Tag Archives: Laurentian University

Whispering in the Dark: Updates from Underground Science a June 12, 2019 talk in Vancouver (Canada)

The Society of Italian Researchers and Professionals in Western Canada (ARPICO) is hosting the intriguing ‘Whispering in the Dark …’ talk about underground science being held prior to the organization’s annual general meeting. From a May 21, 2019 ARPICO announcement (received via email),

… on June 12th, 2019 at the Italian Cultural Centre. ARPICO is proud to host Dr. Silvia Scorza, who will be presenting on the topic of underground science (literally underground) at SNOLAB, where research is conducted in fields of fundamental science that require shielding from external radiation such as cosmic rays. SNOLAB (SNO stands for Sudbury Neutrino Observatory) is a Canadian research laboratory located 2 km underground in Sudbury, Ontario. This presentation will give a unique and interesting perspective into the research that is conducted mostly out of the public view and discussion, but contributes critically to our scientific advances. Applications found in medicine, national security, industry, computing, science, and workforce development, illustrate a long and growing list of beneficial practical applications with contributions from particle physics.

Please read below to learn more about our speaker and topic.

Ahead of the speaking event, ARPICO will be holding its 2019 Annual General Meeting in the same location. We encourage everyone to participate in the AGM, have their say on ARPICO’s matters and possibly volunteer for the Board of Directors. ARPICO is made by all of its members, not just the Board, and it is therefore paramount that you all come, let us know what your wishes are for the Society and tell us how we can do better together as we go forward.

If you are driving to the venue, there is plenty of free parking space.  Please refer to the attached parking map for information on where not to park however, just to be sure.

We look forward to seeing everyone there.

The evening agenda is as follows:
6:00 pm to 6:45 pm – Annual General Meeting  [ Doors Open for Registration at 5:50 pm ]
7:00 pm – Start of the evening event with introductions & lecture by Dr. Silvia Scorza [ Doors Open for Registration at 6:45 pm ]
~8:00 pm – Q & A Period
to follow – Mingling & Refreshments until about 9:30 pm
If you have not already done so, please register for the event by visiting the EventBrite link or RSVPing to info@arpico.ca.

Further details are also available at arpico.ca and Eventbrite.

Whispering in the Dark: Updates from Underground Scienc

Based at a depth of 2 km in the Vale Creighton mine near Sudbury, Ontario, SNOLAB is an underground scientific environment that provides the conditions necessary for experiments dealing with rare interactions that have to be shielded from external radiation. The lab hosts an international community involved in a number of fundamental physics (neutrino and dark matter) as well as new biology and genomic experiments making use of the unique facility. In this lecture, Dr. Scorza will offer an overview on the life of an “underground scientist” and the immense possibilities of discovery that facilities like SNOLAB make available to our society.

Dr. Silvia Scorza was born and raised in Genoa, Italy. She received her B.Sc. and M.Sc. in Physics from the University of Genoa in 2003 and 2006, respectively. She then moved to the University Claude Bernard Lyon1 (UCBL1), France, where she obtained her Ph.D. in 2009. She has then held postdoctoral positions in France at the Institut de Physique Nucléaire de Lyon, in the U.S. at the Southern Methodist University in Dallas (TX) and later in Germany at the Karlsruhe Institute of Technology. Silvia is currently a research scientist at SNOLAB and adjunct professor at Laurentian University working on the SuperCDMS SNOLAB direct dark matter search experiment and the cryogenic test facility CUTE.
 
WHEN (AGM): Wednesday, June 12th, 2019 at 6:00pm (doors open at 5:50pm)
WHEN (EVENT): Wednesday, June 12th, 2019 at 7:00pm (doors open at 6:45pm)
WHERE: Italian Cultural Centre – Museum & Art Gallery – 3075 Slocan St, Vancouver, BC, V5M 3E4

RSVP: Please RSVP at EventBrite (http://whispersinthedark.eventbrite.ca/) or email info@arpico.ca
 
Tickets are Neede

Tickets are FREE, but all individuals are requested to obtain “free-admission” tickets on EventBrite site due to limited seating at the venue. Organizers need accurate registration numbers to manage wait lists and prepare name tags.

All ARPICO events are 100% staffed by volunteer organizers and helpers, however, room rental, stationery, and guest refreshments are costs incurred and underwritten by members of ARPICO. Therefore to be fair, all audience participants are asked to donate to the best of their ability at the door or via EventBrite to “help” defray costs of the event.
 
FAQs
Where can I contact the organizer with any questions? info@arpico.ca
Do I have to bring my printed ticket to the event? No, you do not. Your name will be on our Registration List at the Check-in Desk.
Is my registration/ticket transferrable? If you are unable to attend, another person may use your ticket. Please send us an email at info@arpico.ca of this substitution to correct our audience Registration List and to prepare guest name tags.
Can I update my registration information? Yes. If you have any questions, contact us at info@arpico.ca
I am having trouble using EventBrite and cannot reserve my ticket(s). Can someone at ARPICO help me with my ticket reservation? Of course, simply send your ticket request to us at info@arpico.ca so we help you.
 
What are my transport/parking options?
Bus/Train: The Millenium Line Renfrew Skytrain station is a 5 minute walk from the Italian Cultural Centre.
Parking: Free Parking is vastly available at the ICC’s own parking lot.  …

We look forward to seeing you there.

ARPICO
www.arpico.ca

You can find out more about SNOLAB here. There’s even a virtual tour.

Book commentaries: The Science of Orphan Black: The Official Companion and Star Trek Treknology; The Science of Star Trek from Tricorders to Warp Drive

I got more than I expected from both books (“The Science of Orphan Black: The Official Companion” by Casey Griffin and Nina Nesseth and “Star Trek Treknology; The Science of Star Trek from Tricorders to Warp Drive” by Ethan Siegel) I’m going to discuss by changing my expectations.

The Science of Orphan Black: The Official Companion

I had expected a book about the making of the series with a few insider stories about the production along with some science. Instead, I was treated to a season by season breakdown of the major scientific and related ethical issues in the fields of cloning and genetics.I don’t follow those areas exhaustively but from my inexpert perspective, the authors covered everything I could have hoped for (e.g., CRISPR/CAS9, Henrietta Lacks, etc.) in an accessible but demanding writing style  In other words, it’s a good read but it’s not a light read.

There are many, many pictures of Tatiana Maslany as one of her various clone identities in the book. Unfortunately, the images do not boast good reproduction values. This was disconcerting as it can lead a reader (yes, that was me) to false expectations (e.g., this is a picture book) concerning the contents. The boxed snippets from the scripts and explanatory notes inset into the text helped to break up some of the more heavy going material while providing additional historical/scripting/etc. perspectives. One small niggle, the script snippets weren’t always as relevant to the discussion at hand as the authors no doubt hoped.

I suggest reading both the Foreword by Cosima Herter, the series science consultant, and (although it could have done with a little editing) The Conversation between Cosima Herter and Graeme Manson (one of the producers). That’s where you’ll find that the series seems to have been incubated in Vancouver, Canada. It’s also where you’ll find out how much of Cosima Herter’s real life story is included in the Cosima clone’s life story.

The Introduction tells you how the authors met (as members of ‘the clone club’) and started working together as recappers for the series. (For anyone unfamiliar with the phenomenon or terminology, episodes of popular series are recapitulated [recapped] on one or more popular websites. These may or may not be commercial, i.e., some are fan sites.)

One of the authors, Casey Griffin, is a PhD candidate at the University of Southern California (USC) studying in the field of developmental and stem cell biology. I was not able to get much more information but did find her LinkedIn profile. The other author also has a science background. Nina Nesseth is described as a science communicator on the back cover of the book but she’s described as a staff scientist for Science North, a science centre located in Sudbury, Ontario, Canada. Her LinkedIn profile lists an honours Bachelor of Science (Biological and Medical Sciences) from Laurentian University, also located in Sudbury, Ontario.

It’s no surprise, given the authors’ educational background, that a bibliography (selected) has been included. This is something I very much appreciated. Oddly, given that Nesseth lists a graduate certificate in publishing as one of her credentials (on LinkedIn), there is no index (!?!). Unusually, the copyright page is at the back of the book instead of the front and boasts a fairly harsh copyright notice (summary: don’t copy anything, ever … unless you get written permission from ECW Press and the other copyright owners; Note: Herter is the copyright owner of her Foreword while the authors own the rest).

There are logos on the copyright page—more than I’m accustomed to seeing. Interestingly, two of them are government logos. It seems that taxpayers contributed to the publication of this book. The copyright notice seems a little facey to me since taxpayers (at least partially) subsidized the book, as well, Canadian copyright law has a concept called fair dealing (in the US, there’s something similar: fair use). In other words, if I chose, I could copy portions of the text without asking for permission if there’s no intent to profit from it and as long as I give attributions.

How, for example, could anyone profit from this?

In fact, in January 2017, Jun Wu and colleagues published their success in creating pig-human hybrids. (description of real research on chimeras on p. 98)

Or this snippet of dialogue,

[Charlotte] You’re my big sister.

[Sarah] How old are you? (p. 101)

All the quoted text is from “The Science of Orphan Black: The Official Companion” by Casey Griffin and Nina Nesseth (paperback published August 22, 2017).

On the subject of chimeras, the Canadian Broadcasting Corporation (CBC) featured a January 26, 2017 article about the pig-human chimeras on its website along with a video,

Getting back to the book, copyright silliness aside, it’s a good book for anyone interested in some of the  science and the issues associated with biotechnology, synthetic biology, genomes, gene editing technologies, chimeras, and more. I don’t think you need to have seen the series in order to appreciate the book.

Star Trek Treknology; The Science of Star Trek from Tricorders to Warp Drive

This looks and feels like a coffee table book. The images in this book are of a much higher quality than those in the ‘Orphan Black’ book. With thicker paper and extensive ink coverage lending to its glossy, attractive looks, it’s a physically heavy book. The unusually heavy use of black ink  would seem to be in service of conveying the feeling that you are exploring the far reaches of outer space.

It’s clear that “Star Trek Treknology; The Science of Star Trek from Tricorders to Warp Drive’s” author, Ethan Siegel, PhD., is a serious Star Trek and space travel fan. All of the series and movies are referenced at one time or another in the book in relationship to technology (treknology).

Unlike Siegel, while I love science fiction and Star Trek, I have never been personally interested in space travel. Regardless, Siegel did draw me in with his impressive ability to describe and explain physics-related ideas. Unfortunately, his final chapter on medical and biological ‘treknology’ is not as good. He covers a wide range of topics but no one is an expert on everything.

Siegel has a Wikipedia entry, which notes this (Note: Links have been removed),

Ethan R. Siegel (August 3, 1978, Bronx)[1] is an American theoretical astrophysicist and science writer, who studies Big Bang theory. He is a professor at Lewis & Clark College and he blogs at Starts With a Bang, on ScienceBlogs and also on Forbes.com since 2016.

By contrast with the ‘Orphan Black’ book, the tone is upbeat. It’s one of the reasons Siegel appreciates Star Trek in its various iterations,

As we look at the real-life science and technology behind the greatest advances anticipated by Star Trek, it’s worth remembering that the greatest legacy of the show is its message of hope. The future can be brighter and better than our past or present has ever been. It’s our continuing mission to make it so. (p. 6)

All the quoted text is from “Star Trek Treknology; The Science of Star Trek from Tricorders to Warp Drive” by Ethan Siegel (hard cover published October 15, 2017).

This book too has one of those copyright notices that fail to note you don’t need permission when it’s fair dealing to copy part of the text. While it does have an index, it’s on the anemic side and, damningly, there are neither bibliography nor reference notes of any sort. If Siegel hadn’t done such a good writing job, I might not have been so distressed.

For example, it’s frustrating for someone like me who’s been trying to get information on cortical/neural  implants and finds this heretofore unknown and intriguing tidbit in Siegel’s text,

In 2016, the very first successful cortical implant into a patient with ALS [amyotrophic lateral sclerosis] was completed, marking the very first fully implanted brain-computer interface in a human being. (p. 180)

Are we talking about the Australia team, which announced human clinical trials for their neural/cortical implant (my February 15, 2016 posting) or was it preliminary work by a team in Ohio (US) which later (?) announced a successful implant for a quadriplegic (also known as tetraplegic) patient who was then able to move hands and fingers (see my April 19, 2016 posting)? Or is it an entirely different team?

One other thing, I was a bit surprised to see no mention of quantum or neuromorphic computing in the chapter on computing. I don’t believe either was part of the Star Trek universe but they (neuromorphic and quantum computing) are important developments and Siegel makes a point, on at least a few occasions, of contrasting present day research with what was and wasn’t ‘predicted’ by Star Trek.

As for the ‘predictions’, there’s a longstanding interplay between storytellers and science and sometimes it can be a little hard to figure out which came first. I think Siegel might have emphasized that give and take a bit more.

Regardless of my nitpicking, Siegel is a good writer and managed to put an astonishing amount of ‘educational’ material into a lively and engaging book. That is not easy.

Final thoughts

I enjoyed both books and am very excited to see grounded science being presented along with the fictional stories of both universes (Star Trek and Orphan Black).

Yes, both books have their shortcomings (harsh copyright notices, no index, no bibliography, no reference notes, etc.) but in the main they offer adults who are sufficiently motivated a wealth of current scientific and technical information along with some elucidation of ethical issues.

2017 proceedings for the Canadian Science Policy Conference

I received (via email) a December 11, 2017 notice from the Canadian Science Policy Centre that the 2017 Proceedings for the ninth annual conference (Nov. 1 – 3, 2017 in Ottawa, Canada) can now be accessed,

The Canadian Science Policy Centre is pleased to present you the Proceedings of CSPC 2017. Check out the reports and takeaways for each panel session, which have been carefully drafted by a group of professional writers. You can also listen to the audio recordings and watch the available videos. The proceedings page will provide you with the opportunity to immerse yourself in all of the discussions at the conference. Feel free to share the ones you like! Also, check out the CSPC 2017 reports, analyses, and stats in the proceedings.

Click here for the CSPC 2017 Proceedings

CSPC 2017 Interviews

Take a look at the 70+ one-on-one interviews with prominent figures of science policy. The interviews were conducted by the great team of CSPC 2017 volunteers. The interviews feature in-depth perspectives about the conference, panels, and new up and coming projects.

Click here for the CSPC 2017 interviews

Amongst many others, you can find a video of Governor General Julie Payette’s notorious remarks made at the opening ceremonies and which I highlighted in my November 3, 2017 posting about this year’s conference.

The proceedings are organized by day with links to individual pages for each session held that day. Here’s a sample of what is offered on Day 1: Artificial Intelligence and Discovery Science: Playing to Canada’s Strengths,

Artificial Intelligence and Discovery Science: Playing to Canada’s Strengths

Conference Day:
Day 1 – November 1st 2017

Organized by: Friends of the Canadian Institutes of Health Research

Keynote: Alan Bernstein, President and CEO, CIFAR, 2017 Henry G. Friesen International Prizewinner

Speakers: Brenda Andrews, Director, Andrew’s Lab, University of Toronto; Doina Precup, Associate Professor, McGill University; Dr Rémi Quirion, Chief Scientist of Quebec; Linda Rabeneck, Vice President, Prevention and Cancer Control, Cancer Care Ontario; Peter Zandstra, Director, School of Biomedical Engineering, University of British Columbia

Discussants: Henry Friesen, Professor Emeritus, University of Manitoba; Roderick McInnes, Acting President, Canadian Institutes of Health Research and Director, Lady Davis Institute, Jewish General Hospital, McGill University; Duncan J. Stewart, CEO and Scientific Director, Ottawa Hospital Research Institute; Vivek Goel, Vice President, Research and Innovation, University of Toronto

Moderators: Eric Meslin, President & CEO, Council of Canadian Academies; André Picard, Health Reporter and Columnist, The Globe and Mail

Takeaways and recommendations:

The opportunity for Canada

  • The potential impact of artificial intelligence (AI) could be as significant as the industrial revolution of the 19th century.
  • Canada’s global advantage in deep learning (a subset of machine learning) stems from the pioneering work of Geoffrey Hinton and early support from CIFAR and NSERC.
  • AI could mark a turning point in Canada’s innovation performance, fueled by the highest levels of venture capital financing in nearly a decade, and underpinned by publicly funded research at the federal, provincial and institutional levels.
  • The Canadian AI advantage can only be fully realized by developing and importing skilled talent, accessible markets, capital and companies willing to adopt new technologies into existing industries.
  • Canada leads in the combination of functional genomics and machine learning which is proving effective for predicting the functional variation in genomes.
  • AI promises advances in biomedical engineering by connecting chronic diseases – the largest health burden in Canada – to gene regulatory networks by understanding how stem cells make decisions.
  • AI can be effectively deployed to evaluate health and health systems in the general population.

The challenges

  • AI brings potential ethical and economic perils and requires a watchdog to oversee standards, engage in fact-based debate and prepare for the potential backlash over job losses to robots.
  • The ethical, environmental, economic, legal and social (GEL3S) aspects of genomics have been largely marginalized and it’s important not to make the same mistake with AI.
  • AI’s rapid scientific development makes it difficult to keep pace with safeguards and standards.
  • The fields of AI’s and pattern recognition are strongly connected but here is room for improvement.
  • Self-learning algorithms such as Alphaville could lead to the invention of new things that humans currently don’t know how to do. The field is developing rapidly, leading to some concern over the deployment of such systems.

Training future AI professionals

  • Young researchers must be given the oxygen to excel at AI if its potential is to be realized.
  • Students appreciate the breadth of training and additional resources they receive from researchers with ties to both academia and industry.
  • The importance of continuing fundamental research in AI is being challenged by companies such as Facebook, Google and Amazon which are hiring away key talent.
  • The explosion of AI is a powerful illustration of how the importance of fundamental research may only be recognized and exploited after 20 or 30 years. As a result, support for fundamental research, and the students working in areas related to AI, must continue.

A couple comments

To my knowledge, this is the first year the proceedings have been made so easily accessible. In fact, I can’t remember another year where they have been open access. Thank you!

Of course, I have to make a comment about the Day 2 session titled: Does Canada have a Science Culture? The answer is yes and it’s in the province of Ontario. Just take a look at the panel,

Organized by: Kirsten Vanstone, Royal Canadian Institute for Science and Reinhart Reithmeier, Professor, University of Toronto [in Ontario]

Speakers: Chantal Barriault, Director, Science Communication Graduate Program, Laurentian University [in Ontario] and Science North [in Ontario]; Maurice Bitran, CEO, Ontario Science Centre [take a wild guess as to where this institution is located?]; Kelly Bronson, Assistant Professor, Faculty of Social Sciences, University of Ottawa [in Ontario]; Marc LePage, President and CEO, Genome Canada [in Ontario]

Moderator: Ivan Semeniuk, Science Reporter, The Globe and Mail [in Ontario]

In fact, all of the institutions are in southern Ontario, even, the oddly named Science North.

I know from bitter experience it’s hard to put together panels but couldn’t someone from another province have participated?

Ah well, here’s hoping for 2018 and for a new location. After Ottawa as the CSPC site for three years in a row, please don’t make it a fourth year in a row.

Burning coal produces harmful titanium dioxide nanoparticles

It turns out that Canada has the fifth largest reserve of coal in the world, according to the Coal in Canada Wikipedia entry (Note: Links have been removed),

Coal reserves in Canada rank fifth largest in the world (following the former Soviet Union, the United States, the People’s Republic of China and Australia) at approximately 10 billion tons, 10% of the world total.[1] This represents more energy than all of the oil and gas in the country combined. The coal industry generates CDN$5 billion annually.[2] Most of Canada’s coal mining occurs in the West of the country.[3] British Columbia operates 10 coal mines, Alberta 9, Saskatchewan 3 and New Brunswick one. Nova Scotia operates several small-scale mines, Westray having closed following the 1992 disaster there.[4]

So, this news from Virginia holds more than the usual interest for me (I’m in British Columbia). From an Aug. 8, 2017 Virginia Tech news release (also on EurekAlert),

Environmental scientists led by the Virginia Tech College of Science have discovered that the burning of coal produces incredibly small particles of a highly unusual form of titanium oxide.

When inhaled, these nanoparticles can enter the lungs and potentially the bloodstream.

The particulates — known as titanium suboxide nanoparticles — are unintentionally produced as coal is burned, creating these tiniest of particles, as small as 100 millionths of a meter [emphasis mine], said the Virginia Tech-led team. When the particles are introduced into the air — unless captured by high-tech particle traps — they can float away from power plant stacks and travel on air currents locally, regionally, and even globally.

As an example of this, these nanoparticles were found on city streets, sidewalks, and in standing water in Shanghai, China.

The findings are published in the latest issue of Nature Communications under team leader Michael F. Hochella Jr., University Distinguished Professor of Geosciences with the College of Science, and Yi Yang, a professor at East China Normal University in Shanghai. Other study participants include Duke University, the University of Kentucky, and Laurentian University in Canada.

“The problem with these nanoparticles is that there is no easy or practical way to prevent their formation during coal burning,” Hochella said, adding that in nations with strong environmental regulations, such as the United States, most of the nanoparticles would be caught by particle traps. Not so in Africa [a continent not a nation], China, or India, where regulations are lax or nonexistent, with coal ash and smoke entering the open air.

“Due to advanced technology used at U.S.-based coal burning power plants, mandated by the Clean Air Act and the Environmental Protection Agency, most of these nanoparticles and other tiny particles are removed before the final emission of the plant’s exhaust gases,” Hochella said. “But in countries where the particles from the coal burning are not nearly so efficiently removed, or removed at all, these titanium suboxide nanoparticles and many other particle types are emitted into the atmosphere, in part resulting in hazy skies that plague many countries, especially in China and India.”

Hochella and his team found these previously unknown nanoparticles not only in coal ash from around the world and in the gaseous waste emissions of coal plants, but on city streets, in soils and storm water ponds, and at wastewater treatment plants.

“I could not believe what I have found at the beginning, because they had been reported so extremely rarely in the natural environment,” said Yang, who once worked as a visiting professor in Virginia Tech’s Department of Geosciences with Hochella. “It took me several months to confirm their occurrence in coal ash samples.”

The newly found titanium suboxide — called Magnéli phases — was once thought rare, found only sparingly on Earth in some meteorites, from a small area of rock formations in western Greenland, and occasionally in moon rocks. The findings by Hochella and his team indicate that these nanoparticles are in fact widespread globally. They are only now being studied for the first time in natural environments using powerful electron microscopes.

Why did the discovery occur now? According to the report, nearly all coal contains traces of the minerals rutile and/or anatase, both “normal,” naturally occurring, and relatively inert titanium oxides, especially in the absence of light. When those minerals are burned in the presence of coal, research found they easily and quickly converted to these unusual titanium suboxide nanoparticles. The nanoparticles then become entrained in the gases that leave the power plant.

When inhaled, the nanoparticles enter deep into the lungs, potentially all the way into the air sacs that move oxygen into our bloodstream during the normal breathing process. While human lung toxicity of these particles is not yet known, a preliminary biotoxicity test by Hochella and Richard Di Giulio, professor of environmental toxicology, and Jessica Brandt, a doctoral candidate, both at Duke University, indicates that the particles do indeed have toxicity potential.

According to the team, further study is clearly needed, especially biotoxicity testing directly relevant to the human lung. Partnering with coal-power plants either in the United States or China would be ideal, said Yang.

More troubling, the study shows that titanium suboxide nanoparticles are biologically active in the dark, making the particles highly suspect. Exact human health effects are yet unknown.

“Future studies will need to very carefully investigate and access the toxicity of titanium suboxide nanoparticles in the human lung, and this could take years, a sobering thought considering its potential danger,” Hochella said.

As the titanium suboxide nanoparticle itself is produced incidentally, Hochella and his team came across the nanoparticle by accident while studying a 2014 coal ash spill in the Dan River, North Carolina. During the study of the downstream movement of toxic metals in the ash in the Dan River, the team discovered and recognized the presence of small amounts of the highly unusual titanium suboxide.

The group later produced the titanium suboxide nanoparticles when burning coal in a lab simulation.

This new potential air pollution health hazard builds on already established findings from the World Health Organization. It estimates that 3.3 million premature deaths occur worldwide per year due to polluted air, Hochella said. In China, 1.6 million premature deaths are estimated annually due to cardiovascular and respiratory injury from air pollution. Most Chinese megacities top 100 severely hazy days each year with particle concentrations two to four times higher than WHO guidelines, Yang said.

Direct health effects on humans is only one factor. Findings of thousands of scientists have determined that the biggest driver of warming of the planet and the resulting climate change is industrial-scale coal burning. The impact of titanium suboxide nanoparticles found in the atmosphere, in addition to greenhouse gases, on animals, water, and plants is not yet known.

They’ve used an unusual unit of measurement, “100 millionths of a meter,” nanoparticles are usually described in nanometers.

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

Discovery and ramifications of incidental Magnéli phase generation and release from industrial coal-burning by Yi Yang, Bo Chen, James Hower, Michael Schindler, Christopher Winkler, Jessica Brandt, Richard Di Giulio, Jianping Ge, Min Liu, Yuhao Fu, Lijun Zhang, Yuru Chen, Shashank Priya, & Michael F. Hochella Jr. Nature Communications 8, Article number: 194 (2017) doi:10.1038/s41467-017-00276-2 Published online: 08 August 2017

This paper is behind a paywall.

This put me in mind of the famous London smog, which one doesn’t hear about much anymore. For anyone not familiar with that phenomenon, here’s more from the Great Smog of London Wikipedia entry (Note: Links have been removed),

The Great Smog of London, or Great Smog of 1952 sometimes called the Big Smoke,[1] was a severe air-pollution event [emphasis mine] that affected the British capital of London in December 1952. A period of cold weather, combined with an anticyclone and windless conditions, collected airborne pollutants – mostly arising from the use of coal [emphasis mine]– to form a thick layer of smog over the city. It lasted from Friday, 5 December to Tuesday, 9 December 1952 and then dispersed quickly when the weather changed.

It caused major disruption by reducing visibility and even penetrating indoor areas, far more severe than previous smog events experienced in the past, called “pea-soupers”. Government medical reports in the following weeks, however, estimated that up until 8 December, 4,000 people had died as a direct result of the smog and 100,000 more were made ill by the smog’s effects on the human respiratory tract. More recent research suggests that the total number of fatalities was considerably greater, about 12,000.[2]

London had suffered since the 1200s from poor air quality,[3] which worsened in the 1600s,[4][5] but the Great Smog is known to be the worst air-pollution event in the history of the United Kingdom,[6] and the most significant in terms of its effect on environmental research, government regulation, and public awareness of the relationship between air quality and health.[2][4] It led to several changes in practices and regulations, including the Clean Air Act 1956. …

Frogs: monitoring them, finding new species, and research about the golden ones in Panama

I have three frog-oriented items and while they’re not strictly speaking in my usual range of topics, given this blog’s name and the fact I haven’t posted a frog piece in quite a while, it seems this is a good moment to address that lack.

Monitoring frogs and amphibians at Trent University (Ontario, Canada)

From a March 23, 2015 Trent University news release,

With the decline of amphibian populations around the world, a team of researchers led by Trent University’s Dr. Dennis Murray will seek to establish environmental DNA (eDNA) monitoring of amphibian occupancy and aquatic ecosystem risk assessment with the help of a significant grant of over $596,000 from the Natural Sciences and Engineering Research Council of Canada (NSERC).

Awarded to Professor Murray, a Canada research chair in integrative wildlife conservation, bioinformatics, and ecological modelling and professor at Trent University along with colleagues Dr. Craig Brunetti of the Biology department, and Dr. Chris Kyle of the Forensic Science program, and partners at Laurentian University, University of Toronto, McGill University, Ontario Ministry of Natural Resources and Forestry and Environment Canada, the grant will support the development of tools that will promote a cleaner aquatic environment.

The project will use amphibian DNA found in natural breeding habitats to determine the presence and abundance of amphibians as well as their pathogens. This new technology capitalizes on Trent University’s expertise and infrastructure in the areas of wildlife DNA and water quality.

“We’re honoured to have received the grant to help us drive the project forward,” said Prof. Murray. “Our plan is to place Canada, and Trent, in a leadership position with respect to aquatic wildlife monitoring and amphibian conservation.”

Amphibian populations are declining worldwide, yet in Canada, amphibian numbers are not monitored closely, meaning changes in their distribution or abundance may be unnoticeable. Amphibian monitoring in Canada is conducted by citizen scientists who record frog breeding calls when visiting bodies of water during the spring. However, the lack of formalized amphibian surveys leaves Canada in a vulnerable position regarding the status of its diverse amphibian community.

Prof. Murray believes that the protocols developed from this project could revolutionize how amphibian populations are monitored in Canada and in turn lead to new insights regarding the population trends for several amphibian species across the country.

Here’s more about NSERC and Trent University from the news release,

About NSERC

NSERC is a federal agency that helps make Canada a country of discoverers and innovators. The agency supports almost 30,000 post-secondary students and postdoctoral fellows in their advanced studies. NSERC promotes discovery by funding approximately 12,000 professors every year and fosters innovation by encouraging over 2,400 Canadian companies to participate and invest in post-secondary research projects.

The NSERC Strategic Project Grants aim to increase research and training in areas that could strongly influence Canada’s economy, society or environment in the next 10 years in four target areas: environmental science and technologies; information and communications technologies; manufacturing; and natural resources and energy.

About Trent University

One of Canada’s top universities, Trent University was founded on the ideal of interactive learning that’s personal, purposeful and transformative. Consistently recognized nationally for leadership in teaching, research and student satisfaction, Trent attracts excellent students from across the country and around the world. Here, undergraduate and graduate students connect and collaborate with faculty, staff and their peers through diverse communities that span residential colleges, classrooms, disciplines, hands-on research, co-curricular and community-based activities. Across all disciplines, Trent brings critical, integrative thinking to life every day. As the University celebrates its 50th anniversary in 2014/15, Trent’s unique approach to personal development through supportive, collaborative community engagement is in more demand than ever. Students lead the way by co-creating experiences rooted in dialogue, diverse perspectives and collaboration. In a learning environment that builds life-long passion for inclusion, leadership and social change, Trent’s students, alumni, faculty and staff are engaged global citizens who are catalysts in developing sustainable solutions to complex issues. Trent’s Peterborough campus boasts award-winning architecture in a breathtaking natural setting on the banks of the Otonabee River, just 90 minutes from downtown Toronto, while Trent University Durham delivers a distinct mix of programming in the GTA.

Trent University’s expertise in water quality could be traced to its proximity to Canada’s Experimental Lakes Area (ELA), a much beleaguered research environment due to federal political imperatives. You can read more about the area and the politics in this Wikipedia entry. BTW, I am delighted to learn that it still exists under the auspices of the International Institute for Sustainable Development (IISD),

Taking this post into nanotechnology territory while mentioning the ELA, Trent University published a Dec. 8, 2014 news release about research into silver nanoparticles,

For several years, Trent University’s Dr. Chris Metcalfe and Dr. Maggie Xenopoulos have dedicated countless hours to the study of aquatic contaminants and the threat they pose to our environment.

Now, through the efforts of the International Institute for Sustainable Development (IISD), their research is reaching a wider audience thanks to a new video (Note: A link has been removed).

The video is one of a five-part series being released by the IISD that looks into environmental issues in Canada. The video entitled “Distilling Science at the Experimental Lakes Area: Nanosilver” and featuring Professors Metcalfe and Xenopoulos profiles their research around nanomaterials at the Experimental Lakes Area.

Prof. Xenopolous’ involvement in the project falls in line with other environmental issues she has tackled. In the past, her research has examined how human activities – including climate change, eutrophication and land use – affect ecosystem structure and function in lakes and rivers. She has also taken an interest in how land use affects the material exported and processed in aquatic ecosystems.

Prof. Metcalfe’s ongoing research on the fate and distribution of pharmaceutical and personal care products in the environment has generated considerable attention both nationally and internationally.

Together, their research into nanomaterials is getting some attention. Nanomaterials are submicroscopic particles whose physical and chemical properties make them useful for a variety of everyday applications. They can be found in certain pieces of clothing, home appliances, paint, and kitchenware. Initial laboratory research conducted at Trent University showed that nanosilver could strongly affect aquatic organisms at the bottom of the food chain, such as bacteria, algae and zooplankton.

To further examine these effects in a real ecosystem, a team of researchers from Trent University, Fisheries and Oceans Canada and Environment Canada has been conducting studies at undisclosed lakes in northwestern Ontario. The Lake Ecosystem Nanosilver (LENS) project has been monitoring changes in the lakes’ ecosystem that occur after the addition of nanosilver.

“In our particular case, we will be able to study and understand the effects of only nanosilver because that is the only variable that is going to change,” says Prof. Xenopoulos. “It’s really the only place in the world where we can do that.”

The knowledge gained from the study will help policy-makers make decisions about whether nanomaterials can be a threat to aquatic ecosystems and whether regulatory action is required to control their release into the environment.

You can find the 13 mins. video here: https://www.youtube.com/watch?v=_nJai_B4YH0#action=share

Shapeshifting frogs, a new species in Ecuador

Caption: This image shows skin texture variation in one individual frog (Pristimantis mutabilis) from Reserva Las Gralarias. Note how skin texture shifts from highly tubercular to almost smooth; also note the relative size of the tubercles on the eyelid, lower lip, dorsum and limbs. Credit: Zoological Journal of the Linnean Society

Caption: This image shows skin texture variation in one individual frog (Pristimantis mutabilis) from Reserva Las Gralarias. Note how skin texture shifts from highly tubercular to almost smooth; also note the relative size of the tubercles on the eyelid, lower lip, dorsum and limbs.
Credit: Zoological Journal of the Linnean Society

Here’s more about the shapeshifting and how the scientists figured out what the frogs were doing (from a March 23, 2015 Case Western Research University news release on EurekAlert; Note: A link has been removed),

A frog in Ecuador’s western Andean cloud forest changes skin texture in minutes, appearing to mimic the texture it sits on.

Originally discovered by a Case Western Reserve University PhD student and her husband, a projects manager at Cleveland Metroparks’ Natural Resources Division, the amphibian is believed to be the first known to have this shape-shifting capability.

But the new species, called Pristimantis mutabilis, or mutable rainfrog, has company. Colleagues working with the couple recently found that a known relative of the frog shares the same texture-changing quality–but it was never reported before.

The frogs are found at Reserva Las Gralarias, a nature reserve originally created to protect endangered birds in the Parish of Mindo, in north-central Ecuador.

The researchers, Katherine and Tim Krynak, and colleagues from Universidad Indoamérica and Tropical Herping (Ecuador) co-authored a manuscript describing the new animal and skin texture plasticity in the Zoological Journal of the Linnean Society this week. They believe their findings have broad implications for how species are and have been identified. The process may now require photographs and longer observations in the field to ensure the one species is not mistakenly perceived as two because at least two species of rain frogs can change their appearance.

Katherine Krynak believes the ability to change skin texture to reflect its surroundings may enable P. mutabilis to help camouflage itself from birds and other predators.

The Krynaks originally spotted the small, spiny frog, nearly the width of a marble, sitting on a moss-covered leaf about a yard off the ground on a misty July night in 2009. The Krynaks had never seen this animal before, though Tim had surveyed animals on annual trips to Las Gralarias since 2001, and Katherine since 2005.

They captured the little frog and tucked it into a cup with a lid before resuming their nightly search for wildlife. They nicknamed it “punk rocker” because of the thorn-like spines covering its body.

The next day, Katherine Krynak pulled the frog from the cup and set it on a smooth white sheet of plastic for Tim to photograph. It wasn’t “punk “–it was smooth-skinned. They assumed that, much to her dismay, she must have picked up the wrong frog.

“I then put the frog back in the cup and added some moss,” she said. “The spines came back… we simply couldn’t believe our eyes, our frog changed skin texture!

“I put the frog back on the smooth white background. Its skin became smooth.”

“The spines and coloration help them blend into mossy habitats, making it hard for us to see them,” she said. “But whether the texture really helps them elude predators still needs to be tested.”

During the next three years, a team of fellow biologists studied the frogs. They found the animals shift skin texture in a little more than three minutes.

Juan M. Guayasamin, from Universidad Tecnológica Indoamérica, Ecuador, the manuscript’s first author, performed morphological and genetic analyses showing that P. mutabilis was a unique and undescribed species. Carl R. Hutter, from the University of Kansas, studied the frog’s calls, finding three songs the species uses, which differentiate them from relatives. The fifth author of the paper, Jamie Culebras, assisted with fieldwork and was able to locate a second population of the species. Culebras is a member of Tropical Herping, an organization committed to discovering, and studying reptiles and amphibians.

Guayasamin and Hutter discovered that Prismantis sobetes, a relative with similar markings but about twice the size of P. mutabilis, has the same trait when they placed a spiny specimen on a sheet and watched its skin turn smooth. P. sobetes is the only relative that has been tested so far.

Because the appearance of animals has long been one of the keys to identifying them as a certain species, the researchers believe their find challenges the system, particularly for species identified by one or just a few preserved specimens. With those, there was and is no way to know if the appearance is changeable.

The Krynaks, who helped form Las Gralarias Foundation to support the conservation efforts of the reserve, plan to return to continue surveying for mutable rain frogs and to work with fellow researchers to further document their behaviors, lifecycle and texture shifting, and estimate their population, all in effort to improve our knowledge and subsequent ability to conserve this paradigm shifting species.

Further, they hope to discern whether more relatives have the ability to shift skin texture and if that trait comes from a common ancestor. If P. mutabilis and P. sobetes are the only species within this branch of Pristimantis frogs to have this capability, they hope to learn whether they retained it from an ancestor while relatives did not, or whether the trait evolved independently in each species.

Golden frog of Panama and its skin microbiome

Caption: Researchers studied microbial communities on the skin of Panamanian golden frogs to learn more about amphibian disease resistance. Panamanian golden frogs live only in captivity. Continued studies may help restore them back to the wild. Credit: B. Gratwicke/Smithsonian Conservation Biology Institute

Caption: Researchers studied microbial communities on the skin of Panamanian golden frogs to learn more about amphibian disease resistance. Panamanian golden frogs live only in captivity. Continued studies may help restore them back to the wild.
Credit: B. Gratwicke/Smithsonian Conservation Biology Institute

Among many of the pressures on frog populations, there’s a lethal fungus which has affected some 200 species of frogs. A March 23, 2015 news item on ScienceDaily describes some recent research into the bacterial communities present on frog skin,

A team of scientists including Virginia Tech researchers is one step closer to understanding how bacteria on a frog’s skin affects its likelihood of contracting disease.

A frog-killing fungus known as Batrachochytrium dendrobatidis, or Bd, has already led to the decline of more than 200 amphibian species including the now extinct-in-the-wild Panamanian golden frog.

In a recent study, the research team attempted to apply beneficial bacteria found on the skin of various Bd-resistant wild Panamanian frog species to Panamanian golden frogs in captivity, to see if this would stimulate a defense against the disease.

A March 23, 2015 Virginia Tech University news release on EurekAlert, which originated the news item, provides a twist and a turn in the story (Note: Links have been removed),

They found that while the treatment with beneficial bacteria was not successful due to its inability to stick to the skin, there were some frogs that survived exposure to the fungus.

These survivors actually had unique bacterial communities on their skin before the experiments started.

The next step is to explore these new bacterial communities.

“We were disappointed that the treatment didn’t work, but glad to have discovered new information about the relationship between these symbiotic microbial communities and amphibian disease resistance,” said Lisa Belden, an associate professor of biological sciences in the College of Science, a Fralin Life Science Institute affiliate, and a faculty member with the new Global Change Center at Virginia Tech. “Every bit of information gets us closer to getting these frogs back into nature.”

Studying the microbial communities of Panamanian golden frogs was the dissertation focus of Belden’s former graduate student Matthew Becker, who graduated with a Ph.D. in biological sciences from Virginia Tech in 2014 and is now a fellow at the Smithsonian Conservation Biology Institute.

“Anything that can help us predict resistance to this disease is very useful because the ultimate goal of this research is to establish healthy populations of golden frogs in their native habitat,” Becker told Smithsonian Science News. “I think identifying alternative probiotic treatment methods that optimize dosages and exposure times will be key for moving forward with the use of probiotics to mitigate chytridiomycosis.”

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

Composition of symbiotic bacteria predicts survival in Panamanian golden frogs infected with a lethal fungus by Matthew H. Becker , Jenifer B. Walke , Shawna Cikanek , Anna E. Savage , Nichole Mattheus , Celina N. Santiago , Kevin P. C. Minbiole , Reid N. Harris , Lisa K. Belden , Brian Gratwicke. April 2015 Volume: 282 Issue: 1805 DOI: 10.1098/rspb.2014.2881 Published 18 March 2015

This is an open access paper.

For anyone curious about the article in the Smithsonian mentioned in the news release, you can find it here.