Tag Archives: biology

Whispering in the Dark: Updates from Underground Science a June 12, 2019 talk in Vancouver (Canada)

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The Society of Italian Researchers and Professionals in Western Canada (ARPICO) is hosting the intriguing ‘Whispering in the Dark …’ talk about underground science being held prior to the organization’s annual general meeting. From a May 21, 2019 ARPICO announcement (received via email),

… on June 12th, 2019 at the Italian Cultural Centre. ARPICO is proud to host Dr. Silvia Scorza, who will be presenting on the topic of underground science (literally underground) at SNOLAB, where research is conducted in fields of fundamental science that require shielding from external radiation such as cosmic rays. SNOLAB (SNO stands for Sudbury Neutrino Observatory) is a Canadian research laboratory located 2 km underground in Sudbury, Ontario. This presentation will give a unique and interesting perspective into the research that is conducted mostly out of the public view and discussion, but contributes critically to our scientific advances. Applications found in medicine, national security, industry, computing, science, and workforce development, illustrate a long and growing list of beneficial practical applications with contributions from particle physics.

Please read below to learn more about our speaker and topic.

Ahead of the speaking event, ARPICO will be holding its 2019 Annual General Meeting in the same location. We encourage everyone to participate in the AGM, have their say on ARPICO’s matters and possibly volunteer for the Board of Directors. ARPICO is made by all of its members, not just the Board, and it is therefore paramount that you all come, let us know what your wishes are for the Society and tell us how we can do better together as we go forward.

If you are driving to the venue, there is plenty of free parking space.  Please refer to the attached parking map for information on where not to park however, just to be sure.

We look forward to seeing everyone there.

The evening agenda is as follows:
6:00 pm to 6:45 pm – Annual General Meeting  [ Doors Open for Registration at 5:50 pm ]
7:00 pm – Start of the evening event with introductions & lecture by Dr. Silvia Scorza [ Doors Open for Registration at 6:45 pm ]
~8:00 pm – Q & A Period
to follow – Mingling & Refreshments until about 9:30 pm
If you have not already done so, please register for the event by visiting the EventBrite link or RSVPing to info@arpico.ca.

Further details are also available at arpico.ca and Eventbrite.

Whispering in the Dark: Updates from Underground Scienc

Based at a depth of 2 km in the Vale Creighton mine near Sudbury, Ontario, SNOLAB is an underground scientific environment that provides the conditions necessary for experiments dealing with rare interactions that have to be shielded from external radiation. The lab hosts an international community involved in a number of fundamental physics (neutrino and dark matter) as well as new biology and genomic experiments making use of the unique facility. In this lecture, Dr. Scorza will offer an overview on the life of an “underground scientist” and the immense possibilities of discovery that facilities like SNOLAB make available to our society.

Dr. Silvia Scorza was born and raised in Genoa, Italy. She received her B.Sc. and M.Sc. in Physics from the University of Genoa in 2003 and 2006, respectively. She then moved to the University Claude Bernard Lyon1 (UCBL1), France, where she obtained her Ph.D. in 2009. She has then held postdoctoral positions in France at the Institut de Physique Nucléaire de Lyon, in the U.S. at the Southern Methodist University in Dallas (TX) and later in Germany at the Karlsruhe Institute of Technology. Silvia is currently a research scientist at SNOLAB and adjunct professor at Laurentian University working on the SuperCDMS SNOLAB direct dark matter search experiment and the cryogenic test facility CUTE.
 
WHEN (AGM): Wednesday, June 12th, 2019 at 6:00pm (doors open at 5:50pm)
WHEN (EVENT): Wednesday, June 12th, 2019 at 7:00pm (doors open at 6:45pm)
WHERE: Italian Cultural Centre – Museum & Art Gallery – 3075 Slocan St, Vancouver, BC, V5M 3E4

RSVP: Please RSVP at EventBrite (http://whispersinthedark.eventbrite.ca/) or email info@arpico.ca
 
Tickets are Neede

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.
 
FAQs
Where can I contact the organizer with any questions? info@arpico.ca
Do I have to bring my printed ticket to the event? No, you do not. Your name will be on our Registration List at the Check-in Desk.
Is my registration/ticket transferrable? If you are unable to attend, another person may use your ticket. Please send us an email at info@arpico.ca of this substitution to correct our audience Registration List and to prepare guest name tags.
Can I update my registration information? Yes. If you have any questions, contact us at info@arpico.ca
I am having trouble using EventBrite and cannot reserve my ticket(s). Can someone at ARPICO help me with my ticket reservation? Of course, simply send your ticket request to us at info@arpico.ca so we help you.
 
What are my transport/parking options?
Bus/Train: The Millenium Line Renfrew Skytrain station is a 5 minute walk from the Italian Cultural Centre.
Parking: Free Parking is vastly available at the ICC’s own parking lot.  …

We look forward to seeing you there.

ARPICO
www.arpico.ca

You can find out more about SNOLAB here. There’s even a virtual tour.

Frugal science: ancient toys for state-of-the-art science

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A toy that’s been a plaything for 5,000 years and known as a whirligig (in English, anyway) has inspired a scientific tool for use by field biologists and students interested in creating state-of-the-art experiments. Exciting stuff, eh?

A May 23, 2019 Georgia Tech (Georgia Institute of Technology) news release (also on EurekAlert but published on May 22, 2019) announces this development in ‘frugal science’,

A 5,000-year-old toy still enjoyed by kids today has inspired an inexpensive, hand-powered scientific tool that could not only impact how field biologists conduct their research but also allow high-school students and others with limited resources to realize their own state-of-the-art experiments.

The device, a portable centrifuge for preparing scientific samples including DNA, is reported May 21 [2019] in the journal PLOS Biology. The co-first author of the paper is Gaurav Byagathvalli, a senior at Lambert High School in Georgia. His colleagues are M. Saad Bhamla, an assistant professor at the Georgia Institute of Technology; Soham Sinha, a Georgia Tech undergraduate; Janet Standeven, Byagathvalli’s biology teacher at Lambert; and Aaron F. Pomerantz, a graduate student at the University of California, Berkeley.

“I am exceptionally proud of this paper and will remember it 10, 20, 30 years from now because of the uniquely diverse team we put together,” said Bhamla, who is an assistant professor in Georgia Tech’s School of Chemical and Biomolecular Engineering.

From a Rainforest to a High School

Together the team demonstrated the device, dubbed the 3D-Fuge because it is created through 3D printing, in two separate applications. In a rainforest in Peru the 3D-Fuge was an integral part of a “lab in a backpack” used to identify four previously-unknown plants and insects by sequencing their DNA [deoxyribonucleic acid]. Back in the United States, a slightly different design enabled a new approach to creating living bacterial sensors for the potential detection of disease. That work was conducted at Lambert High School for a synthetic biology competition.

Thanks to social media and a preprint of the PLOS Biology paper on BioRxiv, the 3D-Fuge has already generated interest from around the world, including emails from high-school teachers in Zambia and Kenya. “It’s awesome to see research not just remain isolated to one location but see it spread,” said Byagathvalli. “Through this, we’ve realized how much of an impact simple yet effective tools can have, and hope this technology motivates others to continue along the same path and innovate new solutions to global issues.”

To better share the work, the team has posted the 3D-Fuge designs, videos, and photos online available to anyone.

Frugal Science

One focus of Bhamla’s lab at Georgia Tech is the development of tools for frugal science, or real research that just about anyone can afford. The tools behind state-of-the-art science often cost thousands of dollars that make them inaccessible to those without serious resources.

Centrifuges are a good example.  A small benchtop unit costs between $3,000 and $5,000; larger units cost many times that. Yet the devices are necessary to produce concentrated amounts of, say, genomic materials like DNA. By rapidly spinning samples, they separate materials of interest from biological debris.

The Bhamla team found that the 3D-Fuge works as well as its more expensive cousins, but costs less than $1.

An Ancient Toy

The 3D-Fuge is based on earlier work by Bhamla and colleagues at Stanford University on a simple centrifuge made of paper. The “paperfuge,” in turn, was inspired by a toy composed of string and a button that Bhamla played with as a child. He later discovered that these toys, known as whirligigs, have existed for some 5,000 years.

They consist of a disk – like a button – with two holes, through which is threaded a length of flexible cord whose ends are knotted to create a single loop with the disk in the middle. That simple contraption is then swung with two hands until the button is spinning and whirring at very fast speeds.

The earlier paperfuge uses a disk of paper. To that disk Bhamla glued small plastic tubes filled with a sample. He and colleagues reported that the device did indeed create high-quality samples.

In late 2017 Bhamla was separately approached by the Lambert High team and Pomerantz to see if the paperfuge could be adapted for the larger samples they needed (the paperfuge is limited to small samples of ~1 microliter—or one drop of blood).

Together they came up with the 3D-Fuge, which includes cavities for tubes that can hold some 100 times more of a sample than the paperfuge. The team developed two equally effective designs: one for field biology (led by Pomerantz) and the other for the high-school’s synthetic biology project (led by Byagathvalli).

Bhamla notes that the 3D-Fuge has some limitations. For example, it can only process a few samples at a time (some applications require thousands of samples). Further, because it’s 10 times heavier than the paperfuge, it can’t reach the same speeds or produce the same forces of that device. That said, it still weighs only 20 grams, slightly less than a AA battery.

“But it works,” said Bhamla. “All you need is an [appropriate] application and some creativity.”

Here are a couple of images showing the 3D-Fuge in action,

Using the 3D-Fuge Courtesy: Georgia Tech
Sample vial in 3D-Fuge Courtesy: Georgia Tech

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

A 3D-printed hand-powered centrifuge for molecular biology by Gaurav Byagathvalli, Aaron Pomerantz, Soham Sinha, Janet Standeven, M. Saad Bhamla. PLOS Biology DOI: https://doi.org/10.1371/journal.pbio.3000251 Published: May 21, 2019

As always with a Public Library of Science (PLOS) publication, this paper is open access.

Teaching molecular and synthetic biology in grades K-12

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This* story actually started in 2018 with an August 1, 2018 Harvard University news release (h/t Aug. 1, 2018 news item on phys.org) by Leslie Brownell announcing molecular and synthetic biology educational kits that been tested in the classroom. (In 2019, a new kit was released but more about that later.)

As biologists have probed deeper into the molecular and genetic underpinnings of life, K-12 schools have struggled to provide a curriculum that reflects those advances. Hands-on learning is known to be more engaging and effective for teaching science to students, but even the most basic molecular and synthetic biology experiments require equipment far beyond an average classroom’s budget, and often involve the use of bacteria and other substances that can be difficult to manage outside a controlled lab setting.

Now, a collaboration between the Wyss Institute at Harvard University, MIT [Massachusetts Institute of Technology], and Northwestern University has developed BioBits, new educational biology kits that use freeze-dried cell-free (FD-CF) reactions to enable students to perform a range of simple, hands-on biological experiments. The BioBits kits introduce molecular and synthetic biology concepts without the need for specialized lab equipment, at a fraction of the cost of current standard experimental designs. The kits are described in two papers published in Science Advances [2018].

“The main motivation in developing these kits was to give students fun activities that allow them to actually see, smell, and touch the outcomes of the biological reactions they’re doing at the molecular level,” said Ally Huang, a co-first author on both papers who is an MIT graduate student in the lab of Wyss Founding Core Faculty member Jim Collins, Ph.D. “My hope is that they will inspire more kids to consider a career in STEM [science, technology, engineering, and math] and, more generally, give all students a basic understanding of how biology works, because they may one day have to make personal or policy decisions based on modern science.”

Synthetic and molecular biology frequently make use of the cellular machinery found in E. coli bacteria to produce a desired protein. But this system requires that the bacteria be kept alive and contained for an extended period of time, and involves several complicated preparation and processing steps. The FD-CF reactions pioneered in Collins’ lab for molecular manufacturing, when combined with innovations from the lab of Michael Jewett, Ph.D. at Northwestern University, offer a solution to this problem by removing bacteria from the equation altogether.

“You can think of it like opening the hood of a car and taking the engine out: we’ve taken the ‘engine’ that drives protein production out of a bacterial cell and given it the fuel it needs, including ribosomes and amino acids, to create proteins from DNA outside of the bacteria itself,” explained Jewett, who is the Charles Deering McCormick Professor of Teaching Excellence at Northwestern University’s McCormick School of Engineering and co-director of Northwestern’s Center for Synthetic Biology, and co-corresponding author of both papers. This collection of molecular machinery is then freeze-dried into pellets so that it becomes shelf-stable at room temperature. To initiate the transcription of DNA into RNA and the translation of that RNA into a protein, a student just needs to add the desired DNA and water to the freeze-dried pellets.

The researchers designed a range of molecular experiments that can be performed using this system, and coupled each of them to a signal that the students can easily detect with their sense of sight, smell, or touch. The first, called BioBits Bright, contains six different freeze-dried DNA templates that each encode a protein that fluoresces a different color when illuminated with blue light. To produce the proteins, students simply add these DNA templates and water to the FD-CF machinery and put the reactions in an inexpensive incubator (~$30) for several hours, and then view them with a blue light illuminator (~$15). The students can also design their own experiments to produce a desired collection of colors that they can then arrange into a visual image, a bit like using a Light Brite ©. “Challenging the students to build their own in vitro synthetic programs also allows educators to start to talk about how synthetic biologists might control biology to make important products, such as medicines or chemicals,” explained Jessica Stark, an NSF Graduate Research Fellow in the Jewett lab at Northwestern University who is co-first author on both papers.

An expansion of the BioBits Bright kit, called BioBits Explorer, includes experiments that engage the senses of smell and touch and allow students to probe their environment using designer synthetic biosensors. In the first experiment, the FD-CF reaction pellets contain a gene that drives the conversion of isoamyl alcohol to isoamyl acetate, a compound that produces a strong banana odor. In the second experiment, the FD-CF reactions contain a gene coding for the enzyme sortase, which recognizes and links specific segments of proteins in a liquid solution together to form a squishy, semi-solid hydrogel, which the students can touch and manipulate. The third module uses another Wyss technology, the toehold switch sensor, to identify DNA extracted from a banana or a kiwi. The sensors are hairpin-shaped RNA molecules designed such that when they bind to a “trigger” RNA, they spring open and reveal a genetic sequence that produces a fluorescent protein. When fruit DNA is added to the sensor-containing FD-CF pellets, only the sensors that are designed to open in the presence of each fruit’s RNA will produce the fluorescent protein.

The researchers tested their BioBits kits in the Chicago Public School system, and demonstrated that students and teachers were able to perform the experiments in the kits with the same success as trained synthetic biology researchers. In addition to refining the kits’ design so that they can one day provide them to classrooms around the world, the authors hope to create an open-source online database where teachers and students can share their results and ideas for ways to modify the kits to explore different biological questions.

“Synthetic biology is going to be one of the defining technologies of the century, and yet it has been challenging to teach the fundamental concepts of the field in K-12 classrooms given that such efforts often require expensive, complicated equipment,” said Collins, who is a co-corresponding author of both papers and also the Termeer Professor of Medical Engineering & Science at MIT. “We show that it is possible to use freeze-dried, cell-free extracts along with freeze-dried synthetic biology components to conduct innovative educational experiments in classrooms and other low-resource settings. The BioBits kits enable us to expose young kids, older kids, and even adults to the wonders of synthetic biology and, as a result, are poised to transform science education and society.

“All scientists are passionate about what they do, and we are frustrated by the difficulty our educational system has had in inciting a similar level of passion in young people. This BioBits project demonstrates the kind of out-of-the-box thinking and refusal to accept the status quo that we value and cultivate at the Wyss Institute, and we all hope it will stimulate young people to be intrigued by science,” said Wyss Institute Founding Director Donald Ingber, M.D., Ph.D., who is also the Judah Folkman Professor of Vascular Biology at Harvard Medical School (HMS) and the Vascular Biology Program at Boston Children’s Hospital, as well as Professor of Bioengineering at Harvard’s John A. Paulson School of Engineering and Applied Sciences (SEAS). “It’s exciting to see this project move forward and become available to biology classrooms worldwide and, hopefully some of these students will pursue a path in science because of their experience.”

Additional authors of the papers include Peter Nguyen, Ph.D., Nina Donghia, and Tom Ferrante from the Wyss Institute; Melissa Takahashi, Ph.D. and Aaron Dy from MIT; Karen Hsu and Rachel Dubner from Northwestern University; Keith Pardee, Ph.D., Assistant Professor at the University of Toronto; and a number of teachers and students in the Chicago school system including: Mary Anderson, Ada Kanapskyte, Quinn Mucha, Jessica Packett, Palak Patel, Richa Patel, Deema Qaq, Tyler Zondor, Julie Burke, Tom Martinez, Ashlee Miller-Berry, Aparna Puppala, Kara Reichert, Miriam Schmid, Lance Brand, Lander Hill, Jemima Chellaswamy, Nuhie Faheem, Suzanne Fetherling, Elissa Gong, Eddie Marie Gonzales, Teresa Granito, Jenna Koritsaris, Binh Nguyen, Sujud Ottman, Christina Palffy, Angela Patel, Sheila Skweres, Adriane Slaton, and TaRhonda Woods.

This research was supported by the Army Research Office, the National Science Foundation, the Air Force Research Laboratory Center of Excellence Grant, The Defense Threat Reduction Agency Grant, the David and Lucile Packard Foundation, the Camille Dreyfus Teacher-Scholar Program, the Wyss Institute at Harvard University, the Paul G. Allen Frontiers Group, The Air Force Office of Scientific Research, and the Natural Sciences and Engineering Council of Canada. [emphases mine]

Well, that list of funding agencies is quite interesting. The US Army and Air Force but not the Navy? As for what the Natural Sciences and Engineering Council of Canada is doing on that list, I can only imagine why.

This is what they were doing in 2018,

Now for the latest update, a May 7, 2019 news item on phys.org announces the BioBits Kits have been expanded,

How can high school students learn about a technology as complex and abstract as CRISPR? It’s simple: just add water.

A Northwestern University-led team has developed BioBits, a suite of hands-on educational kits that enable students to perform a range of biological experiments by adding water and simple reagents to freeze-dried cell-free reactions. The kits link complex biological concepts to visual, fluorescent readouts, so students know—after a few hours and with a single glance—the results of their experiments.

A May 7, 2019 Northwestern University news release (also on EurekAlert and received via email) by Amanda Morris, which originated the news item, provides more details,

After launching BioBits last summer, the researchers are now expanding the kit to include modules for CRISPR [clustered regularly interspaced short palindromic repeats] and antibiotic resistance. A small group of Chicago-area teachers and high school students just completed the first pilot study for these new modules, which include interactive experiments and supplementary materials exploring ethics and strategies.

“After we unveiled the first kits, we next wanted to tackle current topics that are important for society,” said Northwestern’s Michael Jewett, principal investigator of the study. “That led us to two areas: antibiotic resistance and gene editing.”

Called BioBits Health, the new kits and pilot study are detailed in a paper published today (May 7 [2019]) in the journal ACS Synthetic Biology.

Jewett is a professor of chemical and biological engineering in Northwestern’s McCormick School of Engineering and co-director of Northwestern’s Center for Synthetic Biology. Jessica Stark, a graduate student in Jewett’s laboratory, led the study.

Test in a tube

Instead of using live cells, the BioBits team removed the essential cellular machinery from inside the cells and freeze-dried them for shelf stability. Keeping cells alive and contained for an extended period of time involves several complicated, time-consuming preparation and processing steps as well as expensive equipment. Freeze-dried cell-free reactions bypass those complications and costs.

“These are essentially test-tube biological reactions,” said Stark, a National Science Foundation graduate research fellow. “We break the cells open and use their guts, which still contain all of the necessary biological machinery to carry out a reaction. We no longer need living cells to demonstrate biology.”

This method to harness biological systems without intact, living cells became possible over the last two decades thanks to multiple innovations, including many in cell-free synthetic biology by Jewett’s lab. Not only are these experiments doable in the classroom, they also only cost pennies compared to standard high-tech experimental designs.

“I’m hopeful that students get excited about engineering biology and want to learn more,” Jewett said.

Conquering CRISPR

One of the biggest scientific breakthroughs of the past decade, CRISPR (pronounced “crisper”) stands for Clustered Regularly Interspaced Short Palindromic Repeats. The powerful gene-editing technology uses enzymes to cut DNA in precise locations to turn off or edit targeted genes. It could be used to halt genetic diseases, develop new medicines, make food more nutritious and much more.

BioBits Health uses three components required for CRISPR: an enzyme called the Cas9 protein, a target DNA sequence encoding a fluorescent protein and an RNA molecule that targets the fluorescent protein gene. When students add all three components — and water — to the freeze-dried cell-free system, it creates a reaction that edits, or cuts, the DNA for the fluorescent protein. If the DNA is cut, the system does not glow. If the DNA is not cut, the fluorescent protein is made, and the system glows fluorescent.

“We have linked this abstract, really advanced biological concept to the presence or absence of a fluorescent protein,” Stark said. “It’s something students can see, something they can visually understand.”

The curriculum also includes activities that challenge students to consider the ethical questions and dilemmas surrounding the use of gene-editing technologies.

“There is a lot of excitement about being able to edit genomes with these technologies,” Jewett said. “BioBits Health calls attention to a lot of important questions — not only about how CRISPR technology works but about ethics that society should be thinking about. We hope that this promotes a conversation and dialogue about such technologies.”

Reducing resistance

Jewett and Stark are both troubled by a prediction that, by the year 2050, drug-resistant bacterial infections could outpace cancer as a leading cause of death. This motivated them to help educate the future generation of scientists about how antibiotic resistance emerges and inspire them to take actions that could help limit the emergence of resistant bacteria.
In this module, students run two sets of reactions to produce a glowing fluorescent protein — one set with an antibiotic resistance gene and one set without. Students then add antibiotics. If the experiment glows, the fluorescent protein has been made, and the reaction has become resistant to antibiotics. If the experiment does not glow, then the antibiotic has worked.

“Because we’re using cell-free systems rather than organisms, we can demonstrate drug resistance in a way that doesn’t create drug-resistant bacteria,” Stark explained. “We can demonstrate these concepts without the risks.”

A supporting curriculum piece challenges students to brainstorm and research strategies for slowing the rate of emerging antibiotic resistant strains.

Part of something cool

After BioBits was launched in summer 2018, 330 schools from around the globe requested prototype kits for their science labs. The research team, which includes members from Northwestern and MIT, has received encouraging feedback from teachers, students and parents.

“The students felt like scientists and doctors by touching and using the laboratory materials provided during the demo,” one teacher said. “Even the students who didn’t seem engaged were secretly paying attention and wanted to take their turn pipetting. They knew they were part of something really cool, so we were able to connect with them in a way that was new to them.”

“My favorite part was using the equipment,” a student said. “It was a fun activity that immerses you into what top scientists are currently doing.”

###

The study, “BioBits Health: Classroom activities exploring engineering, biology and human health with fluorescent readouts,” was supported by the Army Research Office (award number W911NF-16-1-0372), the National Science Foundation (grant numbers MCB-1413563 and MCB-1716766), the Air Force Research Laboratory Center of Excellence (grant number FA8650-15-2-5518), the Defense Threat Reduction Agency (grant number HDTRA1-15-10052/P00001), the Department of Energy (grant number DE-SC0018249), the Human Frontiers Science Program (grant number RGP0015/2017), the David and Lucile Packard Foundation, the Office of Energy Efficiency and Renewable Energy (grant number DE-EE008343) and the Camille Dreyfus Teacher-Scholar Program. [emphases mine]

This is an image you’ll find in the abstract for the 2019 paper,

[downloaded from https://pubs.acs.org/doi/10.1021/acssynbio.8b00381]

Here are links and citations for the 2018 papers and the 2019 paper,

BioBits™ Explorer: A modular synthetic biology education kit by Ally Huang, Peter Q. Nguyen, Jessica C. Stark, Melissa K. Takahashi, Nina Donghia, Tom Ferrante, Aaron J. Dy, Karen J. Hsu, Rachel S. Dubner, Keith Pardee, Michael C. Jewett, and James J. Collins. Science Advances 01 Aug 2018: Vol. 4, no. 8, eaat5105 DOI: 10.1126/sciadv.aat5105

BioBits™ Bright: A fluorescent synthetic biology education kit by Jessica C. Stark, Ally Huang, Peter Q. Nguyen, Rachel S. Dubner, Karen J. Hsu, Thomas C. Ferrante, Mary Anderson, Ada Kanapskyte, Quinn Mucha, Jessica S. Packett, Palak Patel, Richa Patel, Deema Qaq, Tyler Zondor, Julie Burke, Thomas Martinez, Ashlee Miller-Berry, Aparna Puppala, Kara Reichert, Miriam Schmid, Lance Brand, Lander R. Hill, Jemima F. Chellaswamy, Nuhie Faheem, Suzanne Fetherling, Elissa Gong, Eddie Marie Gonzalzles, Teresa Granito, Jenna Koritsaris, Binh Nguyen, Sujud Ottman, Christina Palffy, Angela Patel, Sheila Skweres, Adriane Slaton, TaRhonda Woods, Nina Donghia, Keith Pardee, James J. Collins, and Michael C. Jewett. Science Advances 01 Aug 2018: Vol. 4, no. 8, eaat5107 DOI: 10.1126/sciadv.aat5107

BioBits Health: Classroom Activities Exploring Engineering, Biology, and Human Health with Fluorescent Readouts by Jessica C. Stark, Ally Huang, Karen J. Hsu, Rachel S. Dubner, Jason Forbrook, Suzanne Marshalla, Faith Rodriguez, Mechelle Washington, Grant A. Rybnicky, Peter Q. Nguyen, Brenna Hasselbacher, Ramah Jabri, Rijha Kamran, Veronica Koralewski, Will Wightkin, Thomas Martinez, and Michael C. Jewett. ACS Synth. Biol., Article ASAP
DOI: 10.1021/acssynbio.8b00381 Publication Date (Web): March 29, 2019

Copyright © 2019 American Chemical Society

Both of the 2018 papers appear to be open access while the 2019 paper is behind a paywall.

Should you be interested in acquiring a BioBits kit, you can check out the BioBits website. As for ‘conguering’ CRISPR, do we really need to look at it that way? Maybe a more humble appraoch could work just as well or even better, eh?

*’is’ removed from sentence on May 9, 2019.

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

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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:

INSECTS IN THE CITY: SHRINKING BEETLES AND DISAPPEARING BEES. HOW BUGS
HELP US LEARN ABOUT THE ECOLOGICAL EFFECTS OF URBANIZATION AND CLIMATE
CHANGE

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
development.

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.

Tseng Lab website: http://michelletseng.weebly.com/index.html

Enjoy!

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

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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

CLICK HERE FOR MORE AND TO RSVP

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

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

CLICK HERE FOR MORE AND TO RSVP

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

CLICK HERE FOR MORE AND TO RSVP

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

CLICK HERE FOR MORE AND TO RSVP

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

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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)

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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,

Speakers

Keynote


  • Shobita Parthasarathy

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

Moderator


  • 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

Panelists


  • 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

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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

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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.