Tag Archives: Rice University

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).

Shining a light on flurocarbon bonds and robotic ‘soft’ matter research

Both of these news bits are concerned with light for one reason or another.

Rice University (Texas, US) and breaking fluorocarbon bonds

The secret to breaking fluorocarbon bonds is light according to a June 22, 2020 news item on Nanowerk,

Rice University engineers have created a light-powered catalyst that can break the strong chemical bonds in fluorocarbons, a group of synthetic materials that includes persistent environmental pollutants.

A June 22, 2020 Rice University news release (also on EurekAlert), which originated the news item, describes the work in greater detail,

In a study published this month in Nature Catalysis, Rice nanophotonics pioneer Naomi Halas and collaborators at the University of California, Santa Barbara (UCSB) and Princeton University showed that tiny spheres of aluminum dotted with specks of palladium could break carbon-fluorine (C-F) bonds via a catalytic process known as hydrodefluorination in which a fluorine atom is replaced by an atom of hydrogen.

The strength and stability of C-F bonds are behind some of the 20th century’s most recognizable chemical brands, including Teflon, Freon and Scotchgard. But the strength of those bonds can be problematic when fluorocarbons get into the air, soil and water. Chlorofluorocarbons, or CFCs, for example, were banned by international treaty in the 1980s after they were found to be destroying Earth’s protective ozone layer, and other fluorocarbons were on the list of “forever chemicals” targeted by a 2001 treaty.

“The hardest part about remediating any of the fluorine-containing compounds is breaking the C-F bond; it requires a lot of energy,” said Halas, an engineer and chemist whose Laboratory for Nanophotonics (LANP) specializes in creating and studying nanoparticles that interact with light.

Over the past five years, Halas and colleagues have pioneered methods for making “antenna-reactor” catalysts that spur or speed up chemical reactions. While catalysts are widely used in industry, they are typically used in energy-intensive processes that require high temperature, high pressure or both. For example, a mesh of catalytic material is inserted into a high-pressure vessel at a chemical plant, and natural gas or another fossil fuel is burned to heat the gas or liquid that’s flowed through the mesh. LANP’s antenna-reactors dramatically improve energy efficiency by capturing light energy and inserting it directly at the point of the catalytic reaction.

In the Nature Catalysis study, the energy-capturing antenna is an aluminum particle smaller than a living cell, and the reactors are islands of palladium scattered across the aluminum surface. The energy-saving feature of antenna-reactor catalysts is perhaps best illustrated by another of Halas’ previous successes: solar steam. In 2012, her team showed its energy-harvesting particles could instantly vaporize water molecules near their surface, meaning Halas and colleagues could make steam without boiling water. To drive home the point, they showed they could make steam from ice-cold water.

The antenna-reactor catalyst design allows Halas’ team to mix and match metals that are best suited for capturing light and catalyzing reactions in a particular context. The work is part of the green chemistry movement toward cleaner, more efficient chemical processes, and LANP has previously demonstrated catalysts for producing ethylene and syngas and for splitting ammonia to produce hydrogen fuel.

Study lead author Hossein Robatjazi, a Beckman Postdoctoral Fellow at UCSB who earned his Ph.D. from Rice in 2019, conducted the bulk of the research during his graduate studies in Halas’ lab. He said the project also shows the importance of interdisciplinary collaboration.

“I finished the experiments last year, but our experimental results had some interesting features, changes to the reaction kinetics under illumination, that raised an important but interesting question: What role does light play to promote the C-F breaking chemistry?” he said.

The answers came after Robatjazi arrived for his postdoctoral experience at UCSB. He was tasked with developing a microkinetics model, and a combination of insights from the model and from theoretical calculations performed by collaborators at Princeton helped explain the puzzling results.

“With this model, we used the perspective from surface science in traditional catalysis to uniquely link the experimental results to changes to the reaction pathway and reactivity under the light,” he said.

The demonstration experiments on fluoromethane could be just the beginning for the C-F breaking catalyst.

“This general reaction may be useful for remediating many other types of fluorinated molecules,” Halas said.

Caption: An artist’s illustration of the light-activated antenna-reactor catalyst Rice University engineers designed to break carbon-fluorine bonds in fluorocarbons. The aluminum portion of the particle (white and pink) captures energy from light (green), activating islands of palladium catalysts (red). In the inset, fluoromethane molecules (top) comprised of one carbon atom (black), three hydrogen atoms (grey) and one fluorine atom (light blue) react with deuterium (yellow) molecules near the palladium surface (black), cleaving the carbon-fluorine bond to produce deuterium fluoride (right) and monodeuterated methane (bottom). Credit: H. Robatjazi/Rice University

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

Plasmon-driven carbon–fluorine (C(sp3)–F) bond activation with mechanistic insights into hot-carrier-mediated pathways by Hossein Robatjazi, Junwei Lucas Bao, Ming Zhang, Linan Zhou, Phillip Christopher, Emily A. Carter, Peter Nordlander & Naomi J. Halas. Nature Catalysis (2020) DOI: https://doi.org/10.1038/s41929-020-0466-5 Published: 08 June 2020

This paper is behind a paywall.

Northwestern University (Illinois, US) brings soft robots to ‘life’

This June 22, 2020 news item on ScienceDaily reveals how scientists are getting soft robots to mimic living creatures,

Northwestern University researchers have developed a family of soft materials that imitates living creatures.

When hit with light, the film-thin materials come alive — bending, rotating and even crawling on surfaces.

A June 22, 2020 Northwestern University news release (also on EurekAlert) by Amanda Morris, which originated the news item, delves further into the details,

Called “robotic soft matter by the Northwestern team,” the materials move without complex hardware, hydraulics or electricity. The researchers believe the lifelike materials could carry out many tasks, with potential applications in energy, environmental remediation and advanced medicine.

“We live in an era in which increasingly smarter devices are constantly being developed to help us manage our everyday lives,” said Northwestern’s Samuel I. Stupp, who led the experimental studies. “The next frontier is in the development of new science that will bring inert materials to life for our benefit — by designing them to acquire capabilities of living creatures.”

The research will be published on June 22 [2020] in the journal Nature Materials.

Stupp is the Board of Trustees Professor of Materials Science and Engineering, Chemistry, Medicine and Biomedical Engineering at Northwestern and director of the Simpson Querrey Institute He has appointments in the McCormick School of Engineering, Weinberg College of Arts and Sciences and Feinberg School of Medicine. George Schatz, the Charles E. and Emma H. Morrison Professor of Chemistry in Weinberg, led computer simulations of the materials’ lifelike behaviors. Postdoctoral fellow Chuang Li and graduate student Aysenur Iscen, from the Stupp and Schatz laboratories, respectively, are co-first authors of the paper.

Although the moving material seems miraculous, sophisticated science is at play. Its structure comprises nanoscale peptide assemblies that drain water molecules out of the material. An expert in materials chemistry, Stupp linked the peptide arrays to polymer networks designed to be chemically responsive to blue light.

When light hits the material, the network chemically shifts from hydrophilic (attracts water) to hydrophobic (resists water). As the material expels the water through its peptide “pipes,” it contracts — and comes to life. When the light is turned off, water re-enters the material, which expands as it reverts to a hydrophilic structure.

This is reminiscent of the reversible contraction of muscles, which inspired Stupp and his team to design the new materials.

“From biological systems, we learned that the magic of muscles is based on the connection between assemblies of small proteins and giant protein polymers that expand and contract,” Stupp said. “Muscles do this using a chemical fuel rather than light to generate mechanical energy.”

For Northwestern’s bio-inspired material, localized light can trigger directional motion. In other words, bending can occur in different directions, depending on where the light is located. And changing the direction of the light also can force the object to turn as it crawls on a surface.

Stupp and his team believe there are endless possible applications for this new family of materials. With the ability to be designed in different shapes, the materials could play a role in a variety of tasks, ranging from environmental clean-up to brain surgery.

“These materials could augment the function of soft robots needed to pick up fragile objects and then release them in a precise location,” he said. “In medicine, for example, soft materials with ‘living’ characteristics could bend or change shape to retrieve blood clots in the brain after a stroke. They also could swim to clean water supplies and sea water or even undertake healing tasks to repair defects in batteries, membranes and chemical reactors.”

Fascinating, eh? No batteries, no power source, just light to power movement. For the curious, here’s a link to and a citation for the paper,

Supramolecular–covalent hybrid polymers for light-activated mechanical actuation by Chuang Li, Aysenur Iscen, Hiroaki Sai, Kohei Sato, Nicholas A. Sather, Stacey M. Chin, Zaida Álvarez, Liam C. Palmer, George C. Schatz & Samuel I. Stupp. Nature Materials (2020) DOI: https://doi.org/10.1038/s41563-020-0707-7 Published: 22 June 2020

This paper is behind a paywall.

Double-walled carbon nanotubes have superior electrical properties?

A March 27, 2020 news item on Nanowerk suggests that double-walled carbon nanotubes (DWCNTs) may offer some advantages over single-walled carbon nanotubes (SWCNTs), NOTE: A link has been removed,

One nanotube could be great for electronics applications, but there’s new evidence that two could be tops.

Rice University engineers already knew that size matters when using single-walled carbon nanotubes for their electrical properties. But until now, nobody had studied how electrons act when confronted with the Russian doll-like structure of multiwalled tubes.

There’s a diagram representing the work,

Caption: Rice University theorists have calculated flexoelectric effects in double-walled carbon nanotubes. The electrical potential (P) of atoms on either side of a graphene sheet (top) are identical, but not when the sheet is curved into a nanotube. Double-walled nanotubes (bottom) show unique effects as band gaps in inner and outer tubes are staggered. Credit: Yakobson Research Group/Rice University

A March 27, 2020 Rice University news release (also on EurekAlert), which originated the news item, delves further (NOTE: Links have been removed),

The Rice lab of materials theorist Boris Yakobson has now calculated the impact of curvature of semiconducting double-wall carbon nanotubes on their flexoelectric voltage, a measure of electrical imbalance between the nanotube’s inner and outer walls.

This affects how suitable nested nanotube pairs may be for nanoelectronics applications, especially photovoltaics.

The theoretical research by Yakobson’s Brown School of Engineering group appears in the American Chemical Society journal Nano Letters.

In an 2002 study, Yakobson and his Rice colleagues had revealed how charge transfer, the difference between positive and negative poles that allows voltage to exist between one and the other, scales linearly to the curvature of the nanotube wall. The width of the tube dictates curvature, and the lab found that the thinner the nanotube (and thus larger the curvature), the greater the potential voltage.

When carbon atoms form flat graphene, the charge density of the atoms on either side of the plane are identical, Yakobson said. Curving the graphene sheet into a tube breaks that symmetry, changing the balance.

That creates a flexoelectric local dipole in the direction of, and proportional to, the curvature, according to the researchers, who noted that the flexoelectricity of 2D carbon “is a remarkable but also fairly subtle effect.”

But more than one wall greatly complicates the balance, altering the distribution of electrons. In double-walled nanotubes, the curvature of the inner and outer tubes differ, giving each a distinct band gap. Additionally, the models showed the flexoelectric voltage of the outer wall shifts the band gap of the inner wall, creating a staggered band alignment in the nested system.

“The novelty is that the inserted tube, the ‘baby’ (inside) matryoshka has all of its quantum energy levels shifted because of the voltage created by exterior nanotube,” Yakobson said. The interplay of different curvatures, he said, causes a straddling-to-staggered band gap transition that takes place at an estimated critical diameter of about 2.4 nanometers.

“This is a huge advantage for solar cells, essentially a prerequisite for separating positive and negative charges to create a current,” Yakobson said. “When light is absorbed, an electron always jumps from the top of an occupied valence band (leaving a ‘plus’ hole behind) to the lowest state of empty conductance band.

“But in a staggered configuration they happen to be in different tubes, or layers,” he said. “The ‘plus’ and ‘minus’ get separated between the tubes and can flow away by generating current in a circuit.”

The team’s calculations also showed that modifying the nanotubes’ surfaces with either positive or negative atoms could create “substantial voltages of either sign” up to three volts. “Although functionalization could strongly perturb the electronic properties of nanotubes, it may be a very powerful way of inducing voltage for certain applications,” the researchers wrote.

The team suggested its findings may apply to other types of nanotubes, including boron nitride and molybdenum disulfide, on their own or as hybrids with carbon nanotubes.

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

Flexoelectricity and charge separation in carbon nanotubes by Vasilii I. Artyukhov, Sunny Gupta, Alex Kutana, Boris I. Yakobson. Nano Lett. 2020, XXXX, XXX, XXX-XXX DOI: https://doi.org/10.1021/acs.nanolett.9b05345 [Online] Publication Date:March 10, 2020 Copyright © 2020 American Chemical Society

This paper is behind a paywall.

In the future your clothing may be a health monitor

It’s not ready for the COVID-19 pandemic but if I understand it properly, wearing this clothing will be a little like wearing a thermometer and that could be very useful. A March 4, 2020 news item on Nanowerk announces the research (Note: A link has been removed),

Researchers have reported a new material, pliable enough to be woven into fabric but imbued with sensing capabilities that can serve as an early warning system for injury or illness.

The material, described in a paper published by ACS Applied Nano Materials (“Poly(octadecyl acrylate)-Grafted Multiwalled Carbon Nanotube Composites for Wearable Temperature Sensors”), involves the use of carbon nanotubes and is capable of sensing slight changes in body temperature while maintaining a pliable disordered structure – as opposed to a rigid crystalline structure – making it a good candidate for reusable or disposable wearable human body temperature sensors. Changes in body heat change the electrical resistance, alerting someone monitoring that change to the potential need for intervention.

I think this is an artistic rendering of the research,

Caption: Researchers have reported a new material, pliable enough to be woven into fabric but imbued with sensing capabilities that could serve as an early warning system for injury or illness. Credit: University of Houston

A March 4, 2020 University of Houston (Texas, US) news release (also on EurekAlert) by Jeannie Kever, which originated the news item, describes the work in more detail,

“Your body can tell you something is wrong before it becomes obvious,” said Seamus Curran, a physics professor at the University of Houston and co-author on the paper. Possible applications range from detecting dehydration in an ultra-marathoner to the beginnings of a pressure sore in a nursing home patient.

The researchers said it is also cost-effective because the raw materials required are used in relatively low concentrations.

The discovery builds on work Curran and fellow researchers Kang-Shyang Liao and Alexander J. Wang began nearly a decade ago, when they developed a hydrophobic nanocoating for cloth, which they envisioned as a protective coating for clothing, carpeting and other fiber-based materials.

Wang is now a Ph.D. student at Technological University Dublin, currently working with Curran at UH, and is corresponding author for the paper. In addition to Curran and Liao, other researchers involved include Surendra Maharjan, Brian P. McElhenny, Ram Neupane, Zhuan Zhu, Shuo Chen, Oomman K. Varghese and Jiming Bao, all of UH; Kourtney D. Wright and Andrew R. Barron of Rice University, and Eoghan P. Dillon of Analysis Instruments in Santa Barbara.

The material, created using poly(octadecyl acrylate)-grafted multiwalled carbon nanotubes, is technically known as a nanocarbon-based disordered, conductive, polymeric nanocomposite, or DCPN, a class of materials increasingly used in materials science. But most DCPN materials are poor electroconductors, making them unsuitable for use in wearable technologies that require the material to detect slight changes in temperature.

The new material was produced using a technique called RAFT-polymerization, Wang said, a critical step that allows the attached polymer to be electronically and phononically coupled with the multiwalled carbon nanotube through covalent bonding. As such, subtle structural arrangements associated with the glass transition temperature of the system are electronically amplified to produce the exceptionally large electronic responses reported in the paper, without the negatives associated with solid-liquid phase transitions. The subtle structural changes associated with glass transition processes are ordinarily too small to produce large enough electronic responses.

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

Poly(octadecyl acrylate)-Grafted Multiwalled Carbon Nanotube Composites for Wearable Temperature Sensors by Alexander J. Wang, Surendra Maharjan, Kang-Shyang Liao, Brian P. McElhenny, Kourtney D. Wright, Eoghan P. Dillon, Ram Neupane, Zhuan Zhu, Shuo Chen, Andrew R. Barron, Oomman K. Varghese, Jiming Bao, Seamus A. Curran. ACS Appl. Nano Mater. 2020, XXXX, XXX, XXX-XXX DOI: https://doi.org/10.1021/acsanm.9b02396 (Online) Publication Date:January 28, 2020 Copyright © 2020 American Chemical Society

This paper is behind a paywall.

Graphene fatigue

Graphene fatigue operates under the same principle as metal fatigue. Subject graphene to stress over and over and at some point it (just like metal) will fail. Scientists at the University of Toronto (Ontatrio, Canada) and Rice University (Texas, US) have determined just how much stress graphene can withstand before breaking according to a January 28, 2020 University of Toronto news release by Tyler Irving (also on EurekAlert but published on January 29, 2020),

Graphene is a paradox. It is the thinnest material known to science, yet also one of the strongest. Now, research from University of Toronto Engineering shows that graphene is also highly resistant to fatigue — able to withstand more than a billion cycles of high stress before it breaks.

Graphene resembles a sheet of interlocking hexagonal rings, similar to the pattern you might see in bathroom flooring tiles. At each corner is a single carbon atom bonded to its three nearest neighbours. While the sheet could extend laterally over any area, it is only one atom thick.

The intrinsic strength of graphene has been measured at more than 100 gigapascals, among the highest values recorded for any material. But materials don’t always fail because the load exceeds their maximum strength. Stresses that are small but repetitive can weaken materials by causing microscopic dislocations and fractures that slowly accumulate over time, a process known as fatigue.

“To understand fatigue, imagine bending a metal spoon,” says Professor Tobin Filleter, one of the senior authors of the study, which was recently published in Nature Materials. “The first time you bend it, it just deforms. But if you keep working it back and forth, eventually it’s going to break in two.”

The research team — consisting of Filleter, fellow University of Toronto Engineering professors Chandra Veer Singh and Yu Sun, their students, and collaborators at Rice University — wanted to know how graphene would stand up to repeated stresses. Their approach included both physical experiments and computer simulations.

“In our atomistic simulations, we found that cyclic loading can lead to irreversible bond reconfigurations in the graphene lattice, causing catastrophic failure on subsequent loading,” says Singh, who along with postdoctoral fellow Sankha Mukherjee led the modelling portion of the study. “This is unusual behaviour in that while the bonds change, there are no obvious cracks or dislocations, which would usually form in metals, until the moment of failure.”

PhD candidate Teng Cui, who is co-supervised by Filleter and Sun, used the Toronto Nanofabrication Centre to build a physical device for the experiments. The design consisted of a silicon chip etched with half a million tiny holes only a few micrometres in diameter. The graphene sheet was stretched over these holes, like the head of a tiny drum.

Using an atomic force microscope, Cui then lowered a diamond-tipped probe into the hole to push on the graphene sheet, applying anywhere from 20 to 85 per cent of the force that he knew would break the material.

“We ran the cycles at a rate of 100,000 times per second,” says Cui. “Even at 70 per cent of the maximum stress, the graphene didn’t break for more than three hours, which works out to over a billion cycles. At lower stress levels, some of our trials ran for more than 17 hours.”

As with the simulations, the graphene didn’t accumulate cracks or other tell-tale signs of stress — it either broke or it didn’t.

“Unlike metals, there is no progressive damage during fatigue loading of graphene,” says Sun. “Its failure is global and catastrophic, confirming simulation results.”

The team also tested a related material, graphene oxide, which has small groups of atoms such as oxygen and hydrogen bonded to both the top and bottom of the sheet. Its fatigue behaviour was more like traditional materials, in that the failure was more progressive and localized. This suggests that the simple, regular structure of graphene is a major contributor to its unique properties.

“There are no other materials that have been studied under fatigue conditions that behave the way graphene does,” says Filleter. “We’re still working on some new theories to try and understand this.”

In terms of commercial applications, Filleter says that graphene-containing composites — mixtures of conventional plastic and graphene — are already being produced and used in sports equipment such as tennis rackets and skis.

In the future, such materials may begin to be used in cars or in aircraft, where the emphasis on light and strong materials is driven by the need to reduce weight, improve fuel efficiency and enhance environmental performance.

“There have been some studies to suggest that graphene-containing composites offer improved resistance to fatigue, but until now, nobody had measured the fatigue behaviour of the underlying material,” he says. “Our goal in doing this was to get at that fundamental understanding so that in the future, we’ll be able to design composites that work even better.”

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

Fatigue of graphene by Teng Cui, Sankha Mukherjee, Parambath M. Sudeep, Guillaume Colas, Farzin Najafi, Jason Tam, Pulickel M. Ajayan, Chandra Veer Singh, Yu Sun & Tobin Filleter. Nature Materials (2020) DOI: DOIhttps://doi.org/10.1038/s41563-019-0586-y Published: 20 January 2020

This paper is behind a paywall.

Safe nanomaterial handling on a tiny budget

A June 3, 2019 news item on Nanowerk describes an inexpensive way to safely handle carbon nanotubes (CNTs), Note: A link has been removed,

With a little practice, it doesn’t take much more than 10 minutes, a couple of bags and a big bucket to keep nanomaterials in their place.

The Rice University lab of chemist Andrew Barron works with bulk carbon nanotubes on a variety of projects. Years ago, members of the lab became concerned that nanotubes could escape into the air, and developed a cheap and clean method to keep them contained as they were transferred from large containers into jars for experimental use.

More recently Barron himself became concerned that too few labs around the world were employing best practices to handle nanomaterials. He decided to share what his Rice team had learned.

“There was a series of studies that said if you’re going to handle nanotubes, you really need to use safety protocols,” Barron said. “Then I saw a study that said many labs didn’t use any form of hood or containment system. In the U.S., it was really bad, and in Asia it was even worse. But there are a significant number of labs scaling up to use these materials at the kilogram scale without taking the proper precautions.”

The lab’s inexpensive method is detailed in an open-access paper in the Springer Nature journal SN Applied Sciences (“The safe handling of bulk low-density nanomaterials”).

Here’s a bag and a bucket,

Caption: A plastic bucket and a plastic bag contain a 5-gallon supply of carbon nanotubes in a lab at Rice University, the beginning of the process to safely transfer the nanotubes for experimental use. The Rice lab published its technique in SN Applied Sciences. Credit: Barron Research Group/Rice University

A June 3, 2019 Rice University news release (also on EurekAlert and received separately by email), which originated the news item, provides more detail,

In bulk form, carbon nanotubes are fluffy and disperse easily if disturbed. The Rice lab typically stores the tubes in 5-gallon plastic buckets, and simply opening the lid is enough to send them flying because of their low density.

Varun Shenoy Gangoli, a research scientist in Barron’s lab, and Pavan Raja, a scientist with Rice’s Nanotechnology-Enabled Water Treatment center, developed for their own use a method that involves protecting the worker and sequestering loose tubes when removing smaller amounts of the material for use in experiments.

Full details are available in the paper, but the precautions include making sure workers are properly attired with long pants, long sleeves, lab coats, full goggles and face masks, along with two pairs of gloves duct-taped to the lab coat sleeves. The improvised glove bag involves a 25-gallon trash bin with a plastic bag taped to the rim. The unopened storage container is placed inside, and then the bin is covered with another transparent trash bag, with small holes cut in the top for access.

After transferring the nanotubes, acetone wipes are used to clean the gloves and more acetone is sprayed inside the barrel so settling nanotubes would stick to the surfaces. These can be recovered and returned to the storage container.

Barron said it took lab members time to learn to use the protocol efficiently, “but now they can get their samples in 5 to 10 minutes.” He’s sure other labs can and will enhance the technique for their own circumstances. He noted a poster presented at the Ninth Guadalupe Workshop on the proper handling of carbon nanotubes earned recognition and discussion among the world’s premier researchers in the field, noting the importance of the work for agencies in general.

“When we decided to write about this, we were originally just going to put it on the web and hope somebody would read it occasionally,” Barron said. “We couldn’t imagine who would publish it, but we heard that an editor at Springer Nature was really keen to have published articles like this.

“I think this is something people will use,” he said. “There’s nothing outrageous but it helps everybody, from high schools and colleges that are starting to use nanoparticles for experiments to small companies. That was the goal: Let’s provide a process that doesn’t cost thousands of dollars to install and allows you to transfer nanomaterials safely and on a large scale. Finally, publish said work in an open-access journal to maximize the reach across the globe.”

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

The safe handling of bulk low-density nanomaterials by Varun Shenoy Gangoli, Pavan M. V. Raja, Gibran Liezer Esquenazi, Andrew R. Barron. SN Applied Sciences June 2019, 1:644 DOI: https://doi.org/10.1007/s42452-019-0647-5 First Online 25 May 2019

This paper is open access.

Vitamin C helps gold nanowires grow

This research gives new meaning to ‘Take your vitamin C’ as can be seen in a February 19, 2019 news item on Nanowerk,

A boost of vitamin C helped Rice University scientists turn small gold nanorods into fine gold nanowires.

Common, mild ascorbic acid is the not-so-secret sauce that helped the Rice lab of chemist Eugene Zubarev grow pure batches of nanowires from stumpy nanorods without the drawbacks of previous techniques.

“There’s no novelty per se in using vitamin C to make gold nanostructures because there are many previous examples,” Zubarev said. “But the slow and controlled reduction achieved by vitamin C is surprisingly suitable for this type of chemistry in producing extra-long nanowires.”

A February 19, 2019 Rice University news release (also on EurekAlert), which originated the news item, provides more technical detail about the research

The Rice lab’s nanorods are about 25 nanometers thick at the start of the process – and remain that way while their length grows to become long nanowires. Above 1,000 nanometers in length, the objects are considered nanowires, and that matters. The wires’ aspect ratio – length over width – dictates how they absorb and emit light and how they conduct electrons. Combined with gold’s inherent metallic properties, that could enhance their value for sensing, diagnostic, imaging and therapeutic applications.

Zubarev and lead author Bishnu Khanal, a Rice chemistry alumnus, succeeded in making their particles go far beyond the transition from nanorod to nanowire, theoretically to unlimited length.

The researchers also showed the process is fully controllable and reversible. That makes it possible to produce nanowires of any desired length, and thus the desired configuration for electronic or light-manipulating applications, especially those that involve plasmons, the light-triggered oscillation of electrons on a metal’s surface.

The nanowires’ plasmonic response can be tuned to emit light from visible to infrared and theoretically far beyond, depending on their aspect ratios.

The process is slow, so it takes hours to grow a micron-long nanowire. “In this paper, we only reported structures up to 4 to 5 microns in length,” Zubarev said. “But we’re working to make much longer nanowires.”

The growth process only appeared to work with pentahedrally twinned gold nanorods, which contain five linked crystals. These five-sided rods — “Think of a pencil, but with five sides instead of six,” Zubarev said — are stable along the flat surfaces, but not at the tips.

“The tips also have five faces, but they have a different arrangement of atoms,” he said. “The energy of those atoms is slightly lower, and when new atoms are deposited there, they don’t migrate anywhere else.”

That keeps the growing wires from gaining girth. Every added atom increases the wire’s length, and thus the aspect ratio.

The nanorods’ reactive tips get help from a surfactant, CTAB, that covers the flat surfaces of nanorods. “The surfactant forms a very dense, tight bilayer on the sides, but it cannot cover the tips effectively,” Zubarev said.

That leaves the tips open to an oxidation or reduction reaction. The ascorbic acid provides electrons that combine with gold ions and settle at the tips in the form of gold atoms. And unlike carbon nanotubes in a solution that easily aggregate, the nanowires keep their distance from one another.

“The most valuable feature is that it is truly one-dimensional elongation of nanorods to nanowires,” Zubarev said. “It does not change the diameter, so in principal we can take small rods with an aspect ratio of maybe two or three and elongate them to 100 times the length.”
He said the process should apply to other metal nanorods, including silver.

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

Chemical Transformation of Nanorods to Nanowires: Reversible Growth and Dissolution of Anisotropic Gold Nanostructures by Bishnu P. Khanal and Eugene R. Zubarev. ACS Nano, 2019, 13 (2), pp 2370–2378 DOI: 10.1021/acsnano.8b09203 Publication Date (Web): February 12, 2019

Copyright © 2019 American Chemical Society

This paper is behind a paywall. Below you’ll find an image fo what I believe to be the vitamin C-enhanced gold nanowires.

Caption: Gold nanowires grown in the Rice University lab of chemist Eugene Zubarev promise to provide tunable plasmonic properties for optical and electronic applications. The wires can be controllably grown from nanorods, or reduced. Credit: Zubarev Research Group/Rice University

Let them (Rice University scientists) show you how to restore oil-soaked soil

I did not want to cash in (so to speak) on someone else’s fun headline so I played with it. Hre is the original head, which was likely written by either David Ruth or Mike Williams at Rice University (Texas, US), “Lettuce show you how to restore oil-soaked soil.”

A February 1, 2019 news item on ScienceDaily on the science behind lettuce and oil-soaked soil,

Rice University engineers have figured out how soil contaminated by heavy oil can not only be cleaned but made fertile again.

How do they know it works? They grew lettuce.

Rice engineers Kyriacos Zygourakis and Pedro Alvarez and their colleagues have fine-tuned their method to remove petroleum contaminants from soil through the age-old process of pyrolysis. The technique gently heats soil while keeping oxygen out, which avoids the damage usually done to fertile soil when burning hydrocarbons cause temperature spikes.

Lettuce growing in once oil-contaminated soil revived by a process developed by Rice University engineers. The Rice team determined that pyrolyzing oil-soaked soil for 15 minutes at 420 degrees Celsius is sufficient to eliminate contaminants while preserving the soil’s fertility. The lettuce plants shown here, in treated and fertilized soil, showed robust growth over 14 days. Photo by Wen Song

A February 1, 2019 Rice University news release (also on EurekAlert), which originated the news item, explains more about the work,

While large-volume marine spills get most of the attention, 98 percent of oil spills occur on land, Alvarez points out, with more than 25,000 spills a year reported to the Environmental Protection Agency. That makes the need for cost-effective remediation clear, he said.

“We saw an opportunity to convert a liability, contaminated soil, into a commodity, fertile soil,” Alvarez said.

The key to retaining fertility is to preserve the soil’s essential clays, Zygourakis said. “Clays retain water, and if you raise the temperature too high, you basically destroy them,” he said. “If you exceed 500 degrees Celsius (900 degrees Fahrenheit), dehydration is irreversible.

The researchers put soil samples from Hearne, Texas, contaminated in the lab with heavy crude, into a kiln to see what temperature best eliminated the most oil, and how long it took.

Their results showed heating samples in the rotating drum at 420 C (788 F) for 15 minutes eliminated 99.9 percent of total petroleum hydrocarbons (TPH) and 94.5 percent of polycyclic aromatic hydrocarbons (PAH), leaving the treated soils with roughly the same pollutant levels found in natural, uncontaminated soil.

The paper appears in the American Chemical Society journal Environmental Science and Technology. It follows several papers by the same group that detailed the mechanism by which pyrolysis removes contaminants and turns some of the unwanted hydrocarbons into char, while leaving behind soil almost as fertile as the original. “While heating soil to clean it isn’t a new process,” Zygourakis said, “we’ve proved we can do it quickly in a continuous reactor to remove TPH, and we’ve learned how to optimize the pyrolysis conditions to maximize contaminant removal while minimizing soil damage and loss of fertility.

“We also learned we can do it with less energy than other methods, and we have detoxified the soil so that we can safely put it back,” he said.

Heating the soil to about 420 C represents the sweet spot for treatment, Zygourakis said. Heating it to 470 C (878 F) did a marginally better job in removing contaminants, but used more energy and, more importantly, decreased the soil’s fertility to the degree that it could not be reused.

“Between 200 and 300 C (392-572 F), the light volatile compounds evaporate,” he said. “When you get to 350 to 400 C (662-752 F), you start breaking first the heteroatom bonds, and then carbon-carbon and carbon-hydrogen bonds triggering a sequence of radical reactions that convert heavier hydrocarbons to stable, low-reactivity char.”

The true test of the pilot program came when the researchers grew Simpson black-seeded lettuce, a variety for which petroleum is highly toxic, on the original clean soil, some contaminated soil and several pyrolyzed soils. While plants in the treated soils were a bit slower to start, they found that after 21 days, plants grown in pyrolyzed soil with fertilizer or simply water showed the same germination rates and had the same weight as those grown in clean soil.

“We knew we had a process that effectively cleans up oil-contaminated soil and restores its fertility,” Zygourakis said. “But, had we truly detoxified the soil?”

To answer this final question, the Rice team turned to Bhagavatula Moorthy, a professor of neonatology at Baylor College of Medicine, who studies the effects of airborne contaminants on neonatal development. Moorthy and his lab found that extracts taken from oil-contaminated soils were toxic to human lung cells, while exposing the same cell lines to extracts from treated soils had no adverse effects. The study eased concerns that pyrolyzed soil could release airborne dust particles laced with highly toxic pollutants like PAHs.

”One important lesson we learned is that different treatment objectives for regulatory compliance, detoxification and soil-fertility restoration need not be mutually exclusive and can be simultaneously achieved,” Alvarez said.

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

Pilot-Scale Pyrolytic Remediation of Crude-Oil-Contaminated Soil in a Continuously-Fed Reactor: Treatment Intensity Trade-Offs by Wen Song, Julia E. Vidonish, Roopa Kamath, Pingfeng Yu, Chun Chu, Bhagavatula Moorthy, Baoyu Gao, Kyriacos Zygourakis, and Pedro J. J. Alvarez. Environ. Sci. Technol., 2019, 53 (4), pp 2045–2053 DOI: 10.1021/acs.est.8b05825 Publication Date (Web): January 25, 2019

Copyright © 2019 American Chemical Society

This paper is behind a paywall.

Lifesaving moths and nanomagnets

Rice University bioengineers use a magnetic field to activate nanoparticle-attached baculoviruses in a tissue. The viruses, which normally infect alfalfa looper moths, are modified to deliver gene-editing DNA code only to cells that are targeted with magnetic field-induced local transduction. Courtesy of the Laboratory of Biomolecular Engineering and Nanomedicine

Kudos to whomever put that diagram together! That’s a lot of well conveyed information.

Now for the details about how this technology might save lives. From a November 13, 2018 news item on Nanowerk,

A new technology that relies on a moth-infecting virus and nanomagnets could be used to edit defective genes that give rise to diseases like sickle cell, muscular dystrophy and cystic fibrosis.

Rice University bioengineer Gang Bao has combined magnetic nanoparticles with a viral container drawn from a particular species of moth to deliver CRISPR/Cas9 payloads that modify genes in a specific tissue or organ with spatial control.

A November 12, 2018 Rice University news release (also on EurekAlert published on November 13, 2018), which originated the news item, provides detail,

Because magnetic fields are simple to manipulate and, unlike light, pass easily through tissue, Bao and his colleagues want to use them to control the expression of viral payloads in target tissues by activating the virus that is otherwise inactivated in blood.

The research appears in Nature Biomedical Engineering. In nature, CRISPR/Cas9 bolsters microbes’ immune systems by recording the DNA of invaders. That gives microbes the ability to recognize and attack returning invaders, but scientists have been racing to adapt CRISPR/Cas9 to repair mutations that cause genetic diseases and to manipulate DNA in laboratory experiments.

CRISPR/Cas9 has the potential to halt hereditary disease – if scientists can get the genome-editing machinery to the right cells inside the body. But roadblocks remain, especially in delivering the gene-editing payloads with high efficiency.

Bao said it will be necessary to edit cells in the body to treat many diseases. “But efficiently delivering genome-editing machinery into target tissue in the body with spatial control remains a major challenge,” Bao said. “Even if you inject the viral vector locally, it can leak to other tissues and organs, and that could be dangerous.”

The delivery vehicle developed by Bao’s group is based on a virus that infects Autographa californica, aka the alfalfa looper, a moth native to North America. The cylindrical baculovirus vector (BV), the payload-carrying part of the virus, is considered large at up to 60 nanometers in diameter and 200-300 nanometers in length. That’s big enough to transport more than 38,000 base pairs of DNA, which is enough to supply multiple gene-editing units to a target cell, Bao said.

He said the inspiration to combine BV and magnetic nanoparticles came from discussions with Rice postdoctoral researcher and co-lead author Haibao Zhu, who learned about the virus during a postdoctoral stint in Singapore but knew nothing about magnetic nanoparticles until he joined the Bao lab. The Rice team had previous experience using iron oxide nanoparticles and an applied magnetic field to open blood vessel walls just enough to let large-molecule drugs pass through.

“We really didn’t know if this would work for gene editing or not, but we thought, ‘worth a shot,'” Bao said.

The researchers use the magnetic nanoparticles to activate BV and deliver gene-editing payloads only where they’re needed. To do this, they take advantage of an immune-system protein called C3 that normally inactivates baculoviruses.

“If we combine BV with magnetic nanoparticles, we can overcome this deactivation by applying the magnetic field,” Bao said. “The beauty is that when we deliver it, gene editing occurs only at the tissue, or the part of the tissue, where we apply the magnetic field.”

Application of the magnetic field allows BV transduction, the payload-delivery process that introduces gene-editing cargo into the target cell. The payload is also DNA, which encodes both a reporter gene and the CRISPR/Cas9 system.

In tests, the BV was loaded with green fluorescent proteins or firefly luciferase. Cells with the protein glowed brightly under a microscope, and experiments showed the magnets were highly effective at targeted delivery of BV cargoes in both cell cultures and lab animals.

Bao noted his and other labs are working on the delivery of CRISPR/Cas9 with adeno-associated viruses (AAV), but he said BV’s capacity for therapeutic cargo is roughly eight times larger. “However, it is necessary to make BV transduction into target cells more efficient,” he said.

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

Spatial control of in vivo CRISPR–Cas9 genome editing via nanomagnets by Haibao Zhu, Linlin Zhang, Sheng Tong, Ciaran M. Lee, Harshavardhan Deshmukh, & Gang Bao. Nature Biomedical Engineering (2018) DOI: https://doi.org/10.1038/s41551-018-0318-7 Published: 12 November 2018

This paper is behind a paywall.

Where do I stand? a graphene artwork

A May 2,2019 news item on Nanowerk describes some graphene-based artwork being created at Rice University (Texas, US), Note: A link has been removed,

When you read about electrifying art, “electrifying” isn’t usually a verb. But an artist working with a Rice University lab is in fact making artwork that can deliver a jolt.

The Rice lab of chemist James Tour introduced laser-induced graphene (LIG) to the world in 2014, and now the researchers are making art with the technique, which involves converting carbon in a common polymer or other material into microscopic flakes of graphene.

The “ink” in “Where Do I Stand?” by artist Joseph Cohen is actually laser-induced graphene (LIG). The design shows Cohen’s impression of what LIG looks like at the microscopic level. The work was produced in the Rice University lab where the technique of creating LIG was invented. Photo by Jeff Fitlow
A detail from “Where Do I Stand?” by artist Joseph Cohen, who created the work at Rice University using laser-induced graphene as the medium. Photo by Jeff Fitlow

A May 2, 2019 Rice university news release (also received via email), which originated the news item, describes laser-induced graphene (LIG) and the art in more detail (Note: Links have been removed),

LIG is metallic and conducts electricity. The interconnected flakes are effectively a wire that could empower electronic artworks.

The paper in the American Chemical Society journal ACS Applied Nano Materials – simply titled “Graphene Art” – lays out how the lab and Houston artist and co-author Joseph Cohen generated LIG portraits and prints, including a graphene-inspired landscape called “Where Do I Stand?”

While the work isn’t electrified, Cohen said it lays the groundwork for future possibilities.

“That’s what I would like to do,” he said. “Not make it kitsch or play off the novelty, but to have it have some true functionality that allows greater awareness about the material and opens up the experience.”

Cohen created the design in an illustration program and sent it directly to the industrial engraving laser Tour’s lab uses to create LIG on a variety of materials. The laser burned the artist’s fine lines into the substrate, in this case archive-quality paper treated with fire retardant.

The piece, which was part of Cohen’s exhibit at Rice’s BioScience Research Collaborative last year, peers into the depths of what a viewer shrunken to nanoscale might see when facing a field of LIG, with overlapping hexagons – the basic lattice of atom-thick graphene – disappearing into the distance.

“You’re looking at this image of a 3D foam matrix of laser-induced graphene and it’s actually made of LIG,” he said. “I didn’t base it on anything; I was just thinking about what it would look like. When I shared it with Jim, he said, ‘Wow, that’s what it would look like if you could really blow this up.’”

Cohen said his art is about media specificity.

“In terms of the artistic application, you’re not looking at a representation of something, as traditionally we would in the history of art,” he said. “Each piece is 100% original. That’s the key.”

He developed an interest in nanomaterials as media for his art when he began work with Rice alumnus Daniel Heller, a bioengineer at Memorial Sloan Kettering Cancer Center in New York who established an artist-in-residency position in his lab.

After two years of creating with carbon nanotube-infused paint, Cohen attended an Electrochemical Society conference and met Tour, who in turn introduced him to Rice chemists Bruce Weisman and Paul Cherukuri, who further inspired his investigation of nanotechnology.

The rest is art history.

It would be incorrect to think of the process as “printing,” Tour said. Instead of adding a substance to the treated paper, substance is burned away as the laser turns the surface into foamlike flakes of interconnected graphene.

The art itself can be much more than eye candy, given LIG’s potential for electronic applications like sensors or as triboelectric generators that turn mechanical actions into current.

“You could put LIG on your back and have it flash LEDs with every step you take,” Tour said.

The fact that graphene is a conductor — unlike paint, ink or graphite from a pencil — makes it particularly appealing to Cohen, who expects to take advantage of that capability in future works.

“It’s art with a capital A that is trying to do the most that it can with advancements in science and technology,” he said. “If we look back historically, from the Renaissance to today, the highest forms of art push the limits of human understanding.”

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

Graphene Art by Yieu Chyan, Joseph Cohen, Winston Wang, Chenhao Zhang, and James M. Tour. ACS Appl. Nano Mater., Article ASAP DOI: 10.1021/acsanm.9b00391 Publication Date (Web): April 23, 2019

Copyright © 2019 American Chemical Society

This paper appears to be open access.

Because I can’t resist the delight beaming from these faces,

maging with laser-induced graphene (LIG) was taken to a new level in a Rice University lab. From left, chemist James Tour, holding a portrait of himself in LIG; artist Joseph Cohen, holding his work “Where Do I Stand?”; and Yieu Chyan, a Rice graduate student and lead author of a new paper detailing the process used to create the art. Photo by Jeff Fitlow