Tag Archives: University of Oxford

A transatlantic report highlighting the risks and opportunities associated with synthetic biology and bioengineering

I love e-Life, the open access journal where its editors noted that a submitted synthetic biology and bioengineering report was replete with US and UK experts (along with a European or two) but no expert input from other parts of the world. In response the authors added ‘transatlantic’ to the title. It was a good decision since it was too late to add any new experts if the authors planned to have their paper published in the foreseeable future.

I’ve commented many times here when panels of experts include only Canadian, US, UK, and, sometimes, European or Commonwealth (Australia/New Zealand) experts that we need to broaden our perspectives and now I can add: or at least acknowledge (e.g. transatlantic) that the perspectives taken are reflective of a rather narrow range of countries.

Now getting to the report, here’s more from a November 21, 2017 University of Cambridge press release,

Human genome editing, 3D-printed replacement organs and artificial photosynthesis – the field of bioengineering offers great promise for tackling the major challenges that face our society. But as a new article out today highlights, these developments provide both opportunities and risks in the short and long term.

Rapid developments in the field of synthetic biology and its associated tools and methods, including more widely available gene editing techniques, have substantially increased our capabilities for bioengineering – the application of principles and techniques from engineering to biological systems, often with the goal of addressing ‘real-world’ problems.

In a feature article published in the open access journal eLife, an international team of experts led by Dr Bonnie Wintle and Dr Christian R. Boehm from the Centre for the Study of Existential Risk at the University of Cambridge, capture perspectives of industry, innovators, scholars, and the security community in the UK and US on what they view as the major emerging issues in the field.

Dr Wintle says: “The growth of the bio-based economy offers the promise of addressing global environmental and societal challenges, but as our paper shows, it can also present new kinds of challenges and risks. The sector needs to proceed with caution to ensure we can reap the benefits safely and securely.”

The report is intended as a summary and launching point for policy makers across a range of sectors to further explore those issues that may be relevant to them.

Among the issues highlighted by the report as being most relevant over the next five years are:

Artificial photosynthesis and carbon capture for producing biofuels

If technical hurdles can be overcome, such developments might contribute to the future adoption of carbon capture systems, and provide sustainable sources of commodity chemicals and fuel.

Enhanced photosynthesis for agricultural productivity

Synthetic biology may hold the key to increasing yields on currently farmed land – and hence helping address food security – by enhancing photosynthesis and reducing pre-harvest losses, as well as reducing post-harvest and post-consumer waste.

Synthetic gene drives

Gene drives promote the inheritance of preferred genetic traits throughout a species, for example to prevent malaria-transmitting mosquitoes from breeding. However, this technology raises questions about whether it may alter ecosystems [emphasis mine], potentially even creating niches where a new disease-carrying species or new disease organism may take hold.

Human genome editing

Genome engineering technologies such as CRISPR/Cas9 offer the possibility to improve human lifespans and health. However, their implementation poses major ethical dilemmas. It is feasible that individuals or states with the financial and technological means may elect to provide strategic advantages to future generations.

Defence agency research in biological engineering

The areas of synthetic biology in which some defence agencies invest raise the risk of ‘dual-use’. For example, one programme intends to use insects to disseminate engineered plant viruses that confer traits to the target plants they feed on, with the aim of protecting crops from potential plant pathogens – but such technologies could plausibly also be used by others to harm targets.

In the next five to ten years, the authors identified areas of interest including:

Regenerative medicine: 3D printing body parts and tissue engineering

While this technology will undoubtedly ease suffering caused by traumatic injuries and a myriad of illnesses, reversing the decay associated with age is still fraught with ethical, social and economic concerns. Healthcare systems would rapidly become overburdened by the cost of replenishing body parts of citizens as they age and could lead new socioeconomic classes, as only those who can pay for such care themselves can extend their healthy years.

Microbiome-based therapies

The human microbiome is implicated in a large number of human disorders, from Parkinson’s to colon cancer, as well as metabolic conditions such as obesity and type 2 diabetes. Synthetic biology approaches could greatly accelerate the development of more effective microbiota-based therapeutics. However, there is a risk that DNA from genetically engineered microbes may spread to other microbiota in the human microbiome or into the wider environment.

Intersection of information security and bio-automation

Advancements in automation technology combined with faster and more reliable engineering techniques have resulted in the emergence of robotic ‘cloud labs’ where digital information is transformed into DNA then expressed in some target organisms. This opens the possibility of new kinds of information security threats, which could include tampering with digital DNA sequences leading to the production of harmful organisms, and sabotaging vaccine and drug production through attacks on critical DNA sequence databases or equipment.

Over the longer term, issues identified include:

New makers disrupt pharmaceutical markets

Community bio-labs and entrepreneurial startups are customizing and sharing methods and tools for biological experiments and engineering. Combined with open business models and open source technologies, this could herald opportunities for manufacturing therapies tailored to regional diseases that multinational pharmaceutical companies might not find profitable. But this raises concerns around the potential disruption of existing manufacturing markets and raw material supply chains as well as fears about inadequate regulation, less rigorous product quality control and misuse.

Platform technologies to address emerging disease pandemics

Emerging infectious diseases—such as recent Ebola and Zika virus disease outbreaks—and potential biological weapons attacks require scalable, flexible diagnosis and treatment. New technologies could enable the rapid identification and development of vaccine candidates, and plant-based antibody production systems.

Shifting ownership models in biotechnology

The rise of off-patent, generic tools and the lowering of technical barriers for engineering biology has the potential to help those in low-resource settings, benefit from developing a sustainable bioeconomy based on local needs and priorities, particularly where new advances are made open for others to build on.

Dr Jenny Molloy comments: “One theme that emerged repeatedly was that of inequality of access to the technology and its benefits. The rise of open source, off-patent tools could enable widespread sharing of knowledge within the biological engineering field and increase access to benefits for those in developing countries.”

Professor Johnathan Napier from Rothamsted Research adds: “The challenges embodied in the Sustainable Development Goals will require all manner of ideas and innovations to deliver significant outcomes. In agriculture, we are on the cusp of new paradigms for how and what we grow, and where. Demonstrating the fairness and usefulness of such approaches is crucial to ensure public acceptance and also to delivering impact in a meaningful way.”

Dr Christian R. Boehm concludes: “As these technologies emerge and develop, we must ensure public trust and acceptance. People may be willing to accept some of the benefits, such as the shift in ownership away from big business and towards more open science, and the ability to address problems that disproportionately affect the developing world, such as food security and disease. But proceeding without the appropriate safety precautions and societal consensus—whatever the public health benefits—could damage the field for many years to come.”

The research was made possible by the Centre for the Study of Existential Risk, the Synthetic Biology Strategic Research Initiative (both at the University of Cambridge), and the Future of Humanity Institute (University of Oxford). It was based on a workshop co-funded by the Templeton World Charity Foundation and the European Research Council under the European Union’s Horizon 2020 research and innovation programme.

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

A transatlantic perspective on 20 emerging issues in biological engineering by Bonnie C Wintle, Christian R Boehm, Catherine Rhodes, Jennifer C Molloy, Piers Millett, Laura Adam, Rainer Breitling, Rob Carlson, Rocco Casagrande, Malcolm Dando, Robert Doubleday, Eric Drexler, Brett Edwards, Tom Ellis, Nicholas G Evans, Richard Hammond, Jim Haseloff, Linda Kahl, Todd Kuiken, Benjamin R Lichman, Colette A Matthewman, Johnathan A Napier, Seán S ÓhÉigeartaigh, Nicola J Patron, Edward Perello, Philip Shapira, Joyce Tait, Eriko Takano, William J Sutherland. eLife; 14 Nov 2017; DOI: 10.7554/eLife.30247

This paper is open access and the editors have included their notes to the authors and the authors’ response.

You may have noticed that I highlighted a portion of the text concerning synthetic gene drives. Coincidentally I ran across a November 16, 2017 article by Ed Yong for The Atlantic where the topic is discussed within the context of a project in New Zealand, ‘Predator Free 2050’ (Note: A link has been removed),

Until the 13th century, the only land mammals in New Zealand were bats. In this furless world, local birds evolved a docile temperament. Many of them, like the iconic kiwi and the giant kakapo parrot, lost their powers of flight. Gentle and grounded, they were easy prey for the rats, dogs, cats, stoats, weasels, and possums that were later introduced by humans. Between them, these predators devour more than 26 million chicks and eggs every year. They have already driven a quarter of the nation’s unique birds to extinction.

Many species now persist only in offshore islands where rats and their ilk have been successfully eradicated, or in small mainland sites like Zealandia where they are encircled by predator-proof fences. The songs in those sanctuaries are echoes of the New Zealand that was.

But perhaps, they also represent the New Zealand that could be.

In recent years, many of the country’s conservationists and residents have rallied behind Predator-Free 2050, an extraordinarily ambitious plan to save the country’s birds by eradicating its invasive predators. Native birds of prey will be unharmed, but Predator-Free 2050’s research strategy, which is released today, spells doom for rats, possums, and stoats (a large weasel). They are to die, every last one of them. No country, anywhere in the world, has managed such a task in an area that big. The largest island ever cleared of rats, Australia’s Macquarie Island, is just 50 square miles in size. New Zealand is 2,000 times bigger. But, the country has committed to fulfilling its ecological moonshot within three decades.

In 2014, Kevin Esvelt, a biologist at MIT, drew a Venn diagram that troubles him to this day. In it, he and his colleagues laid out several possible uses for gene drives—a nascent technology for spreading designer genes through groups of wild animals. Typically, a given gene has a 50-50 chance of being passed to the next generation. But gene drives turn that coin toss into a guarantee, allowing traits to zoom through populations in just a few generations. There are a few natural examples, but with CRISPR, scientists can deliberately engineer such drives.

Suppose you have a population of rats, roughly half of which are brown, and the other half white. Now, imagine there is a gene that affects each rat’s color. It comes in two forms, one leading to brown fur, and the other leading to white fur. A male with two brown copies mates with a female with two white copies, and all their offspring inherit one of each. Those offspring breed themselves, and the brown and white genes continue cascading through the generations in a 50-50 split. This is the usual story of inheritance. But you can subvert it with CRISPR, by programming the brown gene to cut its counterpart and replace it with another copy of itself. Now, the rats’ children are all brown-furred, as are their grandchildren, and soon the whole population is brown.

Forget fur. The same technique could spread an antimalarial gene through a mosquito population, or drought-resistance through crop plants. The applications are vast, but so are the risks. In theory, gene drives spread so quickly and relentlessly that they could rewrite an entire wild population, and once released, they would be hard to contain. If the concept of modifying the genes of organisms is already distasteful to some, gene drives magnify that distaste across national, continental, and perhaps even global scales.

These excerpts don’t do justice to this thought-provoking article. If you have time, I recommend reading it in its entirety  as it provides some insight into gene drives and, with some imagination on the reader’s part, the potential for the other technologies discussed in the report.

One last comment, I notice that Eric Drexler is cited as on the report’s authors. He’s familiar to me as K. Eric Drexler, the author of the book that popularized nanotechnology in the US and other countries, Engines of Creation (1986) .

Revisiting the scientific past for new breakthroughs

A March 2, 2017 article on phys.org features a thought-provoking (and, for some of us, confirming) take on scientific progress  (Note: Links have been removed),

The idea that science isn’t a process of constant progress might make some modern scientists feel a bit twitchy. Surely we know more now than we did 100 years ago? We’ve sequenced the genome, explored space and considerably lengthened the average human lifespan. We’ve invented aircraft, computers and nuclear energy. We’ve developed theories of relativity and quantum mechanics to explain how the universe works.

However, treating the history of science as a linear story of progression doesn’t reflect wholly how ideas emerge and are adapted, forgotten, rediscovered or ignored. While we are happy with the notion that the arts can return to old ideas, for example in neoclassicism, this idea is not commonly recognised in science. Is this constraint really present in principle? Or is it more a comment on received practice or, worse, on the general ignorance of the scientific community of its own intellectual history?

For one thing, not all lines of scientific enquiry are pursued to conclusion. For example, a few years ago, historian of science Hasok Chang undertook a careful examination of notebooks from scientists working in the 19th century. He unearthed notes from experiments in electrochemistry whose results received no explanation at the time. After repeating the experiments himself, Chang showed the results still don’t have a full explanation today. These research programmes had not been completed, simply put to one side and forgotten.

A March 1, 2017 essay by Giles Gasper (Durham University), Hannah Smithson (University of Oxford) and Tom Mcleish (Durham University) for The Conversation, which originated the article, expands on the theme (Note: Links have been removed),

… looping back into forgotten scientific history might also provide an alternative, regenerative way of thinking that doesn’t rely on what has come immediately before it.

Collaborating with an international team of colleagues, we have taken this hypothesis further by bringing scientists into close contact with scientific treatises from the early 13th century. The treatises were composed by the English polymath Robert Grosseteste – who later became Bishop of Lincoln – between 1195 and 1230. They cover a wide range of topics we would recognise as key to modern physics, including sound, light, colour, comets, the planets, the origin of the cosmos and more.

We have worked with paleographers (handwriting experts) and Latinists to decipher Grosseteste’s manuscripts, and with philosophers, theologians, historians and scientists to provide intellectual interpretation and context to his work. As a result, we’ve discovered that scientific and mathematical minds today still resonate with Grosseteste’s deeply physical and structured thinking.

Our first intuition and hope was that the scientists might bring a new analytic perspective to these very technical texts. And so it proved: the deep mathematical structure of a small treatise on colour, the De colore, was shown to describe what we would now call a three-dimensional abstract co-ordinate space for colour.

But more was true. During the examination of each treatise, at some point one of the group would say: “Did anyone ever try doing …?” or “What would happen if we followed through with this calculation, supposing he meant …”. Responding to this thinker from eight centuries ago has, to our delight and surprise, inspired new scientific work of a rather fresh cut. It isn’t connected in a linear way to current research programmes, but sheds light on them from new directions.

I encourage you to read the essay in its entirety.

Brown recluse spider, one of the world’s most venomous spiders, shows off unique spinning technique

Caption: American Brown Recluse Spider is pictured. Credit: Oxford University

According to scientists from Oxford University this deadly spider could teach us a thing or two about strength. From a Feb. 15, 2017 news item on ScienceDaily,

Brown recluse spiders use a unique micro looping technique to make their threads stronger than that of any other spider, a newly published UK-US collaboration has discovered.

One of the most feared and venomous arachnids in the world, the American brown recluse spider has long been known for its signature necro-toxic venom, as well as its unusual silk. Now, new research offers an explanation for how the spider is able to make its silk uncommonly strong.

Researchers suggest that if applied to synthetic materials, the technique could inspire scientific developments and improve impact absorbing structures used in space travel.

The study, published in the journal Material Horizons, was produced by scientists from Oxford University’s Department of Zoology, together with a team from the Applied Science Department at Virginia’s College of William & Mary. Their surveillance of the brown recluse spider’s spinning behaviour shows how, and to what extent, the spider manages to strengthen the silk it makes.

A Feb. 15, 2017 University of Oxford press release, which originated the news item,  provides more detail about the research,

From observing the arachnid, the team discovered that unlike other spiders, who produce round ribbons of thread, recluse silk is thin and flat. This structural difference is key to the thread’s strength, providing the flexibility needed to prevent premature breakage and withstand the knots created during spinning which give each strand additional strength.

Professor Hannes Schniepp from William & Mary explains: “The theory of knots adding strength is well proven. But adding loops to synthetic filaments always seems to lead to premature fibre failure. Observation of the recluse spider provided the breakthrough solution; unlike all spiders its silk is not round, but a thin, nano-scale flat ribbon. The ribbon shape adds the flexibility needed to prevent premature failure, so that all the microloops can provide additional strength to the strand.”

By using computer simulations to apply this technique to synthetic fibres, the team were able to test and prove that adding even a single loop significantly enhances the strength of the material.

William & Mary PhD student Sean Koebley adds: “We were able to prove that adding even a single loop significantly enhances the toughness of a simple synthetic sticky tape. Our observations open the door to new fibre technology inspired by the brown recluse.”

Speaking on how the recluse’s technique could be applied more broadly in the future, Professor Fritz Vollrath, of the Department of Zoology at Oxford University, expands: “Computer simulations demonstrate that fibres with many loops would be much, much tougher than those without loops. This right away suggests possible applications. For example carbon filaments could be looped to make them less brittle, and thus allow their use in novel impact absorbing structures. One example would be spider-like webs of carbon-filaments floating in outer space, to capture the drifting space debris that endangers astronaut lives’ and satellite integrity.”

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

Toughness-enhancing metastructure in the recluse spider’s looped ribbon silk by
S. R. Koebley, F. Vollrath, and H. C. Schniepp. Mater. Horiz., 2017, Advance Article DOI: 10.1039/C6MH00473C First published online 15 Feb 2017

This paper is open access although you may need to register with the Royal Society of Chemistry’s publishing site to get access.

Developing cortical implants for future speech neural prostheses

I’m guessing that graphene will feature in these proposed cortical implants since the project leader is a member of the Graphene Flagship’s Biomedical Technologies Work Package. (For those who don’t know, the Graphene Flagship is one of two major funding initiatives each receiving funding of 1B Euros over 10 years from the European Commission as part of their FET [Future and Emerging Technologies)] Initiative.)  A Jan. 12, 2017 news item on Nanowerk announces the new project (Note: A link has been removed),

BrainCom is a FET Proactive project, funded by the European Commission with 8.35M€ [8.3 million Euros] for the next 5 years, holding its Kick-off meeting on January 12-13 at ICN2 (Catalan Institute of Nanoscience and Nanotechnology) and the UAB [ Universitat Autònoma de Barcelona]. This project, coordinated by ICREA [Catalan Institution for Research and Advanced Studies] Research Prof. Jose A. Garrido from ICN2, will permit significant advances in understanding of cortical speech networks and the development of speech rehabilitation solutions using innovative brain-computer interfaces.

A Jan. 12, 2017 ICN2 press release, which originated the news item expands on the theme (it is a bit repetitive),

More than 5 million people worldwide suffer annually from aphasia, an extremely invalidating condition in which patients lose the ability to comprehend and formulate language after brain damage or in the course of neurodegenerative disorders. Brain-computer interfaces (BCIs), enabled by forefront technologies and materials, are a promising approach to treat patients with aphasia. The principle of BCIs is to collect neural activity at its source and decode it by means of electrodes implanted directly in the brain. However, neurorehabilitation of higher cognitive functions such as language raises serious issues. The current challenge is to design neural implants that cover sufficiently large areas of the brain to allow for reliable decoding of detailed neuronal activity distributed in various brain regions that are key for language processing.

BrainCom is a FET Proactive project funded by the European Commission with 8.35M€ for the next 5 years. This interdisciplinary initiative involves 10 partners including technologists, engineers, biologists, clinicians, and ethics experts. They aim to develop a new generation of neuroprosthetic cortical devices enabling large-scale recordings and stimulation of cortical activity to study high level cognitive functions. Ultimately, the BraimCom project will seed a novel line of knowledge and technologies aimed at developing the future generation of speech neural prostheses. It will cover different levels of the value chain: from technology and engineering to basic and language neuroscience, and from preclinical research in animals to clinical studies in humans.

This recently funded project is coordinated by ICREA Prof. Jose A. Garrido, Group Leader of the Advanced Electronic Materials and Devices Group at the Institut Català de Nanociència i Nanotecnologia (Catalan Institute of Nanoscience and Nanotechnology – ICN2) and deputy leader of the Biomedical Technologies Work Package presented last year in Barcelona by the Graphene Flagship. The BrainCom Kick-Off meeting is held on January 12-13 at ICN2 and the Universitat Autònoma de Barcelona (UAB).

Recent developments show that it is possible to record cortical signals from a small region of the motor cortex and decode them to allow tetraplegic [also known as, quadriplegic] people to activate a robotic arm to perform everyday life actions. Brain-computer interfaces have also been successfully used to help tetraplegic patients unable to speak to communicate their thoughts by selecting letters on a computer screen using non-invasive electroencephalographic (EEG) recordings. The performance of such technologies can be dramatically increased using more detailed cortical neural information.

BrainCom project proposes a radically new electrocorticography technology taking advantage of unique mechanical and electrical properties of novel nanomaterials such as graphene, 2D materials and organic semiconductors.  The consortium members will fabricate ultra-flexible cortical and intracortical implants, which will be placed right on the surface of the brain, enabling high density recording and stimulation sites over a large area. This approach will allow the parallel stimulation and decoding of cortical activity with unprecedented spatial and temporal resolution.

These technologies will help to advance the basic understanding of cortical speech networks and to develop rehabilitation solutions to restore speech using innovative brain-computer paradigms. The technology innovations developed in the project will also find applications in the study of other high cognitive functions of the brain such as learning and memory, as well as other clinical applications such as epilepsy monitoring.

The BrainCom project Consortium members are:

  • Catalan Institute of Nanoscience and Nanotechnology (ICN2) – Spain (Coordinator)
  • Institute of Microelectronics of Barcelona (CNM-IMB-CSIC) – Spain
  • University Grenoble Alpes – France
  • ARMINES/ Ecole des Mines de St. Etienne – France
  • Centre Hospitalier Universitaire de Grenoble – France
  • Multichannel Systems – Germany
  • University of Geneva – Switzerland
  • University of Oxford – United Kingdom
  • Ludwig-Maximilians-Universität München – Germany
  • Wavestone – Luxembourg

There doesn’t seem to be a website for the project but there is a BrainCom webpage on the European Commission’s CORDIS (Community Research and Development Information Service) website.

Epic Scottish poetry and social network science

It’s been a while since I’ve run a social network story here and this research into a 250-year controversy piqued my interest anew. From an Oct. 20, 2016 Coventry University (UK) press release (also on EurekAlert) Note: A link has been removed,

The social networks behind one of the most famous literary controversies of all time have been uncovered using modern networks science.

Since James Macpherson published what he claimed were translations of ancient Scottish Gaelic poetry by a third-century bard named Ossian, scholars have questioned the authenticity of the works and whether they were misappropriated from Irish mythology or, as heralded at the time, authored by a Scottish equivalent to Homer.

Now, in a joint study by Coventry University, the National University of Ireland, Galway and the University of Oxford, published today in the journal Advances in Complex Systems, researchers have revealed the structures of the social networks underlying the Ossian’s works and their similarities to Irish mythology.

The researchers mapped the characters at the heart of the works and the relationships between them to compare the social networks found in the Scottish epics with classical Greek literature and Irish mythology.

The study revealed that the networks in the Scottish poems bore no resemblance to epics by Homer, but strongly resembled those in mythological stories from Ireland.

The Ossianic poems are considered to be some of the most important literary works ever to have emerged from Britain or Ireland, given their influence over the Romantic period in literature and the arts. Figures from Brahms to Wordsworth reacted enthusiastically; Napoleon took a copy on his military campaigns and US President Thomas Jefferson believed that Ossian was the greatest poet to have ever existed.

The poems launched the romantic portrayal of the Scottish Highlands which persists, in many forms, to the present day and inspired Romantic nationalism all across Europe.

Professor Ralph Kenna, a statistical physicist based at Coventry University, said:

By working together, it shows how science can open up new avenues of research in the humanities. The opposite also applies, as social structures discovered in Ossian inspire new questions in mathematics.”

Dr Justin Tonra, a digital humanities expert from the National University of Ireland, Galway said:

From a humanities point of view, while it cannot fully resolve the debate about Ossian, this scientific analysis does reveal an insightful statistical picture: close similarity to the Irish texts which Macpherson explicitly rejected, and distance from the Greek sources which he sought to emulate.”

A statistical physicist, eh? I find that specialty quite an unexpected addition to the team stretching my ideas about social networks in new directions.

Getting back to the research, the scientists have supplied this image to illustrate their work,

Caption: In the social network underlying the Ossianic epic, the 325 nodes represent characters appearing in the narratives and the 748 links represent interactions between them. Credit: Coventry University

Caption: In the social network underlying the Ossianic epic, the 325 nodes represent characters appearing in the narratives and the 748 links represent interactions between them. Credit: Coventry University

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

A networks-science investigation into the epic poems of Ossian by Joseph Yose, Ralph Kenna, Pádraig MacCarron, Thierry Platini, Justin Tonra.  Complex Syst. DOI: http://dx.doi.org/10.1142/S0219525916500089 Published: 21 October 2016

This paper is behind a paywall.

Help find some siblings for the Higgs boson

This is the Higgs Hunters’ (or HiggsHunters) second call for volunteers; the first was described in my Dec. 2, 2014 posting. Some 18 months after the first call, over 20,000 volunteers have been viewing images from the Large Hadron Collider in a bid to assist physicists at CERN (European Organization for Nuclear Research).

These images show how particles appear in the ATLAS detector. The lines show the paths of charged particles travelling away from a collision at the centre. Volunteers are looking for tracks appearing 'out of thin air' away from the centre. (Image: CERN)

These images show how particles appear in the ATLAS detector. The lines show the paths of charged particles travelling away from a collision at the centre. Volunteers are looking for tracks appearing ‘out of thin air’ away from the centre. (Image: CERN)

A July 6, 2016 news item on phys.org announces the call for more volunteers (Note: Links have been removed),

A citizen science project, called HiggsHunters gives everyone the chance to help search for the Higgs boson’s relatives.

Volunteers are searching through thousands of images from the ATLAS experiment on the HiggsHunters.org website, which makes use of the Zooniverse  citizen science platform.

They are looking for ‘baby Higgs bosons’, which leave a characteristic trace in the ATLAS detector.

This is the first time that images from the Large Hadron Collider have been examined on such a scale – 60,000 of the most interesting events were selected from collisions recorded throughout 2012 – the year of the Higgs boson discovery. About 20,000 of those collisions have been scanned so far, revealing interesting features.

A July 4, 2016 posting by Harriet Kim Jarlett on Will Kalderon’s CERN blog, which originated the news item, provides more details,

“There are tasks – even in this high-tech world – where the human eye and the human brain simply win out,” says Professor Alan Barr of the University of Oxford, who is leading the project.

Over the past two years, more than twenty thousand amateur scientists, from 179 countries, have been scouring images of LHC collisions,  looking for as-yet unobserved particles.

Dr Will Kalderon, who has been working on the project says “We’ve been astounded both by the number of responses and ability of people to do this so well, I’m really excited to see what we might find”.

July 4, 2016 was the fourth anniversary of the  confirmation that the Higgs Boson almost certainly exists (from the CERN blog),

Today, July 4 2016, is the fourth birthday of the Higgs boson discovery. Here, a toy Higgs is sat on top of a birthday cake decorated with a HiggsHunter event display. On the blackboard behind is the process people are looking for - Higgs-strahlung. (Image: Will Kalderon/CERN)

Today, July 4 2016, is the fourth birthday of the Higgs boson discovery. Here, a toy Higgs is sat on top of a birthday cake decorated with a HiggsHunter event display. On the blackboard behind is the process people are looking for – Higgs-strahlung. (Image: Will Kalderon/CERN)

You can find the Higgs Hunters website here. Should you be interested in other citizen science projects, you can find the Zooniverse website here.

Weather@Home citizen science project

It’s been a while since I’ve featured a citizen science story here. So, here’s more about Weather@Home from a June 9, 2016 Oregon State University news release on EurekAlert,

Tens of thousands of “citizen scientists” have volunteered some use of their personal computer time to help researchers create one of the most detailed, high resolution simulations of weather ever done in the Western United States.

The data, obtained through a project called Weather@Home, is an important step forward for scientifically sound, societally relevant climate science, researchers say in a an article published in the Bulletin of the American Meteorological Society. The analysis covered the years 1960-2009 and future projections of 2030-49.

Caption: The elevation of areas of the American West that were part of recent climate modeling as part of the Weather@Home Program. Credit: Graphic courtesy of Oregon State University

Caption: The elevation of areas of the American West that were part of recent climate modeling as part of the Weather@Home Program. Credit: Graphic courtesy of Oregon State University

The news release expands on the theme,

“When you have 30,000 modern laptop computers at work, you can transcend even what a supercomputer can do,” said Philip Mote, professor and director of the Oregon Climate Change Research Institute at Oregon State University, and lead author on the study.

“With this analysis we have 140,000 one-year simulations that show all of the impacts that mountains, valleys, coasts and other aspects of terrain can have on local weather,” he said. “We can drill into local areas, ask more specific questions about management implications, and understand the physical and biological climate changes in the West in a way never before possible.”

The sheer number of simulations tends to improve accuracy and reduce the uncertainty associated with this type of computer analysis, experts say. The high resolution also makes it possible to better consider the multiple climate forces at work in the West – coastal breezes, fog, cold air in valleys, sunlight being reflected off snow – and vegetation that ranges from wet, coastal rain forests to ice-covered mountains and arid scrublands within a comparatively short distance.

Although more accurate than previous simulations, improvements are still necessary, researchers say. Weather@Home tends to be too cool in a few mountain ranges and too warm in some arid plains, such as the Snake River plain and Columbia plateau, especially in summer. While other models have similar errors, Weather@Home offers the unique capability to improve simulations by improving the physics in the model.

Ultimately, this approach will help improve future predictions of regional climate. The social awareness of these issues has “matured to the point that numerous public agencies, businesses and investors are asking detailed questions about the future impacts of climate change,” the researchers wrote in their report.

This has led to a skyrocketing demand for detailed answers to specific questions – what’s the risk of a flood in a particular area, what will be future wind speeds as wind farms are developed, how should roads and bridges be built to handle extremely intense rainfall? There will be questions about heat stress on humans, the frequency of droughts, future sea levels and the height of local storm surges.

This type of analysis, and more like it, will help answer some of those questions, researchers say.

New participants in this ongoing research are always welcome, officials said. If interested in participating, anyone can go online to “climateprediction.net” and click on “join.” They should then follow the instructions to download and install BOINC, a program that manages the tasks; create an account; and select a project. Participation in climateprediction.net is available, as well as many others.

I checked out the About page on the climateprediction.net website, which hosts the Weather@Home project,

Climateprediction.net is a volunteer computing, climate modelling project based at the University of Oxford in the Environmental Change Institute, the Oxford e-Research Centre and Atmospheric, Oceanic and Planetary Physics.

We have a team of 13 climate scientists, computing experts and graduate students working on this project, as well as our partners and collaborators working at other universities, research and non-profit organisations around the world.

What we do

We run climate modelling experiments using the home computers of thousands of volunteers. This allows us to answer important and difficult questions about how climate change is affecting our world now and how it will affect our world in the future.

Climateprediction.net is a not-for-profit project.

Why we need your help

We run hundreds of thousands of state-of-the-art climate models, each very slightly different from the others, but still plausibly representing the real world.

This technique, known as ensemble modelling, requires an enormous amount of computing power.

Climate models are large and resource-intensive to run and it is not possible to run the large number of models we need on supercomputers.

Our solution is to appeal to volunteer computing, which combines the power of thousands of ordinary computers, each of which tackles one small part of the larger modelling task.

By using your computers, we can improve our understanding of, and confidence in, climate change predictions more than would ever be possible using the supercomputers currently available to scientists.

Please join our project and help us model the climate.

Our Experiments

When climateprediction.net first started, we were running very large, global models to answer questions about how climate change will pan out in the 21st century.

In addition, we are now running a number of smaller, regional experiments, under the umbrella of weather@home.

BOINC

Climateprediction.net uses a volunteer computing platform called BOINC (The Berkeley Open Infrastructure for Network Computing).

BOINC was originally developed to support SETI@home, which uses people’s home computers to analyse radio signals, searching for signs of extra-terrestrial intelligence.

BOINC is now used on over 70 projects covering a wide range of scientific areas, including mathematics, medicine, molecular biology, climatology, environmental science, and astrophysics.

Getting back to Oregon State University and its regional project research, here’s a link to and a citation for the paper,

Superensemble Regional Climate Modeling for the Western United States by Philip W. Mote, Myles R. Allen, Richard G. Jones, Sihan Li, Roberto Mera, David E. Rupp, Ahmed Salahuddin, and Dean Vickers. Bulletin of the American Meteorological Society February 2016, Vol. 97, No. 2 DOI: http://dx.doi.org/10.1175/BAMS-D-14-00090.1 Published online 14 March 2016

This is an open access paper.

Spider webs inspire liquid wire

Courtesy University of Oxford

Courtesy University of Oxford

Usually, when science talk runs to spider webs the focus is on strength but this research from the UK and France is all about resilience. From a May 16, 2016 news item on phys.org,

Why doesn’t a spider’s web sag in the wind or catapult flies back out like a trampoline? The answer, according to new research by an international team of scientists, lies in the physics behind a ‘hybrid’ material produced by spiders for their webs.

Pulling on a sticky thread in a garden spider’s orb web and letting it snap back reveals that the thread never sags but always stays taut—even when stretched to many times its original length. This is because any loose thread is immediately spooled inside the tiny droplets of watery glue that coat and surround the core gossamer fibres of the web’s capture spiral.

This phenomenon is described in the journal PNAS by scientists from the University of Oxford, UK and the Université Pierre et Marie Curie, Paris, France.

The researchers studied the details of this ‘liquid wire’ technique in spiders’ webs and used it to create composite fibres in the laboratory which, just like the spider’s capture silk, extend like a solid and compress like a liquid. These novel insights may lead to new bio-inspired technology.

A May 16, 2016 University of Oxford press release (also on EurekAlert), which originated the news item, provides more detail,

Professor Fritz Vollrath of the Oxford Silk Group in the Department of Zoology at Oxford University said: ‘The thousands of tiny droplets of glue that cover the capture spiral of the spider’s orb web do much more than make the silk sticky and catch the fly. Surprisingly, each drop packs enough punch in its watery skins to reel in loose bits of thread. And this winching behaviour is used to excellent effect to keep the threads tight at all times, as we can all observe and test in the webs in our gardens.’

The novel properties observed and analysed by the scientists rely on a subtle balance between fibre elasticity and droplet surface tension. Importantly, the team was also able to recreate this technique in the laboratory using oil droplets on a plastic filament. And this artificial system behaved just like the spider’s natural winch silk, with spools of filament reeling and unreeling inside the oil droplets as the thread extended and contracted.

Dr Hervé Elettro, the first author and a doctoral researcher at Institut Jean Le Rond D’Alembert, Université Pierre et Marie Curie, Paris, said: ‘Spider silk has been known to be an extraordinary material for around 40 years, but it continues to amaze us. While the web is simply a high-tech trap from the spider’s point of view, its properties have a huge amount to offer the worlds of materials, engineering and medicine.

‘Our bio-inspired hybrid threads could be manufactured from virtually any components. These new insights could lead to a wide range of applications, such as microfabrication of complex structures, reversible micro-motors, or self-tensioned stretchable systems.’

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

In-drop capillary spooling of spider capture thread inspires hybrid fibers with mixed solid–liquid mechanical properties by Hervé Elettro, Sébastien Neukirch, Fritz Vollrath, and Arnaud Antkowiak. PNAS doi: 10.1073/pnas.1602451113

This paper appears to be open access.

3D print the city of Palmyra (Syria)?

Designated a World Heritage Site by UNESCO (United Nations Educational, Scientific and Cultural Organization), Palmyra dates back to Second Century BCE (before the common era) as UNESCO’s Site of Palmyra webpage indicates,

An oasis in the Syrian desert, north-east of Damascus, Palmyra contains the monumental ruins of a great city that was one of the most important cultural centres of the ancient world. From the 1st to the 2nd century, the art and architecture of Palmyra, standing at the crossroads of several civilizations, married Graeco-Roman techniques with local traditions and Persian influences.

First mentioned in the archives of Mari in the 2nd millennium BC, Palmyra was an established caravan oasis when it came under Roman control in the mid-first century AD as part of the Roman province of Syria.  It grew steadily in importance as a city on the trade route linking Persia, India and China with the Roman Empire, marking the crossroads of several civilisations in the ancient world. A grand, colonnaded street of 1100 metres’ length forms the monumental axis of the city, which together with secondary colonnaded cross streets links the major public monuments including the Temple of Ba’al, Diocletian’s Camp, the Agora, Theatre, other temples and urban quarters. Architectural ornament including unique examples of funerary sculpture unites the forms of Greco-roman art with indigenous elements and Persian influences in a strongly original style. Outside the city’s walls are remains of a Roman aqueduct and immense necropolises.

Discovery of the ruined city by travellers in the 17th and 18th centuries resulted in its subsequent influence on architectural styles.

Until recently Palmyra was occupied by ISIS or ISIL or IS (depending on what the group is being called today). A March 31, 2016 news item on phys.org presents a perspective on the city and cultural heritage in a time of strife,

The destruction at the ancient city of Palmyra symbolises the suffering of the Syrian people at the hands of the terrorist group known as Islamic State (IS). Palmyra was a largely Roman city located at a desert oasis on a vital crossroad, and “one of the most important cultural centres of the ancient world”. Its remarkable preservation highlighted an intermingling of cultures that today, as then, came to stand for the tolerance and multiculturalism that pre-conflict Syria was renowned for -– tolerance that IS seeks to eradicate.

A March 31, 2016 essay by Emma Cunliffe (University of Oxford) for The Conversation, which originated the news item, expands on the theme,

Early in the conflict, the area was heavily fortified. Roads and embankments were dug through the necropolises and the Roman walls, and the historic citadel defences were upgraded. Yet the terrorists occupied and desecrated the city from May 2015, systematically destroying monuments such as the Temple of Baalshamin, the Temple of Bel, seven tower tombs, a large Lion goddess statue and two Islamic shrines. They ransacked the museum, tortured and executing the former site director Khaled al-Asaad in search of treasure to sell. According to satellite imagery analysis the site was heavily looted throughout it all.

Now the city has been recaptured, the first damage assessments are underway, and Syrian – and international – attention is already turning to restoration. This work will be greatly aided by the Syrians who risked their lives to transport the contents of the Palmyra museum to safety. The last truck pulled out as IS arrived, with bullets whizzing past.

There is a contrasting view as to how much destruction occurred from a March 29, 2016 essay by Paul Rogers (University of Bradford) for The Conversation,

Syrian Army units have taken back the ancient city of Palmyra from Islamic State. The units are now also trying to extend their control to include al-Qaryatain, to the south west of Palmyra, and Sukhnah, to the north east.

There are indications that the damage done to the ancient world heritage site which lies just outside Palmyra has been much less than feared. It may even have been limited to the destruction of two or three individual ruins – certainly important in their own right but just a small part of a huge complex that stretches over scores of hectares.

Written before some of the latest events, Rogers’ perspective is one of military tactics and strategy which contrasts with Cunliffe’s cultural heritage perspective. Like the answers to the classic question ‘Is the glass is half empty or is the glass is half full?’, both are correct, in their way.

Getting back to the cultural heritage aspect, Cunliffe outlines how Syrians and others in the international community are attempting to restore Palmyra, from her March 31, 2016 essay (Note: Links have been removed),

Even as they were displaced, Syrians have worked to keep a detailed memory of the city alive. Syrian artists created artworks depicting the destruction. In a Jordanian camp, refugees made miniature models of the city and other cultural sites, even measuring out the number and position of Palmyra’s columns from photographs.

The international community is also playing its part. Groups like UNOSAT [UNITAR’s Operational Satellite Applications Programme], the UN’s satellite imagery analysts have used satellite imagery to monitor the damage. On the ground, Syrian-founded NGOs like APSA [Association for the Protection Syrian Archaeology] have linked with universities to assess the site. Groups such as NewPalmyra and Palmyra 3D Model are using the latest technology to create open-access 3D computer models from photographs.

Others have gone even further. The Million Image Database Project at the Oxford Institute for Digital Archaeology distributed cameras to volunteers across the Middle East to collect 3D photos of sites. As well as creating 3D models, they will recreate full-scale artefacts, sites, and architectural features using their own cement-based 3D printing techniques. This will start with a recreation of the arch from Palmyra’s Temple of Bel, due to be unveiled in London in April 2016.

Here’s an artistic representation of the destruction,

A depiction of the destruction. Humam Alsalim and Rami Bakhos

A depiction of the destruction. Humam Alsalim and Rami Bakhos

Of course, there are some ethical issues about the restoration being raised, from Cunliffe’s March 31, 2016 essay (Note: Links have been removed),

It wouldn’t be the first time such large-scale restoration has been undertaken. Historic central Warsaw, for example, was destroyed during World War II, and was almost completely reconstructed and is now a World Heritage site. Reconstruction is costly, but might be accomplished more quickly and cheaply using new digital techniques, showing the world that Syria values its cultural heritage.

But many argue that 3D printing fails to capture the authenticity of the original structures, amounting to little more than the Disneyfication of heritage. They also point out that the fighting is still ongoing: 370,000 Syrians are dead, millions are displaced, and perhaps 50%-70% of the nearby town has been destroyed. Given the pressing humanitarian needs, stabilisation alone should be the priority for now.

Rebuilding also fails to redress the loss caused by the extensive looting of the site, focusing only on the dramatically destroyed monuments. Perhaps most importantly, its worth asking whether returning Palmyra exactly to its pre-conflict state denies a major chapter of its history? There needs to be a wide-ranging discussion on the priorities for the immediate future and the nature of any future reconstruction.

While I grasp most of the arguments I’m not sure why 3D printing raises a greater ethical issue, “… many argue that 3D printing fails to capture the authenticity of the original structures, amounting to little more than the Disneyfication of heritage … .” Couldn’t you say that about any form of restoration? Certainly, I was disconcerted when I saw the Sphinx in Cairo in real life where the restoration is quite obvious from angles not usually seen in tourist pictures.

More tangentially, how big is the 3D printer? If memory serves, building materials from ancient times were often large blocks of stone.

Getting back to the point, both Cunliffe’s and Rogers’ essays are worth reading in their entirety if you have the time. And since those essays have been written there has been an update for Associated Press in an April 1, 2016 article by Albert Aji on phys.org. Apparently, the IS retreat included time to plant thousands of mines throughout Palmyra with trees, doors, animals and more being booby-trapped and, now, being detonated by the Syrian army.

One final comment, The booby-trapping reminded me of a scene in the English Patient (movie) when the allies have won the war, the Germans have withdrawn and British and Canadian soldiers have liberated a town in Italy. They celebrate that night and one exuberant Brit soldier climbs a flagpole (I think) and is killed because the Germans had booby-trapped the top of the flagpole. Some years ago, a friend of mine was peacekeeper in Croatia and he said that everything was booby-trapped, flagpoles, mailboxes, cemetery markers, etc. He never said anything much more about but I have the impression it was demoralizing and stressful. I think the discussion about restoration and the artwork produced by Syrians in response to the happenings in Palmyra are an important way to counteract demoralization and stress. Whether money should be spent on restoration or all of it dedicated to pressing humanitarian needs is a question for other people to answer but a society without art and culture is one that is dying so it is heartening to note the vibrancy in Syria.

ETA April 19, 2016: Palmyra’s Arch of Triumph has been successfully replicated and is standing in London, UK according to an April 19, 2016 news item on phys.org. The replica is about 2/3 the size of the original. No reason for the size change is given in the Associated Press article. The arch scheduled to remain in London for a few more days before moving to New York, Dubai, and other destinations before arriving in Palmyra.

Motor proteins have a stiff-legged walk

An April 23, 2015 news item on Nanowerk calls to mind Monty Python and its Ministry of Silly Walks,

The ‘stiff-legged’ walk of a motor protein along a tightrope-like filament has been captured for the first time.

Because cells are divided in many parts that serve different functions some cellular goodies need to be transported from one part of the cell to another for it to function smoothly. There is an entire class of proteins called ‘molecular motors’, such as myosin 5, that specialise in transporting cargo using chemical energy as fuel.

Remarkably, these proteins not only function like nano-scale lorries, they also look like a two-legged creature that takes very small steps. But exactly how Myosin 5 did this was unclear.

For anyone unfamiliar with The Ministry of Silly Walks (from its Wikipedia entry; Note: Links have been removed),

“The Ministry of Silly Walks” is a sketch from the Monty Python comedy troupe’s television show Monty Python’s Flying Circus, season 2, episode 14, which is entitled “Face the Press”.

Here’s an image from the sketch, which perfectly illustrates a stiff-legged walk,

John Cleese as a Civil Servant in the Ministry of Silly Walks. Screenshot from Monty Python's Flying Circus episode, Dinsdale (Alternate episode title: Face the Press). Ministry_of_Silly_Walks.jpg ‎(300 × 237 pixels, file size: 14 KB, MIME type: image/jpeg) [downloaded from http://en.wikipedia.org/wiki/File:Ministry_of_Silly_Walks.jpg]

John Cleese as a Civil Servant in the Ministry of Silly Walks. Screenshot from Monty Python’s Flying Circus episode, Dinsdale (Alternate episode title: Face the Press). Ministry_of_Silly_Walks.jpg ‎(300 × 237 pixels, file size: 14 KB, MIME type: image/jpeg) [downloaded from http://en.wikipedia.org/wiki/File:Ministry_of_Silly_Walks.jpg]

As far as I can tell, the use of this image would fall under the notion of ‘fair dealing‘ as it’s called in Canada.

Getting back to the Nanowerk news item, it started life as a University of Oxford Science blog April 23, 2015 posting  by Pete Wilton (Note: A link has been removed),

The motion of myosin 5 has now been recorded by a team led by Oxford University scientists using a new microscopy technique that can ‘see’ tiny steps of tens of nanometres captured at up to 1000 frames per second. The findings are of interest for anyone trying to understand the basis of cellular function but could also help efforts aimed at designing efficient nanomachines.

‘Until now, we believed that the sort of movements or steps these proteins made were random and free-flowing because none of the experiments suggested otherwise,’ said Philipp Kukura of Oxford University’s Department of Chemistry who led the research recently reported in the journal eLife. ‘However, what we have shown is that the movements only appeared random; if you have the capability to watch the motion with sufficient speed and precision, a rigid walking pattern emerges.’

One of the key problems for those trying to capture proteins on a walkabout is that not only are these molecules small – with steps much smaller than the wavelength of light and therefore the resolution of most optical microscopes – but they are also move very quickly.

Philipp describes how the team had to move from the microscope equivalent of an iPhone camera to something more like the high speed cameras used to snap speeding bullets. Even with such precise equipment the team had to tag the ‘feet’ of the protein in order to precisely image its gait: one foot was tagged with a quantum dot, the other with a gold particle just 20 nanometres across. (Confusingly, technically speaking, these ‘feet’ are termed the ‘heads’ of the protein because they bind to the actin filament).

I recommend reading Wilton’s post in its entirety. Meanwhile, here’s a 12 secs. video illustrating the motor protein’s stiff-legged walk,

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

Structural dynamics of myosin 5 during processive motion revealed by interferometric scattering microscopy by Joanna Andrecka, Jaime Ortega Arroyo, Yasuharu Takagi, Gabrielle de Wit, Adam Fineberg, Lachlan MacKinnon, Gavin Young, James R Sellers, & Philipp Kukura. eLife 2015;4:e05413 DOI: http://dx.doi.org/10.7554/eLife.05413Published March 6, 2015

This paper is open access.

As for silly walks, there is more than one version of the sketch with John Cleese on YouTube but I was particularly taken with this public homage which took place in Brno (Czech Republic) in Jan. 2013,

Enjoy!