Tag Archives: University of California at Berkeley

Neurotransistor for brainlike (neuromorphic) computing

According to researchers at Helmholtz-Zentrum Dresden-Rossendorf and the rest of the international team collaborating on the work, it’s time to look more closely at plasticity in the neuronal membrane,.

From the abstract for their paper, Intrinsic plasticity of silicon nanowire neurotransistors for dynamic memory and learning functions by Eunhye Baek, Nikhil Ranjan Das, Carlo Vittorio Cannistraci, Taiuk Rim, Gilbert Santiago Cañón Bermúdez, Khrystyna Nych, Hyeonsu Cho, Kihyun Kim, Chang-Ki Baek, Denys Makarov, Ronald Tetzlaff, Leon Chua, Larysa Baraban & Gianaurelio Cuniberti. Nature Electronics volume 3, pages 398–408 (2020) DOI: https://doi.org/10.1038/s41928-020-0412-1 Published online: 25 May 2020 Issue Date: July 2020

Neuromorphic architectures merge learning and memory functions within a single unit cell and in a neuron-like fashion. Research in the field has been mainly focused on the plasticity of artificial synapses. However, the intrinsic plasticity of the neuronal membrane is also important in the implementation of neuromorphic information processing. Here we report a neurotransistor made from a silicon nanowire transistor coated by an ion-doped sol–gel silicate film that can emulate the intrinsic plasticity of the neuronal membrane.

Caption: Neurotransistors: from silicon chips to neuromorphic architecture. Credit: TU Dresden / E. Baek Courtesy: Helmholtz-Zentrum Dresden-Rossendorf

A July 14, 2020 news item on Nanowerk announced the research (Note: A link has been removed),

Especially activities in the field of artificial intelligence, like teaching robots to walk or precise automatic image recognition, demand ever more powerful, yet at the same time more economical computer chips. While the optimization of conventional microelectronics is slowly reaching its physical limits, nature offers us a blueprint how information can be processed and stored quickly and efficiently: our own brain.

For the very first time, scientists at TU Dresden and the Helmholtz-Zentrum Dresden-Rossendorf (HZDR) have now successfully imitated the functioning of brain neurons using semiconductor materials. They have published their research results in the journal Nature Electronics (“Intrinsic plasticity of silicon nanowire neurotransistors for dynamic memory and learning functions”).

A July 14, 2020 Helmholtz-Zentrum Dresden-Rossendorf press release (also on EurekAlert), which originated the news items delves further into the research,

Today, enhancing the performance of microelectronics is usually achieved by reducing component size, especially of the individual transistors on the silicon computer chips. “But that can’t go on indefinitely – we need new approaches”, Larysa Baraban asserts. The physicist, who has been working at HZDR since the beginning of the year, is one of the three primary authors of the international study, which involved a total of six institutes. One approach is based on the brain, combining data processing with data storage in an artificial neuron.

“Our group has extensive experience with biological and chemical electronic sensors,” Baraban continues. “So, we simulated the properties of neurons using the principles of biosensors and modified a classical field-effect transistor to create an artificial neurotransistor.” The advantage of such an architecture lies in the simultaneous storage and processing of information in a single component. In conventional transistor technology, they are separated, which slows processing time and hence ultimately also limits performance.

Silicon wafer + polymer = chip capable of learning

Modeling computers on the human brain is no new idea. Scientists made attempts to hook up nerve cells to electronics in Petri dishes decades ago. “But a wet computer chip that has to be fed all the time is of no use to anybody,” says Gianaurelio Cuniberti from TU Dresden. The Professor for Materials Science and Nanotechnology is one of the three brains behind the neurotransistor alongside Ronald Tetzlaff, Professor of Fundamentals of Electrical Engineering in Dresden, and Leon Chua [emphasis mine] from the University of California at Berkeley, who had already postulated similar components in the early 1970s.

Now, Cuniberti, Baraban and their team have been able to implement it: “We apply a viscous substance – called solgel – to a conventional silicon wafer with circuits. This polymer hardens and becomes a porous ceramic,” the materials science professor explains. “Ions move between the holes. They are heavier than electrons and slower to return to their position after excitation. This delay, called hysteresis, is what causes the storage effect.” As Cuniberti explains, this is a decisive factor in the functioning of the transistor. “The more an individual transistor is excited, the sooner it will open and let the current flow. This strengthens the connection. The system is learning.”

Cuniberti and his team are not focused on conventional issues, though. “Computers based on our chip would be less precise and tend to estimate mathematical computations rather than calculating them down to the last decimal,” the scientist explains. “But they would be more intelligent. For example, a robot with such processors would learn to walk or grasp; it would possess an optical system and learn to recognize connections. And all this without having to develop any software.” But these are not the only advantages of neuromorphic computers. Thanks to their plasticity, which is similar to that of the human brain, they can adapt to changing tasks during operation and, thus, solve problems for which they were not originally programmed.

I highlighted Dr. Leon Chua’s name as he was one of the first to conceptualize the notion of a memristor (memory resistor), which is what the press release seems to be referencing with the mention of artificial synapses. Dr. Chua very kindly answered a few questions for me about his work which I published in an April 13, 2010 posting (scroll down about 40% of the way).

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).

Gecko-like toes needed for climbing robots

Caption: The spotted belly of a Tokay gecko used by UC Berkeley biologists to understand how the animal’s five sticky toes help it climb on many types of surface. Credit: Yi Song

Those are fabulous toes. Geckos and the fine hairs on their toes have been of great interest to researchers looking to increase qualities of adhesion for all kinds of purposes including for robots that climb. The latest foray into the research suggests that it’s not just the fine hairs found on gecko toes that are important.

A May 8, 2020 news item on ScienceDaily makes the proclamation,

Robots with toes? Experiments suggest that climbing robots could benefit from having flexible, hairy toes, like those of geckos, that can adjust quickly to accommodate shifting weight and slippery surfaces.

Biologists from the University of California, Berkeley, and Nanjing University of Aeronautics and Astronautics observed geckos running horizontally along walls to learn how they use their five toes to compensate for different types of surfaces without slowing down.

Close-up look at the toe pads of a Tokay gecko. They have about 15,000 hairs per foot, each of which has split ends that maximize contact with the surface and support the animal’s weight by interacting with surface molecules via van der Waals forces. (Photo by Yi Song)

You can find that image and more embedded in the May 8, 2020 University of California at Berkeley news release (also on EurekAlert) by Robert Sanders. The news release delves further into the work

“The research helped answer a fundamental question: Why have many toes?” said Robert Full, UC Berkeley professor of integrative biology.

As his previous research showed, geckos’ toes can stick to the smoothest surfaces through the use of intermolecular forces, and uncurl and peel in milliseconds. Their toes have up to 15,000 hairs per foot, and each hair has “an awful case of split ends, with as many as a thousand nano-sized tips that allow close surface contact,” he said.

These discoveries have spawned research on new types of adhesives that use intermolecular forces, or van der Waals forces, to stick almost anywhere, even underwater.

One puzzle, he said, is that gecko toes only stick in one direction. They grab when pulled in one direction, but release when peeled in the opposite direction. Yet, geckos move agilely in any orientation.

To determine how geckos have learned to deal with shifting forces as they move on different surfaces, Yi Song, a UC Berkeley visiting student from Nanjing, China, ran geckos sideways along a vertical wall while making high-speed video recordings to show the orientation of their toes. The sideways movement allowed him to distinguish downward gravity from forward running forces to best test the idea of toe compensation.

Using a technique called frustrated total internal reflection, Song, also measured the area of contact of each toe. The technique made the toes light up when they touched a surface.

To the researcher’s surprise, geckos ran sideways just as fast as they climbed upward, easily and quickly realigning their toes against gravity. The toes of the front and hind top feet during sideways wall-running shifted upward and acted just like toes of the front feet during climbing.

To further explore the value of adjustable toes, researchers added slippery patches and strips, as well as irregular surfaces. To deal with these hazards, geckos took advantage of having multiple, soft toes. The redundancy allowed toes that still had contact with the surface to reorient and distribute the load, while the softness let them conform to rough surfaces.

“Toes allowed agile locomotion by distributing control among multiple, compliant, redundant structures that mitigate the risks of moving on challenging terrain,” Full said. “Distributed control shows how biological adhesion can be deployed more effectively and offers design ideas for new robot feet, novel grippers and unique manipulators.”

The team, which also includes Zhendong Dai and Zhouyi Wang of the College of Mechanical and Electrical Engineering at Nanjing University of Aeronautics and Astronautics, published its findings this week in the journal Proceedings of the Royal Society B.

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

Role of multiple, adjustable toes in distributed control shown by sideways wall-running in geckos by Yi Song, Zhendong Dai, Zhouyi Wang, and Robert J. Full. Proceedings of the Royal Society B; Biological Sciences 29 April 2020 Volume 287Issue 1926 DOI: https://doi.org/10.1098/rspb.2020.0123 Published [online]:06 May 2020

This paper is open access.

Controlling agricultural pests with CRISPR-based technology

CRISPR (clustered regularly interspaced short palindromic repeats) technology is often touted as being ‘precise’, which as far as I can tell, is not exactly the case (see my Nov. 28, 2018 posting about the CRISPR babies [scroll down about 30% of the way for the first hint that CRISPR isn’t]). So, it’s a bit odd to see the word ‘precise’ used as part of a new CRISPR-based technology’s name (from a January 8, 2019 news item on ScienceDaily,

Using the CRISPR gene editing tool, Nikolay Kandul, Omar Akbari and their colleagues at UC San Diego [UC is University of California] and UC Berkeley devised a method of altering key genes that control insect sex determination and fertility.

A description of the new “precision-guided sterile insect technique,” [emphasis mine] or pgSIT, is published Jan. 8 [2019] in the journal Nature Communications.

A January 8, 209 UCSD press release (also on EurekAlert) by Mario Aguilera, which originated the news item, delves further into the research,

When pgSIT-derived eggs are introduced into targeted populations, the researchers report, only adult sterile males emerge, resulting in a novel, environmentally friendly and relatively low-cost method of controlling pest populations in the future.

“CRISPR technology has empowered our team to innovate a new, effective, species-specific, self-limiting, safe and scalable genetic population control technology with remarkable potential to be developed and utilized in a plethora of insect pests and disease vectors,” said Akbari, an assistant professor in UC San Diego’s Division of Biological Sciences. “In the future, we strongly believe this technology will be safely used in the field to suppress and even eradicate target species locally, thereby revolutionizing how insects are managed and controlled going forward.”

Since the 1930s, agricultural researchers have used select methods to release sterile male insects into the wild to control and eradicate pest populations. In the 1950s, a method using irradiated males was implemented in the United States to eliminate the pest species known as the New World Screwworm fly, which consumes animal flesh and causes extensive damage to livestock. Such radiation-based methods were later used in Mexico and parts of Central America and continue today.

Instead of radiation, the new pgSIT (precision-guided sterile insect technique), developed over the past year-and-a-half by Kandul and Akbari in the fruit fly Drosophila, uses CRISPR to simultaneously disrupt key genes that control female viability and male fertility in pest species. pgSIT, the researchers say, results in sterile male progeny with 100 percent efficiency. Because the targeted genes are common to a vast cross-section of insects, the researchers are confident the technology can be applied to a range of insects, including disease-spreading mosquitoes.

The researchers envision a system in which scientists genetically alter and produce eggs of a targeted pest species. The eggs are then shipped to a pest location virtually anywhere in the world, circumventing the need for a production facility on-site. Once the eggs are deployed at the pest location, the researchers say, the newly born sterile males will mate with females in the wild and be incapable of producing offspring, driving down the population.

“This is a novel twist of a very old technology,” said Kandul, an assistant project scientist in UC San Diego’s Division of Biological Sciences. “That novel twist makes it extremely portable from one species to another species to suppress populations of mosquitoes or agricultural pests, for example those that feed on valuable wine grapes.”

The new technology is distinct from continuously self-propagating “gene drive” systems that propagate genetic alterations from generation to generation. Instead, pgSIT is considered a “dead end” since male sterility effectively closes the door on future generations.

“The sterile insect technique is an environmentally safe and proven technology,” [emphasis mine] the researchers note in the paper. “We aimed to develop a novel, safe, controllable, non-invasive genetic CRISPR-based technology that could be transferred across species and implemented worldwide in the short-term to combat wild populations.”

With pgSIT proven in fruit flies, the scientists are hoping to develop the technology in Aedes aegypti, the mosquito species responsible for transmitting dengue fever, Zika, yellow fever and other diseases to millions of people.

“The extension of this work to other insect pests could prove to be a general and very useful strategy to deal with many vector-borne diseases that plague humanity and wreak havoc an agriculture globally,” said Suresh Subramani, global director of the Tata Institute for Genetics and Society.

I have one comment about the ‘safety’ of the sterile insect technique. It’s been safe up until now but, assuming this technique works as described: What happens as this new and more powerful technique is more widely deployed possibly eliminating whole species of insects? Might these ‘pests’ have a heretofore unknown beneficial effect somewhere in the food chain or in an ecosystem? Or, there may be other unintended consequences.

Moving on, here’s a link to and a citation for the paper,

Transforming insect population control with precision guided sterile males with demonstration in flies by Nikolay P. Kandul, Junru Liu, Hector M. Sanchez C., Sean L. Wu, John M. Marshall, & Omar S. Akbari. Nature Communications volume 10, Article number: 84 (2019) DOI: https://doi.org/10.1038/s41467-018-07964-7 Published 08 January 2019

This paper is open access.

The researchers have made this illustrative image available,

Caption: This is a schematic of the new precision-guided sterile insect technique (pgSIT), which uses components of the CRISPR/Cas9 system to disrupt key genes that control female viability and male fertility, resulting in sterile male progeny. Credit: Nikolay Kandul, Akbari Lab, UC San Diego

Jiggly jell-o as a new hydrogen fuel catalyst

Jello [uploaded from https://www.organicauthority.com/eco-chic-table/new-jell-o-mold-jiggle-chic-holidays]

I’m quite intrigued by this ‘jell-o’ story. It’s hard to believe a childhood dessert might prove to have an application as a catalyst for producing hydrogen fuel. From a December 14, 2018 news item on Nanowerk,

A cheap and effective new catalyst developed by researchers at the University of California, Berkeley, can generate hydrogen fuel from water just as efficiently as platinum, currently the best — but also most expensive — water-splitting catalyst out there.

The catalyst, which is composed of nanometer-thin sheets of metal carbide, is manufactured using a self-assembly process that relies on a surprising ingredient: gelatin, the material that gives Jell-O its jiggle.

Two-dimensional metal carbides spark a reaction that splits water into oxygen and valuable hydrogen gas. Berkeley researchers have discovered an easy new recipe for cooking up these nanometer-thin sheets that is nearly as simple as making Jell-O from a box. (Xining Zang graphic, copyright Wiley)

A December 13, 2018 University of California at Berkeley (UC Berkeley) news release by Kara Manke (also on EurekAlert but published on Dec. 14, 2018), which originated the news item, provides more technical detail,

“Platinum is expensive, so it would be desirable to find other alternative materials to replace it,” said senior author Liwei Lin, professor of mechanical engineering at UC Berkeley. “We are actually using something similar to the Jell-O that you can eat as the foundation, and mixing it with some of the abundant earth elements to create an inexpensive new material for important catalytic reactions.”

The work appears in the Dec. 13 [2018] print edition of the journal Advanced Materials.

A zap of electricity can break apart the strong bonds that tie water molecules together, creating oxygen and hydrogen gas, the latter of which is an extremely valuable source of energy for powering hydrogen fuel cells. Hydrogen gas can also be used to help store energy from renewable yet intermittent energy sources like solar and wind power, which produce excess electricity when the sun shines or when the wind blows, but which go dormant on rainy or calm days.

A black and white image of metal carbide under high magnification.

When magnified, the two-dimensional metal carbides resemble sheets of cell[o]phane. (Xining Zang photo, copyright Wiley)

But simply sticking an electrode in a glass of water is an extremely inefficient method of generating hydrogen gas. For the past 20 years, scientists have been searching for catalysts that can speed up this reaction, making it practical for large-scale use.

“The traditional way of using water gas to generate hydrogen still dominates in industry. However, this method produces carbon dioxide as byproduct,” said first author Xining Zang, who conducted the research as a graduate student in mechanical engineering at UC Berkeley. “Electrocatalytic hydrogen generation is growing in the past decade, following the global demand to lower emissions. Developing a highly efficient and low-cost catalyst for electrohydrolysis will bring profound technical, economical and societal benefit.”

To create the catalyst, the researchers followed a recipe nearly as simple as making Jell-O from a box. They mixed gelatin and a metal ion — either molybdenum, tungsten or cobalt — with water, and then let the mixture dry.

“We believe that as gelatin dries, it self-assembles layer by layer,” Lin said. “The metal ion is carried by the gelatin, so when the gelatin self-assembles, your metal ion is also arranged into these flat layers, and these flat sheets are what give Jell-O its characteristic mirror-like surface.”

Heating the mixture to 600 degrees Celsius triggers the metal ion to react with the carbon atoms in the gelatin, forming large, nanometer-thin sheets of metal carbide. The unreacted gelatin burns away.

The researchers tested the efficiency of the catalysts by placing them in water and running an electric current through them. When stacked up against each other, molybdenum carbide split water the most efficiently, followed by tungsten carbide and then cobalt carbide, which didn’t form thin layers as well as the other two. Mixing molybdenum ions with a small amount of cobalt boosted the performance even more.

“It is possible that other forms of carbide may provide even better performance,” Lin said.

On the left, an illustration of blue spheres, representing gelatin molecules, arranged in a lattice shape. On the right, an illustration of thin sheets of metal carbide.

Molecules in gelatin naturally self-assemble in flat sheets, carrying the metal ions with them (left). Heating the mixture to 600 degrees Celsius burns off the gelatin, leaving nanometer-thin sheets of metal carbide. (Xining Zang illustration, copyright Wiley)

The two-dimensional shape of the catalyst is one of the reasons why it is so successful. That is because the water has to be in contact with the surface of the catalyst in order to do its job, and the large surface area of the sheets mean that the metal carbides are extremely efficient for their weight.

Because the recipe is so simple, it could easily be scaled up to produce large quantities of the catalyst, the researchers say.

“We found that the performance is very close to the best catalyst made of platinum and carbon, which is the gold standard in this area,” Lin said. “This means that we can replace the very expensive platinum with our material, which is made in a very scalable manufacturing process.”

Co-authors on the study are Lujie Yang, Buxuan Li and Minsong Wei of UC Berkeley, J. Nathan Hohman and Chenhui Zhu of Lawrence Berkeley National Lab; Wenshu Chen and Jiajun Gu of Shanghai Jiao Tong University; Xiaolong Zou and Jiaming Liang of the Shenzhen Institute; and Mohan Sanghasadasa of the U.S. Army RDECOM AMRDEC.

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

Self‐Assembly of Large‐Area 2D Polycrystalline Transition Metal Carbides for Hydrogen Electrocatalysis by Xining Zang, Wenshu Chen, Xiaolong Zou, J. Nathan Hohman, Lujie Yang
Buxuan Li, Minsong Wei, Chenhui Zhu, Jiaming Liang, Mohan Sanghadasa, Jiajun Gu, Liwei Lin. Advanced Materials Volume30, Issue 50 December 13, 2018 1805188 DOI: https://doi.org/10.1002/adma.201805188 First published [online]: 09 October 2018

This paper is behind a paywall.

Greater mortality for the CRISPR twins Lulu and Nana?

Every time I think this CRISPR (clustered regularly interspaced short palindromic repeats) story is winding down, something new happens. The latest (I think) is in a June 3, 2019 news item on ScienceDaily,

A genetic mutation that a Chinese scientist attempted to create in twin babies born last year, ostensibly to help them fend off HIV infection, is also associated with a 21% increase in mortality in later life, according to an analysis by University of California, Berkeley, scientists.

The researchers scanned more than 400,000 genomes and associated health records contained in a British database, UK Biobank, and found that people who had two mutated copies of the gene had a significantly higher death rate between ages 41 and 78 than those with one or no copies.

Sarah Zhang’s June 3, 2019 article for The Atlantic provides an overview of the situation before exploring the current controversy,

In the 1990s, virologists in New York learned of a genetic mutation that would become one of the most famous ever discovered. They found it in a man who could not be infected with HIV. He turned out to be missing just 32 letters in a gene called CCR5, and remarkably, it was enough to make him resistant to the virus killing so many others. About 1 percent of people of European descent carry two copies of this mutation, now known as CCR5-Δ32.

In 2018, a Chinese scientist named He Jiankui made the mutation infamous when he attempted to use CRISPR to edit CCR5-Δ32 (pronounced “CCR5-delta-32”) into human embryos. He chose this mutation, he said, because the babies’ father was HIV-positive, and he wanted to make the resulting twin girls resistant to the virus. CCR5-Δ32 is also, after all, one of the most studied mutations.

He’s work immediately provoked outrage among scientists, who knew enough to know how much they did not know about the risks of altering CCR5. And now a new study suggests that CCR5-Δ32 is indeed harmful overall.

The girls’ CCR5 genes were altered, according to data He presented, but they do not exactly match the 32-letter deletion; it’s unclear whether either of them is actually resistant to HIV. Even if they were unable to get HIV, a body of research already suggested that CCR5-Δ32 made people more vulnerable to the flu and West Nile virus. A “good” mutation in the context of HIV can be “bad” in another context. No one knew, exactly, the net effect of a CCR5-Δ32 mutation.

For some reason, Zhang makes no mention of the possibly enhanced cognitive abilities that the twins may have as a consequence of the gene editing assuming that He Jiankui successfully edited the genes. (To my knowledge, the results and data have not been released for review by colleagues.)

Regardless, Zhang’s article provides a handy overview and update.

For anyone who’s interested in more detail about this latest research into mortality and CCR5, there’s a June 3, 2019 University of California at Berkeley news release (also on EurekAlert) by Robert Sanders, which also originated the ScienceDaily news item, details the latest research,

Previous studies have associated two mutated copies of the gene, CCR5, with a fourfold increase in the death rate after influenza infection, and the higher overall mortality rate may reflect this greater susceptibility to death from the flu. But the researchers say there could be any number of explanations, since the protein that CCR5 codes for, and which no longer works in those having the mutation in both copies of the gene, is involved in many body functions.

“Beyond the many ethical issues involved with the CRISPR babies, the fact is that, right now, with current knowledge, it is still very dangerous to try to introduce mutations without knowing the full effect of what those mutations do,” said Rasmus Nielsen, a UC Berkeley professor of integrative biology. “In this case, it is probably not a mutation that most people would want to have. You are actually, on average, worse off having it.”

“Because one gene could affect multiple traits, and because, depending on the environment, the effects of a mutation could be quite different, I think there can be many uncertainties and unknown effects in any germline editing,” said postdoctoral fellow Xinzhu “April” Wei.
Wei is first author and Nielsen is senior author of a paper describing the research that will appear online on Monday, June 3, in the journal Nature Medicine.

Mutation prevents HIV infection

The gene CCR5 codes for a protein that, among other things, sits on the surface of immune cells and helps some strains of HIV, including the most common ones, to enter and infect them. Jiankui He, the Chinese scientist who last November shocked the world by announcing he had experimented with CCR5 on at least two babies, said he wanted to introduce a mutation in the gene that would prevent this. Naturally-occurring mutations that disable the protein are rare in Asians, but a mutation found in about 11% of Northern Europeans protects them against HIV infection.

The genetic mutation, ∆32 (Delta 32), refers to a missing 32-base-pair segment in the CCR5 gene. This mutation interferes with the localization on the cell surface of the protein for which CCR5 codes, thwarting HIV binding and infection. He was unable to duplicate the natural mutation, but appears to have generated a similar deletion that would also inactivate the protein. One of the twin babies reportedly had one copy of CCR5 modified by CRISPR-Cas9 gene editing, while the other baby had both copies edited.

But inactivating a protein found in all humans and most animals is likely to have negative effects, Nielsen said, especially when done to both copies of the gene — a so-called homozygous mutation

“Here is a functional protein that we know has an effect in the organism, and it is well-conserved among many different species, so it is likely that a mutation that destroys the protein is, on average, not good for you,” he said. “Otherwise, evolutionary mechanisms would have destroyed that protein a long time ago.”

After He’s experiment became public, Nielsen and Wei, who study current genetic variation to understand the origin of human, animal and plant traits, decided to investigate the effect of the CCR5-∆32 mutation using data from UK Biobank. The database houses genomic information on a half million U.K. citizens that is linked to their medical records. The genomic information is much like that acquired by Ancestry.com and 23andMe: details on nearly a million individual variations in the genetic sequence, so-called single nucleotide polymorphisms (SNPs).

Two independent measures indicated a higher mortality rate for those with two mutated genes. Fewer people than expected with two mutations enrolled in the database, indicating that they had died at a higher rate than the general population. And fewer than expected survived from ages 40 to 78.

“Both the proportions before enrollment and the survivorship after enrollment tell the same story, which is that you have lower survivability or higher mortality if you have two copies of the mutation,” Nielsen said. “There is simply a deficiency of individuals with two copies.”

Because the ∆32 mutation is relatively common in Northern Europeans, it must have been favored by natural selection at some point, Nielsen said, though probably not to protect against HIV, since the virus has circulated among humans only since the 1980s.

Wei said that some evidence links the mutation to increased survival after stroke and protection against smallpox and flaviviruses, a group that includes the dengue, Zika and West Nile viruses.

Despite these possible benefits, the potential unintended effects of creating genetic mutations, in both adult somatic cells and in embryonic, germline cells, argue for caution, the researchers said.

“I think there are a lot of things that are unknown at the current stage about genes’ functions,” Wei said. “The CRISPR technology is far too dangerous to use right now for germline editing.”

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

CCR5-∆32 is deleterious in the homozygous state in humans by Xinzhu Wei & Rasmus Nielsen. Nature Medicine (2019) DOI: https://doi.org/10.1038/s41591-019-0459-6 Published 03 June 2019

This paper is behind a paywall.

For those who have an insatiable appetite for detail, there’s my November 28, 2018 posting which covers what happened when the CRISPR twins, Lulu and Nana, was first announced, along with a few updates to January 23, 2019. The May 17, 2019 posting covers the news of possible cognitive advantages for the CCR5-Δ32 gene-edited twins and explores some of the social implications.

Two approaches to memristors

Within one day of each other in October 2018, two different teams working on memristors with applications to neuroprosthetics and neuromorphic computing (brainlike computing) announced their results.

Russian team

An October 15, 2018 (?) Lobachevsky University press release (also published on October 15, 2018 on EurekAlert) describes a new approach to memristors,

Biological neurons are coupled unidirectionally through a special junction called a synapse. An electrical signal is transmitted along a neuron after some biochemical reactions initiate a chemical release to activate an adjacent neuron. These junctions are crucial for cognitive functions, such as perception, learning and memory.

A group of researchers from Lobachevsky University in Nizhny Novgorod investigates the dynamics of an individual memristive device when it receives a neuron-like signal as well as the dynamics of a network of analog electronic neurons connected by means of a memristive device. According to Svetlana Gerasimova, junior researcher at the Physics and Technology Research Institute and at the Neurotechnology Department of Lobachevsky University, this system simulates the interaction between synaptically coupled brain neurons while the memristive device imitates a neuron axon.

A memristive device is a physical model of Chua’s [Dr. Leon Chua, University of California at Berkeley; see my May 9, 2008 posting for a brief description Dr. Chua’s theory] memristor, which is an electric circuit element capable of changing its resistance depending on the electric signal received at the input. The device based on a Au/ZrO2(Y)/TiN/Ti structure demonstrates reproducible bipolar switching between the low and high resistance states. Resistive switching is determined by the oxidation and reduction of segments of conducting channels (filaments) in the oxide film when voltage with different polarity is applied to it. In the context of the present work, the ability of a memristive device to change conductivity under the action of pulsed signals makes it an almost ideal electronic analog of a synapse.

Lobachevsky University scientists and engineers supported by the Russian Science Foundation (project No.16-19-00144) have experimentally implemented and theoretically described the synaptic connection of neuron-like generators using the memristive interface and investigated the characteristics of this connection.

“Each neuron is implemented in the form of a pulse signal generator based on the FitzHugh-Nagumo model. This model provides a qualitative description of the main neurons’ characteristics: the presence of the excitation threshold, the presence of excitable and self-oscillatory regimes with the possibility of a changeover. At the initial time moment, the master generator is in the self-oscillatory mode, the slave generator is in the excitable mode, and the memristive device is used as a synapse. The signal from the master generator is conveyed to the input of the memristive device, the signal from the output of the memristive device is transmitted to the input of the slave generator via the loading resistance. When the memristive device switches from a high resistance to a low resistance state, the connection between the two neuron-like generators is established. The master generator goes into the oscillatory mode and the signals of the generators are synchronized. Different signal modulation mode synchronizations were demonstrated for the Au/ZrO2(Y)/TiN/Ti memristive device,” – says Svetlana Gerasimova.

UNN researchers believe that the next important stage in the development of neuromorphic systems based on memristive devices is to apply such systems in neuroprosthetics. Memristive systems will provide a highly efficient imitation of synaptic connection due to the stochastic nature of the memristive phenomenon and can be used to increase the flexibility of the connections for neuroprosthetic purposes. Lobachevsky University scientists have vast experience in the development of neurohybrid systems. In particular, a series of experiments was performed with the aim of connecting the FitzHugh-Nagumo oscillator with a biological object, a rat brain hippocampal slice. The signal from the electronic neuron generator was transmitted through the optic fiber communication channel to the bipolar electrode which stimulated Schaffer collaterals (axons of pyramidal neurons in the CA3 field) in the hippocampal slices. “We are going to combine our efforts in the design of artificial neuromorphic systems and our experience of working with living cells to improve flexibility of prosthetics,” concludes S. Gerasimova.

The results of this research were presented at the 38th International Conference on Nonlinear Dynamics (Dynamics Days Europe) at Loughborough University (Great Britain).

This diagram illustrates an aspect of the work,

Caption: Schematic of electronic neurons coupling via a memristive device. Credit: Lobachevsky University

US team

The American Institute of Physics (AIP) announced the publication of a ‘memristor paper’ by a team from the University of Southern California (USC) in an October 16, 2018 news item on phys.org,

Just like their biological counterparts, hardware that mimics the neural circuitry of the brain requires building blocks that can adjust how they synapse, with some connections strengthening at the expense of others. One such approach, called memristors, uses current resistance to store this information. New work looks to overcome reliability issues in these devices by scaling memristors to the atomic level.

An October 16, 2018 AIP news release (also on EurekAlert), which originated the news item, delves further into the particulars of this particular piece of memristor research,

A group of researchers demonstrated a new type of compound synapse that can achieve synaptic weight programming and conduct vector-matrix multiplication with significant advances over the current state of the art. Publishing its work in the Journal of Applied Physics, from AIP Publishing, the group’s compound synapse is constructed with atomically thin boron nitride memristors running in parallel to ensure efficiency and accuracy.

The article appears in a special topic section of the journal devoted to “New Physics and Materials for Neuromorphic Computation,” which highlights new developments in physical and materials science research that hold promise for developing the very large-scale, integrated “neuromorphic” systems of tomorrow that will carry computation beyond the limitations of current semiconductors today.

“There’s a lot of interest in using new types of materials for memristors,” said Ivan Sanchez Esqueda, an author on the paper. “What we’re showing is that filamentary devices can work well for neuromorphic computing applications, when constructed in new clever ways.”

Current memristor technology suffers from a wide variation in how signals are stored and read across devices, both for different types of memristors as well as different runs of the same memristor. To overcome this, the researchers ran several memristors in parallel. The combined output can achieve accuracies up to five times those of conventional devices, an advantage that compounds as devices become more complex.

The choice to go to the subnanometer level, Sanchez said, was born out of an interest to keep all of these parallel memristors energy-efficient. An array of the group’s memristors were found to be 10,000 times more energy-efficient than memristors currently available.

“It turns out if you start to increase the number of devices in parallel, you can see large benefits in accuracy while still conserving power,” Sanchez said. Sanchez said the team next looks to further showcase the potential of the compound synapses by demonstrating their use completing increasingly complex tasks, such as image and pattern recognition.

Here’s an image illustrating the parallel artificial synapses,

Caption: Hardware that mimics the neural circuitry of the brain requires building blocks that can adjust how they synapse. One such approach, called memristors, uses current resistance to store this information. New work looks to overcome reliability issues in these devices by scaling memristors to the atomic level. Researchers demonstrated a new type of compound synapse that can achieve synaptic weight programming and conduct vector-matrix multiplication with significant advances over the current state of the art. They discuss their work in this week’s Journal of Applied Physics. This image shows a conceptual schematic of the 3D implementation of compound synapses constructed with boron nitride oxide (BNOx) binary memristors, and the crossbar array with compound BNOx synapses for neuromorphic computing applications. Credit: Ivan Sanchez Esqueda

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

Efficient learning and crossbar operations with atomically-thin 2-D material compound synapses by Ivan Sanchez Esqueda, Huan Zhao and Han Wang. The article will appear in the Journal of Applied Physics Oct. 16, 2018 (DOI: 10.1063/1.5042468).

This paper is behind a paywall.

*Title corrected from ‘Two approaches to memristors featuring’ to ‘Two approaches to memristors’ on May 31, 2019 at 1455 hours PDT.

Unusual appetite for gold

This bacterium (bacteria being the plural) loves gold, which is lucky for anyone trying to develop artificial photosynthesis.From an October 9, 2018 news item on ScienceDaily,

A bacterium named Moorella thermoacetica won’t work for free. But UC Berkeley [University of California at Berkeley] researchers have figured out it has an appetite for gold. And in exchange for this special treat, the bacterium has revealed a more efficient path to producing solar fuels through artificial photosynthesis.

An October 5, 2018 UC Berkeley news release by Theresa Duque (also on EurekAlert but published on October 9, 2018), which originated the news item, expands on the theme,

M. thermoacetica first made its debut as the first non-photosensitive bacterium to carry out artificial photosynthesis (link is external) in a study led by Peidong Yang, a professor in UC Berkeley’s College of Chemistry. By attaching light-absorbing nanoparticles made of cadmium sulfide (CdS) to the bacterial membrane exterior, the researchers turned M. thermoacetica into a tiny photosynthesis machine, converting sunlight and carbon dioxide into useful chemicals.

Now Yang and his team of researchers have found a better way to entice this CO2-hungry bacterium into being even more productive. By placing light-absorbing gold nanoclusters inside the bacterium, they have created a biohybrid system that produces a higher yield of chemical products than previously demonstrated. The research, funded by the National Institutes of Health, was published on Oct. 1 in Nature Nanotechnology (link is external).

For the first hybrid model, M. thermoacetica-CdS, the researchers chose cadmium sulfide as the semiconductor for its ability to absorb visible light. But because cadmium sulfide is toxic to bacteria, the nanoparticles had to be attached to the cell membrane “extracellularly,” or outside the M. thermoacetica-CdS system. Sunlight excites each cadmium-sulfide nanoparticle into generating a charged particle known as an electron. As these light-generated electrons travel through the bacterium, they interact with multiple enzymes in a process known as “CO2 reduction,” triggering a cascade of reactions that eventually turns CO2 into acetate, a valuable chemical for making solar fuels.

But within the extracellular model, the electrons end up interacting with other chemicals that have no part in turning CO2 into acetate. And as a result, some electrons are lost and never reach the enzymes. So to improve what’s known as “quantum efficiency,” or the bacterium’s ability to produce acetate each time it gains an electron, the researchers found another semiconductor: nanoclusters made of 22 gold atoms (Au22), a material that M. thermoacetica took a surprising shine to.

A single nanocluster of 22 gold atoms

Figure: A single nanocluster of 22 gold atoms – Au22 – is only 1 nanometer in diameter, allowing it to easily slip through the bacterial cell wall.

“We selected Au22 because it’s ideal for absorbing visible light and has the potential for driving the CO2 reduction process, but we weren’t sure whether it would be compatible with the bacteria,” Yang said. “When we inspected them under the microscope, we discovered that the bacteria were loaded with these Au22 clusters – and were still happily alive.”

Imaging of the M. thermoacetica-Au22 system was done at UC Berkeley’s Molecular Imaging Center (link is external).

The researchers also selected Au22 ­– dubbed by the researchers as “magic” gold nanoclusters – for its ultrasmall size: A single Au22nanocluster is only 1 nanometer in diameter, allowing each nanocluster to easily slip through the bacterial cell wall.

“By feeding bacteria with Au22 nanoclusters, we’ve effectively streamlined the electron transfer process for the CO2 reduction pathway inside the bacteria, as evidenced by a 2.86 percent quantum efficiency – or 33 percent more acetate produced within the M. thermoacetica-Au22 system than the CdS model,” Yang said.

The magic gold nanocluster is the latest discovery coming out of Yang’s lab, which for the past six years has focused on using biohybrid nanostructures to convert CO2 into useful chemicals as part of an ongoing effort to find affordable, abundant resources for renewable fuels, and potential solutions to thwart the effects of climate change.

“Next, we’d like to find a way to reduce costs, improve the lifetimes for these biohybrid systems, and improve quantum efficiency,” Yang said. “By continuing to look at the fundamental aspect of how gold nanoclusters are being photoactivated, and by following the electron transfer process within the CO2 reduction pathway, we hope to find even better solutions.”

Co-authors with Yang are UC Berkeley graduate student Hao Zhang and former postdoctoral fellow Hao Liu, now at Donghua University in Shanghai, China.

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

Bacteria photosensitized by intracellular gold nanoclusters for solar fuel production by Hao Zhang, Hao Liu, Zhiquan Tian, Dylan Lu, Yi Yu, Stefano Cestellos-Blanco, Kelsey K. Sakimoto, & Peidong Yang. Nature Nanotechnologyvolume 13, pages900–905 (2018). DOI: https://doi.org/10.1038/s41565-018-0267-z Published: 01 October 2018

This paper is behind a paywall.

For lovers of animation, the folks at UC Berkeley have produced this piece about the ‘gold-loving’ bacterium,

Frugal science: ancient toys for state-of-the-art science

A toy that’s been a plaything for 5,000 years and known as a whirligig (in English, anyway) has inspired a scientific tool for use by field biologists and students interested in creating state-of-the-art experiments. Exciting stuff, eh?

A May 23, 2019 Georgia Tech (Georgia Institute of Technology) news release (also on EurekAlert but published on May 22, 2019) announces this development in ‘frugal science’,

A 5,000-year-old toy still enjoyed by kids today has inspired an inexpensive, hand-powered scientific tool that could not only impact how field biologists conduct their research but also allow high-school students and others with limited resources to realize their own state-of-the-art experiments.

The device, a portable centrifuge for preparing scientific samples including DNA, is reported May 21 [2019] in the journal PLOS Biology. The co-first author of the paper is Gaurav Byagathvalli, a senior at Lambert High School in Georgia. His colleagues are M. Saad Bhamla, an assistant professor at the Georgia Institute of Technology; Soham Sinha, a Georgia Tech undergraduate; Janet Standeven, Byagathvalli’s biology teacher at Lambert; and Aaron F. Pomerantz, a graduate student at the University of California, Berkeley.

“I am exceptionally proud of this paper and will remember it 10, 20, 30 years from now because of the uniquely diverse team we put together,” said Bhamla, who is an assistant professor in Georgia Tech’s School of Chemical and Biomolecular Engineering.

From a Rainforest to a High School

Together the team demonstrated the device, dubbed the 3D-Fuge because it is created through 3D printing, in two separate applications. In a rainforest in Peru the 3D-Fuge was an integral part of a “lab in a backpack” used to identify four previously-unknown plants and insects by sequencing their DNA [deoxyribonucleic acid]. Back in the United States, a slightly different design enabled a new approach to creating living bacterial sensors for the potential detection of disease. That work was conducted at Lambert High School for a synthetic biology competition.

Thanks to social media and a preprint of the PLOS Biology paper on BioRxiv, the 3D-Fuge has already generated interest from around the world, including emails from high-school teachers in Zambia and Kenya. “It’s awesome to see research not just remain isolated to one location but see it spread,” said Byagathvalli. “Through this, we’ve realized how much of an impact simple yet effective tools can have, and hope this technology motivates others to continue along the same path and innovate new solutions to global issues.”

To better share the work, the team has posted the 3D-Fuge designs, videos, and photos online available to anyone.

Frugal Science

One focus of Bhamla’s lab at Georgia Tech is the development of tools for frugal science, or real research that just about anyone can afford. The tools behind state-of-the-art science often cost thousands of dollars that make them inaccessible to those without serious resources.

Centrifuges are a good example.  A small benchtop unit costs between $3,000 and $5,000; larger units cost many times that. Yet the devices are necessary to produce concentrated amounts of, say, genomic materials like DNA. By rapidly spinning samples, they separate materials of interest from biological debris.

The Bhamla team found that the 3D-Fuge works as well as its more expensive cousins, but costs less than $1.

An Ancient Toy

The 3D-Fuge is based on earlier work by Bhamla and colleagues at Stanford University on a simple centrifuge made of paper. The “paperfuge,” in turn, was inspired by a toy composed of string and a button that Bhamla played with as a child. He later discovered that these toys, known as whirligigs, have existed for some 5,000 years.

They consist of a disk – like a button – with two holes, through which is threaded a length of flexible cord whose ends are knotted to create a single loop with the disk in the middle. That simple contraption is then swung with two hands until the button is spinning and whirring at very fast speeds.

The earlier paperfuge uses a disk of paper. To that disk Bhamla glued small plastic tubes filled with a sample. He and colleagues reported that the device did indeed create high-quality samples.

In late 2017 Bhamla was separately approached by the Lambert High team and Pomerantz to see if the paperfuge could be adapted for the larger samples they needed (the paperfuge is limited to small samples of ~1 microliter—or one drop of blood).

Together they came up with the 3D-Fuge, which includes cavities for tubes that can hold some 100 times more of a sample than the paperfuge. The team developed two equally effective designs: one for field biology (led by Pomerantz) and the other for the high-school’s synthetic biology project (led by Byagathvalli).

Bhamla notes that the 3D-Fuge has some limitations. For example, it can only process a few samples at a time (some applications require thousands of samples). Further, because it’s 10 times heavier than the paperfuge, it can’t reach the same speeds or produce the same forces of that device. That said, it still weighs only 20 grams, slightly less than a AA battery.

“But it works,” said Bhamla. “All you need is an [appropriate] application and some creativity.”

Here are a couple of images showing the 3D-Fuge in action,

Using the 3D-Fuge Courtesy: Georgia Tech
Sample vial in 3D-Fuge Courtesy: Georgia Tech

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

A 3D-printed hand-powered centrifuge for molecular biology by Gaurav Byagathvalli, Aaron Pomerantz, Soham Sinha, Janet Standeven, M. Saad Bhamla. PLOS Biology DOI: https://doi.org/10.1371/journal.pbio.3000251 Published: May 21, 2019

As always with a Public Library of Science (PLOS) publication, this paper is open access.

The wonder of movement in 3D

Shades of Eadweard Muybridge (English photographer who pioneered photographic motion studies)! A September 19, 2018 news item on ScienceDaily describes the latest efforts to ‘capture motion’,

Patriots quarterback Tom Brady has often credited his success to spending countless hours studying his opponent’s movements on film. This understanding of movement is necessary for all living species, whether it’s figuring out what angle to throw a ball at, or perceiving the motion of predators and prey. But simple videos can’t actually give us the full picture.

That’s because traditional videos and photos for studying motion are two-dimensional, and don’t show us the underlying 3-D structure of the person or subject of interest. Without the full geometry, we can’t inspect the small and subtle movements that help us move faster, or make sense of the precision needed to perfect our athletic form.

Recently, though, researchers from MIT’s [Massachusetts Institute of Technology] Computer Science and Artificial Intelligence Laboratory (CSAIL) have come up with a way to get a better handle on this understanding of complex motion.

There isn’t a single reference to Muybridge, still, this September 18, 2018 Massachusetts Institute of Technology news release (also on EurekAlert but published September 19, 2018), which originated the news item, delves further into the research,

The new system uses an algorithm that can take 2-D videos and turn them into 3-D printed “motion sculptures” that show how a human body moves through space. In addition to being an intriguing aesthetic visualization of shape and time, the team envisions that their “MoSculp” system could enable a much more detailed study of motion for professional athletes, dancers, or anyone who wants to improve their physical skills.

“Imagine you have a video of Roger Federer serving a ball in a tennis match, and a video of yourself learning tennis,” says PhD student Xiuming Zhang, lead author of a new paper about the system. “You could then build motion sculptures of both scenarios to compare them and more comprehensively study where you need to improve.”

Because motion sculptures are 3-D, users can use a computer interface to navigate around the structures and see them from different viewpoints, revealing motion-related information inaccessible from the original viewpoint.

Zhang wrote the paper alongside MIT professors William Freeman and Stefanie Mueller, PhD student Jiajun Wu, Google researchers Qiurui He and Tali Dekel, as well as U.C. Berkeley postdoc and former CSAIL PhD Andrew Owens.

How it works

Artists and scientists have long struggled to gain better insight into movement, limited by their own camera lens and what it could provide.

Previous work has mostly used so-called “stroboscopic” photography techniques, which look a lot like the images in a flip book stitched together. But since these photos only show snapshots of movement, you wouldn’t be able to see as much of the trajectory of a person’s arm when they’re hitting a golf ball, for example.

What’s more, these photographs also require laborious pre-shoot setup, such as using a clean background and specialized depth cameras and lighting equipment. All MoSculp needs is a video sequence.

Given an input video, the system first automatically detects 2-D key points on the subject’s body, such as the hip, knee, and ankle of a ballerina while she’s doing a complex dance sequence. Then, it takes the best possible poses from those points to be turned into 3-D “skeletons.”

After stitching these skeletons together, the system generates a motion sculpture that can be 3-D printed, showing the smooth, continuous path of movement traced out by the subject. Users can customize their figures to focus on different body parts, assign different materials to distinguish among parts, and even customize lighting.

In user studies, the researchers found that over 75 percent of subjects felt that MoSculp provided a more detailed visualization for studying motion than the standard photography techniques.

“Dance and highly-skilled athletic motions often seem like ‘moving sculptures’ but they only create fleeting and ephemeral shapes,” says Courtney Brigham, communications lead at Adobe. “This work shows how to take motions and turn them into real sculptures with objective visualizations of movement, providing a way for athletes to analyze their movements for training, requiring no more equipment than a mobile camera and some computing time.”

The system works best for larger movements, like throwing a ball or taking a sweeping leap during a dance sequence. It also works for situations that might obstruct or complicate movement, such as people wearing loose clothing or carrying objects.

Currently, the system only uses single-person scenarios, but the team soon hopes to expand to multiple people. This could open up the potential to study things like social disorders, interpersonal interactions, and team dynamics.

This work will be presented at the User Interface Software and Technology (UIST) symposium in Berlin, Germany in October 2018 and the team’s paper published as part of the proceedings.

As for anyone wondering about the Muybridge comment, here’s an image the MIT researchers have made available,

A new system uses an algorithm that can take 2-D videos and turn them into 3-D-printed “motion sculptures” that show how a human body moves through space. Image courtesy of MIT CSAIL

Contrast that MIT image with some of the images in this video capturing parts of a theatre production, Studies in Motion: The Hauntings of Eadweard Muybridge,

Getting back to MIT, here’s their MoSculp video,

There are some startling similarities, eh? I suppose there are only so many ways one can capture movement be it in studies of Eadweard Muybridge, a theatre production about his work, or an MIT video the latest in motion capture technology.