Monthly Archives: January 2018

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.

A bioengineered robot hand with its own nervous system: machine/flesh and a job opening

A November 14, 2017 news item on phys.org announces a grant for a research project which will see engineered robot hands combined with regenerative medicine to imbue neuroprosthetic hands with the sense of touch,

The sense of touch is often taken for granted. For someone without a limb or hand, losing that sense of touch can be devastating. While highly sophisticated prostheses with complex moving fingers and joints are available to mimic almost every hand motion, they remain frustratingly difficult and unnatural for the user. This is largely because they lack the tactile experience that guides every movement. This void in sensation results in limited use or abandonment of these very expensive artificial devices. So why not make a prosthesis that can actually “feel” its environment?

That is exactly what an interdisciplinary team of scientists from Florida Atlantic University and the University of Utah School of Medicine aims to do. They are developing a first-of-its-kind bioengineered robotic hand that will grow and adapt to its environment. This “living” robot will have its own peripheral nervous system directly linking robotic sensors and actuators. FAU’s College of Engineering and Computer Science is leading the multidisciplinary team that has received a four-year, $1.3 million grant from the National Institute of Biomedical Imaging and Bioengineering of the [US] National Institutes of Health for a project titled “Virtual Neuroprosthesis: Restoring Autonomy to People Suffering from Neurotrauma.”

A November14, 2017 Florida Atlantic University (FAU) news release by Gisele Galoustian, which originated the news item, goes into more detail,

With expertise in robotics, bioengineering, behavioral science, nerve regeneration, electrophysiology, microfluidic devices, and orthopedic surgery, the research team is creating a living pathway from the robot’s touch sensation to the user’s brain to help amputees control the robotic hand. A neuroprosthesis platform will enable them to explore how neurons and behavior can work together to regenerate the sensation of touch in an artificial limb.

At the core of this project is a cutting-edge robotic hand and arm developed in the BioRobotics Laboratory in FAU’s College of Engineering and Computer Science. Just like human fingertips, the robotic hand is equipped with numerous sensory receptors that respond to changes in the environment. Controlled by a human, it can sense pressure changes, interpret the information it is receiving and interact with various objects. It adjusts its grip based on an object’s weight or fragility. But the real challenge is figuring out how to send that information back to the brain using living residual neural pathways to replace those that have been damaged or destroyed by trauma.

“When the peripheral nerve is cut or damaged, it uses the rich electrical activity that tactile receptors create to restore itself. We want to examine how the fingertip sensors can help damaged or severed nerves regenerate,” said Erik Engeberg, Ph.D., principal investigator, an associate professor in FAU’s Department of Ocean and Mechanical Engineering, and director of FAU’s BioRobotics Laboratory. “To accomplish this, we are going to directly connect these living nerves in vitro and then electrically stimulate them on a daily basis with sensors from the robotic hand to see how the nerves grow and regenerate while the hand is operated by limb-absent people.”

For the study, the neurons will not be kept in conventional petri dishes. Instead, they will be placed in  biocompatible microfluidic chambers that provide a nurturing environment mimicking the basic function of living cells. Sarah E. Du, Ph.D., co-principal investigator, an assistant professor in FAU’s Department of Ocean and Mechanical Engineering, and an expert in the emerging field of microfluidics, has developed these tiny customized artificial chambers with embedded micro-electrodes. The research team will be able to stimulate the neurons with electrical impulses from the robot’s hand to help regrowth after injury. They will morphologically and electrically measure in real-time how much neural tissue has been restored.

Jianning Wei, Ph.D., co-principal investigator, an associate professor of biomedical science in FAU’s Charles E. Schmidt College of Medicine, and an expert in neural damage and regeneration, will prepare the neurons in vitro, observe them grow and see how they fare and regenerate in the aftermath of injury. This “virtual” method will give the research team multiple opportunities to test and retest the nerves without any harm to subjects.

Using an electroencephalogram (EEG) to detect electrical activity in the brain, Emmanuelle Tognoli, Ph.D., co-principal investigator, associate research professor in FAU’s Center for Complex Systems and Brain Sciences in the Charles E. Schmidt College of Science, and an expert in electrophysiology and neural, behavioral, and cognitive sciences, will examine how the tactile information from the robotic sensors is passed onto the brain to distinguish scenarios with successful or unsuccessful functional restoration of the sense of touch. Her objective: to understand how behavior helps nerve regeneration and how this nerve regeneration helps the behavior.

Once the nerve impulses from the robot’s tactile sensors have gone through the microfluidic chamber, they are sent back to the human user manipulating the robotic hand. This is done with a special device that converts the signals coming from the microfluidic chambers into a controllable pressure at a cuff placed on the remaining portion of the amputated person’s arm. Users will know if they are squeezing the object too hard or if they are losing their grip.

Engeberg also is working with Douglas T. Hutchinson, M.D., co-principal investigator and a professor in the Department of Orthopedics at the University of Utah School of Medicine, who specializes in hand and orthopedic surgery. They are developing a set of tasks and behavioral neural indicators of performance that will ultimately reveal how to promote a healthy sensation of touch in amputees and limb-absent people using robotic devices. The research team also is seeking a post-doctoral researcher with multi-disciplinary experience to work on this breakthrough project.

Here’s more about the job opportunity from the FAU BioRobotics Laboratory job posting, (I checked on January 30, 2018 and it seems applications are still being accepted.)

Post-doctoral Opportunity

Dated Posted: Oct. 13, 2017

The BioRobotics Lab at Florida Atlantic University (FAU) invites applications for a NIH NIBIB-funded Postdoctoral position to develop a Virtual Neuroprosthesis aimed at providing a sense of touch in amputees and limb-absent people.

Candidates should have a Ph.D. in one of the following degrees: mechanical engineering, electrical engineering, biomedical engineering, bioengineering or related, with interest and/or experience in transdisciplinary work at the intersection of robotic hands, biology, and biomedical systems. Prior experience in the neural field will be considered an advantage, though not a necessity. Underrepresented minorities and women are warmly encouraged to apply.

The postdoctoral researcher will be co-advised across the department of Mechanical Engineering and the Center for Complex Systems & Brain Sciences through an interdisciplinary team whose expertise spans Robotics, Microfluidics, Behavioral and Clinical Neuroscience and Orthopedic Surgery.

The position will be for one year with a possibility of extension based on performance. Salary will be commensurate with experience and qualifications. Review of applications will begin immediately and continue until the position is filled.

The application should include:

  1. a cover letter with research interests and experiences,
  2. a CV, and
  3. names and contact information for three professional references.

Qualified candidates can contact Erik Engeberg, Ph.D., Associate Professor, in the FAU Department of Ocean and Mechanical Engineering at eengeberg@fau.edu. Please reference AcademicKeys.com in your cover letter when applying for or inquiring about this job announcement.

You can find the apply button on this page. Good luck!

Café Scientifique Vancouver talk on January 30, 2018 and a couple of February 2018 art/sci events in Toronto

Vancouver

This could be a first for Café Scientifique Vancouver. From a January 28, 2018 Café Scientifique Vancouver announcement (received via email)

This is a reminder that our next café with biotech entrepreneur Dr.Andrew Tait (TUESDAY, JANUARY 30TH [2018] at 7:30PM) in the back room of YAGGER'S DOWNTOWN (433 W Pender).

COMBINING TRADITIONAL NATURAL MEDICINES WITH SCIENTIFIC RESEARCH: UNVEILING THE POTENTIAL OF THE MANDARIN ORANGE PEEL

The orange peel is something most of us may think of as a throw-away compost item, but it is so much more. Travel back in time 9,000 years to China, where orange peel was found in the first fermented alcoholic beverage, and return to today, where mandarin orange peel remains one of China’s top selling herbs that promotes digestion. Now meet Tait Laboratories Inc., a company that was founded based on one chemistry Ph.D. student’s idea, that mandarin orange peel has the potential to reverse incurable neurodegenerative diseases like multiple sclerosis. You will learn about the company’s journey through a scientific lens, from its early days to the present, having developed a mandarin orange peel product sold across Canada in over 1,000 stores including 400 Rexall pharmacies. You will leave with a basic understanding of how herbal products like the company’s mandarin orange peel-based product are developed and brought to market in Canada, and about the science that is required to substantiate health claims on this and other exciting new botanical products.

Bio:

Dr. Andrew Tait is the founder of Tait Laboratories Inc., a company devoted to developing natural medicines from agricultural bi-products. After a B.Sc. in Biochemistry and M.Sc. in Chemistry from Concordia University (Montreal), he completed a Ph.D. in Chemistry at the
University of British Columbia [UBC].

Inspired by his thesis work on multiple sclerosis, he subsequently identified Traditional Chinese Medicines as having potential to treat a wide range of chronic diseases; he founded the company while finishing his graduate studies.

In 2012, he was invited to Ottawa to be awarded the NSERC [{Canada} Natural Sciences and Engineering Research Council] Innovation Challenge Award, for successfully translating his Ph.D. research to an entrepreneurial venture. In 2014, he was awarded the BC Food Processors Association “Rising Star” award.

Dr. Tait is a regularly invited speaker on the topics of entrepreneurship and the science supporting natural health products; he was keynote speaker in 2012 at the Annual Symposium of the Boucher Institute of Naturopathic Medicine (Vancouver) and in 2016 at the
Functional Foods and Natural Health Products Graduate Research Symposium (Winnipeg).

Supported by the Futurpreneur Canada, the Bank of Development of Canada, the UBC’s Entrepreneurship@UBC program, and the NSERC  and NRC  [{Canada} National Research Council] Industry Research Assistance Program (IRAP), he works with industrial and academic researchers developing safe, affordable, and clinically proven medicines. He successfully launched MS+ Mandarin Skin PlusÒ, a patent-pending digestive product now on shelf in over 1000 pharmacies and health food stores across Canada, including 400 Rexall pharmacies.

Dr. Tait mentors young companies as an Entrepreneur in Residence at both SFU [Simon Fraser University] Coast Capital Savings Venture Connection and also the Health Tech Innovation Hub and he also volunteers his time to mentor students of the Student Biotechnology Network.

Lest it be forgotten, many drugs and therapeutic agents are based on natural remedies; a fact often ignored in the discussion about drugs and natural remedies. In any event, I am surprised this talk is being hosted by Café Scientifique Vancouver which has tended to more ‘traditional’ (i.e., university academic) presentations without any hint of ‘alternative’ or ‘entrepreneurial’ aspects. I wonder if this is the harbinger of new things to come from the Café Scientifique Vancouver community.

Meanwhile, interested parties can find out more about Tait Laboratories on their company website. They are selling one product at this time (from the MS+ [Mandarin Skin Plus] product webpage,

MS+™ (Mandarin Skin Plus) is a revolutionary natural health product that aids with digestion and promotes gastrointestinal health. It is a patent-pending proprietary extract based on dry-aged mandarin orange peel, an ancient Traditional Chinese Medicine. This remedy has been safely used for centuries to relieve bloating, indigestion, diarrhea, nausea, upset stomach, cough with phlegm. Experience ULTIMATE DIGESTIVE RELIEF and top gastrointestinal health for only about a dollar a day!

Directions: take one capsule twice a day, up to six capsules per day. Swallow capsule directly OR dissolve powder in water.
60 vegan capsules for ~ 1 month supply

I would have liked to have seen a list of research papers and discussion of human clinical trials regarding their ‘digestive’ product. Will Tait be discussing his research and results into what seems to be a new direction (i.e., the use of mandarin skin peel-derived therapeutics for neurodegenerative diseases)?

I don’t think I’m going to make it to the talk but should anyone who attends care to answer the question, please feel free to add a comment.

ArtSci Salon in Toronto

2018 is proving to be an active year for the ArtSci Salon folks in Toronto. They’ve just finished hosting a January 24-25, 2018 workshop and January 26, 2018 panel discussion on the gene-editing tool CRISPR/CAS9 (see my January 10, 2018 posting for a description).

Now they’ve announced another workshop and panel discussion on successive nights in February, the topic being: cells. From a January 29, 2018 ArtSci Salon announcement (received via email), Note: The panel discussion is listed first, then the workshop, then the artists’ biographies,

FROM CELL TO CANVAS: CREATIVE EXPLORATIONS OF THE MICROSCOPIC [panel discussion]

From the complex forms of the cell to the colonies created by the microbiota; from the undetectable chemical reactions activated by enzymes and natural processes to the environmental information captured through data visualization, the five local and international artists presenting tonight have developed a range of very diverse practices all inspired by the invisible, the undetectable and the microscopic.

We invite you to an evening of artist talks and discussion on the creative process of exploring the microscopic and using living organisms in art, on its potentials and implication for science and its popular dissemination, as well as on its ethics.

WITH:
Robyn Crouch
Mellissa Fisher
JULIA KROLIK
SHAVON MADDEN
TOSCA TERAN

FRIDAY, FEB 9, 2018
6:00-8:00 PM
THE FIELDS INSTITUTE
222 COLLEGE STREET,
RM 230

[Go to this page for access to registration]

FROM CELL TO CANVAS: CREATIVE EXPLORATIONS OF THE MICROSCOPIC [workshop]

THE EVENT WILL BE FOLLOWED BY A WORKSHOP BY: MELLISSA FISHER, SHAVON MADDEN AND JULIA KROLIK
FEB. 10, 2018
11:00AM-5:00PM
AT HACKLAB,
1266 Queen St West

[Go to this page for access to registration]

Workshop:

Design My Microbiome

Artist Mellissa Fisher invites participants to mould parts of her body in agar to create their own microbial version of her, alongside producing their own microbial portrait with painting techniques.

Cooking with the Invasive

Artist Shavon Madden invites participants to discuss invasive species like garlic mustard and cook invasive species whilst exploring, do species which we define and brand as invasive simply have no benefits?

Intoduction to Biological Staining

Artist & Scientist Julia Krolik invites participants to learn about 3 different types of biological staining and have a chance to try staining procedures.

BIOS:

ROBYN CROUCH
The symbolic imagery that comes through Robyn’s work invites one’s gaze inward to the cellular realms. There, one discovers playful depictions of chemical processes; the unseen lattice upon which our macro­cosmic world is constructed. Technological advancements create windows into this molecular realm, and human consciousness acts as the interface between the seen and the unseen worlds. In her functional ceramic work, the influence of Chinese and Japanese tea ceremony encourages contem­plation and appreciation of a quiet
moment. The viewer-participant can lose their train of thought while meandering through geometry and biota, con­nected by strands of double-helical DNA. A flash of recognition, a momentary mirror.

MELLISSA FISHER
Mellissa Fisher is a British Bio Artist based in Kent. Her practice explores the invisible world on our skin by using living organisms and by creating sculptures made with agar to show the public what the surface of our skin really looks like. She is best known for her work with bacteria and works extensively with collaborators in microbiology and immunology. She has exhibited an installation _ “Microbial Me”_with Professor Mark Clements and Dr Richard Harvey at The Eden Project for their permanent exhibition _“The Invisible You: The Human
Microbiome”._The installation included a living portrait in bacteria of the artists face as well as a time-lapse film of the sculpture growing.

JULIA KROLIK
Julia Krolik is a creative director, entrepreneur, scientist and award-winning artist. Her diverse background enables a rare cross-disciplinary empathy, and she continuously advocates for both art and science through several initiatives. Julia is the founder of Art the Science, a non-profit organization dedicated to facilitating artist residencies in scientific research laboratories to foster Canadian science-art culture and expand scientific knowledge communication to benefit the public. Through her consulting agency Pixels and Plans, Julia works with private and public organizations, helping them with strategy, data visualization and knowledge mobilization, often utilizing creative technology and skills-transfer workshops.

SHAVON MADDEN
Shavon Madden is a Brampton based artist, specializing in sculptural, performance and instillation based work exploring the social injustices inflicted on the environment and its creatures. Her work focuses on challenging social-environmental and political ethics, through the embodied experience and feelings of self. She graduated from the University of Toronto Specializing in Art and Art History, along with studies in Environmental Science and will be on her way to Edinburgh for her MFA. Shavon has had works shown at Shelly Peterson, the Burlington Art Gallery and the Art Gallery of Mississauga, among many others. Website: www.greenheartartistry.com [4]

TOSCA TERAN
Working with metal for over 30+ years, Tosca was introduced to glass as an artistic medium in 2004. Through developing bodies of work incorporating metal + glass Tosca has been awarded scholarships at The Corning Museum of Glass, Pilchuck Glass School and The Penland school of Crafts. Her work has been featured at SOFA New York, Culture Canada,
Metalsmith Magazine, The Toronto Design Exchange, and the Memphis Metal Museum. She has been awarded residencies at Gullkistan, Nes, and the Ayatana Research Program. A long-term guest artist instructor at the Ontario Science Centre, Tosca continues to explore materials, code, BioArt, SciArt and teach Metal + Glass courses out of her studio in Toronto.

It seems that these February events and the two events with Marta de Menezes are part of the FACTT (transdisciplinary and transnational festival of art and science) Toronto, from the FACTT Toronto webpage,

FACTT Toronto – Festival of Art & Science posted in: blog, events

The Arte Institute, in partnership with Cultivamos Cultura and ArtSi Salon, has the pleasure to announce FACTT – Festival of Art & Science in Toronto.

The Festival took place in Lisbon, New York, Mexico, Berlin and will continue in Toronto.
Exhibition: The Cabinet Project/ Art Sci Salon / FACTT

Artists:

Andrew Carnie
Elaine Whittaker
Erich Berger
Joana Ricou
Ken Rinaldo
Laura Beloff and Maria Antonia Gonzalez Valerio
Marta de Menezes and Luís Graça
Pedro Cruz

Dates: Jan 26- feb 15 [2018 {sic}]

Where: Meet us on Jan 26 [2018] in the Lobby of the Physics Department, 255 Huron Street
University of Toronto
When: 4:45 PM

You may want to keep an eye on the ArtSci Salon website although I find their posting schedule a bit erratic. Sometimes, I get email notices for events that aren’t yet listed on their website.

Editing the genome with CRISPR ((clustered regularly interspaced short palindromic repeats)-carrying nanoparticles

MIT (Massachusetts Institute of Technology) researchers have developed a new nonviral means of delivering CRISPR ((clustered regularly interspaced short palindromic repeats)-CAS9 gene therapy according to a November 13, 2017 news item on Nanowerk,

In a new study, MIT researchers have developed nanoparticles that can deliver the CRISPR genome-editing system and specifically modify genes in mice. The team used nanoparticles to carry the CRISPR components, eliminating the need to use viruses for delivery.

Using the new delivery technique, the researchers were able to cut out certain genes in about 80 percent of liver cells, the best success rate ever achieved with CRISPR in adult animals.

In a new study, MIT researchers have developed nanoparticles that can deliver the CRISPR genome-editing system and specifically modify genes, eliminating the need to use viruses for delivery. Image: MIT News

A November 13, 2017 MIT news release (also on EurekAlert), which originated the news item, provides more details about the research and a good description of and comparison between using a viral system and using a nanoparticle-based system to deliver CRISPR-CAS9,

“What’s really exciting here is that we’ve shown you can make a nanoparticle that can be used to permanently and specifically edit the DNA in the liver of an adult animal,” says Daniel Anderson, an associate professor in MIT’s Department of Chemical Engineering and a member of MIT’s Koch Institute for Integrative Cancer Research and Institute for Medical Engineering and Science (IMES).

One of the genes targeted in this study, known as Pcsk9, regulates cholesterol levels. Mutations in the human version of the gene are associated with a rare disorder called dominant familial hypercholesterolemia, and the FDA recently approved two antibody drugs that inhibit Pcsk9. However these antibodies need to be taken regularly, and for the rest of the patient’s life, to provide therapy. The new nanoparticles permanently edit the gene following a single treatment, and the technique also offers promise for treating other liver disorders, according to the MIT team.

Anderson is the senior author of the study, which appears in the Nov. 13 [2017] issue of Nature Biotechnology. The paper’s lead author is Koch Institute research scientist Hao Yin. Other authors include David H. Koch Institute Professor Robert Langer of MIT, professors Victor Koteliansky and Timofei Zatsepin of the Skolkovo Institute of Science and Technology [Russia], and Professor Wen Xue of the University of Massachusetts Medical School.

Targeting disease

Many scientists are trying to develop safe and efficient ways to deliver the components needed for CRISPR, which consists of a DNA-cutting enzyme called Cas9 and a short RNA that guides the enzyme to a specific area of the genome, directing Cas9 where to make its cut.

In most cases, researchers rely on viruses to carry the gene for Cas9, as well as the RNA guide strand. In 2014, Anderson, Yin, and their colleagues developed a nonviral delivery system in the first-ever demonstration of curing a disease (the liver disorder tyrosinemia) with CRISPR in an adult animal. However, this type of delivery requires a high-pressure injection, a method that can also cause some damage to the liver.

Later, the researchers showed they could deliver the components without the high-pressure injection by packaging messenger RNA (mRNA) encoding Cas9 into a nanoparticle instead of a virus. Using this approach, in which the guide RNA was still delivered by a virus, the researchers were able to edit the target gene in about 6 percent of hepatocytes, which is enough to treat tyrosinemia.

While that delivery technique holds promise, in some situations it would be better to have a completely nonviral delivery system, Anderson says. One consideration is that once a particular virus is used, the patient will develop antibodies to it, so it couldn’t be used again. Also, some patients have pre-existing antibodies to the viruses being tested as CRISPR delivery vehicles.

In the new Nature Biotechnology paper, the researchers came up with a system that delivers both Cas9 and the RNA guide using nanoparticles, with no need for viruses. To deliver the guide RNAs, they first had to chemically modify the RNA to protect it from enzymes in the body that would normally break it down before it could reach its destination.

The researchers analyzed the structure of the complex formed by Cas9 and the RNA guide, or sgRNA, to figure out which sections of the guide RNA strand could be chemically modified without interfering with the binding of the two molecules. Based on this analysis, they created and tested many possible combinations of modifications.

“We used the structure of the Cas9 and sgRNA complex as a guide and did tests to figure out we can modify as much as 70 percent of the guide RNA,” Yin says. “We could heavily modify it and not affect the binding of sgRNA and Cas9, and this enhanced modification really enhances activity.”

Reprogramming the liver

The researchers packaged these modified RNA guides (which they call enhanced sgRNA) into lipid nanoparticles, which they had previously used to deliver other types of RNA to the liver, and injected them into mice along with nanoparticles containing mRNA that encodes Cas9.

They experimented with knocking out a few different genes expressed by hepatocytes, but focused most of their attention on the cholesterol-regulating Pcsk9 gene. The researchers were able to eliminate this gene in more than 80 percent of liver cells, and the Pcsk9 protein was undetectable in these mice. They also found a 35 percent drop in the total cholesterol levels of the treated mice.

The researchers are now working on identifying other liver diseases that might benefit from this approach, and advancing these approaches toward use in patients.

“I think having a fully synthetic nanoparticle that can specifically turn genes off could be a powerful tool not just for Pcsk9 but for other diseases as well,” Anderson says. “The liver is a really important organ and also is a source of disease for many people. If you can reprogram the DNA of your liver while you’re still using it, we think there are many diseases that could be addressed.”

“We are very excited to see this new application of nanotechnology open new avenues for gene editing,” Langer adds.

The research was funded by the National Institutes of Health (NIH), the Russian Scientific Fund, the Skoltech Center, and the Koch Institute Support (core) Grant from the National Cancer Institute.

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

Structure-guided chemical modification of guide RNA enables potent non-viral in vivo genome editing by Hao Yin, Chun-Qing Song, Sneha Suresh, Qiongqiong Wu, Stephen Walsh, Luke Hyunsik Rhym, Esther Mintzer, Mehmet Fatih Bolukbasi, Lihua Julie Zhu, Kevin Kauffman, Haiwei Mou, Alicia Oberholzer, Junmei Ding, Suet-Yan Kwan, Roman L Bogorad, Timofei Zatsepin, Victor Koteliansky, Scot A Wolfe, Wen Xue, Robert Langer, & Daniel G Anderson. Nature Biotechnology doi:10.1038/nbt.4005 Published online: 13 November 2017

This paper is behind a paywall.

Why don’t you CRISPR yourself?

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Canadian content*

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Nano-neurons from a French-Japanese-US research team

This news about nano-neurons comes from a Nov. 8, 2017 news item on defenceweb.co.za,

Researchers from the Joint Physics Unit CNRS/Thales, the Nanosciences and Nanotechnologies Centre (CNRS/Université Paris Sud), in collaboration with American and Japanese researchers, have developed the world’s first artificial nano-neuron with the ability to recognise numbers spoken by different individuals. Just like the recent development of electronic synapses described in a Nature article, this electronic nano-neuron is a breakthrough in artificial intelligence and its potential applications.

A Sept. 19, 2017 Thales press release, which originated the news item, expands on the theme,

The latest artificial intelligence algorithms are able to recognise visual and vocal cues with high levels of performance. But running these programs on conventional computers uses 10,000 times more energy than the human brain. To reduce electricity consumption, a new type of computer is needed. It is inspired by the human brain and comprises vast numbers of miniaturised neurons and synapses. Until now, however, it had not been possible to produce a stable enough artificial nano-neuron which would process the information reliably.

Today [Sept. 19, 2017 or July 27, 2017 when the paper was published in Nature?]], for the first time, researchers have developed a nano-neuron with the ability to recognise numbers spoken by different individuals with 99.6% accuracy. This breakthrough relied on the use of an exceptionally stable magnetic oscillator. Each gyration of this nano-compass generates an electrical output, which effectively imitates the electrical impulses produced by biological neurons. In the next few years, these magnetic nano-neurons could be interconnected via artificial synapses, such as those recently developed, for real-time big data analytics and classification.

The project is a collaborative initiative between fundamental research laboratories and applied research partners. The long-term goal is to produce extremely energy-efficient miniaturised chips with the intelligence needed to learn from and adapt to the constantly ever-changing and ambiguous situations of the real world. These electronic chips will have many practical applications, such as providing smart guidance to robots or autonomous vehicles, helping doctors in their diagnosis’ and improving medical prostheses. This project included researchers from the Joint Physics Unit CNRS/Thales, the AIST, the CNS-NIST, and the Nanosciences and Nanotechnologies Centre (CNRS/Université Paris-Sud).

About the CNRS
The French National Centre for Scientific Research is Europe’s largest public research institution. It produces knowledge for the benefit of society. With nearly 32,000 employees, a budget exceeding 3.2 billion euros in 2016, and offices throughout France, the CNRS is present in all scientific fields through its 1100 laboratories. With 21 Nobel laureates and 12 Fields Medal winners, the organization has a long tradition of excellence. It carries out research in mathematics, physics, information sciences and technologies, nuclear and particle physics, Earth sciences and astronomy, chemistry, biological sciences, the humanities and social sciences, engineering and the environment.

About the Université Paris-Saclay (France)
To meet global demand for higher education, research and innovation, 19 of France’s most renowned establishments have joined together to form the Université Paris-Saclay. The new university provides world-class teaching and research opportunities, from undergraduate courses to graduate schools and doctoral programmes, across most disciplines including life and natural sciences as well as social sciences. With 9,000 masters students, 5,500 doctoral candidates, an equivalent number of engineering students and an extensive undergraduate population, some 65,000 people now study at member establishments.

About the Center for Nanoscale Science & Technology (Maryland, USA)
The CNST is a national user facility purposely designed to accelerate innovation in nanotechnology-based commerce. Its mission is to operate a national, shared resource for nanoscale fabrication and measurement and develop innovative nanoscale measurement and fabrication capabilities to support researchers from industry, academia, NIST and other government agencies in advancing nanoscale technology from discovery to production. The Center, located in the Advanced Measurement Laboratory Complex on NIST’s Gaithersburg, MD campus, disseminates new nanoscale measurement methods by incorporating them into facility operations, collaborating and partnering with others and providing international leadership in nanotechnology.

About the National Institute of Advanced Industrial Science and Technology (Japan)
The National Institute of Advanced Industrial Science and Technology (AIST), one of the largest public research institutes in Japan, focuses on the creation and practical realization of technologies useful to Japanese industry and society, and on bridging the gap between innovative technological seeds and commercialization. For this, AIST is organized into 7 domains (Energy and Environment, Life Science and Biotechnology, Information Technology and Human Factors, Materials and Chemistry, Electronics and Manufacturing, Geological

About the Centre for Nanoscience and Nanotechnology (France)
Established on 1 June 2016, the Centre for Nanosciences and Nanotechnologies (C2N) was launched in the wake of the joint CNRS and Université Paris-Sud decision to merge and gather on the same campus site the Laboratory for Photonics and Nanostructures (LPN) and the Institut d’Electronique Fondamentale (IEF). Its location in the École Polytechnique district of the Paris-Saclay campus will be completed in 2017 while the new C2N buildings are under construction. The centre conducts research in material science, nanophotonics, nanoelectronics, nanobiotechnologies and microsystems, as well as in nanotechnologies.

There is a video featuring researcher Julie Grollier discussing their work but you will need your French language skills,

(If you’re interested, there is an English language video published on youtube on Feb. 19, 2017 with Julie Grollier speaking more generally about the field at the World Economic Forum about neuromorphic computing,  https://www.youtube.com/watch?v=Sm2BGkTYFeQ

Here’s a link to and a citation for the team’s July 2017 paper,

Neuromorphic computing with nanoscale spintronic oscillators by Jacob Torrejon, Mathieu Riou, Flavio Abreu Araujo, Sumito Tsunegi, Guru Khalsa, Damien Querlioz, Paolo Bortolotti, Vincent Cros, Kay Yakushiji, Akio Fukushima, Hitoshi Kubota, Shinji Yuasa, Mark D. Stiles, & Julie Grollier. Nature 547, 428–431 (27 July 2017) doi:10.1038/nature23011 Published online 26 July 2017

This paper is behind a paywall.

What human speech, jazz, and whale song have in common

Credit: iStock/Velvetfish

Seeing connections between what seem to be unrelated activities such as human speech, jazz, and whale song is fascinating to me and I’m not alone. Scientists at the University of California at Merced (UC Merced) have delivered handily on that premise according to an Oct. 13, 2017 news item on phys.org,

Jazz musicians riffing with each other, humans talking to each other and pods of killer whales all have interactive conversations that are remarkably similar to each other, new research reveals.

Cognitive science researchers at UC Merced have developed a new method for analyzing and comparing the sounds of speech, music and complex animal vocalizations like whale song and bird song. The paper detailing their findings is being published today [Oct. 12, 2017] in the Journal of the Royal Society Interface.

Their method is based on the idea that these sounds are complex because they have multiple layers of structure. Every language, for instance, has individuals sounds, roughly corresponding to letters, that combine to form syllables, words, phrases, sentences and so on. It’s a hierarchy that everyone understands intuitively. Musical compositions have their own temporal hierarchies, but until now there hasn’t been a way to directly compare the hierarchies of speech and music, or test whether similar hierarchies might exist in bird song and whale song.

An Oct. 12, 2017 UC Merced news release by Lorena Anderson, which originated the news item, provides more details about the investigation (Note: Links have been removed),

“Playing jazz music has been likened to a conversation among musicians, and killer whales are highly social creatures who vocalize as if they are talking to each other. But does jazz music really sound like a conversation, and do killer whales really sound like they are talking?” asked lead researcher and UC Merced professor Chris Kello. “We know killer whales are highly social and intelligent, but it’s hard to tell that they are interacting when you listen to recordings of them. Our method shows how much their sound patterns are like people talking, but not like other, less social whales or birds.”

The researchers figured out a way to measure and compare sound recordings by converting them into “barcodes” that capture clusters of sound energy, and clusters of clusters, across levels of a hierarchy. These barcodes allowed the researchers to directly compare temporal hierarchies in more than 200 recordings of different kinds of speech in six different languages, different kinds of popular and classical music, four different species of birds and whales singing their songs, and even thunderstorms.

Kello and his colleagues have been using the barcode method for several years. They first developed it in studies of conversations. The study published today is the first time that they applied the method to music and animal vocalizations.

“The method allows us to ask questions about language and music and animal songs that we couldn’t ask without a way to see and compare patterns in all these recordings,” Kello said.

A common song

The researchers compared barcode-style visualizations of recorded sounds.
Credit: UC Merced

Kello, fellow UC Merced cognitive science professor Ramesh Balasubramaniam, graduate student Butovens Me´de´ [or Médé] and collaborator professor Simone Dalla Bella also discovered that the haunting songs of huge humpback whales are remarkably similar to the beautiful songs of tiny nightingales and hermit thrushes in terms of their temporal hierarchies.

“Humpbacks, nightingales and hermit thrushes are solitary singers,” Kello said. “The barcodes show that their songs have similar layers of structure, but we don’t know what it means — yet.”

The idea for this project came from Kello’s sabbatical at the University of Montpellier in France, where he worked and discussed ideas with Dalla Bella. Balasubramaniam, who studies how music is perceived, is in the School of Social Sciences, Humanities and Arts with Kello, who studies speech and language processing. The project was a natural collaboration and is part of a growing research focus at UC Merced that was enabled by the National Science Foundation-funded CHASE summer school on Music and Language in 2014, and a Google Faculty Award to Kello.

Balasubramaniam is interested in continuing the work to better understand how brains distinguish between music and speech, while Kello said there are many different avenues to pursue.

For instance, the researchers found nearly identical temporal hierarchies for six different languages, which may suggest something universal about human speech. However, because this result was based on recordings of TED Talks — which have a common style and progression — Kello said it will be important to keep looking at other forms of speech and language.

One of his graduate students, Sara Schneider, is using the method to study the convergence of Spanish and English barcodes in bilingual conversations. Another graduate student, Adolfo Ramirez-Aristizabal, is working with Kello and Balasubramaniam to study whether the barcode method may shed light on how brains process speech and other complex sounds.

“Listening to music and speech, we can hear some of what we see in the barcodes, and the information may be useful for automatic classification of audio recordings. But that doesn’t mean that our brains process music and speech using these barcodes,” Kello said. “It’s intriguing, but we need to keep asking questions and go where the data lead us.”

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

Hierarchical temporal structure in music, speech and animal vocalizations: jazz is like a conversation, humpbacks sing like hermit thrushes by Christopher T. Kello, Simone Dalla Bella, Butovens Médé, Ramesh Balasubramaniam. Journal of the Royal Society Interface DOI: 10.1098/rsif.2017.0231 Published 11 October 2017

This paper appears to be open access.*

*”This paper is behind a paywall” was changed to “… appears to be open access.” at 1700 hours on January 23, 2018.

Memristors at Masdar

The Masdar Institute of Science and Technology (Abu Dhabi, United Arab Emirates; Masdar Institute Wikipedia entry) featured its work with memristors in an Oct. 1, 2017 Masdar Institute press release by Erica Solomon (for anyone who’s interested, I have a simple description of memristors and links to more posts about them after the press release),

Researchers Develop New Memristor Prototype Capable of Performing Complex Operations at High-Speed and Low Power, Could Lead to Advancements in Internet of Things, Portable Healthcare Sensing and other Embedded Technologies

Computer circuits in development at the Khalifa University of Science and Technology could make future computers much more compact, efficient and powerful thanks to advancements being made in memory technologies that combine processing and memory storage functions into one densely packed “memristor.”

Enabling faster, smaller and ultra-low-power computers with memristors could have a big impact on embedded technologies, which enable Internet of Things (IoT), artificial intelligence, and portable healthcare sensing systems, says Dr. Baker Mohammad, Associate Professor of Electrical and Computer Engineering. Dr. Mohammad co-authored a book on memristor technologies, which has just been released by Springer, a leading global scientific publisher of books and journals, with Class of 2017 PhD graduate Heba Abunahla. The book, titled Memristor Technology: Synthesis and Modeling for Sensing and Security Applications, provides readers with a single-source guide to fabricate, characterize and model memristor devices for sensing applications.

The pair also contributed to a paper on memristor research that was published in IEEE Transactions on Circuits and Systems I: Regular Papers earlier this month with Class of 2017 MSc graduate Muath Abu Lebdeh and Dr. Mahmoud Al-Qutayri, Professor of Electrical and Computer Engineering.PhD student Yasmin Halawani is also an active member of Dr. Mohammad’s research team.

Conventional computers rely on energy and time-consuming processes to move information back and forth between the computer central processing unit (CPU) and the memory, which are separately located. A memristor, which is an electrical resistor that remembers how much current flows through it, can bridge the gap between computation and storage. Instead of fetching data from the memory and sending that data to the CPU where it is then processed, memristors have the potential to store and process data simultaneously.

“Memristors allow computers to perform many operations at the same time without having to move data around, thereby reducing latency, energy requirements, costs and chip size,” Dr. Mohammad explained. “We are focused on extending the logic gate design of the current memristor architecture with one that leads to even greater reduction of latency, energy dissipation and size.”

Logic gates control an electronics logical operation on one or more binary inputs and typically produce a single binary output. That is why they are at the heart of what makes a computer work, allowing a CPU to carry out a given set of instructions, which are received as electrical signals, using one or a combination of the seven basic logical operations: AND, OR, NOT, XOR, XNOR, NAND and NOR.

The team’s latest work is aimed at advancing a memristor’s ability to perform a complex logic operation, known as the XNOR (Exclusive NOR) logic gate function, which is the most complex logic gate operation among the seven basic logic gates types.

Designing memristive logic gates is difficult, as they require that each electrical input and output be in the form of electrical resistance rather than electrical voltage.

“However, we were able to successfully design an XNOR logic gate prototype with a novel structure, by layering bipolar and unipolar memristor types in a novel heterogeneous structure, which led to a reduction in latency and energy consumption for a memristive XNOR logic circuit gate by 50% compared to state-of the art state full logic proposed by leading research institutes,” Dr. Mohammad revealed.

The team’s current work builds on five years of research in the field of memristors, which is expected to reach a market value of US$384 million by 2025, according to a recent report from Research and Markets. Up to now, the team has fabricated and characterized several memristor prototypes, assessing how different design structures influence efficiency and inform potential applications. Some innovative memristor technology applications the team discovered include machine vision, radiation sensing and diabetes detection. Two patents have already been issued by the US Patents and Trademark Office (USPTO) for novel memristor designs invented by the team, with two additional patents pending.

Their robust research efforts have also led to the publication of several papers on the technology in high impact journals, including The Journal of Physical Chemistry, Materials Chemistry and Physics, and IEEE TCAS. This strong technology base paved the way for undergraduate senior students Reem Aldahmani, Amani Alshkeili, and Reem Jassem Jaffar to build novel and efficient memristive sensing prototypes.

The memristor research is also set to get an additional boost thanks to the new University merger, which Dr. Mohammad believes could help expedite the team’s research and development efforts through convenient and continuous access to the wider range of specialized facilities and tools the new university has on offer.

The team’s prototype memristors are now in the laboratory prototype stage, and Dr. Mohammad plans to initiate discussions for internal partnership opportunities with the Khalifa University Robotics Institute, followed by external collaboration with leading semiconductor companies such as Abu Dhabi-owned GlobalFoundries, to accelerate the transfer of his team’s technology to the market.

With initial positive findings and the promise of further development through the University’s enhanced portfolio of research facilities, this project is a perfect demonstration of how the Khalifa University of Science and Technology is pushing the envelope of electronics and semiconductor technologies to help transform Abu Dhabi into a high-tech hub for research and entrepreneurship.

h/t Oct. 4, 2017 Nanowerk news item

Slightly restating it from the press release, a memristor is a nanoscale electrical component which mimics neural plasticity. Memristor combines the word ‘memory’ with ‘resistor’.

For those who’d like a little more, there are three components: capacitors, inductors, and resistors which make up an electrical circuit. The resistor is the circuit element which represents the resistance to the flow of electric current.  As for how this relates to the memristor (from the Memristor Wikipedia entry; Note: Links have been removed),

The memristor’s electrical resistance is not constant but depends on the history of current that had previously flowed through the device, i.e., its present resistance depends on how much electric charge has flowed in what direction through it in the past; the device remembers its history — the so-called non-volatility property.[2] When the electric power supply is turned off, the memristor remembers its most recent resistance until it is turned on again

The memristor could lead to more energy-saving devices but much of the current (pun noted) interest lies in its similarity to neural plasticity and its potential application on neuromorphic engineering (brainlike computing).

Here’s a sampling of some of the more recent memristor postings on this blog:

August 24, 2017: Neuristors and brainlike computing

June 28, 2017: Dr. Wei Lu and bio-inspired ‘memristor’ chips

May 2, 2017: Predicting how a memristor functions

December 30, 2016: Changing synaptic connectivity with a memristor

December 5, 2016: The memristor as computing device

November 1, 2016: The memristor as the ‘missing link’ in bioelectronic medicine?

You can find more by using ‘memristor’ as the search term in the blog search function or on the search engine of your choice.

Crackpot or visionary? Teaching seven-year-olds about intellectual property

It’s been a while since I’ve devoted a posting to intellectual property issues and my focus is usually on science/technology and how intellectual property issues relate to those fields. As a writer, I support a more relaxed approach to copyright and patent law and, in particular, I want to see the continuation of ‘fair use’ as it’s called in the US and ‘fair dealing’ as it’s called in Canada. I support the principle of making money from your work so you can continue to contribute creatively. But, the application of intellectual property law seems to have been turned into a weapon against creativity of all sorts. (At the end of this post you’ll find links to three typical posts from the many I have written on this topic.)

I do take the point being made in the following video (but for seven-year-olds and up!!!) about trademarks/logos and trademark infringement from the UK’s Intellectual Property Office,

Here’s the description from Youtube’s Logo Mania webpage,

Published on Jan 16, 2018

Brian Wheeler’s January 17, 2018 article for BBC (British Broadcasting Corporation) online news on UK Politics sheds a bit of light on this ‘campaign’ (Note: A link has been removed),

A campaign to teach children about copyright infringement on the internet, is employing cartoons and puns on pop stars’ names, to get the message across.

Even its makers admit it is a “dry” and “niche” subject for a cartoon aimed at seven-year-olds.

But the Intellectual Property Office adds learning to “respect” copyrights and trademarks is a “key life skill”.

And it is hoping the adventures of Nancy and the Meerkats can finally make intellectual property “fun”.

The series, which began life five years ago on Fun Kids Radio, was re-launched this week with the aim of getting its message into primary schools.

The Intellectual Property Office is leading the government’s efforts to crack down on internet piracy and protect the revenues of Britain’s creative industries.

The government agency is spending £20,000 of its own money on the latest Nancy campaign, which is part-funded by the UK music industry.

Catherine Davies, head of the IPO’s education outreach department, which already produces teaching materials for GCSE students, admitted IP was a “complex subject” for small children and something of a challenge to make accessible and entertaining.

Wheeler’s article is definitely worth reading in its entirety. In fact, I was so intrigued I chased down the government press release (from the www.gov.uk webpage),

Nancy and the Meerkats logo

Nancy and the Meerkats, with the help of Big Joe, present a new radio series to engage pupils with the concept of intellectual property (IP). Aimed at primary education, the resource guides pupils through the process of setting up a band and recording and releasing a song, which is promoted and performed live on tour.

Building on the success of the previous two series, Nancy and the Meerkats consists of a new radio series, short videos, comic book, lesson plans and competition. The supporting teaching resource also includes themed activities and engaging lesson plans. Together, these support and develop pupils’ understanding of copyright, trade marks and the importance of respecting IP.

Curriculum links are provided for England, Northern Ireland, Scotland and Wales.

The series will launch on Monday 15th January [2018] at 5pm on Fun Kids Radio

Along with ‘Logo Mania’, you can find such gems as ‘Track Attack’ concerning song lyrics and, presumably, copyright issues, ‘The Hum Bone’ concerning patents, and ‘Pirates on the Internet’ about illegal downloading on the Fun Kids Radio website. Previous seasons have included ‘Are forks just for eating with?’, ‘Is a kaleidoscope useful?’, ‘Rubber Bands’, ‘Cornish Pasties’, and more. It seems Fun Kids Radio has moved from its focus on the types of questions and topics that might interest children to topics of interest for the music industry and the UK’s Intellectual Property Office. At a guess, I’m guessing those groups might be maximalists where copyright is concerned.

By the way, for those interested in teaching resources and more, go to http://crackingideas.com/third_party/Nancy+and+the+Meerkats.

Finally, I’m not sure whether to laugh or cry. I do know that I’m curious about how they decided to focus on seven to 11-year-olds. Are children in the UK heavily involved in content piracy? Is there a generation of grade school pop stars about to enter the music market? Where is the data and how did they gather it?

Should anyone be inclined to answer those questions, I look forward to reading your reply in the Comments section.

ETA January 19, 2018 (five minutes later) Oops! Here are the links promised earlier,

October 31, 2011: Patents as weapons and obstacles

June 28, 2012: Billions lost to patent trolls; US White House asks for comments on intellectual property (IP) enforcement; and more on IP

March 28, 2013: Intellectual property, innovation, and hindrances

There are many, many more posts. Just click on the category for ‘intellectual property’.

Implanting a synthetic cornea in your eye

For anyone who needs a refresher, Simon Shapiro in a Nov. 5, 2017 posting on the Sci/Why blog offers a good introduction to how eyes work and further in his post describes Corneat Vision’s corneal implants,

A quick summary of how our eyes work: they refract (bend) light and focus it on the retina. The job of doing the refraction is split between the cornea and the lens. Two thirds of the refraction is done by the cornea, so it’s critical in enabling vision. After light passes through the cornea, it passes through the pupil (in the centre of the iris) to reach the lens. Muscles in the eye (the ciliary muscle) can change the shape of the lens and allow the eye to focus nearer or further. The lens focuses light on the retina, which passes signals to the brain via the optic nerve.

It’s all pretty neat, but some things can go wrong, especially as you get older. Common problems are that the lens and/or the cornea can become cloudy.

CoreNeat Vision, the Israeli ophthalmic devices startup company, released an Oct. 6, 2017 press release about their corneal implant on BusinessWire (Note: Links have been removed),

The CorNeat KPro implant is a patent-pending synthetic cornea that utilizes advanced cell technology to integrate artificial optics within resident ocular tissue. The CorNeat KPro is produced using nanoscale chemical engineering that stimulates cellular growth. Unlike previous devices, which attempted to integrate optics into the native cornea, the CorNeat KPro leverages a virtual space under the conjunctiva that is rich with fibroblast cells that heals quickly and provides robust long-term integration. Combined with a novel and simple 30-minute surgical procedure, the CorNeat KPro provides an esthetic, efficient, scalable remedy for millions of people with cornea-related visual impairments and is far superior to any available biological and synthetic alternatives.

A short animated movie that demonstrates the implantation and integration of the CorNeat KPro device to the human eye is available in the following link: www.corneat.com/product-animation.

“Corneal pathology is the second leading cause of blindness worldwide with 20-30 million patients in need of a remedy and around 2 million new cases/year, said CorNeat Vision CEO and VP R&D, Mr. Almog Aley-Raz. “Though a profound cause of distress and disability, existing solutions, such as corneal transplantation, are carried out only about 200,000 times/year worldwide. Together, corneal transplantation, and to a much lesser extent artificial implants (KPros), address only 5%-10% of cases, “There exists an urgent need for an efficient, long-lasting and affordable solution to corneal pathology, injury and blindness, which would alleviate the suffering and disability of millions of people. We are very excited to reach this important milestone in the development of our solution and are confident that the CorNeat KPro will enable millions to regain their sight”, he added.

“The groundbreaking results obtained in our proof of concept which is backed by conclusive histopathological evidence, are extremely encouraging. We are entering the next phase with great confidence that CorNeat KPro will address corneal blindness just like IOLs (Intra Ocular Lens) addressed cataract”, commented Dr. Gilad Litvin, CorNeat Vision’s Chief Medical Officer and founder and the CorNeat KPro inventor. “Our novel IP, now cleared by the European Patent Office, ensures long-term retention, robust integration into the eye and an operation that is significantly shorter and simpler than Keratoplasty (Corneal transplantation).

“The innovative approach behind CorNeat KPro coupled by the team’s execution ability present a unique opportunity to finally address the global corneal blindness challenge”, added Prof. Ehud Assia., head of the ophthalmic department at the Meir Hospital in Israel, a serial ophthalmic innovator, and a member of CorNeat Vision scientific advisory board. “I welcome our new advisory board members, Prof. David Rootman, a true pioneer in ophthalmic surgery and one of the top corneal specialist surgeons from the University of Toronto, Canada, and Prof. Eric Gabison., who’s a leading cornea surgeon at the Rothschild Ophthalmic Foundation research center at Bichat hospital – Paris, France. We are all looking forward to initiating the clinical trial later in 2018.”

About CorNeat Vision

CorNeat Vision is an ophthalmic medical device company with an overarching mission to promote human health, sustainability and equality worldwide. The objective of CorNeat Vision is to produce, test and market an innovative, safe and long-lasting scalable medical solution for corneal blindness, pathology and injury, a bio-artificial organ: The CorNeat KPro. For more information on CorNeat Vision and the CorNeat KPro device, visit us at www.corneat.com.

Unfortunately, I cannot find any more detail. Presumably the company principals are making sure that no competitive advantages are given away.