Category Archives: science

Getting your brain cells to glow in the dark

The extraordinary effort to colonize our brains continues apace with a new sensor from Vanderbilt University. From an Oct. 27, 2016 news item on ScienceDaily,

A new kind of bioluminescent sensor causes individual brain cells to imitate fireflies and glow in the dark.

The probe, which was developed by a team of Vanderbilt scientists, is a genetically modified form of luciferase, the enzyme that a number of other species including fireflies use to produce light. …

The scientists created the technique as a new and improved method for tracking the interactions within large neural networks in the brain.

“For a long time neuroscientists relied on electrical techniques for recording the activity of neurons. These are very good at monitoring individual neurons but are limited to small numbers of neurons. The new wave is to use optical techniques to record the activity of hundreds of neurons at the same time,” said Carl Johnson, Stevenson Professor of Biological Sciences, who headed the effort.

Individual neuron glowing with bioluminescent light produced by a new genetically engineered sensor. (Johnson Lab / Vanderbilt University)

Individual neuron glowing with bioluminescent light produced by a new genetically engineered sensor. (Johnson Lab / Vanderbilt University)

An Oct. 27, 2016 Vanderbilt University news release (also on EurekAlert) by David Salisbury, which originated the news item, explains the work in more detail,

“Most of the efforts in optical recording use fluorescence, but this requires a strong external light source which can cause the tissue to heat up and can interfere with some biological processes, particularly those that are light sensitive,” he [Carl Johnson] said.

Based on their research on bioluminescence in “a scummy little organism, the green alga Chlamydomonas, that nobody cares much about” Johnson and his colleagues realized that if they could combine luminescence with optogenetics – a new biological technique that uses light to control cells, particularly neurons, in living tissue – they could create a powerful new tool for studying brain activity.

“There is an inherent conflict between fluorescent techniques and optogenetics. The light required to produce the fluorescence interferes with the light required to control the cells,” said Johnson. “Luminescence, on the other hand, works in the dark!”

Johnson and his collaborators – Associate Professor Donna Webb, Research Assistant Professor Shuqun Shi, post-doctoral student Jie Yang and doctoral student Derrick Cumberbatch in biological sciences and Professor Danny Winder and postdoctoral student Samuel Centanni in molecular physiology and biophysics – genetically modified a type of luciferase obtained from a luminescent species of shrimp so that it would light up when exposed to calcium ions. Then they hijacked a virus that infects neurons and attached it to their sensor molecule so that the sensors are inserted into the cell interior.

The researchers picked calcium ions because they are involved in neuron activation. Although calcium levels are high in the surrounding area, normally they are very low inside the neurons. However, the internal calcium level spikes briefly when a neuron receives an impulse from one of its neighbors.

They tested their new calcium sensor with one of the optogenetic probes (channelrhodopsin) that causes the calcium ion channels in the neuron’s outer membrane to open, flooding the cell with calcium. Using neurons grown in culture they found that the luminescent enzyme reacted visibly to the influx of calcium produced when the probe was stimulated by brief light flashes of visible light.

To determine how well their sensor works with larger numbers of neurons, they inserted it into brain slices from the mouse hippocampus that contain thousands of neurons. In this case they flooded the slices with an increased concentration of potassium ions, which causes the cell’s ion channels to open. Again, they found that the sensor responded to the variations in calcium concentrations by brightening and dimming.

“We’ve shown that the approach works,” Johnson said. “Now we have to determine how sensitive it is. We have some indications that it is sensitive enough to detect the firing of individual neurons, but we have to run more tests to determine if it actually has this capability.”

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

Coupling optogenetic stimulation with NanoLuc-based luminescence (BRET) Ca++ sensing by Jie Yang, Derrick Cumberbatch, Samuel Centanni, Shu-qun Shi, Danny Winder, Donna Webb, & Carl Hirschie Johnson. Nature Communications 7, Article number: 13268 (2016)  doi:10.1038/ncomms13268 Published online: 27 October 2016

This paper is open access.

Epic Scottish poetry and social network science

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

This paper is behind a paywall.

Creeping gel does ‘The Loco-Motion’

Now it’s the creeping gel’s turn, from an Oct. 24, 2016 news item on phys.org,

Directed motion seems simple to us, but the coordinated interplay of complex processes is needed, even for seemingly simple crawling motions of worms or snails. By using a gel that periodically swells and shrinks, researchers developed a model for the waves of muscular contraction and relaxation involved in crawling. As reported in the journal Angewandte Chemie, they were able to produce two types of crawling motion by using inhomogeneous irradiation.

 

Courtesy: Angewandte Chemie

Courtesy: Angewandte Chemie

An Oct. 24, 2016 Angewandte Chemie (Wiley) press release (also on EurekAlert), which originated the news item, explains further,

Crawling comes from waves that travel through muscle. These waves can travel in the same direction as the animal is crawling (direct waves), from the tail end toward the head, or in the opposite direction (retrograde waves), from the head toward the tail. While land snails use the former type of wave, earthworms and limpets use the latter. Chitons (polyplacophora) can switch between both types of movement.

With the aid of a chemical model in the form of a self-oscillating gel, researchers working with Qingyu Gao at the China University of Mining and Technology (Jiangsu, China) and Irving R. Epstein at Brandeis University (Waltham, Massachusetts, USA) have been able to answer some of the many questions about these crawling processes.

A gel is a molecular network with liquid bound in the gaps. In this case, the liquid contains all of the ingredients needed for an oscillating chemical reaction (“chemical clock”). The researchers incorporated one component of their reaction system into the network: a ruthenium complex. During the reaction, the ruthenium periodically switches between two oxidation states, Ru2+ and Ru3+. This switch changes the gel so that in one state it can hold more liquid than the other, so the gel swells and shrinks periodically. Like the chemical clock, these regions propagate in waves, similar to the waves of muscle contractions in crawling.

The complex used in this gel also changes oxidation state when irradiated with light. When the right half of the gel is irradiated more strongly than the left, the waves move from right to left, i.e., from a high- to a low-frequency region of gel oscillations. Once the difference in intensity of irradiation reaches a certain threshold, it causes a wormlike motion of the gel from left to right, retrograde wave locomotion. If the difference is increased further, the gel comes to a stop. A further increase in the difference causes the gel to move again, but in the opposite direction, i.e., direct wave locomotion. The nonuniform illumination plays a role analogous to that of anchoring segments and appendages (such as limbs and wings) during cell migration and animal locomotion, which control the direction of locomotion by strengthening direct movement and/or inhibiting the opposite movement.

By using computational models, the researchers were able to describe these processes. Within the gel, there are regions where pulling forces predominate; pushing forces predominate in other areas. Variations in the intensity of the irradiation lead to different changes in the friction forces and the tensions in the gel. When these effects are added up, it is possible to predict in which direction a particular grid element of the gel will move.

One important finding from this model: special changes in the viscoelastic properties of the slime excreted by the snails and worms as they crawl are not required for locomotion, whether retrograde or direct.

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

Retrograde and Direct Wave Locomotion in a Photosensitive Self-Oscillating Gel by Lin Ren, Weibing She, Prof. Dr. Qingyu Gao, Dr. Changwei Pan, Dr. Chen Ji, and Prof. Dr. Irving R. Epstein. Angewandte Chemie International Edition DOI: 10.1002/anie.201608367 Version of Record online: 13 OCT 2016

© 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim

This paper is behind a paywall.

For anyone curious about the song, there’s this from its Wikipedia entry (Note: Links have been removed),

“The Loco-Motion” is a 1962 pop song written by American songwriters Gerry Goffin and Carole King. “The Loco-Motion” was originally written for Dee Dee Sharp but Sharp turned the song down.[1] The song is notable for appearing in the American Top 5 three times – each time in a different decade, performed by artists from three different cultures: originally African American pop singer Little Eva in 1962 (U.S. No. 1);[2] then American band Grand Funk Railroad in 1974 (U.S. No. 1);[3] and finally Australian singer Kylie Minogue in 1988 (U.S. No. 3).[4]

The song is a popular and enduring example of the dance-song genre: much of the lyrics are devoted to a description of the dance itself, usually done as a type of line dance. However, the song came before the dance.

“The Loco-Motion” was also the second song to reach No. 1 by two different musical acts. The earlier song to do this was “Go Away Little Girl”, also written by Goffin and King. It is one of only nine songs to achieve this

I had not realized this song had such a storied past; there’s a lot more about it in the Wikipedia entry.

I hear the proteins singing

Points to anyone who recognized the paraphrasing of the title for the well-loved, Canadian movie, “I heard the mermaids singing.” In this case, it’s all about protein folding and data sonification (from an Oct. 20, 2016 news item on phys.org),

Transforming data about the structure of proteins into melodies gives scientists a completely new way of analyzing the molecules that could reveal new insights into how they work – by listening to them. A new study published in the journal Heliyon shows how musical sounds can help scientists analyze data using their ears instead of their eyes.

The researchers, from the University of Tampere in Finland, Eastern Washington University in the US and the Francis Crick Institute in the UK, believe their technique could help scientists identify anomalies in proteins more easily.

An Oct. 20, 2016 Elsevier Publishing press release on EurekAlert, which originated the news item, expands on the theme,

“We are confident that people will eventually listen to data and draw important information from the experiences,” commented Dr. Jonathan Middleton, a composer and music scholar who is based at Eastern Washington University and in residence at the University of Tampere. “The ears might detect more than the eyes, and if the ears are doing some of the work, then the eyes will be free to look at other things.”

Proteins are molecules found in living things that have many different functions. Scientists usually study them visually and using data; with modern microscopy it is possible to directly see the structure of some proteins.

Using a technique called sonification, the researchers can now transform data about proteins into musical sounds, or melodies. They wanted to use this approach to ask three related questions: what can protein data sound like? Are there analytical benefits? And can we hear particular elements or anomalies in the data?

They found that a large proportion of people can recognize links between the melodies and more traditional visuals like models, graphs and tables; it seems hearing these visuals is easier than they expected. The melodies are also pleasant to listen to, encouraging scientists to listen to them more than once and therefore repeatedly analyze the proteins.

The sonifications are created using a combination of Dr. Middleton’s composing skills and algorithms, so that others can use a similar process with their own proteins. The multidisciplinary approach – combining bioinformatics and music informatics – provides a completely new perspective on a complex problem in biology.

“Protein fold assignment is a notoriously tricky area of research in molecular biology,” said Dr. Robert Bywater from the Francis Crick Institute. “One not only needs to identify the fold type but to look for clues as to its many functions. It is not a simple matter to unravel these overlapping messages. Music is seen as an aid towards achieving this unraveling.”

The researchers say their molecular melodies can be used almost immediately in teaching protein science, and after some practice, scientists will be able to use them to discriminate between different protein structures and spot irregularities like mutations.

Proteins are the first stop, but our knowledge of other molecules could also benefit from sonification; one day we may be able to listen to our genomes, and perhaps use this to understand the role of junk DNA [emphasis mine].

About 97% of our DNA (deoxyribonucleic acid) has been known for some decades as ‘junk DNA’. In roughly 2012, that was notion was challenged as Stephen S. Hall wrote in an Oct. 1, 2012 article (Hidden Treasures in Junk DNA; What was once known as junk DNA turns out to hold hidden treasures, says computational biologist Ewan Birney) for Scientific American.

Getting back to  2016, here’s a link to and a citation for ‘protein singing’,

Melody discrimination and protein fold classification by  Robert P. Bywater, Jonathan N. Middleton. Heliyon 20 Oct 2016, Volume 2, Issue 10 DOI: 10.1016/j.heliyon.2016.e0017

This paper is open access.

Here’s what the proteins sound like,

Supplementary Audio 3 for file for Supplementary Figure 2 1r75 OHEL sonification full score. [downloaded from the previously cited Heliyon paper]

Joanna Klein has written an Oct. 21, 2016 article for the New York Times providing a slightly different take on this research (Note: Links have been removed),

“It’s used for the concert hall. It’s used for sports. It’s used for worship. Why can’t we use it for our data?” said Jonathan Middleton, the composer at Eastern Washington University and the University of Tampere in Finland who worked with Dr. Bywater.

Proteins have been around for billions of years, but humans still haven’t come up with a good way to visualize them. Right now scientists can shoot a laser at a crystallized protein (which can distort its shape), measure the patterns it spits out and simulate what that protein looks like. These depictions are difficult to sift through and hard to remember.

“There’s no simple equation like e=mc2,” said Dr. Bywater. “You have to do a lot of spade work to predict a protein structure.”

Dr. Bywater had been interested in assigning sounds to proteins since the 1990s. After hearing a song Dr. Middleton had composed called “Redwood Symphony,” which opens with sounds derived from the tree’s DNA, he asked for his help.

Using a process called sonification (which is the same thing used to assign different ringtones to texts, emails or calls on your cellphone) the team took three proteins and turned their folding shapes — a coil, a turn and a strand — into musical melodies. Each shape was represented by a bunch of numbers, and those numbers were converted into a musical code. A combination of musical sounds represented each shape, resulting in a song of simple patterns that changed with the folds of the protein. Later they played those songs to a group of 38 people together with visuals of the proteins, and asked them to identify similarities and differences between them. The two were surprised that people didn’t really need the visuals to detect changes in the proteins.

Plus, I have more about data sonification in a Feb. 7, 2014 posting regarding a duet based on data from Voyager 1 & 2 spacecraft.

Finally, I hope my next Steep project will include  sonification of data on gold nanoparticles. I will keep you posted on any developments.

FrogHeart presents: Steep (1) A digital poetry of gold nanoparticles on Nov. 17, 2016 in Vancouver (Canada)

For anyone who has wanted to hear about the videopoem or poetryfilm, Steep (1): A digital poetry of gold nanoparticles, that I presented at the 2015 International Symposium on Electronic Arts (ISEA) in Vancouver, your wait is over. From the Canadian Academy of Independent Scholars Nov. 7, 2016 announcement (received via email),

Date:  Thursday, November 17th, 2016
Time:  7:30 pm
Place:  Simon Fraser University, Vancouver, BC Campus, 515 West Hastings Street (between Seymour and Richards Streets) in the Diamond Lounge
Speaker:  Maryse de la Giroday
Topic:  A digital poetry of gold nanoparticles: a Steep art/science project

Outline:

An object of desire, the stuff of myth and legend, and a cross-cultural icon, gold is now being perceived in a whole new way at the nanoscale where its properties and colour undergo a change. Increasingly used as a component in biomedical applications, gold nanoparticles are entering the environment (air, soil, and water).  ‘Steep (1): A digital poetry of gold nanoparticles’ is a short videopoem exploring the good and the bad about gold at the macroscale and at the nanoscale.

Presented at the 2015 International Symposium on Electronic Arts, the Steep (1) videopoem is an art/sci collaboration between Maryse de la Giroday (science writer and poet) from Canada and Raewyn Turner (video artist) from New Zealand. In addition to a look at the video, the presentation offers an inside perspective on incorporating science, poetry, and video in an art/sci piece. As well, there’ll be some discussion regarding one or more of Maryse’s and Raewyn’s current art/sci projects.

Brief Biography:
Maryse de la Giroday writes and publishes the largest, independent, science blog in Canada. Her main focus is nanotechnology (the Canadian kind when she can find it). She has also written several pieces for local visual arts magazine, Preview. Maryse holds an undergraduate Communications (honours) degree from Simon Fraser University and a Master’s degree (Creative Writing and New Media) from De Montfort University (UK). (Unfortunately, Raewyn will either be in New Zealand or on the US East Coast and unable to attend.)

You can preview the video here at steep.nz or here on Vimeo.

Superconductivity with spin

Vivid lines of light tracing a pattern reminiscent of a spinning top toy Courtesy: Harvard University

Vivid lines of light tracing a pattern reminiscent of a spinning top toy Courtesy: Harvard University

An Oct. 14, 2016 Harvard University John A. Paulson School of Engineering and Applied Sciences (SEAS) press release (also on EurekAlert) by Leah Burrows describes how scientists have discovered a way to transmit spin information through supercapacitors,

Researchers from the Harvard John A. Paulson School of Engineering and Applied Sciences (SEAS) have made a discovery that could lay the foundation for quantum superconducting devices. Their breakthrough solves one the main challenges to quantum computing: how to transmit spin information through superconducting materials.

Every electronic device — from a supercomputer to a dishwasher — works by controlling the flow of charged electrons. But electrons can carry so much more information than just charge; electrons also spin, like a gyroscope on axis.

Harnessing electron spin is really exciting for quantum information processing because not only can an electron spin up or down — one or zero — but it can also spin any direction between the two poles. Because it follows the rules of quantum mechanics, an electron can occupy all of those positions at once. Imagine the power of a computer that could calculate all of those positions simultaneously.

A whole field of applied physics, called spintronics, focuses on how to harness and measure electron spin and build spin equivalents of electronic gates and circuits.

By using superconducting materials through which electrons can move without any loss of energy, physicists hope to build quantum devices that would require significantly less power.

But there’s a problem.

According to a fundamental property of superconductivity, superconductors can’t transmit spin. Any electron pairs that pass through a superconductor will have the combined spin of zero.

In work published recently in Nature Physics, the Harvard researchers found a way to transmit spin information through superconducting materials.

“We now have a way to control the spin of the transmitted electrons in simple superconducting devices,” said Amir Yacoby, Professor of Physics and of Applied Physics at SEAS and senior author of the paper.

It’s easy to think of superconductors as particle super highways but a better analogy would be a super carpool lane as only paired electrons can move through a superconductor without resistance.

These pairs are called Cooper Pairs and they interact in a very particular way. If the way they move in relation to each other (physicists call this momentum) is symmetric, then the pair’s spin has to be asymmetric — for example, one negative and one positive for a combined spin of zero. When they travel through a conventional superconductor, Cooper Pairs’ momentum has to be zero and their orbit perfectly symmetrical.

But if you can change the momentum to asymmetric — leaning toward one direction — then the spin can be symmetric. To do that, you need the help of some exotic (aka weird) physics.

Superconducting materials can imbue non-superconducting materials with their conductive powers simply by being in close proximity. Using this principle, the researchers built a superconducting sandwich, with superconductors on the outside and mercury telluride in the middle. The atoms in mercury telluride are so heavy and the electrons move so quickly, that the rules of relativity start to apply.

“Because the atoms are so heavy, you have electrons that occupy high-speed orbits,” said Hechen Ren, coauthor of the study and graduate student at SEAS. “When an electron is moving this fast, its electric field turns into a magnetic field which then couples with the spin of the electron. This magnetic field acts on the spin and gives one spin a higher energy than another.”

So, when the Cooper Pairs hit this material, their spin begins to rotate.

“The Cooper Pairs jump into the mercury telluride and they see this strong spin orbit effect and start to couple differently,” said Ren. “The homogenous breed of zero momentum and zero combined spin is still there but now there is also a breed of pairs that gains momentum, breaking the symmetry of the orbit. The most important part of that is that the spin is now free to be something other than zero.”

The team could measure the spin at various points as the electron waves moved through the material. By using an external magnet, the researchers could tune the total spin of the pairs.

“This discovery opens up new possibilities for storing quantum information. Using the underlying physics behind this discovery provides also new possibilities for exploring the underlying nature of superconductivity in novel quantum materials,” said Yacoby.

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

Controlled finite momentum pairing and spatially varying order parameter in proximitized HgTe quantum wells by Sean Hart, Hechen Ren, Michael Kosowsky, Gilad Ben-Shach, Philipp Leubner, Christoph Brüne, Hartmut Buhmann, Laurens W. Molenkamp, Bertrand I. Halperin, & Amir Yacoby. Nature Physics (2016) doi:10.1038/nphys3877 Published online 19 September 2016

This paper is behind a paywall.

Creative destruction for Canada’s fundamental science

After receiving an ‘invitation’ from the Canadian Science Policy Centre, I wrote an opinion piece, drawing on my submission for the public consultation on Canada’s fundamental science research. It seems the invitation was more of a ‘call’ for submissions and my piece did not end up being selected for inclusion on the website. So rather than waste the piece, here it is,

Creative destruction for Canada’s fundamental science

At a time when we are dealing with the consequences of our sins and virtues, fundamental science, at heart, an exercise in imagination, can seem a waste of precious time. Pollution and climate change (sins: ill-considered uses of technology) and food security and water requirements (virtues: efforts to improve health and save more lives) would seem to demand solutions not the flights of fancy associated with basic science. After all, what does the ‘big bang’ have to do with potable water?

It’s not an unfair question despite the impatience some might feel when answering it by citing a number of practical applications which are the result of all that ‘fanciful’ or ‘blue sky’ science. The beauty and importance of the question is that it will always be asked and can never be definitively answered, rendering it a near constant goad or insurance against complacency.

In many ways Canada’s review of fundamental science (deadline for comments was Sept. 30, 2016) is not just an examination of the current funding schemes but an opportunity to introduce more ‘goads’ or ‘anti-complacency’ measures into Canada’s fundamental science efforts for a kind of ‘creative destruction’.

Introduced by economist Joseph Schumpeter, the concept is derived from Karl Marx’s work but these days is associated with disruptive, painful, and regenerative innovation of all kinds and Canadian fundamental science needs more ‘creative destruction’. There’s at least one movement in this direction (found both in Canada and internationally) which takes us beyond uncomfortable, confrontative questions and occasional funding reviews—the integration of arts and humanities as an attempt at ‘creative destruction’ of the science endeavour.

At one point in the early 2000s, Canada developed a programme where the National Research Council could get joint funding with the Canada Council for the Arts for artists to work with their scientists. It was abandoned a few years later, as a failure. But, since then, several informal attempts at combining arts, sciences, and humanities have sprung up.

For example, Curiosity Collider (founded in 2015) hosts artists and scientists presenting their art/science pieces at various events in Vancouver. Beakerhead has mashed up science, engineering, arts, and entertainment in a festival founded and held in Calgary since 2013. Toronto’s ArtSci Salon hosts events and installations for local, national, and international collaborations of artists and scientists. And, getting back to Vancouver, Anecdotal Evidence is a science storytelling series which has been appearing sporadically since 2015.

There is a tendency to dismiss these types of collaboration as a form of science outreach designed to amuse or entertain but they can be much more than that. Illustrators have taught botanists a thing or two about plants. Markus Buehler at the Massachusetts Institute of Technology has used his understanding of music to explore material science (spider’s webs). Domenico Vicinanza has sonified data from space vehicle, Voyager 1, to produce a symphony, which is also a highly compressed means of communicating data.

C. P. Snow’s ‘The Two Cultures’ (lecture and book) covered much of the same territory in 1959 noting the idea that the arts and sciences (and humanities) can and should be linked in some fashion was not new. For centuries the sciences were referred to as Natural Philosophy (humanities), albeit only chemistry and physics were considered sciences, and many universities have or had faculties of arts and sciences or colleges of arts and science (e.g., the University of Saskatchewan still has such a college).

The current art/sci or sci-art movement can be seen as more than an attempt to resuscitate a ‘golden’ period from the past. It could be a means of embedding a continuous state of regeneration or ‘creative destruction’ for fundamental science in Canada.

A computer that intuitively predicts a molecule’s chemical properties

First, we have emotional artificial intelligence from MIT (Massachusetts Institute of Technology) with their Kismet [emotive AI] project and now we have intuitive computers according to an Oct. 14, 2016 news item on Nanowerk,

Scientists from Moscow Institute of Physics and Technology (MIPT)’s Research Center for Molecular Mechanisms of Aging and Age-Related Diseases together with Inria research center, Grenoble, France have developed a software package called Knodle to determine an atom’s hybridization, bond orders and functional groups’ annotation in molecules. The program streamlines one of the stages of developing new drugs.

An Oct. 14, 2016 Moscow Institute of Physics and Technology press release (also on EurekAlert), which originated the news item, expands on the theme,

Imagine that you were to develop a new drug. Designing a drug with predetermined properties is called drug-design. Once a drug has entered the human body, it needs to take effect on the cause of a disease. On a molecular level this is a malfunction of some proteins and their encoding genes. In drug-design these are called targets. If a drug is antiviral, it must somehow prevent the incorporation of viral DNA into human DNA. In this case the target is viral protein. The structure of the incorporating protein is known, and we also even know which area is the most important – the active site. If we insert a molecular “plug” then the viral protein will not be able to incorporate itself into the human genome and the virus will die. It boils down to this: you find the “plug” – you have your drug.

But how can we find the molecules required? Researchers use an enormous database of substances for this. There are special programs capable of finding a needle in a haystack; they use quantum chemistry approximations to predict the place and force of attraction between a molecular “plug” and a protein. However, databases only store the shape of a substance; information about atom and bond states is also needed for an accurate prediction. Determining these states is what Knodle does. With the help of the new technology, the search area can be reduced from hundreds of thousands to just a hundred. These one hundred can then be tested to find drugs such as Reltagravir – which has actively been used for HIV prevention since 2011.

From science lessons at school everyone is used to seeing organic substances as letters with sticks (substance structure), knowing that in actual fact there are no sticks. Every stick is a bond between electrons which obeys the laws of quantum chemistry. In the case of one simple molecule, like the one in the diagram [diagram follows], the experienced chemist intuitively knows the hybridizations of every atom (the number of neighboring atoms which it is connected to) and after a few hours looking at reference books, he or she can reestablish all the bonds. They can do this because they have seen hundreds and hundreds of similar substances and know that if oxygen is “sticking out like this”, it almost certainly has a double bond. In their research, Maria Kadukova, a MIPT student, and Sergei Grudinin, a researcher from Inria research center located in Grenoble, France, decided to pass on this intuition to a computer by using machine learning.

Compare “A solid hollow object with a handle, opening at the top and an elongation at the side, at the end of which there is another opening” and “A vessel for the preparation of tea”. Both of them describe a teapot rather well, but the latter is simpler and more believable. The same is true for machine learning, the best algorithm for learning is the simplest. This is why the researchers chose to use a nonlinear support vector machines (SVM), a method which has proven itself in recognizing handwritten text and images. On the input it was given the positions of neighboring atoms and on the output collected hybridization.

Good learning needs a lot of examples and the scientists did this using 7605 substances with known structures and atom states. “This is the key advantage of the program we have developed, learning from a larger database gives better predictions. Knodle is now one step ahead of similar programs: it has a margin of error of 3.9%, while for the closest competitor this figure is 4.7%”, explains Maria Kadukova. And that is not the only benefit. The software package can easily be modified for a specific problem. For example, Knodle does not currently work with substances containing metals, because those kind of substances are rather rare. But if it turns out that a drug for Alzheimer’s is much more effective if it has metal, the only thing needed to adapt the program is a database with metallic substances. We are now left to wonder what new drug will be found to treat a previously incurable disease.

Scientists from MIPT's Research Center for Molecular Mechanisms of Aging and Age-Related Diseases together with Inria research center, Grenoble, France have developed a software package called Knodle to determine an atom's hybridization, bond orders and functional groups' annotation in molecules. The program streamlines one of the stages of developing new drugs. Credit: MIPT Press Office

Scientists from MIPT’s Research Center for Molecular Mechanisms of Aging and Age-Related Diseases together with Inria research center, Grenoble, France have developed a software package called Knodle to determine an atom’s hybridization, bond orders and functional groups’ annotation in molecules. The program streamlines one of the stages of developing new drugs. Credit: MIPT Press Office

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

Knodle: A Support Vector Machines-Based Automatic Perception of Organic Molecules from 3D Coordinates by Maria Kadukova and Sergei Grudinin. J. Chem. Inf. Model., 2016, 56 (8), pp 1410–1419 DOI: 10.1021/acs.jcim.5b00512 Publication Date (Web): July 13, 2016

Copyright © 2016 American Chemical Society

This paper is behind a paywall.

Monster science (a book announcement and interview)

Helaine Becker has launched a new children’s science book incorporating monsters with science. The title, unsurprisingly, is: ‘Monster Science’. Here’s more about the book from Helaine’s Oct. 14, 2016 post on Sci/Why where she shares two reviews,

“From Frankenstein’s creation to Nessie, Becker uses the creatures of our scariest stories as a springboard for an introduction to the scientific understandings that might make such creatures possible—or impossible. In addition to man-made monsters and legendary sea creatures, she covers vampires, zombies, werewolves, and wild, humanlike creatures like Bigfoot. Chapter by chapter, she provides references from literature, film, and popular culture, including a bit of science, a bit of history, and a plentiful helping of humor. She includes numerous monster facts, suggests weapons of defense, and concludes each section with a test-yourself quiz. Science topics covered range widely: electricity, genetic engineering, “demonic diseases,” the nature of our blood and the circulatory system, the possibility of immortality, animal classification, evolution, cannibalism, optical illusions, heredity, hoaxes, and the very real profession of cryptozoology, or the search for hitherto unidentified creatures. … Kirkus

Then, there’s this one,

A highlight of this work is its exploration of the often symbiotic relationship between culture and science; figures such as Shelley, John Polidori (The Vampyre), and filmmaker George Romero (Night of the Living Dead) merged cultural fascination with scientific development to create truly inspiring works and further public interest in science… School Library Journal

Interview with Helaine Becker

Not to be confused with ‘Interview with a vampire’, this one is not novel-length and includes a scoop about an upcoming book in 2017,

Were you surprised by anything when you were researching and/or witting the book?

I learned so much while writing Monster Science – it’s one of the reasons I enjoy writing nonfiction, especially for kids. I always turn up fascinating stuff. I was surprised to learn that werewolves were rounded up and burned at the stake, just like witches, during the period of the Inquisition. Werewolves, it turns out, were thought to be witches – usually male ones – who could shape shift.

My fave fact of all is that vampires would still have to eat their vegetables.

Did you have to leave any monsters/pop culture references/science out of the book? And, why?

Children’s books have very tight space constraints, but my research is comprehensive and complete. That means we have to pick and choose what stays in. It’s gotta be the very best! I work closely with my editors on this, and sometimes we have, shall we say, “heated” discussions.” For Monster Science, I was particularly sorry to see the fascinating back story of the mad scientist trope end up with a stake in its heart.

Did you have a favourite monster before you started? If so, has your favourite changed? Or if you didn’t have one before writing the book, have you since developed a favourite monster?

I’ve had an uneasy relationship with vampires from the age of about 7, after watching an episode of Gilligan’s Island. It featured a “humorous” dream sequence with Gilligan as the vampire. I failed to see the humor at that tender age, and was terrified out of my socks. And anyone remember the original Dark Shadows? Barnabus Collins? Yeah. That show should have never been on in the afternoon. I slept with the blankies up to my ears until my mid-thirties. (Who am I kidding? I still do!)

Are you hoping to tie this book into the Frankenstein bicentennial celebrations?

Illustrated children’s books have very long time lines from concept to finished book. I wrote Monster Science several years ago, before I had any notion of Frankenstein bicentennials. But now that we’ve arrived at this auspicious date, I’m excited! I’d love to participate in some way. I will put on my zzz zzzz zzzt thinking cap.

Where can your fans come to a reading or some other event?

I do dozens of school visits and festival events every year. Some of them might be focused on a specific book, like Monster Science, but most usually feature discussions around several of my titles. This holiday season, for example, I will be doing events around my latest picture book, a very Canadian Christmas-themed title called Deck the Halls. It’s the third in a very popular series. Anyone can drop in to the Sherway Gardens branch of Indigo Book Store [in Toronto] at noon on Sunday, Dec. 4 [2016], to take part in that.

I’ll be doing many events in association with the Forest of Reading, one of North America’s largest children’s choice award programs this spring. More than 250,000 children participate! I am honored to have two science-related books nominated this year, Worms for Breakfast: How to Feed a Zoo (Owlkids) and Everything: Space (National Geographic Kids). I will also be the keynote at the Killaloe Literary Festival in beautiful northern Ontario at the end of May. Best place to look for my latest book and schedule info is my blog, http://helainebecker.blogspot.ca/.

Is there anything you’d like to add?

For insiders only: Coming soon! Look for my upcoming picture book biography of William Playfair, the Victorian era scoundrel who single-handedly invented the field of infographics. It’s called Lines, Bars and Circles and will be published by Kids Can Press early in 2017.

Thank you, Helaine! (I usually don’t get funny interviews. It makes for a good change of pace.)

Getting back to ‘Monster Science’, you can purchase the book here.