Category Archives: science

Loop quantum cosmology connects the tiniest with the biggest in a cosmic tango

Caption: Tiny quantum fluctuations in the early universe explain two major mysteries about the large-scale structure of the universe, in a cosmic tango of the very small and the very large. A new study by researchers at Penn State used the theory of quantum loop gravity to account for these mysteries, which Einstein’s theory of general relativity considers anomalous.. Credit: Dani Zemba, Penn State

A July 29, 2020 news item on ScienceDaily announces a study showing that quantum loop cosmology can account for some large-scale mysteries,

While [1] Einstein’s theory of general relativity can explain a large array of fascinating astrophysical and cosmological phenomena, some aspects of the properties of the universe at the largest-scales remain a mystery. A new study using loop quantum cosmology — a theory that uses quantum mechanics to extend gravitational physics beyond Einstein’s theory of general relativity — accounts for two major mysteries. While the differences in the theories occur at the tiniest of scales — much smaller than even a proton — they have consequences at the largest of accessible scales in the universe. The study, which appears online July 29 [2020] in the journal Physical Review Letters, also provides new predictions about the universe that future satellite missions could test.

A July 29, 2020 Pennsylvania State University (Penn State) news release (also on EurekAlert) by Gail McCormick, which originated the news item, describes how this work helped us avoid a crisis in cosmology,

While [2] a zoomed-out picture of the universe looks fairly uniform, it does have a large-scale structure, for example because galaxies and dark matter are not uniformly distributed throughout the universe. The origin of this structure has been traced back to the tiny inhomogeneities observed in the Cosmic Microwave Background (CMB)–radiation that was emitted when the universe was 380 thousand years young that we can still see today. But the CMB itself has three puzzling features that are considered anomalies because they are difficult to explain using known physics.

“While [3] seeing one of these anomalies may not be that statistically remarkable, seeing two or more together suggests we live in an exceptional universe,” said Donghui Jeong, associate professor of astronomy and astrophysics at Penn State and an author of the paper. “A recent study in the journal Nature Astronomy proposed an explanation for one of these anomalies that raised so many additional concerns, they flagged a ‘possible crisis in cosmology‘ [emphasis mine].’ Using quantum loop cosmology, however, we have resolved two of these anomalies naturally, avoiding that potential crisis.”

Research over the last three decades has greatly improved our understanding of the early universe, including how the inhomogeneities in the CMB were produced in the first place. These inhomogeneities are a result of inevitable quantum fluctuations in the early universe. During a highly accelerated phase of expansion at very early times–known as inflation–these primordial, miniscule fluctuations were stretched under gravity’s influence and seeded the observed inhomogeneities in the CMB.

“To understand how primordial seeds arose, we need a closer look at the early universe, where Einstein’s theory of general relativity breaks down,” said Abhay Ashtekar, Evan Pugh Professor of Physics, holder of the Eberly Family Chair in Physics, and director of the Penn State Institute for Gravitation and the Cosmos. “The standard inflationary paradigm based on general relativity treats space time as a smooth continuum. Consider a shirt that appears like a two-dimensional surface, but on closer inspection you can see that it is woven by densely packed one-dimensional threads. In this way, the fabric of space time is really woven by quantum threads. In accounting for these threads, loop quantum cosmology allows us to go beyond the continuum described by general relativity where Einstein’s physics breaks down–for example beyond the Big Bang.”

The researchers’ previous investigation into the early universe replaced the idea of a Big Bang singularity, where the universe emerged from nothing, with the Big Bounce, where the current expanding universe emerged from a super-compressed mass that was created when the universe contracted in its preceding phase. They found that all of the large-scale structures of the universe accounted for by general relativity are equally explained by inflation after this Big Bounce using equations of loop quantum cosmology.

In the new study, the researchers determined that inflation under loop quantum cosmology also resolves two of the major anomalies that appear under general relativity.

“The primordial fluctuations we are talking about occur at the incredibly small Planck scale,” said Brajesh Gupt, a postdoctoral researcher at Penn State at the time of the research and currently at the Texas Advanced Computing Center of the University of Texas at Austin. “A Planck length is about 20 orders of magnitude smaller than the radius of a proton. But corrections to inflation at this unimaginably small scale simultaneously explain two of the anomalies at the largest scales in the universe, in a cosmic tango of the very small and the very large.”

The researchers also produced new predictions about a fundamental cosmological parameter and primordial gravitational waves that could be tested during future satellite missions, including LiteBird and Cosmic Origins Explorer, which will continue improve our understanding of the early universe.

That’s a lot of ‘while’. I’ve done this sort of thing, too, and whenever I come across it later; it’s painful.

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

Alleviating the Tension in the Cosmic Microwave Background Using Planck-Scale Physics by Abhay Ashtekar, Brajesh Gupt, Donghui Jeong, and V. Sreenath. Phys. Rev. Lett. 125, 051302 DOI: Published 29 July 2020 © 2020 American Physical Society

This paper is behind a paywall.

Taxonomies (classification schemes) rouse passions

There seems to have been some lively debate among biologists about matters most of us treat as invisible: naming, establishing, and classifying categories. These activities can become quite visible when learning a new language, e.g., French which divides nouns into two genders or German which classifies nouns with any of three genders.

A July 26, 2020 essay by Stephen Garnett (Professor of Conservation and Sustainable Livelihoods, Charles Darwin University, Australia), Les Christidis (Professor, Southern Cross University, Australia), Richard L. Pyle (Associate lecturer, University of Hawaii, US), and Scott Thomson (Research associate, Universidade de São Paulo, Brazil) for The Conversation (also on but published July 27, 2020) describes a very heated debate over taxonomy,

Taxonomy, or the naming of species, is the foundation of modern biology. It might sound like a fairly straightforward exercise, but in fact it’s complicated and often controversial.

Why? Because there’s no one agreed list of all the world’s species. Competing lists exist for organisms such as mammals and birds, while other less well-known groups have none. And there are more than 30 definitions of what constitutes a species [emphasis mine]. This can make life difficult for biodiversity researchers and those working in areas such as conservation, biosecurity and regulation of the wildlife trade.

In the past few years, a public debate erupted among global taxonomists, including those who authored and contributed to this article, about whether the rules of taxonomy should be changed. Strongly worded ripostes were exchanged. A comparison to Stalin [emphasis mine] was floated.

Here’s how it started,

In May 2017 two of the authors, Stephen Garnett and Les Christidis, published an article in Nature. They argued taxonomy needed rules around what should be called a species, because currently there are none. They wrote:

” … for a discipline aiming to impose order on the natural world, taxonomy (the classification of complex organisms) is remarkably anarchic […] There is reasonable agreement among taxonomists that a species should represent a distinct evolutionary lineage. But there is none about how a lineage should be defined.

‘Species’ are often created or dismissed arbitrarily, according to the individual taxonomist’s adherence to one of at least 30 definitions. Crucially, there is no global oversight of taxonomic decisions — researchers can ‘split or lump’ species with no consideration of the consequences.”

Garnett and Christidis proposed that any changes to the taxonomy of complex organisms be overseen by the highest body in the global governance of biology, the International Union of Biological Sciences (IUBS), which would “restrict […] freedom of taxonomic action.”

… critics rejected the description of taxonomy as “anarchic”. In fact, they argued there are detailed rules around the naming of species administered by groups such as the International Commission on Zoological Nomenclature and the International Code of Nomenclature for algae, fungi, and plants. For 125 years, the codes have been almost universally adopted by scientists.

So in March 2018, 183 researchers – led by Scott Thomson and Richard Pyle – wrote an animated response to the Nature article, published in PLoS Biology [PLoS is Public Library of Science; it is an open access journal].

They wrote that Garnett and Christidis’ IUBS proposal was “flawed in terms of scientific integrity […] but is also untenable in practice”. They argued:

“Through taxonomic research, our understanding of biodiversity and classifications of living organisms will continue to progress. Any system that restricts such progress runs counter to basic scientific principles, which rely on peer review and subsequent acceptance or rejection by the community, rather than third-party regulation.”

In a separate paper, another group of taxonomists accused Garnett and Christidis of trying to suppress freedom of scientific thought, likening them to Stalin’s science advisor Trofim Lysenko.

The various parties did come together,

We hope by 2030, a scientific debate that began with claims of anarchy might lead to a clear governance system – and finally, the world’s first endorsed global list of species.

As for how they got to a “clear governance system”, there’s the rest of the July 26, 2020 essay on The Conversation or there’s the copy on (published July 27, 2020).

Science fiction, interconnectedness (globality), and pandemics

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

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

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

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

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

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

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

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


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

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

Filmmaking beetles wearing teeny, tiny wireless cameras

Researchers at the University of Washington have developed a tiny camera that can ride aboard an insect. Here a Pinacate beetle explores the UW campus with the camera on its back. Credit: Mark Stone/University of Washington

Scientists at Washington University have created a removable wireless camera backpack for beetles and for tiny robots resembling beetles. I’m embedding a video shot by a beetle later in this post with a citation and link for the paper, near the end of this post where you’ll also find links to my other posts on insects and technology.

As for the latest on insects and technology, there’s a July 15, 2020 news item on ScienceDaily,

In the movie “Ant-Man,” the title character can shrink in size and travel by soaring on the back of an insect. Now researchers at the University of Washington have developed a tiny wireless steerable camera that can also ride aboard an insect, giving everyone a chance to see an Ant-Man view of the world.

The camera, which streams video to a smartphone at 1 to 5 frames per second, sits on a mechanical arm that can pivot 60 degrees. This allows a viewer to capture a high-resolution, panoramic shot or track a moving object while expending a minimal amount of energy. To demonstrate the versatility of this system, which weighs about 250 milligrams — about one-tenth the weight of a playing card — the team mounted it on top of live beetles and insect-sized robots.

A July 15, 2020 University of Washington news release (also on EurekAlert), which originated the news item, provides more technical detail (although I still have a few questions) about the work,

“We have created a low-power, low-weight, wireless camera system that can capture a first-person view of what’s happening from an actual live insect or create vision for small robots,” said senior author Shyam Gollakota, a UW associate professor in the Paul G. Allen School of Computer Science & Engineering. “Vision is so important for communication and for navigation, but it’s extremely challenging to do it at such a small scale. As a result, prior to our work, wireless vision has not been possible for small robots or insects.”

Typical small cameras, such as those used in smartphones, use a lot of power to capture wide-angle, high-resolution photos, and that doesn’t work at the insect scale. While the cameras themselves are lightweight, the batteries they need to support them make the overall system too big and heavy for insects — or insect-sized robots — to lug around. So the team took a lesson from biology.

“Similar to cameras, vision in animals requires a lot of power,” said co-author Sawyer Fuller, a UW assistant professor of mechanical engineering. “It’s less of a big deal in larger creatures like humans, but flies are using 10 to 20% of their resting energy just to power their brains, most of which is devoted to visual processing. To help cut the cost, some flies have a small, high-resolution region of their compound eyes. They turn their heads to steer where they want to see with extra clarity, such as for chasing prey or a mate. This saves power over having high resolution over their entire visual field.”

To mimic an animal’s vision, the researchers used a tiny, ultra-low-power black-and-white camera that can sweep across a field of view with the help of a mechanical arm. The arm moves when the team applies a high voltage, which makes the material bend and move the camera to the desired position. Unless the team applies more power, the arm stays at that angle for about a minute before relaxing back to its original position. This is similar to how people can keep their head turned in one direction for only a short period of time before returning to a more neutral position.

“One advantage to being able to move the camera is that you can get a wide-angle view of what’s happening without consuming a huge amount of power,” said co-lead author Vikram Iyer, a UW doctoral student in electrical and computer engineering. “We can track a moving object without having to spend the energy to move a whole robot. These images are also at a higher resolution than if we used a wide-angle lens, which would create an image with the same number of pixels divided up over a much larger area.”

The camera and arm are controlled via Bluetooth from a smartphone from a distance up to 120 meters away, just a little longer than a football field.

The researchers attached their removable system to the backs of two different types of beetles — a death-feigning beetle and a Pinacate beetle. Similar beetles have been known to be able to carry loads heavier than half a gram, the researchers said.

“We made sure the beetles could still move properly when they were carrying our system,” said co-lead author Ali Najafi, a UW doctoral student in electrical and computer engineering. “They were able to navigate freely across gravel, up a slope and even climb trees.”

The beetles also lived for at least a year after the experiment ended. [emphasis mine]

“We added a small accelerometer to our system to be able to detect when the beetle moves. Then it only captures images during that time,” Iyer said. “If the camera is just continuously streaming without this accelerometer, we could record one to two hours before the battery died. With the accelerometer, we could record for six hours or more, depending on the beetle’s activity level.”

The researchers also used their camera system to design the world’s smallest terrestrial, power-autonomous robot with wireless vision. This insect-sized robot uses vibrations to move and consumes almost the same power as low-power Bluetooth radios need to operate.

The team found, however, that the vibrations shook the camera and produced distorted images. The researchers solved this issue by having the robot stop momentarily, take a picture and then resume its journey. With this strategy, the system was still able to move about 2 to 3 centimeters per second — faster than any other tiny robot that uses vibrations to move — and had a battery life of about 90 minutes.

While the team is excited about the potential for lightweight and low-power mobile cameras, the researchers acknowledge that this technology comes with a new set of privacy risks.

“As researchers we strongly believe that it’s really important to put things in the public domain so people are aware of the risks and so people can start coming up with solutions to address them,” Gollakota said.

Applications could range from biology to exploring novel environments, the researchers said. The team hopes that future versions of the camera will require even less power and be battery free, potentially solar-powered.

“This is the first time that we’ve had a first-person view from the back of a beetle while it’s walking around. There are so many questions you could explore, such as how does the beetle respond to different stimuli that it sees in the environment?” Iyer said. “But also, insects can traverse rocky environments, which is really challenging for robots to do at this scale. So this system can also help us out by letting us see or collect samples from hard-to-navigate spaces.”


Johannes James, a UW mechanical engineering doctoral student, is also a co-author on this paper. This research was funded by a Microsoft fellowship and the National Science Foundation.

I’m surprised there’s no funding from a military agency as the military and covert operation applications seem like an obvious pairing. In any event, here’s a link to and a citation for the paper,

Wireless steerable vision for live insects and insect-scale robots by Vikram Iyer, Ali Najafi, Johannes James, Sawyer Fuller, and Shyamnath Gollakota. Science Robotics 15 Jul 2020: Vol. 5, Issue 44, eabb0839 DOI: 10.1126/scirobotics.abb0839

This paper is behind a paywall.

Video and links

As promised, here’s the video the scientists have released,

These posts feature some fairly ruthless uses of the insects.

  1. The first mention of insects and technology here is in a July 27, 2009 posting titled: Nanotechnology enables robots and human enhancement: part 4. The mention is in the second to last paragraph of the post. Then,.
  2. A November 23, 2011 post titled: Cyborg insects and trust,
  3. A January 9, 2012 post titled: Controlling cyborg insects,
  4. A June 26, 2013 post titled: Steering cockroaches in the lab and in your backyard—cutting edge neuroscience, and, finally,
  5. An April 11, 2014 post titled: Computerized cockroaches as precursors to new healing techniques.

As for my questions (how do you put the backpacks on the beetles? is there a strap, is it glue, is it something else? how heavy is the backpack and camera? how old are the beetles you use for this experiment? where did you get the beetles from? do you have your own beetle farm where you breed them?), I’ll see if I can get some answers.

Replacing nanotechnology-enabled oil spill solutions with dog fur?

Coincidentally or not, this research from Australia was announced a little more than a month after reports of a major oil spill in the Russian Arctic. A July 10, 2020 news item on announces a new technology for mopping up oil spills (Note: Links have been removed),

Oil spill disasters on land cause long-term damage for communities and the natural environment, polluting soils and sediments and contaminating groundwater.

Current methods using synthetic sorbent materials can be effective for cleaning up oil spills, but these materials are often expensive and generate large volumes of non-biodegradable plastic wastes. Now the first comparison of natural-origin sorbent materials for land-based oil spills, including peat moss, recycled human hair, and dog fur, shows that sustainable, cheaper and biodegradable options can be developed.

The University of Technology Sydney (UTS) project found that dog fur and human hair products—recycled from salon wastes and dog groomers—can be just as good as synthetic fabrics at cleaning up crude oil spills on hard land surfaces like highway roads, pavement, and sealed concrete floors. Polypropylene, a plastic, is a widely-used fabric used to clean up oil spills in aquatic environments.

A July 9, 2020 Univesity of Technology Sydney press release on EurekAlert completes the story,

“Dog fur in particular was surprisingly good at oil spill clean-up, and felted mats from human hair and fur were very easy to apply and remove from the spills.” lead author of the study, UTS Environmental Scientist Dr Megan Murray, said. Dr Murray investigates environmentally-friendly solutions for contamination and leads The Phyto Lab research group at UTS School of Life Sciences.

“This is a very exciting finding for land managers who respond to spilled oil from trucks, storage tanks, or leaking oil pipelines. All of these land scenarios can be treated effectively with sustainable-origin sorbents,” she said.

The sorbents tested included two commercially-available products, propylene and loose peat moss, as well as sustainable-origin prototypes including felted mats made of dog fur and human hair. Prototype oil-spill sorbent booms filled with dog fur and human hair were also tested. Crude oil was used to replicate an oil spill. The results of the study are published in Environments.

The research team simulated three types of land surfaces; non-porous hard surfaces, semi-porous surfaces, and sand, to recreate common oil-spill scenarios.

“We found that loose peat moss is not as effective at cleaning up oil spills on land compared to dog fur and hair products, and it is not useful at all for sandy environments.” Dr Murray said.

“Based on this research, we recommend peat moss is no longer used for this purpose. Given that peat moss is a limited resource and harvesting it requires degrading wetland ecosystems, we think this is a very important finding.” she said.

The research concluded that, for now, sandy environments like coastal beaches can still benefit from the use of polypropylene sorbents, but further exploration of sustainable-origin sorbents is planned.

The researchers say that future applications from the research include investigating felted mats of sustainable-origin sorbents for river bank stabilisation, [emphases mine] as well as the removal of pollutants from flowing polluted waters, similar to existing membrane technology.

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

Decontaminating Terrestrial Oil Spills: A Comparative Assessment of Dog Fur, Human Hair, Peat Moss and Polypropylene Sorbents by Megan L. Murray, Soeren M. Poulsen and Brad R. Murray. Environments 2020, 7(7), 52; DOI: Published: 8 July 2020 (This article belongs to the Special Issue Pollution Prevention/Environmental Sustainability for Industry)

This paper is open access.

As for the Russian oil spill

A June 4, 2020 British Broadcasting Corporation (BBC) news online article outlines the situation regarding the oil spill and the steps being taken to deal with it,

Russia’s President Vladimir Putin has declared a state of emergency after 20,000 tonnes of diesel oil leaked into a river within the Arctic Circle.

The spill happened when a fuel tank at a power plant near the Siberian city of Norilsk collapsed last Friday [May 29, 2020].

The power plant’s director Vyacheslav Starostin has been taken into custody until 31 July, but not yet charged.

The plant is owned by a subsidiary of Norilsk Nickel, which is the world’s leading nickel and palladium producer.

The Russian Investigative Committee (SK) has launched a criminal case over the pollution and alleged negligence, as there was reportedly a two-day delay in informing the Moscow authorities about the spill.

Ground subsidence beneath the fuel storage tanks is believed to have caused the spill. Arctic permafrost has been melting in exceptionally warm weather [more information about the weather towards the end of this posting] for this time of year.

Russian Minister for Emergencies Yevgeny Zinichev told Mr Putin that the Norilsk plant had spent two days trying to contain the spill, before alerting his ministry.

The leaked oil drifted some 12km (7.5 miles) from the accident site, turning long stretches of the Ambarnaya river crimson red.

The leaked diesel oil drifted some 12km (7.5 miles) from the site of the accident [downloaded from]

Getting back to the June 4, 2020 British Broadcasting Corporation (BBC) news online article,

“Why did government agencies only find out about this two days [May 29, 2020?) after the fact?” he asked the subsidiary’s chief, Sergei Lipin. “Are we going to learn about emergency situations from social media?”

The region’s governor, Alexander Uss, had earlier told President Putin that he became aware of the oil spill on Sunday [May 31, 2020] after “alarming information appeared in social media”.

The spill has contaminated a 350 sq km (135 sq mile) area, state media report.

The state of emergency means extra forces are going to the area to assist with the clean-up operation.

The accident is believed to be the second largest in modern Russian history in terms of volume, an expert from the World Wildlife Fund, Alexei Knizhnikov, told the AFP [Agence France Presse] news agency.

The incident has prompted stark warnings from environmental groups, who say the scale of the spill and geography of the river mean it will be difficult to clean up.

Greenpeace has compared it to the 1989 Exxon Valdez disaster in Alaska.

Oleg Mitvol, former deputy head of Russia’s environmental watchdog Rosprirodnadzor, said there had “never been such an accident in the Arctic zone”.

He said the clean-up could cost 100bn roubles (£1.2bn; $1.5bn) and take between five and 10 years.

Minister of Natural Resources Dmitry Kobylkin warned against trying to burn off such a vast quantity of fuel oil.

He proposed trying to dilute the oil with reagents. Only the emergencies ministry with military support could deal with the pollution, he said.

Barges with booms could not contain the slick because the Ambarnaya river was too shallow, he warned.

He suggested pumping the oil on to the adjacent tundra, although President Putin added: “The soil there is probably saturated [with oil] already.”

An update of the situation can be found in a July 8, 2020 Canadian Broadcasting Corporation (CBC) article (issued by Thomson Reuters),

Russia’s environmental watchdog has asked a power subsidiary of Russian mining giant Norilsk Nickel to pay almost 148 billion rubles, or $2.8 billion Cdn, in damages over an Arctic fuel spill in Siberia.

Rosprirodnadzor, the Federal Service for Supervision of Use of Natural Resources, said in a statement on Monday [July 8, 2020] that it had already sent a request for “voluntary compensation” to the subsidiary, NTEK, after calculating the damage caused by the May 29 [2020] fuel spill.

Norilsk Nickel’s Moscow-listed shares fell by 3 per cent after the watchdog’s statement.

A fuel tank at the power plant lost pressure and released 21,000 tonnes of diesel into rivers and subsoil near the city of Norilsk, 2,900 kilometres northeast of Moscow. Russian President Vladimir Putin subsequently declared a state of emergency in the region, and investigators detained three staff at the power plant.

Norilsk, a remote city of 180,000 people situated 300 kilometres inside the Arctic Circle, is built around Norilsk Nickel, the world’s leading nickel and palladium producer, and has a reputation for its pollution.

Rosprirodnadzor said the damages included the cost for nearby water bodies, estimated at 147.05 billion rubles, $2.8 billion Cdn, and for subsoil, estimated at 738.62 million roubles, $14 million Cdn.

I can’t find any August 2020 updates for the oil spill situation in Russia. (Note: There is now an oil spill in a ecologically sensitive region near Mauritius; see August 13, 2020 news item on CBC news online website.)

Exceptionally warm weather

The oil spill isn’t the only problem in the Arctic.Here’s more from a June 23, 2020 article by Matt Simon for Wired magazine (Note: A link has been removed),

On Saturday [June 20, 2020], the residents of Verkhoyansk, Russia, marked the first day of summer with 100 degree Fahrenheit temperatures. Not that they could enjoy it, really, as Verkhoyansk is in Siberia, hundreds of miles from the nearest beach. That’s much, much hotter than towns inside the Arctic Circle usually get. That 100 degrees appears to be a record, well above the average June high temperature of 68 degrees. Yet it’s likely the people of Verkhoyansk will see that record broken again in their lifetimes: The Arctic is warming twice as fast as the rest of the planet—if not faster—creating ecological chaos for the plants and animals that populate the north.

“The events over the weekend—in the last few weeks, really—with the heatwave in Siberia, all are unprecedented in terms of the magnitude of the extremes in temperature,” says Sophie Wilkinson, a wildfire scientist at McMaster University who studies northern peat fires, which themselves have grown unusually frequent in recent years as temperatures climb.

The Arctic’s extreme warming, known as Arctic amplification or polar amplification, may be due to three factors. One, the region’s reflectivity, or albedo—how much light it bounces back into space—is changing as the world warms. “What we’ve been seeing over the last 30 years is some relatively dramatic declines in sea ice in the summertime,” says University of Edinburgh global change ecologist Isla Myers-Smith, who studies the Arctic.

Since ice is white, it reflects the sun’s energy, something you’re already probably familiar with when it comes to staying cool in the summer. If you had to pick the color of T-shirt to wear when going hiking on a hot day, she says, “most of us would pick the white T-shirt, because that’s going to reflect the sun’s heat off of our back.” Similarly, Myers-Smith says, “If the sea ice melts in the Arctic, that will remove that white surface off of the ocean, and what will be exposed is this darker ocean surface that will absorb more of the sun’s heat.”

If you’re interested in the environmental consequences of the warming of the Arctic, this is a very good article.

Finishing up, I wish the clean-up crews (in Russia and near Mauritius) all the best as they work in the midst of a pandemic, as well as, an environmental disaster (both the oil spill and the warming of the Arctic).

Branched flows of light look like trees say “explorers of experimental science” at Technion

Enhancing soap bubbles for your science explorations? It sounds like an entertaining activity you might give children for ‘painless’ science education. In this case, researchers at Technion – Israel Institute of Technology have made an exciting discovery, The following video is where I got the phrase “explorers of experimental science,”

A July 1, 2020 news item on Nanowerk announces the work (Note: A link has been removed),

A team of researchers from the Technion – Israel Institute of Technology has observed branched flow of light for the very first time. The findings are published in Nature and are featured on the cover of the July 2, 2020 issue (“Observation of branched flow of light”).

The study was carried out by Ph.D. student Anatoly (Tolik) Patsyk, in collaboration with Miguel A. Bandres, who was a postdoctoral fellow at Technion when the project started and is now an Assistant Professor at CREOL, College of Optics and Photonics, University of Central Florida. The research was led by Technion President Professor Uri Sivan and Distinguished Professor Mordechai (Moti) Segev of the Technion’s Physics and Electrical Engineering Faculties, the Solid State Institute, and the Russell Berrie Nanotechnology Institute.

A July 2, 2020 Technion press release, which originated the news item, delves further into the research,

When waves travel through landscapes that contain disturbances, they naturally scatter, often in all directions. Scattering of light is a natural phenomenon, found in many places in nature. For example, the scattering of light is the reason for the blue color of the sky. As it turns out, when the length over which disturbances vary is much larger than the wavelength, the wave scatters in an unusual fashion: it forms channels (branches) of enhanced intensity that continue to divide or branch out, as the wave propagates.  This phenomenon is known as branched flow. It was first observed in 2001 in electrons and had been suggested to be ubiquitous and occur also for all waves in nature, for example – sound waves and even ocean waves. Now, Technion researchers are bringing branched flow to the domain of light: they have made an experimental observation of the branched flow of light.

“We always had the intention of finding something new, and we were eager to find it. It was not what we started looking for, but we kept looking and we found something far better,” says Asst. Prof. Miguel Bandres. “We are familiar with the fact that waves spread when they propagate in a homogeneous medium. But for other kinds of mediums, waves can behave in very different ways. When we have a disordered medium where the variations are not random but smooth, like a landscape of mountains and valleys, the waves will propagate in a peculiar way. They will form channels that keep dividing as the wave propagates, forming a beautiful pattern resembling the branches of a tree.” 

In their research, the team coupled a laser beam to a soap membrane, which contains random variations in membrane thickness. They discovered that when light propagates within the soap film, rather than being scattered, the light forms elongated branches, creating the branched flow phenomenon for light.

“In optics we usually work hard to make light stay focused and propagate as a collimated beam, but here the surprise is that the random structure of the soap film naturally caused the light to stay focused. It is another one of nature’s surprises,” says Tolik Patsyk. 

The ability to create branched flow in the field of optics offers new and exciting opportunities for investigating and understanding this universal wave phenomenon.

“There is nothing more exciting than discovering something new and this is the first demonstration of this phenomenon with light waves,” says Technion President Prof. Uri Sivan. “This goes to show that intriguing phenomena can also be observed in simple systems and one just has to be perceptive enough to uncover them. As such, bringing together and combining the views of researchers from different backgrounds and disciplines has led to some truly interesting insights.”

“The fact that we observe it with light waves opens remarkable new possibilities for research, starting with the fact that we can characterize the medium in which light propagates to very high precision and the fact that we can also follow those branches accurately and study their properties,” he adds.

Distinguished Prof. Moti Segev looks to the future. “I always educate my team to think beyond the horizon,” he says, “to think about something new, and at the same time – look at the experimental facts as they are, rather than try to adapt the experiments to meet some expected behavior. Here, Tolik was trying to measure something completely different and was surprised to see these light branches which he could not initially explain. He asked Miguel to join in the experiments, and together they upgraded the experiments considerably – to the level they could isolate the physics involved. That is when we started to understand what we see. It took more than a year until we understood that what we have is the strange phenomenon of “branched flow”, which at the time was never considered in the context of light waves. Now, with this observation – we can think of a plethora of new ideas. For example, using these light branches to control the fluidic flow in liquid, or to combine the soap with fluorescent material and cause the branches to become little lasers. Or to use the soap membranes as a platform for exploring fundamentals of waves, such as the transitions from ordinary scattering which is always diffusive, to branched flow, and subsequently to Anderson localization. There are many ways to continue this pioneering study. As we did many times in the past, we would like to boldly go where no one has gone before.” 

The project is now continuing in the laboratories of Profs. Segev and Sivan at Technion, and in parallel in the newly established lab of Prof. Miguel Bandres at UCF. 

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

Observation of branched flow of light by Anatoly Patsyk, Uri Sivan, Mordechai Segev & Miguel A. Bandres Nature volume 583, pages60–65 (2020) DOI: Published: 01 July 2020 Issue Date: 02 July 2020

This paper is behind a paywall.

Off-target CRISPR-Cas9 gene-editing changes closer to home than originally believed according to three studies

Heidi Ledford’s June 25, 2020 article (Note: Links have been removed) for Nature focuses on three studies (not yet peer-reviewed) that viewed together suggest CRISPR (clustered regularly interspaced short palindromic repeats) gene-editing is less like using a pair of scissors to cut out unwanted mutations and more like using a catalyst (a chemical agent which increases chemical reactions) and getting unanticipated and unwatned reactions. Except, it’s an unpredictable catalyst.

A suite of experiments that use the gene-editing tool CRISPR–Cas9 to modify human embryos have revealed how the process can make large, unwanted changes to the genome at or near the target site. [emphasis mine]

The studies were published this month on the preprint server bioRxiv, and have not yet been peer-reviewed1,2,3. But taken together, they give scientists a good look at what some say is an underappreciated risk of CRISPR–Cas9 editing. Previous experiments have revealed that the tool can make ‘off target’ gene mutations far from the target site, but the nearby changes identified in the latest studies can be missed by standard assessment methods.

These safety concerns are likely to inform the ongoing debate over whether scientists should edit human embryos to prevent genetic diseases — a process that is controversial because it creates a permanent change to the genome that can be passed down for generations. “If human embryo editing for reproductive purposes or germline editing were space flight, the new data are the equivalent of having the rocket explode at the launch pad before take-off,” says Fyodor Urnov, who studies genome editing at the University of California, Berkeley, but was not involved in any of the latest research.

These studies,if borne out, offer new concerns (from Ledford’s June 25, 2020 article),

The changes are the result of DNA-repair processes harnessed by genome-editing tools. CRISPR–Cas9 uses a small strand of RNA to direct the Cas9 enzyme to a site in the genome with a similar sequence. The enzyme then cuts both strands of DNA at that site, and the cell’s repair systems heal the gap.

The edits occur during that repair: most often, the cell seals up the cut using an error-prone mechanism that can insert or delete a small number of DNA letters. If researchers provide a DNA template, the cell might sometimes use that sequence to mend the cut, resulting in a true rewrite. But broken DNA can also cause shuffling or loss of a large region of the chromosome.

Previous work using CRISPR in mouse embryos and other kinds of human cell had already demonstrated that editing chromosomes can cause large, unwanted effects4,5. But it was important to demonstrate the work in human embryos as well, says Urnov, because different cell types might respond to genome editing differently.

Such rearrangements could be missed in many experiments, which typically look for other unwanted edits, such as single DNA-letter changes or small insertions or deletions of only a few letters. The latest studies, however, looked specifically for large deletions and chromosomal rearrangements near the target site. [emphasis mine] “This is something that all of us in the scientific community will, starting immediately, take more seriously than we already have,” says Urnov. “This is not a one-time fluke.”

Ledford’s article offers some description and analysis of each of the three papers.Note: All of the research was done with nonviable embryos. For anyone who wants to read the papers for themselves here are links and citations for each of the three,

Frequent loss-of-heterozygosity in CRISPR-Cas9-edited early human embryos by Gregorio Alanis-Lobato, Jasmin Zohren, Afshan McCarthy, Norah M.E. Fogarty, Nada Kubikova, Emily Hardman, Maria Greco, Dagan Wells, James M.A. Turner, Kathy K. Niakan. bioRxiv DOI: Posted: June 5, 2020

Reading frame restoration at the EYS locus, and allele-specific chromosome removal after Cas9 cleavage in human embryos by Michael V. Zuccaro, Jia Xu, Carl Mitchell, Diego Marin, Raymond Zimmerman, Bhavini Rana, Everett Weinstein, Rebeca T. King, Morgan Smith, Stephen H. Tsang, Robin Goland, Maria Jasin, Rogerio Lobo, Nathan Treff, Dieter Egli. bioRxiv DOI: Posted June 18, 2020

FREQUENT GENE CONVERSION IN HUMAN EMBRYOS INDUCED BY DOUBLE STRAND BREAKS by Dan Liang, Nuria Marti Gutierrez, Tailai Chen, Yeonmi Lee, Sang-Wook Park, Hong Ma, Amy Koski, Riffat Ahmed, Hayley Darby, Ying Li, Crystal Van Dyken, Aleksei Mikhalchenko, Thanasup Gonmanee, Tomonari Hayama, Han Zhao, Keliang Wu, Jingye Zhang, Zhenzhen Hou, Jumi Park, Chong-Jai Kim, Jianhui Gong, Yilin Yuan, Ying Gu, Yue Shen, Susan B. Olson, Hui Yang, David Battaglia, Thomas O’Leary, Sacha A. Krieg, David M. Lee, Diana H. Wu, P. Barton Duell, Sanjiv Kaul, Jin-Soo Kim, Stephen B. Heitner, Eunju Kang, Zi-Jiang Chen, Paula Amato, Shoukhrat Mitalipov. bioRxiv DOI: Posted June 20, 2020

These papers are open access.

A July 17, 2018 posting is probably the first time I featured work showing that CRISPR gene-editing can result in off-target effects; it was followed up by a September 20, 2019 posting on the topic.

Live music by teleportation? Catch up. It’s already happened.

Dr. Alexis Kirke first graced this blog about four years ago, in a July 8, 2016 posting titled, Cornwall (UK) connects with University of Southern California for performance by a quantum computer (D-Wave) and mezzo soprano Juliette Pochin.

Kirke now returns with a study showing how teleportation helped to create a live performance piece, from a July 2, 2020 news item on ScienceDaily,

Teleportation is most commonly the stuff of science fiction and, for many, would conjure up the immortal phrase “Beam me up, Scotty.”

However, a new study has described how its status in science fact could actually be employed as another, and perhaps unlikely, form of entertainment — live music.

Dr Alexis Kirke, Senior Research Fellow in the Interdisciplinary Centre for Computer Music Research at the University of Plymouth (UK), has for the first time shown that a human musician can communicate directly with a quantum computer via teleportation.

The result is a high-tech jamming session, through which a blend of live human and computer-generated sounds come together to create a unique performance piece.

A July 2, 2020 Plymouth University press release (also on EurekAlert), which originated the news item, offers more detail about this latest work along with some information about the 2016 performance and how it all provides insight into how quantum computing might function in the future,

Speaking about the study, published in the current issue of the Journal of New Music Research, Dr Kirke said: “The world is racing to build the first practical and powerful quantum computers, and whoever succeeds first will have a scientific and military advantage because of the extreme computing power of these machines. This research shows for the first time that this much-vaunted advantage can also be helpful in the world of making and performing music. No other work has shown this previously in the arts, and it demonstrates that quantum power is something everyone can appreciate and enjoy.”

Quantum teleportation is the ability to instantaneously transmit quantum information over vast distances, with scientists having previously used it to send information from Earth to an orbiting satellite over 870 miles away.

In the current study, Dr Kirke describes how he used a system called MIq (Multi-Agent Interactive qgMuse), in which an IBM quantum computer executes a methodology called Grover’s Algorithm.

Discovered by Lov Grover at Bell Labs in 1996, it was the second main quantum algorithm (after Shor’s algorithm) and gave a huge advantage over traditional computing.

In this instance, it allows the dynamic solving of musical logical rules which, for example, could prevent dissonance or keep to ¾ instead of common time.

It is significantly faster than any classical computer algorithm, and Dr Kirke said that speed was essential because there is actually no way to transmit quantum information other than through teleportation.

The result was that when played the theme from Game of Thrones on the piano, the computer – a 14-qubit machine housed at IBM in Melbourne – rapidly generated accompanying music that was transmitted back in response.

Dr Kirke, who in 2016 staged the first ever duet between a live singer and a quantum supercomputer, said: “At the moment there are limits to how complex a real-time computer jamming system can be. The number of musical rules that a human improviser knows intuitively would simply take a computer too long to solve to real-time music. Shortcuts have been invented to speed up this process in rule-based AI music, but using the quantum computer speed-up has not be tried before. So while teleportation cannot move information faster than the speed of light, if remote collaborators want to connect up their quantum computers – which they are using to increase the speed of their musical AIs – it is 100% necessary. Quantum information simply cannot be transmitted using normal digital transmission systems.”

Caption: Dr Alexis Kirke (right) and soprano Juliette Pochin during the first duet between a live singer and a quantum supercomputer. Credit: University of Plymouth

Here’s a link to and a citation for the latest research,

Testing a hybrid hardware quantum multi-agent system architecture that utilizes the quantum speed advantage for interactive computer music by Alexis Kirke. Journal of New Music Research Volume 49, 2020 – Issue 3 Pages 209-230 DOI: Published online: 13 Apr 2020

This paper appears to be open access.

July 2020 update on Dr. He Jiankui (the CRISPR twins) situation

This was going to be written for January 2020 but sometimes things happen (e.g., a two-part overview of science culture in Canada from 2010-19 morphed into five parts with an addendum and, then, a pandemic). By now (July 28, 2020), Dr. He’s sentencing to three years in jail announced by the Chinese government in January 2020 is old news.

Regardless, it seems a neat and tidy ending to an international scientific scandal concerned with germline-editing which resulted in at least one set of twins, Lulu and Nana. He claimed to have introduced a variant (“Delta 32” variation) of their CCR5 gene. This does occur naturally and scientists have noted that people with this mutation seem to be resistant to HIV and smallpox.

For those not familiar with the events surrounding the announcement, here’s a brief recap. News of the world’s first gene-edited twins’ birth was announced in November 2018 just days before an international meeting group of experts who had agreed on a moratorium in 2015 on exactly that kind of work. The scientist making the announcement about the twins was scheduled for at least one presentation at the meeting, which was to be held in Hong Kong. He did give his presentation but left the meeting shortly afterwards as shock was beginning to abate and fierce criticism was rising. My November 28, 2018 posting (First CRISPR gene-edited babies? Ethics and the science story) offers a timeline of sorts and my initial response.

I subsequently followed up with two mores posts as the story continued to develop. My May 17, 2019 posting (Genes, intelligence, Chinese CRISPR (clustered regularly interspaced short palindromic repeats) babies, and other children) featured news that Dr. He’s gene-editing may have resulted in the twins having improved cognitive skills. Then, more news broke. The title for my June 20, 2019 posting (Greater mortality for the CRISPR twins Lulu and Nana?) is self-explanatory.

I have roughly organized my sources for this posting into two narratives, which I’m contrasting with each other. First, there is one found in the mainstream media (English language), ‘The Popular Narrative’. Second, there is story where Dr. He is viewed more sympathetically and as part of a larger community where there isn’t nearly as much consensus over what should or shouldn’t be done as ‘the popular narrative’ insists.

The popular narrative: Dr. He was a rogue scientist

A December 30, 2019 article for Fast Company by Kristin Toussaint lays out the latest facts (Note: A link has been removed),

… Now, a court in China has sentenced He to three years in prison, according to Xinhua, China’s state-run press agency, for “illegal medical practices.”

The court in China’s southern city of Shenzhen says that He’s team, which included colleagues Zhang Renli and Qin Jinzhou from two medical institutes in Guangdong Province, falsified ethical approval documents and violated China’s “regulations and ethical principles” with their gene-editing work. Zhang was sentenced to two years in jail, and Qin to 18 months with a two-year reprieve, according to Xinhau.

Ian Sample’s December 31, 2020 article for the Guardian offers more detail (Note: Links have been removed),

The court in Shenzhen found He guilty of “illegal medical practices” and in addition to the prison sentence fined him 3m yuan (£327,360), according to the state news agency, Xinhua. Two others on He’s research team received lesser fines and sentences.

“The three accused did not have the proper certification to practise medicine, and in seeking fame and wealth, deliberately violated national regulations in scientific research and medical treatment,” the court said, according to Xinhua. “They’ve crossed the bottom line of ethics in scientific research and medical ethics.”

[…] the court found He had forged documents from an ethics review panel that were used to recruit couples for the research. The couples that enrolled had a man with HIV and a woman without and were offered IVF in return for taking part.

Zhang Renli, who worked with He, was sentenced to two years in prison and fined 1m yuan. Colleague Qin Jinzhou received an 18-month sentence, but with a two-year reprieve, and a 500,000 yuan fine.

He’s experiments, which were carried out on seven embryos in late 2018, sent shockwaves through the medical and scientific world. The work was swiftly condemned for deceiving vulnerable patients and using a risky, untested procedure with no medical justification. Earlier this month, MIT Technology Review released excerpts from an early manuscript of He’s work. It casts serious doubts on his claims to have made the children immune to HIV.

Even as the scientific community turned against He, the scientist defended his work and said he was proud of having created Lulu and Nana. A third child has since been born as a result of the experiments.

Robin Lovell-Badge at the Francis Crick Institute in London said it was “far too premature” for anyone to pursue genome editing on embryos that are intended to lead to pregnancies. “At this stage we do not know if the methods will ever be sufficiently safe and efficient, although the relevant science is progressing rapidly, and new methods can look promising. It is also important to have standards established, including detailed regulatory pathways, and appropriate means of governance.”

A December 30, 2019 article, by Carolyn Y. Johnson for the Washington Post, covers much the same ground although it does go on to suggest that there might be some blame to spread around (Note: Links have been removed),

The Chinese researcher who stunned and alarmed the international scientific community with the announcement that he had created the world’s first gene-edited babies has been sentenced to three years in prison by a court in China.

He Jiankui sparked a bioethical crisis last year when he claimed to have edited the DNA of human embryos, resulting in the birth of twins called Lulu and Nana as well as a possible third pregnancy. The gene editing, which was aimed at making the children immune to HIV, was excoriated by many scientists as a reckless experiment on human subjects that violated basic ethical principles.

The judicial proceedings were not public, and outside experts said it is hard to know what to make of the punishment without the release of the full investigative report or extensive knowledge of Chinese law and the conditions under which He will be incarcerated.

Jennifer Doudna, a biochemist at the University of California at Berkeley who co-invented CRISPR, the gene editing technology that He utilized, has been outspoken in condemning the experiments and has repeatedly said CRISPR is not ready to be used for reproductive purposes.

R. Alta Charo, a fellow at Stanford’s Center for Advanced Study in the Behavioral Sciences, was among a small group of experts who had dinner with He the night before he unveiled his controversial research in Hong Kong in November 2018.

“He Jiankui is an example of somebody who fundamentally didn’t understand, or didn’t want to recognize, what have become international norms around responsible research,” Charo said. “My impression is he allowed his personal ambition to completely cloud rational thinking and judgment.”

Scientists have been testing an array of powerful biotechnology tools to fix genetic diseases in adults. There is tremendous excitement about the possibility of fixing genes that cause serious disease, and the first U.S. patients were treated with CRISPR this year.

But scientists have long drawn a clear moral line between curing genetic diseases in adults and editing and implanting human embryos, which raises the specter of “designer babies.” Those changes and any unanticipated ones could be inherited by future generations — in essence altering the human species.

“The fact that the individual at the center of the story has been punished for his role in it should not distract us from examining what supporting roles were played by others, particularly in the international scientific community and also the environment that shaped and encouraged him to push the limits,” said Benjamin Hurlbut [emphasis mine], associate professor in the School of Life Sciences at Arizona State University.

Stanford University cleared its scientists, including He’s former postdoctoral adviser, Stephen Quake, finding that Quake and others did not participate in the research and had expressed “serious concerns to Dr. He about his work.” A Rice University spokesman said an investigation continues into bioengineering professor Michael Deem, He’s former academic adviser. Deem was listed as a co-author on a paper called “Birth of Twins After Genome Editing for HIV Resistance,” submitted to scientific journals, according to MIT Technology Review.

It’s interesting that it’s only the Chinese scientists who are seen to be punished, symbolically at least. Meanwhile, Stanford clears its scientists of any wrongdoing and Rice University continues to investigate.

Watch for the Hurlbut name (son, Benjamin and father, William) to come up again in the ‘complex narrative’ section.

Criticism of the ‘twins’ CRISPR editing’ research

Antonio Regalado’s December 3, 2020 article for the MIT (Massachusetts Institute of Technology) Technology Review features comments from various experts on an unpublished draft of Dr. He Jiankui’s research

Earlier this year a source sent us a copy of an unpublished manuscript describing the creation of the first gene-edited babies, born last year in China. Today, we are making excerpts of that manuscript public for the first time.

Titled “Birth of Twins After Genome Editing for HIV Resistance,” and 4,699 words long, the still unpublished paper was authored by He Jiankui, the Chinese biophysicist who created the edited twin girls. A second manuscript we also received discusses laboratory research on human and animal embryos.

The metadata in the files we were sent indicate that the two draft papers were edited by He in late November 2018 and appear to be what he initially submitted for publication. Other versions, including a combined manuscript, may also exist. After consideration by at least two prestigious journals, Nature and JAMA, his research remains unpublished.

The text of the twins paper is replete with expansive claims of a medical breakthrough that can “control the HIV epidemic.” It claims “success”—a word used more than once—in using a “novel therapy” to render the girls resistant to HIV. Yet surprisingly, it makes little attempt to prove that the twins really are resistant to the virus. And the text largely ignores data elsewhere in the paper suggesting that the editing went wrong.

We shared the unpublished manuscripts with four experts—a legal scholar, an IVF doctor, an embryologist, and a gene-editing specialist—and asked them for their reactions. Their views were damning. Among them: key claims that He and his team made are not supported by the data; the babies’ parents may have been under pressure to agree to join the experiment; the supposed medical benefits are dubious at best; and the researchers moved forward with creating living human beings before they fully understood the effects of the edits they had made.

1. Why aren’t the doctors among the paper’s authors?

The manuscript begins with a list of the authors—10 of them, mostly from He Jiankui’s lab at the Southern University of Science and Technology, but also including Hua Bai, director of an AIDS support network, who helped recruit couples, and Michael Deem, an American biophysicist whose role is under review by Rice University. (His attorney previously said Deem never agreed to submit the manuscript and sought to remove his name from it.)

It’s a small number of people for such a significant project, and one reason is that some names are missing—notably, the fertility doctors who treated the patients and the obstetrician who delivered the babies. Concealing them may be an attempt to obscure the identities of the patients. However, it also leaves unclear whether or not these doctors understood they were helping to create the first gene-edited babies.

To some, the question of whether the manuscript is trustworthy arises immediately.

Hank Greely, professor of law, Stanford University: We have no, or almost no, independent evidence for anything reported in this paper. Although I believe that the babies probably were DNA-edited and were born, there’s very little evidence for that. Given the circumstances of this case, I am not willing to grant He Jiankui the usual presumption of honesty. 

That last article by Regalado is the purest example I have of how fierce the criticism is and how almost all of it is focused on Dr. He and his Chinese colleagues.

A complex, measured narrative: multiple players in the game

The most sympathetic and, in many ways, the most comprehensive article is an August 1, 2019 piece by Jon Cohen for Science magazine (Note: Links have been removed),

On 10 June 2017, a sunny and hot Saturday in Shenzhen, China, two couples came to the Southern University of Science and Technology (SUSTech) to discuss whether they would participate in a medical experiment that no researcher had ever dared to conduct. The Chinese couples, who were having fertility problems, gathered around a conference table to meet with He Jiankui, a SUSTech biophysicist. Then 33, He (pronounced “HEH”) had a growing reputation in China as a scientist-entrepreneur but was little known outside the country. “We want to tell you some serious things that might be scary,” said He, who was trim from years of playing soccer and wore a gray collared shirt, his cuffs casually unbuttoned.

He simply meant the standard in vitro fertilization (IVF) procedures. But as the discussion progressed, He and his postdoc walked the couples through informed consent forms [emphasis mine] that described what many ethicists and scientists view as a far more frightening proposition. Seventeen months later, the experiment triggered an international controversy, and the worldwide scientific community rejected him. The scandal cost him his university position and the leadership of a biotech company he founded. Commentaries labeled He, who also goes by the nickname JK, a “rogue,” “China’s Frankenstein,” and “stupendously immoral.” [emphases mine]

But that day in the conference room, He’s reputation remained untarnished. As the couples listened and flipped through the forms, occasionally asking questions, two witnesses—one American, the other Chinese—observed [emphasis mine]. Another lab member shot video, which Science has seen [emphasis mine], of part of the 50-minute meeting. He had recruited those couples because the husbands were living with HIV infections kept under control by antiviral drugs. The IVF procedure would use a reliable process called sperm washing to remove the virus before insemination, so father-to-child transmission was not a concern. Rather, He sought couples who had endured HIV-related stigma and discrimination and wanted to spare their children that fate by dramatically reducing their risk of ever becoming infected. [emphasis mine]

He, who for much of his brief career had specialized in sequencing DNA, offered a potential solution: CRISPR, the genome-editing tool that was revolutionizing biology, could alter a gene in IVF embryos to cripple production of an immune cell surface protein, CCR5, that HIV uses to establish an infection. “This technique may be able to produce an IVF baby naturally immunized against AIDS,” one consent form read.[emphasis mine]

The couples’ children could also pass the protective mutation to future generations. The prospect of this irrevocable genetic change is why, since the advent of CRISPR as a genome editor 5 years earlier, the editing of human embryos, eggs, or sperm has been hotly debated. The core issue is whether such germline editing would cross an ethical red line because it could ultimately alter our species. Regulations, some with squishy language, arguably prohibited it in many countries, China included.

Yet opposition was not unanimous. A few months before He met the couples, a committee convened by the U.S. National Academies of Sciences, Engineering, and Medicine (NASEM) concluded in a well-publicized report that human trials of germline editing “might be permitted” if strict criteria were met. The group of scientists, lawyers, bioethicists, and patient advocates spelled out a regulatory framework but cautioned that “these criteria are necessarily vague” because various societies, caregivers, and patients would view them differently. The committee notably did not call for an international ban, arguing instead for governmental regulation as each country deemed appropriate and “voluntary self-regulation pursuant to professional guidelines.”

[…] He hid his plans and deceived his colleagues and superiors, as many people have asserted? A preliminary investigation in China stated that He had forged documents, “dodged supervision,” and misrepresented blood tests—even though no proof of those charges was released [emphasis mine], no outsiders were part of the inquiry, and He has not publicly admitted to any wrongdoing. (CRISPR scientists in China say the He fallout has affected their research.) Many scientists outside China also portrayed He as a rogue actor. “I think there has been a failure of self-regulation by the scientific community because of a lack of transparency,” virologist David Baltimore, a Nobel Prize–winning researcher at the California Institute of Technology (Caltech) in Pasadena and co-chair of the Hong Kong summit, thundered at He after the biophysicist’s only public talk on the experiment.

Because the Chinese government has revealed little and He is not talking, key questions about his actions are hard to answer. Many of his colleagues and confidants also ignored Science‘s requests for interviews. But Ryan Ferrell, a public relations specialist He hired, has cataloged five dozen people who were not part of the study but knew or suspected what He was doing before it became public. Ferrell calls it He’s circle of trust. [emphasis mine]

That circle included leading scientists—among them a Nobel laureate—in China and the United States, business executives, an entrepreneur connected to venture capitalists, authors of the NASEM report, a controversial U.S. IVF specialist [John Zhang] who discussed opening a gene-editing clinic with He [emphasis mine], and at least one Chinese politician. “He had an awful lot of company to be called a ‘rogue,’” says geneticist George Church [emphases mine], a CRISPR pioneer at Harvard University who was not in the circle of trust and is one of the few scientists to defend at least some aspects of He’s experiment.

Some people sharply criticized He when he brought them into the circle; others appear to have welcomed his plans or did nothing. Several went out of their way to distance themselves from He after the furor erupted. For example, the two onlookers in that informed consent meeting were Michael Deem, He’s Ph.D. adviser at Rice University in Houston, Texas, and Yu Jun, a member of the Chinese Academy of Sciences (CAS) and co-founder of the Beijing Genomics Institute, the famed DNA sequencing company in Shenzhen. Deem remains under investigation by Rice for his role in the experiment and would not speak with Science. In a carefully worded statement, Deem’s lawyers later said he “did not meet the parents of the reported CCR5-edited children, or anyone else whose embryos were edited.” But earlier, Deem cooperated with the Associated Press (AP) for its exclusive story revealing the birth of the babies, which reported that Deem was “present in China when potential participants gave their consent and that he ‘absolutely’ thinks they were able to understand the risks. [emphasis mine]”

Yu, who works at CAS’s Beijing Institute of Genomics, acknowledges attending the informed consent meeting with Deem, but he told Science he did not know that He planned to implant gene-edited embryos. “Deem and I were chatting about something else,” says Yu, who has sequenced the genomes of humans, rice, silkworms, and date palms. “What was happening in the room was not my business, and that’s my personality: If it’s not my business, I pay very little attention.”

Some people who know He and have spoken to Science contend it is time for a more open discussion of how the biophysicist formed his circle of confidants and how the larger circle of trust—the one between the scientific community and the public—broke down. Bioethicist William Hurlbut at Stanford University [emphasis mine] in Palo Alto, California, who knew He wanted to conduct the embryo-editing experiment and tried to dissuade him, says that He was “thrown under the bus” by many people who once supported him. “Everyone ran for the exits, in both the U.S. and China. I think everybody would do better if they would just openly admit what they knew and what they did, and then collectively say, ‘Well, people weren’t clear what to do. We should all admit this is an unfamiliar terrain.’”

Steve Lombardi, a former CEO of Helicos, reacted far more charitably. Lombardi, who runs a consulting business in Bridgewater, Connecticut, says Quake introduced him to He to help find investors for Direct Genomics. “He’s your classic, incredibly bright, naïve entrepreneur—I run into them all the time,” Lombardi says. “He had the right instincts for what to do in China and just didn’t know how to do it. So I put him in front of as many people as I could.” Lombardi says He told him about his embryo-editing ambitions in August 2017, asking whether Lombardi could find investors for a new company that focused on “genetic medical tourism” and was based in China or, because of a potentially friendlier regulatory climate, Thailand. “I kept saying to him, ‘You know, you’ve got to deal with the ethics of this and be really sure that you know what you’re doing.’”

In April 2018, He asked Ferrell to handle his media full time. Ferrell was a good fit—he had an undergraduate degree in neuroscience, had spent a year in Beijing studying Chinese, and had helped another company using a pre-CRISPR genome editor. Now that a woman in the trial was pregnant, Ferrell says, He’s “understanding of the gravity of what he had done increased.” Ferrell had misgivings about the experiment, but he quit HDMZ and that August moved to Shenzhen. With the pregnancy already underway, Ferrell reasoned, “It was going to be the biggest science story of that week or longer, no matter what I did.”

MIT Technology Review had broken a story early that morning China time, saying human embryos were being edited and implanted, after reporter Antonio Regalado discovered descriptions of the project that He had posted online, without Ferrell’s knowledge, in an official Chinese clinical trial registry. Now, He gave AP the green light to post a detailed account, which revealed that twin girls—whom He, to protect their identifies, named Lulu and Nana—had been born. Ferrell and He also posted five unfinished YouTube videos explaining and justifying the unprecedented experiment.

“He was fearful that he’d be unable to communicate to the press and the onslaught in a way that would be in any way manageable for him,” Ferrell says. One video tried to forestall eugenics accusations, with He rejecting goals such as enhancing intelligence, changing skin color, and increasing sports performance as “not love.” Still, the group knew it had lost control of the news. [emphasis mine]

… On 7 March 2017, 5 weeks after the California gathering, He submitted a medical ethics approval application to the Shenzhen HarMoniCare Women and Children’s Hospital that outlined the planned CCR5 edit of human embryos. The babies, it claimed, would be resistant to HIV as well as to smallpox and cholera. (The natural CCR5 mutation may have been selected for because it helps carriers survive smallpox and plague, some studies suggest—but they don’t mention cholera.) “This is going to be a great science and medicine achievement ever since the IVF technology which was awarded the Nobel Prize in 2010, and will also bring hope to numerous genetic disease patients,” the application says. Seven people on the ethics committee, chaired by Lin Zhitong—a one-time Direct Genomics director and a HarMoniCare administrator—signed the application, indicating they approved it.

[…] John Zhang, […] [emphasis mine] earned his medical degree in China and a Ph.D. in reproductive biology at the University of Cambridge in the United Kingdom. Zhang had made international headlines himself in September 2016, when New Scientist revealed that he had created the world’s first “three-parent baby” by using mitochondrial DNA from a donor egg to revitalize the egg of a woman with infertility and then inseminating the resulting egg. “This technology holds great hope for ladies with advanced maternal age to have their own children with their own eggs,” Zhang explains in the center’s promotional video, which alternates between Chinese and English. It does not mention that Zhang did the IVF experiment in Mexico because it is not now allowed in the United States. [emphasis mine]

When Science contacted Zhang, the physician initially said he barely knew He: [emphases mine] “I know him just like many people know him, in an academic meeting.”

After his talk [November 2018 at Hong Kong meeting], He immediately drove back to Shenzhen, and his circle of trust began to disintegrate. He has not spoken publicly since. “I don’t think he can recover himself through PR,” says Ferrell, who no longer works for He but recently started to do part-time work for He’s wife. “He has to do other service to the world.”

Calls for a moratorium on human germline editing have increased, although at the end of the Hong Kong summit, the organizing committee declined in its consensus to call for a ban. China has stiffened its regulations on work with human embryos, and Chinese bioethicists in a Nature editorial about the incident urged the country to confront “the eugenic thinking that has persisted among a small proportion of Chinese scholars.”

Church, who has many CRISPR collaborations in China, finds it inconceivable that He’s work surprised the Chinese government. China has “the best surveillance system in the world,” he says. “I conclude that they were totally aware of what he was doing at every step of the way, especially because he wasn’t particularly secretive about it.”

Benjamin Hurlbut, William’s son and a historian of biomedicine at Arizona State University in Tempe, says leaders in the scientific community should take a hard look at their actions, too. [emphases mine] He thinks the 2017 NASEM report helped give rise to He by following a well-established approach to guiding science: appointing an elite group to decide how scientists should be regulated. Benjamin Hurlbut, whose book Experiments in Democracy explores the governance of embryo research and bioethics, questions why small, scientist-led groups—à la the totemic Asilomar conference held in 1975 to discuss the future of recombinant DNA research—are seen as the best way to shape thinking about new technologies. Hurlbut has called for a “global observatory for gene editing” to convene meetings with diverse perspectives.

The prevailing notion that the scientific community simply “failed to see the rogue among the responsible,” Hurlbut says, is a convenient narrative for those scientific leaders and inhibits their ability to learn from such failures. [emphases mine] “It puts them on the right side of history,” he says. They failed to paint a bright enough red line, Hurlbut contends. “They are not on the right side of history because they contributed to this.”

If you have the time, I strongly recommend reading Cohen’s piece in its entirety. You’ll find links to the reports and more articles with in-depth reporting on this topic.

A little kindness and no regrets

William Hurlbut was interviewed in an As it happens (Canadian Broadcasting Corporation’ CBC) radio programme segment on December 30, 2020. This is an excerpt from the story transcript written by Sheena Goodyear (Note: A link has been removed),

Dr. William Hurlbut, a physician and professor of neural-biology at Stanford University, says he tried to warn He to slow down before it was too late. Here is part of his conversation with As It Happens guest host Helen Mann.

What was your reaction to the news that Dr. He had been sentenced to three years in prison?

My first reaction was one of sadness because I know Dr. He — who we call J.K., that’s his nickname.

I spent quite a few hours talking with him, and I’m just sad that this worked out this way. It didn’t work out well for him or for his country or for the world, in some sense.

Except the one good thing is it’s alerted us, it’s awakened the world, to the seriousness of the issues that are coming down toward us with biotechnology, especially in genetics.

How does he feel about [how] not just the Chinese government, but the world generally, responded to his experiment?

He was surprised, personally. But I had actually warned him that he was proceeding too fast, and I didn’t know he had implanted embryos.

We had several conversations before this was disclosed, and I warned him to go more slowly and to keep in conversation with the rest of the international scientific community, and more broadly the international perspectives on social and ethical matters.

He was doing that to some extent, but not deeply enough and not transparently enough.

It sounds like you were very thoughtful in the conversations you had with him and the advice you gave him. And I guess you operated with what you had. But do you have any regrets yourself?

I don’t have any regrets about the way I conducted myself. I regret that this happened this way for J.K., who is a very bright person, and a very nice person, a humble person.

He grew up in a poor urban farming village. He told me that at one point he wanted to ask out a certain girl that he thought was really pretty … but he was embarrassed to do so because her family owned the restaurant. And so you see how humble his origins were.

By the way, he did end up asking her out and he ended up marrying her, which is a happy story, except now they’re separated for years of crucial time, and they have little children. 

I know this is a bigger story than just J.K. and his family. But there’s a personal story to it too.

What happens He Jiankui? … Is his research career over?

It’s hard to imagine that a nation like China would not give him some some useful role in their society. A very intelligent and very well-educated young man. 

But on the other hand, he will be forever a sign of a very crucial and difficult moment for the human species. He’s not going outlive that.

It’s going to be interesting. I hope I get a chance to have good conversations with him again and hear his internal ruminations and perspectives on it all.

This (“I don’t have any regrets about the way I conducted myself”) is where Hurlbut lost me. I think he could have suggested that he’d reviewed and rethought everything and feels that he and others could have done better and maybe they need to rethink how scientists are trained and how we talk about science, genetics, and emerging technology. Interestingly, it’s his son who comes up with something closer to what I’m suggesting (this excerpt was quoted earlier in this posting from a December 30, 2019 article, by Carolyn Y. Johnson for the Washington Post),

“The fact that the individual at the center of the story has been punished for his role in it should not distract us from examining what supporting roles were played by others, particularly in the international scientific community and also the environment that shaped and encouraged him to push the limits,” said Benjamin Hurlbut [emphasis mine], associate professor in the School of Life Sciences at Arizona State University.

The man who CRISPRs himself approves

Josiah Zayner publicly injected himself with CRISPR in a demonstration (see my January 25, 2018 posting for details about Zayner, his demonstration, and his plans). As you might expect, his take on the He affair is quite individual. From a January 2, 2020 article for STAT, Zayner presents the case for Dr. He’s work (Note: Links have been removed),

When I saw the news that He Jiankui and colleagues had been sentenced to three years in prison for the first human embryo gene editing and implantation experiments, all I could think was, “How will we look back at what they had done in 100 years?”

When the scientist described his research and revealed the births of gene edited twin girls at the [Second] International Summit on Human Genome Editing in Hong Kong in late November 2018, I stayed up into the early hours of the morning in Oakland, Calif., watching it. Afterward, I couldn’t sleep for a few days and couldn’t stop thinking about his achievement.

This was the first time a viable human embryo was edited and allowed to live past 14 days, much less the first time such an embryo was implanted and the baby brought to term.

The majority of scientists were outraged at the ethics of what had taken place, despite having very little information on what had actually occurred.

To me, no matter how abhorrent one views [sic] the research, it represents a substantial step forward in human embryo editing. Now there is a clear path forward that anyone can follow when before it had been only a dream.

As long as the children He Jiankui engineered haven’t been harmed by the experiment, he is just a scientist who forged some documents to convince medical doctors to implant gene-edited embryos. The 4-minute mile of human genetic engineering has been broken. It will happen again.

The academic establishment and federal funding regulations have made it easy to control the number of heretical scientists. We rarely if ever hear of individuals pushing the ethical and legal boundaries of science.

The rise of the biohacker is changing that.

A biohacker is a scientist who exists outside academia or an institution. By this definition, He Jiankui is a biohacker. I’m also part of this community, and helped build an organization to support it.

Such individuals have much more freedom than “traditional” scientists because scientific regulation in the U.S. is very much institutionally enforced by the universities, research organizations, or grant-giving agencies. But if you are your own institution and don’t require federal grants, who can police you? If you don’t tell anyone what you are doing, there is no way to stop you — especially since there is no government agency actively trying to stop people from editing embryos.

… When a human embryo being edited and implanted is no longer interesting enough for a news story, will we still view He Jiankui as a villain?

I don’t think we will. But even if we do, He Jiankui will be remembered and talked about more than any scientist of our day. Although that may seriously aggravate many scientists and bioethicists, I think he deserves that honor.

Josiah Zayner is CEO of The ODIN, a company that teaches people how to do genetic engineering in their homes.

You can find The ODIN here.

Final comments

There can’t be any question that this was inevitable. One needs only to take a brief stroll through the history of science to know that scientists are going to push boundaries or, as in this case, press past an ill-defined grey zone.

The only scientists who are being publicly punished for hubris are Dr. He Jiankui and his two colleagues in China. Dr. Michael Deem is still working for Rice University as far as I can determine. Here’s how the Wikipedia entry for the He Jiankui Affair describes the investigation (Note: Links have been removed),

Michael W. Deem, an American bioengineering professor at Rice University and He’s doctoral advisor, was involved in the research, and was present when people involved in He’s study gave consent.[24] He was the only non-Chinese out of 10 authors listed in the manuscript submitted to Nature.[30] Deem came under investigation by Rice University after news of the work was made public.[58] As of 31 December 2019, the university had not released a decision.[59] [emphasis mine]

Meanwhile the scientists at Stanford are cleared. While there are comments about the Chinese government not being transparent, it seems to me that US universities are just as opaque.

What seems missing from all this discussion and opprobrium is that the CRISPR technology itself is problematic. My September 20, 2019 post features research into off-target results from CRISPR gene-editing and, prior, there was this July 17, 2018 posting (The CRISPR [clustered regularly interspaced short palindromic repeats]-CAS9 gene-editing technique may cause new genetic damage kerfuffle).

I’d like to see more discussion and, in line with Benjamin Hurlbut’s thinking, I’d like to see more than a small group of experts talking to each other as part of the process especially here in Canada and in light of efforts to remove our ban on germline-editing (see my April 26, 2019 posting for more about those efforts).

Worried your ‘priceless’ art could be ruined? Genomics could be the answer

First, there was the story about art masterpieces turning into soap (my June 22, 2017 posting) and now, it seems that microbes may also constitute a problem. Before getting to the latest research, here’s are some images the researchers are using to illustrate their work,

Caption: Leonardo da Vinci noted that the fore and hind wings of a dragonfly are out of phase — verified centuries later by slow motion photography. Thaler suggests further study to compare individuals and species with high “flicker fusion frequency” ability. Credit: PXFuel

I’m not sure what that has to do with anything but I do love dragonflies. This next image seems more relevant to the research,

Caption: Photo summary of the various artworks sampled for the study “”Characterizing microbial signatures on sculptures and paintings of similar provenance.” Circles indicate swabbed areas on each sample artwork Credit: JCVI

It turns out, the researchers are releasing two pieces of research in the same press release, neither having much to do with the other. They (art conservation rresearch, first and, then, research into vision [hence the dragonfly] and da Vinci’s eyes) are both described in a June 18, 2020 J. Craig Venter Institute (JCVI)-Leonardo Da Vinci DNA Project press release (also on EurekAlert),

A new study of the microbial settlers on old paintings, sculptures, and other forms of art charts a potential path for preserving, restoring, and confirming the geographic origin of some of humanity’s greatest treasures.

Genetics scientists with the J. Craig Venter Institute (JCVI), collaborating with the Leonardo da Vinci DNA Project and supported by the Richard Lounsbery Foundation, say identifying and managing communities of microbes on art may offer museums and collectors a new way to stem the deterioration of priceless possessions, and to unmask counterfeits in the $60 billion a year art market.

Manolito G. Torralba, Claire Kuelbs, Kelvin Jens Moncera, and Karen E. Nelson of the JCVI, La Jolla, California, and Rhonda Roby of the Alameda California County Sheriff’s Office Crime Laboratory, used small, dry polyester swabs to gently collect microbes from centuries-old, Renaissance-style art in a private collector’s home in Florence, Italy. Their findings are published in the journal Microbial Ecology .

The genetic detectives caution that additional time and research are needed to formally convict microbes as a culprit in artwork decay but consider their most interesting find to be “oxidase positive” microbes primarily on painted wood and canvas surfaces.

These species can dine on organic and inorganic compounds often found in paints, in glue, and in the cellulose in paper, canvas, and wood. Using oxygen for energy production, they can produce water or hydrogen peroxide, a chemical used in disinfectants and bleaches.

“Such byproducts are likely to influence the presence of mold and the overall rate of deterioration,” the paper says.

“Though prior studies have attempted to characterize the microbial composition associated with artwork decay, our results summarize the first large scale genomics-based study to understand the microbial communities associated with aging artwork.”

The study builds on an earlier one in which the authors compared hairs collected from people in the Washington D.C., and San Diego, CA. areas, finding that microbial signatures and patterns are geographically distinguishable.

In the art world context, studying microbes clinging to the surface of a work of art may help confirm its geographic origin and authenticity or identify counterfeits.

Lead author Manolito G. Torralba notes that, as art’s value continues to climb, preservation is increasingly important to museums and collectors alike, and typically involves mostly the monitoring and adjusting of lighting, heat, and moisture.

Adding genomics science to these efforts offers advantages of “immense potential.”

The study says microbial populations “were easily discernible between the different types of substrates sampled,” with those on stone and marble art more diverse than wood and canvas. This is “likely due to the porous nature of stone and marble harboring additional organisms and potentially moisture and nutrients, along with the likelihood of biofilm formation.”

As well, microbial diversity on paintings is likely lower because few organisms can metabolize the meagre nutrients offered by oil-based paint.

“Though our sample size is low, the novelty of our study has provided the art and scientific communities with evidence that microbial signatures are capable of differentiating artwork according to their substrate,” the paper says.

“Future studies would benefit from working with samples whose authorship, ownership, and care are well-documented, although documentation about care of works of art (e.g., whether and how they were cleaned) seems rare before the mid-twentieth century.”

“Of particular interest would be the presence and activity of oil-degrading enzymes. Such approaches will lead to fully understanding which organism(s) are responsible for the rapid decay of artwork while potentially using this information to target these organisms to prevent degradation.”

“Focusing on reducing the abundance of such destructive organisms has great potential in preserving and restoring important pieces of human history.”

Biology in Art

The paper was supported by the US-based Richard Lounsbery Foundation as part of its “biology in art” research theme, which has also included seed funding efforts to obtain and sequence the genome of Leonardo da Vinci.

The Leonardo da Vinci DNA Project involves scientists in France (where Leonardo lived during his final years and was buried), Italy (where his father and other relatives were buried, and descendants of his half-brothers still live), Spain (whose National Library holds 700 pages of his notebooks), and the US (where forensic DNA skills flourish).

The Leonardo project has convened molecular biologists, population geneticists, microbiologists, forensic experts, and physicians working together with other natural scientists and with genealogists, historians, artists, and curators to discover and decode previously inaccessible knowledge and to preserve cultural heritage.  

Related news release: Leonardo da Vinci’s DNA: Experts unite to shine modern light on a Renaissance master

Measuring Leonardo da Vinci’s “quick eye” 500 years later.

Could he have played major-league baseball?

Famous art historians and biographers such as Sir Kenneth Clark and Walter Isaacson have written about Leonardo da Vinci’s “quick eye” because of the way he accurately captured fleeting expressions, wings during bird flight, and patterns in swirling water. But until now no one had tried to put a number on this aspect of Leonardo’s extraordinary visual acuity.

David S. Thaler of the University of Basel, and a guest investigator in the Program for the Human Environment at The Rockefeller University, does, allowing comparison of Leonardo with modern measures. Leonardo fares quite well.

Thaler’s estimate hinges on Leonardo’s observation that the fore and hind wings of a dragonfly are out of phase — not verified until centuries later by slow motion photography (see e.g.

To quote Isaacson’s translation of Leonardo’s notebook: “The dragonfly flies with four wings, and when those in front are raised those behind are lowered.”

Thaler challenged himself and friends to try seeing if that’s true, but they all saw only blurs.

High-speed camera studies by others show the fore and hind wingbeats of dragonflies vary by 20 to 10 milliseconds — one fiftieth to one hundredth of a second — beyond average human perception.

Thaler notes that “flicker fusion frequency” (FFF) — akin to a motion picture’s frames per second — is used to quantify and measure “temporal acuity” in human vision.

When frames per second exceed the number of frames the viewer can perceive individually, the brain constructs the illusion of continuous movement. The average person’s FFF is between 20 to 40 frames per second; current motion pictures present 48 or 72 frames per second.

To accurately see the angle between dragonfly wings would require temporal acuity in the range of 50 to 100 frames per second.

Thaler believes genetics will account for variations in FFF among different species, which range from a low of 12 in some nocturnal insects to over 300 in Fire Beetles. We simply do not know what accounts for human variation. Training and genetics may both play important roles.

“Perhaps the clearest contemporary case for a fast flicker fusion frequency in humans is in American baseball, because it is said that elite batters can see the seams on a pitched baseball,” even when rotating 30 to 50 times per second with two or four seams facing the batter. A batter would need Leonardo-esque FFF to spot the seams on most inbound baseballs.  

Thaler suggests further study to compare the genome of individuals and species with unusually high FFF, including, if possible, Leonardo’s DNA.  

Flicker fusion for focus, attention, and affection   

In a companion paper, Thaler describes how Leonardo used psychophysics that would only be understood centuries later — and about which a lot remains to be learned today — to communicate deep beauty and emotion. 

Leonardo was master of a technique known as sfumato (the word derived from the Italian sfumare, “to tone down” or “to evaporate like smoke”), which describes a subtle blur of edges and blending of colors without sharp focus or distinct lines.

Leonardo expert Martin Kemp has noted that Leonardo’s sfumato sometimes involves a distance dependence which is akin to the focal plane of a camera. Yet, at other times, features at the same distance have selective sfumato so simple plane of focus is not the whole answer.

Thaler suggests that Leonardo achieved selective soft focus in portraits by painting in overcast or evening light, where the eyes’ pupils enlarge to let in more light but have a narrow plane of sharp focus. 

To quote Leonardo’s notebook, under the heading “Selecting the light which gives most grace to faces”: “In the evening and when the weather is dull, what softness and delicacy you may perceive in the faces of men and women.”  In dim light pupils enlarge to let in more light but their depth of field decreases.  

By measuring the size of the portrait’s pupils, Thaler inferred Leonardo’s depth of focus. He says Leonardo likely sensed this effect, perhaps unconsciously in the realm of his artistic sensibility. The pupil / aperture effect on depth of focus wasn’t explained until the mid-1800s, centuries after Leonardo’s birth in Vinci, Italy in 1452.

What about selective focus at equal distance? In this case Leonardo may have taken advantage of the fovea, the small area on the back of the eye where detail is sharpest.

Most of us move our eyes around and because of our slower flicker fusion frequency we construct a single 3D image of the world by jamming together many partially in-focus images. Leonardo realized and “froze” separate snapshots with which we construct ordinary perception.

Says Thaler: “We study Leonardo not only to learn about him but to learn about ourselves and further human potential.”

Thaler’s papers (at and evolved from talks at meetings of the Leonardo da Vinci DNA Project in Italy (2018), Spain and France (2019).

They form part of a collection of papers presented at a recent colloquium in Amboise, France, now being readied for publication in a book: Actes du Colloque International d’Amboise: Leonardo de Vinci, Anatomiste. Pionnier de l’Anatomie comparée, de la Biomécanique, de la Bionique et de la Physiognomonie. Edited by Henry de Lumley, President, Institute of Human Paleontology, Paris, and originally planned for release in late spring, 2020, publication was delayed by the global virus pandemic but should be available at CNRS Editions in the second half of the summer.

Other papers in the collection cover a range of topics, including how Leonardo used his knowledge of anatomy, gained by performing autopsies on dozens of cadavers, to achieve Mona Lisa’s enigmatic smile.

Leonardo also used it to exact revenge on academics and scientists who ridiculed him for lacking a classical education, sketching them with absurdly deformed faces to resemble birds, dogs, or goats. 

De Lumley earlier co-authored a 72-page monograph for the Leonardo DNA Project: “Leonardo da Vinci: Pioneer of comparative anatomy, biomechanics and physiognomy.”.

Here’s a link to and a citation for the paper featuring microbes and art masterpiece,

Characterizing Microbial Signatures on Sculptures and Paintings of Similar Provenance by Manolito G. Torralba, Claire Kuelbs, Kelvin Jens Moncera, Rhonda Roby & Karen E. Nelson. Microbial Ecology (2020) DOI: Published: 21 May 2020

This paper is open access.