this latest pandemic (COVID-19), she explains what a virus actually is and suggests we all calm down in her March 17, 2020 posting. BTW, she has an interdisciplinary PhD for work largely focused on health economics. She is also a lecturer in the health sciences programme at Simon Fraser University (Vancouver, Canada). Full disclosure: She and I have a longstanding friendship.

Marilyn J. Roossinck, a professor of Plant Pathology and Environmental Microbiology at Pennsylvania State University, wrote a February 20, 2020 essay for The Conversation titled, “What are viruses anyway, and why do they make us so sick? 5 questions answered,”

4. SARS was a formidable foe, and then seemed to disappear. Why?

Measures to contain SARS started early, and they were very successful. The key is to stop the chain of transmission by isolating infected individuals. SARS had a short incubation period; people generally showed symptoms in two to seven days. There were no documented cases of anyone being a source of SARS without showing symptoms.

Stopping the chain of transmission is much more difficult when the incubation time is much longer, or when some people don’t get symptoms at all. This may be the case with the virus causing CoVID-19, so stopping it may take more time.

1918/19 pandemic vs. COVID-19

Angela Betsaida B. Laguipo, with a Bachelor of Nursing degree from the University of Baguio, Philippine is currently completing her Master’s Degree, has written a March 9, 2020 article for News Medical comparing the two pandemics,

The COVID-19 is fast spreading because traveling is an everyday necessity today, with flights from one country to another accessible to most.

Some places did manage to keep the virus at bay in 1918 with traditional and effective methods, such as closing schools, banning public gatherings, and locking down villages, which has been performed in Wuhan City, in Hubei province, China, where the coronavirus outbreak started. The same method is now being implemented in Northern Italy, where COVID-19 had killed more than 400 people.

The 1918 Spanish flu has a higher mortality rate of an estimated 10 to 20 percent, compared to 2 to 3 percent in COVID-19. The global mortality rate of the Spanish flu is unknown since many cases were not reported back then. About 500 million people or one-third of the world’s population contracted the disease, while the number of deaths was estimated to be up to 50 million.

During that time, public funds are mostly diverted to military efforts, and a public health system was still a budding priority in most countries. In most places, only the middle class or the wealthy could afford to visit a doctor. Hence, the virus has [sic] killed many people in poor urban areas where there are poor nutrition and sanitation. Many people during that time had underlying health conditions, and they can’t afford to receive health services.

I recommend reading Laguipo’s article in its entirety right down to the sources she cites at the end of her article.

Ed Yong’s March 20, 2020 article for The Atlantic, “Why the Coronavirus Has Been So Successful; We’ve known about SARS-CoV-2 for only three months, but scientists can make some educated guesses about where it came from and why it’s behaving in such an extreme way,” provides more information about what is currently know about the coronavirus, SATS-CoV-2,

One of the few mercies during this crisis is that, by their nature, individual coronaviruses are easily destroyed. Each virus particle consists of a small set of genes, enclosed by a sphere of fatty lipid molecules, and because lipid shells are easily torn apart by soap, 20 seconds of thorough hand-washing can take one down. Lipid shells are also vulnerable to the elements; a recent study shows that the new coronavirus, SARS-CoV-2, survives for no more than a day on cardboard, and about two to three days on steel and plastic. These viruses don’t endure in the world. They need bodies.

But why do some people with COVID-19 get incredibly sick, while others escape with mild or nonexistent symptoms? Age is a factor. Elderly people are at risk of more severe infections possibly because their immune system can’t mount an effective initial defense, while children are less affected because their immune system is less likely to progress to a cytokine storm. But other factors—a person’s genes, the vagaries of their immune system, the amount of virus they’re exposed to, the other microbes in their bodies—might play a role too. In general, “it’s a mystery why some people have mild disease, even within the same age group,” Iwasaki [Akiko Iwasaki of the Yale School of Medicine] says.

We still have a lot to learn about this.

Going nuts and finding balance with numbers

Generally speaking,. I find numbers help me to put this situation into perspective. It seems I’m not alone; Dr. Daniel Gillis’ (Guelph University in Ontario, Canada) March 18, 2020 blog post is titled, Statistics In A Time of Crisis.

Hearkening back in history, the Wikipedia entry for Spanish flu offers a low of 17M deaths in a 2018 estimate to a high of !00M deaths in a 2005 estimate. At this writing (Friday, March 20, 2020 at 3 pm PT), the number of coronovirus cases worldwide is 272,820 with 11, 313 deaths.

Articles like Michael Schulman’s March 16, 2020 article for the New Yorker might not be as helpful as one hope (Note: Links have been removed),

Last Wednesday night [March 11, 2020], not long after President Trump’s Oval Office address, I called my mother to check in about the, you know, unprecedented global health crisis [emphasis mine] that’s happening. She told me that she and my father were in a cab on the way home from a fun dinner at the Polo Bar, in midtown Manhattan, with another couple who were old friends.

“You went to a restaurant?!” I shrieked. This was several days after she had told me, through sniffles, that she was recovering from a cold but didn’t see any reason that she shouldn’t go to the school where she works. Also, she was still hoping to make a trip to Florida at the end of the month. My dad, a lawyer, was planning to go into the office on Thursday, but thought that he might work from home on Friday, if he could figure out how to link up his personal computer. …

… I’m thirty-eight, and my mother and father are sixty-eight and seventy-four, respectively. Neither is retired, and both are in good shape. But people sixty-five and older—more than half of the baby-boomer population—are more susceptible to COVID-19 and have a higher mortality rate, and my parents’ blithe behavior was as unsettling as the frantic warnings coming from hospitals in Italy.

Clearly, Schulman is concerned about his parents’ health and well being but the tone of near hysteria is a bit off-putting. We’re not in a crisis (exception: the Italians and, possibly, the Spanish and the French)—yet.

Tyler Dawson’s March 20, 2020 article in The Province newspaper (in Vancouver, British Columbia) offers dire consequences from COVID-19 before pivoting,

COVID-19 will leave no Canadian untouched.

Travel plans halted. First dates postponed. School semesters interrupted. Jobs lost. Retirement savings decimated. Some of us will know someone who has gotten sick, or tragically, died from the virus.

By now we know the terminology: social distancing, flatten the curve. Across the country, each province is taking measures to prepare, to plan for care, and the federal government has introduced financial measures amounting to more than three per cent of the country’s GDP to float the economy onward.

The response, says Steven Taylor, a University of British Columbia psychiatry professor and author of The Psychology of Pandemics, is a “balancing act.” [emphasis mine] Keep people alert, but neither panicked nor tuned out.

“You need to generate some degree of anxiety that gets people’s attention,” says Taylor. “If you overstate the message it could backfire.”

Prepare for uncertainty

In the same way experts still cannot come up with a definitive death rate for the 1918/19 pandemic, they are having trouble with this one too although, now, they’re trying to model the future rather than trying to establish what happened in the past. David Adam’s March 12, 2020 article forThe Scientist, provides some insight into the difficulties (Note: Links have been removed)

Like any other models, the projections of how the outbreak will unfold, how many people will become infected, and how many will die, are only as reliable as the scientific information they rest on. And most modelers’ efforts so far have focused on improving these data, rather than making premature predictions.

“Most of the work that modelers have done recently or in the first part of the epidemic hasn’t really been coming up with models and predictions, which is I think how most people think of it,” says John Edmunds, who works in the Centre for the Mathematical Modelling of Infectious Diseases at the London School of Hygiene & Tropical Medicine. “Most of the work has really been around characterizing the epidemiology, trying to estimate key parameters. I don’t really class that as modeling but it tends to be the modelers that do it.”

These variables include key numbers such as the disease incubation period, how quickly the virus spreads through the population, and, perhaps most contentiously, the case-fatality ratio. This sounds simple: it’s the proportion of infected people who die. But working it out is much trickier than it looks. “The non-specialists do this all the time and they always get it wrong,” Edmunds says. “If you just divide the total numbers of deaths by the total numbers of cases, you’re going to get the wrong answer.”

Earlier this month, Tedros Adhanom Ghebreyesus, the head of the World Health Organization, dismayed disease modelers when he said COVID-19 (the disease caused by the SARS-CoV-2 coronavirus) had killed 3.4 percent of reported cases, and that this was more severe than seasonal flu, which has a death rate of around 0.1 percent. Such a simple calculation does not account for the two to three weeks it usually takes someone who catches the virus to die, for example. And it assumes that reported cases are an accurate reflection of how many people are infected, when the true number will be much higher and the true mortality rate much lower.

Edmunds calls this kind of work “outbreak analytics” rather than true modeling, and he says the results of various specialist groups around the world are starting to converge on COVID-19’s true case-fatality ratio, which seems to be about 1 percent.[emphasis mine]

The 1% estimate in Adam’s article accords with Jeremy Samuel Faust’s (an emergency medicine physician at Brigham and Women’s Hospital in Boston, faculty in its division of health policy and public health, and an instructor at Harvard Medical School) estimates in a March 4, 2020 article (COVID-19 Isn’t As Deadly As We Think featured in my March 9, 2020 posting).

In a March 17, 2020 article by Steven Lewis (a health policy consultant formerly based in Saskatchewan, Canada; now living in Australia) for the Canadian Broadcasting Corporation’s (CBC) news online website, he covers some of the same ground and offers a somewhat higher projected death rate while refusing to commit,

Imagine you’re a chief public health officer and you’re asked the question on everyone’s mind: how deadly is the COVID-19 outbreak?

With the number of cases worldwide approaching 200,000, and 1,000 or more cases in 15 countries, you’d think there would be an answer. But the more data we see, the tougher it is to come up with a hard number.

Overall, the death rate is around four per cent — of reported cases. That’s also the death rate in China, which to date accounts for just under half the total number of global cases.

China is the only country where a) the outcome of almost all cases is known (85 per cent have recovered), and b) the spread has been stopped (numbers plateaued about a month ago). 

A four per cent death rate is pretty high — about 40 times more deadly than seasonal flu — but no experts believe that is the death rate. The latest estimate is that it is around 1.5 per cent. [emphasis mine] Other models suggest that it may be somewhat lower. 

The true rate can be known only if every case is known and confirmed by testing — including the asymptomatic or relatively benign cases, which comprise 80 per cent or more of the total — and all cases have run their course (people have either recovered or died). Aside from those in China, almost all cases identified are still active. 

Unless a jurisdiction systematically tests a large random sample of its population, we may never know the true rate of infection or the real death rate. 

Yet for all this unavoidable uncertainty, it is still odd that the rates vary so widely by country.

His description of the situation in Europe is quite interesting and worthwhile if you have the time to read it.

In the last article I’m including here, Murray Brewster offers some encouraging words in his March 20, 2020 piece about the preparations being made by the Canadian Armed Forces (CAF),

The Canadian military is preparing to respond to multiple waves of the COVID-19 pandemic which could stretch out over a year or more, the country’s top military commander said in his latest planning directive.

Gen. Jonathan Vance, chief of the defence staff, warned in a memo issued Thursday that requests for assistance can be expected “from all echelons of government and the private sector and they will likely come to the Department [of National Defence] through multiple points of entry.”

The directive notes the federal government has not yet directed the military to move into response mode, but if or when it does, a single government panel — likely a deputy-minister level inter-departmental task force — will “triage requests and co-ordinate federal responses.”

It also warns that members of the military will contract the novel coronavirus, “potentially threatening the integrity” of some units.

The notion that the virus caseload could recede and then return is a feature of federal government planning.

The Public Health Agency of Canada has put out a notice looking for people to staff its Centre for Emergency Preparedness and Response during the crisis and the secondment is expected to last between 12 and 24 months.

The Canadian military, unlike those in some other nations, has high-readiness units available. Vance said they are already set to reach out into communities to help when called.

Planners are also looking in more detail at possible missions — such as aiding remote communities in the Arctic where an outbreak could cripple critical infrastructure.

Defence analyst Dave Perry said this kind of military planning exercise is enormously challenging and complicated in normal times, let alone when most of the federal civil service has been sent home.

“The idea that they’re planning to be at this for year is absolutely bang on,” said Perry, a vice-president at the Canadian Global Affairs Institute.

In other words, concern and caution are called for not panic. I realize this post has a strongly Canada-centric focus but I’m hopeful others elsewhere will find this helpful.