A Nov.27, 2015 news item on Nanowerk announces a new UK (United Kingdom) research project designed to answer the question: what impact could nanoscale plastic particles have on the marine environment?,
As England brings in pricing on plastic carrier bags, and Scotland reveals that similar changes a little over a year ago have reduced the use of such bags by 80%, new research led by Heriot-Watt University in conjunction with Plymouth University will look at the effect which even the most microscopic plastic particles can have on the marine environment.
While images of large ‘islands’ of plastic rubbish or of large marine animals killed or injured by the effects of such discards have brought home some of the obvious negative effects of plastics in the marine environment, it is known that there is more discarded plastic out there than we can account for, and much of it will have degraded into small or even microscopic particles.
It is the effect of these latter, known as nano-plastics, which will be studied under a £1.1m research project, largely funded by NERC [UKNatural Environment Research Council] and run by Heriot-Watt and Plymouth Universities.
The project, RealRiskNano, will look at the risks these tiny plastic particles pose to the food web including filter-feeding organisms like mussels, clams and sediment dwelling organisms. It will focus on providing information to improve environmental risk assessment for nanoplastics, based on real-world exposure scenarios replicated in the laboratory.
Team leader Dr Theodore Henry, Associate Professor of Toxicology at Heriot-Watt’s School of Life Sciences, said that the study will build on previous research on nano-material toxicology, but will provide information which the earlier studies did not include.
“Pieces of plastic of all sizes have been found in even the most remote marine environments. It’s relatively easy to see some of the results: turtles killed by easting plastic bags which they take for jelly fish, or large marine mammals drowned when caught in discarded ropes and netting.
“But when plastics fragment into microscopic particles, what then? It’s easy to imagine that they simply disappear, but we know that nano-particles pose their own distinct threats purely because of their size. They’re small enough to be transported throughout the environment with unknown effects on organisms including toxicity and interference with processes of the digestive system.
An important component of the project, to be investigated by Dr Tony Gutierrez at Heriot-Watt, will be the study of interactions between microorganisms and the nanoplastics to reveal how these interactions affect their fate and toxicology.
The aim, said Dr Henry, is to provide the information which is needed to effect real change.“We simply don’t know what effects these nano-plastic particles may pose to the marine environment, to filter-feeders and on to fish, and through the RealRiskNano project we aim to provide this urgently needed information to the people whose job it is to assess risk to the marine ecosystem and decide what steps need to be taken to mitigate it.”
My introduction to the term, Afrofuturism was in a March 11, 2015 posting by Jessica Bland for the Guardian in the Technology/Political Science section. It was written on the occasion of a then upcoming FutureFest event,
This is unapologetically connected to FutureFest, the festival Nesta (where I work) is holding this weekend in London Bridge. These thoughts represent the ideas that piqued my interest while curating talks and exhibits based on the thought experiment of a future African city-superpower. George Clinton, Spoek Mathambo, Tegan Bristow and Fabian-Carlos Guhl (from Ampion Venture Bus) will be speaking during the weekend. Thomas Aquilina is displaying photographs from his trip and the architects of the Lagos 2060 project will take part in a debate on whether their fiction can lead to a different kind of future.
In anticipation of the March 2015 FutureFest event, Bland had written a roundup piece about “New sounds from South Africa and Nigeria’s urban science fiction [that] could change the future of technology and the city.” Here are some excerpts from her piece (Note: Links have been removed),
Strong stories or visions of the future stick around. The 1920s sci-fi fantasy of a jetpack commute still pops up in discussions about the future of technology, not to mention as an option on the Citymapper travel app. By co-opting or creating new visions of the future, it seems possible to influence the development of new products and services – from consumer tech to urban infrastructure. A new generation of African artists is taking over the mantle of Afrofuturist arts from a US-centred crowd. They could bring a welcome change to how technology is developed in the region, as well as a challenge to the dominance of imported plans for urban development.
Last Thursday’s London gig from Fantasma was sweaty and boisterous. It was also very different from the remix of Joy Division’s She’s Lost Control that brought front man Spoek Mathambo to the attention of a global audience a couple of years ago. Fantasma is a group of South African musicians with different backgrounds. Guitarist Bhekisenzo Cele started the gig with three of his own songs, introducing the traditional Zulu maskandi music that they went on to mix with shangaan electro, hiphop, punk, electronica and everything in between.
The gig had a buzz about it. But the performance was from a new collective trying things out; it wasn’t as genre-smashing as expected. And expectations ride high for Spoek. In 2011, he titled a collection from his back catalogue ‘Beyond Afrofuturism’. He took on, at least in name, a whole Afro-American cultural movement: embodied by musicians like Sun Ra, George Clinton and Drexciya. A previous post on this blog by Chardine Taylor-Stone describes the roots of Afrofuturism in science fiction that centres on space travel and human enhancement. But she goes on to say: “Afrofuturism also goes beyond spaceships, androids and aliens, and encompasses African mythology and cosmology with an aim to connect those from across the Black Diaspora to their forgotten African ancestry.” Spoek shares what he calls a cultural lineage with this movement. But he is not Afro-American. He also shares a cultural lineage with the sounds of South African musicians he grew up listening to.
Other forms of art are taking an increasingly activist role in the future of technology. Lydia Nicholas’s description of the relationship between Douglas Adam’s fictional Hitchhiker’s Guide and the real life development of the iPad shows how science fiction can effortlessly influence the development of new technology.
The science fiction collection Lagos 2060 is a more purposeful intervention. Published in 2013, it speculates about what it will be like to live in Lagos 100 years after Nigeria gained independence from the UK. It was born out of a creative writing workshop initiated by DADA books in Lagos. Foundation director of DADA, Ayodele Arigbabu, described the collection and other similar video and visual art work (in an email): “Far more than aesthetic indulgence, these renditions are a calibration of the changes deemed necessary in today’s political, technical and cultural infrastructure.”
Bland also explores a history of this movement,
Gaston Berger was the Senegalese founder of the academic journal Prospectiv in 1957. To many, he was the first futurist, or at least one of the first people to describe themselves as one. He founded promotes the practice of playing out the human consequences of today’s action. This is about avoiding a fatalistic approach to the future: about being proactive and provoking change, as much as anticipating it.
Berger’s early work spawned a generation, and then another and another, of professional futurists. They work in different ways and different places. Some are in government, enticing and frightening politicians with the prospect of a different transport system, healthcare sector or national security regime. Some are consultants to large companies, offering advice on the way that trends like 3D printing or flying robots will change their sector. An article from 1996 does a good job of summarising the principles of this movement: don’t act like an ostrich and ignore the future by putting your head in the sand; don’t act like a fireman and just respond to threats to your future; and don’t focus just on insurance against for the future.
Bland has written an interesting and sprawling piece, which in some way reflects the subject. Africa is a huge and sprawling continent.
Slate, a US online magazine, is hosting along with New America and Arizona State University a Future Tense event on Afrofuturism but this seems to be quite US-centric. From the Future Tense Afrofuturism event webpage on the Slate website (Note: Links have been removed),
Future Tense is hosting a conversation about Afrofuturism in New York City on December 3rd, 2015 from 6:30-8:30 p.m.
Afrofuturism emphasizes the intersection of black cultures with questions of imagination, liberation, and technology. Rooted in works like those of science fiction author Octavia Butler, avant-garde jazz legend Sun Ra, and George Clinton, Afrofuturism explores concepts of race, space and time in order to ask the existential question posed by critic Mark Dery: “Can a community whose past has been deliberately erased imagine possible futures?”
Will the alternative futures and realities Afrofuturism describes transform and reshape the concept of black identity? Join Future Tense for a discussion on Afrofuturism and its unique vantage on the challenges faced by black Americans and others throughout the African diaspora.
During the event, enjoy an Afrofuturist inspired drink from 67 Orange Street. Follow the discussion online using #Afrofuturism and by following @NewAmericaNYC and @FutureTenseNow.
Click here to RSVP. Space is limited so register now!
Principal Investigator, School for the Future of Innovation in Society, Arizona State University
Author, Afrofuturism: The World of Black Sci-Fi and Fantasy Culture and Post Black: How A New Generation is Redefining African American Identity
DJ and Artist
Designer and Creative Director, Ikire Jones
Staff writer, Slate
It seems we have one word, Afrofuturism, and two definitions. One where Africa is referenced and one where African-American experience is referenced.
For anyone curious about Nesta, where Jessica Bland works and the Future Fest host (from its Wikipedia entry),
Nesta (formerly NESTA, National Endowment for Science, Technology and the Arts) is an independent charity that works to increase the innovation capacity of the UK.
The organisation acts through a combination of practical programmes, investment, policy and research, and the formation of partnerships to promote innovation across a broad range of sectors.
It’s the 150th anniversary for a series of equations electric charges and electric and magnetic fields that are still being explored. Jon Butterworth in a Nov. 22, 2015 posting on the Guardian science blog network explains (Note: A link has been removed),
The chances are that you are reading this article on some kind of electronic technology. You are definitely seeing it via visible light, unless you have a braille or audio converter. And it probably got to you via wifi or a mobile phone signal. All of those things are understood in terms of the relationships between electric charges and electric and magnetic fields summarised in Maxwell’s [James Clerk Maxwell] equations, published by the Royal Society in 1865, 150 years ago.
Verbally, the equations can be summarised as something like:
Electric and magnetic fields make electric charges move. Electric charges cause electric fields, but there are no magnetic charges. Changes in magnetic fields cause electric fields, and vice versa.
The equations specify precisely how it all happens, but that is the gist of it.
Butterworth got a rare opportunity to see the original manuscript,
Original manuscript of Maxwell’s seminal paper Photograph: Jon Butterworth/Royal Society [downloaded from http://www.theguardian.com/science/life-and-physics/2015/nov/22/maxwells-equations-150-years-of-light]
I love this description from Butterworth,
It was submitted in 1864 but, in a situation familiar to scientists everywhere, was held up in peer review. There’s a letter, dated March 1865, from William Thomson (later Lord Kelvin) saying he was sorry for being slow, that he’d read most of it and it seemed pretty good (“decidely suitable for publication”).
Then, there’s this,
The equations seem to have been very much a bottom-up affair, in that Maxwell collected together a number of known laws which were used to describe various experimental results, and (with a little extra ingredient of his own) fitted them into a unified framework. What is amazing is how much that framework then reveals, both in terms of deep physical principles, and rich physical phenomena.
I’m not excerpting any part of Butterworth’s description of how Maxwell fit these equations together for his unification theory as I think it should be read in its totality.
The section on quantum mechanics is surprising,
Now, one thing Maxwell’s equations don’t contain is quantum mechanics [emphasis mine]. They are classical equations. But if you take the quantum mechnical description of an electron, and you enforce the same charge conservation law/voltage symmetry that was contained in the classical Maxwell’s equations, something marvellous happens [emphasis mine]. The symmetry is denoted “U(1)”, and if you enforce it locally – that it, you say that you have to be allowed make different U(1) type changes to electrons at different points in space, you actually generate the quantum mechanical version of Maxwell’s equations out of nowhere [emphasis mine]. You produce the equations that describe the photon, and the whole of quantum electrodynamics.
I encourage you to read Butterworth’s Nov. 22, 2015 posting where he also mention two related art/science projects and has embedded a video animation of the principles discussed in his posting.
For anyone unfamiliar with Butterworth, there’s this description at the Guardian,
An international graphene measurement centre opened in Oct. 2015 but the official launch seems to have just started. A Nov. 23, 2015 news item on Nanowerk makes the announcement,
The China-UK collaborative effort to support the development an international graphene standards and testing centre was officially launched at Zhongguancun Fengtai Science Park, Beijing, China, in October 2015. As the demand for international standards for testing graphene increases, the Centre in Beijing will lay the foundation for the development of graphene industry and high-end applications in China.
A China-UK graphene conference was held as part of the launch activities on the 24 October 2015 and graphene experts from China and the UK’s National Physical Laboratory (NPL) discussed graphene R&D progress and the development of graphene international standards; the discussions included NPL’s work in this area and the related testing methods.
The graphene conference was part of a programme of activities between NPL, Beijing Zhongguancun Fengtai Science Park and the associated Beijing Fengtai New Materials Inspection Institute (BFM) agreed in a Memorandum of Understanding signed in Spring 2015, to support the development of standards and testing in China. Efforts are being made to promote the implementation of standards in China and to introduce new methods of measurement by establishing non-contact and contact-type testing facilities for electrical and structural properties of graphene and other 2D materials at the centre. During the conference, the Chinese Association for Promoting Cooperation between Universities and Industries agreed a strategic cooperation for the centre, which will enable the integration and utilisation of the resources of universities and research institutes. This will lead to knowledge transfer and dissemination of testing standards for the establishment of China’s graphene characterisation platform and applications platform.
The Vice Mayor of Fengtai District, and Fengtai Park director, Jie Zhang (张婕), said that the Zhongguancun Fengtai Park is now actively building an international graphene centre, and that the cooperation of NPL and other international research teams will be instrumental to the success of the centre. NPL’s Principal Research Scientist, Ling Hao (郝玲), added that the partnership with Fengtai Science Park, BFM and other Chinese organisations will be “a win-win collaboration” for graphene research, development and application for both the UK and China.
Executive Chairman of the China Industry-University-Research Institute Collaboration Association (CIUR) Prof Wang Jianhua (王建华) said that graphene international standards and testing is key to national development of a graphene industry. He continued that the China-UK conference will further promote cooperation in graphene research, strengthening resource integration in graphene certification through testing and standards, all will contribute to these exciting R&D developments.
Stephanie Kitchen, Andrew Pollard, Tim Prior and Ling Hao of NPL also made presentations at the China-UK conference and delegates from China National Institute of Standardization, Beijing Institute of Metrology, Beijing Institute of Technology gave presentations and many other research and development institutions attended this conference.
The Brits have been amazing where graphene is concerned. They have been tireless about promoting it and themselves as leaders in the field and this is one more notch on their belt. Just prior to the Graphene Flagship winning one of two places (in 2013) for 1B Euros in research funding over 10 years, I wrote a series of posts (Feb. 2, 2012 starts the series, followed by Feb. 6, 2012, and then there was Feb. 21, 2012) where I expressed my admiration for the Brits’ stellar efforts.
Despite all the excitement and claims for nanoparticles as vehicles for drug delivery to ‘sick’ cells there is at least one substantive problem, the drug-laden nanoparticles don’t actually enter the interior of the cell. They are held in a kind of cellular ‘waiting room’.
Leonid Schneider in a Nov. 20, 2015 posting on his For Better Science blog describes the process in more detail,
A large body of scientific nanotechnology literature is dedicated to the biomedical aspect of nanoparticle delivery into cells and tissues. The functionalization of the nanoparticle surface is designed to insure their specificity at targeting only a certain type of cells, such as cancers cells. Other technological approaches aim at the cargo design, in order to ensure the targeted release of various biologically active agents: small pharmacological substances, peptides or entire enzymes, or nucleotides such as regulatory small RNAs or even genes. There is however a main limitation to this approach: though cells do readily take up nanoparticles through specific membrane-bound receptor interaction (endocytosis) or randomly (pinocytosis), these nanoparticles hardly ever truly reach the inside of the cell, namely its nucleocytoplasmic space. Solid nanoparticles are namely continuously surrounded by the very same membrane barrier they first interacted with when entering the cell. These outer-cell membrane compartments mature into endosomal and then lysosomal vesicles, where their cargo is subjected to low pH and enzymatic digestion. The nanoparticles, though seemingly inside the cell, remain actually outside. …
What follows is a stellar piece featuring counterclaims about and including Schneider’s own journalistic research into scientific claims that the problem of gaining entry to a cell’s true interior has been addressed by technologies developed in two different labs.
Having featured one of the technologies here in a July 24, 2015 posting titled: Sticky-flares nanotechnology to track and observe RNA (ribonucleic acid) regulation and having been contacted a couple of times by one of the scientists, Raphaël Lévy from the University of Liverpool (UK), challenging the claims made (Lévy’s responses can be found in the comments section of the July 2015 posting), I thought a followup of sorts was in order.
Leviathan and the Air-Pump: Hobbes, Boyle, and the Experimental Life (published 1985) is a book by Steven Shapin and Simon Schaffer. It examines the debate between Robert Boyle and Thomas Hobbes over Boyle’s air-pump experiments in the 1660s.
The style seems more genteel than what a contemporary Canadian or US audience is accustomed to but Hobbes and Boyle (and proponents of both sides) engaged in bruising communication.
There was a lot at stake then and now. It’s not just the power, prestige, and money, as powerfully motivating as they are, it’s the research itself. Scientists work for years to achieve breakthroughs or to add more to our common store of knowledge. It’s painstaking and if you work at something for a long time, you tend to be invested in it. Saying you’ve wasted ten years of your life looking at the problem the wrong way or have misunderstood your data is not easy.
As for the current debate, Schneider’s description gives no indication that there is rancour between any of the parties but it does provide a fascinating view of two scientists challenging one of the US’s nanomedicine rockstars, Chad Mirkin. The following excerpt follows the latest technical breakthroughs to the interior portion of the cell through three phases of the naming conventions (Nano-Flares, also known by its trade name, SmartFlares, which is a precursor technology to Sticky-Flares), Note: Links have been removed,
The next family of allegedly nucleocytoplasmic nanoparticles which Lévy turned his attention to, was that of the so called “spherical nucleic acids”, developed in the lab of Chad Mirkin, multiple professor and director of the International Institute for Nanotechnology at the Northwestern University, USA. These so called “Nano-Flares” are gold nanoparticles, functionalized with fluorophore-coupled oligonucleotides matching the messenger RNA (mRNA) of interest (Prigodich et al., ACS Nano 3:2147-2152, 2009; Seferos et al., J Am. Chem.Soc. 129:15477-15479, 2007). The mRNA detection method is such that the fluorescence is initially quenched by the gold nanoparticle proximity. Yet when the oligonucleotide is displaced by the specific binding of the mRNA molecules present inside the cell, the fluorescence becomes detectable and serves thus as quantitative read-out for the intracellular mRNA abundance. Exactly this is where concerns arise. To find and bind mRNA, spherical nucleic acids must leave the endosomal compartments. Is there any evidence that Nano-Flares ever achieve this and reach intact the nucleocytoplasmatic space, where their target mRNA is?
Lévy’s lab has focused its research on the commercially available analogue of the Nano-Flares, based on the patent to Mirkin and Northwestern University and sold by Merck Millipore under the trade name of SmartFlares. These were described by Mirkin as “a powerful and prolific tool in biology and medical diagnostics, with ∼ 1,600 unique forms commercially available today”. The work, led by Lévy’s postdoctoral scientist David Mason, now available in post-publication process at ScienceOpen and on Figshare, found no experimental evidence for SmartFlares to be ever found outside the endosomal membrane vesicles. On the contrary, the analysis by several complementary approaches, i.e., electron, fluorescence and photothermal microscopy, revealed that the probes are retained exclusively within the endosomal compartments.
In fact, even Merck Millipore was apparently well aware of this problem when the product was developed for the market. As I learned, Merck performed a number of assays to address the specificity issue. Multiple hundred-fold induction of mRNA by biological cell stimulation (confirmed by quantitative RT-PCR) led to no significant changes in the corresponding SmartFlare signal. Similarly, biological gene downregulation or experimental siRNA knock-down had no effect on the corresponding SmartFlare fluorescence. Cell lines confirmed as negative for a certain biomarker proved highly positive in a SmartFlare assay. Live cell imaging showed the SmartFlare signal to be almost entirely mitochondrial, inconsistent with reported patterns of the respective mRNA distributions. Elsewhere however, cyanine dye-labelled oligonucleotides were found to unspecifically localise to mitochondria (Orio et al., J. RNAi Gene Silencing 9:479-485, 2013), which might account to the often observed punctate Smart Flare signal.
More recently, Mirkin lab has developed a novel version of spherical nucleic acids, named Sticky-Flares (Briley et al., PNAS 112:9591-9595, 2015), which has also been patented for commercial use. The claim is that “the Sticky-flare is capable of entering live cells without the need for transfection agents and recognizing target RNA transcripts in a sequence-specific manner”. To confirm this, Lévy used the same approach as for the striped nanoparticles [not excerpted here]: he approached Mirkin by email and in person, requesting the original microscopy data from this publication. As Mirkin appeared reluctant, Lévy invoked the rules for data sharing by the journal PNAS, the funder NSF as well as the Northwestern University. After finally receiving Mirkin’s thin-optical microscopy data by air mail, Lévy and Mason re-analyzed it and determined the absence of any evidence for endosomal escape, while all Sticky-Flare particles appeared to be localized exclusively inside vesicular membrane compartments, i.e., endosomes (Mason & Levy, bioRxiv 2015).
I encourage you to read Schneider’s Nov. 20, 2015 posting in its entirety as these excerpts can’t do justice to it.
The PNAS surprise
PNAS (Proceedings of the National Academy of Science) published one of Mirkin’s papers on ‘Sticky-flares’ and is where scientists, Raphaël Lévy and David Mason, submitted a letter outlining their concerns with the ‘Sticky-flares’ research. Here’s the response as reproduced in Lévy’s Nov. 16, 2015 posting on his Rapha-Z-Lab blog
Dear Dr. Levy,
I regret to inform you that the PNAS Editorial Board has declined to publish your Letter to the Editor. After careful consideration, the Board has decided that your letter does not contribute significantly to the discussion of this paper.
Thank you for submitting your comments to PNAS.
Judge for yourself, Lévy’s and Mason’s letter can be found here (pdf) and here.
My primary interest in this story is in the view it provides of the scientific process and the importance of and difficulty associated with the debates.
I can’t venture an opinion about the research or the counterarguments other than to say that Lévy’s and Mason’s thoughtful challenge bears more examination than PNAS is inclined to accord. If their conclusions or Chad Mirkin’s are wrong, let that be determined in an open process.
I’ll leave the very last comment to Schneider who is both writer and cartoonist, from his Nov. 20, 2015 posting,
The story of science in the Muslim world is extraordinary, influencing science to this day, and is not well known even within its own community. The days when Muslim or Islamic scientists led the world are long gone and that is cause for concern. An Oct. 29, 2015 Malaysian Industry-Government Group for High Technology press release on EurekAlert argues that universities in Muslim countries must reinvent themselves to transform society and achieve scientific excellence,
A Task Force of international experts, formed by the Muslim World Science Initiative, today released a report [Science at Universities of the Muslim World] on the state of science at universities of the Muslim world.
To assess the state of science at universities of the Muslim world, the Task Force reviewed the rankings of Muslim-world’s universities globally, scientific production (number of papers published and citations), the level of spending on research and development (R&D), female participation in the scientific workforce, and other indicators.
The results were compared to those of countries deemed comparable in terms of gross domestic product (GDP) per capita, e.g. Brazil, Israel, Spain, South Africa, and South Korea.
The Task Force noted recent improvements in scientific publishing across a number of countries and a relatively healthy gender ratio among university students, even though the overall state of science in the Muslim World remains ‘poor,’ as depicted by
the disproportionately small number of Nobel Laureates
the small number of universities in top global rankings
the low spending on R&D, and
the abysmal performance of pre-university students on math and science tests
Seeking to assess if universities were the ‘main culprits’ in this sorry state of affairs, the Task Force highlighted significant challenges at the Universities of the Muslim World.
In particular, the Task Force lamented the fact that science education in most Organization of Islamic Cooperation (OIC) member countries was extremely narrow in focus and did little to enable students to think critically, especially beyond their respective domains of specialty.
The Task Force calls for broad liberal education for scientists and engineers to enable them to function effectively in addressing complex multi-disciplinary challenges that the world faces today.
The Task Force also noted that self-censorship was often practiced in the selection of topics to be taught, particularly regarding controversial subjects such as the theory of evolution.
The Task Force called for the introduction and systematic study of philosophy of science and history of the sciences of the Muslim ‘Golden Age’ and beyond for students to navigate and develop a perspective on these difficult disciplinary boundaries and overlaps. The language of instruction also created significant challenges.
Faculty members were also ill-trained to teach using cutting-edge methods such as inquiry-based science education and had little autonomy to innovate.
While the Task Force called for greater autonomy for the universities, it also emphasized that they must become meritocracies and aspire for true scientific excellence rather than playing for temporary gains in numbers or rankings. It also calls for zero tolerance on plagiarism and other forms of academic misconduct.
The Report of the Task Force includes: a foreword by the Chair, Tan Sri Zakri Abdul Hamid, the main assessment and recommendations, and individual essays written by the Task Force members on issues, including
Science, Society & the University
Are universities of the Muslim world helping spread a culture of science through society?
Should Religion Be Kept Out of the Science Classroom?
STEM Education and the Muslim Gender Divide and
The Need of Liberal Education for Science and Engineering
The Task Force is putting out an open call for universities across the Muslim world to join a voluntary Network of Excellence of Universities for Science (NEXUS), to be launched early next year.
This peer group will be managed by the task force and housed in Tan Sri Zakri’s office. NEXUS will run summer schools for university administrators, monitor the progress of reforms at participating universities, and issue a peer report card that will assess the performance of the universities in meeting milestones, thus recognizing and inspiring further improvements. True transformation will require much broader action from ministries, regulators and funding agencies, and these may be the most resistant to change.
Releasing the Report of the Task Force, Tan Sri Zakri Abdul Hamid stressed that “universities must reinvent themselves to lead the scientific reforms in the Muslim World, and as they do so they must embrace key ideas of merit and transparency, engagement with society, and pedagogical and curricular innovation.”
Professor Nidhal Guessoum, the Task Force’s Convenor, noted that “Task Force members strongly believe that the most appropriate venue for action on our recommendations is the university itself. The most essential ingredient in creating excellence in science and science teaching at a university is a realization, within a university’s highest leadership and its faculty, of the need to give up the old and dated ways, renew the purpose, and re-write the genetic code of their university.
Dr. Athar Osama, the Director of the Project noted that “the purpose of Muslim World Science Initiative is to jumpstart a dialogue within the society on critical issues at the intersection of science, society, and Islam. The Task Force has done a commendable job in laying the groundwork for a very important conversation about our universities.”
The divide between science/technology/engineering/mathematics (STEM) education and other fields of interest such as social sciences, the arts, and the humanities may be larger in the Islamic world (and to some extent reversed with humanities looking down on science) but it is a problem elsewhere, often expressed as a form of snobbery, as I alluded to in my Aug. 7, 2015 posting titled: Science snobbery and the problem of accessibility.
An Oct. 28, 2015 Nature essay about Islam, science, and the report by Nidhal Guessou and Athar Osama (two members of the Task Force; Note: Links have been removed) provides more context,
The Islamic civilization lays claim to the world’s oldest continually operational university. The University of Qarawiyyin was founded in Fes, Morocco, in ad 859, at the beginning of an Islamic Golden Age. Despite such auspicious beginnings, universities in the region are now in dire straits, as demonstrated by a report we have authored, released this week (see go.nature.com/korli3).
The 57 countries of the Muslim world — those with a Muslim-majority population, and part of the Organisation of Islamic Cooperation (OIC) — are home to nearly 25% of the world’s people. But as of 2012, they had contributed only 1.6% of the world’s patents, 6% of its academic publications, and 2.4% of the global research expenditure1, 2.
The authors note problems and at least one success with regard to curriculum (from the Nature essay; Note: Links have been removed),
Science classes themselves have serious problems. The textbooks used in OIC universities are often imported from the United States or Europe. Although the content is of a high standard, they assume a Western experience and use English or French as the language of instruction. This disadvantages many students, and creates a disconnect between their education and culture. To encourage the production of higher-quality, local textbooks and other academic material, universities need to reward staff for producing these at least as much as they do for research publication.
Some basic facts are seen as controversial, and marginalized. Evolution, for example, is usually taught only to biology students, often as “a theory”, and is rarely connected to the rest of the body of knowledge. One ongoing study has found, for example, that most Malaysian physicians and medical students reject evolution (see go.nature.com/38cswo). Evolution needs to be taught widely and shown to be compatible with Islam and its culture6. Teaching the philosophy and history of science would help, too.
The global consensus is that enquiry-based science education fosters the deepest understanding of scientific concepts and laws. But in most OIC universities, lecture-based teaching still prevails. Exceptions are rare. One is the Petroleum Institute, an engineering university in Abu Dhabi, UAE, where the faculty has created a hands-on experience with positive results on student interest and enrolment, particularly of women.
For anyone interested in the full report, it can be requested from the Muslim Science website.
One final comment, here’s the list of task force members in the Oct. 29, 2015 news release which includes someone from Mauritius (my father was born there),
Tan Sri Zakri Abdul Hamid, Science Advisor to Prime Minister of Malaysia, Chair of the Task Force on Science at the Universities of the Muslim World
Prof. Nidhal Guessoum, American University of Sharjah, UAE, Convenor of the Task Force on Science at Universities of the Muslim World
Dr. Mohammad Yusoff Sulaiman, President and CEO, MiGHT, Malaysia, Co-Convenor of the Task Force on Science at Universities of the Muslim World.
Dr. Moneef Zou’bi, Executive Director, Islamic World Academy of Science (IAS)
Prof. Adil Najam, Dean Frederick S. Pardee School of Global Studies, Boston University and former Vice Chancellor, Lahore University of Management Sciences (LUMS)
Prof. Ameenah Gurib-Fakim, Fellow of IAS, President of the Republic of Mauritius, and Professor at University of Mauritius
Prof. Mustafa El-Tayeb, President , Future University, Khartoum, Sudan
Prof. Abdur Razak Dzulkifli, President of International Association of Universities (IAU), and former Vice Chancellor USM, Malaysia
Dr. Nadia Alhasani, Dean of Student Life (formerly Dean of Women in Science and Engineering (WiSE), The Petroleum Institute, Abu Dhabi, UAE
Prof. Jamal Mimouni, Professor, University of Constantine-1, Algeria
Dr. Dato Lee Yee Cheong, Chair ISTIC Governing Board / Chair IAP SEP Global Council
Prof. Michael Reiss, Professor of Science Education, UCL Institute of Education, University College, London, Expert Advisor to the Muslim-Science.Com Task Force on Science at Universities of the Muslim World
Prof. Bruce Alberts, Professor of Biochemistry, University of California, San Francisco; President Emeritus, National Academy of Sciences, and Recipient, 2014 US Presidential Medal of Science, Expert Advisor to the Muslim-Science.Com Task Force on Science at Universities of the Muslim World
Professor Shoaib S. H. Zaidi, Professor and Dean of School of Sciences and Engineering, Habib University, Karachi
Dr. Athar Osama, Founder Muslim World Science Initiative, and Project Director of the Task Forces Project.
This show is still making its way around the world with the latest stop, as of Oct. 20, 2015, at the Library of Alexandria in Egypt.
A Jan. 21, 2010 article by Nick Higham and Margaret Ryan for BBC (British Broadcasting Corporation) news online describes some of the exhibit highlights,
From about 700 to 1700, many of history’s finest scientists and technologists were to be found in the Muslim world.
In Christian Europe the light of scientific inquiry had largely been extinguished with the collapse of the Roman empire. But it survived, and indeed blazed brightly, elsewhere.
From Moorish Spain across North Africa to Damascus, Baghdad, Persia and all the way to India, scientists in the Muslim world were at the forefront of developments in medicine, astronomy, engineering, hydraulics, mathematics, chemistry, map-making and exploration.
Salim Al-Hassani, a former professor of engineering at Umist (University of Manchester Institute of Science and Technology) is a moving force behind the exhibition, 1001 Inventions.
Visitors to the exhibition will be greeted by a 20 ft high replica of a spectacular clock designed in 1206 by the inventor Al-Jazari.
It incorporates elements from many cultures, representing the different cultural and scientific traditions which combined and flowed through the Muslim world.
The clock’s base is an elephant, representing India; inside the elephant the water-driven works of the clock derive from ancient Greece.
A Chinese dragon swings down from the top of the clock to mark the hours. At the top is a phoenix, representing ancient Egypt.
Sitting astride the elephant and inside the framework of the clock are automata, or puppets, wearing Arab turbans.
Elsewhere in the exhibition are displays devoted to water power, the spread of education (one of the world’s first universities was founded by a Muslim woman, Fatima al-Fihri), Muslim architecture and its influence on the modern world and Muslim explorers and geographers.
There is a display of 10th Century surgeons’ instruments, a lifesize model of a man called Abbas ibn Firnas, allegedly the first person to have flown with wings, and a model of the vast 100 yard-long junk commanded by the Muslim Chinese navigator, Zheng He.
The description of the exhibition items is compelling.
Science and the modern world debate (Humanism and Islam)
Yasmin Khan has written up a transcript of sorts in a Nov. 6, 2015 posting on the Guardian science blogs about a science debate (which took place Wednesday, Oct. 28, 2015 in London, UK) where Humanist and Islamic perspectives were being discussed (Note: Links have been removed),
Two important figures came head-to-head at Conway Hall, to discuss Islamic versus Humanist perspectives on science and the modern world. Jim Al-Khalili made the final public appearance of his term as president of the British Humanist Association during this stimulating, and at times provoking, debate with Ziauddin Sardar, chair of the Muslim Institute.
Al-Khalili advocated the values of the European Enlightenment, arguing that ever since the “Age of Reason” took hold during the 18th century, Humanists have looked to science instead of religion to explore and comprehend the world. Sardar upheld the view that it is the combination of faith and reason that offers a fuller understanding of the world, maintaining that it was this worldview that enabled the development of science in the Islamic golden Age.
A practising Muslim, Sardar is on an independent mission to promote rational, considered thought in interpreting the Qur’an. He explained that when he came to the UK from Pakistan, he found comfort in the familiar language of mathematics, which set him on a trajectory to train as a physicist: “God doesn’t need me, I need him. It makes me a better person and a better scientist”, he said.
In short, Sardar’s view is that although human knowledge at times converges with the Qur’an, the text should certainly not be treated as a scientific encyclopaedia. In support of this view, Sardar lamented the emergence of the I’jaz movement, which insists the Qur’an contains descriptions of modern scientific phenomena ranging from quantum mechanics to accurate descriptions of the stages of embryology and geology. In Sardar’s opinion, this stems from insecurity and a personal need to vindicate Islam to others.
Jim Al-Khalili agreed that ascribing literal meanings to religious texts can be perilous and that these verses should be interpreted more metaphorically. Likewise, when Einstein famously said “God does not play dice” he was using a figure of speech to acknowledge that there are things we don’t yet understand but this shouldn’t stop us from trying to find out more.
Whilst Al-Khalili is a staunch atheist, he adopts what he describes as an “accommodationist” approach in his interactions with people of religious faith: “I don’t think people who believe in God are irrational, I just don’t see a need to believe there is a purpose for why things are the way they are.” Born in Bagdad, Al-Khalili grew up in Iraq. His mother was Christian and his father was Shia, but he never heard them quarrel about religion. By the time he reached his teens he felt that he had distanced himself from needing any form of spirituality and his subsequent scientific training cemented this worldview. He asserted that his core values are empathy, humility and respect, without being driven by a reward in an afterlife: “It’s not just people of religious faith that have a moral compass – morality is what makes us human.”
I encourage you to read Khan’s piece (Nov. 6, 2015 posting) in its entirety as she provides historical and contemporary context to what seems to have been a fascinating and nuanced debate. Plus, there’s a bit of a bonus at the end where Khan is described as the producer of Sindbad Sci-Fi, a website where they are Reimagining Arab Science Fiction. From the website’s About page,
Sindbad Sci-Fi is an initiative for spurring the discovery of and engagement with Arab Science Fiction through dialogue. Our aim is to sustain a growing community of interest through brokering face-to-face and online discussion, building new partnerships and project collaborations along the way.
Many of us know and love Sindbad the sailor as the fictional sailor from the Arabian Book of OneThousand and One Nights, considered as being an early composite work of proto-science fiction and fantasy. His extraordinary voyages led him to adventures in magical places whilst meeting monsters and encountering supernatural phenomena.
Sindbad Sci-Fi is reviving Sindbad’s adventurous spirit for exploration and discovery. Join us as we continue star trekking across the Middle East, North Africa, South Asia and beyond. Together, we will boldly go where no one else has gone before!
I’m pretty sure somebody associated with this site is a Star Trek fan.
It’s been a while since I last (in a March 17, 2015 post) featured PoetryFilm. Here’s the latest from the organization’s Oct. 2015 newsletter,
I have been invited to join the International Jury for the CYCLOP International Videopoetry Festival, 20-22 November 2015 (Kiev, Ukraine)
PoetryFilm Paradox events, featuring poetry films about love, as part of the BFI LOVE season, 6 and 22 December 2015 (London, UK)
PoetryFilm screening + Zata Banks in conversation with filmmaker Roxana Vilk at The Scottish Poetry Library, 3 December 2015 (Scotland, UK)
I have been invited to judge the Carbon Culture Review poetry film competition (USA)
poetryfilmkanal in Germany recently invited me to write an article about the poetry film artform – it can be read here
FYI, the “I” in the announcement’s text is for Zata Banks, the founder and director of PoetryFilm since 2002.
There’s more about the CYCLOP International Videopoetry Festival in a Sept. 13, 2015 posting on the PoetryFilm website,
*The 5th CYCLOP International Videopoetry Festival will take place on 20 – 22 November 2015 in Ukraine (Kyiv). The festival programme features video poetry-related lectures, workshops, round tables, discussions, presentations of international contests and festivals, as well as a demonstration of the best examples of Ukrainian and world videopoetry, a competitive programme, an awards ceremony and other related projects.
One of the projects is a new Contest for International poetry films within the framework of the CYCLOP festival. The International Jury: Alastair Cook (Filmpoem Festival, Edinburgh, Scotland), Zata Banks (PoetryFilm, London, United Kingdom), Javier Robledo (VideoBardo, Buenos Aires, Argentina), John Bennet (videopoet, USA), Alice Lyons (Videopoet, Sligo, Ireland), Sigrun Hoellrigl (Art Visuals & Poetry, Vienna, Austria), Lucy English (Liberated Words, Bristol, United Kingdom), Tom Konyves (poet, video producer, educator and a pioneer in the field of videopoetry, British Columbia, Canada), Polina Horodyska (CYCLOP Videopoetry Festival, Kyiv, Ukraine) and Thomas Zandegiacomo (ZEBRA Poetry Film Festival, Berlin, Germany).
I can’t find a website for the Carbon Culture Review poetry film competition or a webpage for it on the Carbon Culture Review website but here’s what they have to say about themselves on the journal’s About page,
Carbon Culture Review is a journal at the intersection of new literature, art, technology and contemporary culture. We define culture broadly as the values, attitudes, actions and inventions of our global society and its subcultures in our modern age. Carbon Culture Review is distributed in the United States and countries throughout the world by Publisher’s Distribution Group, Inc. and Annas International as well as digitally through 0s&1s, Magzter and Amazon. CCR is a member of Councils of Literary Magazines and Presses and also publishes monthly online issues.
The last item from the announcement that I’m highlighting is Zata’s essay for poetryfilmkanal ,
Poetry films offer creative opportunities for exploring new semiotic modes and for communicating messages and meanings in innovative ways. Poetry films open up new methods of engagement, new audiences, and new means of self-expression, and also provide rich potential for the creation, perception and experience of emotion and meaning.
We are surrounded by communicative signs in literature, art, culture and in the world at large. Whilst words represent one system of communicating, there are many other ways of making meanings, for instance, colour semiotics, typographic design, and haptic, olfactive, gustatory and durational experiences – indeed, a comprehensive list could be infinite. The uses of spoken and written words to communicate represent just two approaches among many. Through using meaning-making systems other than words, by communicating without words, or by not using words alone, we can bypass these direct signifiers and tap directly into pools of meaning, or the signifieds, associated with those words. Different combinations of systems, or modes, can reinforce each other, render meanings more complex and subtle, or contrast with each other to illuminate different perspectives. Powerful juxtapositions, associations and new meanings can therefore emerge.
The essay is a good introduction for beginners and a good refresher for those in need. Btw, I understand Zata got married in March 2015. Congratulations to Zata and Joe!
On Tuesday, October 27, 2015 Café Scientifique, in the back room of The Railway Club (2nd floor of 579 Dunsmuir St. [at Seymour St.]), will be hosting a talk on the history of noise (from the Oct. 13, 2015 announcement),
Our speaker for the evening will be Dr. Shawn Bullock. The title of his talk is:
The History of Noise: Perspectives from Physics and Engineering
The word “noise” is often synonymous with “nuisance,” which implies something to be avoided as much as possible. We label blaring sirens, the space between stations on the radio dial and the din of a busy street as “noise.” Is noise simply a sound we don’t like? We will consider the evolution of how scientists and engineers have thought about noise, beginning in the 19th-century and continuing to the present day. We will explore the idea of noise both as a social construction and as a technological necessity. We’ll also touch on critical developments in the study of sound, the history of physics and engineering, and the development of communications technology.
I used ideas from the history of physics, the history of music, the discipline of sound studies, and the history of electrical engineering to make the point that understanding “noise” is essential to understanding advancements in physics and engineering in the last century. We began with a discussion of 19th-century attitudes toward noise (and its association with “progress” and industry) before moving on to examine the early history of recorded sound and music, early attempts to measure noise, and the noise abatement movement. I concluded with a brief overview of my recent work on the role of noise in the development of the modem during the early Cold War.
You can find out more about Dr. Bullock who is an assistant professor of science education at Simon Fraser University here at his website.
On the subject of noise, although not directly related to Bullock’s work, there’s some research suggesting that noise may be having a serious impact on marine life. From an Oct. 8, 2015 Elsevier press release on EurekAlert,
Quiet areas should be sectioned off in the oceans to give us a better picture of the impact human generated noise is having on marine animals, according to a new study published in Marine Pollution Bulletin. By assigning zones through which ships cannot travel, researchers will be able to compare the behavior of animals in these quiet zones to those living in noisier areas, helping decide the best way to protect marine life from harmful noise.
The authors of the study, from the University of St Andrews, UK, the Oceans Initiative, Cornell University, USA, and Curtin University, Australia, say focusing on protecting areas that are still quiet will give researchers a better insight into the true impact we are having on the oceans.
Almost all marine organisms, including mammals like whales and dolphins, fish and even invertebrates, use sound to find food, avoid predators, choose mates and navigate. Chronic noise from human activities such as shipping can have a big impact on these animals, since it interferes with their acoustic signaling – increased background noise can mean animals are unable to hear important signals, and they tend to swim away from sources of noise, disrupting their normal behavior.
The number of ships in the oceans has increased fourfold since 1992, increasing marine noise dramatically. Ships are also getting bigger, and therefore noisier: in 2000 the biggest cargo ships could carry 8,000 containers; today’s biggest carry 18,000.
“Marine animals, especially whales, depend on a naturally quiet ocean for survival, but humans are polluting major portions of the ocean with noise,” said Dr. Christopher Clark from the Bioacoustics Research Program, Cornell University. “We must make every effort to protect quiet ocean regions now, before they grow too noisy from the din of our activities.”
For the new study, lead author Dr. Rob Williams and the team mapped out areas of high and low noise pollution in the oceans around Canada. Using shipping route and speed data from Environment Canada, the researchers put together a model of noise based on ships’ location, size and speed, calculating the cumulative sound they produce over the course of a year. They used the maps to predict how noisy they thought a particular area ought to be.
To test their predictions, in partnership with Cornell University, they deployed 12 autonomous hydrophones – devices that can measure noise in water – and found a correlation in terms of how the areas ranked from quietest to noisiest. The quiet areas are potential noise conservation zones.
“We tend to focus on problems in conservation biology. This was a fun study to work on, because we looked for opportunities to protect species by working with existing patterns in noise and animal distribution, and found that British Colombia offers many important habitat for whales that are still quiet,” said Dr. Rob Williams, lead author of the study. “If we think of quiet, wild oceans as a natural resource, we are lucky that Canada is blessed with globally rare pockets of acoustic wilderness. It makes sense to talk about protecting acoustic sanctuaries before we lose them.”
Although it is clear that noise has an impact on marine organisms, the exact effect is still not well understood. By changing their acoustic environment, we could be inadvertently choosing winners and losers in terms of survival; researchers are still at an early stage of predicting who will win or lose under different circumstances. The quiet areas the team identified could serve as experimental control sites for research like the International Quiet Ocean Experiment to see what effects ocean noise is having on marine life.
“Sound is perceived differently by different species, and some are more affected by noise than others,” said Christine Erbe, co-author of the study and Director of the Marine Science Center, Curtin University, Australia.
So far, the researchers have focused on marine mammals – whales, dolphins, porpoises, seals and sea lions. With a Pew Fellowship in Marine Conservation, Dr. Williams now plans to look at the effects of noise on fish, which are less well understood. By starting to quantify that and let people know what the likely economic effect on fisheries or on fish that are culturally important, Dr. Williams hopes to get the attention of the people who make decisions that affect ocean noise.
“When protecting highly mobile and migratory species that are poorly studied, it may make sense to focus on threats rather than the animals themselves. Shipping patterns decided by humans are often more predictable than the movements of whales and dolphins,” said Erin Ashe, co-author of the study and co-founder of the Oceans Initiative from the University of St Andrews.
Keeping areas of the ocean quiet is easier than reducing noise in already busy zones, say the authors of the study. However, if future research that stems from noise protected zones indicates that overall marine noise should be reduced, there are several possible approaches to reducing noise. The first is speed reduction: the faster a ship goes, the noisier it gets, so slowing down would reduce overall noise. The noisiest ships could also be targeted for replacement: by reducing the noise produced by the noisiest 10% of ships in use today, overall marine noise could be reduced by more than half. The third, more long-term, option would be to build quieter ships from the outset.
I can’t help wondering why Canadian scientists aren’t involved in this research taking place off our shores. Regardless, here’s a link to and a citation for the paper,
Quiet(er) marine protected areas by Rob Williams, Christine Erbe, Erin Ashe, & Christopher W. Clark. Marine Pollution Bulletin Available online 16 September 2015 In Press, Corrected Proof doi:10.1016/j.marpolbul.2015.09.012
The accuracy and reliability of expert advice is often compromised by “cognitive frailties”, and needs to be interrogated with the same tenacity as research data to avoid weak and ill-informed policy, warn two leading risk analysis and conservation researchers in the journal Nature today.
While many governments aspire to evidence-based policy [emphasis mine], the researchers say the evidence on experts themselves actually shows that they are highly susceptible to “subjective influences” – from individual values and mood, to whether they stand to gain or lose from a decision – and, while highly credible, experts often vastly overestimate their objectivity and the reliability of peers.
They appear to be conflating evidence and expertise. Evidence usually means data while expertise is a more ephemeral concept. (Presumably, an expert is someone whose opinion is respected for one reason or another and who has studied the evidence and drawn some conclusions from it.)
The study described in the press release notes that one of the weaknesses of relying on experts is that they are subject to bias. They don’t mention that evidence or data can also be subject to bias but perhaps that’s why they suggest the experts should provide and assess the evidence on which they are basing their advice,
The researchers caution that conventional approaches of informing policy by seeking advice from either well-regarded individuals or assembling expert panels needs to be balanced with methods that alleviate the effects of psychological and motivational bias.
They offer a straightforward framework for improving expert advice, and say that experts should provide and assess [emphasis mine] evidence on which decisions are made – but not advise decision makers directly, which can skew impartiality.
“We are not advocating replacing evidence with expert judgements, rather we suggest integrating and improving them,” write professors William Sutherland and Mark Burgman from the universities of Cambridge and Melbourne respectively.
“Policy makers use expert evidence as though it were data. So they should treat expert estimates with the same critical rigour that must be applied to data,” they write.
“Experts must be tested, their biases minimised, their accuracy improved, and their estimates validated with independent evidence. Put simply, experts should be held accountable for their opinions.”
Sutherland and Burgman point out that highly regarded experts are routinely shown to be no better than novices at making judgements.
However, several processes have been shown to improve performances across the spectrum, they say, such as ‘horizon scanning’ – identifying all possible changes and threats – and ‘solution scanning’ – listing all possible options, using both experts and evidence, to reduce the risk of overlooking valuable alternatives.
To get better answers from experts, they need better, more structured questions, say the authors. “A seemingly straightforward question, ‘How many diseased animals are there in the area?’ for example, could be interpreted very differently by different people. Does it include those that are infectious and those that have recovered? What about those yet to be identified?” said Sutherland, from Cambridge’s Department of Zoology.
“Structured question formats that extract upper and lower boundaries, degrees of confidence and force consideration of alternative theories are important for shoring against slides into group-think, or individuals getting ascribed greater credibility based on appearance or background,” he said.
When seeking expert advice, all parties must be clear about what they expect of each other, says Burgman, Director of the Centre of Excellence for Biosecurity Risk Analysis. “Are policy makers expecting estimates of facts, predictions of the outcome of events, or advice on the best course of action?”
“Properly managed, experts can help with estimates and predictions, but providing advice assumes the expert shares the same values and objectives as the decision makers. Experts need to stick to helping provide and assess evidence on which such decisions are made,” he said.
Sutherland and Burgman have created a framework of eight key ways to improve the advice of experts. These include using groups – not individuals – with diverse, carefully selected members well within their expertise areas.
They also caution against being bullied or “starstruck” by the over-assertive or heavyweight. “People who are less self-assured will seek information from a more diverse range of sources, and age, number of qualifications and years of experience do not explain an expert’s ability to predict future events – a finding that applies in studies from geopolitics to ecology,” said Sutherland.
Added Burgman: “Some experts are much better than others at estimation and prediction. However, the only way to tell a good expert from a poor one is to test them. Qualifications and experience don’t help to tell them apart.”
“The cost of ignoring these techniques – of using experts inexpertly – is less accurate information and so more frequent, and more serious, policy failures,” write the researchers.
If you want to learn how something works, one strategy is to take it apart and put it back together again [also known as reverse engineering]. For 10 years, a global initiative called the Blue Brain Project–hosted at the Ecole Polytechnique Federale de Lausanne (EPFL)–has been attempting to do this digitally with a section of juvenile rat brain. The project presents a first draft of this reconstruction, which contains over 31,000 neurons, 55 layers of cells, and 207 different neuron subtypes, on October 8  in Cell.
Heroic efforts are currently being made to define all the different types of neurons in the brain, to measure their electrical firing properties, and to map out the circuits that connect them to one another. These painstaking efforts are giving us a glimpse into the building blocks and logic of brain wiring. However, getting a full, high-resolution picture of all the features and activity of the neurons within a brain region and the circuit-level behaviors of these neurons is a major challenge.
Henry Markram and colleagues have taken an engineering approach to this question by digitally reconstructing a slice of the neocortex, an area of the brain that has benefitted from extensive characterization. Using this wealth of data, they built a virtual brain slice representing the different neuron types present in this region and the key features controlling their firing and, most notably, modeling their connectivity, including nearly 40 million synapses and 2,000 connections between each brain cell type.
“The reconstruction required an enormous number of experiments,” says Markram, of the EPFL. “It paves the way for predicting the location, numbers, and even the amount of ion currents flowing through all 40 million synapses.”
Once the reconstruction was complete, the investigators used powerful supercomputers to simulate the behavior of neurons under different conditions. Remarkably, the researchers found that, by slightly adjusting just one parameter, the level of calcium ions, they could produce broader patterns of circuit-level activity that could not be predicted based on features of the individual neurons. For instance, slow synchronous waves of neuronal activity, which have been observed in the brain during sleep, were triggered in their simulations, suggesting that neural circuits may be able to switch into different “states” that could underlie important behaviors.
“An analogy would be a computer processor that can reconfigure to focus on certain tasks,” Markram says. “The experiments suggest the existence of a spectrum of states, so this raises new types of questions, such as ‘what if you’re stuck in the wrong state?'” For instance, Markram suggests that the findings may open up new avenues for explaining how initiating the fight-or-flight response through the adrenocorticotropic hormone yields tunnel vision and aggression.
The Blue Brain Project researchers plan to continue exploring the state-dependent computational theory while improving the model they’ve built. All of the results to date are now freely available to the scientific community at https://bbp.epfl.ch/nmc-portal.
Published by the renowned journal Cell, the paper is the result of a massive effort by 82 scientists and engineers at EPFL and at institutions in Israel, Spain, Hungary, USA, China, Sweden, and the UK. It represents the culmination of 20 years of biological experimentation that generated the core dataset, and 10 years of computational science work that developed the algorithms and built the software ecosystem required to digitally reconstruct and simulate the tissue.
The Hebrew University of Jerusalem’s Prof. Idan Segev, a senior author of the research paper, said: “With the Blue Brain Project, we are creating a digital reconstruction of the brain and using supercomputer simulations of its electrical behavior to reveal a variety of brain states. This allows us to examine brain phenomena within a purely digital environment and conduct experiments previously only possible using biological tissue. The insights we gather from these experiments will help us to understand normal and abnormal brain states, and in the future may have the potential to help us develop new avenues for treating brain disorders.”
Segev, a member of the Hebrew University’s Edmond and Lily Safra Center for Brain Sciences and director of the university’s Department of Neurobiology, sees the paper as building on the pioneering work of the Spanish anatomist Ramon y Cajal from more than 100 years ago: “Ramon y Cajal began drawing every type of neuron in the brain by hand. He even drew in arrows to describe how he thought the information was flowing from one neuron to the next. Today, we are doing what Cajal would be doing with the tools of the day: building a digital representation of the neurons and synapses, and simulating the flow of information between neurons on supercomputers. Furthermore, the digitization of the tissue is open to the community and allows the data and the models to be preserved and reused for future generations.”
While a long way from digitizing the whole brain, the study demonstrates that it is feasible to digitally reconstruct and simulate brain tissue, and most importantly, to reveal novel insights into the brain’s functioning. Simulating the emergent electrical behavior of this virtual tissue on supercomputers reproduced a range of previous observations made in experiments on the brain, validating its biological accuracy and providing new insights into the functioning of the neocortex. This is a first step and a significant contribution to Europe’s Human Brain Project, which Henry Markram founded, and where EPFL is the coordinating partner.
Cell has made a video abstract available (it can be found with the Hebrew University of Jerusalem press release)
Here’s a link to and a citation for the paper,
Reconstruction and Simulation of Neocortical Microcircuitry by Henry Markram, Eilif Muller, Srikanth Ramaswamy, Michael W. Reimann, Marwan Abdellah, Carlos Aguado Sanchez, Anastasia Ailamaki, Lidia Alonso-Nanclares, Nicolas Antille, Selim Arsever, Guy Antoine Atenekeng Kahou, Thomas K. Berger, Ahmet Bilgili, Nenad Buncic, Athanassia Chalimourda, Giuseppe Chindemi, Jean-Denis Courcol, Fabien Delalondre, Vincent Delattre, Shaul Druckmann, Raphael Dumusc, James Dynes, Stefan Eilemann, Eyal Gal, Michael Emiel Gevaert, Jean-Pierre Ghobril, Albert Gidon, Joe W. Graham, Anirudh Gupta, Valentin Haenel, Etay Hay, Thomas Heinis, Juan B. Hernando, Michael Hines, Lida Kanari, Daniel Keller, John Kenyon, Georges Khazen, Yihwa Kim, James G. King, Zoltan Kisvarday, Pramod Kumbhar, Sébastien Lasserre, Jean-Vincent Le Bé, Bruno R.C. Magalhães, Angel Merchán-Pérez, Julie Meystre, Benjamin Roy Morrice, Jeffrey Muller, Alberto Muñoz-Céspedes, Shruti Muralidhar, Keerthan Muthurasa, Daniel Nachbaur, Taylor H. Newton, Max Nolte, Aleksandr Ovcharenko, Juan Palacios, Luis Pastor, Rodrigo Perin, Rajnish Ranjan, Imad Riachi, José-Rodrigo Rodríguez, Juan Luis Riquelme, Christian Rössert, Konstantinos Sfyrakis, Ying Shi, Julian C. Shillcock, Gilad Silberberg, Ricardo Silva, Farhan Tauheed, Martin Telefont, Maria Toledo-Rodriguez, Thomas Tränkler, Werner Van Geit, Jafet Villafranca Díaz, Richard Walker, Yun Wang, Stefano M. Zaninetta, Javier DeFelipe, Sean L. Hill, Idan Segev, Felix Schürmann. Cell, Volume 163, Issue 2, p456–492, 8 October 2015 DOI: http://dx.doi.org/10.1016/j.cell.2015.09.029
This paper appears to be open access.
My most substantive description of the Blue Brain Project , previous to this, was in a Jan. 29, 2013 posting featuring the European Union’s (EU) Human Brain project and involvement from countries that are not members.
* I edited a redundant lede (That’s a virtual slice of a rat brain.), moved the second sentence to the lede while adding this: *about this virtual brain slice* on Oct. 16, 2015 at 0955 hours PST.