Tag Archives: US

Could CRISPR (clustered regularly interspaced short palindromic repeats) be weaponized?

On the occasion of an American team’s recent publication of research where they edited the germline (embryos), I produced a three-part series about CRISPR (clustered regularly interspaced short palindromic repeats), sometimes referred to as CRISPR/Cas9, (links offered at end of this post).

Somewhere in my series, there’s a quote about how CRISPR could be used as a ‘weapon of mass destruction’ and it seems this has been a hot topic for the last year or so as James Revill, research fellow at the University of Sussex, references in his August 31, 2017 essay on theconversation.com (h/t phys.org August 31, 2017 news item), Note: Links have been removed,

The gene editing technique CRISPR has been in the limelight after scientists reported they had used it to safely remove disease in human embryos for the first time. This follows a “CRISPR craze” over the last couple of years, with the number of academic publications on the topic growing steadily.

There are good reasons for the widespread attention to CRISPR. The technique allows scientists to “cut and paste” DNA more easily than in the past. It is being applied to a number of different peaceful areas, ranging from cancer therapies to the control of disease carrying insects.

Some of these applications – such as the engineering of mosquitoes to resist the parasite that causes malaria – effectively involve tinkering with ecosystems. CRISPR has therefore generated a number of ethical and safety concerns. Some also worry that applications being explored by defence organisations that involve “responsible innovation in gene editing” may send worrying signals to other states.

Concerns are also mounting that gene editing could be used in the development of biological weapons. In 2016, Bill Gates remarked that “the next epidemic could originate on the computer screen of a terrorist intent on using genetic engineering to create a synthetic version of the smallpox virus”. More recently, in July 2017, John Sotos, of Intel Health & Life Sciences, stated that gene editing research could “open up the potential for bioweapons of unimaginable destructive potential”.

An annual worldwide threat assessment report of the US intelligence community in February 2016 argued that the broad availability and low cost of the basic ingredients of technologies like CRISPR makes it particularly concerning.

A Feb. 11, 2016 news item on sciencemagazine.org offers a précis of some of the reactions while a February 9, 2016 article by Antonio Regalado for the Massachusetts Institute of Technology’s MIT Technology Review delves into the matter more deeply,

Genome editing is a weapon of mass destruction.

That’s according to James Clapper, [former] U.S. director of national intelligence, who on Tuesday, in the annual worldwide threat assessment report of the U.S. intelligence community, added gene editing to a list of threats posed by “weapons of mass destruction and proliferation.”

Gene editing refers to several novel ways to alter the DNA inside living cells. The most popular method, CRISPR, has been revolutionizing scientific research, leading to novel animals and crops, and is likely to power a new generation of gene treatments for serious diseases (see “Everything You Need to Know About CRISPR’s Monster Year”).

It is gene editing’s relative ease of use that worries the U.S. intelligence community, according to the assessment. “Given the broad distribution, low cost, and accelerated pace of development of this dual-use technology, its deliberate or unintentional misuse might lead to far-reaching economic and national security implications,” the report said.

The choice by the U.S. spy chief to call out gene editing as a potential weapon of mass destruction, or WMD, surprised some experts. It was the only biotechnology appearing in a tally of six more conventional threats, like North Korea’s suspected nuclear detonation on January 6 [2016], Syria’s undeclared chemical weapons, and new Russian cruise missiles that might violate an international treaty.

The report is an unclassified version of the “collective insights” of the Central Intelligence Agency, the National Security Agency, and half a dozen other U.S. spy and fact-gathering operations.

Although the report doesn’t mention CRISPR by name, Clapper clearly had the newest and the most versatile of the gene-editing systems in mind. The CRISPR technique’s low cost and relative ease of use—the basic ingredients can be bought online for $60—seems to have spooked intelligence agencies.

….

However, one has to be careful with the hype surrounding new technologies and, at present, the security implications of CRISPR are probably modest. There are easier, cruder methods of creating terror. CRISPR would only get aspiring biological terrorists so far. Other steps, such as growing and disseminating biological weapons agents, would typically be required for it to become an effective weapon. This would require additional skills and places CRISPR-based biological weapons beyond the reach of most terrorist groups. At least for the time being.

A July 5, 2016 opinion piece by Malcolm Dando for Nature argues for greater safeguards,

In Geneva next month [August 2016], officials will discuss updates to the global treaty that outlaws the use of biological weapons. The 1972 Biological Weapons Convention (BWC) was the first agreement to ban an entire class of weapons, and it remains a crucial instrument to stop scientific research on viruses, bacteria and toxins from being diverted into military programmes.

The BWC is the best route to ensure that nations take the biological-weapons threat seriously. Most countries have struggled to develop and introduce strong and effective national programmes — witness the difficulty the United States had in agreeing what oversight system should be applied to gain-of-function experiments that created more- dangerous lab-grown versions of common pathogens.

As scientific work advances — the CRISPR gene-editing system has been flagged as the latest example of possible dual-use technology — this treaty needs to be regularly updated. This is especially important because it has no formal verification system. Proposals for declarations, monitoring visits and inspections were vetoed by the United States in 2001, on the grounds that such verification threatened national security and confidential business information.

Even so, issues such as the possible dual-use threat from gene-editing systems will not be easily resolved. But we have to try. Without the involvement of the BWC, codes of conduct and oversight systems set up at national level are unlikely to be effective. The stakes are high, and after years of fumbling, we need strong international action to monitor and assess the threats from the new age of biological techniques.

Revill notes the latest BWC agreement and suggests future directions,

This convention is imperfect and lacks a way to ensure that states are compliant. Moreover, it has not been adequately “tended to” by its member states recently, with the last major meeting unable to agree a further programme of work. Yet it remains the cornerstone of an international regime against the hostile use of biology. All 178 state parties declared in December of 2016 their continued determination “to exclude completely the possibility of the use of (biological) weapons, and their conviction that such use would be repugnant to the conscience of humankind”.

These states therefore need to address the hostile potential of CRISPR. Moreover, they need to do so collectively. Unilateral national measures, such as reasonable biological security procedures, are important. However, preventing the hostile exploitation of CRISPR is not something that can be achieved by any single state acting alone.

As such, when states party to the convention meet later this year, it will be important to agree to a more systematic and regular review of science and technology. Such reviews can help with identifying and managing the security risks of technologies such as CRISPR, as well as allowing an international exchange of information on some of the potential benefits of such technologies.

Most states supported the principle of enhanced reviews of science and technology under the convention at the last major meeting. But they now need to seize the opportunity and agree on the practicalities of such reviews in order to prevent the convention being left behind by developments in science and technology.

Experts (military, intelligence, medical, etc.) are not the only ones concerned about CRISPR according to a February 11, 2016 article by Sharon Begley for statnews.com (Note: A link has been removed),

Most Americans oppose using powerful new technology to alter the genes of unborn babies, according to a new poll — even to prevent serious inherited diseases.

They expressed the strongest disapproval for editing genes to create “designer babies” with enhanced intelligence or looks.

But the poll, conducted by STAT and Harvard T.H. Chan School of Public Health, found that people have mixed, and apparently not firm, views on emerging genetic techniques. US adults are almost evenly split on whether the federal government should fund research on editing genes before birth to keep children from developing diseases such as cystic fibrosis or Huntington’s disease.

“They’re not against scientists trying to improve [genome-editing] technologies,” said Robert Blendon, professor of health policy and political analysis at Harvard’s Chan School, perhaps because they recognize that one day there might be a compelling reason to use such technologies. An unexpected event, such as scientists “eliminating a terrible disease” that a child would have otherwise inherited, “could change people’s views in the years ahead,” Blendon said.

But for now, he added, “people are concerned about editing the genes of those who are yet unborn.”

A majority, however, wants government regulators to approve gene therapy to treat diseases in children and adults.

The STAT-Harvard poll comes as scientists and policy makers confront the ethical, social, and legal implications of these revolutionary tools for changing DNA. Thanks to a technique called CRISPR-Cas9, scientists can easily, and with increasing precision, modify genes through the genetic analog of a computer’s “find and replace” function.

I find it surprising that there’s resistance to removing diseases found in the germline (embryos). When they were doing public consultations on nanotechnology, the one area where people tended to be quite open to research was health and medicine. Where food was concerned however, people had far more concerns.

If you’re interested in the STAT-Harvard poll, you can find it here. As for James Revill, he has written a more substantive version of this essay as a paper, which is available here.

On a semi-related note, I found STAT (statnews.com) to be a quite interesting and accessibly written online health science journal. Here’s more from the About Us page (Note: A link has been removed),

What’s STAT all about?
STAT is a national publication focused on finding and telling compelling stories about health, medicine, and scientific discovery. We produce daily news, investigative articles, and narrative projects in addition to multimedia features. We tell our stories from the places that matter to our readers — research labs, hospitals, executive suites, and political campaigns.

Why did you call it STAT?
In medical parlance, “stat” means important and urgent, and that’s what we’re all about — quickly and smartly delivering good stories. Read more about the origins of our name here.

Who’s behind the new publication?
STAT is produced by Boston Globe Media. Our headquarters is located in Boston but we have bureaus in Washington, New York, Cleveland, Atlanta, San Francisco, and Los Angeles. It was started by John Henry, the owner of Boston Globe Media and the principal owner of the Boston Red Sox. Rick Berke is executive editor.

So is STAT part of The Boston Globe?
They’re distinct properties but the two share content and complement one another.

Is it free?
Much of STAT is free. We also offer STAT Plus, a premium subscription plan that includes exclusive reporting about the pharmaceutical and biotech industries as well as other benefits. Learn more about it here.

Who’s working for STAT?
Some of the best-sourced science, health, and biotech journalists in the country, as well as motion graphics artists and data visualization specialists. Our team includes talented writers, editors, and producers capable of the kind of explanatory journalism that complicated science issues sometimes demand.

Who’s your audience?
You. Even if you don’t work in science, have never stepped foot in a hospital, or hated high school biology, we’ve got something for you. And for the lab scientists, health professionals, business leaders, and policy makers, we think you’ll find coverage here that interests you, too. The world of health, science, and medicine is booming and yielding fascinating stories. We explore how they affect us all.

….

As promised, here are the links to my three-part series on CRISPR,

Part 1 opens the series with a basic description of CRISPR and the germline research that occasioned the series along with some of the other (non-weapon) ethical issues and patent disputes that are arising from this new technology. CRISPR and editing the germline in the US (part 1 of 3): In the beginning

Part 2 covers three critical responses to the reporting and between them describe the technology in more detail and the possibility of ‘designer babies’.  CRISPR and editing the germline in the US (part 2 of 3): ‘designer babies’?

Part 3 is all about public discussion or, rather, the lack of and need for according to a couple of social scientists. Informally, there is some discussion via pop culture and Joelle Renstrom notes although she is focused on the larger issues touched on by the television series, Orphan Black and as I touch on in my final comments. CRISPR and editing the germline in the US (part 3 of 3): public discussions and pop culture

Finally, I hope to stumble across studies from other countries about how they are responding to the possibilities presented by CRISPR/Cas9 so that I can offer a more global perspective than this largely US perspective. At the very least, it would be interesting to find it if there differences.

World heritage music stored in DNA

It seems a Swiss team from the École Polytechnique de Lausanne (EPFL) have collaborated with American companies Twist Bioscience and Microsoft, as well as, the University of Washington (state) to preserve two iconic jazz pieces on DNA (deoxyribonucleic acid) according to a Sept. 29, 2017 news item on phys.org,,

Thanks to an innovative technology for encoding data in DNA strands, two items of world heritage – songs recorded at the Montreux Jazz Festival [held in Switzerland] and digitized by EPFL – have been safeguarded for eternity. This marks the first time that cultural artifacts granted UNESCO heritage status have been saved in such a manner, ensuring they are preserved for thousands of years. The method was developed by US company Twist Bioscience and is being unveiled today in a demonstrator created at the EPFL+ECAL Lab.

“Tutu” by Miles Davis and “Smoke on the Water” by Deep Purple have already made their mark on music history. Now they have entered the annals of science, for eternity. Recordings of these two legendary songs were digitized by the Ecole Polytechnique Fédérale de Lausanne (EPFL) as part of the Montreux Jazz Digital Project, and they are the first to be stored in the form of a DNA sequence that can be subsequently decoded and listened to without any reduction in quality.

A Sept. 29, 2017 EPFL press release by Emmanuel Barraud, which originated the news item, provides more details,

This feat was achieved by US company Twist Bioscience working in association with Microsoft Research and the University of Washington. The pioneering technology is actually based on a mechanism that has been at work on Earth for billions of years: storing information in the form of DNA strands. This fundamental process is what has allowed all living species, plants and animals alike, to live on from generation to generation.

The entire world wide web in a shoe box

All electronic data storage involves encoding data in binary format – a series of zeros and ones – and then recording it on a physical medium. DNA works in a similar way, but is composed of long strands of series of four nucleotides (A, T, C and G) that make up a “code.” While the basic principle may be the same, the two methods differ greatly in terms of efficiency: if all the information currently on the internet was stored in the form of DNA, it would fit in a shoe box!

Recent advances in biotechnology now make it possible for humans to do what Mother Nature has always done. Today’s scientists can create artificial DNA strands, “record” any kind of genetic code on them and then analyze them using a sequencer to reconstruct the original data. What’s more, DNA is extraordinarily stable, as evidenced by prehistoric fragments that have been preserved in amber. Artificial strands created by scientists and carefully encapsulated should likewise last for millennia.

To help demonstrate the feasibility of this new method, EPFL’s Metamedia Center provided recordings of two famous songs played at the Montreux Jazz Festival: “Tutu” by Miles Davis, and “Smoke on the Water” by Deep Purple. Twist Bioscience and its research partners encoded the recordings, transformed them into DNA strands and then sequenced and decoded them and played them again – without any reduction in quality.

The amount of artificial DNA strands needed to record the two songs is invisible to the naked eye, and the amount needed to record all 50 years of the Festival’s archives, which have been included in UNESCO’s [United Nations Educational, Scientific and Cultural Organization] Memory of the World Register, would be equal in size to a grain of sand. “Our partnership with EPFL in digitizing our archives aims not only at their positive exploration, but also at their preservation for the next generations,” says Thierry Amsallem, president of the Claude Nobs Foundation. “By taking part in this pioneering experiment which writes the songs into DNA strands, we can be certain that they will be saved on a medium that will never become obsolete!”

A new concept of time

At EPFL’s first-ever ArtTech forum, attendees got to hear the two songs played after being stored in DNA, using a demonstrator developed at the EPFL+ECAL Lab. The system shows that being able to store data for thousands of years is a revolutionary breakthrough that can completely change our relationship with data, memory and time. “For us, it means looking into radically new ways of interacting with cultural heritage that can potentially cut across civilizations,” says Nicolas Henchoz, head of the EPFL+ECAL Lab.

Quincy Jones, a longstanding Festival supporter, is particularly enthusiastic about this technological breakthrough: “With advancements in nanotechnology, I believe we can expect to see people living prolonged lives, and with that, we can also expect to see more developments in the enhancement of how we live. For me, life is all about learning where you came from in order to get where you want to go, but in order to do so, you need access to history! And with the unreliability of how archives are often stored, I sometimes worry that our future generations will be left without such access… So, it absolutely makes my soul smile to know that EPFL, Twist Bioscience and their partners are coming together to preserve the beauty and history of the Montreux Jazz Festival for our future generations, on DNA! I’ve been a part of this festival for decades and it truly is a magnificent representation of what happens when different cultures unite for the sake of music. Absolute magic. And I’m proud to know that the memory of this special place will never be lost.

A Sept. 29, 2017 Twist Bioscience news release is repetitive in some ways but interesting nonetheless,

Twist Bioscience, a company accelerating science and innovation through rapid, high-quality DNA synthesis, today announced that, working with Microsoft and University of Washington researchers, they have successfully stored archival-quality audio recordings of two important music performances from the archives of the world-renowned Montreux Jazz Festival.
These selections are encoded and stored in nature’s preferred storage medium, DNA, for the first time. These tiny specks of DNA will preserve a part of UNESCO’s Memory of the World Archive, where valuable cultural heritage collections are recorded. This is the first time DNA has been used as a long-term archival-quality storage medium.
Quincy Jones, world-renowned Entertainment Executive, Music Composer and Arranger, Musician and Music Producer said, “With advancements in nanotechnology, I believe we can expect to see people living prolonged lives, and with that, we can also expect to see more developments in the enhancement of how we live. For me, life is all about learning where you came from in order to get where you want to go, but in order to do so, you need access to history! And with the unreliability of how archives are often stored, I sometimes worry that our future generations will be left without such access…So, it absolutely makes my soul smile to know that EPFL, Twist Bioscience and others are coming together to preserve the beauty and history of the Montreux Jazz Festival for our future generations, on DNA!…I’ve been a part of this festival for decades and it truly is a magnificent representation of what happens when different cultures unite for the sake of music. Absolute magic. And I’m proud to know that the memory of this special place will never be lost.”
“Our partnership with EPFL in digitizing our archives aims not only at their positive exploration, but also at their preservation for the next generations,” says Thierry Amsallem, president of the Claude Nobs Foundation. “By taking part in this pioneering experiment which writes the songs into DNA strands, we can be certain that they will be saved on a medium that will never become obsolete!”
The Montreux Jazz Digital Project is a collaboration between the Claude Nobs Foundation, curator of the Montreux Jazz Festival audio-visual collection and the École Polytechnique Fédérale de Lausanne (EPFL) to digitize, enrich, store, show, and preserve this notable legacy created by Claude Nobs, the Festival’s founder.
In this proof-of-principle project, two quintessential music performances from the Montreux Jazz Festival – Smoke on the Water, performed by Deep Purple and Tutu, performed by Miles Davis – have been encoded onto DNA and read back with 100 percent accuracy. After being decoded, the songs were played on September 29th [2017] at the ArtTech Forum (see below) in Lausanne, Switzerland. Smoke on the Water was selected as a tribute to Claude Nobs, the Montreux Jazz Festival’s founder. The song memorializes a fire and Funky Claude’s rescue efforts at the Casino Barrière de Montreux during a Frank Zappa concert promoted by Claude Nobs. Miles Davis’ Tutu was selected for the role he played in music history and the Montreux Jazz Festival’s success. Miles Davis died in 1991.
“We archived two magical musical pieces on DNA of this historic collection, equating to 140MB of stored data in DNA,” said Karin Strauss, Ph.D., a Senior Researcher at Microsoft, and one of the project’s leaders.  “The amount of DNA used to store these songs is much smaller than one grain of sand. Amazingly, storing the entire six petabyte Montreux Jazz Festival’s collection would result in DNA smaller than one grain of rice.”
Luis Ceze, Ph.D., a professor in the Paul G. Allen School of Computer Science & Engineering at the University of Washington, said, “DNA, nature’s preferred information storage medium, is an ideal fit for digital archives because of its durability, density and eternal relevance. Storing items from the Montreux Jazz Festival is a perfect way to show how fast DNA digital data storage is becoming real.”
Nature’s Preferred Storage Medium
Nature selected DNA as its hard drive billions of years ago to encode all the genetic instructions necessary for life. These instructions include all the information necessary for survival. DNA molecules encode information with sequences of discrete units. In computers, these discrete units are the 0s and 1s of “binary code,” whereas in DNA molecules, the units are the four distinct nucleotide bases: adenine (A), cytosine (C), guanine (G) and thymine (T).
“DNA is a remarkably efficient molecule that can remain stable for millennia,” said Bill Peck, Ph.D., chief technology officer of Twist Bioscience.  “This is a very exciting project: we are now in an age where we can use the remarkable efficiencies of nature to archive master copies of our cultural heritage in DNA.   As we develop the economies of this process new performances can be added any time.  Unlike current storage technologies, nature’s media will not change and will remain readable through time. There will be no new technology to replace DNA, nature has already optimized the format.”
DNA: Far More Efficient Than a Computer 
Each cell within the human body contains approximately three billion base pairs of DNA. With 75 trillion cells in the human body, this equates to the storage of 150 zettabytes (1021) of information within each body. By comparison, the largest data centers can be hundreds of thousands to even millions of square feet to hold a comparable amount of stored data.
The Elegance of DNA as a Storage Medium
Like music, which can be widely varied with a finite number of notes, DNA encodes individuality with only four different letters in varied combinations. When using DNA as a storage medium, there are several advantages in addition to the universality of the format and incredible storage density. DNA can be stable for thousands of years when stored in a cool dry place and is easy to copy using polymerase chain reaction to create back-up copies of archived material. In addition, because of PCR, small data sets can be targeted and recovered quickly from a large dataset without needing to read the entire file.
How to Store Digital Data in DNA
To encode the music performances into archival storage copies in DNA, Twist Bioscience worked with Microsoft and University of Washington researchers to complete four steps: Coding, synthesis/storage, retrieval and decoding. First, the digital files were converted from the binary code using 0s and 1s into sequences of A, C, T and G. For purposes of the example, 00 represents A, 10 represents C, 01 represents G and 11 represents T. Twist Bioscience then synthesizes the DNA in short segments in the sequence order provided. The short DNA segments each contain about 12 bytes of data as well as a sequence number to indicate their place within the overall sequence. This is the process of storage. And finally, to ensure that the file is stored accurately, the sequence is read back to ensure 100 percent accuracy, and then decoded from A, C, T or G into a two-digit binary representation.
Importantly, to encapsulate and preserve encoded DNA, the collaborators are working with Professor Dr. Robert Grass of ETH Zurich. Grass has developed an innovative technology inspired by preservation of DNA within prehistoric fossils.  With this technology, digital data encoded in DNA remains preserved for millennia.
About UNESCO’s Memory of the World Register
UNESCO established the Memory of the World Register in 1992 in response to a growing awareness of the perilous state of preservation of, and access to, documentary heritage in various parts of the world.  Through its National Commissions, UNESCO prepared a list of endangered library and archive holdings and a world list of national cinematic heritage.
A range of pilot projects employing contemporary technology to reproduce original documentary heritage on other media began. These included, for example, a CD-ROM of the 13th Century Radzivill Chronicle, tracing the origins of the peoples of Europe, and Memoria de Iberoamerica, a joint newspaper microfilming project involving seven Latin American countries. These projects enhanced access to this documentary heritage and contributed to its preservation.
“We are incredibly proud to be a part of this momentous event, with the first archived songs placed into the UNESCO Memory of the World Register,” said Emily Leproust, Ph.D., CEO of Twist Bioscience.
About ArtTech
The ArtTech Foundation, created by renowned scientists and dignitaries from Crans-Montana, Switzerland, wishes to stimulate reflection and support pioneering and innovative projects beyond the known boundaries of culture and science.
Benefitting from the establishment of a favorable environment for the creation of technology companies, the Foundation aims to position itself as key promoter of ideas and innovative endeavors within a landscape of “Culture and Science” that is still being shaped.
Several initiatives, including our annual global platform launched in the spring of 2017, are helping to create a community that brings together researchers, celebrities in the world of culture and the arts, as well as investors and entrepreneurs from Switzerland and across the globe.
 
About EPFL
EPFL, one of the two Swiss Federal Institutes of Technology, based in Lausanne, is Europe’s most cosmopolitan technical university with students, professors and staff from over 120 nations. A dynamic environment, open to Switzerland and the world, EPFL is centered on its three missions: teaching, research and technology transfer. EPFL works together with an extensive network of partners including other universities and institutes of technology, developing and emerging countries, secondary schools and colleges, industry and economy, political circles and the general public, to bring about real impact for society.
About Twist Bioscience
At Twist Bioscience, our expertise is accelerating science and innovation by leveraging the power of scale. We have developed a proprietary semiconductor-based synthetic DNA manufacturing process featuring a high throughput silicon platform capable of producing synthetic biology tools, including genes, oligonucleotide pools and variant libraries. By synthesizing DNA on silicon instead of on traditional 96-well plastic plates, our platform overcomes the current inefficiencies of synthetic DNA production, and enables cost-effective, rapid, high-quality and high throughput synthetic gene production, which in turn, expedites the design, build and test cycle to enable personalized medicines, pharmaceuticals, sustainable chemical production, improved agriculture production, diagnostics and biodetection. We are also developing new technologies to address large scale data storage. For more information, please visit www.twistbioscience.com. Twist Bioscience is on Twitter. Sign up to follow our Twitter feed @TwistBioscience at https://twitter.com/TwistBioscience.

If you hadn’t read the EPFL press release first, it might have taken a minute to figure out why EPFL is being mentioned in the Twist Bioscience news release. Presumably someone was rushing to make a deadline. Ah well, I’ve seen and written worse.

I haven’t been able to find any video or audio recordings of the DNA-preserved performances but there is an informational video (originally published July 7, 2016) from Microsoft and the University of Washington describing the DNA-based technology,

I also found this description of listening to the DNA-preserved music in an Oct. 6, 2017 blog posting for the Canadian Broadcasting Corporation’s (CBC) Day 6 radio programme,

To listen to them, one must first suspend the DNA holding the songs in a solution. Next, one can use a DNA sequencer to read the letters of the bases forming the molecules. Then, algorithms can determine the digital code those letters form. From that code, comes the music.

It’s complicated but Ceze says his team performed this process without error.

You can find out more about UNESCO’s Memory of the World and its register here , more about the EPFL+ECAL Lab here, and more about Twist Bioscience here.

What helps you may hurt you (titanium dioxide nanoparticles and orthopedic implants)

From a Sept. 16, 2017 news item on Nanotechnology Now,

Researchers from the Mayo Clinic have proposed that negative cellular responses to titanium-based nanoparticles released from metal implants interfere in bone formation and resorption at the site of repair, resulting in implant loosening and joint pain. [emphasis mine]Their review of recent scientific evidence and call for further research to characterize the biological, physical, and chemical interactions between titanium dioxide nanoparticles and bone-forming cells is published in BioResearch Open Access, a peer-reviewed open access journal from Mary Ann Liebert, Inc., publishers. The article is available free on theBioResearch Open Access website.

A Sept. 14, 2017 Mary Anne Liebert (Publishing) news release, which originated the news item,  mentions the authors,

Jie Yao, Eric Lewallen, PhD, David Lewallen, MD, Andre van Wijnen, PhD, and colleagues from the Mayo Clinic, Rochester, MN and Second Affiliated Hospital of Soochow University, China, coauthored the article entitled “Local Cellular Responses to Titanium Dioxide from Orthopedic Implants The authors examined the results of recently published studies of titanium-based implants, focusing on the direct and indirect effects of titanium dioxide nanoparticles on the viability and behavior of multiple bone-related cell types. They discuss the impact of particle size, aggregation, structure, and the specific extracellular and intracellular (if taken up by the cells) effects of titanium particle exposure.

“The adverse effects of metallic orthopedic particles generated from implants are of significant clinical interest given the large number of procedures carried out each year. This article reviews our current understanding of the clinical issues and highlights areas for future research,” says BioResearch Open Access Editor Jane Taylor, PhD, MRC Centre for Regenerative Medicine, University of Edinburgh, Scotland.

Before getting to the abstract, here’s a link to and a citation for the paper,

Local Cellular Responses to Titanium Dioxide from Orthopedic Implants by Yao, Jie J.; Lewallen, Eric A.; Trousdale, William H.; Xu, Wei; Thaler, Roman; Salib, Christopher G.; Reina, Nicolas; Abdel, Matthew P.; Lewallen, David G.; and van Wijnenm, Andre J.. BioResearch Open Access. July 2017, 6(1): 94-103. https://doi.org/10.1089/biores.2017.0017 Published July 1, 2017

This paper is open access.

Hallucinogenic molecules and the brain

Psychedelic drugs seems to be enjoying a ‘moment’. After decades of being vilified and  declared illegal (in many jurisdictions), psychedelic (or hallucinogenic) drugs are once again being tested for use in therapy. A Sept. 1, 2017 article by Diana Kwon for The Scientist describes some of the latest research (I’ve excerpted the section on molecules; Note: Links have been removed),

Mind-bending molecules

© SEAN MCCABE

All the classic psychedelic drugs—psilocybin, LSD, and N,N-dimethyltryptamine (DMT), the active component in ayahuasca—activate serotonin 2A (5-HT2A) receptors, which are distributed throughout the brain. In all likelihood, this receptor plays a key role in the drugs’ effects. Krähenmann [Rainer Krähenmann, a psychiatrist and researcher at the University of Zurich]] and his colleagues in Zurich have discovered that ketanserin, a 5-HT2A receptor antagonist, blocks LSD’s hallucinogenic properties and prevents individuals from entering a dreamlike state or attributing personal relevance to the experience.12,13

Other research groups have found that, in rodent brains, 2,5-dimethoxy-4-iodoamphetamine (DOI), a highly potent and selective 5-HT2A receptor agonist, can modify the expression of brain-derived neurotrophic factor (BDNF)—a protein that, among other things, regulates neuronal survival, differentiation, and synaptic plasticity. This has led some scientists to hypothesize that, through this pathway, psychedelics may enhance neuroplasticity, the ability to form new neuronal connections in the brain.14 “We’re still working on that and trying to figure out what is so special about the receptor and where it is involved,” says Katrin Preller, a postdoc studying psychedelics at the University of Zurich. “But it seems like this combination of serotonin 2A receptors and BDNF leads to a kind of different organizational state in the brain that leads to what people experience under the influence of psychedelics.”

This serotonin receptor isn’t limited to the central nervous system. Work by Charles Nichols, a pharmacology professor at Louisiana State University, has revealed that 5-HT2A receptor agonists can reduce inflammation throughout the body. Nichols and his former postdoc Bangning Yu stumbled upon this discovery by accident, while testing the effects of DOI on smooth muscle cells from rat aortas. When they added this drug to the rodent cells in culture, it blocked the effects of tumor necrosis factor-alpha (TNF-α), a key inflammatory cytokine.

“It was completely unexpected,” Nichols recalls. The effects were so bewildering, he says, that they repeated the experiment twice to convince themselves that the results were correct. Before publishing the findings in 2008,15 they tested a few other 5-HT2A receptor agonists, including LSD, and found consistent anti-inflammatory effects, though none of the drugs’ effects were as strong as DOI’s. “Most of the psychedelics I have tested are about as potent as a corticosteroid at their target, but there’s something very unique about DOI that makes it much more potent,” Nichols says. “That’s one of the mysteries I’m trying to solve.”

After seeing the effect these drugs could have in cells, Nichols and his team moved on to whole animals. When they treated mouse models of system-wide inflammation with DOI, they found potent anti-inflammatory effects throughout the rodents’ bodies, with the strongest effects in the small intestine and a section of the main cardiac artery known as the aortic arch.16 “I think that’s really when it felt that we were onto something big, when we saw it in the whole animal,” Nichols says.

The group is now focused on testing DOI as a potential therapeutic for inflammatory diseases. In a 2015 study, they reported that DOI could block the development of asthma in a mouse model of the condition,17 and last December, the team received a patent to use DOI for four indications: asthma, Crohn’s disease, rheumatoid arthritis, and irritable bowel syndrome. They are now working to move the treatment into clinical trials. The benefit of using DOI for these conditions, Nichols says, is that because of its potency, only small amounts will be required—far below the amounts required to produce hallucinogenic effects.

In addition to opening the door to a new class of diseases that could benefit from psychedelics-inspired therapy, Nichols’s work suggests “that there may be some enduring changes that are mediated through anti-inflammatory effects,” Griffiths [Roland Griffiths, a psychiatry professor at Johns Hopkins University] says. Recent studies suggest that inflammation may play a role in a number of psychological disorders, including depression18 and addiction.19

“If somebody has neuroinflammation and that’s causing depression, and something like psilocybin makes it better through the subjective experience but the brain is still inflamed, it’s going to fall back into the depressed rut,” Nichols says. But if psilocybin is also treating the inflammation, he adds, “it won’t have that rut to fall back into.”

If it turns out that psychedelics do have anti-inflammatory effects in the brain, the drugs’ therapeutic uses could be even broader than scientists now envision. “In terms of neurodegenerative disease, every one of these disorders is mediated by inflammatory cytokines,” says Juan Sanchez-Ramos, a neuroscientist at the University of South Florida who in 2013 reported that small doses of psilocybin could promote neurogenesis in the mouse hippocampus.20 “That’s why I think, with Alzheimer’s, for example, if you attenuate the inflammation, it could help slow the progression of the disease.”

For anyone who was never exposed to the anti-hallucinogenic drug campaigns, this turn of events is mindboggling. There was a great deal of concern especially with LSD in the 1960s and it was not entirely unfounded. In my own family, a distant cousin, while under the influence of the drug, jumped off a building believing he could fly.  So, Kwon’s story opening with a story about someone being treated successfully for depression with a psychedelic drug was surprising to me . Why these drugs are being used successfully for psychiatric conditions when so much damage was apparently done under the influence in decades past may have something to do with taking the drugs in a controlled environment and, possibly, smaller dosages.

Alan Copperman and Amanda Marcotte have a very US-centric discussion about CRISPR and germline editing (designer babies?)

For anyone who needs more information, I ran a three part series on CRISPR germline editing on August 15, 2017:

Part 1 opens the series with a basic description of CRISPR and the germline research that occasioned the series along with some of the ethical issues and patent disputes that are arising from this new technology. CRISPR and editing the germline in the US (part 1 of 3): In the beginning

Part 2 covers three critical responses to the reporting and between them describe the technology in more detail and the possibility of ‘designer babies’.  CRISPR and editing the germline in the US (part 2 of 3): ‘designer babies’?

Part 3 is all about public discussion or, rather, the lack of and need for according to a couple of social scientists. Informally, there is some discussion via pop culture and Joelle Renstrom notes although she is focused on the larger issues touched on by the television series, Orphan Black and as I touch on in my final comments. CRISPR and editing the germline in the US (part 3 of 3): public discussions and pop culture

The news about CRISPR and germline editing by a US team made a bit of a splash even being mentioned on Salon.com, which hardly ever covers any science news (except for some occasional climate change pieces). In a Sept. 4, 2017 salon.com item (an excerpt from the full interview) Amanda Marcotte talks with Dr. Alan Copperman director of the division of reproductive endocrinology and infertility at Mount Sinai Medical Center about the technology and its implications.  As noted in the headline, it’s a US-centric discussion where assumptions are made about who will be leading discussions about the future of the technology.

It’s been a while since I’ve watched it but I believe they do mention in passing that Chinese scientists published two studies about using CRISPR to edit the germline (i think there’s a third Chinese paper in the pipeline) before the American team announced its accomplishment in August 2017. By the way, the first paper by the Chinese caused quite the quandary in April 2015. (My May 14, 2015 posting covers some of the ethical issues; scroll down about 50% of the way for more about the impact of the published Chinese research.)

Also, you might want notice just how smooth Copperman’s responses are almost always emphasizing the benefits of the technology before usually answering the question. He’s had media training and he’s good at this.

They also talk about corn and CRISPR just about the time that agricultural research was announced. Interesting timing, non? (See my Oct. 11, 2017 posting about CRISPR edited corn coming to market in 2020.)

For anyone who wants to skip to the full Marcotte/Cooperman interview, go here on Facebook.

‘Nano-hashtags’ for Majorana particles?

The ‘nano-hashtags’ are in fact (assuming a minor leap of imagination) nanowires that resemble hashtags.

Scanning electron microscope image of the device wherein clearly a ‘hashtag’ is formed. Credit: Eindhoven University of Technology

An August 23, 2017 news item on ScienceDaily makes the announcement,

In Nature, an international team of researchers from Eindhoven University of Technology [Netherlands], Delft University of Technology [Netherlands] and the University of California — Santa Barbara presents an advanced quantum chip that will be able to provide definitive proof of the mysterious Majorana particles. These particles, first demonstrated in 2012, are their own antiparticle at one and the same time. The chip, which comprises ultrathin networks of nanowires in the shape of ‘hashtags’, has all the qualities to allow Majorana particles to exchange places. This feature is regarded as the smoking gun for proving their existence and is a crucial step towards their use as a building block for future quantum computers.

An August 23, 2017 Eindhoven University press release (also on EurekAlert), which originated the news item, provides some context and information about the work,

In 2012 it was big news: researchers from Delft University of Technology and Eindhoven University of Technology presented the first experimental signatures for the existence of the Majorana fermion. This particle had been predicted in 1937 by the Italian physicist Ettore Majorana and has the distinctive property of also being its own anti-particle. The Majorana particles emerge at the ends of a semiconductor wire, when in contact with a superconductor material.

Smoking gun

While the discovered particles may have properties typical to Majoranas, the most exciting proof could be obtained by allowing two Majorana particles to exchange places, or ‘braid’ as it is scientifically known. “That’s the smoking gun,” suggests Erik Bakkers, one of the researchers from Eindhoven University of Technology. “The behavior we then see could be the most conclusive evidence yet of Majoranas.”

Crossroads

In the Nature paper that is published today [August 23, 2017], Bakkers and his colleagues present a new device that should be able to show this exchanging of Majoranas. In the original experiment in 2012 two Majorana particles were found in a single wire but they were not able to pass each other without immediately destroying the other. Thus the researchers quite literally had to create space. In the presented experiment they formed intersections using the same kinds of nanowire so that four of these intersections form a ‘hashtag’, #, and thus create a closed circuit along which Majoranas are able to move.

Etch and grow

The researchers built their hashtag device starting from scratch. The nanowires are grown from a specially etched substrate such that they form exactly the desired network which they then expose to a stream of aluminium particles, creating layers of aluminium, a superconductor, on specific spots on the wires – the contacts where the Majorana particles emerge. Places that lie ‘in the shadow’ of other wires stay uncovered.

Leap in quality

The entire process happens in a vacuum and at ultra-cold temperature (around -273 degree Celsius). “This ensures very clean, pure contacts,” says Bakkers, “and enables us to make a considerable leap in the quality of this kind of quantum device.” The measurements demonstrate for a number of electronic and magnetic properties that all the ingredients are present for the Majoranas to braid.

Quantum computers

If the researchers succeed in enabling the Majorana particles to braid, they will at once have killed two birds with one stone. Given their robustness, Majoranas are regarded as the ideal building block for future quantum computers that will be able to perform many calculations simultaneously and thus many times faster than current computers. The braiding of two Majorana particles could form the basis for a qubit, the calculation unit of these computers.

Travel around the world

An interesting detail is that the samples have traveled around the world during the fabrication, combining unique and synergetic activities of each research institution. It started in Delft with patterning and etching the substrate, then to Eindhoven for nanowire growth and to Santa Barbara for aluminium contact formation. Finally back to Delft via Eindhoven for the measurements.

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

Epitaxy of advanced nanowire quantum devices by Sasa Gazibegovic, Diana Car, Hao Zhang, Stijn C. Balk, John A. Logan, Michiel W. A. de Moor, Maja C. Cassidy, Rudi Schmits, Di Xu, Guanzhong Wang, Peter Krogstrup, Roy L. M. Op het Veld, Kun Zuo, Yoram Vos, Jie Shen, Daniël Bouman, Borzoyeh Shojaei, Daniel Pennachio, Joon Sue Lee, Petrus J. van Veldhoven, Sebastian Koelling, Marcel A. Verheijen, Leo P. Kouwenhoven, Chris J. Palmstrøm, & Erik P. A. M. Bakkers. Nature 548, 434–438 (24 August 2017) doi:10.1038/nature23468 Published online 23 August 2017

This paper is behind a paywall.

Dexter Johnson has some additional insight (interview with one of the researchers) in an Aug. 29, 2017 posting on his Nanoclast blog (on the IEEE [institute of Electrical and Electronics Engineers] website).

Announcing Canada’s Chief Science Advisor: Dr. Mona Nemer

Thanks to the Canadian Science Policy Centre’s September 26, 2017 announcement (received via email) a burning question has been answered,

After great anticipation, Prime Minister Trudeau along with Minister Duncan have announced Canada’s Chief Science Advisor, Dr. Mona Nemer, [emphasis mine]  at a ceremony at the House of Commons. The Canadian Science Policy Centre welcomes this exciting news and congratulates Dr. Nemer on her appointment in this role and we wish her the best in carrying out her duties in this esteemed position. CSPC is looking forward to working closely with Dr. Nemer for the Canadian science policy community. Mehrdad Hariri, CEO & President of the CSPC, stated, “Today’s historic announcement is excellent news for science in Canada, for informed policy-making and for all Canadians. We look forward to working closely with the new Chief Science Advisor.”

In fulfilling our commitment to keep the community up to date and informed regarding science, technology, and innovation policy issues, CSPC has been compiling all news, publications, and editorials in recognition of the importance of the Federal Chief Science Officer as it has been developing, as you may see by clicking here.

We invite your opinions regarding the new Chief Science Advisor, to be published on our CSPC Featured Editorial page. We will publish your reactions on our website, sciencepolicy.ca on our Chief Science Advisor page.

Please send your opinion pieces to editorial@sciencepolicy.ca.

Here are a few (very few) details from the Prime Minister’s (Justin Trudeau) Sept. 26, 2017 press release making the official announcement,

The Government of Canada is committed to strengthen science in government decision-making and to support scientists’ vital work.

In keeping with these commitments, the Prime Minister, Justin Trudeau, today announced Dr. Mona Nemer as Canada’s new Chief Science Advisor, following an open, transparent, and merit-based selection process.  

We know Canadians value science. As the new Chief Science Advisor, Dr. Nemer will help promote science and its real benefits for Canadians—new knowledge, novel technologies, and advanced skills for future jobs. These breakthroughs and new opportunities form an essential part of the Government’s strategy to secure a better future for Canadian families and to grow Canada’s middle class.

Dr. Nemer is a distinguished medical researcher whose focus has been on the heart, particularly on the mechanisms of heart failure and congenital heart diseases. In addition to publishing over 200 scholarly articles, her research has led to new diagnostic tests for heart failure and the genetics of cardiac birth defects. Dr. Nemer has spent more than ten years as the Vice-President, Research at the University of Ottawa, has served on many national and international scientific advisory boards, and is a Fellow of the Royal Society of Canada, a Member of the Order of Canada, and a Chevalier de l’Ordre du Québec.

As Canada’s new top scientist, Dr. Nemer will provide impartial scientific advice to the Prime Minister and the Minister of Science. She will also make recommendations to help ensure that government science is fully available and accessible to the public, and that federal scientists remain free to speak about their work. Once a year, she will submit a report about the state of federal government science in Canada to the Prime Minister and the Minister of Science, which will also be made public.

Quotes

“We have taken great strides to fulfill our promise to restore science as a pillar of government decision-making. Today, we took another big step forward by announcing Dr. Mona Nemer as our Chief Science Advisor. Dr. Nemer brings a wealth of expertise to the role. Her advice will be invaluable and inform decisions made at the highest levels. I look forward to working with her to promote a culture of scientific excellence in Canada.”
— The Rt. Hon. Justin Trudeau, Prime Minister of Canada

“A respect for science and for Canada’s remarkable scientists is a core value for our government. I look forward to working with Dr. Nemer, Canada’s new Chief Science Advisor, who will provide us with the evidence we need to make decisions about what matters most to Canadians: their health and safety, their families and communities, their jobs, environment and future prosperity.”
— The Honourable Kirsty Duncan, Minister of Science

“I am honoured and excited to be Canada’s Chief Science Advisor. I am very pleased to be representing Canadian science and research – work that plays a crucial role in protecting and improving the lives of people everywhere. I look forward to advising the Prime Minister and the Minister of Science and working with the science community, policy makers, and the public to make science part of government policy making.”
— Dr. Mona Nemer, Chief Science Advisor, Canada

Quick Facts

  • Dr. Nemer is also a Knight of the Order of Merit of the French Republic, and has been awarded honorary doctorates from universities in France and Finland.
  • The Office of the Chief Science Advisor will be housed at Innovation, Science and Economic Development and supported by a secretariat.

Nemers’ Wikipedia entry does not provide much additional information although you can find out a bit more on her University of Ottawa page. Brian Owens in a Sept. 26, 2017 article for the American Association for the Advancement of Science’s (AAAS) Science Magazine provides a bit more detail, about this newly created office and its budget

Nemer’s office will have a $2 million budget, and she will report to both Trudeau and science minister Kirsty Duncan. Her mandate includes providing scientific advice to government ministers, helping keep government-funded science accessible to the public, and protecting government scientists from being muzzled.

Ivan Semeniuk’s Sept. 26, 2017 article for the Globe and Mail newspaper about Nemer’s appointment is the most informative (that I’ve been able to find),

Mona Nemer, a specialist in the genetics of heart disease and a long time vice-president of research at the University of Ottawa, has been named Canada’s new chief science advisor.

The appointment, announced Tuesday [Sept. 26, 2017] by Prime Minister Justin Trudeau, comes two years after the federal Liberals pledged to reinstate the position during the last election campaign and nearly a decade after the previous version of the role was cut by then prime minister Stephen Harper.

Dr. Nemer steps into the job of advising the federal government on science-related policy at a crucial time. Following a landmark review of Canada’s research landscape [Naylor report] released last spring, university-based scientists are lobbying hard for Ottawa to significantly boost science funding, one of the report’s key recommendations. At the same time, scientists and science-advocacy groups are increasingly scrutinizing federal actions on a range of sensitive environment and health-related issues to ensure the Trudeau government is making good on promises to embrace evidence-based decision making.

A key test of the position’s relevance for many observers will be the extent to which Dr. Nemer is able to speak her mind on matters where science may run afoul of political expediency.

Born in 1957, Dr. Nemer grew up in Lebanon and pursued an early passion for chemistry at a time and place where women were typically discouraged from entering scientific fields. With Lebanon’s civil war making it increasingly difficult for her to pursue her studies, her family was able to arrange for her to move to the United States, where she completed an undergraduate degree at Wichita State University in Kansas.

A key turning point came in the summer of 1977 when Dr. Nemer took a trip with friends to Montreal. She quickly fell for the city and, in short order, managed to secure acceptance to McGill University, where she received a PhD in 1982. …

It took a lot of searching to find out that Nemer was born in Lebanon and went to the United States first. A lot of immigrants and their families view Canada as a second choice and Nemer and her family would appear to have followed that pattern. It’s widely believed (amongst Canadians too) that the US is where you go for social mobility. I’m not sure if this is still the case but at one point in the 1980s Israel ranked as having the greatest social mobility in the world. Canada came in second while the US wasn’t even third or fourth ranked.

It’s the second major appointment by Justin Trudeau in the last few months to feature a woman who speaks French. The first was Julie Payette, former astronaut and Québecker, as the upcoming Governor General (there’s more detail and a whiff of sad scandal in this Aug. 21, 2017 Canadian Broadcasting Corporation online news item). Now there’s Dr. Mona Nemer who’s lived both in Québec and Ontario. Trudeau and his feminism, eh? Also, his desire to keep Québeckers happy (more or less).

I’m not surprised by the fact that Nemer has been based in Ottawa for several years. I guess they want someone who’s comfortable with the government apparatus although I for one think a little fresh air might be welcome. After all, the Minister of Science, Kirsty Duncan, is from Toronto which between Nemer and Duncan gives us the age-old Canadian government trifecta (geographically speaking), Ottawa-Montréal-Toronto.

Two final comments, I am surprised that Duncan did not make the announcement. After all, it was in her 2015 mandate letter.But perhaps Paul Wells in his acerbic June 29, 2017 article for Macleans hints at the reason as he discusses the Naylor report (review of fundamental science mentioned in Semeniuk’s article and for which Nemer is expected to provide advice),

The Naylor report represents Canadian research scientists’ side of a power struggle. The struggle has been continuing since Jean Chrétien left office. After early cuts, he presided for years over very large increases to the budgets of the main science granting councils. But since 2003, governments have preferred to put new funding dollars to targeted projects in applied sciences. …

Naylor wants that trend reversed, quickly. He is supported in that call by a frankly astonishingly broad coalition of university administrators and working researchers, who until his report were more often at odds. So you have the group representing Canada’s 15 largest research universities and the group representing all universities and a new group representing early-career researchers and, as far as I can tell, every Canadian scientist on Twitter. All backing Naylor. All fundamentally concerned that new money for research is of no particular interest if it does not back the best science as chosen by scientists, through peer review.

The competing model, the one preferred by governments of all stripes, might best be called superclusters. Very large investments into very large projects with loosely defined scientific objectives, whose real goal is to retain decorated veteran scientists and to improve the Canadian high-tech industry. Vast and sprawling labs and tech incubators, cabinet ministers nodding gravely as world leaders in sexy trendy fields sketch the golden path to Jobs of Tomorrow.

You see the imbalance. On one side, ribbons to cut. On the other, nerds experimenting on tapeworms. Kirsty Duncan, a shaky political performer, transparently a junior minister to the supercluster guy, with no deputy minister or department reporting to her, is in a structurally weak position: her title suggests she’s science’s emissary to the government, but she is not equipped to be anything more than government’s emissary to science.

Second,  our other science minister, Navdeep Bains, Minister of Innovation, Science  and Economic Development does not appear to have been present at the announcement. Quite surprising given where her office will located (from the government’s Sept. 26, 2017 press release in Quick Facts section ) “The Office of the Chief Science Advisor will be housed at Innovation, Science and Economic Development and supported by a secretariat.”

Finally, Wells’ article is well worth reading in its entirety and for those who are information gluttons, I have a three part series on the Naylor report, published June 8, 2017,

INVESTING IN CANADA’S FUTURE; Strengthening the Foundations of Canadian Research (Review of fundamental research final report): 1 of 3

INVESTING IN CANADA’S FUTURE; Strengthening the Foundations of Canadian Research (Review of fundamental research final report): 2 of 3

INVESTING IN CANADA’S FUTURE; Strengthening the Foundations of Canadian Research (Review of fundamental research final report): 3 of 3

Carbon nanotubes for water desalination

In discussions about water desalination and carbon nanomaterials,  it’s graphene that’s usually mentioned these days. By contrast, scientists from the US Department of Energy’s Lawrence Livermore National Laboratory (LLNL) have turned to carbon nanotubes,

There are two news items about the work at LLNL on ScienceDaily, this first one originated by the American Association for the Advancement of Science (AAAS) offers a succinct summary of the work (from an August 24, 2017 news item on ScienceDaily,

At just the right size, carbon nanotubes can filter water with better efficiency than biological proteins, a new study reveals. The results could pave the way to new water filtration systems, at a time when demands for fresh water pose a global threat to sustainable development.

A class of biological proteins, called aquaporins, is able to effectively filter water, yet scientists have not been able to manufacture scalable systems that mimic this ability. Aquaporins usually exhibit channels for filtering water molecules at a narrow width of 0.3 nanometers, which forces the water molecules into a single-file chain.

Here, Ramya H. Tunuguntla and colleagues experimented with nanotubes of different widths to see which ones are best for filtering water. Intriguingly, they found that carbon nanotubes with a width of 0.8 nanometers outperformed aquaporins in filtering efficiency by a factor of six.

These narrow carbon nanotube porins (nCNTPs) were still slim enough to force the water molecules into a single-file chain. The researchers attribute the differences between aquaporins and nCNTPS to differences in hydrogen bonding — whereas pore-lining residues in aquaporins can donate or accept H bonds to incoming water molecules, the walls of CNTPs cannot form H bonds, permitting unimpeded water flow.

The nCNTPs in this study maintained permeability exceeding that of typical saltwater, only diminishing at very high salt concentrations. Lastly, the team found that by changing the charges at the mouth of the nanotube, they can alter the ion selectivity. This advancement is highlighted in a Perspective [in Science magazine] by Zuzanna Siwy and Francesco Fornasiero.

The second Aug. 24, 2017 news item on ScienceDaily offers a more technical  perspective,

Lawrence Livermore scientists, in collaboration with researchers at Northeastern University, have developed carbon nanotube pores that can exclude salt from seawater. The team also found that water permeability in carbon nanotubes (CNTs) with diameters smaller than a nanometer (0.8 nm) exceeds that of wider carbon nanotubes by an order of magnitude.

The nanotubes, hollow structures made of carbon atoms in a unique arrangement, are more than 50,000 times thinner than a human hair. The super smooth inner surface of the nanotube is responsible for their remarkably high water permeability, while the tiny pore size blocks larger salt ions.

There’s a rather lovely illustration for this work,

An artist’s depiction of the promise of carbon nanotube porins for desalination. The image depicts a stylized carbon nanotube pipe that delivers clean desalinated water from the ocean to a kitchen tap. Image by Ryan Chen/LLNL

An Aug. 24, 2017 LLNL news release (also on EurekAlert), which originated the second news item, proceeds

Increasing demands for fresh water pose a global threat to sustainable development, resulting in water scarcity for 4 billion people. Current water purification technologies can benefit from the development of membranes with specialized pores that mimic highly efficient and water selective biological proteins.

“We found that carbon nanotubes with diameters smaller than a nanometer bear a key structural feature that enables enhanced transport. The narrow hydrophobic channel forces water to translocate in a single-file arrangement, a phenomenon similar to that found in the most efficient biological water transporters,” said Ramya Tunuguntla, an LLNL postdoctoral researcher and co-author of the manuscript appearing in the Aug. 24 [2017]edition of Science.

Computer simulations and experimental studies of water transport through CNTs with diameters larger than 1 nm showed enhanced water flow, but did not match the transport efficiency of biological proteins and did not separate salt efficiently, especially at higher salinities. The key breakthrough achieved by the LLNL team was to use smaller-diameter nanotubes that delivered the required boost in performance.

“These studies revealed the details of the water transport mechanism and showed that rational manipulation of these parameters can enhance pore efficiency,” said Meni Wanunu, a physics professor at Northeastern University and co-author on the study.

“Carbon nanotubes are a unique platform for studying molecular transport and nanofluidics,” said Alex Noy, LLNL principal investigator on the CNT project and a senior author on the paper. “Their sub-nanometer size, atomically smooth surfaces and similarity to cellular water transport channels make them exceptionally suited for this purpose, and it is very exciting to make a synthetic water channel that performs better than nature’s own.”

This discovery by the LLNL scientists and their colleagues has clear implications for the next generation of water purification technologies and will spur a renewed interest in development of the next generation of high-flux membranes.

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

Enhanced water permeability and tunable ion selectivity in subnanometer carbon nanotube porins by Ramya H. Tunuguntla, Robert Y. Henley, Yun-Chiao Yao, Tuan Anh Pham, Meni Wanunu, Aleksandr Noy. Science 25 Aug 2017: Vol. 357, Issue 6353, pp. 792-796 DOI: 10.1126/science.aan2438

This paper is behind a paywall.

And, Northeastern University issued an August 25, 2017 news release (also on EurekAlert) by Allie Nicodemo,

Earth is 70 percent water, but only a tiny portion—0.007 percent—is available to drink.

As potable water sources dwindle, global population increases every year. One potential solution to quenching the planet’s thirst is through desalinization—the process of removing salt from seawater. While tantalizing, this approach has always been too expensive and energy intensive for large-scale feasibility.

Now, researchers from Northeastern have made a discovery that could change that, making desalinization easier, faster and cheaper than ever before. In a paper published Thursday [August 24, 2017] in Science, the group describes how carbon nanotubes of a certain size act as the perfect filter for salt—the smallest and most abundant water contaminant.

Filtering water is tricky because water molecules want to stick together. The “H” in H2O is hydrogen, and hydrogen bonds are strong, requiring a lot of energy to separate. Water tends to bulk up and resist being filtered. But nanotubes do it rapidly, with ease.

A carbon nanotube is like an impossibly small rolled up sheet of paper, about a nanometer in diameter. For comparison, the diameter of a human hair is 50 to 70 micrometers—50,000 times wider. The tube’s miniscule size, exactly 0.8 nm, only allows one water molecule to pass through at a time. This single-file lineup disrupts the hydrogen bonds, so water can be pushed through the tubes at an accelerated pace, with no bulking.

“You can imagine if you’re a group of people trying to run through the hallway holding hands, it’s going to be a lot slower than running through the hallway single-file,” said co-author Meni Wanunu, associate professor of physics at Northeastern. Wanunu and post doctoral student Robert Henley collaborated with scientists at the Lawrence Livermore National Laboratory in California to conduct the research.

Scientists led by Aleksandr Noy at Lawrence Livermore discovered last year [2016] that carbon nanotubes were an ideal channel for proton transport. For this new study, Henley brought expertise and technology from Wanunu’s Nanoscale Biophysics Lab to Noy’s lab, and together they took the research one step further.

In addition to being precisely the right size for passing single water molecules, carbon nanotubes have a negative electric charge. This causes them to reject anything with the same charge, like the negative ions in salt, as well as other unwanted particles.

“While salt has a hard time passing through because of the charge, water is a neutral molecule and passes through easily,” Wanunu said. Scientists in Noy’s lab had theorized that carbon nanotubes could be designed for specific ion selectivity, but they didn’t have a reliable system of measurement. Luckily, “That’s the bread and butter of what we do in Meni’s lab,” Henley said. “It created a nice symbiotic relationship.”

“Robert brought the cutting-edge measurement and design capabilities of Wanunu’s group to my lab, and he was indispensable in developing a new platform that we used to measure the ion selectivity of the nanotubes,” Noy said.

The result is a novel system that could have major implications for the future of water security. The study showed that carbon nanotubes are better at desalinization than any other existing method— natural or man-made.

To keep their momentum going, the two labs have partnered with a leading water purification organization based in Israel. And the group was recently awarded a National Science Foundation/Binational Science Foundation grant to conduct further studies and develop water filtration platforms based on their new method. As they continue the research, the researchers hope to start programs where students can learn the latest on water filtration technology—with the goal of increasing that 0.007 percent.

As is usual in these cases there’s a fair degree of repetition but there’s always at least one nugget of new information, in this case, a link to Israel. As I noted many times, the Middle East is experiencing serious water issues. My most recent ‘water and the Middle East’ piece is an August 21, 2017 post about rainmaking at the Masdar Institute in United Arab Emirates. Approximately 50% of the way down the posting, I mention Israel and Palestine’s conflict over water.

Measurably fewer nanoparticles in São Paulo’s (Brazil) air after ethanol use

An Aug. 28, 2017 news item on Nanotechnology Now features news about nanoparticles and the environment in São Paulo, Brazil,

When ethanol prices at the pump rise for whatever reason, it becomes economically advantageous for drivers of dual-fuel vehicles to fill up with gasoline. However, the health of the entire population pays a high price: substitution of gasoline for ethanol leads to a 30% increase in the atmospheric concentration of ultrafine particulate matter, which consists of particles with a diameter of less than 50 nanometers (nm).

An Aug. 23, 2017 Fundação de Amparo à Pesquisa do Estado de São Paulo (The São Paulo Research Foundation [FAPESP]) press release, which originated the news item, explains further,

The phenomenon was detected in São Paulo City, Brazil, in a study supported by FAPESP and published in July 2017 in Nature Communications.

“These polluting nanoparticles are so tiny that they behave like gas molecules. When inhaled, they can penetrate the respiratory system’s defensive barriers and reach the pulmonary alveoli, so that potentially toxic substances enter the bloodstream and may increase the incidence of respiratory and cardiovascular problems,” said Paulo Artaxo, Full Professor at the University of São Paulo’s Physics Institute (IF-USP) and a co-author of the study.

Levels of ultrafine particulate matter in the atmosphere are neither monitored nor regulated by environmental agencies not only in Brazil but practically anywhere in the world, according to Artaxo. The São Paulo State Environmental Corporation (CETESB), for example, routinely monitors only solid particles with diameters of 10,000 nm (PM10) and 2,500 nm (PM2.5) – as well as other gaseous pollutants such as ozone (O3), carbon monoxide (CO) and nitrogen dioxide (NO2).

“Between 75% and 80% of the mass of the nanoparticles we measured in this study corresponds to organic compounds emitted by motor vehicles – carbon in different chemical forms. What these compounds are exactly and how they affect health are questions that require further research,” Artaxo said.

He added that a consensus is forming in the United States and Europe based on recent research indicating that these emissions are a potential health hazard and should be regulated. Several US states, such as California, have laws requiring a 20%-30% ethanol blend in gasoline, which also helps reduce emissions of ultrafine particulate matter.

Methodology

The data analyzed in the study were collected during the period of January-May 2011, when ethanol prices fluctuated sharply compared with gasoline prices, owing to macroeconomic factors such as variations in the international price of sugar (Brazilian ethanol is made from sugarcane).

Collection was performed at the top of a ten-story building belonging to IF-USP in the western part of São Paulo City. According to Artaxo, the site was chosen because it is relatively distant from the main traffic thoroughfares so that the aerosols there are “older” in the sense that they have already interacted with other substances present in the atmosphere.

“Generally speaking, the pollution we inhale every day at home or at work isn’t what comes out of vehicular exhaust pipes but particles already processed in the atmosphere,” he explained. “For this reason, we chose a site that isn’t directly impacted by primary vehicle emissions.”

The study was conducted during Joel Ferreira de Brito’s postdoctoral research, which Artaxo supervised. The model used to analyze the data was developed by Brazilian economist Alberto Salvo, a professor at the National University of Singapore and first author of the article. Franz Geiger, a chemist at Northwestern University in the US, also collaborated.

“We adapted a sophisticated statistical model originally developed for economic analysis and used here for the first time to analyze the chemistry of atmospheric nanoparticles,” Artaxo said. “The main strength of this tool is that it can work with a large number of variables, such as the presence or absence of rainfall, wind direction, traffic intensity, and levels of ozone, carbon monoxide and other pollutants.”

Analyses were performed before, during and after a sharp fluctuation in ethanol prices leading consumers to switch motor fuels in São Paulo City. While no significant changes were detected in levels of inhalable fine particulate matter (PM2.5 and PM10), the study proved in a real, day-to-day situation that choosing ethanol reduces emissions of ultrafine particles. To date, this phenomenon had only been observed in the laboratory.

“These results reinforce the need for public policies to encourage the use of biofuels, as they clearly show that the public lose in health what they save at the pump when opting for gasoline,” Artaxo said.

In São Paulo, a city with 7 million motor vehicles and the largest urban fleet of flexible-fuel cars, it would be feasible to run all buses on biofuel. “We have the technology for this in Brazil – and at a competitive price,” he said.

The fact that the city’s bus fleet still depends on diesel, Artaxo warned, creates an even worse health hazard in the shape of emissions of black carbon, one of the main components of soot and a pollutant that contributes to global warming. Alongside electricity generation, the transportation sector is the largest emitter of pollutants produced by the burning of fossil fuels.

For Artaxo, incentives for electric, hybrid or biofuel vehicles are vital to reduce greenhouse gas emissions. “By incentivizing biofuels, we could solve several problems at once,” he said. “We could combat climate change, reduce harm to health and foster advances in automotive technology by offering a stimulus for auto makers to develop more economical and efficient cars fueled by ethanol.”

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

Reduced ultrafine particle levels in São Paulo’s atmosphere during shifts from gasoline to ethanol use by Alberto Salvo, Joel Brito, Paulo Artaxo, & Franz M. Geiger. Nature Communications 8, Article number: 77 (2017) doi:10.1038/s41467-017-00041-5 Published online: 18 July 2017

This paper is open access.

Yarns that harvest and generate energy

The researchers involved in this work are confident enough about their prospects that they will be  patenting their research into yarns. From an August 25, 2017 news item on Nanowerk,

An international research team led by scientists at The University of Texas at Dallas and Hanyang University in South Korea has developed high-tech yarns that generate electricity when they are stretched or twisted.

In a study published in the Aug. 25 [2017] issue of the journal Science (“Harvesting electrical energy from carbon nanotube yarn twist”), researchers describe “twistron” yarns and their possible applications, such as harvesting energy from the motion of ocean waves or from temperature fluctuations. When sewn into a shirt, these yarns served as a self-powered breathing monitor.

“The easiest way to think of twistron harvesters is, you have a piece of yarn, you stretch it, and out comes electricity,” said Dr. Carter Haines, associate research professor in the Alan G. MacDiarmid NanoTech Institute at UT Dallas and co-lead author of the article. The article also includes researchers from South Korea, Virginia Tech, Wright-Patterson Air Force Base and China.

An August 25, 2017 University of Texas at Dallas news release, which originated the news item, expands on the theme,

Yarns Based on Nanotechnology

The yarns are constructed from carbon nanotubes, which are hollow cylinders of carbon 10,000 times smaller in diameter than a human hair. The researchers first twist-spun the nanotubes into high-strength, lightweight yarns. To make the yarns highly elastic, they introduced so much twist that the yarns coiled like an over-twisted rubber band.

In order to generate electricity, the yarns must be either submerged in or coated with an ionically conducting material, or electrolyte, which can be as simple as a mixture of ordinary table salt and water.

“Fundamentally, these yarns are supercapacitors,” said Dr. Na Li, a research scientist at the NanoTech Institute and co-lead author of the study. “In a normal capacitor, you use energy — like from a battery — to add charges to the capacitor. But in our case, when you insert the carbon nanotube yarn into an electrolyte bath, the yarns are charged by the electrolyte itself. No external battery, or voltage, is needed.”

When a harvester yarn is twisted or stretched, the volume of the carbon nanotube yarn decreases, bringing the electric charges on the yarn closer together and increasing their energy, Haines said. This increases the voltage associated with the charge stored in the yarn, enabling the harvesting of electricity.

Stretching the coiled twistron yarns 30 times a second generated 250 watts per kilogram of peak electrical power when normalized to the harvester’s weight, said Dr. Ray Baughman, director of the NanoTech Institute and a corresponding author of the study.

“Although numerous alternative harvesters have been investigated for many decades, no other reported harvester provides such high electrical power or energy output per cycle as ours for stretching rates between a few cycles per second and 600 cycles per second.”

Lab Tests Show Potential Applications

In the lab, the researchers showed that a twistron yarn weighing less than a housefly could power a small LED, which lit up each time the yarn was stretched.

To show that twistrons can harvest waste thermal energy from the environment, Li connected a twistron yarn to a polymer artificial muscle that contracts and expands when heated and cooled. The twistron harvester converted the mechanical energy generated by the polymer muscle to electrical energy.

“There is a lot of interest in using waste energy to power the Internet of Things, such as arrays of distributed sensors,” Li said. “Twistron technology might be exploited for such applications where changing batteries is impractical.”

The researchers also sewed twistron harvesters into a shirt. Normal breathing stretched the yarn and generated an electrical signal, demonstrating its potential as a self-powered respiration sensor.

“Electronic textiles are of major commercial interest, but how are you going to power them?” Baughman said. “Harvesting electrical energy from human motion is one strategy for eliminating the need for batteries. Our yarns produced over a hundred times higher electrical power per weight when stretched compared to other weavable fibers reported in the literature.”

Electricity from Ocean Waves

“In the lab we showed that our energy harvesters worked using a solution of table salt as the electrolyte,” said Baughman, who holds the Robert A. Welch Distinguished Chair in Chemistry in the School of Natural Sciences and Mathematics. “But we wanted to show that they would also work in ocean water, which is chemically more complex.”

In a proof-of-concept demonstration, co-lead author Dr. Shi Hyeong Kim, a postdoctoral researcher at the NanoTech Institute, waded into the frigid surf off the east coast of South Korea to deploy a coiled twistron in the sea. He attached a 10 centimeter-long yarn, weighing only 1 milligram (about the weight of a mosquito), between a balloon and a sinker that rested on the seabed.

Every time an ocean wave arrived, the balloon would rise, stretching the yarn up to 25 percent, thereby generating measured electricity.

Even though the investigators used very small amounts of twistron yarn in the current study, they have shown that harvester performance is scalable, both by increasing twistron diameter and by operating many yarns in parallel.

“If our twistron harvesters could be made less expensively, they might ultimately be able to harvest the enormous amount of energy available from ocean waves,” Baughman said. “However, at present these harvesters are most suitable for powering sensors and sensor communications. Based on demonstrated average power output, just 31 milligrams of carbon nanotube yarn harvester could provide the electrical energy needed to transmit a 2-kilobyte packet of data over a 100-meter radius every 10 seconds for the Internet of Things.”

Researchers from the UT Dallas Erik Jonsson School of Engineering and Computer Science and Lintec of America’s Nano-Science & Technology Center also participated in the study.

The investigators have filed a patent on the technology.

In the U.S., the research was funded by the Air Force, the Air Force Office of Scientific Research, NASA, the Office of Naval Research and the Robert A. Welch Foundation. In Korea, the research was supported by the Korea-U.S. Air Force Cooperation Program and the Creative Research Initiative Center for Self-powered Actuation of the National Research Foundation and the Ministry of Science.

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

Harvesting electrical energy from carbon nanotube yarn twist by Shi Hyeong Kim, Carter S. Haines, Na Li, Keon Jung Kim, Tae Jin Mun, Changsoon Choi, Jiangtao Di, Young Jun Oh, Juan Pablo Oviedo, Julia Bykova, Shaoli Fang, Nan Jiang, Zunfeng Liu, Run Wang, Prashant Kumar, Rui Qiao, Shashank Priya, Kyeongjae Cho, Moon Kim, Matthew Steven Lucas, Lawrence F. Drummy, Benji Maruyama, Dong Youn Lee, Xavier Lepró, Enlai Gao, Dawood Albarq, Raquel Ovalle-Robles, Seon Jeong Kim, Ray H. Baughman. Science 25 Aug 2017: Vol. 357, Issue 6353, pp. 773-778 DOI: 10.1126/science.aam8771

This paper is behind a paywall.

Dexter Johnson in an Aug. 25, 2017 posting on his Nanoclast blog (on the IEEE [Institute of Electrical and Electronics Engineers] website) delves further into the research,

“Basically what’s happening is when we stretch the yarn, we’re getting a change in capacitance of the yarn. It’s that change that allows us to get energy out,” explains Carter Haines, associate research professor at UT Dallas and co-lead author of the paper describing the research, in an interview with IEEE Spectrum.

This makes it similar in many ways to other types of energy harvesters. For instance, in other research, it has been demonstrated—with sheets of rubber with coated electrodes on both sides—that you can increase the capacitance of a material when you stretch it and it becomes thinner. As a result, if you have charge on that capacitor, you can change the voltage associated with that charge.

“We’re more or less exploiting the same effect but what we’re doing differently is we’re using an electric chemical cell to do this,” says Haines. “So we’re not changing double layer capacitance in normal parallel plate capacitors. But we’re actually changing the electric chemical capacitance on the surface of a super capacitor yarn.”

While there are other capacitance-based energy harvesters, those other devices require extremely high voltages to work because they’re using parallel plate capacitors, according to Haines.

Dexter asks good questions and his post is very informative.