Tag Archives: UCL

Robot radiologists (artificially intelligent doctors)

Mutaz Musa, a physician at New York Presbyterian Hospital/Weill Cornell (Department of Emergency Medicine) and software developer in New York City, has penned an eyeopening opinion piece about artificial intelligence (or robots if you prefer) and the field of radiology. From a June 25, 2018 opinion piece for The Scientist (Note: Links have been removed),

Although artificial intelligence has raised fears of job loss for many, we doctors have thus far enjoyed a smug sense of security. There are signs, however, that the first wave of AI-driven redundancies among doctors is fast approaching. And radiologists seem to be first on the chopping block.

Andrew Ng, founder of online learning platform Coursera and former CTO of “China’s Google,” Baidu, recently announced the development of CheXNet, a convolutional neural net capable of recognizing pneumonia and other thoracic pathologies on chest X-rays better than human radiologists. Earlier this year, a Hungarian group developed a similar system for detecting and classifying features of breast cancer in mammograms. In 2017, Adelaide University researchers published details of a bot capable of matching human radiologist performance in detecting hip fractures. And, of course, Google achieved superhuman proficiency in detecting diabetic retinopathy in fundus photographs, a task outside the scope of most radiologists.

Beyond single, two-dimensional radiographs, a team at Oxford University developed a system for detecting spinal disease from MRI data with a performance equivalent to a human radiologist. Meanwhile, researchers at the University of California, Los Angeles, reported detecting pathology on head CT scans with an error rate more than 20 times lower than a human radiologist.

Although these particular projects are still in the research phase and far from perfect—for instance, often pitting their machines against a limited number of radiologists—the pace of progress alone is telling.

Others have already taken their algorithms out of the lab and into the marketplace. Enlitic, founded by Aussie serial entrepreneur and University of San Francisco researcher Jeremy Howard, is a Bay-Area startup that offers automated X-ray and chest CAT scan interpretation services. Enlitic’s systems putatively can judge the malignancy of nodules up to 50 percent more accurately than a panel of radiologists and identify fractures so small they’d typically be missed by the human eye. One of Enlitic’s largest investors, Capitol Health, owns a network of diagnostic imaging centers throughout Australia, anticipating the broad rollout of this technology. Another Bay-Area startup, Arterys, offers cloud-based medical imaging diagnostics. Arterys’s services extend beyond plain films to cardiac MRIs and CAT scans of the chest and abdomen. And there are many others.

Musa has offered a compelling argument with lots of links to supporting evidence.

[downloaded from https://www.the-scientist.com/news-opinion/opinion–rise-of-the-robot-radiologists-64356]

And evidence keeps mounting, I just stumbled across this June 30, 2018 news item on Xinhuanet.com,

An artificial intelligence (AI) system scored 2:0 against elite human physicians Saturday in two rounds of competitions in diagnosing brain tumors and predicting hematoma expansion in Beijing.

The BioMind AI system, developed by the Artificial Intelligence Research Centre for Neurological Disorders at the Beijing Tiantan Hospital and a research team from the Capital Medical University, made correct diagnoses in 87 percent of 225 cases in about 15 minutes, while a team of 15 senior doctors only achieved 66-percent accuracy.

The AI also gave correct predictions in 83 percent of brain hematoma expansion cases, outperforming the 63-percent accuracy among a group of physicians from renowned hospitals across the country.

The outcomes for human physicians were quite normal and even better than the average accuracy in ordinary hospitals, said Gao Peiyi, head of the radiology department at Tiantan Hospital, a leading institution on neurology and neurosurgery.

To train the AI, developers fed it tens of thousands of images of nervous system-related diseases that the Tiantan Hospital has archived over the past 10 years, making it capable of diagnosing common neurological diseases such as meningioma and glioma with an accuracy rate of over 90 percent, comparable to that of a senior doctor.

All the cases were real and contributed by the hospital, but never used as training material for the AI, according to the organizer.

Wang Yongjun, executive vice president of the Tiantan Hospital, said that he personally did not care very much about who won, because the contest was never intended to pit humans against technology but to help doctors learn and improve [emphasis mine] through interactions with technology.

“I hope through this competition, doctors can experience the power of artificial intelligence. This is especially so for some doctors who are skeptical about artificial intelligence. I hope they can further understand AI and eliminate their fears toward it,” said Wang.

Dr. Lin Yi who participated and lost in the second round, said that she welcomes AI, as it is not a threat but a “friend.” [emphasis mine]

AI will not only reduce the workload but also push doctors to keep learning and improve their skills, said Lin.

Bian Xiuwu, an academician with the Chinese Academy of Science and a member of the competition’s jury, said there has never been an absolute standard correct answer in diagnosing developing diseases, and the AI would only serve as an assistant to doctors in giving preliminary results. [emphasis mine]

Dr. Paul Parizel, former president of the European Society of Radiology and another member of the jury, also agreed that AI will not replace doctors, but will instead function similar to how GPS does for drivers. [emphasis mine]

Dr. Gauden Galea, representative of the World Health Organization in China, said AI is an exciting tool for healthcare but still in the primitive stages.

Based on the size of its population and the huge volume of accessible digital medical data, China has a unique advantage in developing medical AI, according to Galea.

China has introduced a series of plans in developing AI applications in recent years.

In 2017, the State Council issued a development plan on the new generation of Artificial Intelligence and the Ministry of Industry and Information Technology also issued the “Three-Year Action Plan for Promoting the Development of a New Generation of Artificial Intelligence (2018-2020).”

The Action Plan proposed developing medical image-assisted diagnostic systems to support medicine in various fields.

I note the reference to cars and global positioning systems (GPS) and their role as ‘helpers’;, it seems no one at the ‘AI and radiology’ competition has heard of driverless cars. Here’s Musa on those reassuring comments abut how the technology won’t replace experts but rather augment their skills,

To be sure, these services frame themselves as “support products” that “make doctors faster,” rather than replacements that make doctors redundant. This language may reflect a reserved view of the technology, though it likely also represents a marketing strategy keen to avoid threatening or antagonizing incumbents. After all, many of the customers themselves, for now, are radiologists.

Radiology isn’t the only area where experts might find themselves displaced.

Eye experts

It seems inroads have been made by artificial intelligence systems (AI) into the diagnosis of eye diseases. It got the ‘Fast Company’ treatment (exciting new tech, learn all about it) as can be seen further down in this posting. First, here’s a more restrained announcement, from an August 14, 2018 news item on phys.org (Note: A link has been removed),

An artificial intelligence (AI) system, which can recommend the correct referral decision for more than 50 eye diseases, as accurately as experts has been developed by Moorfields Eye Hospital NHS Foundation Trust, DeepMind Health and UCL [University College London].

The breakthrough research, published online by Nature Medicine, describes how machine-learning technology has been successfully trained on thousands of historic de-personalised eye scans to identify features of eye disease and recommend how patients should be referred for care.

Researchers hope the technology could one day transform the way professionals carry out eye tests, allowing them to spot conditions earlier and prioritise patients with the most serious eye diseases before irreversible damage sets in.

An August 13, 2018 UCL press release, which originated the news item, describes the research and the reasons behind it in more detail,

More than 285 million people worldwide live with some form of sight loss, including more than two million people in the UK. Eye diseases remain one of the biggest causes of sight loss, and many can be prevented with early detection and treatment.

Dr Pearse Keane, NIHR Clinician Scientist at the UCL Institute of Ophthalmology and consultant ophthalmologist at Moorfields Eye Hospital NHS Foundation Trust said: “The number of eye scans we’re performing is growing at a pace much faster than human experts are able to interpret them. There is a risk that this may cause delays in the diagnosis and treatment of sight-threatening diseases, which can be devastating for patients.”

“The AI technology we’re developing is designed to prioritise patients who need to be seen and treated urgently by a doctor or eye care professional. If we can diagnose and treat eye conditions early, it gives us the best chance of saving people’s sight. With further research it could lead to greater consistency and quality of care for patients with eye problems in the future.”

The study, launched in 2016, brought together leading NHS eye health professionals and scientists from UCL and the National Institute for Health Research (NIHR) with some of the UK’s top technologists at DeepMind to investigate whether AI technology could help improve the care of patients with sight-threatening diseases, such as age-related macular degeneration and diabetic eye disease.

Using two types of neural network – mathematical systems for identifying patterns in images or data – the AI system quickly learnt to identify 10 features of eye disease from highly complex optical coherence tomography (OCT) scans. The system was then able to recommend a referral decision based on the most urgent conditions detected.

To establish whether the AI system was making correct referrals, clinicians also viewed the same OCT scans and made their own referral decisions. The study concluded that AI was able to make the right referral recommendation more than 94% of the time, matching the performance of expert clinicians.

The AI has been developed with two unique features which maximise its potential use in eye care. Firstly, the system can provide information that helps explain to eye care professionals how it arrives at its recommendations. This information includes visuals of the features of eye disease it has identified on the OCT scan and the level of confidence the system has in its recommendations, in the form of a percentage. This functionality is crucial in helping clinicians scrutinise the technology’s recommendations and check its accuracy before deciding the type of care and treatment a patient receives.

Secondly, the AI system can be easily applied to different types of eye scanner, not just the specific model on which it was trained. This could significantly increase the number of people who benefit from this technology and future-proof it, so it can still be used even as OCT scanners are upgraded or replaced over time.

The next step is for the research to go through clinical trials to explore how this technology might improve patient care in practice, and regulatory approval before it can be used in hospitals and other clinical settings.

If clinical trials are successful in demonstrating that the technology can be used safely and effectively, Moorfields will be able to use an eventual, regulatory-approved product for free, across all 30 of their UK hospitals and community clinics, for an initial period of five years.

The work that has gone into this project will also help accelerate wider NHS research for many years to come. For example, DeepMind has invested significant resources to clean, curate and label Moorfields’ de-identified research dataset to create one of the most advanced eye research databases in the world.

Moorfields owns this database as a non-commercial public asset, which is already forming the basis of nine separate medical research studies. In addition, Moorfields can also use DeepMind’s trained AI model for future non-commercial research efforts, which could help advance medical research even further.

Mustafa Suleyman, Co-founder and Head of Applied AI at DeepMind Health, said: “We set up DeepMind Health because we believe artificial intelligence can help solve some of society’s biggest health challenges, like avoidable sight loss, which affects millions of people across the globe. These incredibly exciting results take us one step closer to that goal and could, in time, transform the diagnosis, treatment and management of patients with sight threatening eye conditions, not just at Moorfields, but around the world.”

Professor Sir Peng Tee Khaw, director of the NIHR Biomedical Research Centre at Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology said: “The results of this pioneering research with DeepMind are very exciting and demonstrate the potential sight-saving impact AI could have for patients. I am in no doubt that AI has a vital role to play in the future of healthcare, particularly when it comes to training and helping medical professionals so that patients benefit from vital treatment earlier than might previously have been possible. This shows the transformative research than can be carried out in the UK combining world leading industry and NIHR/NHS hospital/university partnerships.”

Matt Hancock, Health and Social Care Secretary, said: “This is hugely exciting and exactly the type of technology which will benefit the NHS in the long term and improve patient care – that’s why we fund over a billion pounds a year in health research as part of our long term plan for the NHS.”

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

Clinically applicable deep learning for diagnosis and referral in retinal disease by Jeffrey De Fauw, Joseph R. Ledsam, Bernardino Romera-Paredes, Stanislav Nikolov, Nenad Tomasev, Sam Blackwell, Harry Askham, Xavier Glorot, Brendan O’Donoghue, Daniel Visentin, George van den Driessche, Balaji Lakshminarayanan, Clemens Meyer, Faith Mackinder, Simon Bouton, Kareem Ayoub, Reena Chopra, Dominic King, Alan Karthikesalingam, Cían O. Hughes, Rosalind Raine, Julian Hughes, Dawn A. Sim, Catherine Egan, Adnan Tufail, Hugh Montgomery, Demis Hassabis, Geraint Rees, Trevor Back, Peng T. Khaw, Mustafa Suleyman, Julien Cornebise, Pearse A. Keane, & Olaf Ronneberger. Nature Medicine (2018) DOI: https://doi.org/10.1038/s41591-018-0107-6 Published 13 August 2018

This paper is behind a paywall.

And now, Melissa Locker’s August 15, 2018 article for Fast Company (Note: Links have been removed),

In a paper published in Nature Medicine on Monday, Google’s DeepMind subsidiary, UCL, and researchers at Moorfields Eye Hospital showed off their new AI system. The researchers used deep learning to create algorithm-driven software that can identify common patterns in data culled from dozens of common eye diseases from 3D scans. The result is an AI that can identify more than 50 diseases with incredible accuracy and can then refer patients to a specialist. Even more important, though, is that the AI can explain why a diagnosis was made, indicating which part of the scan prompted the outcome. It’s an important step in both medicine and in making AIs slightly more human

The editor or writer has even highlighted the sentence about the system’s accuracy—not just good but incredible!

I will be publishing something soon [my August 21, 2018 posting] which highlights some of the questions one might want to ask about AI and medicine before diving headfirst into this brave new world of medicine.

How does sticky tape make graphene?

As I understand it, Andre Geim one of the two men (the other was Konstantin Novoselov) to first isolate graphene from a block of graphite by using sticky tape is not thrilled that it’s known in some quarters as the graphene sticky tape method. Still, the technique caught the imagination as Steve Connor’s March 18, 2013 article for the Independent made clear.

It seems scientists are still just as fascinated as anyone else as a February 27, 2018 news item for Nanowerk describes,

Scientists at UCL [University College London] have explained for the first time the mystery of why adhesive tape is so useful for graphene production.

The study, published in Advanced Materials (“Graphene–Graphene Interactions: Friction, Superlubricity, and Exfoliation”), used supercomputers to model the process through which graphene sheets are exfoliated from graphite, the material in pencils.

A February 26, 2018 UCL press release, which originated the news item, provides more detail,

There are various methods for exfoliating graphene, including the famous adhesive tape method developed by Nobel Prize winner Andre Geim. However little has been known until now about how the process of exfoliating graphene using sticky tape works.

Academics at UCL are now able to demonstrate how individual flakes of graphite can be exfoliated to make one atom thick layers. They also reveal that the process of peeling a layer of graphene demands 40% less energy than that of another common method called shearing. This is expected to have far reaching impacts for the commercial production of graphene.

“The sticky tape method works rather like peeling egg boxes apart with a vertical motion, it is easier than pulling one horizontally across another when they are neatly stacked,” explained Professor Peter Coveney, Director of the Centre for Computational Science (UCL Chemistry).

“If shearing, then you get held up by this egg carton configuration. But if you peel, you can get them apart much more easily. The polymethyl methacrylate adhesive on traditional sticky tape is ideal for picking up the edge of the graphene sheet so it can be lifted and peeled,” added Professor Coveney.

Graphite occurs naturally, its basic crystalline structure is stacks of flat sheets of strongly bonded carbon atoms in a honeycomb pattern. Graphite’s many layers are bound together by weak interactions and can easily slide large distances over one another with little friction due to their superlubricity.

The scientists at UCL simulated an experiment conducted in 2015 at Lawrence Berkeley Laboratory in Berkeley, California, which used a special microscope with atomic resolution to see how graphene flakes move around on a graphite surface.

The supercomputer’s results matched Berkeley’s observations showing that there is less movement when the graphene atoms neatly line up with the atoms below.

“Despite the vast amount of research carried out on graphene since its discovery, it is clear that until now our understanding of its behaviour on an atomic length scale was very poor,” explains PhD student Robert Sinclair (UCL Chemistry).

“The one reason above all others why the material is difficult to use is because it is hard to make. Even now, a dozen years after its discovery, companies have to apply sticky tape methods to pull it apart, as the Laureates did to uncover it; hardly a hi-tech and industrially simple process to implement. We’re now in a position to assist experimentalists to figure out how to prise it apart, or make it to order. That could have big cost implications for the emerging graphene industry,” said Professor Coveney.

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

Graphene–Graphene Interactions: Friction, Superlubricity, and Exfoliation by Robert C. Sinclair, James L. Suter, and Peter V. Coveney. Advanced Materials DOI: 10.1002/adma.201705791 First published: 13 February 2018

This paper is open access.

Cosmopolitanism and the Local in Science and Nature (a three year Canadian project nearing its end date)

Working on a grant from Canada’s Social Sciences and Humanities Research Council (SSHRC), the  Cosmopolitanism and the Local in Science and Nature project has been establishing a ‘cosmopolitanism’ research network that critiques the eurocentric approach so beloved of Canadian academics and has set up nodes across Canada and in India and Southeast Asia.

I first wrote about the project in a Dec. 12, 2014 posting which also featured a job listing. It seems I was there for the beginning and now for the end. For one of the project’s blog postings in its final months, they’re profiling one of their researchers (Dr. Letitia Meynell, Sept. 6, 2017 posting),

1. What is your current place of research?

I am an associate professor in philosophy at Dalhousie University, cross appointed with gender and women studies.

2. Could you give us some details about your education background?

My 1st degree was in Theater, which I did at York University. I did, however, minor in Philosophy and I have always had a particular interest in philosophy of science. So, my minor was perhaps a little anomalous, comprising courses on philosophy of physics, philosophy of nature, and the philosophy of Karl Popper along with courses on aesthetics and existentialism. After taking a few more courses in philosophy at the University of Calgary, I enrolled there for a Master’s degree, writing a thesis on conceptualization, with a view to its role in aesthetics and epistemology. From there I moved to the University of Western Ontario where I brought these three interests together, writing a thesis on the epistemology of pictures in science. Throughout these studies I maintained a keen interest in feminist philosophy, especially the politics of knowledge, and I have always seen my work on pictures in science as fitting into broader feminist commitments.

3. What projects are you currently working on and what are some projects you’ve worked on in the past?

4. What’s one thing you particularly enjoy about working in your field?

5. How do you relate your work to the broader topic of ‘cosmopolitanism and the local’?

As feminist philosophers have long realized, having perspectives on a topic that are quite different to your own is incredibly powerful for critically assessing both your own views and those of others. So, for instance, if you want to address the exploitation of nonhuman animals in our society it is incredibly powerful to consider how people from, say, South Asian traditions have thought about the differences, similarities, and relationships between humans and other animals. Keeping non-western perspectives in mind, even as one works in a western philosophical tradition, helps one to be both more rigorous in one’s analyses and less dogmatic. Rigor and critical openness are, in my opinion, central virtues of philosophy and, indeed, science.

Dr. Maynell will be speaking at the ‘Bridging the Gap: Scientific Imagination Meets Aesthetic Imagination‘ conference Oct. 5-6, 2017 at the London School of Economics,

On 5–6 October, this 2-day conference aims to connect work on artistic and scientific imagination, and to advance our understanding of the epistemic and heuristic roles that imagination can play.

Why, how, and when do scientists imagine, and what epistemological roles does the imagination play in scientific progress? Over the past few years, many philosophical accounts have emerged that are relevant to these questions. Roman Frigg, Arnon Levy, and Adam Toon have developed theories of scientific models that place imagination at the heart of modelling practice. And James R. Brown, Tamar Gendler, James McAllister, Letitia Meynell, and Nancy Nersessian have developed theories that recognize the indispensable role of the imagination in the performance of thought experiments. On the other hand, philosophers like Michael Weisberg dismiss imagination-based views of scientific modelling as mere “folk ontology”, and John D. Norton seems to claim that thought experiments are arguments whose imaginary components are epistemologically irrelevant.

In this conference we turn to aesthetics for help in addressing issues concerning scientific imagination-use. Aesthetics is said to have begun in 1717 with an essay called “The Pleasures of the Imagination” by Joseph Addison, and ever since imagination has been what Michael Polyani called “the cornerstone of aesthetic theory”. In recent years Kendall Walton has fruitfully explored the fundamental relevance of imagination for understanding literary, visual and auditory fictions. And many others have been inspired to do the same, including Greg Currie, David Davies, Peter Lamarque, Stein Olsen, and Kathleen Stock.

This conference aims to connect work on artistic and scientific imagination, and to advance our understanding of the epistemic and heuristic roles that imagination can play. Specific topics may include:

  • What kinds of imagination are involved in science?
  • What is the relation between scientific imagination and aesthetic imagination?
  • What are the structure and limits of knowledge and understanding acquired through imagination?
  • From a methodological point of view, how can aesthetic considerations about imagination play a role in philosophical accounts of scientific reasoning?
  • What can considerations about scientific imagination contribute to our understanding of aesthetic imagination?

The conference will include eight invited talks and four contributed papers. Two of the four slots for contributed papers are being reserved for graduate students, each of whom will receive a travel bursary of £100.

Invited speakers

Margherita Arcangeli (Humboldt University, Berlin)

Andrej Bicanski (Institute of Cognitive Neuroscience, University College London)

Gregory Currie (University of York)

Jim Faeder (University of Pittsburgh School of Medicine)

Tim de Mey (Erasmus University of Rotterdam)

Laetitia Meynell (Dalhousie University, Canada)

Adam Toon (University of Exeter)

Margot Strohminger (Humboldt University, Berlin)

This event is organised by LSE’s Centre for Philosophy of Natural and Social Science and it is co-sponsored by the British Society of Aesthetics, the Mind Association, the Aristotelian Society and the Marie Skłodowska-Curie grant agreement No 654034.

I wonder if they’ll be rubbing shoulders with Angelina Jolie? She is slated to be teaching there in Fall 2017 according to a May 23, 2016 news item in the Guardian (Note: Links have been removed),

The Hollywood actor and director has been appointed a visiting professor at the London School of Economics, teaching a course on the impact of war on women.

From 2017, Jolie will join the former foreign secretary William Hague as a “professor in practice”, the university announced on Monday, as part of a new MSc course on women, peace and security, which LSE says is the first of its kind in the world.

The course, it says, is intended to “[develop] strategies to promote gender equality and enhance women’s economic, social and political participation and security”, with visiting professors playing an active part in giving lectures, participating in workshops and undertaking their own research.

Getting back to ‘Cosmopolitanism’, some of the principals organized a summer 2017 event (from a Sept. 6, 2017 posting titled: Summer Events – 25th International Congress of History of Science and Technology),

CosmoLocal partners Lesley Cormack (University of Alberta, Canada), Gordon McOuat (University of King’s College, Halifax, Canada), and Dhruv Raina (Jawaharlal Nehru University, India) organized a symposium “Cosmopolitanism and the Local in Science and Nature” as part of the 25th International Congress of History of Science and Technology.  The conference was held July 23-29, 2017, in Rio de Janeiro, Brazil.  The abstract of the CosmoLocal symposium is below, and a pdf version can be found here.

Science, and its associated technologies, is typically viewed as “universal”. At the same time we were also assured that science can trace its genealogy to Europe in a period of rising European intellectual and imperial global force, ‘going outwards’ towards the periphery. As such, it is strikingly parochial. In a kind of sad irony, the ‘subaltern’ was left to retell that tale as one of centre-universalism dominating a traditionalist periphery. Self-described ‘modernity’ and ‘the west’ (two intertwined concepts of recent and mutually self-supporting origin) have erased much of the local engagement and as such represent science as emerging sui generis, moving in one direction. This story is now being challenged within sociology, political theory and history.

… Significantly, scholars who study the history of science in Asia and India have been examining different trajectories for the origin and meaning of science. It is now time for a dialogue between these approaches. Grounding the dialogue is the notion of a “cosmopolitical” science. “Cosmopolitics” is a term borrowed from Kant’s notion of perpetual peace and modern civil society, imagining shared political, moral and economic spaces within which trade, politics and reason get conducted.  …

The abstract is a little ‘high falutin’ but I’m glad to see more efforts being made in  Canada to understand science and its history as a global affair.

CRISPR and editing the germline in the US (part 3 of 3): public discussions and pop culture

After giving a basic explanation of the technology and some of the controversies in part 1 and offering more detail about the technology and about the possibility of designer babies in part 2; this part covers public discussion, a call for one and the suggestion that one is taking place in popular culture.

But a discussion does need to happen

In a move that is either an exquisite coincidence or has been carefully orchestrated (I vote for the latter), researchers from the University of Wisconsin-Madison have released a study about attitudes in the US to human genome editing. From an Aug. 11, 2017 University of Wisconsin-Madison news release (also on EurekAllert),

In early August 2017, an international team of scientists announced they had successfully edited the DNA of human embryos. As people process the political, moral and regulatory issues of the technology — which nudges us closer to nonfiction than science fiction — researchers at the University of Wisconsin-Madison and Temple University show the time is now to involve the American public in discussions about human genome editing.

In a study published Aug. 11 in the journal Science, the researchers assessed what people in the United States think about the uses of human genome editing and how their attitudes may drive public discussion. They found a public divided on its uses but united in the importance of moving conversations forward.

“There are several pathways we can go down with gene editing,” says UW-Madison’s Dietram Scheufele, lead author of the study and member of a National Academy of Sciences committee that compiled a report focused on human gene editing earlier this year. “Our study takes an exhaustive look at all of those possible pathways forward and asks where the public stands on each one of them.”

Compared to previous studies on public attitudes about the technology, the new study takes a more nuanced approach, examining public opinion about the use of gene editing for disease therapy versus for human enhancement, and about editing that becomes hereditary versus editing that does not.

The research team, which included Scheufele and Dominique Brossard — both professors of life sciences communication — along with Michael Xenos, professor of communication arts, first surveyed study participants about the use of editing to treat disease (therapy) versus for enhancement (creating so-called “designer babies”). While about two-thirds of respondents expressed at least some support for therapeutic editing, only one-third expressed support for using the technology for enhancement.

Diving even deeper, researchers looked into public attitudes about gene editing on specific cell types — somatic or germline — either for therapy or enhancement. Somatic cells are non-reproductive, so edits made in those cells do not affect future generations. Germline cells, however, are heritable, and changes made in these cells would be passed on to children.

Public support of therapeutic editing was high both in cells that would be inherited and those that would not, with 65 percent of respondents supporting therapy in germline cells and 64 percent supporting therapy in somatic cells. When considering enhancement editing, however, support depended more upon whether the changes would affect future generations. Only 26 percent of people surveyed supported enhancement editing in heritable germline cells and 39 percent supported enhancement of somatic cells that would not be passed on to children.

“A majority of people are saying that germline enhancement is where the technology crosses that invisible line and becomes unacceptable,” says Scheufele. “When it comes to therapy, the public is more open, and that may partly be reflective of how severe some of those genetically inherited diseases are. The potential treatments for those diseases are something the public at least is willing to consider.”

Beyond questions of support, researchers also wanted to understand what was driving public opinions. They found that two factors were related to respondents’ attitudes toward gene editing as well as their attitudes toward the public’s role in its emergence: the level of religious guidance in their lives, and factual knowledge about the technology.

Those with a high level of religious guidance in their daily lives had lower support for human genome editing than those with low religious guidance. Additionally, those with high knowledge of the technology were more supportive of it than those with less knowledge.

While respondents with high religious guidance and those with high knowledge differed on their support for the technology, both groups highly supported public engagement in its development and use. These results suggest broad agreement that the public should be involved in questions of political, regulatory and moral aspects of human genome editing.

“The public may be split along lines of religiosity or knowledge with regard to what they think about the technology and scientific community, but they are united in the idea that this is an issue that requires public involvement,” says Scheufele. “Our findings show very nicely that the public is ready for these discussions and that the time to have the discussions is now, before the science is fully ready and while we have time to carefully think through different options regarding how we want to move forward.”

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

U.S. attitudes on human genome editing by Dietram A. Scheufele, Michael A. Xenos, Emily L. Howell, Kathleen M. Rose, Dominique Brossard1, and Bruce W. Hardy. Science 11 Aug 2017: Vol. 357, Issue 6351, pp. 553-554 DOI: 10.1126/science.aan3708

This paper is behind a paywall.

A couple of final comments

Briefly, I notice that there’s no mention of the ethics of patenting this technology in the news release about the study.

Moving on, it seems surprising that the first team to engage in germline editing in the US is in Oregon; I would have expected the work to come from Massachusetts, California, or Illinois where a lot of bleeding edge medical research is performed. However, given the dearth of financial support from federal funding institutions, it seems likely that only an outsider would dare to engage i the research. Given the timing, Mitalipov’s work was already well underway before the recent about-face from the US National Academy of Sciences (Note: Kaiser’s Feb. 14, 2017 article does note that for some the recent recommendations do not represent any change).

As for discussion on issues such as editing of the germline, I’ve often noted here that popular culture (including advertising with the science fiction and other dramas laid in various media) often provides an informal forum for discussion. Joelle Renstrom in an Aug. 13, 2017 article for slate.com writes that Orphan Black (a BBC America series featuring clones) opened up a series of questions about science and ethics in the guise of a thriller about clones. She offers a précis of the first four seasons (Note: A link has been removed),

If you stopped watching a few seasons back, here’s a brief synopsis of how the mysteries wrap up. Neolution, an organization that seeks to control human evolution through genetic modification, began Project Leda, the cloning program, for two primary reasons: to see whether they could and to experiment with mutations that might allow people (i.e., themselves) to live longer. Neolution partnered with biotech companies such as Dyad, using its big pharma reach and deep pockets to harvest people’s genetic information and to conduct individual and germline (that is, genetic alterations passed down through generations) experiments, including infertility treatments that result in horrifying birth defects and body modification, such as tail-growing.

She then provides the article’s thesis (Note: Links have been removed),

Orphan Black demonstrates Carl Sagan’s warning of a time when “awesome technological powers are in the hands of a very few.” Neolutionists do whatever they want, pausing only to consider whether they’re missing an opportunity to exploit. Their hubris is straight out of Victor Frankenstein’s playbook. Frankenstein wonders whether he ought to first reanimate something “of simpler organisation” than a human, but starting small means waiting for glory. Orphan Black’s evil scientists embody this belief: if they’re going to play God, then they’ll control not just their own destinies, but the clones’ and, ultimately, all of humanity’s. Any sacrifices along the way are for the greater good—reasoning that culminates in Westmoreland’s eugenics fantasy to genetically sterilize 99 percent of the population he doesn’t enhance.

Orphan Black uses sci-fi tropes to explore real-world plausibility. Neolution shares similarities with transhumanism, the belief that humans should use science and technology to take control of their own evolution. While some transhumanists dabble in body modifications, such as microchip implants or night-vision eye drops, others seek to end suffering by curing human illness and aging. But even these goals can be seen as selfish, as access to disease-eradicating or life-extending technologies would be limited to the wealthy. Westmoreland’s goal to “sell Neolution to the 1 percent” seems frighteningly plausible—transhumanists, who statistically tend to be white, well-educated, and male, and their associated organizations raise and spend massive sums of money to help fulfill their goals. …

On Orphan Black, denial of choice is tantamount to imprisonment. That the clones have to earn autonomy underscores the need for ethics in science, especially when it comes to genetics. The show’s message here is timely given the rise of gene-editing techniques such as CRISPR. Recently, the National Academy of Sciences gave germline gene editing the green light, just one year after academy scientists from around the world argued it would be “irresponsible to proceed” without further exploring the implications. Scientists in the United Kingdom and China have already begun human genetic engineering and American scientists recently genetically engineered a human embryo for the first time. The possibility of Project Leda isn’t farfetched. Orphan Black warns us that money, power, and fear of death can corrupt both people and science. Once that happens, loss of humanity—of both the scientists and the subjects—is inevitable.

In Carl Sagan’s dark vision of the future, “people have lost the ability to set their own agendas or knowledgeably question those in authority.” This describes the plight of the clones at the outset of Orphan Black, but as the series continues, they challenge this paradigm by approaching science and scientists with skepticism, ingenuity, and grit. …

I hope there are discussions such as those Scheufele and Brossard are advocating but it might be worth considering that there is already some discussion underway, as informal as it is.

-30-

Part 1: CRISPR and editing the germline in the US (part 1 of 3): In the beginning

Part 2: CRISPR and editing the germline in the US (part 2 of 3): ‘designer babies’?

CRISPR and editing the germline in the US (part 2 of 3): ‘designer babies’?

Having included an explanation of CRISPR-CAS9 technology along with the news about the first US team to edit the germline and bits and pieces about ethics and a patent fight (part 1), this part hones in on the details of the work and worries about ‘designer babies’.

The interest flurry

I found three articles addressing the research and all three concur that despite some of the early reporting, this is not the beginning of a ‘designer baby’ generation.

First up was Nick Thieme in a July 28, 2017 article for Slate,

MIT Technology Review reported Thursday that a team of researchers from Portland, Oregon were the first team of U.S.-based scientists to successfully create a genetically modified human embryo. The researchers, led by Shoukhrat Mitalipov of Oregon Health and Science University, changed the DNA of—in MIT Technology Review’s words—“many tens” of genetically-diseased embryos by injecting the host egg with CRISPR, a DNA-based gene editing tool first discovered in bacteria, at the time of fertilization. CRISPR-Cas9, as the full editing system is called, allows scientists to change genes accurately and efficiently. As has happened with research elsewhere, the CRISPR-edited embryos weren’t implanted—they were kept sustained for only a couple of days.

In addition to being the first American team to complete this feat, the researchers also improved upon the work of the three Chinese research teams that beat them to editing embryos with CRISPR: Mitalipov’s team increased the proportion of embryonic cells that received the intended genetic changes, addressing an issue called “mosaicism,” which is when an embryo is comprised of cells with different genetic makeups. Increasing that proportion is essential to CRISPR work in eliminating inherited diseases, to ensure that the CRISPR therapy has the intended result. The Oregon team also reduced the number of genetic errors introduced by CRISPR, reducing the likelihood that a patient would develop cancer elsewhere in the body.

Separate from the scientific advancements, it’s a big deal that this work happened in a country with such intense politicization of embryo research. …

But there are a great number of obstacles between the current research and the future of genetically editing all children to be 12-foot-tall Einsteins.

Ed Yong in an Aug. 2, 2017 article for The Atlantic offered a comprehensive overview of the research and its implications (unusually for Yong, there seems to be mildly condescending note but it’s worth ignoring for the wealth of information in the article; Note: Links have been removed),

… the full details of the experiment, which are released today, show that the study is scientifically important but much less of a social inflection point than has been suggested. “This has been widely reported as the dawn of the era of the designer baby, making it probably the fifth or sixth time people have reported that dawn,” says Alta Charo, an expert on law and bioethics at the University of Wisconsin-Madison. “And it’s not.”

Given the persistent confusion around CRISPR and its implications, I’ve laid out exactly what the team did, and what it means.

Who did the experiments?

Shoukhrat Mitalipov is a Kazakhstani-born cell biologist with a history of breakthroughs—and controversy—in the stem cell field. He was the scientist to clone monkeys. He was the first to create human embryos by cloning adult cells—a move that could provide patients with an easy supply of personalized stem cells. He also pioneered a technique for creating embryos with genetic material from three biological parents, as a way of preventing a group of debilitating inherited diseases.

Although MIT Tech Review name-checked Mitalipov alone, the paper splits credit for the research between five collaborating teams—four based in the United States, and one in South Korea.

What did they actually do?

The project effectively began with an elevator conversation between Mitalipov and his colleague Sanjiv Kaul. Mitalipov explained that he wanted to use CRISPR to correct a disease-causing gene in human embryos, and was trying to figure out which disease to focus on. Kaul, a cardiologist, told him about hypertrophic cardiomyopathy (HCM)—an inherited heart disease that’s commonly caused by mutations in a gene called MYBPC3. HCM is surprisingly common, affecting 1 in 500 adults. Many of them lead normal lives, but in some, the walls of their hearts can thicken and suddenly fail. For that reason, HCM is the commonest cause of sudden death in athletes. “There really is no treatment,” says Kaul. “A number of drugs are being evaluated but they are all experimental,” and they merely treat the symptoms. The team wanted to prevent HCM entirely by removing the underlying mutation.

They collected sperm from a man with HCM and used CRISPR to change his mutant gene into its normal healthy version, while simultaneously using the sperm to fertilize eggs that had been donated by female volunteers. In this way, they created embryos that were completely free of the mutation. The procedure was effective, and avoided some of the critical problems that have plagued past attempts to use CRISPR in human embryos.

Wait, other human embryos have been edited before?

There have been three attempts in China. The first two—in 2015 and 2016—used non-viable embryos that could never have resulted in a live birth. The third—announced this March—was the first to use viable embryos that could theoretically have been implanted in a womb. All of these studies showed that CRISPR gene-editing, for all its hype, is still in its infancy.

The editing was imprecise. CRISPR is heralded for its precision, allowing scientists to edit particular genes of choice. But in practice, some of the Chinese researchers found worrying levels of off-target mutations, where CRISPR mistakenly cut other parts of the genome.

The editing was inefficient. The first Chinese team only managed to successfully edit a disease gene in 4 out of 86 embryos, and the second team fared even worse.

The editing was incomplete. Even in the successful cases, each embryo had a mix of modified and unmodified cells. This pattern, known as mosaicism, poses serious safety problems if gene-editing were ever to be used in practice. Doctors could end up implanting women with embryos that they thought were free of a disease-causing mutation, but were only partially free. The resulting person would still have many tissues and organs that carry those mutations, and might go on to develop symptoms.

What did the American team do differently?

The Chinese teams all used CRISPR to edit embryos at early stages of their development. By contrast, the Oregon researchers delivered the CRISPR components at the earliest possible point—minutes before fertilization. That neatly avoids the problem of mosaicism by ensuring that an embryo is edited from the very moment it is created. The team did this with 54 embryos and successfully edited the mutant MYBPC3 gene in 72 percent of them. In the other 28 percent, the editing didn’t work—a high failure rate, but far lower than in previous attempts. Better still, the team found no evidence of off-target mutations.

This is a big deal. Many scientists assumed that they’d have to do something more convoluted to avoid mosaicism. They’d have to collect a patient’s cells, which they’d revert into stem cells, which they’d use to make sperm or eggs, which they’d edit using CRISPR. “That’s a lot of extra steps, with more risks,” says Alta Charo. “If it’s possible to edit the embryo itself, that’s a real advance.” Perhaps for that reason, this is the first study to edit human embryos that was published in a top-tier scientific journal—Nature, which rejected some of the earlier Chinese papers.

Is this kind of research even legal?

Yes. In Western Europe, 15 countries out of 22 ban any attempts to change the human germ line—a term referring to sperm, eggs, and other cells that can transmit genetic information to future generations. No such stance exists in the United States but Congress has banned the Food and Drug Administration from considering research applications that make such modifications. Separately, federal agencies like the National Institutes of Health are banned from funding research that ultimately destroys human embryos. But the Oregon team used non-federal money from their institutions, and donations from several small non-profits. No taxpayer money went into their work. [emphasis mine]

Why would you want to edit embryos at all?

Partly to learn more about ourselves. By using CRISPR to manipulate the genes of embryos, scientists can learn more about the earliest stages of human development, and about problems like infertility and miscarriages. That’s why biologist Kathy Niakan from the Crick Institute in London recently secured a license from a British regulator to use CRISPR on human embryos.

Isn’t this a slippery slope toward making designer babies?

In terms of avoiding genetic diseases, it’s not conceptually different from PGD, which is already widely used. The bigger worry is that gene-editing could be used to make people stronger, smarter, or taller, paving the way for a new eugenics, and widening the already substantial gaps between the wealthy and poor. But many geneticists believe that such a future is fundamentally unlikely because complex traits like height and intelligence are the work of hundreds or thousands of genes, each of which have a tiny effect. The prospect of editing them all is implausible. And since genes are so thoroughly interconnected, it may be impossible to edit one particular trait without also affecting many others.

“There’s the worry that this could be used for enhancement, so society has to draw a line,” says Mitalipov. “But this is pretty complex technology and it wouldn’t be hard to regulate it.”

Does this discovery have any social importance at all?

“It’s not so much about designer babies as it is about geographical location,” says Charo. “It’s happening in the United States, and everything here around embryo research has high sensitivity.” She and others worry that the early report about the study, before the actual details were available for scrutiny, could lead to unnecessary panic. “Panic reactions often lead to panic-driven policy … which is usually bad policy,” wrote Greely [bioethicist Hank Greely].

As I understand it, despite the change in stance, there is no federal funding available for the research performed by Mitalipov and his team.

Finally, University College London (UCL) scientists Joyce Harper and Helen O’Neill wrote about CRISPR, the Oregon team’s work, and the possibilities in an Aug. 3, 2017 essay for The Conversation (Note: Links have been removed),

The genome editing tool used, CRISPR-Cas9, has transformed the field of biology in the short time since its discovery in that it not only promises, but delivers. CRISPR has surpassed all previous efforts to engineer cells and alter genomes at a fraction of the time and cost.

The technology, which works like molecular scissors to cut and paste DNA, is a natural defence system that bacteria use to fend off harmful infections. This system has the ability to recognise invading virus DNA, cut it and integrate this cut sequence into its own genome – allowing the bacterium to render itself immune to future infections of viruses with similar DNA. It is this ability to recognise and cut DNA that has allowed scientists to use it to target and edit specific DNA regions.

When this technology is applied to “germ cells” – the sperm and eggs – or embryos, it changes the germline. That means that any alterations made would be permanent and passed down to future generations. This makes it more ethically complex, but there are strict regulations around human germline genome editing, which is predominantly illegal. The UK received a licence in 2016 to carry out CRISPR on human embryos for research into early development. But edited embryos are not allowed to be inserted into the uterus and develop into a fetus in any country.

Germline genome editing came into the global spotlight when Chinese scientists announced in 2015 that they had used CRISPR to edit non-viable human embryos – cells that could never result in a live birth. They did this to modify the gene responsible for the blood disorder β-thalassaemia. While it was met with some success, it received a lot of criticism because of the premature use of this technology in human embryos. The results showed a high number of potentially dangerous, off-target mutations created in the procedure.

Impressive results

The new study, published in Nature, is different because it deals with viable human embryos and shows that the genome editing can be carried out safely – without creating harmful mutations. The team used CRISPR to correct a mutation in the gene MYBPC3, which accounts for approximately 40% of the myocardial disease hypertrophic cardiomyopathy. This is a dominant disease, so an affected individual only needs one abnormal copy of the gene to be affected.

The researchers used sperm from a patient carrying one copy of the MYBPC3 mutation to create 54 embryos. They edited them using CRISPR-Cas9 to correct the mutation. Without genome editing, approximately 50% of the embryos would carry the patients’ normal gene and 50% would carry his abnormal gene.

After genome editing, the aim would be for 100% of embryos to be normal. In the first round of the experiments, they found that 66.7% of embryos – 36 out of 54 – were normal after being injected with CRIPSR. Of the remaining 18 embryos, five had remained unchanged, suggesting editing had not worked. In 13 embryos, only a portion of cells had been edited.

The level of efficiency is affected by the type of CRISPR machinery used and, critically, the timing in which it is put into the embryo. The researchers therefore also tried injecting the sperm and the CRISPR-Cas9 complex into the egg at the same time, which resulted in more promising results. This was done for 75 mature donated human eggs using a common IVF technique called intracytoplasmic sperm injection. This time, impressively, 72.4% of embryos were normal as a result. The approach also lowered the number of embryos containing a mixture of edited and unedited cells (these embryos are called mosaics).

Finally, the team injected a further 22 embryos which were grown into blastocyst – a later stage of embryo development. These were sequenced and the researchers found that the editing had indeed worked. Importantly, they could show that the level of off-target mutations was low.

A brave new world?

So does this mean we finally have a cure for debilitating, heritable diseases? It’s important to remember that the study did not achieve a 100% success rate. Even the researchers themselves stress that further research is needed in order to fully understand the potential and limitations of the technique.

In our view, it is unlikely that genome editing would be used to treat the majority of inherited conditions anytime soon. We still can’t be sure how a child with a genetically altered genome will develop over a lifetime, so it seems unlikely that couples carrying a genetic disease would embark on gene editing rather than undergoing already available tests – such as preimplantation genetic diagnosis or prenatal diagnosis – where the embryos or fetus are tested for genetic faults.

-30-

As might be expected there is now a call for public discussion about the ethics about this kind of work. See Part 3.

For anyone who started in the middle of this series, here’s Part 1 featuring an introduction to the technology and some of the issues.

CRISPR and editing the germline in the US (part 1 of 3): In the beginning

There’s been a minor flurry of interest in CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats; also known as CRISPR-CAS9), a gene-editing technique, since a team in Oregon announced a paper describing their work editing the germline. Since I’ve been following the CRISPR-CAS9 story for a while this seems like a good juncture for a more in-depth look at the topic. In this first part I’m including an introduction to CRISPR, some information about the latest US work, and some previous writing about ethics issues raised when Chinese scientists first announced their work editing germlines in 2015 and during the patent dispute between the University of California at Berkeley and Harvard University’s Broad Institute.

Introduction to CRISPR

I’ve been searching for a good description of CRISPR and this helped to clear up some questions for me (Thank you to MIT Review),

For anyone who’s been reading about science for a while, this upbeat approach to explaining how a particular technology will solve all sorts of problems will seem quite familiar. It’s not the most hyperbolic piece I’ve seen but it barely mentions any problems associated with research (for some of the problems see: ‘The interest flurry’ later in part 2).

Oregon team

Steve Connor’s July 26, 2017 article for the MIT (Massachusetts Institute of Technology) Technology Review breaks the news (Note: Links have been removed),

The first known attempt at creating genetically modified human embryos in the United States has been carried out by a team of researchers in Portland, Oregon, MIT Technology Review has learned.

The effort, led by Shoukhrat Mitalipov of Oregon Health and Science University, involved changing the DNA of a large number of one-cell embryos with the gene-editing technique CRISPR, according to people familiar with the scientific results.

Until now, American scientists have watched with a combination of awe, envy, and some alarm as scientists elsewhere were first to explore the controversial practice. To date, three previous reports of editing human embryos were all published by scientists in China.

Now Mitalipov is believed to have broken new ground both in the number of embryos experimented upon and by demonstrating that it is possible to safely and efficiently correct defective genes that cause inherited diseases.

Although none of the embryos were allowed to develop for more than a few days—and there was never any intention of implanting them into a womb—the experiments are a milestone on what may prove to be an inevitable journey toward the birth of the first genetically modified humans.

In altering the DNA code of human embryos, the objective of scientists is to show that they can eradicate or correct genes that cause inherited disease, like the blood condition beta-thalassemia. The process is termed “germline engineering” because any genetically modified child would then pass the changes on to subsequent generations via their own germ cells—the egg and sperm.

Some critics say germline experiments could open the floodgates to a brave new world of “designer babies” engineered with genetic enhancements—a prospect bitterly opposed by a range of religious organizations, civil society groups, and biotech companies.

The U.S. intelligence community last year called CRISPR a potential “weapon of mass destruction.”

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

Correction of a pathogenic gene mutation in human embryos by Hong Ma, Nuria Marti-Gutierrez, Sang-Wook Park, Jun Wu, Yeonmi Lee, Keiichiro Suzuki, Amy Koski, Dongmei Ji, Tomonari Hayama, Riffat Ahmed, Hayley Darby, Crystal Van Dyken, Ying Li, Eunju Kang, A.-Reum Park, Daesik Kim, Sang-Tae Kim, Jianhui Gong, Ying Gu, Xun Xu, David Battaglia, Sacha A. Krieg, David M. Lee, Diana H. Wu, Don P. Wolf, Stephen B. Heitner, Juan Carlos Izpisua Belmonte, Paula Amato, Jin-Soo Kim, Sanjiv Kaul, & Shoukhrat Mitalipov. Nature (2017) doi:10.1038/nature23305 Published online 02 August 2017

This paper appears to be open access.

CRISPR Issues: ethics and patents

In my May 14, 2015 posting I mentioned a ‘moratorium’ on germline research, the Chinese research paper, and the stance taken by the US National Institutes of Health (NIH),

The CRISPR technology has reignited a discussion about ethical and moral issues of human genetic engineering some of which is reviewed in an April 7, 2015 posting about a moratorium by Sheila Jasanoff, J. Benjamin Hurlbut and Krishanu Saha for the Guardian science blogs (Note: A link has been removed),

On April 3, 2015, a group of prominent biologists and ethicists writing in Science called for a moratorium on germline gene engineering; modifications to the human genome that will be passed on to future generations. The moratorium would apply to a technology called CRISPR/Cas9, which enables the removal of undesirable genes, insertion of desirable ones, and the broad recoding of nearly any DNA sequence.

Such modifications could affect every cell in an adult human being, including germ cells, and therefore be passed down through the generations. Many organisms across the range of biological complexity have already been edited in this way to generate designer bacteria, plants and primates. There is little reason to believe the same could not be done with human eggs, sperm and embryos. Now that the technology to engineer human germlines is here, the advocates for a moratorium declared, it is time to chart a prudent path forward. They recommend four actions: a hold on clinical applications; creation of expert forums; transparent research; and a globally representative group to recommend policy approaches.

The authors go on to review precedents and reasons for the moratorium while suggesting we need better ways for citizens to engage with and debate these issues,

An effective moratorium must be grounded in the principle that the power to modify the human genome demands serious engagement not only from scientists and ethicists but from all citizens. We need a more complex architecture for public deliberation, built on the recognition that we, as citizens, have a duty to participate in shaping our biotechnological futures, just as governments have a duty to empower us to participate in that process. Decisions such as whether or not to edit human genes should not be left to elite and invisible experts, whether in universities, ad hoc commissions, or parliamentary advisory committees. Nor should public deliberation be temporally limited by the span of a moratorium or narrowed to topics that experts deem reasonable to debate.

I recommend reading the post in its entirety as there are nuances that are best appreciated in the entirety of the piece.

Shortly after this essay was published, Chinese scientists announced they had genetically modified (nonviable) human embryos. From an April 22, 2015 article by David Cyranoski and Sara Reardon in Nature where the research and some of the ethical issues discussed,

In a world first, Chinese scientists have reported editing the genomes of human embryos. The results are published1 in the online journal Protein & Cell and confirm widespread rumours that such experiments had been conducted — rumours that sparked a high-profile debate last month2, 3 about the ethical implications of such work.

In the paper, researchers led by Junjiu Huang, a gene-function researcher at Sun Yat-sen University in Guangzhou, tried to head off such concerns by using ‘non-viable’ embryos, which cannot result in a live birth, that were obtained from local fertility clinics. The team attempted to modify the gene responsible for β-thalassaemia, a potentially fatal blood disorder, using a gene-editing technique known as CRISPR/Cas9. The researchers say that their results reveal serious obstacles to using the method in medical applications.

“I believe this is the first report of CRISPR/Cas9 applied to human pre-implantation embryos and as such the study is a landmark, as well as a cautionary tale,” says George Daley, a stem-cell biologist at Harvard Medical School in Boston, Massachusetts. “Their study should be a stern warning to any practitioner who thinks the technology is ready for testing to eradicate disease genes.”

….

Huang says that the paper was rejected by Nature and Science, in part because of ethical objections; both journals declined to comment on the claim. (Nature’s news team is editorially independent of its research editorial team.)

He adds that critics of the paper have noted that the low efficiencies and high number of off-target mutations could be specific to the abnormal embryos used in the study. Huang acknowledges the critique, but because there are no examples of gene editing in normal embryos he says that there is no way to know if the technique operates differently in them.

Still, he maintains that the embryos allow for a more meaningful model — and one closer to a normal human embryo — than an animal model or one using adult human cells. “We wanted to show our data to the world so people know what really happened with this model, rather than just talking about what would happen without data,” he says.

This, too, is a good and thoughtful read.

There was an official response in the US to the publication of this research, from an April 29, 2015 post by David Bruggeman on his Pasco Phronesis blog (Note: Links have been removed),

In light of Chinese researchers reporting their efforts to edit the genes of ‘non-viable’ human embryos, the National Institutes of Health (NIH) Director Francis Collins issued a statement (H/T Carl Zimmer).

“NIH will not fund any use of gene-editing technologies in human embryos. The concept of altering the human germline in embryos for clinical purposes has been debated over many years from many different perspectives, and has been viewed almost universally as a line that should not be crossed. Advances in technology have given us an elegant new way of carrying out genome editing, but the strong arguments against engaging in this activity remain. These include the serious and unquantifiable safety issues, ethical issues presented by altering the germline in a way that affects the next generation without their consent, and a current lack of compelling medical applications justifying the use of CRISPR/Cas9 in embryos.” …

The US has modified its stance according to a February 14, 2017 article by Jocelyn Kaiser for Science Magazine (Note: Links have been removed),

Editing the DNA of a human embryo to prevent a disease in a baby could be ethically allowable one day—but only in rare circumstances and with safeguards in place, says a widely anticipated report released today.

The report from an international committee convened by the U.S. National Academy of Sciences (NAS) and the National Academy of Medicine in Washington, D.C., concludes that such a clinical trial “might be permitted, but only following much more research” on risks and benefits, and “only for compelling reasons and under strict oversight.” Those situations could be limited to couples who both have a serious genetic disease and for whom embryo editing is “really the last reasonable option” if they want to have a healthy biological child, says committee co-chair Alta Charo, a bioethicist at the University of Wisconsin in Madison.

Some researchers are pleased with the report, saying it is consistent with previous conclusions that safely altering the DNA of human eggs, sperm, or early embryos—known as germline editing—to create a baby could be possible eventually. “They have closed the door to the vast majority of germline applications and left it open for a very small, well-defined subset. That’s not unreasonable in my opinion,” says genome researcher Eric Lander of the Broad Institute in Cambridge, Massachusetts. Lander was among the organizers of an international summit at NAS in December 2015 who called for more discussion before proceeding with embryo editing.

But others see the report as lowering the bar for such experiments because it does not explicitly say they should be prohibited for now. “It changes the tone to an affirmative position in the absence of the broad public debate this report calls for,” says Edward Lanphier, chairman of the DNA editing company Sangamo Therapeutics in Richmond, California. Two years ago, he co-authored a Nature commentary calling for a moratorium on clinical embryo editing.

One advocacy group opposed to embryo editing goes further. “We’re very disappointed with the report. It’s really a pretty dramatic shift from the existing and widespread agreement globally that human germline editing should be prohibited,” says Marcy Darnovsky, executive director of the Center for Genetics and Society in Berkeley, California.

Interestingly, this change of stance occurred just prior to a CRISPR patent decision (from my March 15, 2017 posting),

I have written about the CRISPR patent tussle (Harvard & MIT’s [Massachusetts Institute of Technology] Broad Institute vs the University of California at Berkeley) previously in a Jan. 6, 2015 posting and in a more detailed May 14, 2015 posting. I also mentioned (in a Jan. 17, 2017 posting) CRISPR and its patent issues in the context of a posting about a Slate.com series on Frankenstein and the novel’s applicability to our own time. This patent fight is being bitterly fought as fortunes are at stake.

It seems a decision has been made regarding the CRISPR patent claims. From a Feb. 17, 2017 article by Charmaine Distor for The Science Times,

After an intense court battle, the US Patent and Trademark Office (USPTO) released its ruling on February 15 [2017]. The rights for the CRISPR-Cas9 gene editing technology was handed over to the Broad Institute of Harvard University and the Massachusetts Institute of Technology (MIT).

According to an article in Nature, the said court battle was between the Broad Institute and the University of California. The two institutions are fighting over the intellectual property right for the CRISPR patent. The case between the two started when the patent was first awarded to the Broad Institute despite having the University of California apply first for the CRISPR patent.

Heidi Ledford’s Feb. 17, 2017 article for Nature provides more insight into the situation (Note: Links have been removed),

It [USPTO] ruled that the Broad Institute of Harvard and MIT in Cambridge could keep its patents on using CRISPR–Cas9 in eukaryotic cells. That was a blow to the University of California in Berkeley, which had filed its own patents and had hoped to have the Broad’s thrown out.

The fight goes back to 2012, when Jennifer Doudna at Berkeley, Emmanuelle Charpentier, then at the University of Vienna, and their colleagues outlined how CRISPR–Cas9 could be used to precisely cut isolated DNA1. In 2013, Feng Zhang at the Broad and his colleagues — and other teams — showed2 how it could be adapted to edit DNA in eukaryotic cells such as plants, livestock and humans.

Berkeley filed for a patent earlier, but the USPTO granted the Broad’s patents first — and this week upheld them. There are high stakes involved in the ruling. The holder of key patents could make millions of dollars from CRISPR–Cas9’s applications in industry: already, the technique has sped up genetic research, and scientists are using it to develop disease-resistant livestock and treatments for human diseases.

….

I also noted this eyebrow-lifting statistic,  “As for Ledford’s 3rd point, there are an estimated 763 patent families (groups of related patents) claiming CAS9 leading to the distinct possibility that the Broad Institute will be fighting many patent claims in the future.)

-30-

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

Preserving heritage smells (scents)

Preserving a smell? It’s an intriguing idea and forms the research focus for scientists at the University College London’s (UCL) Institute for Sustainable Heritage according to an April 6, 2017 Biomed Central news release on EurekAlert,

A ‘Historic Book Odour Wheel’ which has been developed to document and archive the aroma associated with old books, is being presented in a study in the open access journal Heritage Science. Researchers at UCL Institute for Sustainable Heritage created the wheel as part of an experiment in which they asked visitors to St Paul’s Cathedral’s Dean and Chapter library in London to characterize its smell.

The visitors most frequently described the aroma of the library as ‘woody’ (selected by 100% of the visitors who were asked), followed by ‘smoky’ (86%), ‘earthy'(71%) and ‘vanilla’ (41%). The intensity of the smells was assessed as between ‘strong odor’ and ‘very strong odor’. Over 70% of the visitors described the smell as pleasant, 14% as ‘mildly pleasant’ and 14% as ‘neutral’.

In a separate experiment, the researchers presented visitors to the Birmingham Museum and Art Gallery with an unlabelled historic book smell – sampled from a 1928 book they obtained from a second-hand bookshop in London – and collected the terms used to describe the smell. The word ‘chocolate’ – or variations such as ‘cocoa’ or ‘chocolatey’ – was used most often, followed by ‘coffee’, ‘old’, ‘wood’ and ‘burnt’. Participants also mentioned smells including ‘fish’, ‘body odour’, ‘rotten socks’ and ‘mothballs’.

Cecilia Bembibre, heritage scientist at UCL and corresponding author of the study said: “Our odour wheel provides an example of how scientists and historians could begin to identify, analyze and document smells that have cultural significance, such as the aroma of old books in historic libraries. The role of smells in how we perceive heritage has not been systematically explored until now.”

Attempting to answer the question of whether certain smells could be considered part of our cultural heritage and if so how they could be identified, protected and conserved, the researchers also conducted a chemical analysis of volatile organic compounds (VOCs) which they sampled from books in the library. VOCs are chemicals that evaporate at low temperatures, many of which can be perceived as scents or odors.

Combining their findings from the VOC analysis with the visitors’ characterizations, the authors created their Historic Book Odour wheel, which shows the chemical description of a smell (such as acetic acid) together with the sensory descriptions provided by the visitors (such as ‘vinegar’).

Cecilia Bembibre said: “By documenting the words used by the visitors to describe a heritage smell, our study opens a discussion about developing a vocabulary to identify aromas that have cultural meaning and significance.”

She added: “The Historic Book Odour Wheel also has the potential to be used as a diagnostic tool by conservators, informing on the condition of an object, for example its state of decay, through its olfactory profile.”

The authors suggest that, in addition to its use for the identification and conservation of smells, the Historic Book Odour Wheel could potentially be used to recreate smells and aid the design of olfactory experiences in museums, allowing visitors to form a personal connection with exhibits by allowing them to understand what the past smelled like.

Before this can be done, further research is needed to build on the preliminary findings in this study to allow them to inform and benefit heritage management, conservation, visitor experience design and heritage policy making.

Here’s what the Historic Book Odour Wheel looks like,

Odour wheel of historic book containing general aroma categories, sensory descriptors and chemical information on the smells as sampled (colours are arbitrary) Courtesy: Heritage Science [downloaded from https://heritagesciencejournal.springeropen.com/articles/10.1186/s40494-016-0114-1

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

Smell of heritage: a framework for the identification, analysis and archival of historic odours by Cecilia Bembibre and Matija Strlič. Heritage Science20175:2 DOI: 10.1186/s40494-016-0114-1 Published: 7 April 2017

©  The Author(s) 2017

This paper is open access.

Science literacy, science advice, the US Supreme Court, and Britain’s House of Commons

This ‘think’ piece is going to cover a fair bit of ground including science literacy in the general public and in the US Supreme Court, and what that might mean for science advice and UK Members of Parliament (MPs).

Science literacy generally and in the US Supreme Court

A science literacy report for the US National Academy of Sciences (NAS), due sometime from early to mid 2017, is being crafted with an eye to capturing a different perspective according to a March 24, 2016 University of Wisconsin-Madison news release by Terry Dewitt,

What does it mean to be science literate? How science literate is the American public? How do we stack up against other countries? What are the civic implications of a public with limited knowledge of science and how it works? How is science literacy measured?

These and other questions are under the microscope of a 12-member National Academy of Sciences (NAS) panel — including University of Wisconsin—Madison Life Sciences Communication Professor Dominique Brossard and School of Education Professor Noah Feinstein — charged with sorting through the existing data on American science and health literacy and exploring the association between knowledge of science and public perception of and support for science.

The committee — composed of educators, scientists, physicians and social scientists — will take a hard look at the existing data on the state of U.S. science literacy, the questions asked, and the methods used to measure what Americans know and don’t know about science and how that knowledge has changed over time. Critically for science, the panel will explore whether a lack of science literacy is associated with decreased public support for science or research.

Historically, policymakers and leaders in the scientific community have fretted over a perceived lack of knowledge among Americans about science and how it works. A prevailing fear is that an American public unequipped to come to terms with modern science will ultimately have serious economic, security and civic consequences, especially when it comes to addressing complex and nuanced issues like climate change, antibiotic resistance, emerging diseases, environment and energy choices.

While the prevailing wisdom, inspired by past studies, is that Americans don’t stack up well in terms of understanding science, Brossard is not so convinced. Much depends on what kinds of questions are asked, how they are asked, and how the data is analyzed.

It is very easy, she argues, to do bad social science and past studies may have measured the wrong things or otherwise created a perception about the state of U.S. science literacy that may or may not be true.

“How do you conceptualize scientific literacy? What do people need to know? Some argue that scientific literacy may be as simple as an understanding of how science works, the nature of science, [emphasis mine]” Brossard explains. “For others it may be a kind of ‘civic science literacy,’ where people have enough knowledge to be informed and make good decisions in a civics context.”

Science literacy may not be just for the public, it would seem that US Supreme Court judges may not have a basic understanding of how science works. David Bruggeman’s March 24, 2016 posting (on his Pasco Phronesis blog) describes a then current case before the Supreme Court (Justice Antonin Scalia has since died), Note: Links have been removed,

It’s a case concerning aspects of the University of Texas admissions process for undergraduates and the case is seen as a possible means of restricting race-based considerations for admission.  While I think the arguments in the case will likely revolve around factors far removed from science and or technology, there were comments raised by two Justices that struck a nerve with many scientists and engineers.

Both Justice Antonin Scalia and Chief Justice John Roberts raised questions about the validity of having diversity where science and scientists are concerned [emphasis mine].  Justice Scalia seemed to imply that diversity wasn’t esential for the University of Texas as most African-American scientists didn’t come from schools at the level of the University of Texas (considered the best university in Texas).  Chief Justice Roberts was a bit more plain about not understanding the benefits of diversity.  He stated, “What unique perspective does a black student bring to a class in physics?”

To that end, Dr. S. James Gates, theoretical physicist at the University of Maryland, and member of the President’s Council of Advisers on Science and Technology (and commercial actor) has an editorial in the March 25 [2016] issue of Science explaining that the value of having diversity in science does not accrue *just* to those who are underrepresented.

Dr. Gates relates his personal experience as a researcher and teacher of how people’s background inform their practice of science, and that two different people may use the same scientific method, but think about the problem differently.

I’m guessing that both Scalia and Roberts and possibly others believe that science is the discovery and accumulation of facts. In this worldview science facts such as gravity are waiting for discovery and formulation into a ‘law’. They do not recognize that most science is a collection of beliefs and may be influenced by personal beliefs. For example, we believe we’ve proved the existence of the Higgs boson but no one associated with the research has ever stated unequivocally that it exists.

For judges who are under the impression that scientific facts are out there somewhere waiting to be discovered diversity must seem irrelevant. It is not. Who you are affects the questions you ask and how you approach science. The easiest example is to look at how women were viewed when they were subjects in medical research. The fact that women’s physiology is significantly different (and not just in child-bearing ways) was never considered relevant when reporting results. Today, researchers consider not only gender, but age (to some extent), ethnicity, and more when examining results. It’s still not a perfect but it was a step forward.

So when Brossard included “… an understanding of how science works, the nature of science …” as an aspect of science literacy, the judges seemed to present a good example of how not understanding science can have a major impact on how others live.

I’d almost forgotten this science literacy piece as I’d started the draft some months ago but then I spotted a news item about a science advice/MP ‘dating’ service in the UK.

Science advice and UK MPs

First, the news, then, the speculation (from a June 6, 2016 news item on ScienceDaily),

MPs have expressed an overwhelming willingness to use a proposed new service to swiftly link them with academics in relevant areas to help ensure policy is based on the latest evidence.

A June 6, 2016 University of Exeter press release, which originated the news item, provides more detail about the proposed service and the research providing the supporting evidence (Note: A link has been removed),

The government is pursuing a drive towards evidence-based policy, yet policy makers still struggle to incorporate evidence into their decisions. One reason for this is limited easy access to the latest research findings or to academic experts who can respond to questions about evidence quickly.

Researchers at Cardiff University, the University of Exeter and University College London have today published results of the largest study to date reporting MPs’ attitudes to evidence in policy making and their reactions to a proposed Evidence Information Service (EIS) – a rapid match-making advisory service that would work alongside existing systems to put MPs in touch with relevant academic experts.

Dr Natalia Lawrence, of the University of Exeter, said: “It’s clear from our study that politicians want to ensure their decisions incorporate the most reliable evidence, but it can sometimes be very difficult for them to know how to access the latest research findings. This new matchmaking service could be a quick and easy way for them to seek advice from cutting-edge researchers and to check their understanding and facts. It could provide a useful complement to existing highly-valued information services.”

The research, published today in the journal Evidence and Policy, reports the findings of a national consultation exercise between politicians and the public. The researchers recruited members of the public to interview their local parliamentary representative. In total 86, politicians were contacted with 56 interviews completed. The MPs indicated an overwhelming willingness to use a service such as the EIS, with 85% supporting the idea, but noted a number of potential reservations related to the logistics of the EIS such as response time and familiarity with the service. Yet, the MPs indicated that their logistical reservations could be overcome by accessing the EIS via existing highly-valued parliamentary information services such as those provided by the House of Commons and Lords Libraries. Furthermore prior to rolling out the EIS on a nationwide basis it would first need to be piloted.

Developing the proposed EIS in line with feedback from this consultation of MPs would offer the potential to provide policy makers with rapid, reliable and confidential evidence from willing volunteers from the research community.

Professor Chris Chambers, of Cardiff University, said: “The government has given a robust steer that MPs need to link in more with academics to ensure decisions shaping the future of the country are evidence-based. It’s heartening to see that there is a will to adopt this system and we now need to move into a phase of developing a service that is both simple and effective to meet this need.”

The next steps for the project are parallel consultations of academics and members of the public and a pilot of the EIS, using funding from GW4 alliance of universities, made up of Bath, Bristol, Cardiff and Exeter.

What this study shows:
• The consultation shows that politicians recognise the importance of evidence-based policy making and agree on the need for an easier and more direct linkage between academic experts and policy makers.
• Politicians would welcome the creation of the EIS as a provider of rapid, reliable and confidential evidence.

What this study does not show:
• This study does not show how academics would provide evidence. This was a small-scale study which consulted politicians and has not attempted to give voice to the academic community.
• This study does not detail the mechanism of an operational EIS. Instead it indicates the need for a service such as the EIS and suggests ways in which the EIS can be operationalized.

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

Service as a new platform for supporting evidence-based policy: a consultation of UK parliamentarians by Natalia Lawrence, Jemma Chambers, Sinead Morrison, Sven Bestmann, Gerard O’Grady, Christopher Chambers, Andrew Kythreotis. Evidence & Policy: A Journal of Research, Debate and Practice DOI: http://dx.doi.org/10.1332/174426416X14643531912169 Appeared or available online: June 6, 2016

This paper is behind a paywall open access. *Corrected June 17, 2016.*

It’s an interesting idea and I can understand the appeal. However, operationalizing this ‘dating’ or ‘matchmaking’ service could prove quite complex. I appreciate the logistics issues but I’m a little more concerned about the MPs’ science literacy. Are they going to be like the two US justices who believe that science is the pursuit of immutable facts? What happens if two MPs are matched up with a different scientist and those two scientists didn’t agree about what the evidence says. Or, what happens if one scientist is more cautious than the other. There are all kinds of pitfalls. I’m not arguing against the idea but it’s going to require a lot of careful consideration.

Drone fly larvae avoid bacterial contamination due to their nanopillars

This is some fascinating bug research. From an April 6, 2016 news item on phys.org,

The immature stage of the drone fly (Eristalis tenax) is known as a “rat-tailed maggot” because it resembles a hairless baby rodent with a “tail” that is actually used as a breathing tube. Rat-tailed maggots are known to live in stagnant, fetid water that is rich in bacteria, fungi, and algae. However, despite this dirty environment, they are able to avoid infection by these microorganisms.

An April 6, 2016 Entomological Society of America news release on EurekAlert, which originated the news item, describes the findings,

Recently, Matthew Hayes, a cell biologist at the Institute of Ophthalmology at University College London in England, discovered never-before-seen structures that appear to keep the maggot mostly free of bacteria, despite living where microorganisms flourish. …

With scanning and transmission electron microscopes, Hayes carefully examined the larva and saw that much of its body is covered with thin spines, or “nanopillars,” that narrow to sharp points. Once he confirmed the spiky structures were indeed part of the maggot, he noticed a direct relationship between the presence of the spines and the absence of bacteria on the surface of the larva. He speculated that the carpet of spines simply makes it impossible for the bacteria to find enough room to adhere to the larva’s body surface.

Here’s an image of the nanopillars,

Caption: This electron-microscope image expose the spines, or "nanopillars," that poke up from the body of the rat-tailed maggot. The length and density of the spines vary as shown in this cross-section image of the cuticle. Credit: Matthew Hayes

Caption: This electron-microscope image expose the spines, or “nanopillars,” that poke up from the body of the rat-tailed maggot. The length and density of the spines vary as shown in this cross-section image of the cuticle. Credit: Matthew Hayes

Back to the news release,

“They’re much like anti-pigeon spikes that keep the birds away because they can’t find a nice surface to land on,” he said.

Hayes also ventured that the spines could possibly have superoleophobic properties (the ability to repel oils), which would also impede the bacteria from colonizing and forming a biofilm that could ultimately harm or kill the maggot. The composition of the spines is as unique as the structures themselves, Hayes said. Each spine appears to consist of a stack of hollow-cored disks, the largest at the bottom and the smallest at the top.

“What I really think they look like is the baby’s toy with the stack of rings of decreasing size, but on a very small scale,” he said. “I’ve worked in many different fields and looked at lots of different things, and I’ve never seen anything that looks like it.”

This work with the rat-tailed maggot is leading him to examine other insects as well, including the ability of another aquatic invertebrate — the mosquito larva — to thwart bacteria. Such antibacterial properties have applications in many different fields, including ophthalmology and other medical fields where biofilms can foul surgical instruments or implanted devices.

For now, though, he’s thrilled about shedding light on the underappreciated rat-tailed maggot and revealing its spiny armor.

“I’ve loved insects since I was a child, when I would breed butterflies and moths,” he said. “I’m just so chuffed to have discovered something a bit new about insects!”

I am charmed by Hayes’s admission of being “chuffed.”

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

Identification of Nanopillars on the Cuticle of the Aquatic Larvae of the Drone Fly (Diptera: Syrphidae) by Matthew J. Hayes, Timothy P. Levine, Roger H. Wilson. DOI: http://dx.doi.org/10.1093/jisesa/iew019 36 First published online: 30 March 2016

This is an open access paper.

Observing silica microspheres leads to theories about schools of fish and human crowds

Researchers developing theories about the crowd behaviour of tiny particles believe the theories may have some relevance to macro world phenomena.

[downloaded from http://www.ucl.ac.uk/news/news-articles/0316/090316-crowd-control]

[downloaded from http://www.ucl.ac.uk/news/news-articles/0316/090316-crowd-control]

From a March 9, 2016 news item on Nanowerk,

Crowds formed from tiny particles disperse as their environment becomes more disordered, according to scientists from UCL [University College London, UK], Bilkent University [Turkey] and Université Pierre et Marie Curie [France].

The new mechanism is counterintuitive and might help describe crowd behaviour in natural, real-world systems where many factors impact on individuals’ responses to either gather or disperse.

“Bacterial colonies, schools of fish, flocking birds, swarming insects and pedestrian flow all show collective and dynamic behaviours which are sensitive to changes in the surrounding environment and their dispersal or gathering can be sometimes the difference between life and death,” said lead researcher, Dr Giorgio Volpe, UCL Chemistry.

A March 9, 2016 UCL press release (also on EurekAlert), which originated the news item, expands on the theme,

“The crowd often has different behaviours to the individuals within it and we don’t know what the simple rules of motion are for this. If we understood these and how they are adapted in complex environments, we could externally regulate active systems. Examples include controlling the delivery of biotherapeutics in nanoparticle carriers to the target in the body, or improving crowd security in a panic situation.”

The study, published today in Nature Communications, investigated the behaviour of active colloidal particles in a controllable system to find out the rules of motion for individuals gathering or dispersing in response to external factors.

Colloidal particles are free to diffuse through a solution and for this study suspended silica microspheres were used. The colloidal particles became active with the addition of E. coli bacteria to the solution. Active colloidal particles were chosen as a model system because they move of their own accord using the energy from their environment, which is similar to how animals move to get food.

Initially, the active colloidal particles gathered at the centre of the area illuminated by a smooth beam which provided an active potential. Disorder was introduced using a speckle beam pattern which disordered the attractive potential and caused the colloids to disperse from the area at a rate of 0.6 particles per minute over 30 minutes. The particles switched between gathering and dispersing proportional to the level of external disorder imposed.

Erçağ Pinçe, who is first author of the study with Dr Sabareesh K. P. Velu, both Bilkent University, said: “We didn’t expect to see this mechanism as it’s counterintuitive but it might already be at play in natural systems. Our finding suggests there may be a way to control active matter through external factors. We could use it to control an existing system, or to design active agents that exploit the features of the environment to perform a given task, for example designing distinct depolluting agents for different types of polluted terrains and soils.”

Co-author, Dr Giovanni Volpe, Bilkent University, added: “Classical statistical physics allows us to understand what happens when a system is at equilibrium but unfortunately for researchers, life happens far from equilibrium. Behaviours are often unpredictable as they strongly depend on the characteristic of the environment. We hope that understanding these behaviours will help reveal the physics behind living organisms, but also help deliver innovative technologies in personalised healthcare, environmental sustainability and security.”

The team now plan on applying their findings to real-life situations to improve society. In particular, they want to exploit the main conclusions from their work to develop intelligent nanorobots for applications in drug-delivery and environmental sustainability that are capable of efficiently navigate through complex natural environments.

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

Disorder-mediated crowd control in an active matter system by Erçağ Pinçe, Sabareesh K. P. Velu, Agnese Callegari, Parviz Elahi, Sylvain Gigan, Giovanni Volpe, & Giorgio Volpe. Nature Communications 7, Article number: 10907 doi:10.1038/ncomms10907 Published 09 March 2016

This is an open access paper.