Tag Archives: biology

Café Scientifique Vancouver (Canada) talk on May 29th, 2018: Insects in the City: Shrinking Beetles and Disappearing Bees. How Bugs Help Us Learn About the Ecological Effects of Urbanization and Climate Change

I received this Café Scientifique April 30, 2018 notice (received via email),

Our next café will happen on TUESDAY, MAY 29TH at 7:30PM in the back
room at YAGGER'S DOWNTOWN (433 W Pender). Our speaker for the
evening will be DR. MICHELLE TSENG, Assistant Professor in the Zoology
department at UBC. Her topic will be:


Living in the city, we don’t always see the good bugs amongst the
pesky ones. In this presentation, I’ll take you on a trip down insect
lane and share with you the incredible diversity of insects that have
lived in Vancouver over the last 100 years. Many of these bugs have been
collected and preserved in museums and these collections provide us with
a historical snapshot of insect communities from the past. My students
and I have made some remarkable discoveries using museum insect
collections, and these findings help us understand how these fascinating
creatures are changing in response to warming climates and increased

Michelle Tseng is a professor of insect ecology at the UBC Biodiversity
Research Centre. She and her students study the impacts of habitat and
climate change on plankton and insects. Her group’s work has been
featured in national and international media, and on CBC’s Quirks and
Quarks. Michelle is also the zoologist on the award-winning CBC kids
show Scout and the Gumboot Kids.

We hope to see you there!

It says Dr. Tseng is in the zoology department but I also found a profile page for her in the botany department and that one had a little more information,

The Tseng lab investigates ecological and evolutionary responses of populations and communities to novel environments.  We test and refine theory related to predator-prey dynamics, body size variation, intra- and interspecific competition, and the maintenance of genetic variation, using laboratory and field experiments with freshwater plant and animal communities.  We also use museum collections to investigate long term patterns in organism phenotype.


Emergence in Toronto and Ottawa and brains in Vancouver (Canada): three April 2018 events

April 2018 is shaping up to be quite the month where art/sci events are concerned. I just published a March 27, 2018 posting titled ‘Curiosity collides with the quantum and with the Science Writers and Communicators of Canada in Vancouver (Canada)‘ and I’ve now received news about more happenings in Toronto and Ottawa.  Plus, there’s a science-themed meeting organized by ARPICO (Society of Italian Researchers &; Professionals in Western Canada) featuring brains and brain imaging in Vancouver.

Toronto’s and Ottawa’s Emergence

There’s an art/sci exhibit opening, from a March 27, 2018 Art/Sci Salon announcement (received via email),

You are invited!

FaceBook event:

The Oakwood Village Library and Arts Centre event:

341 Oakwood Avenue, Toronto, ON  M6E 2W1

I check the library webpage listed in the above and found this artist’s statement,

Artist / Scientist Statement [Stephen Morris]

I am interested in self-organized, emergent patterns and textures. I make images of patterns both from the natural world and of experiments in my laboratory in the Department of Physics at the University of Toronto. Patterns naturally attract casual attention but are also the subject of serious scientific research. Some things just evolve all by themselves into strikingly regular shapes and textures. Why? These shapes emerge spontaneously from a dynamic process of growing, folding, cracking, wrinkling, branching, flowing and other kinds of morphological development. My photos are informed by the scientific aesthetic of nonlinear physics, and celebrate the subtle interplay of order and complexity in emergent patterns. They are a kind of “Scientific Folk Art” of the science of Emergence.

While the official opening is April 5, 2018, the event itself runs from April 1 – 30, 2018.

Next, there’s another March 27, 2018 announcement (received via email) from the Art/Sci Salon but this one concerns a series of talks about ’emergence’, Note: Some of the event information was a little difficult to decipher so I’ve added a note to the relevant section).

What is Emergent Form?

Nature teems with self-organized forms that seem to spring spontaneously from the smooth background of things, by mechanisms that are not always apparent. Think of rippled sand on a beach or regular stripes in the clouds.  Plants, insects and animals exhibit spirals and spots and stripes in an exuberant riot of colours.  Fluid flows in amazingly regular swirls and eddies.  The emergence of form is ubiquitous, and presents a challenge and an inspiration to both artists and scientists. In mathematics, patterns appear as solutions of the nonlinear partial differential equations in the continuum limit of classical physics, chemistry and biology. In the arts and humanities, “emergent form” addresses the entangled ways in which humans, plants animals, microorganisms inevitably co-exist in the universe; the way that human intervention and natural transformation can generate new landscapes and new forms of life.

With Emergent Form, we want to question the idea of a fixed world.

For us, Emergent Form is not just a series of natural and human phenomena too complicated to understand, measure or predict, but also a concept to help us identify ways in which we can come to term with, and embrace their complexity as a source of inspiration.

Join us in Toronto and Ottawa for a series of interdisciplinary discussions, performances and exhibitions on Emergent Form on Apr 10, 11, 12 (Toronto) and Apr. 14 [2018] (Ottawa).

This series is the result of a collaboration among several parties. Each event of the series is different and has its dedicated RSVP 

Tue. Apr 10 The Fields Institute, 222 College Street

Emergent form: an interdisciplinary concept 6:00-8:00 pm Pier Luigi Capucci, Accademia di Belle Arti Urbino. Founder and director, Noemalab*, Charles Sowers, Independent artist and exhibit designer, the Exploratorium, Stephen Morris, Professor of of Physics University of Toronto, Ron Wild, smART Maps


Wed. Apr 11 The Fields Institute6:00-8:00 pm

Anatomy of an Interconnected SystemA Performative Lecture with Margherita Pevere, Aalto University, Helsinki


Thu. Apr 12 (Note: I believe that from 5 – 6 pm, you’re invited to see Pevere’s exhibit and then proceed to Luella Massey Studio Theatre for performances)

5:00 pm  Cabinets in the Koffler Student Centre [I believe this is at the University of Toronto] Anatomy of an Interconnected System An exhibition by Margherita Pevere

6:00 pm Luella Massey Studio Theatre, 4 Glen Morris Ave., Toronto biopoetriX – conFiGURing AI

6:00-8:00 pm Performance: 

6:00pm Performance “Corpus Nil. A Ritual of Birth for a Modified Body” conceived and performed by Marco Donnarumma

6.30pm LAB dance: Blitz media posters on labs in the arts, sciences and engineering

7.10pm Panel: Performing AI, hybrid media and humans in/as technologyMarco Donnarumma, Doug van Nort (Dispersion Lab, York U.), Jane Tingley (Stratford User Research & Gameful Experiences Lab –SURGE-, U of Waterloo), Angela Schoellig (Dynamic Systems Lab, U of T)

Panel animators: Antje Budde (Digital Dramaturgy Lab) and Roberta Buiani (ArtSci Salon)

8.15pm Reception at the Italian Cultural Institute, 496 Huron St, Toronto


Ottawa. Sat. Apr. 14 National Arts Centre, 1 Elgin Street11:00 am-1:00 pm

Emergent Form and complex phenomenaA creative panel discussion and surprise demonstrationsWith Pier Luigi Capucci, Margherita Pevere, Marco Donnarumma, Stephen Morris


This event would not be possible without the support of The Fields Institute for Research in Mathematical Science, The Italian Embassy, the Centre for Drama, Theatre and Performance Studies at the University of Toronto, the Digital Dramaturgy Lab, and the Istituto Italiano di Cultura. Many thanks to our community partner BYOR (Bring your own Robot)

I wonder if some of the funding from Italy is in support of Italian Research in World Day. This is the inaugural year for the event, which will be held annually on April 15.

Vancouver’s brains

The Society of Italian Researchers and Professionals in Western Canada (ARPICO) is hosting an event in Vancouver (from a March 22, 2018 ARICO announcement received via email),

Our second speaking event of the year, in collaboration with the Consulate General of Italy in Vancouver, has been scheduled for Wednesday, April 11th, 2018 at the Roundhouse Community Centre. Professor Vesna Sossi’s talk will be examining how positron emission tomography (PET) imaging has contributed to better understanding of the brain function and disease with particular focus on Parkinson’s disease. You can read a summary of Prof. Sossi’s lecture as well as her short professional biography at the bottom of this message.

This event is organized in collaboration with the Consulate General of Italy in Vancouver to celebrate the newly instituted Italian Research in the World Day, as part of the Piano Straordinario “Vivere all’Italiana” – Giornata della ricerca Italiana nel mondo. You can read more on our website event page.

We look forward to seeing everyone there.

Please register for the event by visiting the EventBrite link or RSVPing to info@arpico.ca.

The evening agenda is as follows:

  • 6:45 pm – Doors Open
  • 7:00 pm – Lecture by Prof. Vesna Sossi
  • ~8:00 pm – Q & A Period
  • Mingling & Refreshments until about 9:30 pm

If you have not yet RSVP’d, please do so on our EventBrite page.

Further details are also available at arpico.ca, our facebook page, and Eventbrite.

Imaging: A Window into the Brain

Brain illness, comprising neurological disorders, mental illness and addiction, is considered the major health challenge in the 21st century with a socio-economic cost greater than cancer and cardiovascular disease combined. There are at least three unique challenges hampering brain disease management: relative inaccessibility, disease onset often preceding the onset of clinical symptoms by many years and overlap between clinical and pathological symptoms that makes accurate disease identification often difficult. This talk will give examples of how positron emission tomography (PET) imaging has contributed to better understanding of the brain function and disease with particular focus on Parkinson’s disease. Emphasis will be placed on the interplay between scientific discoveries and instrumentation and data analysis development as exemplified by the current understanding of the brain function as comprised by interactions between connectivity networks and neurochemistry and advancement in multi-modal imaging such as simultaneous PET and magnetic resonance imaging (MRI).

Vesna Sossi is a Professor in the University of British Columbia (UBC) Physics and Astronomy Department and at the UBC Djavad Mowafaghian Center for Brain Health. She directs the UBC Positron Emission Tomography (PET) imaging centre, which is known for its use of imaging as applied to neurodegeneration with emphasis on Parkinson’s disease. Her main areas of interest comprise development of imaging methods to enhance the investigation of neurochemical mechanisms that lead to an increased risk of Parkinson’s disease (PD) and mechanisms that contribute to treatment-related complications. She uses PET imaging to explore how alterations of the different neurotransmitter systems contribute to different trajectories of disease progression. Her other areas of interest are PET image analysis, instrumentation and multi-modal, multi-parameter data analysis. She published more than 180 peer review papers, is funded by several granting agencies, including the Michael J Fox Foundation, and sits on several national and international review panels.

WHEN: Wednesday, April 11th, 2018 at 7:00pm (doors open at 6:45pm)
WHERE: Roundhouse Community Centre, Room B – 181 Roundhouse Mews, Vancouver, BC, V6Z 2W3
RSVP: Please RSVP at EventBrite (https://imaging-a-window-into-the-brain.eventbrite.ca) or email info@arpico.ca

Tickets are Needed

  • Tickets are FREE, but all individuals are requested to obtain “free-admission” tickets on EventBrite site due to limited seating at the venue. Organizers need accurate registration numbers to manage wait lists and prepare name tags.
  • All ARPICO events are 100% staffed by volunteer organizers and helpers, however, room rental, stationery, and guest refreshments are costs incurred and underwritten by members of ARPICO. Therefore to be fair, all audience participants are asked to donate to the best of their ability at the door or via EventBrite to “help” defray costs of the event.

You can find directions for the Roundhouse Community Centre here

I have one idle question. What’s going to happen these groups if Canadians change their use of  Facebook or abandon the platform as they are threatening to do in the face of Cambridge Analytica’s use of their data? A March 25, 2018 article on huffingtonpost.ca outlines the latest about Canadians’ reaction to the Cambridge Analytical news according to an Angus Reid poll,

A survey by Angus Reid Institute suggests 73 per cent of Canadian Facebook users say they will make changes, while 27 per cent say it will be “business as usual.”

Nearly a quarter (23 per cent) said they would use Facebook less in the future, and 41 per cent of users said they would check and/or change their privacy settings.

The survey also found that one in 10 say they plan to abandon the platform, at least temporarily.

Facebook has been under fire for its ability to protect user privacy after Cambridge Analytica was accused of lifting the Facebook profiles of more than 50 million users without their permission.

There you have it.

*Well, a bit more information about one of the “Emergent’ speakers was received in an April 4, 2018 ArtSci Salon email announcement,

Do make sure to check out Pier Luigi Capucci’s EU-based (but with international breadth) Noemalab platform. https://noemalab.eu/ since the mid-nineties, this platform has been an important node of information for New Media Art and the relation between the arts and science.

noemalab’s blog regularly hosts reviews of events and conferences occurring around the world, including  the Subtle Technologies Festival between 2007 and 2014. you can search its archives here http://blogs.noemalab.eu/

Capucci has been writing several reflections on emergent forms of Life and theorized what he called the “third life”. See a recent essay https://noemalab.eu/memo/events/evolutionary-creativity-the-inner-life-and-meaning-of-art/ here is a picture which I would love him to explain during Emergent Form. Intrigued? come listen to him!

Of musical parodies, Despacito, and evolution

What great timing, I just found out about a musical science parody featuring evolution and biology and learned of the latest news about the study of evolution on one of the islands in the Galapagos (where Charles Darwin made some of his observations). Thanks to Stacey Johnson for her November 24, 2017 posting on the Signals blog for featuring Evo-Devo (Despacito Biology Parody), an A Capella Science music video from Tim Blais,

Now, for the latest regarding the Galapagos and evolution (from a November 24, 2017 news item on ScienceDaily),

The arrival 36 years ago of a strange bird to a remote island in the Galapagos archipelago has provided direct genetic evidence of a novel way in which new species arise.

In this week’s issue of the journal Science, researchers from Princeton University and Uppsala University in Sweden report that the newcomer belonging to one species mated with a member of another species resident on the island, giving rise to a new species that today consists of roughly 30 individuals.

The study comes from work conducted on Darwin’s finches, which live on the Galapagos Islands in the Pacific Ocean. The remote location has enabled researchers to study the evolution of biodiversity due to natural selection.

The direct observation of the origin of this new species occurred during field work carried out over the last four decades by B. Rosemary and Peter Grant, two scientists from Princeton, on the small island of Daphne Major.

A November 23, 2017 Princeton University news release on EurekAlert, which originated the news item, provides more detail,

“The novelty of this study is that we can follow the emergence of new species in the wild,” said B. Rosemary Grant, a senior research biologist, emeritus, and a senior biologist in the Department of Ecology and Evolutionary Biology. “Through our work on Daphne Major, we were able to observe the pairing up of two birds from different species and then follow what happened to see how speciation occurred.”

In 1981, a graduate student working with the Grants on Daphne Major noticed the newcomer, a male that sang an unusual song and was much larger in body and beak size than the three resident species of birds on the island.

“We didn’t see him fly in from over the sea, but we noticed him shortly after he arrived. He was so different from the other birds that we knew he did not hatch from an egg on Daphne Major,” said Peter Grant, the Class of 1877 Professor of Zoology, Emeritus, and a professor of ecology and evolutionary biology, emeritus.

The researchers took a blood sample and released the bird, which later bred with a resident medium ground finch of the species Geospiz fortis, initiating a new lineage. The Grants and their research team followed the new “Big Bird lineage” for six generations, taking blood samples for use in genetic analysis.

In the current study, researchers from Uppsala University analyzed DNA collected from the parent birds and their offspring over the years. The investigators discovered that the original male parent was a large cactus finch of the species Geospiza conirostris from Española island, which is more than 100 kilometers (about 62 miles) to the southeast in the archipelago.

The remarkable distance meant that the male finch was not able to return home to mate with a member of his own species and so chose a mate from among the three species already on Daphne Major. This reproductive isolation is considered a critical step in the development of a new species when two separate species interbreed.

The offspring were also reproductively isolated because their song, which is used to attract mates, was unusual and failed to attract females from the resident species. The offspring also differed from the resident species in beak size and shape, which is a major cue for mate choice. As a result, the offspring mated with members of their own lineage, strengthening the development of the new species.

Researchers previously assumed that the formation of a new species takes a very long time, but in the Big Bird lineage it happened in just two generations, according to observations made by the Grants in the field in combination with the genetic studies.

All 18 species of Darwin’s finches derived from a single ancestral species that colonized the Galápagos about one to two million years ago. The finches have since diversified into different species, and changes in beak shape and size have allowed different species to utilize different food sources on the Galápagos. A critical requirement for speciation to occur through hybridization of two distinct species is that the new lineage must be ecologically competitive — that is, good at competing for food and other resources with the other species — and this has been the case for the Big Bird lineage.

“It is very striking that when we compare the size and shape of the Big Bird beaks with the beak morphologies of the other three species inhabiting Daphne Major, the Big Birds occupy their own niche in the beak morphology space,” said Sangeet Lamichhaney, a postdoctoral fellow at Harvard University and the first author on the study. “Thus, the combination of gene variants contributed from the two interbreeding species in combination with natural selection led to the evolution of a beak morphology that was competitive and unique.”

The definition of a species has traditionally included the inability to produce fully fertile progeny from interbreeding species, as is the case for the horse and the donkey, for example. However, in recent years it has become clear that some closely related species, which normally avoid breeding with each other, do indeed produce offspring that can pass genes to subsequent generations. The authors of the study have previously reported that there has been a considerable amount of gene flow among species of Darwin’s finches over the last several thousands of years.

One of the most striking aspects of this study is that hybridization between two distinct species led to the development of a new lineage that after only two generations behaved as any other species of Darwin’s finches, explained Leif Andersson, a professor at Uppsala University who is also affiliated with the Swedish University of Agricultural Sciences and Texas A&M University. “A naturalist who came to Daphne Major without knowing that this lineage arose very recently would have recognized this lineage as one of the four species on the island. This clearly demonstrates the value of long-running field studies,” he said.

It is likely that new lineages like the Big Birds have originated many times during the evolution of Darwin’s finches, according to the authors. The majority of these lineages have gone extinct but some may have led to the evolution of contemporary species. “We have no indication about the long-term survival of the Big Bird lineage, but it has the potential to become a success, and it provides a beautiful example of one way in which speciation occurs,” said Andersson. “Charles Darwin would have been excited to read this paper.”

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

Rapid hybrid speciation in Darwin’s finches by Sangeet Lamichhaney, Fan Han, Matthew T. Webster, Leif Andersson, B. Rosemary Grant, Peter R. Grant. Science 23 Nov 2017: eaao4593 DOI: 10.1126/science.aao4593

This paper is behind a paywall.

Happy weekend! And for those who love their Despacito, there’s this parody featuring three Italians in a small car (thanks again to Stacey Johnson’s blog posting),

Patent Politics: a June 23, 2017 book launch at the Wilson Center (Washington, DC)

I received a June 12, 2017 notice (via email) from the Wilson Center (also know as the Woodrow Wilson Center for International Scholars) about a book examining patents and policies in the United States and in Europe and its upcoming launch,

Patent Politics: Life Forms, Markets, and the Public Interest in the United States and Europe

Over the past thirty years, the world’s patent systems have experienced pressure from civil society like never before. From farmers to patient advocates, new voices are arguing that patents impact public health, economic inequality, morality—and democracy. These challenges, to domains that we usually consider technical and legal, may seem surprising. But in Patent Politics, Shobita Parthasarathy argues that patent systems have always been deeply political and social.

To demonstrate this, Parthasarathy takes readers through a particularly fierce and prolonged set of controversies over patents on life forms linked to important advances in biology and agriculture and potentially life-saving medicines. Comparing battles over patents on animals, human embryonic stem cells, human genes, and plants in the United States and Europe, she shows how political culture, ideology, and history shape patent system politics. Clashes over whose voices and which values matter in the patent system, as well as what counts as knowledge and whose expertise is important, look quite different in these two places. And through these debates, the United States and Europe are developing very different approaches to patent and innovation governance. Not just the first comprehensive look at the controversies swirling around biotechnology patents, Patent Politics is also the first in-depth analysis of the political underpinnings and implications of modern patent systems, and provides a timely analysis of how we can reform these systems around the world to maximize the public interest.

Join us on June 23 [2017] from 4-6 pm [elsewhere the time is listed at 4-7 pm] for a discussion on the role of the patent system in governing emerging technologies, on the launch of Shobita Parthasarathy’s Patent Politics: Life Forms, Markets, and the Public Interest in the United States and Europe (University of Chicago Press, 2017).

You can find more information such as this on the Patent Politics event page,



  • Shobita Parthasarathy

    Associate Professor of Public Policy and Women’s Studies, and Director of the Science, Technology, and Public Policy Program, at University of Michigan


  • Eleonore Pauwels

    Senior Program Associate and Director of Biology Collectives, Science and Technology Innovation Program
    Formerly European Commission, Directorate-General for Research and Technological Development, Directorate on Science, Economy and Society


  • Daniel Sarewitz

    Co-Director, Consortium for Science, Policy & Outcomes Professor of Science and Society, School for the Future of Innovation in Society

  • Richard Harris

    Award-Winning Journalist National Public Radio Author of “Rigor Mortis: How Sloppy Science Creates Worthless Cures, Crushes Hope, and Wastes Billions”

For those who cannot attend in person, there will be a live webcast. If you can be there in person, you can RSVP here (Note: The time frame for the event is listed in some places as 4-7 pm.) I cannot find any reason for the time frame disparity. My best guess is that the discussion is scheduled for two hours with a one hour reception afterwards for those who can attend in person.

Evolution of literature as seen by a classicist, a biologist and a computer scientist

Studying intertextuality shows how books are related in various ways and are reorganized and recombined over time. Image courtesy of Elena Poiata.

I find the image more instructive when I read it from the bottom up. For those who prefer to prefer to read from the top down, there’s this April 5, 2017 University of Texas at Austin news release (also on EurekAlert),

A classicist, biologist and computer scientist all walk into a room — what comes next isn’t the punchline but a new method to analyze relationships among ancient Latin and Greek texts, developed in part by researchers from The University of Texas at Austin.

Their work, referred to as quantitative criticism, is highlighted in a study published in the Proceedings of the National Academy of Sciences. The paper identifies subtle literary patterns in order to map relationships between texts and more broadly to trace the cultural evolution of literature.

“As scholars of the humanities well know, literature is a system within which texts bear a multitude of relationships to one another. Understanding what is distinctive about one text entails knowing how it fits within that system,” said Pramit Chaudhuri, associate professor in the Department of Classics at UT Austin. “Our work seeks to harness the power of quantification and computation to describe those relationships at macro and micro levels not easily achieved by conventional reading alone.”

In the study, the researchers create literary profiles based on stylometric features, such as word usage, punctuation and sentence structure, and use techniques from machine learning to understand these complex datasets. Taking a computational approach enables the discovery of small but important characteristics that distinguish one work from another — a process that could require years using manual counting methods.

“One aspect of the technical novelty of our work lies in the unusual types of literary features studied,” Chaudhuri said. “Much computational text analysis focuses on words, but there are many other important hallmarks of style, such as sound, rhythm and syntax.”

Another component of their work builds on Matthew Jockers’ literary “macroanalysis,” which uses machine learning to identify stylistic signatures of particular genres within a large body of English literature. Implementing related approaches, Chaudhuri and his colleagues have begun to trace the evolution of Latin prose style, providing new, quantitative evidence for the sweeping impact of writers such as Caesar and Livy on the subsequent development of Roman prose literature.

“There is a growing appreciation that culture evolves and that language can be studied as a cultural artifact, but there has been less research focused specifically on the cultural evolution of literature,” said the study’s lead author Joseph Dexter, a Ph.D. candidate in systems biology at Harvard University. “Working in the area of classics offers two advantages: the literary tradition is a long and influential one well served by digital resources, and classical scholarship maintains a strong interest in close linguistic study of literature.”

Unusually for a publication in a science journal, the paper contains several examples of the types of more speculative literary reading enabled by the quantitative methods introduced. The authors discuss the poetic use of rhyming sounds for emphasis and of particular vocabulary to evoke mood, among other literary features.

“Computation has long been employed for attribution and dating of literary works, problems that are unambiguous in scope and invite binary or numerical answers,” Dexter said. “The recent explosion of interest in the digital humanities, however, has led to the key insight that similar computational methods can be repurposed to address questions of literary significance and style, which are often more ambiguous and open ended. For our group, this humanist work of criticism is just as important as quantitative methods and data.”

The paper is the work of the Quantitative Criticism Lab (www.qcrit.org), co-directed by Chaudhuri and Dexter in collaboration with researchers from several other institutions. It is funded in part by a 2016 National Endowment for the Humanities grant and the Andrew W. Mellon Foundation New Directions Fellowship, awarded in 2016 to Chaudhuri to further his education in statistics and biology. Chaudhuri was one of 12 scholars selected for the award, which provides humanities researchers the opportunity to train outside of their own area of special interest with a larger goal of bridging the humanities and social sciences.

Here’s another link to the paper along with a citation,

Quantitative criticism of literary relationships by Joseph P. Dexter, Theodore Katz, Nilesh Tripuraneni, Tathagata Dasgupta, Ajay Kannan, James A. Brofos, Jorge A. Bonilla Lopez, Lea A. Schroeder, Adriana Casarez, Maxim Rabinovich, Ayelet Haimson Lushkov, and Pramit Chaudhuri. PNAS Published online before print April 3, 2017, doi: 10.1073/pnas.1611910114

This paper appears to be open access.

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.