Tag Archives: biology

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.

What’s a science historian doing in the field of synthetic biology?

Dominic Berry’s essay on why he, a science historian, is involved in a synthetic biology project takes some interesting twists and turns, from a Sept. 2, 2016 news item on phys.org,

What are synthetic biologists doing to plants, and what are plants doing to synthetic biology? This question frames a series of laboratory observations that I am pursuing across the UK as part of the Engineering Life project, which is dedicated to exploring what it might mean to engineer biology. I contribute to the project through a focus on plant scientists and my training in the history and philosophy of science. For plant scientists the engineering of biology can take many forms not all of which are captured by the category ‘synthetic biology’. Scientists that aim to create modified organisms are more inclined to refer to themselves as the latter, while other plant scientists will emphasise an integration of biological work with methods or techniques from engineering without adopting the identity of synthetic biologist. Accordingly, different legacies in the biosciences (from molecular biology to biomimetics) can be drawn upon depending on the features of the project at hand. These category and naming problems are all part of a larger set of questions that social and natural scientists continue to explore together. For the purposes of this post the distinctions between synthetic biology and the broader engineering of biology do not matter greatly, so I will simply refer to synthetic biology throughout.

Berry’s piece was originally posted Sept. 1, 2016 by Stephen Burgess on the PLOS (Public Library of Science) Synbio (Synthetic Biology blog). In this next bit Berry notes briefly why science historians and scientists might find interaction and collaboration fruitful (Note: Links have been removed),

It might seem strange that a historian is focused so closely on the present. However, I am not alone, and one recent author has picked out projects that suggest it is becoming a trend. This is only of interest for readers of the PLOS Synbio blog because it flags up that there are historians of science available for collaboration (hello!), and plenty of historical scholarship to draw upon to see your work in a new light, or rediscover forgotten research programs, or reconsider current practices, precisely as a recent Nature editorial emphasised for all sciences.

The May 17, 2016 Nature editorial ‘Second Thoughts’, mentioned in Berry’s piece, opens provocatively and continues in that vein (Note: A link has been removed),

The thought experiment has a noble place in research, but some thoughts are deemed more noble than others. Darwin and Einstein could let their minds wander and imagine the consequences of certain actions or natural laws. But scientists and historians who try to estimate what might have happened if, say, Darwin had fallen off the Beagle and drowned, are often accused of playing parlour games.

What if Darwin had toppled overboard before he joined the evolutionary dots? That discussion seems useful, because it raises interesting questions about the state of knowledge, then and now, and how it is communicated and portrayed. In his 2013 book Darwin Deleted — in which the young Charles is, indeed, lost in a storm — the historian Peter Bowler argued that the theory of evolution would have emerged just so, but with the pieces perhaps placed in a different order, and therefore less antagonistic to religious society.

In this week’s World View, another historian offers an alternative pathway for science: what if the ideas of Gregor Mendel on the inheritance of traits had been challenged more robustly and more successfully by a rival interpretation by the scientist W. F. R. Weldon? Gregory Radick argues that a twentieth-century genetics driven more by Weldon’s emphasis on environmental context would have weakened the dominance of the current misleading impression that nature always trumps nurture.

Here is Berry on the importance of questions,

The historian can ask: What traditions and legacies are these practitioners either building on or reacting against? How do these ideas cohere (or remain incoherent) for individuals and laboratories? Is a new way of understanding and investigating biology being created, and if so, where can we find evidence of it? Have biologists become increasingly concerned with controlling biological phenomena rather than understanding them? How does the desire to integrate engineering with biology sit within the long history of the establishment of biological science over the course of the 19th and 20th centuries?

Berry is an academic and his piece reflects an academic writing style with its complicated sentence structures and muted conclusions. If you have the patience, it is a good read on a topic that isn’t discussed all that often.

Artists classified the animal kingdom?

Where taxonomy and biology are concerned, my knowledge begins and end with Carl Linnaeus, the Swedish scientist who ushered in modern taxonomy. It was with some surprise that I find out artists also helped develop the field. From a June 21, 2016 news item on ScienceDaily,

In the sixteenth and seventeenth centuries artists were fascinated by how the animal kingdom was classified. They were in some instances ahead of natural historians.

This is one of the findings of art historian Marrigje Rikken. She will defend her PhD on 23 June [2016] on animal images in visual art. In recent years she has studied how images of animals between 1550 and 1630 became an art genre in themselves. ‘The close relationship between science and art at that time was remarkable,’ Rikken comments. ‘Artists tried to bring some order to the animal kingdom, just as biologists did.’

A June 21, 2016 Universiteit Leiden (Leiden University, Netherlands) press release, which originated the news item, expands on the theme,

In some cases the artists were ahead of their times. They became interested in insects, for example, before they attracted the attention of natural historians. It was artist Joris Hoefnagel who in 1575 made the first miniatures featuring beetles, butterflies and dragonflies, indicating how they were related to one another. In his four albums Hoefnagel divided the animal species according to the elements of fire, water, air and earth, but within these classifications he grouped animals on the basis of shared characteristics.

Courtesy: Universiteit Leiden

Beetles, butterflies, and dragonflies by Joris Hoefnagel. Courtesy: Universiteit Leiden

The press release goes on,

Other illustrators, print-makers and painters tried to bring some cohesion to the animal kingdom.  Some of them used an alphabetical system but artist Marcus Gheeraerts  published a print as early as 1583 [visible below, Ed.] in which grouped even-toed ungulates together. The giraffe and sheep – both visible on Gheeraerts’ print – belong to this species of animals. This doesn’t apply to all Gheeraerts’ animals. The mythical unicorn, which was featured by Gheeraerts, no longer appears in contemporary biology books.

Wealthy courtiers

According to Rikken, the so-called menageries played an important role historically in how animals were represented. These forerunners of today’s zoos were popular in the sixteenth and seventeenth centuries particularly among wealthy rulers and courtiers. Unfamiliar exotic animals regularly arrived that were immediately committed to paper by artists. Rikken: ‘The toucan, for example, was immortalised in 1615 by Jan Brueghel the Elder, court painter in Brussels.’  [See the main image, Ed.].’

In the flesh

Rikken also discovered that the number of animals featured in a work gradually increased. ‘Artists from the 1570s generally included one or just a few animals per work. With the arrival of print series a decade later, each illustration tended to include more and more animals. This trend reached its peak in the lavish paintings produced around 1600.’ These paintings are also much more varied than the drawings and prints. Illustrators and print-makers often blindly copied one another’s motifs, even showing the animals in an identical pose. Artists had no hesitation in including the same animal in different positions. Rikken: ‘This allowed them to show that they had observed the animal in the flesh.’

Even-toed ungulates by Marcus Gheeraerts. Courtesy: Leiden Universiteit

Even-toed ungulates by Marcus Gheeraerts. Courtesy: Leiden Universiteit

Yet more proof or, at least, a very strong suggestion that art and science are tightly linked.

ISEA (International Symposium on Electronic Arts) 2015 and the pronoun ‘I’

The 2015 International Symposium on Electronic Arts (or ISEA 2015) held  in Vancouver ended yesterday, Aug. 19, 2015. It was quite an experience both as a participant and as a presenter (mentioned in my Aug. 14, 2015 posting, Sneak peek: Steep (1): a digital poetry of gold nanoparticles). Both this ISEA and the one I attended previously in 2009 (Belfast, Northern Ireland, and Dublin, Ireland) were jampacked with sessions, keynote addresses, special events, and exhibitions of various artworks. Exhilarating and exhausting, that is the ISEA experience for me and just about anyone else I talked to here in Vancouver (Canada). In terms of organization, I have to give props to the Irish. Unfortunately, the Vancouver team didn’t seem to have given their volunteers any training and technical difficulties abounded. Basics such as having a poster outside a room noting what session was taking place, signage indicating which artist’s work was being featured, and good technical support (my guy managed to plug in a few things but seemed disinclined or perhaps didn’t have the technical expertise (?) to troubleshoot prior to the presentation) seemed elusive (a keynote presentation had to be moved due to technical requirements [!] plus no one told the volunteer staff who consequently misdirected people). Ooops.

Despite the difficulties, people remained enthusiastic and that’s a tribute to both the participants and, importantly, the organizers. The Vancouver ISEA was a huge undertaking with over 1000 presentation submissions made and over 1800 art work submissions. They had 900+ register and were the first ISEA able to offer payment to artists for their installations. Bravo to Philippe Pasquier, Thecla Schiphorst, Kate Armstrong, Malcolm Levy, and all the others who worked hard to pull this off.

Moving on to ‘I’, while the theme for ISEA 2015 was Disruption, I noticed a number of presentations focused on biology and on networks (in particular, generative networks). In some ways this parallels what’s happening in the sciences where more notice is being given to networks and network communications of all sorts.  For example, there’s an Aug. 19, 2015 news item on ScienceDaily suggesting that our use of the pronoun ‘I’ may become outdated.  What we consider to be an individual may be better understood as a host for a number of communities or networks,

Recent microbiological research has shown that thinking of plants and animals, including humans, as autonomous individuals is a serious over-simplification.

A series of groundbreaking studies have revealed that what we have always thought of as individuals are actually “biomolecular networks” that consist of visible hosts plus millions of invisible microbes that have a significant effect on how the host develops, the diseases it catches, how it behaves and possibly even its social interactions.

“It’s a case of the whole being greater than the sum of its parts,” said Seth Bordenstein, associate professor of biological sciences at Vanderbilt University, who has contributed to the body of scientific knowledge that is pointing to the conclusion that symbiotic microbes play a fundamental role in virtually all aspects of plant and animal biology, including the origin of new species.

In this case, the parts are the host and its genome plus the thousands of different species of bacteria living in or on the host, along with all their genomes, collectively known as the microbiome. (The host is something like the tip of the iceberg while the bacteria are like the part of the iceberg that is underwater: Nine out of every 10 cells in plant and animal bodies are bacterial. But bacterial cells are so much smaller than host cells that they have generally gone unnoticed.)

An Aug. 19, 2015 Vanderbilt University news release, which originated the news item, describes this provocative idea (no more ‘I’)  further,

Microbiologists have coined new terms for these collective entities — holobiont — and for their genomes — hologenome. “These terms are needed to define the assemblage of organisms that makes up the so-called individual,” said Bordenstein.

In the article “Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes” published online Aug. 18 [2015] in the open access journal PLOS Biology, Bordenstein and his colleague Kevin Theis from the University of Michigan take the general concepts involved in this new paradigm and break them down into underlying principles that apply to the entire field of biology.

They make specific and refutable predictions based on these principles and call for other biologists to test them theoretically and experimentally.

“One of the basic expectations from this conceptual framework is that animal and plant experiments that do not account for what is happening at the microbiological level will be incomplete and, in some cases, will be misleading as well,” said Bordenstein.

The first principle they advance is that holobionts and hologenomes are fundamental units of biological organization.

Another is that evolutionary forces such as natural selection and drift may act on the hologenome not just on the genome. So mutations in the microbiome that affect the fitness of a holobiont are just as important as mutations in the host’s genome. However, they argue that this does not change the basic rules of evolution but simply upgrades the types of biological units that the rules may act upon.

Although it does not change the basic rules of evolution, holobionts do have a way to respond to environmental challenges that is not available to individual organisms: They can alter the composition of their bacterial communities. For example, if a holobiont is attacked by a pathogen that the host cannot defend against, another symbiont may fulfill the job by manufacturing a toxin that can kill the invader. In this light, the microbes are as much part of the holobiont immune system as the host immune genes themselves.

According to Bordenstein, these ideas are gaining acceptance in the microbiology community. At the American Society of Microbiology General Meeting in June [2015], he convened the inaugural session on “Holobionts and Their Hologenomes” and ASM’s flagship journal mBio plans to publish a special issue on the topic in the coming year. [emphases are mine]

However, adoption of these ideas has been slower in other fields.

“Currently, the field of biology has reached an inflection point. The silos of microbiology, zoology and botany are breaking down and we hope that this framework will help further unify these fields,” said Bordenstein.

Not only will this powerful holistic approach affect the basic biological sciences but it also is likely to impact the practice of personalized medicine as well, Bordenstein said.

Take the missing heritability problem, for example. Although genome-wide studies have provided valuable insights into the genetic basis of a number of simple diseases, they have only found a small portion of the genetic causes of a number of more complex conditions such as autoimmune and metabolic diseases.

These may in part be “missing” because the genetic factors that cause them are in the microbiome, he pointed out.

“Instead of being so ‘germophobic,’ we need to accept the fact that we live in and benefit from a microbial world. We are as much an environment for microbes as microbes are for us,” said Bordenstein.

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

Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes by Seth R. Bordenstein and Kevin R. Theis. PLOS DOI: 10.1371/journal.pbio.1002226 Published: August 18, 2015

This is an open access paper.

It’s intriguing to see artists and scientists exploring ideas that resonate with each other. In fact, ISEA 2015 hosted a couple of sessions on BioArt, as well as, having sessions devoted to networks. While, I wasn’t thinking about networks or biological systems when I wrote my poem on gold nanoparticles, I did pose this possibility (how we become the sum of our parts) at the end:

Nature’s alchemy
breathing them
eating them
drinking them
we become gold
discovering what we are

As for how Raewyn handled the idea, words fail, please do go here to see the video here.

Genes and jazz: a July 17, 2015 performance in Vancouver (Canada)

A geneticist and a jazz musician first combined forces for Genes and Jazz at a 2008 Guggenheim museum event where it was first conceptualized (and performed?). Vancouver will be lucky enough to enjoy a live performance on July 17, 2015 as part of the 2015 Indian Summer Festival (July 9 – 18, 2015). Here’s more from the festival event page,

What happens when you cross a Nobel prize-winning geneticist with one of New York’s most sought after jazz quintets? Genes & Jazz. Part jazz concert, part scientific talk by one of the world’s finest scientific minds, Genes & Jazz is where the seemingly dichotomous worlds of science and the arts meet.

Dr. Harold Varmus won the Nobel Prize in 1989 for his work on the proto-oncogene, which enhanced our understanding of cancer. [emphasis mine] His son, jazz trumpeter Jacob leads the Jacob Varmus Quintet. [emphasis mine] Together they explore the ways that genes and notes affect complex organisms and compelling music. The father-son duo compares cell biology to the development of musical compositions.

“Mutation is essential to species diversity just as stylistic variation is essential to the arts,” says Dr. Varmus. “Without genetic error, there would be no evolution. Without variety, there would be no development in art, literature or music. Variety is essential to progress.”

Genes & Jazz was sparked in 2008 as part of the ‘Works & Process’ series at the Guggenheim Museum in New York.

Logistics (from the ticket purchase page),

    July 17 – July 17 [2015]
Vancouver Playhouse
600 Hamilton Street at Dunsmuir
Vancouver, BC
Admission: $25 / $40 / $60

For anyone wondering about how the jazz might sound, there’s this from the ticket purchase page,

“…lyrical and self-assured, more Miles Davis than Dr. John.” – The New Yorker

I think the first  person to link jazz with biology was Dr. Mae-Won Ho in a 2006 Institute of Science in Society (ISIS) lecture: Quantum Jazz; the meaning of life, the universe, and everything (free version). The fully referenced and illustrated lecture is available for members only. Here’s an excerpt  from the lecture,

Quantum jazz is the music of the organism dancing life into being, from the top of her head to her toes and fingertips, every single cell, molecule and atom taking part in a remarkable ensemble that spins and sways to rhythms from pico (10-12) seconds to minutes, hours, a day, a month, a year and longer, emitting light and sound waves from atomic dimensions of nanometres up to metres, spanning a musical range of 70 octaves (for that is the range of living activities). And each and every player, the tinniest molecule not withstanding, is improvising spontaneously and freely, yet keeping in tune and in step with the whole.

There is no conductor, no choreographer, the organism is creating and recreating herself afresh with each passing moment.

That’s why ordinary folks like us can walk and chew gum at the same time, why top athletes can run a mile in under four minutes, and kung fu experts can move with lightning speed and perhaps even fly effortlessly through the air, like in the movie Crouching Tiger and Hidden Dragon. This perfect coordination of multiple tasks carried out simultaneously depends on a special state of wholeness or coherence best described as “quantum coherence”, hence quantum jazz.

Quantum coherent action is effortless action, effortless creation, the Taoist ideal of art and poetry, of life itself.

Dr. Ho also gave an interview about her influences and ‘quantum jazz’ which is reproduced in ISIS report 23/06/10 (presumably 23 June 2010),

ATHM [Alternative therapies in health and medicine]: Please tell us a little bit about your background and schooling.

Ho: I was born in Hong Kong; started school in Chinese and then transferred to an English school for girls, run by Italian nuns. I got exposed to serious Western ideas late-ish in life, when I was about 10 or 11 years old. I was quite good in school, and the nuns let me do whatever I liked; didn’t have to listen if I got bored. So I escaped the worst of reductionist Western education because ideas that didn’t fit just rolled off my back. I guess that explains why I’m always at odds with whatever the conventional theory is in every single field that I go into.

I was in the convent school until I entered Hong Kong University to read biology and then biochemistry as a PhD. Again, I learned almost nothing useful during that time. Maybe I exaggerate: I learned, by myself, of things I liked to learn about. After I finished university, I got a postdoctoral fellowship, and began to change fields because I didn’t like the kind of research I was doing. I began to revolt against neo-Darwinism and the reductionist way of looking at things in bits.

I had gone into biochemistry for my Ph.D. because of something I heard from one of the professors who quoted Albert St. Györgyi – the father of biochemistry—that life was interposed between two energy levels of an electron. I thought that was sheer poetry. That made me want to know, “what is life?”

So I went into biochemistry thinking I would find the answer there. But it was very dull because biochemistry then was about cutting up and grinding up everything, separating, purifying. Nothing to tell you about what life is about.

Biology as a whole was studying dead, pinned specimens. There was nothing that answered the question, what is biological organization? What makes organisms tick? What is being alive? I especially detested neo-Darwinism because it was the most mind-numbing theory that purports to explain anything and everything by “selective advantage”, competition and selective advantage.

I spent a lot of time criticizing neo-Darwinism until I got bored. What neo-Darwinism leaves out is the whole of chemistry, physics, and mathematics, all science in fact. You don’t even need any physiology or developmental biology if everything can be explained in terms of selective advantage and a gene for any and every character, real or imaginary.

Finally, I met some remarkable people and learned a lot from them, and completely changed my field of research to try and answer that haunting question, “what is life?” I wrote a book on the ‘physics of organisms’, not ‘biophysics’, which is largely about the structure of dead biological materials and physical methods used in characterizing them. The physics of organisms is about living organization, quantum coherence and other important concepts.

Varmus and Ho may or may not be familiar with each other’s work linking jazz with biology. It wouldn’t be the first time that two or more people came to similar conclusions without reference to each other. At a guess, I’d say Ho’s approach is more about the poetry or the metaphor while Varmus’ approach is more about the music.

Animation: art and science

Being in the process of developing an art/science piece involving poetry and visual metaphors as realized through video, I was quite fascinated to read about someone else’s process and issues in Stephen Curry’s and Drew Berry’s June 9, 2015 joint post on the Guardian science blogs (Note: Links have been removed),

Yesterday [June 8, 2015] I [Stephen Curry] was trying to figure out why it seems to be so difficult to connect to the biological molecules that we are made of – proteins, DNA and such like. My piece might have ended on a frustrated note but I have no wish to be negative, especially since the problem has only arisen because animators like Drew Berry are now able to use the results of structural biology to make quite exquisite movies of the molecules of life at work inside the cells of our bodies. As I was working though my difficulties, I wrote to ask Berry how he approached the task of representing molecular complexity in ways that would make sense to people. This is his considered and insightful reply:

“The goal of my [Drew Berry] work is to show non-experts – the general public aged 4 to 99, students of biology, journalists and politicians, and so on – what is being discovered in biology, in a format that is accessible, meaningful, and engaging. I hope that my work provides some sense of what biologists and medical researchers are discovering and thinking about, to provide the public with a framework of understanding to discuss these important new discoveries and the impact it will have on us as a society as we head into the future.

These passages, in particular, caught my attention as they are descriptive of the art and the science inherent in Berry’s work,

… I should avoid overstating how accurately I have depicted the reality of the molecular world. It is vastly messier, random and crowded, and it’s physical nature is unimaginably alien to our normal perception of the world around us. That said, my work is not intended to be a lab-bench-calculated model for research use, it is an impressionistic, artist-generated crude sketch of phenomena and structures science is measuring and discovering at the molecular scale.

… I would then assert that the animations are firmly founded on real data and are as accurate as I can possibly make them, while making them watchable and interpretable to a human audience. By far the largest portion of my time is spent conducting broad ranging literature reviews of the topic I am working on, gathering the fragments of data scattered throughout the journals, and holistically reconstructing what currently we know and do not know. Wherever data and models are available, I incorporate them directly into the construction of the animation, including molecular structures, dynamics simulations, speed measurements, and so on. My work is most akin to a ‘review’ paper in the literature, presented in visual form.

Here is one of the problems Berry and other animators struggle with,

… I am friends with the dozen or so people who are at the top of the game at creating biomedical animations (most have a PhD scientific background) and we all struggle with the problem of having a molecule arrive at a particular location from the thick molecular soup of the cytoplasm and not look directed. I can make the molecule wander around in a Brownian type manner, but for story telling and visual explanations, I need it to get to a certain point and do it’s thing at a certain time to move the story along. This can make it look determined and directed.

Berry also discusses the unexpected,

An unexpected outcome I stumbled across more than a decade ago is that the public loves it when ‘real time’ speeds are displayed and the structures and reactions are derived from research data. This takes a lot of time to build, but then the animations have a remarkable longevity of use and strongly resonate with the audience.

For the last excerpt from this essay, I include Berry’s description of one of his most challenging projects and the video he produced,

The most heavily researched and technically challenging animation I have ever built is the kinetochore which can be seen in the video below . The kinetochore is a gigantic structure that assembles on chromosomes just after they have been duplicated and helps them to be pulled apart during cell division (mitosis). It has about 200 proteins of which I depicted about 50. I gathered data from more than 180 scientific papers with everything built as accurately as possible with hundreds of little scientific details built into the structure and dynamics.”

There are more illustrations and one more video embedded along with more from Berry in the essay, which includes these biographical details (Note: Links have been removed),

Drew Berry is the Biomedical Animations Manager at the Walter and Eliza Hall Institute of Medical Research in Melbourne, Australia. @Stephen_Curry is a professor of structural biology at Imperial College [London, UK].

Motor proteins have a stiff-legged walk

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

This paper is open access.

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

Enjoy!

Citizen science = crowdsourced science?

Deirdre Lockwood’s Nov. 12, 2012 article (Crowdsourcing Chemistry) for Chemical & Engineering News (C&EN) offers a good overview of the various citizen science projects and organizations while using the terms citizen science and crowdsourcing science interchangeably. For me, it’s  a ‘poodles and dogs’ situation; all poodles are dogs but not all dogs are poodles.

Here are two examples from the article,

Although the public has participated in scientific research since at least the first Audubon Christmas Bird Count of 1900, so-called citizen science has gained momentum in the past decade through funding, enthusiasm, and technology. This trend is dominated by projects in biology, but chemists are getting on board, too. NSF’s funding of citizen-science projects has grown from a handful each year in the early 2000s to at least 25 per year today.

Online gaming project Foldit has attracted many participants to find the lowest-energy configuration of proteins. Foldit players recently solved the structure of a retroviral protease that had long stumped structural biologists (Nat. Struct. Mol. Biol., DOI: 10.1038/nsmb.2119).

There’s a difference between going out and counting birds (citizen science) and 50,000 or more people solving a problem in biology (citizen science and crowdsourcing science). In the first instance, you’re gathering data for the scientist and in the second instance, you’re gathering, analyzing, and solving a science problem alongside the scientists. There is, of course, a great big grey zone but if you’re looking to participate in projects, the distinction may be useful to you. Do take a look at Lockwood’s article as she mentions some very exciting projects.

H/T to the Nov. 14, 2012 news item about Lockwood’s article on phys.org.

Take control of a 17th century scientific genius (Newton, Galileo, Keppler, Liebniz, or Kircher) in The New Science board game

Thank you to David Bruggeman (Pasco Phronesis) for the Sept. 16, 2012 posting (by way of Twitter and @JeanLucPiquant) about The New Science Game currently listed on the Kickstarter crowdfunding site. From the description of The New Science board game on Kickstarter,

The New Science gives you control of one of five legendary geniuses from the scientific revolution in a race to research, successfully experiment on, and finally publish some of the critical early advances that shaped modern science.

This fun, fast, easy-to-learn worker placement game for 2-5 players is ideal for casual and serious gamers alike. The rules are easy to learn and teach, but the many layers of shifting strategy make each game a new challenge that tests your mind and gets your competitive juices flowing.

Each scientist has their own unique strengths and weaknesses. No two scientists play the same way, so each time you try someone new it provides a different and satisfying play experience. Your scientist’s mat also serves as a player aid, repeating all of the key technology information from the game board for your easy reference.

The “five legendary geniuses’ are Isaac Newton, Galileo Galilei, Johannes Kepler, Gottfried Liebniz, and Athanasius Kircher. The Kickstarter campaign to take control of the five has raised $5,058 US of the $16,000 requested and it ends on Oct. 17, 2012.

The game is listed on boardgamegeek.com with additional details such as this,

Designer: Dirk Knemeyer

Artist: Heiko Günther

Publisher: Conquistador Games

# of players: 2-5

User suggested ages: 12 and up

Description:

Players control one of the great scientists during the 17th century Scientific Revolution in Europe. Use your limited time and energy to make discoveries, test hypotheses, publish papers, correspond with other famous scientists, hire assistants into your laboratory and network with other people who can help your progress. ’emphasis mine] Discoveries follow historical tech trees in the key sciences of the age: Astronomy, Mathematics, Physics, Biology and Chemistry. The scientist who accumulates the most prestige will be appointed the first President of the Royal Society.

The activities listed in the game description “make discoveries, test hypotheses,” etc. must sound very familiar to a contemporary scientist.

There’s also an explanatory video as seen on the Kickstarter campaign page and embedded here below,

David notes this about game quality in his Sept. 16, 2012 posting (Note: I have removed a link),

The game was heavily tested by the folks at Game Salute, and comes with the kind of quality details you might expect from games like Ticket to Ride or the various version of Catan.  If you’re interested in getting a copy of the game, it will run $49 U.S., plus shipping for destinations outside the U.S.  See the Kickstarter page for more details.

You can find out more about Conquistador Games here.