Tag Archives: biology

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

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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

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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

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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?

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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

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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.

Biology is the new physics?

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Robin McKie, writing on the Guardian’s Science Desk blog (Notes & Theories), remarks on the fact that Paul Nurse, Nobel laureate for Medicine, is about be installed as president of the Royal Society at the end of November. From the Nov. 12, 2010 posting,

Paul Nurse has a modest way with his ideas. “Are you like me when you read books on relativity?” he asks. “You think you have got it and then you close the book, and you find it has all slipped away from you. And if you think you have trouble with relativity, wait till you take on quantum mechanics. It is utterly incomprehensible.” Not a bad admission for a Nobel prizewinner.

The point for Nurse is that biology is facing a similar leap into the incomprehensible as physics did at the beginning of the 20th century when the ordered world of Newtonian theory was replaced by relativity and quantum mechanics. [emphasis mine] Now a revolution awaits the study of living creatures.

There is a video of Paul Nurse talking about biology as a system on the Guardian site or you can take a look at this video (part 1 of 8 for a discussion on physics and unification theories that Nurse moderated  amongst Peter Galison, Sylvester James Gates Jr., Janna Levin and Leonard Susskind, at the 2008 World Science Festival in New York).

I find Nurse’s idea about biology facing some of the same issues as physics particularly interesting as I once found a piece written by a physicist who declared that science at the nanoscale meant that the study of biology was no longer necessary as we could amalgamate it with the study of chemistry and physics, i.e., we could return to the study of natural philosophy. About a year later I came across something written by a biologist declaring that physics and chemistry could be abolished as we could now fold them into the study of biology.

As I understand it, Nurse is not trying to abolish anything but merely pointing out that our understanding of biology may well undergo the same kind of transformation that physics did during the early part of the 20th century.

Darwin theme: Rap about Darwin & evolutionary biology and Darwinism in quantum dots

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You wouldn’t expect someone with this pedigree,

… Professor of Microbial Genomics at the University of Birmingham since July 2001. … is dually qualified as a scientist (PhD) and as a medic/clinical bacteriologist (MBBS, MRCPath), and benefits from Research-Council funding for both bioinformatics and laboratory-based molecular bacteriology projects. His interests focus on bacterial pathogenesis and the exploitation of sequence data, particularly genome sequence data.

to commission a piece of rap music but that’s just what Professor Mark Pallen did last year to honour Darwin’s anniversary (150 years since the publication of Darwin’s theory and 200 years isnce his birth). He contacted Baba Brinkman, a Vancouver, Canada -based rap artist, to commission a series of raps about Darwin and evolutionary biology. The project has become The Rap Guide to Evolution. You can find more about the work at Pasco Phronesis (thank you for the pointer) which also features a number of Brinkman’s videos. There’s also a Brinkman ‘evolutionary’ video on the CBC 3 (Canadian Broadcasting Corporation) site. In that video, Brinkman spontaneously adds some lines to his rap. I don’t know if you’ve ever tried to improvise while you’re presenting for any length of time but it’s not easy and Brinkman actually manages to do this while rhyming about evolutionary biology in front of an audience that’s somewhere between 200 and 500 people (I can’t be sure of the number).

There are some places I don’t expect to see any mention of the theory of evolution and quantum theory is one of those places. From the news item on physorg.com,

Physicists have found new evidence that supports the theory of quantum Darwinism, the idea that the transition from the quantum to the classical world occurs due to a quantum form of natural selection. By explaining how the classical world emerges from the quantum world, quantum Darwinism could shed light on one of the most challenging questions in physics of the past century.

The basis of almost any theoretical quantum-to-classical transition lies in the concept of decoherence. In the quantum world, many possible quantum states “collapse” into a single state due to interactions with the environment. To quantum Darwinists, decoherence is a selection process, and the final, stable state is called a “pointer state.” Although pointer states are quantum states, they are “fit enough” to be transmitted through the environment without collapsing and can then make copies of themselves that can be observed on the macroscopic scale. Although everything in our world is quantum at its core, our classical view of the universe is ultimately determined by these pointer states.

How researchers have used quantum dots  to provide evidence of quantum Darwinism and the link from quantum physics to classical physics is covered in the rest of the news item. The researchers’ study is published here,

A.M. Burke. “Periodic Scarred States in Open Quantum Dots as Evidence of Quantum Darwinism.” Physical Review Letters 104, 176801 (2010). Doi:10.1103/PhysRevLett.104.176801

Cool science; where are the women?; biology discovers graphical notations

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Popular Science’s Future of .., a programme [developed in response to a question “What’s missing from science programming?” posed by Debbie Myers, {US} Science Channel general manager] , was launched last night (Aug. 11, 2009). From the Fast Company posting by Lynne D. Johnston,

The overall response from the 50-plus room full of mostly New York digerati, was resoundingly, “a show that was both entertaining and smart–not dumbed down.”

Their host, Baratunde Thurston, offers an interesting combination of skills as he is a comedian, political pundit, and author. If you go to the posting, you can find the trailer. (It’s gorgeous and, I suspect, quite expensive due to the effects, and as you’d expect from a teaser, it’s short on science content.)

It does seem as if there’s some sort of campaign to make science ‘cool’ in the US. I say campaign because there was also, a few months ago, the World Science Festival in New York (mentioned in my June 12, 2009 posting). Thanks to Darren Barefoot’s blog I see they have posted some highlights and videos from the festival. Barefoot features one of musician Bobby McFerrin’s presentations here.

Barefoot comments on the oddity of having a musician presenting at a science event. The clip doesn’t clarify why McFerrin would be on the panel but neuroscientists have been expressing a lot of interest in musician’s brains and I noticed that there was at least one neuroscientist on the panel. Still, it would have been nice to have understood the thinking behind the panel composition. If you’re interested in more clips and information about the World Science Festival, go here.

Back to my thoughts on the ‘cool’ science campaign, there have been other initiatives including the ‘Dancing with scientists’ video contest put on by the American Association for the Advancement of Science and the nanotechnology video contests put on by the American Chemical Society. All of these initiatives have taken place this year. By contrast, nothing of a similar nature appears to be taking place in Canada. (If you know of a ‘cool science’ project in Canada, please do contact me as I’d be happy to feature it here.)

On the subject of putting together panels, there’s an interesting blog posting by Allyson Kapin (Fast Company) on the dearth of women on technology and/or social media panels. She points out that the problem has many aspects and requires more than one tactic for viable solutions.

She starts by talking about the lack of diversity and she very quickly shifts her primary focus to women. (I’ve seen this before in other writing and I think it happens because the diversity topic is huge so writers want to acknowledge the breadth but have time and expertise to discuss only a small piece of it.) On another tack altogether, I’ve been in the position of assembling a panel and trying to get a diverse group of people can be incredibly difficult. That said, I think more work needs to be done to make sure that panels are as diverse as possible.

Following on my interest in multimodal discourse and new ways of communicating science, a new set of standards for graphically representing biology has been announced. From Physorg.com,

Researchers at the European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI) and their colleagues in 30 labs worldwide have released a new set of standards for graphically representing biological information – the biology equivalent of the circuit diagram in electronics. This visual language should make it easier to exchange complex information, so that models are accurate, efficient and readily understandable. The new standard, called the Systems Biology Graphical Notation (SBGN), is published today (August 11, 2009) in Nature Biotechnology.

There’s more here and the article in Nature Biotechnology is here (keep scrolling).