Tag Archives: University of British Columbia

Synthetic Aesthetics update and an informal Canadian synthetic biology roundup

Amanda Ruggeri has written a very good introduction to synthetic biology for nonexperts in her May 20, 2015 Globe and Mail article about ‘Designing for the Sixth Extinction’, an exhibit showcasing designs and thought experiments focused on synthetic biology ,

In a corner of Istanbul’s Design Biennial late last year [2014], photographs of bizarre creatures sat alongside more conventional displays of product design and typefaces. Diaphanous globes, like transparent balloons, clung to the mossy trunk of an oak tree. Rust-coloured patterns ran across green leaves, as if the foliage had been decorated with henna. On the forest floor, a slug-like creature slithered, its back dotted with gold markings; in another photograph, what looked like a porcupine without a head crawled over the dirt, its quills tipped blood-red.

But as strange as the creatures looked, what they actually are is even stranger. Not quite living things, not quite machines, these imagined prototypes inhabit a dystopic, future world – a world in which they had been created to solve the problems of the living. The porcupine, for example, is an Autonomous Seed Disperser, described as a device that would collect and disperse seeds to increase biodiversity. The slug would be programmed to seek out acidic soils and neutralize them by dispersing an alkali hygroscopic fluid.

They are the designs – and thought experiments – of London-based Alexandra Daisy Ginsberg, designer, artist and lead author of the book Synthetic Aesthetics: Investigating Synthetic Biology’s Designs on Nature. In her project Designing for the Sixth Extinction, which after Istanbul is now on display at the Design Museum in London, Ginsberg imagines what a synthetic biology-designed world would look like – and whether it’s desirable. “

I have a couple of comments. First, the ‘Synthetic Aesthetics: Investigating Synthetic Biology’s Designs on Nature’ book launch last year was covered here in a May 5, 2014 post. where you’ll notice a number of the academics included in Ruggeri’s article are contributors to the book (but not mentioned as such). Second, I cannot find ‘Design for the Sixth Extinction’ listed as an exhibition on London’s Design Museum website.

Getting back to the matter at hand, not all of the projects mentioned in Ruggeri’s article are ‘art’ projects, there is also this rather practical and controversial initiative,

Designing even more complex organisms is the inevitable, and controversial, next step. And those designs have already begun. The British company Oxitec has designed a sterile male mosquito. When the bugs are released into nature and mate, no offspring result, reducing the population or eliminating it altogether. This could be a solution to dengue fever, a mosquito-carried disease that infects more than 50 million people each year: In field trials in Cayman, Panama and Brazil, the wild population of the dengue-carrying mosquito species was reduced by 90 per cent. Yet, as a genetically engineered solution, it also makes some skittish. The consequences of such manipulations remain unforeseen, they say. Proponents counter that the solution is more elegant, and safer, than the current practice of spraying chemicals.

Even so, the engineered mosquito leads to overarching questions: What are the dangers of tinkering with life? Could this cause a slide toward eugenics? Currently, the field doesn’t have an established ethics oversight process, something some critics are pushing to change.

It’s a surprising piece for the Globe and Mail newspaper to run since it doesn’t have a Canadian angle to it and the Globe and Mail doesn’t specialize in science (not withstanding Ivan Semeniuk’s science articles) or art/science or synthetic biology writing, for that matter. Perhaps it bodes an interest and more pieces on emerging science and technology and on art/science projects?

In any event, it seems like a good time to review some of the synthetic biology work or the centres of activity in Canada.  I believe the last time I tackled this particular topic was in a May 24, 2010 post titled, Canada and synthetic biology in the wake of the first ‘synthetic’ bacteria.

After a brief search, I found three centres for research:

Concordia [University] Centre for Applied Synthetic Biology (CASB)

[University of Toronto] The Synthetic Biology and Cellular Control Lab

[University of British Columbia] Centre for High-Throughput Biology (CHiBi)

Following an Oct. 27 – 28, 2014 UK-Canada Synthetic Biology Workshop held at Concordia University, Rémi Quirion, Vincent Martin, Pierre Meulien and Marc LePage co-wrote a Nov. 4, 2014 Concordia University post titled, How Canada is poised to revolutionize synthetic biology,

Rémi Quirion is the Chief Scientist of Québec, Fonds de recherche du Québec. Vincent Martin is Canada Research Chair in Microbial Genomics and Engineering and a professor in the Department of Biology at Concordia University in Montreal. Pierre Meulien is President and CEO of Genome Canada. Marc LePage is the President and CEO of Génome Québec.

Canada’s research and business communities have an opportunity to become world leaders in a burgeoning field that is fast shaping how we deal with everything from climate change to global food security and the production of lifesaving medications. The science of synthetic biology has the transformative capacity to equip us with novel technology tools and products to build a more sustainable society, while creating new business and employment opportunities for the economy of tomorrow.

We can now decipher the code of life for any organism faster and less expensively than ever before. Canadian scientists are producing anti-malarial drugs from organic materials that increase the availability and decrease the cost of lifesaving medicines. They are also developing energy efficient biofuels to dramatically reduce environmental and manufacturing costs, helping Canadian industry to thrive in the global marketplace.

The groundwork has also been laid for a Canadian revolution in the field. Canada’s scientific community is internationally recognized for its leadership in genomics research and strong partnerships with key industries. Since 2000, Genome Canada and partners have invested more than $2.3 billion in deciphering the genomes of economically important plants, animals and microbes in order to understand how they function. A significant proportion of these funds has been invested in building the technological toolkits that can be applied to synthetic biology.

But science cannot do it alone. Innovation on this scale requires multiple forms of expertise in order to be successful. Research in law, business, social sciences and humanities is vital to addressing questions of ethics, supply chain management, social innovation and cultural adaptation to new technologies. Industry knowledge and investments, as well as the capacity to incentivize entrepreneurship, are key to devising business models that will enable new products to thrive. Governments and funding agencies also need to do their part by supporting multidisciplinary research, training and infrastructure.

It’s a bit ‘hype happy’ for my taste but it does provide some fascinating insight in what seems to be a male activity in Canada.

Counterbalancing that impression is an Oct. 6, 2013 article by Ivan Semeniuk for the Globe and Mail about a University of Lethbridge team winning the top prize in a synthetic biology contest,

If you want to succeed in the scientific revolution of the future, it helps to think about life as a computer program.

That strategy helped University of Lethbridge students walk away with the top prize in a synthetic biology competition Sunday. Often touted as the genetic equivalent of the personal computer revolution, synthetic biology involves thinking about cells as programmable machines that can be designed and built to suit a particular need – whether it’s mass producing a vaccine or breaking down a hazardous chemical in the environment.

The five member Lethbridge team came up with a way to modify how cells translate genetic information into proteins. Rather than one bit of DNA carrying the information to make one protein – the usual way cells go about their business – the method involves inserting a genetic command that jiggles a cell’s translational machinery while it’s in mid-operation, coaxing it to produce two proteins out of the same DNA input.

“We started off with a computer analogy – kind of like zipping your files together – so you’d zip two protein sequences together and therefore save space,” said Jenna Friedt, a graduate student in biochemistry at Lethbridge. [emphasis mine]

There are concerns other than gender issues, chief amongst them, ethics. The Canadian Biotechnology Action Network maintains an information page on Synthetic Biology which boasts this as its latest update,

October 2014: In a unanimous decision of 194 countries, the United Nation’s Convention on Biological Diversity formally urged countries to regulate synthetic biology, a new extreme form of genetic engineering. The landmark decision follows ten days of hard-fought negotiations between developing countries and a small group of wealthy biotech-friendly economies. Until now, synthetic organisms have been developed and commercialized without international regulations. …

Finally, there’s a June 2014 synthetic biology timeline from the University of Ottawa’s Institute for Science, Society, and Policy (ISSP) which contextualizes Canadian research, policy and regulation with Australia, the European Union, the UK, and the US.

(On a closely related note, there’s my May 14, 2015 post about genetic engineering and newly raised concerns.)

Research2Reality: a science media engagement experience dedicated to Canadian science

As of May 11, 2015, Canadians will be getting an addition to their science media environment (from the May 4, 2015 news release),

Research2Reality to celebrate Canadian research stars

Social media initiative to popularize scientific innovation

May 4, 2015, TORONTO – On Monday, May 11, Research2Reality.com goes live and launches a social media initiative that will make the scientist a star. Following in the footsteps of popular sites like IFLScience and How Stuff Works, Research2Reality uses a video series and website to engage the community in the forefront of scientific discoveries made here in Canada.

The interviews feature some of Canada’s leading researchers such as Dick Peltier – director of the Centre for Global Change Science at the University of Toronto, Sally Aitken – director of the Centre for Forest Conservation Genetics at the University of British Columbia and Raymond Laflamme – executive director of the Institute for Quantum Computing at the University of Waterloo.

“Right now many Canadians don’t understand the scope of cutting-edge work being done in our backyards,” says Research2Reality co-founder and award-winning professor Molly Shoichet. “This initiative will bridge that gap between researchers and the public.”

Also launching Monday, May 11, courtesy of Research2Reality’s official media partner, Discovery Science, is a complementary website www.sciencechannel.ca/Shows/Research2Reality. The new website will feature the exclusive premieres of a collection of interview sessions. In addition, Discovery Science and Discovery will broadcast an imaginative series of public service announcements through the end of the year, while social media accounts will promote Research2Reality, including Discovery’s flagship science and technology program DAILY PLANET.

About Research2Reality:
Research2Reality is a social media initiative designed to popularize the latest Canadian research. It was founded by Molly Shoichet, Professor of Chemical Engineering & Applied Chemistry and Canada Research Chair in Tissue Engineering at the University of Toronto, and Mike MacMillan, founder and producer of Lithium Studios Productions. Research2Reality’s founding partners are leading research-intensive universities – the University of Alberta, the University of British Columbia, McMaster University, the University of Toronto, the University of Waterloo, and Western University – along with the Ontario Government and Discovery Networks. Discovery Science is the official media partner. Research2Reality is also supported by The Globe and Mail.

Research2Reality details

A Valentine of sorts to Canadian science researchers from Molly Shoichet (pronounced shoy [and] quette as in David Arquette)  and her producing partner Mike MacMillan of Lithium Studios, Research2Reality gives Canadians an opportunity to discover online some of the extraordinary work done by scientists of all stripes, including (unusually) social scientists, in this country. The top tier in this effort is the interview video series ‘The Orange Chair Sessions‘  which can be found and shared across

Shoichet and MacMillan are convinced there’s an appetite for more comprehensive science information. Supporting The Orange Chair Sessions is a complementary website operated by Discovery Channel where there are

  • more interviews
  • backgrounders,
  • biographies,
  • blogs, and
  • links to other resources

Discovery Channel is also going to be airing special one minute  public service announcements (PSA) on topics like water, quantum computing, and cancer. Here’s one of the first of those PSAs,

“I’m very excited about this and really hope that other people will be too,” says Shoichet. The audience for the Research2Reality endeavour is for people who like to know more and have questions when they see news items about science discoveries that can’t be answered by investigating mainstream media programmes or trying to read complex research papers.

This is a big undertaking. ” Mike and I thought about this for about two years.” Building on the support they received from the University of Toronto, “We reached out to the vice-presidents of research at the top fifteen universities in the country.” In the end, six universities accepted the invitation to invest in this project,

  • the University of British Columbia,
  • the University of Alberta,
  • Western University (formerly the University of Western Ontario),
  • McMaster University,
  • Waterloo University, and, of course,
  • the University of Toronto

(Unfortunately, Shoichet was not able to answer a question about the cost for an individual episode but perhaps when there’s time that detail and more about the financing will be made available. [ETA May 11, 2015 1625 PDT: Ivan Semeniuk notes this is a $400,000 project in his Globe and Mail May 11, 2015 article.]) As part of their involvement, the universities decide which of their researchers/projects should be profiled then Research2Reality swings into action. “We shoot our own video, that is, we (Mike and I) come out and conduct interviews that take approximately fifteen minutes. We also shoot a b-roll, that is, footage of the laboratories and other relevant sites so it’s not all ‘talking heads’.” Shoichet and MacMillan are interested in the answer to two questions, “What are you doing? and Why do we care?” Neither interviewer/producer is seen or heard on camera as they wanted to keep the focus on the researcher.

Three videos are being released initially with another 67 in the pipeline for a total of 70.  The focus is on research of an international calibre and one of the first interviews to be released (Shoichet’s will be release later) is Raymond Laflamme’s (he’s also featured in the ‘quantum PSA’.

Raymond Laflamme

Who convinces a genius that he’s gotten an important cosmological concept wrong or ignored it? Alongside Don Page, Laflamme accomplished that feat as one of Stephen Hawking’s PhD students at the University of Cambridge. Today (May 11, 2015), Laflamme is (from his Wikipedia entry)

… co-founder and current director of the Institute for Quantum Computing at the University of Waterloo. He is also a professor in the Department of Physics and Astronomy at the University of Waterloo and an associate faculty member at Perimeter Institute for Theoretical Physics. Laflamme is currently a Canada Research Chair in Quantum Information.

Laflamme changed his focus from quantum cosmology to quantum information while at Los Alamos, “To me, it seemed natural. Not much of a change.” It is the difference between being a theoretician and an experimentalist and anyone who’s watched The Big Bang Theory (US television programme) knows that Laflamme made a big leap.

One of his major research interests is quantum cryptography, a means of passing messages you can ensure are private. Laflamme’s team and a team in Vienna (Austria) have enabled two quantum communication systems, one purely terrestrial version, which can exchange messages with another such system up to 100 km. away. There are some problems yet to be solved with terrestrial quantum communication. First, buildings, trees, and other structures provide interference as does the curvature of the earth. Second, fibre optic cables absorb some of the photons en route.

Satellite quantum communication seems more promising as these problems are avoided altogether. The joint Waterloo/Vienna team of researchers has  conducted successful satellite experiments in quantum communication in the Canary Islands.

While there don’t seem to be any practical, commercial quantum applications, Laflamme says that isn’t strictly speaking the truth, “In the last 10  to 15 years many ideas have been realized.” The talk turns to quantum sensing and Laflamme mentions two startups and notes he can’t talk about them yet. But there is Universal Quantum Devices (UQD), a company that produces parts for quantum sensors. It is Laflamme’s startup, one he co-founded with two partners. (For anyone unfamiliar with the Canadian academic scene, Laflamme’s home institution, the University of Waterloo, is one of the most actively ‘innovative’ and business-oriented universities in Canada.)

LaFlamme’s interests extend beyond laboratory work and business. He’s an active science communicator as can be seen in this 2010 TEDxWaterloo presentation where he takes his audience from the discovery of fire to quantum physics concepts such as a ‘quantum superposition’ and the ‘observer effect’ to the question, ‘What is reality?’ in approximately 18 mins.

For anyone who needs a little more information, a quantum superposition is a term referring the ability of a quantum object to inhabit two states simultaneously, e.g., on/off. yes/no, alive/dead, as in Schrödinger’s cat. (You can find out more about quantum superpositions in this Wikipedia essay and about Schrodinger’s cat in this Wikipedia essay.) The observer effect is a phenomenon whereby the observer of a quantum experiment affects that experiment by the act of observing it. (You can find out more about the observer effect in this Wikipedia essay.)

The topic of reality is much trickier to explain. No one has yet been able to offer a viable theory for why the world at the macro scale behaves one way (classical physics) and the world at the quantum scale behaves another way (quantum physics). As Laflamme notes, “There is no such thing as a superposition in classical physics but we can prove in the laboratory that it exists in quantum physics.” He goes on to suggest that children, raised in an environment where quantum physics and its applications are commonplace, will have an utterly different notion as to what constitutes reality.

Laflamme is also interested in music and consulted on a ‘quantum symphony’. He has this to say about it in an Sept. 20, 2012 piece on the University of Waterlo website,

Science and art share a common goal — to help us understand our universe and ourselves.  Research at IQC [Institute for Quantum Computing] aims to provide important new understanding of nature’s building blocks, and devise methods to turn that understanding into technologies beneficial for society.Since founding IQC a decade ago, I have sought ways to bridge science and the arts, with the belief that scientific discovery itself is a source of beauty and inspiration.  Our collaboration with the Kitchener-Waterloo Symphony was an example — one of many yet to come — of how science and the arts provide different but complementary insights into our universe and ourselves.

I wrote about the IQC and the symphony which debuted at the IQC’s opening in a Sept. 25, 2012 posting.

Music is not the only art which has attracted Laflamme’s talents. He consulted on a documentary, The Quantum Tamers: Revealing our weird and wired future, a co-production between Canada’s Perimeter Institute and Title Entertainment,

From deep inside the sewers of Vienna, site of groundbreaking quantum teleportation experiments, to cutting-edge quantum computing labs, to voyages into the minds of the world’s brightest thinkers, including renowned British scientist Stephen Hawking, this documentary explores the coming quantum technological revolution.

All of this suggests an interest in science not seen since the 19th century when scientists could fill theatres for their lectures. Even Hollywood is capitalizing on this interest. Laflamme, who saw ‘Interstellar’, ‘The Imitation Game’ (Alan Turing), and ‘The Theory of Everything’ (Stephen Hawking) in fall 2014 comments, “I was surprised by how much science there was in The Imitation Game and Interstellar.” As for the Theory of Everything, “I was apprehensive since I know Stephen well. But, the actor, Eddie Redmayne, and the movie surprised me. There were times when he moved his head or did something in a particular way—he was Stephen. Also, most people don’t realize what an incredible sense of humour Stephen has and the movie captured that well.” Laflamme also observed that it was a movie about a relationship and not really concerned with science and its impacts (good and ill) or scientific accomplishments.  Although he allows, “It could have had more science.”

Research2Reality producers

Molly Shoichet

Co-producer Shoichet has sterling scientific credentials of her own. In addition to this science communication project, she runs the Shoichet Lab at the University of Toronto (from the Dr. Molly Shoichet bio page),

Dr. Molly Shoichet holds the Tier 1 Canada Research Chair in Tissue Engineering and is University Professor of Chemical Engineering & Applied Chemistry, Chemistry and Biomaterials & Biomedical Engineering at the University of Toronto. She is an expert in the study of Polymers for Drug Delivery & Regeneration which are materials that promote healing in the body.

Dr. Shoichet has published over to 480 papers, patents and abstracts and has given over 310 lectures worldwide.  She currently leads a laboratory of 25 researchers and has graduated 134 researchers over the past 20 years.  She founded two spin-off companies from research in her laboratory.

Dr. Shoichet is the recipient of many prestigious distinctions and the only person to be a Fellow of Canada’s 3 National Academies: Canadian Academy of Sciences of the Royal Society of Canada, Canadian Academy of Engineering, and Canadian Academy of Health Sciences. Dr. Shoichet holds the Order of Ontario, Ontario’s highest honour and is a Fellow of the American Association for the Advancement of Science. In 2013, her contributions to Canada’s innovation agenda and the advancement of knowledge were recognized with the QEII Diamond Jubilee Award. In 2014, she was given the University of Toronto’s highest distinction, University Professor, a distinction held by less than 2% of the faculty.

Mike MacMillan

MacMIllan’s biography (from the Lithium Studios website About section hints this is his first science-oriented series (Note: Links have been removed),

Founder of Lithium Studios Productions
University of Toronto (‘02)
UCLA’s Professional Producing Program (‘11)

His first feature, the dark comedy / thriller I Put a Hit on You (2014, Telefilm Canada supported), premiered at this year’s Slamdance Film Festival in Park City. Guidance (2014, Telefilm Canada supported, with super producer Alyson Richards over at Edyson), a dark comedy/coming of age story is currently in post-production, expected to join the festival circuit in September 2014.

Mike has produced a dozen short films with Toronto talents Dane Clark and Linsey Stewart (CAN – Long Branch, Margo Lily), Samuel Fluckiger (SWISS – Terminal, Nightlight) and Darragh McDonald (CAN – Love. Marriage. Miscarriage.). They’ve played at the top film fests around the world and won a bunch of awards.

Special skills include kickass hat collection and whiskey. Bam.

Final comments

It’s nice to see the Canadian scene expanding; I’m particularly pleased to learn social scientists will be included.Too often researchers from the physical sciences or natural sciences and researchers from the social sciences remain aloof from each other. In April 2013, I attended a talk by Evelyn Fox Keller, physicist, feminist, and philosopher, who read from a paper she’d written based on a then relatively recent experience in South Africa where researchers had aligned themselves in two different groups and refused to speak to each other. They were all anthropologists but the sticking point was the type of science they practiced. One group were physical anthropologists and the other were cultural anthropologists. That’s an extreme example unfortunately symptomatic of a great divide. Bravo to Research2Reality for bringing the two groups together.

As for the science appetite Shoichet and MacMillan see in Canada, this is not the only country experiencing a resurgence of interest; they’ve been experiencing a science media expansion in the US.  Neil deGrasse Tyson’s Star Talk television talk show, which also exists as a radio podcast, debuted on April 19, 2015 (Yahoo article by Calla Cofield); Public Radio Exchange’s (PRX) Transistor; a STEM (science, technology, engineering, and mathematics) audio project debuted in Feb. 2015; and video podcast Science Goes to the Movies also debuted in Feb. 2015 (more about the last two initiatives in my March 6, 2015 posting [scroll down about 40% of the way]). Finally (for the burgeoning US science media scene) and neither least nor new, David Bruggeman has a series of posts titled, Science and Technology Guests on Late Night, Week of …, on his Pasco Phronesis blog which has been running for many years. Bruggeman’s series is being included here because most people don’t realize that US late night talk shows have jumped into the science scene. You can check  David’s site here as he posts this series on Mondays and this is Monday, May 11, 2015.

It’s early days for Research2Reality and it doesn’t yet have the depth one might wish. The videos are short (the one featured on the Discovery Channel’s complementary website is less than 2 mins. and prepare yourself for ads). They may not be satisfying from an information perspective but what makes The Orange Chair Series fascinating is the peek into the Canadian research scene. Welcome to Research2Reality and I hope to hear more about you in the coming months.

[ETA May 11, 2015 at 1625 PDT: Semeniuk’s May 11, 2015 article mentions a few other efforts to publicize Canadian research (Note: Links have been removed),

For example, Research Matters, a promotional effort by the Council of Ontario Universities, has built up a large bank of short articles on its website that highlight researchers across the province. Similarly, the Canada Foundation for Innovation, which channels federal dollars toward research infrastructure and projects, produces features stories with embedded videos about the scientists who are enabled by their investments.

What makes Research2Reality different, said Dr. Shoichet, is an approach that doesn’t speak for one region, field of research of  [sic] funding stream.

One other aspect which distinguishes Research2Reality from the other science promotion efforts is the attempt to reach out to the audience. The Canada Foundation for Innovation and Council for Ontario Universities are not known for reaching out directly to the general public.]

Café Scientifique (Vancouver, Canada) makes a ‘happy’ change: new speaker for April 28, 2015

For the first time since I’ve started posting about Vancouver’s Café Scientifique there’s been a last minute change of speakers. It’s due to an addition to Dr. Kramer’s family. Congratulations!

So, Tuesday, April 28, 2015’s  Café Scientifique, held in the back room of The Railway Club (2nd floor of 579 Dunsmuir St. [at Seymour St.], will be hosting a talk from a different speaker and on a different topic,

Ph.D candidate and Vanier Scholar, Kostadin Kushlev from the Department of Psychology at UBC presenting his exciting research. Details are as follows:

Always Connected: How Smartphones May be Disconnecting Us From the People Around Us.

Smartphones have transformed where and how we access information and connect with our family and friends. But how might these powerful pocket computers be affecting how and when we interact with others in person? In this talk, I will present recent data from our lab suggesting that smartphones can compromise how connected we feel to close others, peers, and strangers. Parents spending time with their children felt more distracted and less socially connected when they used their phones a lot. Peers waiting together for an appointment connected with each other less and felt less happy when they had access to their phones as compared to when they did not. And, people looking for directions trusted members of their community less when they relied on their phones for directions rather than on the kindness of strangers. These findings highlight some of the perils of being constantly connected for our nonvirtual social lives and for the social fabric of society more generally.

On looking up the speaker online, I found that the main focus of his research is happiness, from the University of British Columbia’s (UBC) Graduate and PostGraduate webpage for Kostadin Kushlev,

 Research topic: Happiness and well-being
Research group: Social Cognition and Emotion Lab
Research location: UBC Vancouver, Kenny Building, 2136 West Mall
Research supervisor: Elizabeth Dunn

Research description
My research focuses on the emotional experience of people. The topics that I am currently investigating range from what gives (or takes away from) people’s experience of meaning in life to how people react to shame and guilt, and to what extent new technologies introduce stress and anxiety in our lives.

Home town: Madan
Country: Bulgaria

Given that the United Nations’ 2015 World Happiness Report (co-authored by UBC professor emeritus John Helliwell) was released on April 23, 2015,  the same day that the Museum of Vancouver’s The Happy Show (Stefan Sagmeister: The Happy Show) opened, Kostadin Kushlev seems like a ‘happy’ choice for a substitute speaker just days later on April 28, 2015, especially since the original topic was ‘pain’.

Centralized depot (Wikipedia style) for data on neurons

The decades worth of data that has been collected about the billions of neurons in the brain is astounding. To help scientists make sense of this “brain big data,” researchers at Carnegie Mellon University have used data mining to create http://www.neuroelectro.org, a publicly available website that acts like Wikipedia, indexing physiological information about neurons.

opens a March 30, 2015 news item on ScienceDaily (Note: A link has been removed),

The site will help to accelerate the advance of neuroscience research by providing a centralized resource for collecting and comparing data on neuronal function. A description of the data available and some of the analyses that can be performed using the site are published online by the Journal of Neurophysiology

A March 30, 2015 Carnegie Mellon University news release on EurekAlert, which originated the news item, describes, in more detail,  the endeavour and what the scientists hope to achieve,

The neurons in the brain can be divided into approximately 300 different types based on their physical and functional properties. Researchers have been studying the function and properties of many different types of neurons for decades. The resulting data is scattered across tens of thousands of papers in the scientific literature. Researchers at Carnegie Mellon turned to data mining to collect and organize these data in a way that will make possible, for the first time, new methods of analysis.

“If we want to think about building a brain or re-engineering the brain, we need to know what parts we’re working with,” said Nathan Urban, interim provost and director of Carnegie Mellon’s BrainHubSM neuroscience initiative. “We know a lot about neurons in some areas of the brain, but very little about neurons in others. To accelerate our understanding of neurons and their functions, we need to be able to easily determine whether what we already know about some neurons can be applied to others we know less about.”

Shreejoy J. Tripathy, who worked in Urban’s lab when he was a graduate student in the joint Carnegie Mellon/University of Pittsburgh Center for the Neural Basis of Cognition (CNBC) Program in Neural Computation, selected more than 10,000 published papers that contained physiological data describing how neurons responded to various inputs. He used text mining algorithms to “read” each of the papers. The text mining software found the portions of each paper that identified the type of neuron studied and then isolated the electrophysiological data related to the properties of that neuronal type. It also retrieved information about how each of the experiments in the literature was completed, and corrected the data to account for any differences that might be caused by the format of the experiment. Overall, Tripathy, who is now a postdoc at the University of British Columbia, was able to collect and standardize data for approximately 100 different types of neurons, which he published on the website http://www.neuroelectro.org.

Since the data on the website was collected using text mining, the researchers realized that it was likely to contain errors related to extraction and standardization. Urban and his group validated much of the data, but they also created a mechanism that allows site users to flag data for further evaluation. Users also can contribute new data with minimal intervention from site administrators, similar to Wikipedia.

“It’s a dynamic environment in which people can collect, refine and add data,” said Urban, who is the Dr. Frederick A. Schwertz Distinguished Professor of Life Sciences and a member of the CNBC. “It will be a useful resource to people doing neuroscience research all over the world.”

Ultimately, the website will help researchers find groups of neurons that share the same physiological properties, which could provide a better understanding of how a neuron functions. For example, if a researcher finds that a type of neuron in the brain’s neocortex fires spontaneously, they can look up other neurons that fire spontaneously and access research papers that address this type of neuron. Using that information, they can quickly form hypotheses about whether or not the same mechanisms are at play in both the newly discovered and previously studied neurons.

To demonstrate how neuroelectro.org could be used, the researchers compared the electrophysiological data from more than 30 neuron types that had been most heavily studied in the literature. These included pyramidal neurons in the hippocampus, which are responsible for memory, and dopamine neurons in the midbrain, thought to be responsible for reward-seeking behaviors and addiction, among others. The site was able to find many expected similarities between the different types of neurons, and some similarities that were a surprise to researchers. Those surprises represent promising areas for future research.

In ongoing work, the Carnegie Mellon researchers are comparing the data on neuroelectro.org with other kinds of data, including data on neurons’ patterns of gene expression. For example, Urban’s group is using another publicly available resource, the Allen Brain Atlas, to find whether groups of neurons with similar electrical function have similar gene expression.

“It would take a lot of time, effort and money to determine both the physiological properties of a neuron and its gene expression,” Urban said. “Our website will help guide this research, making it much more efficient.”

The researchers have produced a brief video describing neurons and their project,

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

Brain-wide analysis of electrophysiological diversity yields novel categorization of mammalian neuron types by Shreejoy J Tripathy, Shawn D. Burton, Matthew Geramita, Richard C. Gerkin, and Nathaniel N. Urban. Journal of Neurophysiology Published 25 March 2015 DOI: 10.1152/jn.00237.2015

This paper is behind a paywall.

Tune in, turn on, and drop out—LSD and psychedelic talk at Vancouver’s (Canada) Café Scientifique on March 31, 2015

There seems to be a lot of interest in psychedelics these days and not least here in Vancouver. Next Tuesday, March 31, 2015 Cafe Scientifique, held in the back room of The Railway Club (2nd floor of 579 Dunsmuir St. [at Seymour St.], will be hosting a talk on LSD (from the March 16, 2015 announcement,

Our speaker for the evening will be Dr. Michael Hughesa Research Associate in the Department of Medical Genetics at UBC (University of British Columbia) …

Psychedelic Medicine: The History & Science of LSD in the Clinic

Ergot is a fungus that grows on rye and other grains that has been blamed (rightly or wrongly) for episodes of mass hysteria throughout history. Lysergic acid diethylamide (LSD) was first synthesized from ergot in 1938 by a Swiss chemist named Albert Hoffman, who, at the height of World War II, also discovered (somewhat mysteriously) its psychedelic properties. LSD soon came to the attention of the U.S. Army who quickly proceeds to buy up all the supply – primarily to keep it out of the hands of its enemies. Throughout the Cold War, elements in U.S. defense and security agencies engage in experiments by secretly slipping LSD to citizens with dangerous (and sometimes comical) consequences with the goal of perfecting brainwashing and mind control. Canadian scientists at McGill participated in some of these studies, thinking they could use LSD to cure psychoses. These unethical and largely unscientific experiments were akin to psychological torture. Meanwhile, the public discovered the recreational benefits of LSD and the hippie movement adopted the drug as a symbol and vehicle to enlightenment. Largely for this reason, in the early ‘70s LSD was classified as a Schedule-1 drug in the U.S. restricted legal access stopped most research and hopes of the clinical benefits of LSD was abandoned and all but forgotten. Recently, scientists, mostly working outside of the U.S. and Canada, have rediscovered LSD’s efficacy for the treatment of psychiatric disorders including post-traumatic stress syndrome (PTSD) and existential fear in terminally ill patients. Are we ready for a new wave of ethical human research to (re)-discover the clinical benefits of LSD? Take a journey through the strange history of LSD research and learn about its potential applications in medicine. What a long, strange trip it’s been.

Hughes works as a team member in the Hematopoietic Cell Development laboratory at the University of British Columbia’s (UBC) Biomedical Research Centre.

Last week on March 18, 2015, The UBC Neuroscience Graduate Student Association hosted a screening of Neurons to Nirvana: Understanding Psychedelic Medicines at the Pacific Cinematheque theatre in Vancouver (Note: Links have been removed),

A thought-provoking and visually-stunning documentary that explores the potential of five powerful psychedelic substances (LSD, psilocybin, MDMA, ayahuasca, and cannabis) as psychotherapeutic medicines. Despite the potential promise shown by such drugs in research conducted in the 1950s, the increasingly restrictive anti-drug policies of successive governments effectively shut down further enquiry. As one of the many world-renowned researchers, writers, psychologists, and scientists interviewed in the film says: “The government does not allow this research to take place, and then says there’s no research to support it. It’s beyond hypocrisy.” The film is a cogent call to put irrational, fear-based beliefs aside in order to allow clinical, evidence-based research into psychedelics in areas such as addictions, PTSD, anxiety, depression, and end-of-life care.

– – – – – – – – – – – – – – – – – –

Post-screening discussion with co-director Oliver Hockenhull and Mark Haden.

A teacher and essayist as well as a filmmaker, Oliver Hockenhull has presented at numerous universities in Canada, the US, and Europe. He has blended the documentary, essay, and experimental genres in such previous works as Aldous Huxley: The Gravity of Light (1996), Building Heaven, Remembering Earth (1999), and Evo (2002).

Mark Haden worked for Vancouver Coastal Health Addiction Services for 28 years and is now an Adjunct Professor at the UBC School of Population and Public Health. He is a pivotal voice in the drug policy reform movement, providing viable models for reforming drug education and regulating markets for currently illegal substances. Mark is also the Chair of the Board of MAPS Canada (Multidisciplinary Association for Psychedelic Studies).

Moderated by Dr. Harry Karlinsky, Clinical Professor, Department of Psychiatry, University of British Columbia.

Perhaps popular demand will lead to another showing. In the meantime, there’s Hughes’ talk and if his description is indicative it should be fascinating.

For anyone who did not recognize it,  ‘tune in, turn on, and drop out’, is a phrase that Timothy Leary, the high priest of psychedelics, psychologist, and former lecturer at Harvard University popularized during the 1960s and 70s. According to the ‘tune in, turn on, and drop out‘ entry in Wikipedia, the phrase was given to Leary by Canadian media theorist, Marshall McLuhan.

ETA March 27, 2015 at 1610 PDT: I just received a newsletter from Canada’s National Film Board where the feature item is this,

All About Acid: Hofmann’s Potion

Open your mind with this powerful feature documentary that retraces the history of LSD, a substance first used to treat addiction and mental illness that became the self-understanding tool of a generation.

For more on Hofmann’s Potion, read Meet the Lab Coat-Clad Granddaddies of LSD on the NFB/ blog.

Watch Now

* ‘tun’ changed to ‘turn’ (sigh) March 27, 2015 at 1615 PDT

The secret life of leaves at Vancouver’s (Canada) Café Scientifique on Jan. 27, 2015

Vancouver’s next Café Scientifique is being held in the back room of the The Railway Club (2nd floor of 579 Dunsmuir St. [at Seymour St.], Vancouver, Canada), on Jan. 27,  2015*. Here’s the meeting description (from the Jan. 19, 2015 announcement),

Happy New Year!  We hope you all had an enjoyable and relaxing holiday season.  We’d like to send out a big thank you for your generosity in our crowdfunding campaign and your help in its promotion.  Your donations and support will help to keep us running for another year and more!

Speaking of which, our next café will happen on Tuesday, January 27th, at 7:30pm at The Railway Club. Our speaker for the evening will be Dr. Chris Muir, a Postdoctoral Fellow in the Biodiversity Research Centre at the University of British Columbia.  The title of his talk is:

More than salad: the inner lives of leaves

To most of us, leaves are the green things in a salad or the emblem on our flag. To a biologist, leaves are the critical interface between a plant and its environment. I will talk about some of the remarkable ways that leaves adapt plants to their environment. First, I will cover some basic functions that leaves perform for a plant: How do plants eat? How do plants avoid being eaten? What goes on inside a leaf? Next, I will talk about some of the unorthodox ways that leaves help plants make a living: How do plants without roots get water? Why do leaves track the sun? How did the Swiss Cheese Plant get its holes? The close connection between a leaf’s form and its function to the plant attests to the relentless action of natural selection in adapting organisms to their environment.

Muir has an eponymous website where you can find out more about his work and about him.

* Jan. 27, 2014 corrected to Jan. 27, 2015 on Feb. 12, 2015.

Art project (autonomous bot purchases illegal goods) seized by Swiss law enforcement

Having just attended a talk on Robotics and Rehabilitation which included a segment on Robo Ethics, news of an art project where an autonomous bot (robot) is set loose on the darknet to purchase goods (not all of them illegal) was fascinating in itself (it was part of an art exhibition which also displayed the proceeds of the darknet activity). But things got more interesting when the exhibit attracted legal scrutiny in the UK and occasioned legal action in Switzerland.

Here’s more from a Jan. 23, 2015 article by Mike Masnick for Techdirt (Note: A link has been removed),

… some London-based Swiss artists, !Mediengruppe Bitnik [(Carmen Weisskopf and Domagoj Smoljo)], presented an exhibition in Zurich of The Darknet: From Memes to Onionland. Specifically, they had programmed a bot with some Bitcoin to randomly buy $100 worth of things each week via a darknet market, like Silk Road (in this case, it was actually Agora). The artists’ focus was more about the nature of dark markets, and whether or not it makes sense to make them illegal:

The pair see parallels between copyright law and drug laws: “You can enforce laws, but what does that mean for society? Trading is something people have always done without regulation, but today it is regulated,” says ays [sic] Weiskopff.

“There have always been darkmarkets in cities, online or offline. These questions need to be explored. But what systems do we have to explore them in? Post Snowden, space for free-thinking online has become limited, and offline is not a lot better.”

Interestingly the bot got excellent service as Mike Power wrote in his Dec. 5, 2014 review of the show. Power also highlights some of the legal, ethical, and moral implications,

The gallery is next door to a police station, but the artists say they are not afraid of legal repercussions of their bot buying illegal goods.

“We are the legal owner of the drugs [the bot purchased 10 ecstasy pills along with a baseball cap, a pair of sneaker/runners/trainers among other items] – we are responsible for everything the bot does, as we executed the code, says Smoljo. “But our lawyer and the Swiss constitution says art in the public interest is allowed to be free.”

The project also aims to explore the ways that trust is built between anonymous participants in a commercial transaction for possibly illegal goods. Perhaps most surprisingly, not one of the 12 deals the robot has made has ended in a scam.

“The markets copied procedures from Amazon and eBay – their rating and feedback system is so interesting,” adds Smojlo. “With such simple tools you can gain trust. The service level was impressive – we had 12 items and everything arrived.”

“There has been no scam, no rip-off, nothing,” says Weiskopff. “One guy could not deliver a handbag the bot ordered, but he then returned the bitcoins to us.”

The exhibition scheduled from Oct. 18, 2014 – Jan. 11, 2015 enjoyed an uninterrupted run but there were concerns in the UK (from the Power article),

A spokesman for the National Crime Agency, which incorporates the National Cyber Crime Unit, was less philosophical, acknowledging that the question of criminal culpability in the case of a randomised software agent making a purchase of an illegal drug was “very unusual”.

“If the purchase is made in Switzerland, then it’s of course potentially subject to Swiss law, on which we couldn’t comment,” said the NCA. “In the UK, it’s obviously illegal to purchase a prohibited drug (such as ecstasy), but any criminal liability would need to assessed on a case-by-case basis.”

Masnick describes the followup,

Apparently, that [case-by[case] assessment has concluded in this case, because right after the exhibit closed in Switzerland, law enforcement showed up to seize stuff …

!Mediengruppe Bitnik  issued a Jan. 15, 2015 press release (Note: Links have been removed),

«Can a robot, or a piece of software, be jailed if it commits a crime? Where does legal culpability lie if code is criminal by design or default? What if a robot buys drugs, weapons, or hacking equipment and has them sent to you, and police intercept the package?» These are some of the questions Mike Power asked when he reviewed the work «Random Darknet Shopper» in The Guardian. The work was part of the exhibition «The Darknet – From Memes to Onionland. An Exploration» in the Kunst Halle St. Gallen, which closed on Sunday, January 11, 2015. For the duration of the exhibition, !Mediengruppe Bitnik sent a software bot on a shopping spree in the Deepweb. Random Darknet Shopper had a budget of $100 in Bitcoins weekly, which it spent on a randomly chosen item from the deepweb shop Agora. The work and the exhibition received wide attention from the public and the press. The exhibition was well-attended and was discussed in a wide range of local and international press from Saiten to Vice, Arte, Libération, CNN, Forbes. «There’s just one problem», The Washington Post wrote in January about the work, «recently, it bought 10 ecstasy pills».

What does it mean for a society, when there are robots which act autonomously? Who is liable, when a robot breaks the law on its own initiative? These were some of the main questions the work Random Darknet Shopper posed. Global questions, which will now be negotiated locally.

On the morning of January 12, the day after the three-month exhibition was closed, the public prosecutor’s office of St. Gallen seized and sealed our work. It seems, the purpose of the confiscation is to impede an endangerment of third parties through the drugs exhibited by destroying them. This is what we know at present. We believe that the confiscation is an unjustified intervention into freedom of art. We’d also like to thank Kunst Halle St. Gallen for their ongoing support and the wonderful collaboration. Furthermore, we are convinced, that it is an objective of art to shed light on the fringes of society and to pose fundamental contemporary questions.

This project brings to mind Isaac Asimov’s three laws of robotics and a question (from the Wikipedia entry; Note: Links have been removed),

The Three Laws of Robotics (often shortened to The Three Laws or Three Laws, also known as Asimov’s Laws) are a set of rules devised by the science fiction author Isaac Asimov. The rules were introduced in his 1942 short story “Runaround”, although they had been foreshadowed in a few earlier stories. The Three Laws are:

A robot may not injure a human being or, through inaction, allow a human being to come to harm.
A robot must obey the orders given it by human beings, except where such orders would conflict with the First Law.
A robot must protect its own existence as long as such protection does not conflict with the First or Second Law.

Here’s my question, how do you programme a robot to know what would injure a human being? For example, if a human ingests an ecstasy pill the bot purchased, would that be covered in the first law?

Getting back to the robot ethics talk I recently attended, it was given by Ajung Moon (Ph.D. student at the University of British Columbia [Vancouver, Canada] studying Human-Robot Interaction and Roboethics. Mechatronics engineer with a sprinkle of Philosophy background). She has a blog,  Roboethic info DataBase where you can read more on robots and ethics.

I strongly recommend reading both Masnick’s post (he positions this action in a larger context) and Power’s article (more details and images from the exhibit).

Canada’s federal scientists bargain for the right to present scientific results without government interference

I believe this latest bargaining round (h/t Dec. 3, 2014 news item on phys.org) between the Canadian federal government (Treasury Board) and the Professional Institute of the Public Service of Canada (PIPSC; a multi-disciplinary professional union representing 60,000 members employed by the Canadian federal government) is extraordinary. To my knowledge, no other union in this country has ever bargained for the right to present information without political interference or, more briefly, integrity. (Should you know otherwise, please let me know.)

Kathryn May in a Dec. 2, 2014 article for the Ottawa Citizen seems to have broken the news,

The Professional Institute of the Public Service of Canada, which represents more than 15,000 scientists, researchers and engineers, is tabling a negotiating position for managing science in the “public interest” with a list of demands for Treasury Board negotiators that dramatically push the boundaries of traditional collective bargaining in the public service.

The 7,000 members of PIPSC’s large applied science and patent examination group are the first at the table with Treasury Board this week, followed by 2,300 members of the research group next week.

A document obtained by the Citizen shows the union is looking for changes to deal with the ongoing spending cuts in science and “interference” in the integrity of scientific work.

The integrity policies will ensure science is done in the public interest; information and data is shared; scientists can collaborate, seek peer review and be protected from political meddling, “intimidation,” “coercion” or pressure to alter data.

It’s hard to tell how much of this is political grandstanding but it should be noted that there has been international notice of the situation in Canada (from the news article),

About a month ago [late October or early November 2014], hundreds of scientists from around the world signed an open letter appealing to Prime Minister Stephen Harper to end the “burdensome restrictions” Canada’s scientists face in talking about their work and collaborating with international colleagues.

The letter, signed by 800 scientists from 32 countries, was drafted by the Union of Concerned Scientists, which represents U.S. scientists.

May’s article goes on to note,

The union has extensively surveyed federal scientists in recent years and issued two major reports that found scientists don’t feel they can freely speak and that spending cuts are affecting Canadians’ health, safety and environment.

A quarter of scientists surveyed said they have been asked to exclude or alter information. That request, whether explicit or implicit, came from the department, ministers’ offices or the Prime Minister’s Office. At the same time, nearly three-quarters of scientists believe policy is being compromised by political interference.

Specifically, PIPSC wants a scientific integrity policy for Treasury Board and the 40 science-based departments and agencies. The union would be consulted in the drafting and the final policy would be part of the collective agreements and made public.

The policy would touch on a range of issues and existing policies, but the key proposal is the “right to speak.” The union wants a clause guaranteeing scientists the right to express their personal views while making clear they don’t speak for government.

The other big demand is professional development, allowing scientists to attend meetings, conferences and courses to maintain their professional standards.

Do please read May’s article in its entirety (assuming the news paper continues to make it freely available) as it is riveting for anyone interested in this topic.

A Dec. 3, 2014 PIPSC news release provides more details about specific negotiating points,

The proposal being tabled would see enforceable policies negotiated that, among other things, ensure:

  • federal scientists have the right to speak;
  • reinvestment in research programs;
  • adequate national and international collaboration among scientists;
  • preservation of government science knowledge and libraries, and;
  • a guaranteed role in informing evidence-based public policy.

“It’s sad, frankly, that it’s come to this,” added Daviau [Debi Daviau, PIPSC president]. “But negotiating provisions in our collective agreements seems to be the only way to get this government’s attention and adopt meaningful, enforceable scientific integrity standards. At least this way our members would have the chance to grieve violations of standards they argue are essential to maintaining adequate public science services.”

The negotiating point (4th bullet) about libraries seems to have arisen from a specific cost-cutting exercise involving the Dept. of Fisheries and Oceans libraries mentioned in my Jan. 30,  2014 posting. (The disbursement of some priceless volumes along with standard texts appeared to have been done with all the grace and thoughtfulness one would expect from a mindless mob.)

On a related note, I attended a four-day international congress in August 2014 and was surprised by the lack of Canadian scientists at this meeting. Perhaps this is not an area (alternatives to animal testing) where we have invested much research money but it was surprising and somehow shocking that so few Canadian scientists were giving presentations; there was one scientific presentation from a group at the University of British Columbia.

The issues around scientific integrity are complex and I’m not comfortable with the notion of including the principles in a union contract. My experience is that unions can be just as repressive and reductive as any government agency. That said, I think the practice of scientific integrity in Canada needs to be addressed in some fashion and if the only means we have is a union contract then, so be it.

It may be a few weeks before I get back to the topic of scientific integrity and the right to speak as I’m still catching up from all that teaching but I hope to have a more thoughtful and complex piece on these issues written before the year’s end.

ETA Dec. 4, 2014 1245 hours (PDT), coincidentally or not the Canadian federal government announced today * a $1.5 billlion fund (over 10 years) for research (from a Dec. 4, 2014 University of British Columbia [UBC) news release),

The University of British Columbia [UBC] welcomes today’s announcement of the $1.5-billion Canada First Research Excellence Fund (CFREF), designed to significantly enhance the capabilities and competitiveness of Canada’s post-secondary institutions, says President Arvind Gupta.

“Thanks to this investment by the Government of Canada, our universities have an extraordinary opportunity to foster globally significant research on issues that have the capacity to change people’s lives and shape our future,” said Gupta. “Excellence in research makes our reputation, and enables us to attract the best faculty, students and staff from around the world.”

UBC will be among Canada’s top universities competing for up to tens of millions of dollars annually in CFREF funding over the course of the 10-year program. These new funds could support UBC’s emerging research and innovation strategy, designed to put students at the cutting edge of knowledge, providing access to the latest discoveries and revelations, noted Gupta.

UBC is internationally recognized for research excellence in such areas as: Quantum materials; translational genomics and precision oncology; economics; neurosciences; biodiversity; bio-economics; and microbial diversity, among others.

You can read the full UBC news release here. There were a few details more to be had in a U15 Group of Canadian Research Universities Dec. 4, 2014 news release,

The U15 Group of Canadian Research Universities applauds the official launch of the Canada First Research Excellence Fund (CFREF). Prime Minister Stephen Harper launched the Fund today, accompanied by Ed Holder, minister of state for science and technology, at an event attended by representatives from the post-secondary education sector and industry.

“Since its announcement in Budget 2014, The U15 has been looking forward to the official launch of CFREF as a significant commitment by Canada to support globally competitive research excellence,” said Dr. Feridun Hamdullahpur, chair of The U15 and president and vice-chancellor of the University of Waterloo. “This Fund will allow successful institutions to better compete on the international stage in established areas of research strength as well as new and emerging areas that will support Canada’s scientific standing and long-term economic advantage.”

Interesting timing, non?

* ‘of’ removed from sentence on Dec. 4, 2014.