Monthly Archives: March 2014

Researchers at Purdue University (Indiana, US) and at the Indian Institute of Technology Madras (Chennai, India) develop Star Trek-type ‘tricorders’

To be clear, the Star Trek-type ‘tricorder’ referred to in the heading is, in fact, a hand-held spectrometer and the research from Purdue University and the Indian Institute of Technology Madras represents a developmental leap forward, not a new product. From a March 26, 2014 news item on Azonano,

Nanotechnology is advancing tools likened to Star Trek’s “tricorder” that perform on-the-spot chemical analysis for a range of applications including medical testing, explosives detection and food safety.

Researchers found that when paper used to collect a sample was coated with carbon nanotubes, the voltage required was 1,000 times reduced, the signal was sharpened and the equipment was able to capture far more delicate molecules.

Dexter Johnson in his March 26, 2014 posting (Nanoclast blog on the IEEE [Institute of Electrical and Electronics Engineers] website) provides some background information about the race to miniaturize spectrometers (Note: A link has been removed),

Recent research has been relying on nanomaterials to build smaller spectrometers. Late last year, a group at the Technische Universität Dresden and the Fraunhofer Institute in Germany developed a novel, miniature spectrometer, based on metallic nanowires, that was small enough to fit into a mobile phone.

Dexter goes on to provide a summary about this latest research, which I strongly recommend reading, especially if you don’t have the patience to read the rest of the news release. The March 25, 2014 Purdue University news release by Elizabeth K. Gardner, which originated the news item, provides insight from the researchers,

“This is a big step in our efforts to create miniature, handheld mass spectrometers for the field,” said R. Graham Cooks, Purdue’s Henry B. Hass Distinguished Professor of Chemistry. “The dramatic decrease in power required means a reduction in battery size and cost to perform the experiments. The entire system is becoming lighter and cheaper, which brings it that much closer to being viable for easy, widespread use.”

Cooks and Thalappil Pradeep, a professor of chemistry at the Indian Institute of Technology Madras, Chennai, led the research.

“Taking science to the people is what is most important,” Pradeep said. “Mass spectrometry is a fantastic tool, but it is not yet on every physician’s table or in the pocket of agricultural inspectors and security guards. Great techniques have been developed, but we need to hone them into tools that are affordable, can be efficiently manufactured and easily used.”

The news release goes on to describe the research,

The National Science Foundation-funded study used an analysis technique developed by Cooks and his colleagues called PaperSpray™ ionization. The technique relies on a sample obtained by wiping an object or placing a drop of liquid on paper wet with a solvent to capture residues from the object’s surface. A small triangle is then cut from the paper and placed on a special attachment of the mass spectrometer where voltage is applied. The voltage creates an electric field that turns the mixture of solvent and residues into fine droplets containing ionized molecules that pop off and are vacuumed into the mass spectrometer for analysis. The mass spectrometer then identifies the sample’s ionized molecules by their mass.

The technique depends on a strong electric field and the nanotubes act like tiny antennas that create a strong electric field from a very small voltage. One volt over a few nanometers creates an electric field equivalent to 10 million volts over a centimeter, Pradeep said.

“The trick was to isolate these tiny, nanoscale antennae and keep them from bundling together because individual nanotubes must project out of the paper,” he said. “The carbon nanotubes work well and can be dispersed in water and applied on suitable substrates.”

The Nano Mission of the Government of India supported the research at the Indian Institute of Technology Madras and graduate students Rahul Narayanan and Depanjan Sarkar performed the experiments.

In addition to reducing the size of the battery required and energy cost to run the tests, the new technique also simplified the analysis by nearly eliminating background noise, Cooks said.

“Under these conditions, the analysis is nearly noise free and a sharp, clear signal of the sample is delivered,” he said. “We don’t know why this is – why background molecules that surround us in the air or from within the equipment aren’t being ionized and entering into the analysis. It’s a puzzling, but pleasant surprise.”

The reduced voltage required also makes the method gentler than the standard PaperSpray™ ionization techniques.

“It is a very soft method,” Cooks said. “Fragile molecules and complexes are able to hold together here when they otherwise wouldn’t. This could lead to other potential applications.”

The team plans to investigate the mechanisms behind the reduction in background noise and potential applications of the gentle method, but the most promising aspect of the new technique is its potential to miniaturize the mass spectrometry system, Cooks said.

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

Molecular Ionization from Carbon Nanotube Paper by Rahul Narayanan, Depanjan Sarkar, Prof. R. Graham Cooks, and Prof. Thalappil Pradeep. Angewandte Chemie International Edition Article first published online: 18 MAR 2014 DOI: 10.1002/anie.201311053

© 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

This paper is behind a paywall.

Greg Rickford, we hardly knew ya; hello to Ed Holder, Canada’s new Minister of State (Science and Technology)

A shakeup in the Stephen Harper (Conservative party) government’s cabinet was destined when Jim Flaherty, Minister of Finance, announced his resignation in a surprise move earlier this March (2014). Greg Rickford was promoted from Minister of State (Science and Technology), considered a junior ministry, to Minister of Natural Resources, a more important portfolio.

A March 20, 2014 posting by David Bruggeman on his Pasco Phronesis blog first alerted me to the change (Note: A link has been removed,

… Taking his responsibilities for science and technology will be MP Ed Holder from Ontario.  Holder represents parts of London, Ontario, and has stood in Parliament since 2008.  His background is in insurance, where he established a successful brokerage company, and contributed time and resources to several charitable causes.  In other words, the appointment reflects the second-tier status the science minister holds within the Canadian government.

(To be fair, science ministers who are elected politicians in many other nations hold a similar status.)

I did find some commentary about Holder and his move, from the March 19, 2014 article by John Miner for the London Free Press,

Eight years after Stephen Harper’s Conservatives won power, the London region — turf they’ve since sewn up — finally has its first Tory cabinet minister.

The question is, why has it taken so long?

London West MP Ed Holder’s appointment Wednesday [March 19, 2014] as minister of state for science and technology makes him the government’s first London minister and its first in the 10-riding region.

Holder’s move from the back benches, part of a cabinet mini-shuffle triggered by Jim Flaherty’s surprise resignation as finance minister, also makes him ­London’s first Conservative ­minister in Ottawa in 21 years.

Holder wasn’t doing interviews Wednesday [March 19, 2014], but in a statement said “I have always believed that investments in science and research create good jobs and drive economic growth.”

On social media, some questioned why Holder was given the science and technology beat when he has a philosophy degree and an insurance background. But others, including former London Liberal MP Glen Pearson, praised the move on Twitter.

I was hoping for a little more insight into Holder’s approach to the portfolio and his personal thoughts on science and technology as opposed to the regional pique and the government rhetoric being reiterated in the article. (The curious can find out more about Ed Holder here.) As noted in my July 17, 2013 posting when Rickford was appointed to the Science and Technology portfolio in July 2013, I don’t believe that the minister has to have a science degree and/or research experience. However, I do like to think they’ve given or will give the matter some thought.

As befitting the Natural Resources’ portfolio’s importance I have found some commentary about Rickford’s move, from the March 19, 2014 article by Alex Boutillier for thestar.com,

Newly minted Natural Resources Minister Greg Rickford gives the Harper government a new face on the energy portfolio as a number of key projects hang in the balance.

Prime Minister Stephen Harper promoted the Kenora [Ontario] MP from a junior minister to one of the most important and sensitive portfolios in the Conservative government in a mini cabinet shuffle Wednesday [March 19, 2014].

Rickford replaces Joe Oliver, who was moved to finance after the surprise departure of Jim [Jim] Flaherty on Tuesday. The move gives the Conservatives a chance to change the tone of debate surrounding a number of large-scale pipeline and mining projects; a debate that turned toxic at times under Oliver’s watch.

The bilingual 46-year old has a nursing degree, a MBA from Laval, and civil and common law degrees from McGill. He worked as a nurse on reserves in northern Ontario, giving him an instinctive feel for communicating with aboriginal communities as well as a degree of credibility in relations with those communities.

That experience can only help Rickford as he navigates difficult negotiations with First Nations groups on the Keystone XL pipeline, the proposed Northern Gateway project, and the prospective Ring of Fire mining development in northern Ontario.

As Rickford prepares for the negotiations, Holder makes announcements such as this one, from a March 28, 2014 University of British Columbia (UBC) news release (I’ve trimmed the list down to the two ‘sciencish’ appointments),

UBC gets $8.5M boost for eight Canada Research Chairs

Research ranging from Latin poetry to neuroethics at the University of British Columbia has received an $8.5 million boost in federal funding for eight professors appointed or renewed as Canada Research Chairs.

The UBC contingent is among the 102 new and renewed chairs announced Friday [March 28, 2014] by Ed Holder, Minister of State for Science and Technology, at the University of Alberta. [emphasis mine]

The Minister of National Revenue Kerry-Lynne Findlay announced UBC’s two new recipients and six renewals at an event on the Vancouver campus to recognize B.C. appointees. The event featured the work of Martin Ordonez, an assistant professor in the Department of Electrical and Computer Engineering, who was named a new Chair in Power Converters and Renewable Systems. His work aims to maximize the use of renewable energy from wind, solar, and the ocean by developing the next generation of power conversion and storage solutions to produce low emissions power.

“The CRC program strengthens UBC’s leading role in world-class research, attracting the best and the brightest minds to work here,” said John Hepburn, UBC vice-president, research and international. “The work of these professors creates lasting change within Canada and beyond.”

Renewed CRCs at UBC are:

Judy Illes, Chair in Neuroethics
Illes studies the ethics of neuroscience, a field that allows us to understand, monitor and potentially manipulate human thought using technology.

For a full list of UBC’s Canada Research Chairs mentioned in the announcement, go here.

Longtime readers know I sometimes make connections between ideas that are at best tenuous and the ‘we hardly knew ya’ phrase which leaped into my mind while considering a head for this post led me, eventually, to punk rock band, Dropkick Murphys,

The song, also known as ‘Johnny, I Hardly Knew Ye’ has a long history as per its Wikipedia entry (Note: Links have been removed),

“Johnny I Hardly Knew Ye” (also known as “Johnny We Hardly Knew Ye” or “Johnny I Hardly Knew Ya”) is a popular traditional song, sung to the same tune as “When Johnny Comes Marching Home”. First published in London in 1867 and written by Joseph B. Geoghegan, a prolific English songwriter and successful music hall figure,[1] it remained popular in Britain and Ireland and the United States into the early years of the 20th century. The song was recorded by The Clancy Brothers & Tommy Makem on their self-titled album in 1961,[2][3] leading to a renewal of its popularity.

Originally seen as humorous, the song today is considered a powerful anti-war song. …

Lyrics

While goin’ the road to sweet Athy, hurroo, hurroo
While goin’ the road to sweet Athy, hurroo, hurroo
While goin’ the road to sweet Athy
A stick in me hand and a tear in me eye
A doleful damsel I heard cry,
Johnny I hardly knew ye.

Chorus:

With your drums and guns and guns and drums, hurroo, hurroo
With your drums and guns and guns and drums, hurroo, hurroo
With your drums and guns and guns and drums
The enemy nearly slew ye
Oh my darling dear, Ye look so queer
Johnny I hardly knew ye.

Where are the eyes that looked so mild, hurroo, hurroo
Where are the eyes that looked so mild, hurroo, hurroo
Where are the eyes that looked so mild
When my poor heart you first beguiled
Why did ye scadaddle from me and the child
Oh Johnny, I hardly knew ye.

(Chorus)

Where are your legs that used to run, hurroo, hurroo
Where are your legs that used to run, hurroo, hurroo
Where are your legs that used to run
When you went to carry a gun
Indeed your dancing days are done
Oh Johnny, I hardly knew ye.

(Chorus)

I’m happy for to see ye home, hurroo, hurroo
I’m happy for to see ye home, hurroo, hurroo
I’m happy for to see ye home
All from the island of Ceylon
So low in the flesh, so high in the bone
Oh Johnny I hardly knew ye.

(Chorus)

Ye haven’t an arm, ye haven’t a leg, hurroo, hurroo
Ye haven’t an arm, ye haven’t a leg, hurroo, hurroo
Ye haven’t an arm, ye haven’t a leg
Ye’re an armless, boneless, chickenless egg
Ye’ll have to be put with a bowl out to beg
Oh Johnny I hardly knew ye.

(Chorus)

They’re rolling out the guns again, hurroo, hurroo
They’re rolling out the guns again, hurroo, hurroo
They’re rolling out the guns again
But they never will take my sons again
No they’ll never take my sons again
Johnny I’m swearing to ye.

As for the Dropkick Murphys, here’s an excerpt from their Wikipedia entry (Note: Links have been removed),

Dropkick Murphys are an American Celtic punk band formed in Quincy, Massachusetts, in 1996.[1] The band was initially signed to independent punk record label Hellcat Records, releasing five albums for the label, and making a name for themselves locally through constant touring and yearly St. Patrick’s Day week shows, held in and around Boston. The 2004 single “Tessie” became the band’s first hit and one of their biggest charting singles to date. The band’s final Hellcat release, 2005’s The Warrior’s Code, included the song “I’m Shipping Up to Boston”; the song was featured in the 2006 Academy Award-winning movie The Departed, and went on to become the band’s only Platinum-selling single to date, and remains one of their best-known songs.

In 2007, the band signed with Warner Bros. Records and began releasing music through their own vanity label, Born & Bred. 2007’s The Meanest of Times made its debut at No. 20 on the Billboard charts and featured the successful single, “The State of Massachusetts”, while 2011’s Going Out in Style was an even bigger success, making its debut at No. 6, giving the band their highest-charting album to date.[2][3] The band’s eighth studio album, Signed and Sealed in Blood was released in 2013 making its debut at No. 9 on the Billboard charts.[4]

US National Nanotechnology Initiative’s 2015 budget request shows a decrease of $200M

A March 27, 2014 news item on Nanowerk highlights the US National Nanotechnology Initiative’s (NNI) document titled “NNI Supplement to the President’s 2015 Budget” (86 pp. PDF; Note: A link has been removed),

This document (pdf) is a supplement to the President’s 2015 Budget request submitted to Congress on March 4, 2014. It gives a description of the activities underway in 2013 and 2014 and planned for 2015 by the Federal Government agencies participating in the National Nanotechnology Initiative (NNI), primarily from a programmatic and budgetary perspective.

The March 25, 2014 NNI announcement provides more details about the current request and funding over the years since the NNI’s inception,

The President’s 2015 Budget provides over $1.5 billion for the National Nanotechnology Initiative (NNI), a continued investment in support of the President’s priorities and innovation strategy. Cumulatively totaling nearly $21 billion since the inception of the NNI in 2001 (including the 2015 request), this support reflects nanotechnology’s potential to significantly improve our fundamental understanding and control of matter at the nanoscale and to translate that knowledge into solutions for critical national issues. The NNI investments in 2013 and 2014 and those proposed for 2015 continue the emphasis on accelerating the transition from basic R&D to innovations that support national priorities, while maintaining a strong base of foundational research, to provide a pipeline for future nanotechnology-based innovations.

The President’s 2015 Budget supports nanoscale science, engineering, and technology R&D at 11 agencies. Another 9 agencies have nanotechnology-related mission interests or regulatory responsibilities. The NNI Supplement to the President’s 2015 Budget documents progress of these NNI participating agencies in addressing the goals and objectives of the NNI. (See the Acronyms page for agency abbreviations.)

Courtesy: NNI [downloaded from http://www.nano.gov/node/1128]

Courtesy: NNI [downloaded from http://www.nano.gov/node/1128]

One significant change for the 2015 Budget, which is reflected in the figures provided in this document for 2013 and 2014, is a revision in the Program Component Areas (PCAs), budget categories under which the NNI investments are reported. Note that this represents an update of how NNI investments by the Federal Government are tabulated, but not a change in the overall scope of the Initiative. As outlined in the 2014 NNI Strategic Plan, the new PCAs are more broadly strategic, fully inclusive, and consistent with Federal research categories, while correlating well with the NNI goals and high-level objectives. Of particular note is the creation of a separate PCA for the Nanotechnology Signature Initiatives (NSIs), reflecting the high priority placed on NSIs in the 2015 OMB/OSTP R&D Priorities Memo.

The 2014 budget for the NNI was $1.7B (as per the NNI Supplement to the President’s 2014 Budget),

The President’s 2014 Budget provides over $1.7 billion for the National Nanotechnology Initiative (NNI), a sustained investment in support of the President’s priorities and innovation strategy. Cumulatively totaling almost $20 billion since the inception of the NNI in 2001 (including the 2014 request), …

So this year’s request represents a decrease of $200M. Coincidentally, the US BRAIN (Brain Research through Advancing Innovative Neurotechnologies) initiative (originally named BAM for brain activity map) is going to have its budget doubled from $100M in 2014 to $200M in 2015 (as per David Bruggeman’s March 25, 2014 posting on his Pasco Phronesis blog),

The President’s Fiscal Year 2015 (which starts on October 1, but likely won’t get funded until next February) budget rollout includes doubling support for the BRAIN (Brain Research though Advancing Innovative Neurotechnologies) Initiative.  The $100 million multi-agency (National Institutes of Health, Defense Advanced Research Projects Agency and National Science Foundation) public-private effort will have some of its first funding awards later this year.

Interesting, non?

For anyone interested in more specifics about the 2015 NNI budget request but who doesn’t want to read the supplementary document, you can visit this page.

UK’s National Physical Laboratory reaches out to ‘BioTouch’ MIT and UCL

This March 27, 2014 news item on Azonano is an announcement for a new project featuring haptics and self-assembly,

NPL (UK’s National Physical Laboratory) has started a new strategic research partnership with UCL (University College of London) and MIT (Massachusetts Institute of Technology) focused on haptic-enabled sensing and micromanipulation of biological self-assembly – BioTouch.

The NPL March 27, 2014 news release, which originated the news item, is accompanied by a rather interesting image,

A computer operated dexterous robotic hand holding a microscope slide with a fluorescent human cell (not to scale) embedded into a synthetic extracellular matrix. Courtesy: NPL

A computer operated dexterous
robotic hand holding a microscope
slide with a fluorescent human cell
(not to scale) embedded into a
synthetic extracellular matrix. Courtesy: NPL

The news release goes on to describe the BioTouch project in more detail (Note: A link has been removed),

The project will probe sensing and application of force and related vectors specific to biological self-assembly as a means of synthetic biology and nanoscale construction. The overarching objective is to enable the re-programming of self-assembled patterns and objects by directed micro-to-nano manipulation with compliant robotic haptic control.

This joint venture, funded by the European Research Council, EPSRC and NPL’s Strategic Research Programme, is a rare blend of interdisciplinary research bringing together expertise in robotics, haptics and machine vision with synthetic and cell biology, protein design, and super- and high-resolution microscopy. The research builds on the NPL’s pioneering developments in bioengineering and imaging and world-leading haptics technologies from UCL and MIT.

Haptics is an emerging enabling tool for sensing and manipulation through touch, which holds particular promise for the development of autonomous robots that need to perform human-like functions in unstructured environments. However, the path to all such applications is hampered by the lack of a compliant interface between a predictably assembled biological system and a human user. This research will enable human directed micro-manipulation of experimental biological systems using cutting-edge robotic systems and haptic feedback.

Recently the UK government has announced ‘eight great technologies’ in which Britain is to become a world leader. Robotics, synthetic biology, regenerative medicine and advanced materials are four of these technologies for which this project serves as a merging point providing thus an excellent example of how multidisciplinary collaborative research can shape our future.

If it read this rightly, it means they’re trying to design systems where robots will work directly with materials in the labs while humans direct the robots’ actions from a remote location. My best example of this (it’s not a laboratory example) would be of a surgery where a robot actually performs the work while a human directs the robot’s actions based on haptic (touch) information the human receives from the robot. Surgeons don’t necessarily see what they’re dealing with, they may be feeling it with their fingers (haptic information). In effect, the robot’s hands become an extension of the surgeon’s hands. I imagine using a robot’s ‘hands’ would allow for less invasive procedures to be performed.

Sanofi BioGENEius Challenge Canada (SBCC) 2014 regional competitions

The Sanofi BioGENEius Challenge competitions seem to have been scheduled a little later this year. I announced the 2013 national winners of the Sanofi BioGENEius Challenge Canada (SBCC) competition in an April 9, 2013 posting and, for this year, I’ve just received word the regional competitions start today, March 27, 2014, and end April 29, 2014 with the national competition being held in Ottawa on May 23, 2014 and the international competition held in San Diego, California, June 22 – 25, 2014.

Here’s more about the competitions from the March 26, 2014 SBCC news release,

Hundreds of Canada’s most gifted high school and CEGEP students and their mentors, teachers and parents, will come together for the 2014 “Sanofi BioGENEius Challenge Canada (SBCC)”, Canada’s only national  biotechnology competition with mentors from Canada’s top universities and research institutes. Inspired by the question “How will you change the world?”, these Canadian teens aim to create astounding and life-changing discoveries.

  • This year, over 200 proposals were received from high school and CEGEP students from Victoria to Saskatoon to St. John’s, focused on biotechnology fields of discovery and study.
  • Now in its 21st year, over 4,700 high school students across Canada have participated in the “Sanofi BioGENEius Challenge Canada (SBCC)”.
    • Working closely with mentors, these students have conducted research in diverse areas such as telomeres, diabetes, stress management, Alzheimers, autism and pulp production.
  • The first place winner of the competition will advance to the International BioGENEius Challenge held in San Diego, CA on June 22-25. For a full schedule of dates, locations and judges, click here.

I believe it is possible for members of the public to view the competitions, here’s a list of cities along with the dates (just click on a date to find details about the location),

Regional competitions begin in Montreal, Quebec on March 27. Over the next few weeks, the SBCC will take place in Winnipeg, MB (April 22), Vancouver, BC (April 17), Edmonton, AB (April 28), Saskatoon, SK (April 28), Southwestern Ontario/Guelph, ON (May 1), Toronto, ON (April 29), Eastern Ontario/Ottawa, ON (April 28) and Atlantic Canada/Sackville, NB (April 29). The competition will conclude at the Partners In Research National Awards (PIRNA) in Ottawa on May 23, 2014.

Good luck to all the entrants!

Wilkinson Prize for numerical software: call for 2015 submissions

The Wilkinson Prize is not meant to recognize a nice, shiny new algorithm, rather it’s meant for the implementation phase and, as anyone who have ever been involved in that phase of a project can tell you, that phase is often sadly neglected. So, bravo for the Wilkinson Prize!

From the March 27, 2014 Numerical Algorithms Group (NAG) news release, here’s a brief history of the Wilkinson Prize,

Every four years the Numerical Algorithms Group (NAG), the National Physical Laboratory (NPL) and Argonne National Laboratory award the prestigious Wilkinson Prize in honour of the outstanding contributions of Dr James Hardy Wilkinson to the field of numerical software. The next Wilkinson Prize will be awarded at the [2015] International Congress on Industrial and Applied Mathematics in Beijing, and will consist of a $3000 cash prize.

NAG, NPL [UK National Physical Laboratory] and Argonne [US Dept. of Energy, Argonne National Laboratory] are committed to encouraging innovative, insightful and original work in numerical software in the same way that Wilkinson inspired many throughout his career. Wilkinson worked on the Automatic Computing Engine (ACE) while at NPL and later authored numerous papers on his speciality, numerical analysis. He also authored many of the routines for matrix computation in the early marks of the NAG Library.

The most recent Wilkinson Prize was awarded in 2011 to Andreas Waechter and Carl D. Laird for IPOPT. Commenting on winning the Wilkinson Prize Carl D. Laird, Associate Professor at the School of Chemical Engineering, Purdue University, said “I love writing software, and working with Andreas on IPOPT was a highlight of my career. From the beginning, our goal was to produce great software that would be used by other researchers and provide solutions to real engineering and scientific problems.

The Wilkinson Prize is one of the few awards that recognises the importance of implementation – that you need more than a great algorithm to produce high-impact numerical software. It rewards the tremendous effort required to ensure reliability, efficiency, and usability of the software.

Here’s more about the prize (list of previous winners, eligibility, etc.), from the Wilkinson Prize for Numerical Software call for submissions webpage,

Previous Prize winners:

  • 2011: Andreas Waechter and Carl D. Laird for Ipopt
  • 2007: Wolfgang Bangerth for deal.II
  • 2003: Jonathan Shewchuch for Triangle
  • 1999: Matteo Frigo and Steven Johnson for FFTW.
  • 1995: Chris Bischof and Alan Carle for ADIFOR 2.0.
  • 1991: Linda Petzold for DASSL.

Eligibility

The prize will be awarded to the authors of an outstanding piece of numerical software, or to individuals who have made an outstanding contribution to an existing piece of numerical software. In the latter case applicants must clearly be able to distinguish their personal contribution and to have that contribution authenticated, and the submission must be written in terms of that personal contribution and not of the software as a whole. To encourage researchers in the earlier stages of their career all applicants must be at most 40 years of age on January 1, 2014.
Rules for Submission

Each entry must contain the following:

Software written in a widely available high-level programming language.
A two-page summary of the main features of the algorithm and software implementation.
A paper describing the algorithm and the software implementation. The paper should give an analysis of the algorithm and indicate any special programming features.
Documentation of the software which describes its purpose and method of use.
Examples of use of the software, including a test program and data.

Submissions

The preferred format for submissions is a gzipped, tar archive or a zip file. Please contact us if you would like to use a different submission mechanism. Submissions should include a README file describing the contents of the archive and scripts for executing the test programs. Submissions can be sent by email to wilkinson-prize@nag.co.uk. Contact this address for further information.

The closing date for submissions is July 1, 2014.

Good luck to you all!

Learn to love slime; it may help you to compute in the future

Eeeewww! Slime or slime mold is not well loved and yet scientists seem to retain a certain affection for it, if their efforts at researching ways to make it useful could be termed affection. A March 27, 2014 news item on Nanowerk highlights a project where scientists have used slime and nanoparticles to create logic units (precursors to computers; Note: A link has been removed),

A future computer might be a lot slimier than the solid silicon devices we have today. In a study published in the journal Materials Today (“Slime mold microfluidic logical gates”), European researchers reveal details of logic units built using living slime molds, which might act as the building blocks for computing devices and sensors.

The March 27, 2014 Elsevier press release, which originated the news item, describes the researchers and their work in more detail,

Andrew Adamatzky (University of the West of England, Bristol, UK) and Theresa Schubert (Bauhaus-University Weimar, Germany) have constructed logical circuits that exploit networks of interconnected slime mold tubes to process information.

One is more likely to find the slime mold Physarum polycephalum living somewhere dark and damp rather than in a computer science lab. In its “plasmodium” or vegetative state, the organism spans its environment with a network of tubes that absorb nutrients. The tubes also allow the organism to respond to light and changing environmental conditions that trigger the release of reproductive spores.

In earlier work, the team demonstrated that such a tube network could absorb and transport different colored dyes. They then fed it edible nutrients – oat flakes – to attract tube growth and common salt to repel them, so that they could grow a network with a particular structure. They then demonstrated how this system could mix two dyes to make a third color as an “output”.

Using the dyes with magnetic nanoparticles and tiny fluorescent beads, allowed them to use the slime mold network as a biological “lab-on-a-chip” device. This represents a new way to build microfluidic devices for processing environmental or medical samples on the very small scale for testing and diagnostics, the work suggests. The extension to a much larger network of slime mold tubes could process nanoparticles and carry out sophisticated Boolean logic operations of the kind used by computer circuitry. The team has so far demonstrated that a slime mold network can carry out XOR or NOR Boolean operations. Chaining together arrays of such logic gates might allow a slime mold computer to carry out binary operations for computation.

“The slime mold based gates are non-electronic, simple and inexpensive, and several gates can be realized simultaneously at the sites where protoplasmic tubes merge,” conclude Adamatzky and Schubert.

Are we entering the age of the biological computer? Stewart Bland, Editor of Materials Today, believes that “although more traditional electronic materials are here to stay, research such as this is helping to push and blur the boundaries of materials science, computer science and biology, and represents an exciting prospect for the future.

I did look at the researchers’ paper and it is fascinating even to someone (me) who doesn’t understand the science very well. Here’s a link to and a citation for the paper,

Slime mold microfluidic logical gates by Andrew Adamatzky and Theresa Schubert. Materials Today, Volume 17, Issue 2, March 2014, Pages 86–91 (2014) published by Elsevier. http://dx.doi.org/10.1016/j.mattod.2014.01.018 The article is available for free at www.materialstoday.com

Yes, it’s an open access paper published by Elsevier, good on them!

An exploration of the grotesque: Glenn Brown and Rebecca Warren at the Rennie Collection

Before launching into my impressions of the current show (Oct. 26, 2013 – March 29, 2014) at the Rennie Collection (located in Vancouver, Canada) I’m providing an excerpt from the Wikipedia entry on the word grotesque (Note: Links have been removed),

The word grotesque comes from the same Latin root as “grotto”, which originated from Greek krypte “hidden place”,[1] meaning a small cave or hollow. The original meaning was restricted to an extravagant style of Ancient Roman decorative art rediscovered and then copied in Rome at the end of the 15th century. The “caves” were in fact rooms and corridors of the Domus Aurea, the unfinished palace complex started by Nero after the Great Fire of Rome in AD 64, which had become overgrown and buried, until they were broken into again, mostly from above. Spreading from Italian to the other European languages, the term was long used largely interchangeably with arabesque and moresque for types of decorative patterns using curving foliage elements.

Since at least the 18th century (in French and German as well as English), grotesque has come to be used as a general adjective for the strange, fantastic, ugly, incongruous, unpleasant, or disgusting, and thus is often used to describe weird shapes and distorted forms such as Halloween masks. In art, performance, and literature, grotesque, however, may also refer to something that simultaneously invokes in an audience a feeling of uncomfortable bizarreness as well as empathic pity. [emphases mine] More specifically, the grotesque forms on Gothic buildings, when not used as drain-spouts, should not be called gargoyles, but rather referred to simply as grotesques, or chimeras.[2]

While my understanding of the word is rooted in its meaning since the 18th century, I couldn’t resist the look backwards to ancient Rome and Greece. In any event, the heading for my post abut the Rennie Collection’s current exhibition concerns the grotesque which is “strange, fantastic, ugly, incongruous, unpleasant, or disgusting” and which “invokes in an audience a feeling of uncomfortable bizarreness as well as empathic pity.”

The entry to the show (main floor) gets the experience off to a deceptive start. The Rebecca Warren (she’s a sculptor) piece showcased here is a series of three vitrines (boxes) with plexiglass covers protecting the artwork within. Arranged in a row, they are small, oblong boxes mounted  at about 5 ft. (?) high on the wall. Rusty nails protrude at odd angles from the boxes, electronic devices of some sort are mounted below the boxes and there are bits of found objects and relatively unshaped clay on top of the boxes, as well as, twigs, more found objects, a neon object, and clay objects inside the boxes, behind the plexiglass covers.

Samantha (or Sam), an Emily Carr University of Art + Design student, sculptor, and our guide (one visits the Collection as part of a group at a prearranged time), provided some context for viewing this piece and the rest of the show. She was very illuminating and, unfortunately, it has been some weeks since I viewed the show and retain only bits and pieces remain (somehow this seems reflective of the vitrines). The one piece of information that I retain about Warren’s first piece is that the middle box has a layer of dust covering the objects within. Sam noted this is deliberate and the artist has specific instructions about how much dust there should be on the objects and on the base of the middle box in the row.

One moves deeper into the first floor’s display areas to view Brown’s first piece, a painting, a rather strange painting. It had a weirdly yellowish cast and it’s main feature looked like a skull to me but others saw something else,  a bit like Rorschach test where everything is open to interpretation.

We proceeded upstairs to a glorious room with dizzyingly high ceilings where the rest of Warren’s pieces were shown,

Rebecca Warren sculpture. Courtesy: Rennie Collection

Rebecca Warren sculptures. Courtesy: Rennie Collection

I don’t think the photograph, which shows three of the eight (?) sculptures in the room, quite conveys the impact of walking into a space occupied by these lumpen things with twisted and partial spinal columns, breasts in peculiar places, and other oddities shaped out of a type of clay that is fragile and obviously deteriorating.

The exhibit has a contrasting piece, one made of bronze and cast in a square of sorts. Interestingly, Warren likes to work with pom poms and there are two rather small examples, one each affixed to two different pieces. As I recall, Sam told us it was meant to be humorous and Warren keeps a large supply of pom poms on hand for when she might want to add one to a piece.

There are two more rooms on the second floor and those housed Glenn Brown’s work,

Glenn Brown, The Ever Popular Dead (after 'Jupiter Cloudscape' 1982 by Adolf Schaller), 2000 Oil on canvas 85 5/8 × 132 5/8 inches (217.49 × 336.87 cm) Courtesy: Rennie Collection

Glenn Brown, The Ever Popular Dead (after ‘Jupiter Cloudscape’ 1982 by Adolf Schaller), 2000. Oil on canvas: 85 5/8 × 132 5/8 inches (217.49 × 336.87 cm) Courtesy: Rennie Collection

If it looks like science fiction, that’s because it is. This piece was inspired by some science fiction art associated with Cosmos: A Personal Voyage, both a television series hosted by Carl Sagan and a book by Sagan. (Note: All of this type of information was provided by our guide, Sam, who also did some extra research to buttress her presentation, which was interactive. Thank you for doing that Sam.)

This painting, along with Brown’s other work in this show, rendered me physically nauseous. There was something about the colours and swirls and, possibly, the juxtapostion with Warren’s work that left me feeling ill. (Art can have physical effects. Stendhal famously passed out when visiting Florence, Italy due to a surfeit of art. Apparently, he’s not the only one; you can read more about Stendhal syndrome in this Wikipedia entry.)

Brown’s other paintings featured ‘portraits’ of odd looking people. You could almost recognize the portrait but the person was rendered in odd colours or it was the back of someone’s head—a head which featured many eyes and other oddities, calling to mind science fiction tropes about aliens.

While Brown was referencing classical work, for the most part, he, like Warren, rendered it as a grotesquerie. He even had a picture of two dogs seated at what appears to be a table. At one time, Brown worked in one of the Tate Museum’s (in London, UK) stores and the most popular items for purchase was a print of these two dogs which Brown reproduced in shades of a bilious green.

One of the interesting contrasts in the exhibition, other than sculptor/painter contrast, is that Warren’s work has human origins where Brown’s subject matter seems extraterrestrial. Adding to that impression is Brown’s painting style. There is no sign of a brush stroke; his paintings look as if they were digitally rendered, an effect made possible by his use of paintbrushes containing only a few hairs.

There were two pieces from Brown which didn’t fit this ‘extraterrestial and inhuman’ theme as I’ve described it. One piece, which bore a resemblance of sorts to Warren’s work, was a mound of material that was splattered and laden with paint sitting in the middle of one of the two rooms holding Brown’s work. Despite its sculptural quality, Brown describes the piece as a painting. The other piece was a painting which was cantilevered from the wall, like a pop-up which mimics the shape of what it being depicted. It was the one ‘pretty’ painting of Brown’s pieces. Titled ‘Zombies of the Stratosphere’ (1999), it depicts someone rowing a boat to a forested island.  The yellow in the picture reputedly gets its colour from urine. I now belatedly wonder if the first painting we saw on the bottom floor and which I described as having “a weirdly yellowish cast” also features this paint.

The Brits (Brown is from Britain) have a phrase “taking the piss” which I gather means ‘mocking’. It seems that in the one ‘pretty’ painting, Brown is almost literally ‘taking the piss’. Whether he’s mocking the art world or the fools who wander around art exhibits and/or purchase prints of dogs (considered banal subjects by many artists) from the Tate is not obvious to me.  Well, it’s never good to take yourself too seriously so there’s not much point to getting my ‘knickers in a twist’ over the matter, especially since I have no way of knowing if that was the artist’s intention.

In the end and after the nausea subsided, I was left with the notion that I was looking at two possible futures, one in which humans return to dust (Warren’s work) or we cease to be human as we understand the term (Brown’s work).

There’s not much time left to see the current exhibition, it ends March 29, 2014 and last I looked both scheduled tours were fully booked. You could try to organize and book your own tour, keep checking to see if someone cancels, or go here to see some images from the show.

Finally, I’m not sure either artist could be described as trying to “invoke empathic pity” as per Wikipedia’s ‘grotesque’ but here’s a video (originally an 8mm film) using the old Kansas song, Dust in the Wind as a soundtrack, which may that effect on you,

Like Warren’s work it looks rough and unpolished. Here’s what uselessdirector who uploaded the video had to say about it,

Uploaded on May 30, 2006

Filmed in 1977 by my dad, this music video nearly became “dust in the wind” until it was restored from its failing 8mm format.

Nano news from Malaysia and from Nigeria

I have two nanotechnology news bits, one concerning Malaysia and the other concerning Nigeria.

There’s a March 24, 2014 news item on Bernama ((national news agency of Malaysia) about a recent signing of a memorandum of understanding (MOU),

NanoMalaysia Bhd [aka, NanoMalaysia Berhad] is looking at jumpstarting nanotechnology development to enable it to contribute one per cent to Malaysia’s gross national income (GNI) by 2020, said Chief Executive Officer, Rezal Khairi Ahmad.

“The company would use four sectors — electronic devices and systems; energy and environment; food and agriculture; and, healthcare, medicine and wellness — to achieve the target, which would be equivalent to RM15 to RM17 billion then,” he said.

Rezal said this at the signing of memorandum of understanding (MOU) with Universiti Teknologi Petronas (UTP) here Monday [March 24, 2014].

I took a look at the NanoMalaysia site and found this on their ABOUT US page (Note: A link has been removed),

Nanotechnology was identified as one of the new growth engines for the New Economic Model (NEM).

NanoMalaysia Berhad was incorporated in 2011 as a company limited by guarantee (CLG) to act as a business entity entrusted with nanotechnology commercialisation activities. It will also support the operations of the NanoMalaysia Centre. Some of its roles include:

Managing and developing NanoMalaysia Centre and other approved Strategic Infrastructure and Facilities for the NND [National Nanotechnology Directorate Division]
Pre-commercialisation and commercialisation of nanotechnology products
Education and public awareness programmes
Bringing in venture funds and international investments in nanotechnology
Building capacity and R&D facilities
Health, safety and environmental initiatives
International linkages and networking

NanoMalaysia Berhad is Malaysia’s Lead Agency for the:

Commercialization of Nanotechnology Research and Development
Industrialization of Nanotechnology
Facilitation of Investments in Nanotechnology
Human Capital Development in Nanotechnology

On the other side of the world in Nigeria, a nanotechnology conference is being held, March 24 – 28, 2014 at the University of Nigeria at Nsukka. Here’s a bit more about the African International Conference/Workshop ON Applications Of Nanotechnology To Energy, Environment And Health, from its homepage,

The economic, social and developmental arguments for organizing the African International Conference/Workshop at the University of Nigeria, Nsukka (UNN) are strong, compelling and urgent.

First, it is an incontrovertible fact that science and technology have emerged to become critical to economic growth and sustainability in modern economy. The developments in materials science have contributed significantly in man’s quest to conquer his environment. More importantly, renewable energy is likely to be man’s long term solution to increasing demand for energy.

The conference/workshop is being organized by the Nano Research Group, University of Nigeria at Nsukka In collaboration with Energy Materials, Materials Science and Manufacturing, CSIR [Council for Scientific and Industrial Research] Pretoria, South Africa.

In a March 25, 2014 news item on leadership.ng, Minister of Power, Prof. Chinedu Nebo commented on the conference and the importance of nanotechnology to Nigeria’s plans,

The Minister of Power, Prof. Chinedu Nebo, on Tuesday said increase access to electricity was crucial and fundamental to economic and social development of Nigeria.

Nebo made this known at the “1st African International Conference/Workshop on Application of Nanotechnology to Energy, Health and Environment’’, at the University of Nigeria (UNN), Nsukka.

Represented by Mr Albert Okorogu, his Senior Special Assistant to Access to Power and Renewable Energy, Nebo said about 30 million households in Nigeria had no access to electricity.

Nebo quoting the United Nations said about 600 million people of Sub-Sahara Africa lacked access to electricity.

“In Nigeria, 30 million households have no access to electricity. This is the reason why the Federal Ministry of Power is rolling out comprehensive roadmap on access to power.

“This roadmap will systematically connect households through grid and off-grid solutions,’’ he said.

Nebo said that President Goodluck Jonathan had in January [2014] inaugurated “Operation Light Up Rural Nigeria Initiatives’’, as part of efforts to ensure that all households had access to electricity.

“The pilot programme will provide energy-efficient lighting to homes, streets and community centres and villages with up-to-dates solar technologies.

“There is plan [sic] to replicate this pilot project across the 36 states of the federation,’’ he said.

He said that solar system made from nanoparticles had been used to produce steam, purify water and disinfected dental device. [sic]

According to him, the exploitation of nanotechnology in Nigeria will provide sustainable solutions to our environment, social responsibility, overall wellbeing as well as increase access to electricity.

I think someone was in a rush to write the news item hence the errors I’ve noted; there may be more.

Bone goo

Most of us think of our bones as being solid matter and in the light of some new research at the University of Cambridge, it seems that we (including scientists and doctors) have not entirely understood the true nature of bone matter. From a March 24, 2014 University of Cambridge news release (also on EurekAlert),

Latest research shows that the chemical citrate – a by-product of natural cell metabolism – is mixed with water to create a viscous fluid that is trapped between the nano-scale crystals that form our bones.

This fluid allows enough movement, or ‘slip’, between these crystals so that bones are flexible, and don’t shatter under pressure. It is the inbuilt shock absorber in bone that, until now, was unknown.

If citrate leaks out, the crystals – made of calcium phosphate – fuse together into bigger and bigger clumps that become inflexible, increasingly brittle and more likely to shatter. This could be the root cause of osteoporosis.

The team from Cambridge’s Department of Chemistry used a combination of NMR spectroscopy, X-ray diffraction, imaging and high-level molecular modelling to reveal the citrate layers in bone.

They say that this is the start of what needs to be an entire shift in focus for studying the cause of brittle bone diseases like osteoporosis, and bone pathologies in general. The study is published today [March 24, 2014] in the journal Proceedings of the National Academy of Sciences.

“Bone mineral was thought to be closely related to this substance called hydroxyapatite. But what we’ve shown is that a large part of bone mineral – possibly as much as half of it in fact – is made up of this goo, where citrate is binding like a gel between mineral crystals,” said Dr Melinda Duer, who led the study.

“This nano-scopic layering of citrate fluid and mineral crystals in bone means that the crystals stay in flat, plate-like shapes that have the facility to slide with respect to each other. Without citrate, all crystals in bone mineral would collapse together, become one big crystal and shatter.

“It’s this layered structure that’s been missing from our knowledge, and we can now see that without it you’re stuffed.”

I appreciate the lively quotes (“… without it you’re stuffed”) and the description which follows,

Duer compares it to two panes of glass with water in the middle, which stick together but are able to slide: “it’s the same thing in these flat bone crystals. But you’ve got to have something that keeps the water there, stops it from drying out and stops the plates from either flying apart or sticking fast together. We now know that thing is citrate.”

Citrate is a ‘spidery’ molecule with four arms, all of which can bond easily to calcium – which bone is packed with, explains Duer. This means that citrate can hold the mineral crystals together at the same time as preventing them from fusing, while trapping the water that allows for the slippery movement which provides bone flexibility. “Without citrate, water would just flow straight through these gaps,” she said.

The body actually delivers bone calcium wrapped in citrate, to prevent it fusing with phosphate and forming large solid – and brittle – mineral crystals in the wrong places. Bone tissue has a protein mesh with holes where the calcium is deposited. In healthy tissue, the holes are very small, so that when the calcium is deposited, the citrate that comes with it can’t escape and is trapped between crystals – creating the flexible layers of fluid and bone plates.

As people age or suffer repeated bone trauma, the protein mesh isn’t repaired so well by the cells that try to replace damaged tissue, but often end up chewing away tissue faster than it can be re-deposited. This causes progressively larger holes in the protein mesh, citrate fluid escapes and crystals fuse together.

What happens then is pure chemistry, says Duer, with little biological control.

The body instigates a form of biological control through the tiny holes in the protein mesh that trap the citrate fluid, along with other molecules that normally control the deposit of mineral. These small spaces force the molecules to be involved with the forming mineral, controlling the process. But if you haven’t got the confined space the chemical reactions spiral out of control.

“In the bigger holes in damaged tissue, pure chemistry takes over. Pretty much the moment calcium and phosphate touch, they form a solid. You end up with these expanding clumps of brittle crystal, with water and citrate relegated to the outside of them,” she said.

“In terms of chemistry, that solid clump of mineral is the most stable structure. Biomechanically, however, it’s hopeless – as soon as you stand on it, it shatters. If we want to cure osteoporosis, we need to figure out how to stop the bigger holes forming in the protein matrix.”

The study is the first in a series of findings, with other studies from the team’s work on bone chemistry expected to come out later in the year.

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

Citrate bridges between mineral platelets in bone by Erika Davies, Karin H. Müller, Wai Ching Wong, Chris J. Pickard, David G. Reid, Jeremy N. Skepper, and Melinda J. Duer. PNAS doi: 10.1073/pnas.1315080111

This paper is made available through the PNAS open access option.