Data science guide from Sense about Science

Sense about Science, headquartered in the UK, is in its own words (from its homepage)

Sense about Science is an independent campaigning charity that challenges the misrepresentation of science and evidence in public life. …

According to an October 1, 2019 announcement from Sense about Science (received via email), the organization has published a new guide,

Our director warned yesterday [September 30, 2019] that data science is being given a free
pass on quality in too many arenas. From flood predictions to mortgage offers to the prediction of housing needs, we are not asking enough about whether AI solutions and algorithms can bear the weight we want to put on them.

It was the UK launch of our ‘Data Science: a guide for society’ at the Institute of Physics, where we invited representatives from different sectors to take up the challenge of creating a more questioning culture. Tracey Brown said the situation was like medicine 50 years ago: it seems that some people have become too clever to explain and the rest of us are feeling too dumb to ask.

At the end of the event we had a lot of proposals for how to make different communities aware of the guide’s three fundamental questions from the people who attended. There are many hundreds of people among our friends who could do something along these lines:

     * Publicise the guide
     * Incorporate it into your own work
     * Send it to people who are involved in procurement, licensing or
reporting or decision making at community, national and international
levels
     * Undertake a project with us to equip particular groups such as
parliamentary advisers, journalists and small charities.

Would you take a look at the guide [1] here and tell me if there’s something you can do? (alex@senseaboutscience.org)

There are launches planned in other countries over the rest of this year and into 2020. We are drawing up a map of offers to reach different communities. I’ll share all your suggestions with my colleague Errin Riley at the end of this week and we will get back to you quickly.

Before linking you to the guide, here’s a brief description from the Patterns in Data webpage,

In recent years, phrases like ‘big data’, ‘machine learning’, ‘algorithms’ and ‘pattern recognition’ have started slipping into everyday discussion. We’ve worked with researchers and experts to generate an open and informed public discussion on patterns in data across a wide range of projects.

Data Science: A guide for society

According to the headlines, we’re in the middle of a ‘data revolution: large, detailed datasets and complex algorithms allow us to make predictions on anything from who will win the league to who is likely to commit a crime. Our ability to question the quality of evidence – as the public, journalists, politicians or decision makers – needs to be expanded to meet this. To know the questions to ask and how to press for clarity about the strengths and weaknesses of using analysis from data models to make decisions. This is a guide to having more of those conversations, regardless of how much you don’t know about data science.

Here’s Data Science: A Guide for Society.

‘Smart’ windows in Vancouver (Canada): engineering issues?

This post was going to focus on the first building in Canada to feature ‘smart’ windows. In this case, they are electrochromic windows and the company, View Dynamic Glass, was mentioned here in a September 17, 2018 posting about the windows’ use at the Dallas/Fort Worth Airport. (The posting includes a link to the View Dynamic Glass report on the windows’ use and a short video.)

However, things changed but, first, let’s start with an explanation as to what electrochromic glass ir. Chris Woodford in a December 5, 2018 article on explainthatstuff.com offers a great overview which includes an explanation, a description of how they work, and more. What follows is a brief excerpt from Woodford’s overview (Note: Links have been removed),

What is electrochromic glass?

Glass is an amazing material and our buildings would be dark, dingy, cold, and damp without it. But it has its drawbacks too. It lets in light and heat even when you don’t want it to. On a blinding summer’s day, the more heat (“solar gain”) that enters your building the more you’ll need to use your air-conditioning—a horrible waste of energy that costs you money and harms the environment. That’s why most of the windows in homes and offices are fitted with curtains or blinds. If you’re into interior design and remodeling, you might think furnishings like this are neat and attractive—but in cold, practical, scientific terms they’re a nuisance. Let’s be honest about this: curtains and blinds are a technological kludge to make up for glass’s big, built-in drawback: it’s transparent (or translucent) even when you don’t want it to be.

Since the early 20th century, people have got used to the idea of buildings that are increasingly automated. We have electric clothes washing machines, dishwashers, vacuum cleaners and much more. So why not fit our homes with electric windows that can change from clear to dark automatically? Smart windows (also referred to by the names smart glass, switchable windows, and dynamic windows) do exactly that using a scientific idea called electrochromism, in which materials change color (or switch from transparent to opaque) when you apply an electrical voltage across them. Typically smart windows start off a blueish color and gradually (over a few minutes) turn transparent when the electric current passes through them.

As for the news about its Vancouver debut, I was very excited to see this April 28, 2019 article by Kenneth Chan for dailyhive.com/vancouver,

BlueSky Properties’ 10-storey office building at 988 West Broadway [in Vancouver, Canada; emphasis mine] is home to the new Vancouver offices of Industrial Alliance Financial Group, which has leased nine stories and 93,700-sq-ft of office space.



One of the building’s unique design features is its use of View Dynamic Glass technology [emphases mine] — a glass technology that controls heat and glare, reduces overall energy consumption and costs, and improves the health and wellness of individuals working inside the building.

These smart windows optimize the amount of natural light to enhance mental and physical well-being without the need for shades or blinds. The application of the technology on this building, the first of its kind in Canada, will result in energy savings of up to 20%, [emphasis mine] with the amount of sunlight streaming through automatically tinted to block glare.

Blue Sky Properties (a Bosa Family Company), the local developer for this building, was very excited about the building and the ‘smart’ glass technology, according to its April 23, 2019 news release (here for a short version and here for the full version).

Other than being happy to see the technology being employed in Vancouver, I didn’t spend a lot of time thinking about the property. That changed on reading a May 8, 2019 article by Kenneth Chan for dailyhive.com/vancouver,

A structural engineer based in Vancouver has been stripped of his license to work in British Columbia [emphasis mine] following an investigation that determined his design for a condominium tower in Surrey fell short of the provincial building code.

According to a disciplinary notice posted by Engineers and Geoscientists British Columbia Association (EGBCA) on April 30, John Bryson, a managing partner of Bryson Markulin Zickmantel Structural Engineers (BMZSE), [emphases mine] admitted to unprofessional conduct and acted contrary to the association’s code of ethics that requires its members to “hold paramount the safety, health, and welfare of the public.”

“Mr. Bryson admitted that his structural design for the building did not comply with the 2006 BC Building Code, to which he certified it had been designed, in particular with respect to seismic and wind loads,” reads the notice. [emphases mine]

BMZSE has been involved in the design work of a number of projects across Metro Vancouver, including Station Square, Rogers Arena South Tower, Lougheed Heights, River District Parcel 17, The Jervis, Harwood, Plaza 88, Solo District, Burrard Place, Centreview Place, Trump International Hotel & Tower Vancouver, Central, Sovereign, Kings Crossing, and 988 West Broadway. [emphases mine]

You can find the ‘disciplinary notice’ (it’s an account of what Bryson failed to do and the punishment for the failure) here on the Association of Professional Engineers and Geoscientists of the Province of British Columbia (also known as Engineers and Geoscientists British Columbia) website.

Presumably, all of Bryson’s projects have been reviewed since the disciplinary action.

Revival of dead pig brains raises moral questions about life and death

The line between life and death may not be what we thought it was according to some research that was reported in April 2019. Ed Wong’s April 17, 2019 article (behind a paywall) for The Atlantic was my first inkling about the life-death questions raised by some research performed at Yale University, (Note: Links have been removed)

The brain, supposedly, cannot long survive without blood. Within seconds, oxygen supplies deplete, electrical activity fades, and unconsciousness sets in. If blood flow is not restored, within minutes, neurons start to die in a rapid, irreversible, and ultimately fatal wave.

But maybe not? According to a team of scientists led by Nenad Sestan at Yale School of Medicine, this process might play out over a much longer time frame, and perhaps isn’t as inevitable or irreparable as commonly believed. Sestan and his colleagues showed this in dramatic fashion—by preserving and restoring signs of activity in the isolated brains of pigs that had been decapitated four hours earlier.

The team sourced 32 pig brains from a slaughterhouse, placed them in spherical chambers, and infused them with nutrients and protective chemicals, using pumps that mimicked the beats of a heart. This system, dubbed BrainEx, preserved the overall architecture of the brains, preventing them from degrading. It restored flow in their blood vessels, which once again became sensitive to dilating drugs. It stopped many neurons and other cells from dying, and reinstated their ability to consume sugar and oxygen. Some of these rescued neurons even started to fire. “Everything was surprising,” says Zvonimir Vrselja, who performed most of the experiments along with Stefano Daniele.

… “I don’t see anything in this report that should undermine confidence in brain death as a criterion of death,” says Winston Chiong, a neurologist at the University of California at San Francisco. The matter of when to declare someone dead has become more controversial since doctors began relying more heavily on neurological signs, starting around 1968, when the criteria for “brain death” were defined. But that diagnosis typically hinges on the loss of brainwide activity—a line that, at least for now, is still final and irreversible. After MIT Technology Review broke the news of Sestan’s work a year ago, he started receiving emails from people asking whether he could restore brain function to their loved ones. He very much cannot. BrainEx isn’t a resurrection chamber.

“It’s not going to result in human brain transplants,” adds Karen Rommelfanger, who directs Emory University’s neuroethics program. “And I don’t think this means that the singularity is coming, or that radical life extension is more possible than before.”

So why do the study? “There’s potential for using this method to develop innovative treatments for patients with strokes or other types of brain injuries, and there’s a real need for those kinds of treatments,” says L. Syd M Johnson, a neuroethicist at Michigan Technological University. The BrainEx method might not be able to fully revive hours-dead brains, but Yama Akbari, a critical-care neurologist at the University of California at Irvine, wonders whether it would be more successful if applied minutes after death. Alternatively, it could help to keep oxygen-starved brains alive and intact while patients wait to be treated. “It’s an important landmark study,” Akbari says.

Yong notes that the study still needs to be replicated in his article which also probes some of the ethical issues associated with the latest neuroscience research.

Nature published the Yale study,

Restoration of brain circulation and cellular functions hours post-mortem by Zvonimir Vrselja, Stefano G. Daniele, John Silbereis, Francesca Talpo, Yury M. Morozov, André M. M. Sousa, Brian S. Tanaka, Mario Skarica, Mihovil Pletikos, Navjot Kaur, Zhen W. Zhuang, Zhao Liu, Rafeed Alkawadri, Albert J. Sinusas, Stephen R. Latham, Stephen G. Waxman & Nenad Sestan. Nature 568, 336–343 (2019) DOI: https://doi.org/10.1038/s41586-019-1099-1 Published 17 April 2019 Issue Date 18 April 2019

This paper is behind a paywall.

Two neuroethicists had this to say (link to their commentary in Nature follows) as per an April 71, 2019 news release from Case Western Reserve University (also on EurekAlert), Note: Links have been removed,

The brain is more resilient than previously thought. In a groundbreaking experiment published in this week’s issue of Nature, neuroscientists created an artificial circulation system that successfully restored some functions and structures in donated pig brains–up to four hours after the pigs were butchered at a USDA food processing facility. Though there was no evidence of restored consciousness, brains from the pigs were without oxygen for hours, yet could still support key functions provided by the artificial system. The result challenges the notion that mammalian brains are fully and irreversibly damaged by a lack of oxygen.

“The assumptions have always been that after a couple minutes of anoxia, or no oxygen, the brain is ‘dead,'” says Stuart Youngner, MD, who co-authored a commentary accompanying the study with Insoo Hyun, PhD, both professors in the Department of Bioethics at Case Western Reserve University School of Medicine. “The system used by the researchers begs the question: How long should we try to save people?”

In the pig experiment, researchers used an artificial perfusate (a type of cell-free “artificial blood”), which helped brain cells maintain their structure and some functions. Resuscitative efforts in humans, like CPR, are also designed to get oxygen to the brain and stave off brain damage. After a period of time, if a person doesn’t respond to resuscitative efforts, emergency medical teams declare them dead.

The acceptable duration of resuscitative efforts is somewhat uncertain. “It varies by country, emergency medical team, and hospital,” Youngner said. Promising results from the pig experiment further muddy the waters about the when to stop life-saving efforts.

At some point, emergency teams must make a critical switch from trying to save a patient, to trying to save organs, said Youngner. “In Europe, when emergency teams stop resuscitation efforts, they declare a patient dead, and then restart the resuscitation effort to circulate blood to the organs so they can preserve them for transplantation.”

The switch can involve extreme means. In the commentary, Youngner and Hyun describe how some organ recovery teams use a balloon to physically cut off blood circulation to the brain after declaring a person dead, to prepare the organs for transplantation.

The pig experiment implies that sophisticated efforts to perfuse the brain might maintain brain cells. If technologies like those used in the pig experiment could be adapted for humans (a long way off, caution Youngner and Hyun), some people who, today, are typically declared legally dead after a catastrophic loss of oxygen could, tomorrow, become candidates for brain resuscitation, instead of organ donation.

Said Youngner, “As we get better at resuscitating the brain, we need to decide when are we going to save a patient, and when are we going to declare them dead–and save five or more who might benefit from an organ.”

Because brain resuscitation strategies are in their infancy and will surely trigger additional efforts, the scientific and ethics community needs to begin discussions now, says Hyun. “This study is likely to raise a lot of public concerns. We hoped to get ahead of the hype and offer an early, reasoned response to this scientific advance.”

Both Youngner and Hyun praise the experiment as a “major scientific advancement” that is overwhelmingly positive. It raises the tantalizing possibility that the grave risks of brain damage caused by a lack of oxygen could, in some cases, be reversible.
“Pig brains are similar in many ways to human brains, which makes this study so compelling,” Hyun said. “We urge policymakers to think proactively about what this line of research might mean for ongoing debates around organ donation and end of life care.”

Here’s a link to and a citation to the Nature commentary,

Pig experiment challenges assumptions around brain damage in people by Stuart Youngner and Insoo Hyun. Nature 568, 302-304 (2019) DOI: 10.1038/d41586-019-01169-8 April 17, 2019

This paper is open access.

I was hoping to find out more about BrainEx, but this April 17, 2019 US National Institute of Mental Health news release is all I’ve been able to find in my admittedly brief online search. The news release offers more celebration than technical detail.

Quick comment

Interestingly, there hasn’t been much of a furor over this work. Not yet.

October 2019 science and art/science events in Vancouver and other parts of Canada

This is a scattering of events, which I’m sure will be augmented as we properly start the month of October 2019.

October 2, 2019 in Waterloo, Canada (Perimeter Institute)

If you want to be close enough to press the sacred flesh (Sir Martin Rees), you’re out of luck. However, there are still options ranging from watching a live webcast from the comfort of your home to watching the lecture via closed circuit television with other devoted fans at a licensed bistro located on site at the Perimeter Institute (PI) to catching the lecture at a later date via YouTube.

That said, here’s why you might be interested,

Here’s more from a September 11, 2019 Perimeter Institute (PI) announcement received via email,

Surviving the Century
MOVING TOWARD A POST-HUMAN FUTURE
Martin Rees, UK Astronomer Royal
Wednesday, Oct. 2 at 7:00 PM ET

Advances in technology and space exploration could, if applied wisely, allow a bright future for the 10 billion people living on earth by the end of the century.

But there are dystopian risks we ignore at our peril: our collective “footprint” on our home planet, as well as the creation and use of technologies so powerful that even small groups could cause a global catastrophe.

Martin Rees, the UK Astronomer Royal, will explore this unprecedented moment in human history during his lecture on October 2, 2019. A former president of the Royal Society and master of Trinity College, Cambridge, Rees is a cosmologist whose work also explores the interfaces between science, ethics, and politics. Read More.

Mark your calendar! Tickets will be available on Monday, Sept. 16 at 9 AM ET

Didn’t get tickets for the lecture? We’ve got more ways to watch.
Join us at Perimeter on lecture night to watch live in the Black Hole Bistro.
Catch the live stream on Inside the Perimeter or watch it on Youtube the next day
Become a member of our donor thank you program! Learn more.

It took me a while to locate an address for PI venue since I expect that information to be part of the announcement. (insert cranky emoticon here) Here’s the address: Perimeter Institute, Mike Lazaridis Theatre of Ideas, 31 Caroline St. N., Waterloo, ON

Before moving onto the next event, I’m including a paragraph from the event description that was not included in the announcement (from the PI Outreach Surviving the Century webpage),

In his October 2 [2019] talk – which kicks off the 2019/20 season of the Perimeter Institute Public Lecture Series – Rees will discuss the outlook for humans (or their robotic envoys) venturing to other planets. Humans, Rees argues, will be ill-adapted to new habitats beyond Earth, and will use genetic and cyborg technology to transform into a “post-human” species.

I first covered Sir Martin Rees and his concerns about technology (robots and cyborgs run amok) in this November 26, 2012 posting about existential risk. He and his colleagues at Cambridge University, UK, proposed a Centre for the Study of Existential Risk, which opened in 2015.

Straddling Sept. and Oct. at the movies in Vancouver

The Vancouver International Film Festival (VIFF) opened today, September 26, 2019. During its run to October 11, 2019 there’ll be a number of documentaries that touch on science. Here are three of the documentaries most closely adhere to the topics I’m most likely to address on this blog. There is a fourth documentary included here as it touches on ecology in a more hopeful fashion than is the current trend.

Human Nature

From the VIFF 2019 film description and ticket page,

One of the most significant scientific breakthroughs in history, the discovery of CRISPR has made it possible to manipulate human DNA, paving the path to a future of great possibilities.

The implications of this could mean the eradication of disease or, more controversially, the possibility of genetically pre-programmed children.

Breaking away from scientific jargon, Human Nature pieces together a complex account of bio-research for the layperson as compelling as a work of science-fiction. But whether the gene-editing powers of CRISPR (described as “a word processor for DNA”) are used for good or evil, they’re reshaping the world as we know it. As we push past the boundaries of what it means to be human, Adam Bolt’s stunning work of science journalism reaches out to scientists, engineers, and people whose lives could benefit from CRISPR technology, and offers a wide-ranging look at the pros and cons of designing our futures.

Tickets
Friday, September 27, 2019 at 11:45 AM
Vancity Theatre

Saturday, September 28, 2019 at 11:15 AM
International Village 10

Thursday, October 10, 2019 at 6:45 PM
SFU Goldcorp

According to VIFF, the tickets for the Sept. 27, 2019 show are going fast.

Resistance Fighters

From the VIFF 2019 film description and ticket page,

Since mass-production in the 1940s, antibiotics have been nothing less than miraculous, saving countless lives and revolutionizing modern medicine. It’s virtually impossible to imagine hospitals or healthcare without them. But after years of abuse and mismanagement by the medical and agricultural communities, superbugs resistant to antibiotics are reaching apocalyptic proportions. The ongoing rise in multi-resistant bacteria – unvanquishable microbes, currently responsible for 700,000 deaths per year and projected to kill 10 million yearly by 2050 if nothing changes – and the people who fight them are the subjects of Michael Wech’s stunning “science-thriller.”

Peeling back the carefully constructed veneer of the medical corporate establishment’s greed and complacency to reveal the world on the cusp of a potential crisis, Resistance Fighters sounds a clarion call of urgency. It’s an all-out war, one which most of us never knew we were fighting, to avoid “Pharmageddon.” Doctors, researchers, patients, and diplomats testify about shortsighted medical and economic practices, while Wech offers refreshingly original perspectives on environment, ecology, and (animal) life in general. As alarming as it is informative, this is a wake-up call the world needs to hear.

Sunday, October 6, 2019 at 5:45 PM
International Village 8

Thursday, October 10, 2019 at 2:15 PM
SFU Goldcorp

According to VIFF, the tickets for the Oct. 6, 2019 show are going fast.

Trust Machine: The Story of Blockchain

Strictly speaking this is more of a technology story than science story but I have written about blockchain and cryptocurrencies before so I’m including this. From the VIFF 2019 film description and ticket page,

For anyone who has questions about cryptocurrencies like Bitcoin (and who doesn’t?), Alex Winter’s thorough documentary is an excellent introduction to the blockchain phenomenon. Trust Machine offers a wide range of expert testimony and a variety of perspectives that explicate the promises and the risks inherent in this new manifestation of high-tech wizardry. And it’s not just money that blockchains threaten to disrupt: innovators as diverse as UNICEF and Imogen Heap make spirited arguments that the industries of energy, music, humanitarianism, and more are headed for revolutionary change.

A propulsive and subversive overview of this little-understood phenomenon, Trust Machine crafts a powerful and accessible case that a technologically decentralized economy is more than just a fad. As the aforementioned experts – tech wizards, underground activists, and even some establishment figures – argue persuasively for an embrace of the possibilities offered by blockchains, others criticize its bubble-like markets and inefficiencies. Either way, Winter’s film suggests a whole new epoch may be just around the corner, whether the powers that be like it or not.

Tuesday, October 1, 2019 at 11:00 AM
Vancity Theatre

Thursday, October 3, 2019 at 9:00 PM
Vancity Theatre

Monday, October 7, 2019 at 1:15 PM
International Village 8

According to VIFF, tickets for all three shows are going fast

The Great Green Wall

For a little bit of hope, From the VIFF 2019 film description and ticket page,

“We must dare to invent the future.” In 2007, the African Union officially began a massively ambitious environmental project planned since the 1970s. Stretching through 11 countries and 8,000 km across the desertified Sahel region, on the southern edges of the Sahara, The Great Green Wall – once completed, a mosaic of restored, fertile land – would be the largest living structure on Earth.

Malian musician-activist Inna Modja embarks on an expedition through Senegal, Mali, Nigeria, Niger, and Ethiopia, gathering an ensemble of musicians and artists to celebrate the pan-African dream of realizing The Great Green Wall. Her journey is accompanied by a dazzling array of musical diversity, celebrating local cultures and traditions as they come together into a community to stand against the challenges of desertification, drought, migration, and violent conflict.

An unforgettable, beautiful exploration of a modern marvel of ecological restoration, and so much more than a passive source of information, The Great Green Wall is a powerful call to take action and help reshape the world.

Sunday, September 29, 2019 at 11:15 AM
International Village 10

Wednesday, October 2, 2019 at 6:00 PM
International Village 8
Standby – advance tickets are sold out but a limited number are likely to be released at the door

Wednesday, October 9, 2019 at 11:00 AM
International Village 9

As you can see, one show is already offering standby tickets only and the other two are selling quickly.

For venue locations, information about what ‘standby’ means and much more go here and click on the Festival tab. As for more information the individual films, you’ll links to trailers, running times, and more on the pages for which I’ve supplied links.

Brain Talks on October 16, 2019 in Vancouver

From time to time I get notices about a series titled Brain Talks from the Dept. of Psychiatry at the University of British Columbia. A September 11, 2019 announcement (received via email) focuses attention on the ‘guts of the matter’,

YOU ARE INVITED TO ATTEND:

BRAINTALKS: THE BRAIN AND THE GUT

WEDNESDAY, OCTOBER 16TH, 2019 FROM 6:00 PM – 8:00 PM

Join us on Wednesday October 16th [2019] for a series of talks exploring the
relationship between the brain, microbes, mental health, diet and the
gut. We are honored to host three phenomenal presenters for the evening:
Dr. Brett Finlay, Dr. Leslie Wicholas, and Thara Vayali, ND.

DR. BRETT FINLAY [2] is a Professor in the Michael Smith Laboratories at
the University of British Columbia. Dr. Finlay’s  research interests are
focused on host-microbe interactions at the molecular level,
specializing in Cellular Microbiology. He has published over 500 papers
and has been inducted into the Canadian  Medical Hall of Fame. He is the
co-author of the  books: Let Them Eat Dirt and The Whole Body
Microbiome.

DR. LESLIE WICHOLAS [3]  is a psychiatrist with an expertise in the
clinical understanding of the gut-brain axis. She has become
increasingly involved in the emerging field of Nutritional Psychiatry,
exploring connections between diet, nutrition, and mental health.
Currently, Dr. Wicholas is the director of the Food as Medicine program
at the Mood Disorder Association of BC.

THARA VAYALI, ND [4] holds a BSc in Nutritional Sciences and a MA in
Education and Communications. She has trained in naturopathic medicine
and advocates for awareness about women’s physiology and body literacy.
Ms. Vayali is a frequent speaker and columnist that prioritizes
engagement, understanding, and community as pivotal pillars for change.

Our event on Wednesday, October 16th [2019] will start with presentations from
each of the three speakers, and end with a panel discussion inspired by
audience questions. After the talks, at 7:30 pm, we host a social
gathering with a rich spread of catered healthy food and non-alcoholic
drinks. We look forward to seeing you there!

Paetzhold Theater

Vancouver General Hospital; Jim Pattison Pavilion, Vancouver, BC

Attend Event

That’s it for now.

Mushroom compost as a biobased nanocarrier for curing plant diseases

Scientists in Europe have just cured a plant disease Esca (fungi that destroy grapevines) for the first time ever. A May 22, 2019 news item on Nanowerk announces the research success,

Plant diseases, though a normal part of nature, can have disastrous effects in agriculture. They reduce food for people and revenues in rural areas. In the worst cases they result in hunger and starvation, as many famines in history show. About 16% of all crops are lost to plant diseases each year across the world.

The Max Planck Institute for Polymer Research in Mainz has just delivered a double novelty to the scientific world: nanocarriers made of “waste”, which release drugs in a way that cured a plant disease for the first time.

Nanocarriers are very tiny degradable capsules that have been studied for medical applications in the last 30 years. These nanocapsules are considered the “magic bullet” to cure human cancer, because they discharge the drug directly to the targeted cells.

A May 20, 2019 BIOrescue project press release, which originated the news item, delves further into the research,

Treating plant diseases that have never been cured before

Thanks to the European research funds of the BIOrescue project, the researchers at the Max Plank Institute investigated the possibility to transpose the same principle to cure plant diseases. They have been testing these nanocapsules to treat ESCA, a fungi disease that affects 2 billion grapevine plants across the world for which there has not been a cure so far.
Dr Frederik Wurm, who is leading this research at Max Planck said “After two years of testing in our labs and then on Riesling vineyards in Germany, it looks like we have managed to reduce the symptoms of the disease. Further tests will confirm if this cure is a solution in the long term. If the effects are confirmed the same method can be extended potentially to any other disease in agriculture”.

“Circular” nanocarriers made of waste

The second novelty of these nanoscopic capsules is that they can be made of waste material – in this case used mushrooms compost.

“Normally nanocarriers are made of polymers based on fossil fuels. In the past, we have developed biobased nanocarriers made of lignin coming from the paper and pulp industry. But this is the very first time we try to develop them from agricultural residues, which makes them a truly “circular” product, from used plant fertiliser to plant cure. Nothing is going to be wasted!” said Wurm.

To obtain these tiny biodegradable capsules, the Max Planck researchers carried out a chemical conversion to transform the soluble lignin obtained after the pretreatment of used mushroom compost.

Afterwards the nanocarriers have been loaded with the drug that is usually sprayed on the plant with very limited effects. Thanks to the natural enzymatic degradation of the nanocarriers, the drug is released inside the plant in a controlled and progressive way. With this effective method the drug only targets the fungi, which destroy the plant from inside. Tests demonstrated that these nanocarriers are not toxic for the plants and do not reach the crop.

“Beyond the agricultural sector, the capsules have a myriad of other potential applications from food enhancement to pharmaceutical products. It’s only a matter of time until we find biobased nanocarriers available on the market for any of these uses” said Wurm.

Bio-based nanocarrier Courtesy: BIOrescue

You can find out more about the BIOrescue project here, including interesting facts such as this,

To satisfy consumer demand for mushrooms, European farmers use over three million tonnes of compost each year. Though the compost contains valuable organic components, it is only suitable for one to three mushroom harvests, and disposing of it creates significant economic and logistical problems for Europe’s farmers.

Apparently, this is is a ‘circular economy’ project. ‘Circular economy’ being one of the latest buzz terms. Let’s hope it graduates to something ‘beyond buzz’, as it were.

Ghosts, mechanical turks, and pseudo-AI (artificial intelligence)—Is it all a con game?

There’s been more than one artificial intelligence (AI) story featured here on this blog but the ones featured in this posting are the first I’ve stumbled across that suggest the hype is even more exaggerated than even the most cynical might have thought. (BTW, the 2019 material is later as I have taken a chronological approach to this posting.)

It seems a lot of companies touting their AI algorithms and capabilities are relying on human beings to do the work, from a July 6, 2018 article by Olivia Solon for the Guardian (Note: A link has been removed),

It’s hard to build a service powered by artificial intelligence. So hard, in fact, that some startups have worked out it’s cheaper and easier to get humans to behave like robots than it is to get machines to behave like humans.

“Using a human to do the job lets you skip over a load of technical and business development challenges. It doesn’t scale, obviously, but it allows you to build something and skip the hard part early on,” said Gregory Koberger, CEO of ReadMe, who says he has come across a lot of “pseudo-AIs”.

“It’s essentially prototyping the AI with human beings,” he said.

In 2017, the business expense management app Expensify admitted that it had been using humans to transcribe at least some of the receipts it claimed to process using its “smartscan technology”. Scans of the receipts were being posted to Amazon’s Mechanical Turk crowdsourced labour tool, where low-paid workers were reading and transcribing them.

“I wonder if Expensify SmartScan users know MTurk workers enter their receipts,” said Rochelle LaPlante, a “Turker” and advocate for gig economy workers on Twitter. “I’m looking at someone’s Uber receipt with their full name, pick-up and drop-off addresses.”

Even Facebook, which has invested heavily in AI, relied on humans for its virtual assistant for Messenger, M.

In some cases, humans are used to train the AI system and improve its accuracy. …

The Turk

Fooling people with machines that seem intelligent is not new according to a Sept. 10, 2018 article by Seth Stevenson for Slate.com (Note: Links have been removed),

It’s 1783, and Paris is gripped by the prospect of a chess match. One of the contestants is François-André Philidor, who is considered the greatest chess player in Paris, and possibly the world. Everyone is so excited because Philidor is about to go head-to-head with the other biggest sensation in the chess world at the time.

But his opponent isn’t a man. And it’s not a woman, either. It’s a machine.

This story may sound a lot like Garry Kasparov taking on Deep Blue, IBM’s chess-playing supercomputer. But that was only a couple of decades ago, and this chess match in Paris happened more than 200 years ago. It doesn’t seem like a robot that can play chess would even be possible in the 1780s. This machine playing against Philidor was making an incredible technological leap—playing chess, and not only that, but beating humans at chess.

In the end, it didn’t quite beat Philidor, but the chess master called it one of his toughest matches ever. It was so hard for Philidor to get a read on his opponent, which was a carved wooden figure—slightly larger than life—wearing elaborate garments and offering a cold, mean stare.

It seems like the minds of the era would have been completely blown by a robot that could nearly beat a human chess champion. Some people back then worried that it was black magic, but many folks took the development in stride. …

Debates about the hottest topic in technology today—artificial intelligence—didn’t starts in the 1940s, with people like Alan Turing and the first computers. It turns out that the arguments about AI go back much further than you might imagine. The story of the 18th-century chess machine turns out to be one of those curious tales from history that can help us understand technology today, and where it might go tomorrow.

[In future episodes our podcast, Secret History of the Future] we’re going to look at the first cyberattack, which happened in the 1830s, and find out how the Victorians invented virtual reality.

Philidor’s opponent was known as The Turk or Mechanical Turk and that ‘machine’ was in fact a masterful hoax as The Turk held a hidden compartment from which a human being directed his moves.

People pretending to be AI agents

It seems that today’s AI has something in common with the 18th century Mechanical Turk, there are often humans lurking in the background making things work. From a Sept. 4, 2018 article by Janelle Shane for Slate.com (Note: Links have been removed),

Every day, people are paid to pretend to be bots.

In a strange twist on “robots are coming for my job,” some tech companies that boast about their artificial intelligence have found that at small scales, humans are a cheaper, easier, and more competent alternative to building an A.I. that can do the task.

Sometimes there is no A.I. at all. The “A.I.” is a mockup powered entirely by humans, in a “fake it till you make it” approach used to gauge investor interest or customer behavior. Other times, a real A.I. is combined with human employees ready to step in if the bot shows signs of struggling. These approaches are called “pseudo-A.I.” or sometimes, more optimistically, “hybrid A.I.”

Although some companies see the use of humans for “A.I.” tasks as a temporary bridge, others are embracing pseudo-A.I. as a customer service strategy that combines A.I. scalability with human competence. They’re advertising these as “hybrid A.I.” chatbots, and if they work as planned, you will never know if you were talking to a computer or a human. Every remote interaction could turn into a form of the Turing test. So how can you tell if you’re dealing with a bot pretending to be a human or a human pretending to be a bot?

One of the ways you can’t tell anymore is by looking for human imperfections like grammar mistakes or hesitations. In the past, chatbots had prewritten bits of dialogue that they could mix and match according to built-in rules. Bot speech was synonymous with precise formality. In early Turing tests, spelling mistakes were often a giveaway that the hidden speaker was a human. Today, however, many chatbots are powered by machine learning. Instead of using a programmer’s rules, these algorithms learn by example. And many training data sets come from services like Amazon’s Mechanical Turk, which lets programmers hire humans from around the world to generate examples of tasks like asking and answering questions. These data sets are usually full of casual speech, regionalisms, or other irregularities, so that’s what the algorithms learn. It’s not uncommon these days to get algorithmically generated image captions that read like text messages. And sometimes programmers deliberately add these things in, since most people don’t expect imperfections of an algorithm. In May, Google’s A.I. assistant made headlines for its ability to convincingly imitate the “ums” and “uhs” of a human speaker.

Limited computing power is the main reason that bots are usually good at just one thing at a time. Whenever programmers try to train machine learning algorithms to handle additional tasks, they usually get algorithms that can do many tasks rather badly. In other words, today’s algorithms are artificial narrow intelligence, or A.N.I., rather than artificial general intelligence, or A.G.I. For now, and for many years in the future, any algorithm or chatbot that claims A.G.I-level performance—the ability to deal sensibly with a wide range of topics—is likely to have humans behind the curtain.

Another bot giveaway is a very poor memory. …

Bringing AI to life: ghosts

Sidney Fussell’s April 15, 2019 article for The Atlantic provides more detail about the human/AI interface as found in some Amazon products such as Alexa ( a voice-control system),

… Alexa-enabled speakers can and do interpret speech, but Amazon relies on human guidance to make Alexa, well, more human—to help the software understand different accents, recognize celebrity names, and respond to more complex commands. This is true of many artificial intelligence–enabled products. They’re prototypes. They can only approximate their promised functions while humans help with what Harvard researchers have called “the paradox of automation’s last mile.” Advancements in AI, the researchers write, create temporary jobs such as tagging images or annotating clips, even as the technology is meant to supplant human labor. In the case of the Echo, gig workers are paid to improve its voice-recognition software—but then, when it’s advanced enough, it will be used to replace the hostess in a hotel lobby.

A 2016 paper by researchers at Stanford University used a computer vision system to infer, with 88 percent accuracy, the political affiliation of 22 million people based on what car they drive and where they live. Traditional polling would require a full staff, a hefty budget, and months of work. The system completed the task in two weeks. But first, it had to know what a car was. The researchers paid workers through Amazon’s Mechanical Turk [emphasis mine] platform to manually tag thousands of images of cars, so the system would learn to differentiate between shapes, styles, and colors.

It may be a rude awakening for Amazon Echo owners, but AI systems require enormous amounts of categorized data, before, during, and after product launch. ..,

Isn’t interesting that Amazon also has a crowdsourcing marketplace for its own products. Calling it ‘Mechanical Turk’ after a famous 18th century hoax would suggest a dark sense of humour somewhere in the corporation. (You can find out more about the Amazon Mechanical Turk on this Amazon website and in its Wikipedia entry.0

Anthropologist, Mary L. Gray has coined the phrase ‘ghost work’ for the work that humans perform but for which AI gets the credit. Angela Chan’s May 13, 2019 article for The Verge features Gray as she promotes her latest book with Siddarth Suri ‘Ghost Work: How to Stop Silicon Valley from Building a New Global Underclass’ (Note: A link has been removed),

“Ghost work” is anthropologist Mary L. Gray’s term for the invisible labor that powers our technology platforms. When Gray, a senior researcher at Microsoft Research, first arrived at the company, she learned that building artificial intelligence requires people to manage and clean up data to feed to the training algorithms. “I basically started asking the engineers and computer scientists around me, ‘Who are the people you pay to do this task work of labeling images and classification tasks and cleaning up databases?’” says Gray. Some people said they didn’t know. Others said they didn’t want to know and were concerned that if they looked too closely they might find unsavory working conditions.

So Gray decided to find out for herself. Who are the people, often invisible, who pick up the tasks necessary for these platforms to run? Why do they do this work, and why do they leave? What are their working conditions?

The interview that follows is interesting although it doesn’t seem to me that the question about working conditions is answered in any great detail. However, there is this rather interesting policy suggestion,

If companies want to happily use contract work because they need to constantly churn through new ideas and new aptitudes, the only way to make that a good thing for both sides of that enterprise is for people to be able to jump into that pool. And people do that when they have health care and other provisions. This is the business case for universal health care, for universal education as a public good. It’s going to benefit all enterprise.

I want to get across to people that, in a lot of ways, we’re describing work conditions. We’re not describing a particular type of work. We’re describing today’s conditions for project-based task-driven work. This can happen to everybody’s jobs, and I hate that that might be the motivation because we should have cared all along, as this has been happening to plenty of people. For me, the message of this book is: let’s make this not just manageable, but sustainable and enjoyable. Stop making our lives wrap around work, and start making work serve our lives.

Puts a different spin on AI and work, doesn’t it?

AI (artificial intelligence) and a hummingbird robot

Every once in a while I stumble across a hummingbird robot story (my August 12, 2011 posting and my August 1, 2014 posting). Here’s what the hummingbird robot looks like now (hint: there’s a significant reduction in size),

Caption: Purdue University researchers are building robotic hummingbirds that learn from computer simulations how to fly like a real hummingbird does. The robot is encased in a decorative shell. Credit: Purdue University photo/Jared Pike

I think this is the first time I’ve seen one of these projects not being funded by the military, which explains why the researchers are more interested in using these hummingbird robots for observing wildlife and for rescue efforts in emergency situations. Still, they do acknowledge theses robots could also be used in covert operations.

From a May 9, 2019 news item on ScienceDaily,

What can fly like a bird and hover like an insect?

Your friendly neighborhood hummingbirds. If drones had this combo, they would be able to maneuver better through collapsed buildings and other cluttered spaces to find trapped victims.

Purdue University researchers have engineered flying robots that behave like hummingbirds, trained by machine learning algorithms based on various techniques the bird uses naturally every day.

This means that after learning from a simulation, the robot “knows” how to move around on its own like a hummingbird would, such as discerning when to perform an escape maneuver.

Artificial intelligence, combined with flexible flapping wings, also allows the robot to teach itself new tricks. Even though the robot can’t see yet, for example, it senses by touching surfaces. Each touch alters an electrical current, which the researchers realized they could track.

“The robot can essentially create a map without seeing its surroundings. This could be helpful in a situation when the robot might be searching for victims in a dark place — and it means one less sensor to add when we do give the robot the ability to see,” said Xinyan Deng, an associate professor of mechanical engineering at Purdue.

The researchers even have a video,

A May 9, 2019 Purdue University news release (also on EurekAlert), which originated the news item, provides more detail,


The researchers [presented] their work on May 20 at the 2019 IEEE International Conference on Robotics and Automation in Montreal. A YouTube video is available at https://www.youtube.com/watch?v=hl892dHqfA&feature=youtu.be. [it’s the video I’ve embedded in the above]

Drones can’t be made infinitely smaller, due to the way conventional aerodynamics work. They wouldn’t be able to generate enough lift to support their weight.

But hummingbirds don’t use conventional aerodynamics – and their wings are resilient. “The physics is simply different; the aerodynamics is inherently unsteady, with high angles of attack and high lift. This makes it possible for smaller, flying animals to exist, and also possible for us to scale down flapping wing robots,” Deng said.

Researchers have been trying for years to decode hummingbird flight so that robots can fly where larger aircraft can’t. In 2011, the company AeroVironment, commissioned by DARPA, an agency within the U.S. Department of Defense, built a robotic hummingbird that was heavier than a real one but not as fast, with helicopter-like flight controls and limited maneuverability. It required a human to be behind a remote control at all times.

Deng’s group and her collaborators studied hummingbirds themselves for multiple summers in Montana. They documented key hummingbird maneuvers, such as making a rapid 180-degree turn, and translated them to computer algorithms that the robot could learn from when hooked up to a simulation.

Further study on the physics of insects and hummingbirds allowed Purdue researchers to build robots smaller than hummingbirds – and even as small as insects – without compromising the way they fly. The smaller the size, the greater the wing flapping frequency, and the more efficiently they fly, Deng says.

The robots have 3D-printed bodies, wings made of carbon fiber and laser-cut membranes. The researchers have built one hummingbird robot weighing 12 grams – the weight of the average adult Magnificent Hummingbird – and another insect-sized robot weighing 1 gram. The hummingbird robot can lift more than its own weight, up to 27 grams.

Designing their robots with higher lift gives the researchers more wiggle room to eventually add a battery and sensing technology, such as a camera or GPS. Currently, the robot needs to be tethered to an energy source while it flies – but that won’t be for much longer, the researchers say.

The robots could fly silently just as a real hummingbird does, making them more ideal for covert operations. And they stay steady through turbulence, which the researchers demonstrated by testing the dynamically scaled wings in an oil tank.

The robot requires only two motors and can control each wing independently of the other, which is how flying animals perform highly agile maneuvers in nature.

“An actual hummingbird has multiple groups of muscles to do power and steering strokes, but a robot should be as light as possible, so that you have maximum performance on minimal weight,” Deng said.

Robotic hummingbirds wouldn’t only help with search-and-rescue missions, but also allow biologists to more reliably study hummingbirds in their natural environment through the senses of a realistic robot.

“We learned from biology to build the robot, and now biological discoveries can happen with extra help from robots,” Deng said.
Simulations of the technology are available open-source at https://github.com/
purdue-biorobotics/flappy
.

Early stages of the work, including the Montana hummingbird experiments in collaboration with Bret Tobalske’s group at the University of Montana, were financially supported by the National Science Foundation.

The researchers have three paper on arxiv.org for open access peer review,

Learning Extreme Hummingbird Maneuvers on Flapping Wing Robots
Fan Fei, Zhan Tu, Jian Zhang, and Xinyan Deng
Purdue University, West Lafayette, IN, USA
https://arxiv.org/abs/1902.0962

Biological studies show that hummingbirds can perform extreme aerobatic maneuvers during fast escape. Given a sudden looming visual stimulus at hover, a hummingbird initiates a fast backward translation coupled with a 180-degree yaw turn, which is followed by instant posture stabilization in just under 10 wingbeats. Consider the wingbeat frequency of 40Hz, this aggressive maneuver is carried out in just 0.2 seconds. Inspired by the hummingbirds’ near-maximal performance during such extreme maneuvers, we developed a flight control strategy and experimentally demonstrated that such maneuverability can be achieved by an at-scale 12- gram hummingbird robot equipped with just two actuators. The proposed hybrid control policy combines model-based nonlinear control with model-free reinforcement learning. We use model-based nonlinear control for nominal flight control, as the dynamic model is relatively accurate for these conditions. However, during extreme maneuver, the modeling error becomes unmanageable. A model-free reinforcement learning policy trained in simulation was optimized to ‘destabilize’ the system and maximize the performance during maneuvering. The hybrid policy manifests a maneuver that is close to that observed in hummingbirds. Direct simulation-to-real transfer is achieved, demonstrating the hummingbird-like fast evasive maneuvers on the at-scale hummingbird robot.

Acting is Seeing: Navigating Tight Space Using Flapping Wings
Zhan Tu, Fan Fei, Jian Zhang, and Xinyan Deng
Purdue University, West Lafayette, IN, USA
https://arxiv.org/abs/1902.0868

Wings of flying animals can not only generate lift and control torques but also can sense their surroundings. Such dual functions of sensing and actuation coupled in one element are particularly useful for small sized bio-inspired robotic flyers, whose weight, size, and power are under stringent constraint. In this work, we present the first flapping-wing robot using its flapping wings for environmental perception and navigation in tight space, without the need for any visual feedback. As the test platform, we introduce the Purdue Hummingbird, a flapping-wing robot with 17cm wingspan and 12 grams weight, with a pair of 30-40Hz flapping wings driven by only two actuators. By interpreting the wing loading feedback and its variations, the vehicle can detect the presence of environmental changes such as grounds, walls, stairs, obstacles and wind gust. The instantaneous wing loading can be obtained through the measurements and interpretation of the current feedback by the motors that actuate the wings. The effectiveness of the proposed approach is experimentally demonstrated on several challenging flight tasks without vision: terrain following, wall following and going through a narrow corridor. To ensure flight stability, a robust controller was designed for handling unforeseen disturbances during the flight. Sensing and navigating one’s environment through actuator loading is a promising method for mobile robots, and it can serve as an alternative or complementary method to visual perception.

Flappy Hummingbird: An Open Source Dynamic Simulation of Flapping Wing Robots and Animals
Fan Fei, Zhan Tu, Yilun Yang, Jian Zhang, and Xinyan Deng
Purdue University, West Lafayette, IN, USA
https://arxiv.org/abs/1902.0962

Insects and hummingbirds exhibit extraordinary flight capabilities and can simultaneously master seemingly conflicting goals: stable hovering and aggressive maneuvering, unmatched by small scale man-made vehicles. Flapping Wing Micro Air Vehicles (FWMAVs) hold great promise for closing this performance gap. However, design and control of such systems remain challenging due to various constraints. Here, we present an open source high fidelity dynamic simulation for FWMAVs to serve as a testbed for the design, optimization and flight control of FWMAVs. For simulation validation, we recreated the hummingbird-scale robot developed in our lab in the simulation. System identification was performed to obtain the model parameters. The force generation, open- loop and closed-loop dynamic response between simulated and experimental flights were compared and validated. The unsteady aerodynamics and the highly nonlinear flight dynamics present challenging control problems for conventional and learning control algorithms such as Reinforcement Learning. The interface of the simulation is fully compatible with OpenAI Gym environment. As a benchmark study, we present a linear controller for hovering stabilization and a Deep Reinforcement Learning control policy for goal-directed maneuvering. Finally, we demonstrate direct simulation-to-real transfer of both control policies onto the physical robot, further demonstrating the fidelity of the simulation.

Enjoy!

Detecting off-target effects of CRISPR gene-editing

In amidst all the hyperbole about CRISPR (clustered regularly interspaced short palindromic repeats), the gene editing technology, you will sometimes find a mild cautionary note. It seems that CRISPR is not as precise as you might think.

Some months ago there was a story about research into detecting possible unanticipated (off target) effects from using CRISPR, from an April 19, 2019 news item on ScienceDaily,

Since the CRISPR genome editing technology was invented in 2012, it has shown great promise to treat a number of intractable diseases. However, scientists have struggled to identify potential off-target effects in therapeutically relevant cell types, which remains the main barrier to moving therapies to the clinic. Now, a group of scientists at the Gladstone Institutes and the Innovative Genomics Institute (IGI), with collaborators at AstraZeneca, have developed a reliable method to do just that.

An April 19, 2019 Gladstone Institutes press release by Julie Langelier, which originated the press release, provides details,

CRISPR edits a person’s genome by cutting the DNA at a specific location. The challenge is to ensure the tool doesn’t also make cuts elsewhere along the DNA—damage referred to as “off-target effects,” which could have unforeseen consequences.

In a study published in the journal Science, the two first authors, Beeke Wienert and Stacia Wyman, found a new way to approach the problem.

“When CRISPR makes a cut, the DNA is broken,” says Wienert, PhD, who began the work in Jacob E. Corn’s IGI laboratory and who is now a postdoctoral scholar in Bruce R. Conklin’s laboratory at Gladstone. “So, in order to survive, the cell recruits many different DNA repair factors to that particular site in the genome to fix the break and join the cut ends back together. We thought that if we could find the locations of these DNA repair factors, we could identify the sites that have been cut by CRISPR.”

To test their idea, the researchers studied a panel of different DNA repair factors. They found that one of them, called MRE11, is one of the first responders to the site of the cut. Using MRE11, the scientists developed a new technique, named DISCOVER-Seq, that can identify the exact sites in the genome where a cut has been made by CRISPR.

“The human genome is extremely large—if you printed the entire DNA sequence, you would end up with a novel as tall as a 16-story building,” explains Conklin, MD, senior investigator at Gladstone and deputy director at IGI. “When we want to cut DNA with CRISPR, it’s like we’re trying to remove one specific word on a particular page in that novel.”

“You can think of the DNA repair factors as different types of bookmarks added to the book,” Conklin adds. “While some may bookmark an entire chapter, MRE11 is a bookmark that drills down to the exact letter than has been changed.”

Different methods currently exist to detect CRISPR off-target effects. However, they come with limitations that range from producing false-positive results to killing the cells they’re examining. In addition, the most common method used to date is currently limited to cultured cells in the laboratory, excluding its use in patient-derived stem cells or animal tissue.

“Because our method relies on the cell’s natural repair process to identify cuts, it has proven to be much less invasive and much more reliable,” says Corn, PhD, who now runs a laboratory at ETH Zurich. “We were able to test our new DISCOVER-Seq method in induced pluripotent stem cells, patient cells, and mice, and our findings indicate that this method could potentially be used in any system, rather than just in the lab.”

The DISCOVER-Seq method, by being applied to new cell types and systems, has also revealed new insights into the mechanisms used by CRISPR to edit the genome, which will lead to a better understanding of the biology of how this tool works.

“The new method greatly simplifies the process of identifying off-target effects while also increasing the accuracy of the results,” says Conklin, who is also a professor of medical genetics and molecular pharmacology at UC San Francisco (UCSF). “This could allow us to better predict how genome editing would work in a clinical setting. As a result, it represents an essential step in improving pre-clinical studies and bringing CRISPR-based therapies closer to the patients in need.”

###

About the Study

The paper “Unbiased detection of CRISPR off-targets in vivo 1 using DISCOVER-Seq” was published by the journal Science on April 19, 2019. Gladstone’s Hannah L. Watry and Luke M. Judge (who is also at UCSF) contributed to this study. Other authors also include Christopher D. Richardson, Jonathan T. Vu, and Katelynn R. Kazane from IGI, Charles D. Yeh from ETH Zurich, as well as Pinar Akcakaya, Michelle J. Porritt, and Michaela Morlock from AstraZeneca.

The work was supported by Gladstone, the National Institutes of Health (grants EY028249 and HL13535801), the Li Ka Shing Foundation, the Heritage Medical Research Institute, the Fanconi Anemia Research Foundation, a Sir Keith Murdoch Fellowship from the American Australian Association, and an Early Career Fellowship from the National Health and Medical Research Council.

About the Gladstone Institute

To ensure our work does the greatest good, the Gladstone Institutes focuses on conditions with profound medical, economic, and social impact—unsolved diseases. Gladstone is an independent, nonprofit life science research organization that uses visionary science and technology to overcome disease. It has an academic affiliation with the University of California, San Francisco.

Before getting to the link and citation that I usually offer you might find this July 17, 2018 posting, The CRISPR ((clustered regularly interspaced short palindromic repeats)-CAS9 gene-editing technique may cause new genetic damage kerfuffle of interest. I wonder if this latest news affected the CRISPR market as the did the news in 2018.

In addition to the link in the press release, I am including a link and a citation for the study,

Unbiased detection of CRISPR off-targets in vivo using DISCOVER-Seq by Beeke Wienert, Stacia K. Wyman, Christopher D. Richardson, Charles D. Yeh, Pinar Akcakaya, Michelle J. Porritt, Michaela Morlock, Jonathan T. Vu, Katelynn R. Kazane, Hannah L. Watry, Luke M. Judge, Bruce R. Conklin, Marcello Maresca, Jacob E. Corn. Science 19 Apr 2019: Vol. 364, Issue 6437, pp. 286-289 DOI: 10.1126/science.aav9023

This paper is behind a paywall.

Money

Over the last 10 or more years, I have, on occasion made a point, of finding out about the funding for various non-profit agencies and projects. I find that sort of thing interesting and have hoped that my readers might feel the same way.

It seems that my readers and I might not be the only ones to care about the source of funding. Joi Ito who held appointments with Harvard University and the Massachusetts Institute of Technology (MIT) resigned from his various appointments on Sept. 7, 2019 after news of major donations from Jeffrey Epstein (a disgraced financier and sex offender) to MIT were revealed. From the Joi Ito’s entry on Wikipedia (Note: Links have been removed),

Joichi “Joi” Ito (伊藤 穰一 Itō Jōichi, born June 19, 1966) is a Japanese activist, entrepreneur and venture capitalist. He is the former director of the MIT Media Lab, and a former professor of the practice of media arts and sciences at MIT. He is a former visiting professor of practice at the Harvard Law School.[1][2]

Ito has received recognition for his role as an entrepreneur focused on Internet and technology companies and has founded, among other companies, PSINet Japan, Digital Garage and Infoseek Japan. Ito is a strategic advisor to Sony Corporation[3] and general partner of Neoteny Labs.[4] Ito writes a monthly column in the Ideas section of Wired.[5]

Ito resigned from his roles at MIT, Harvard, the John D. and Catherine T. MacArthur Foundation, the Knight Foundation, PureTech Health and The New York Times Company on September 7, 2019, following allegations of financial ties to sex offender and financier Jeffrey Epstein.[2][6][7]

Many, many institutions have accepted funds from sketchy characters and orgnaizations. It’s not new to academia, the sciences, or the arts. For a contemporary view of how some of this works, take a look at Anand Giridharadas’s 2018 book, Winners Take All. From the webepage for the book,

WINNERS TAKE ALL
The Elite Charade of Changing the World
 
An insider’s groundbreaking investigation of how the global elite’s efforts to “change the world” preserve the status quo and obscure their role in causing the problems they later seek to solve.

Former New York Times columnist Anand Giridharadas takes us into the inner sanctums of a new gilded age, where the rich and powerful fight for equality and justice any way they can–except ways that threaten the social order and their position atop it. We see how they rebrand themselves as saviors of the poor; how they lavishly reward “thought leaders” who redefine “change” in winner-friendly ways; and how they constantly seek to do more good, but never less harm. We hear the limousine confessions of a celebrated foundation boss; witness an American president hem and haw about his plutocratic benefactors; and attend a cruise-ship conference where entrepreneurs celebrate their own self-interested magnanimity.

I don’t recall any mention of Epstein in Giridharadas’s book but he did have this to say on Twitter about Epstein,

Anand Giridharadas‏Verified account @AnandWrites



Everything that made Epstein’s life possible remains in place after his arrest: the Caribbean tax havens, the hidden real-estate deals, the buying of politicians, the nonprofits that sell reputational glow, the editors who cover for people of their class.

7:34 PM – 8 Jul 2019

it can’t be easy to withstand the temptation to take the money and hope that the misdoings have been exaggerated or that they have stopped. I imagine Ito and others are under constant pressure to get funds.

AstraZeneca

One of the partners in this research about CRISPR, AstraZeneca, is a pharmaceutical company. In fact, it’s one of the largest in the world (from the AstraZeneca Wikipedia entry; Note: Links have been removed),

AstraZeneca plc[4] is a British-Swedish multinational pharmaceutical and biopharmaceutical company. In 2013, it moved its headquarters to Cambridge, UK, and concentrated its R&D in three sites: Cambridge; Gaithersburg, Maryland, USA (location of MedImmune) for work on biopharmaceuticals; and Mölndal (near Gothenburg) in Sweden, for research on traditional chemical drugs.[5] AstraZeneca has a portfolio of products for major disease areas including cancer, cardiovascular, gastrointestinal, infection, neuroscience, respiratory and inflammation.[6]

The company was founded in 1999 through the merger of the Swedish Astra AB and the British Zeneca Group[7][8] (itself formed by the demerger of the pharmaceutical operations of Imperial Chemical Industries in 1993). Since the merger it has been among the world’s largest pharmaceutical companies and has made numerous corporate acquisitions, including Cambridge Antibody Technology (in 2006), MedImmune (in 2007), Spirogen (in 2013) and Definiens (by MedImmune in 2014).

Controversies

Seroquel
In April 2010 AstraZeneca settled a qui tam lawsuit brought by Stefan P. Kruszewski for $520 million to settle allegations that the company defrauded Medicare, Medicaid, and other government-funded health care programs in connection with its marketing and promotional practices for the blockbuster atypical antipsychotic, Seroquel.[76]
In March 2011, AstraZeneca settled a lawsuit in the United States totalling $68.5 million to be divided up to 38 states.[77]
Nexium
The company’s most commercially successful medication is esomeprazole (Nexium). The primary uses are treatment of gastroesophageal reflux disease, treatment and maintenance of erosive esophagitis, treatment of duodenal ulcers caused by Helicobacter pylori, prevention of gastric ulcers in those on chronic NSAID therapy, and treatment of gastrointestinal ulcers associated with Crohn’s disease. When it is manufactured the result is a mixture of two mirror-imaged molecules, R and S. Two years before the omeprazole patent expired, AstraZeneca patented S-omeprazole in pure form, pointing out that since some people metabolise R-omeprazole slowly, pure S-omeprazole treatment would give higher dose efficiency and less variation between individuals.[78] In March 2001, the company began to market Nexium, as it would a brand new drug.[79]

In 2007, Marcia Angell, former editor-in-chief of the New England Journal of Medicine and a lecturer in social medicine at the Harvard Medical School, said in Stern, a German-language weekly newsmagazine, that AstraZeneca’s scientists had misrepresented their research on the drug’s efficiency, saying “Instead of using presumably comparable doses [of each drug], the company’s scientists used Nexium in higher dosages. They compared 20 and 40 mg Nexium with 20 mg Prilosec. With the cards having been marked in that way, Nexium looked like an improvement – which however was only small and shown in only two of the three studies.”[83]
Bildman fraud, and faithless servant clawback

Study
In 2004, University of Minnesota research participant Dan Markingson committed suicide while enrolled in an industry-sponsored pharmaceutical trial comparing three FDA-approved atypical antipsychotics: Seroquel (quetiapine), Zyprexa (olanzapine), and Risperdal (risperidone). University of Minnesota Professor of Bioethics Carl Elliott noted that Markingson was enrolled in the study against the wishes of his mother, Mary Weiss, and that he was forced to choose between enrolling in the study or being involuntarily committed to a state mental institution.[89] Further investigation revealed financial ties to AstraZeneca by Markingson’s psychiatrist, Stephen C. Olson, oversights and biases in AstraZeneca’s trial design, and the inadequacy of university Institutional Review Board (IRB) protections for research subjects.[90][unreliable source?] A 2005 FDA investigation cleared the university. Nonetheless, controversy around the case has continued. A Mother Jones article[89] resulted in a group of university faculty members sending a public letter to the university Board of Regents urging an external investigation into Markingson’s death.[91]

Is it ok to take money and/or other goods and services from them?

Innovative Genomics Institute (IGI)

Also mentioned as a partner in the research, is the Innovative Genomics Institute (IGI). Here’s more from the company’s Overview webpage (Note: Links have been removed),,

The IGI began in 2014 through the Li Ka Shing Center for Genetic Engineering, which was created thanks to a generous donation from the Li Ka Shing Foundation. [emphasis mine] The Innovative Genomics Initiative formed as a partnership between the University of California, Berkeley and the University of California, San Francisco. Combining the fundamental research expertise and the biomedical talent at UCB and UCSF, the Innovative Genomics Initiative focused on unraveling the mechanisms underlying CRISPR-based genome editing and applying this technology to improve human health. Early achievements include improving the efficiency of gene replacement and foundational work toward a treatment for sickle cell disease.

In late 2015, generous philanthropic donations enabled a bolder vision and broader mission for the IGI. With this expansion came a significant enhancement of the organization, and in January 2017, the IGI officially re-launched as the Innovative Genomics Institute.

As it turns out, there is a Li Ka-shing and he has a bit of a history with Vancouver (Canada). First, here’s more about him from the Li Ka-shing Wikipedia entry,(Note: Links have been removed),

Sir Li Ka-shing GBM KBE JP[4] (born 13 June 1928)[5][6] is a Hong Kong business magnate, investor, and philanthropist. As of June 2019, Li is the 30th richest person in the world, with an estimated net wealth of US$29.4 billion.[3] He is the senior advisor for CK Hutchison Holdings,[7] after he retired from the Chairman of the Board in May 2018;[8] through it, he is the world’s leading port investor, developer, and operator of the largest health and beauty retailer in Asia and Europe.[9]

Besides business through his flagship companies Cheung Kong Property Holdings and CK Hutchison Holdings Limited, Li Ka-shing has also personally invested extensively in real estate in Singapore and Canada. He was the single largest shareholder of Canadian Imperial Bank of Commerce (CIBC), the fifth largest bank in Canada, until the sale of his share in 2005 (with all proceedings donated, see below). He is also the majority shareholder of a major energy company, Husky Energy, based in Alberta, Canada.[48]

In January 2005, Li announced plans to sell his $1.2 billion CAD stake in the Canadian Imperial Bank of Commerce, with all proceeds going to private charitable foundations established by Li, including the Li Ka Shing Foundation in Hong Kong and the Li Ka Shing (Canada) Foundation based in Toronto, Ontario.[49]

His son Victor Li was kidnapped in 1996 on his way home after work by gangster “Big Spender” Cheung Tze-keung. Li Ka-shing paid a ransom of HK$1 billion, directly to Cheung who had come to his house.[53] A report was never filed with Hong Kong police. Instead the case was pursued by Mainland authorities, leading to Cheung’s execution in 1998, an outcome not possible under Hong Kong law. Rumours circulated of a deal between Li and the Mainland.[53] In interviews, when this rumor was brought up, Li brushed it off and dismissed it completely.

Li Ka-shing was well known here in Vancouver due to his purchase of a significant chunk of land in the city. This January 9, 2015 article by Glen Korstrum for Business in Vancouver notes some rather interesting news and contextualizes with Li’s Vancouver history,

Hong Kong billionaire Li Ka-shing is restructuring his empire and shifting his base to the Cayman Islands and away from the Chinese special administrative region.

His January 9 [2015] announcement came the same day that Forbes ranked him as Hong Kong’s richest man for the 17th consecutive year, with a total wealth of US$33.5 billion.

Li is best known in Vancouver for buying an 82.5-hectare parcel of land around False Creek for $328 million in 1988 along with partners, who included fellow Hong Kong tycoons, Lee Shau Kee and Cheng Yu Tung.

The group formed Concord Pacific, which redeveloped the site that had been home to Vancouver’s 1986 world’s fair, Expo ’86.

Li cashed out of Concord Pacific in the late 1990s and, in 2007, invested in Deltaport through his Hutchison Port Holdings.

Li’s biggest Canadian holding is his controlling stake in Husky Energy. …

Intriguing, yes? It also makes the prospect of deciding whose money you’re going to accept a bit more complicated than it might seem.

Gladstone Institutes

In what seems to be a decided contrast to the previous two partners, here’s more from the Gladstone Institutes, About Us, History webpage,

Born in London in 1910, J. David Gladstone was orphaned as a boy and came to North America at age 10. He began a career in real estate in Southern California at age 28, eventually making his fortune as the first developer to create the region’s enclosed shopping malls (such as the Northridge Fashion Center mall). His accidental death in 1971 left an estate valued at about $8 million to support medical students interested in research.

It soon became clear to the three trustees administering Mr. Gladstone’s trust that his legacy could support a far more substantial philanthropic enterprise. In 1979, they launched The J. David Gladstone Institutes under the leadership of Robert W. Mahley, MD, PhD, a leading cardiovascular scientist who at the time was working at the National Institutes of Health.

In 2010, after three decades of leading Gladstone, Dr. Mahley stepped down in order to return to more active research. That same year, R. Sanders “Sandy” Williams, MD, left Duke University, where he had been Dean of the School of Medicine—as well as Senior Vice Chancellor and Senior Advisor for International Strategy—to become Gladstone’s new president. The following year, the S.D. Bechtel, Jr. Foundation [emphasis mine] helped launch the Center for Comprehensive Alzheimer’s Disease Research with a generous $6M lead gift, while the Roddenberry Foundation [emphasis mine] gave $5 million to launch the Roddenberry Center for Stem Cell Biology and Medicine. Also in 2011, the independent and philanthropic Gladstone Foundation formed with the mission of expanding the financial resources available to drive’s Gladstone’s mission.

The S. D. Bechtel jr. mentioned is associated with Bechtel, an international engineering firm. I did not find any scandals or controversies in the Bechtel Wikipedia entry. That seemed improbable so I did a little digging and found a January 30, 2015 (?) article by Matthew Brunwasser for foreignpolicy.com (Note: A link has been removed),

Steamrolled; A special investigation into the diplomacy of doing business abroad.

One of Europe’s poorest countries wanted a road, so U.S. mega-contractor Bechtel sold it a $1.3 billion highway, with the backing of a powerful American ambassador. Funny thing is, the highway is barely being used—and the ambassador is now working for Bechtel.

Bechtel, the largest contractor by revenue in the United States and the third-largest internationally, according to an annual list compiled by the Engineering News-Record, has in recent years constructed expensive highways in Kosovo, Croatia, Romania, and Albania. A six-month investigation by the Investigative Reporting Program at the University of California at Berkeley Graduate School of Journalism has found that these highways were boondoggles for the countries in which they were constructed, and that members of governments and international institutions often saw problems coming before Bechtel (along with its Turkish joint venture partner, Enka) even began work on the roads.

My other source is a May 8, 1988 article by Walter Russell Mead for the Los Angeles Time,s

From San Francisco to Saudi Arabia, the Bechtel Group Inc. has left its mark around the world. Yet the privately owned Bechtel Group is one of the country’s most mysterious operations–or was, until the publication of Laton McCartney’s critical and controversial “Friends in High Places.”

Those who believe that “Dynasty” and “Falcon Crest” describe life at the top of America’s corporate pyramids will find a picture here that makes the most far-fetched TV plots look dull. One Bechtel executive was torn to pieces by an angry mob; another, kidnaped, survived two days in the trunk of a Mercedes that had been driven over the edge of a cliff but caught on an obstacle half way down. Wheeling and dealing from Beirut to the Bohemian Grove, Bechtel executives fought off Arab and Jewish nationalists, angry senators, bitter business rivals, and furious consumer groups to build the world’s largest construction and engineering firm.

Poor Bechtel sometimes seems damned if it does and damned if it doesn’t. No major corporation could undertake foreign operations on Bechtel’s scale without some cooperation from the U.S. government–and few companies could refuse a government request that, in return, they provide cover for intelligence agents. Given the enormous scope of Bechtel’s operations in global trouble spots–a $20-billion industrial development in Saudi Arabia, for example–it could only proceed with assurances that its relations with both Saudi and American governments were good. Where, exactly, is the line between right and wrong? [emphasis mine]

… The white elephants Bechtel scattered across the American landscape–particularly the nuclear power plants that threaten to bankrupt some of the country’s largest utility systems–are monuments to wasted talent and misdirected resources.

Finally, I get to the Roddenberry Foundation, which was founded by Gene Roddenberry’s (Star Trek) son. Here’s more from the About Us, Origin webpage,

Gene Roddenberry, creator of the Star Trek series, brought to his audiences meaningful and thought-provoking science fiction to “think, question, and challenge the status quo” with the intention of creating “a brighter future”. His work has touched countless lives and continues to entertain and inspire audiences worldwide. In 2010, Gene’s son Rod established the Roddenberry Foundation to build on his father’s legacy and philosophy of inclusion, diversity, and respect for life to drive social change and meaningfully improve the lives of people around the world.

While there are many criticisms of Mr. Roddenberry, there doesn’t seem to be anything that would be considered a serious scandal on the order of a Jeffrey Epstein or the whisper of scandal on the order of Sir Li Ka-shing or Bechtel.

Final comments

It’s a good thing when research is funded and being able to detect off-target effects from CRISPR is very good, assuming the research holds up to closer scrutiny.

As for vetting your donors, that’s tricky. Of course, Epstein was already a convicted sex offender when Ito accepted his funding for MIT but I cannot emphasize enough the amount of pressure these folks are under. Academia is always hungry for money. Hopefully this incident will introduce checks and balances in the donor process.

Colo(u)r-changing building surfaces thanks to gold nanoparticles

Gold, at the nanoscale, has different properties than it has at the macroscale and research at the University of Cambridge has found a new way to exploit gold’s unique properties at the nanoscale according to a May 13, 2019 news item item on ScienceDaily,

The smallest pixels yet created — a million times smaller than those in smartphones, made by trapping particles of light under tiny rocks of gold — could be used for new types of large-scale flexible displays, big enough to cover entire buildings.

The colour pixels, developed by a team of scientists led by the University of Cambridge, are compatible with roll-to-roll fabrication on flexible plastic films, dramatically reducing their production cost. The results are reported in the journal Science Advances [May 10, 2019].

A May 10,2019 University of Cambridge press release (also on EurekAlert), which originated the news item, delves further into the research,

It has been a long-held dream to mimic the colour-changing skin of octopus or squid, allowing people or objects to disappear into the natural background, but making large-area flexible display screens is still prohibitively expensive because they are constructed from highly precise multiple layers.

At the centre of the pixels developed by the Cambridge scientists is a tiny particle of gold a few billionths of a metre across. The grain sits on top of a reflective surface, trapping light in the gap in between. Surrounding each grain is a thin sticky coating which changes chemically when electrically switched, causing the pixel to change colour across the spectrum.

The team of scientists, from different disciplines including physics, chemistry and manufacturing, made the pixels by coating vats of golden grains with an active polymer called polyaniline and then spraying them onto flexible mirror-coated plastic, to dramatically drive down production cost.

The pixels are the smallest yet created, a million times smaller than typical smartphone pixels. They can be seen in bright sunlight and because they do not need constant power to keep their set colour, have an energy performance that makes large areas feasible and sustainable. “We started by washing them over aluminized food packets, but then found aerosol spraying is faster,” said co-lead author Hyeon-Ho Jeong from Cambridge’s Cavendish Laboratory.

“These are not the normal tools of nanotechnology, but this sort of radical approach is needed to make sustainable technologies feasible,” said Professor Jeremy J Baumberg of the NanoPhotonics Centre at Cambridge’s Cavendish Laboratory, who led the research. “The strange physics of light on the nanoscale allows it to be switched, even if less than a tenth of the film is coated with our active pixels. That’s because the apparent size of each pixel for light is many times larger than their physical area when using these resonant gold architectures.”

The pixels could enable a host of new application possibilities such as building-sized display screens, architecture which can switch off solar heat load, active camouflage clothing and coatings, as well as tiny indicators for coming internet-of-things devices.
The team are currently working at improving the colour range and are looking for partners to develop the technology further.

The research is funded as part of a UK Engineering and Physical Sciences Research Council (EPSRC) investment in the Cambridge NanoPhotonics Centre, as well as the European Research Council (ERC) and the China Scholarship Council.

This image accompanies the press release,

Caption: eNPoMs formed from gold nanoparticles (Au NPs) encapsulated in a conductive polymer shell. Credit: NanoPhotonics Cambridge/Hyeon-Ho Jeong, Jialong Peng Credit: NanoPhotonics Cambridge/Hyeon-Ho Jeong, Jialong Peng

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

Scalable electrochromic nanopixels using plasmonics by Jialong Peng, Hyeon-Ho Jeong, Qianqi Lin, Sean Cormier, Hsin-Ling Liang, Michael F. L. De Volder, Silvia Vignolini, and Jeremy J. Baumberg. Science Advances Vol. 5, no. 5, eaaw2205 DOI: 10.1126/sciadv.aaw2205 Published: 01 May 2019

This paper appears to be open access.