Teaching grammar and syntax to artificial intelligence (AI) algorithms (specifically natural language processing (NLP) algorithms) has helped researchers understand and predict viral mutations more speedily. This facility is especially useful at a time when the Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus seems to be mutating into more easily transmissible variants.
Will Douglas Heaven’s Jan. 14, 2021 article for the Massachusetts Institute of Technology’s MIT Technology Review describes the work that links AI, grammar, and mutating viruses (Note: Links have been removed),
Galileo once observed that nature is written in math. Biology might be written in words. Natural-language processing (NLP) algorithms are now able to generate protein sequences and predict virus mutations, including key changes that help the coronavirus evade the immune system.
The key insight making this possible is that many properties of biological systems can be interpreted in terms of words and sentences. “We’re learning the language of evolution,” says Bonnie Berger, a computational biologist at the Massachusetts Institute of Technology [MIT].
In the last few years, a handful of researchers—including teams from geneticist George Church’s [Professor of Health Sciences and Technology at Harvard University and MIT, etc.] lab and Salesforce [emphasis mine]—have shown that protein sequences and genetic codes can be modeled using NLP techniques.
In a study published in Science today, Berger and her colleagues pull several of these strands together and use NLP to predict mutations that allow viruses to avoid being detected by antibodies in the human immune system, a process known as viral immune escape. The basic idea is that the interpretation of a virus by an immune system is analogous to the interpretation of a sentence by a human.
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Berger’s team uses two different linguistic concepts: grammar and semantics (or meaning). The genetic or evolutionary fitness of a virus—characteristics such as how good it is at infecting a host—can be interpreted in terms of grammatical correctness. A successful, infectious virus is grammatically correct; an unsuccessful one is not.
Similarly, mutations of a virus can be interpreted in terms of semantics. Mutations that make a virus appear different to things in its environment—such as changes in its surface proteins that make it invisible to certain antibodies—have altered its meaning. Viruses with different mutations can have different meanings, and a virus with a different meaning may need different antibodies to read it.
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Instead of millions of sentences, they trained the NLP model on thousands of genetic sequences taken from three different viruses: 45,000 unique sequences for a strain of influenza, 60,000 for a strain of HIV, and between 3,000 and 4,000 for a strain of Sars-Cov-2, the virus that causes covid-19. “There’s less data for the coronavirus because there’s been less surveillance,” says Brian Hie, a graduate student at MIT, who built the models.
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The overall aim of the approach is to identify mutations that might let a virus escape an immune system without making it less infectious—that is, mutations that change a virus’s meaning without making it grammatically incorrect.
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But it’s also just the beginning. Treating genetic mutations as changes in meaning could be applied in different ways across biology. “A good analogy can go a long way,” says Bryson [Bryan Bryson, a biologist at MIT].
If you have time, I recommend reading Heaven’s Jan. 14, 2021 article in its entirety as it’s well written with clear explanations. As for the article’s mentions of George Church and Salesforce, the former could be expected while the latter is not (by me, I speak for no one else).
I find it fascinating that a company which describes itself (from What is Salesforce?) as providing “… customer relationship management, or CRM. It gives all your departments — including marketing, sales, commerce, and service — a shared view of your customers … ” seems to be conducting investigations into one (or more?) areas of biology.
For those who’d like to dive into the science as described in Heaven’s article, here’s a link to and a citation for the paper,
Caption: Forward burrowers use pointed snouts and powerful forelimbs bolstered by strong pectoral muscles to scrabble into the earth. They’re often orb-shaped to improve their ability to hold water. Credit: Rachel Keeffe
It’s always enjoyable to see the scientific community indulge in a little fun and I’m using that as an excuse for including a frog story here.
You might think the buffest frogs would be high jumpers, but if you want shredded pecs, you should train like a burrowing frog. Though famously round, these diggers are the unsung bodybuilders of the frog world. We bring you tips from frog expert Rachel Keeffe, a doctoral student at the University of Florida, and physical therapist Penny Goldberg to help you get the burrowing body of your dreams.
But first, a caveat: According to Keeffe, no workout regimen can help you train your way into a highly specialized frog physique honed by 200 million years of evolution. To better understand burrowing frog anatomy, Keeffe and her adviser David Blackburn, Florida Museum of Natural History curator of herpetology, analyzed CT scans from all 54 frog families to show these frogs boast a robust and quirky skeleton that is more variable than previously thought.
“People think about frogs as being clean and smooth and slimy, or the classic ‘green frog on a lily pad,’ but a lot of them are dirty – they like to scoot around and be in the dirt,” Keeffe said. “Burrowing frogs are really diverse and can do a lot of cool things. And when you look at the skeletons of known burrowers, they’re very different from what you would call a ‘normal frog.'”
Burrowing frogs are found all over the world from deserts to swamps, but their underground lifestyle makes them difficult to study, Keeffe said. Most tunnel hind end-first with their back legs. But a few species are forward burrowers, using pointed snouts and powerful forelimbs bolstered by strong pectoral muscles to scrabble into the earth.
Keeffe’s sample of 89 frog species revealed radical differences in burrowing bone structure, from clavicles the size of eyelashes to other bones that are unusually thick.
“They’re so diverse that it’s challenging to think about even comparing them. It’s almost a black hole of work that we can do with forward burrowers because we tend to focus on the legs,” she said.
Some burrow to seek refuge, whether from arid temperatures or predators, and underground habitats can be hunting grounds or secluded hiding places. Other burrowing frogs can spend months at a time as deep as 3 feet belowground, surviving on a high-protein diet of termites and ants. The takeaway: If you want to compete for resources with the pros, don’t be afraid to put in the work.
Get the burly burrowing body
To train like a burrowing frog, Goldberg, assistant director of ReQuest Physical Therapy in Gainesville, recommended dedicating time to strengthening your upper back.
“In humans, the most important muscle group to focus on if you were to train like one of these frogs would be the scapular stabilizers,” she said. “These include 17 muscles, such as the lats and rotator cuff, with attachments all the way down to the pelvis that allow the upper back to generate power. To burrow like a forward burrower, you need to strengthen this entire region.”
One strengthening move Goldberg recommended is the “Prone W.” Lie facedown with elbows bent and palms on the floor. Squeeze your shoulder blades down and toward your spine as you lift your arms to the ceiling for a couple seconds at a time.
Like any elite athlete, burrowing frogs also maintain an optimal form. They’re often orb-shaped to improve their ability to hold water.
“Personally, if I were a sphere, I think it would be hard for me to dig, but it doesn’t seem to affect these frogs at all,” Keeffe said. “However, frogs with stumpy legs are definitely worse at jumping, and they tend to stagger when they walk.”
For these frogs, time away from the tunnels might be spent swimming instead, Keeffe said. To compete here, Goldberg recommends the breaststroke, adding that her top training tips for getting the upper back and pecs of a forward burrower would include pullups and pushups to develop the shoulder blade area.
“In my world, we would use resistance bands and pushing or pulling motions to train this area,” Goldberg said. “Anything focusing predominantly on building strength in the upper back region.”
If resistance bands are part of your workout routine, try grasping one with both hands and extending your arms while keeping your elbows straight. For best results, Goldberg recommended starting with three sets of 10.
Burrowing frogs might also hold key answers to gaps in scientists’ understanding of amphibian evolution at large. Keeffe’s analysis also found that forward-burrowing behavior evolved independently at least eight times in about one-fifth of frog families, and the trait’s persistence in the frog family tree suggests it’s a beneficial adaptation. Keeffe also found that forward burrowers tended to have a highly contoured humerus, the bone that connects the shoulder to the elbow in humans.
Understanding how bone shape relates to musculature can help scientists identify which frogs, both modern and extinct, are forward burrowers, a helpful tool given their covert behavior.
“Even though it can be frustrating, I like them because they’re secretive,” Keeffe said. “But the whole thing underlying this study is that frogs can do a lot of cool things – they don’t just jump and they’re not just green.”
CT scans were generated from the National Science Foundation-funded oVert project.
Do take a look at the August 31, 2020 Florida Museum of Natural History news release as the researchers have provided pictures of real ‘forward burrowing frogs’ along with more cartoons and other other images that have been embedded in Marchese’s release.
Depending on how you feel about bodily fluids, sex, orgasms, and beauty care products being discussed as part of an event that is both workshop and performance, you may feel you’ve read enough now.
What follows is not especially graphic but it’s not for everybody. First, here’s more about the Oct. 29, 2020 event followed by a call for participants (it’s open until Oct. 15, 2020).
ArtSci Salon’s Beauty Kit – eco-erogenous para-pharmaceutics; a workshop/performance
Beauty Kit is part of Boundary-Crossings: Multiscalar Entanglements in Art, Science and Society, a public Outreach [sic] program supported by the Fiends [sic;] Institute for Research in Mathematical Science.
In this workshop /performance, Isabel Burr Raty explores the energetic potentials of bodily fluids. Modern culture tends to consider bodily fluids as superfluous and wasteful, as unholy and unspeakable taboos, as something that should be discarded because it has no apparent use except in the personal sphere of intimacy.
By revealing the chemical, biological and nutritional potentials of a variety of bodily fluids and by encouraging the participants to explore and harvest their own, Burr Raty engages in a fierce critique of consumption and industrial mass production, and in a clever journey to cross many boundaries: she breaks the taboo that prevents us from speaking about bodily fluids; she shows how bodily fluids are profoundly entangled with the body and its surrounding environment; she demonstrates how far from waste they are, and how they participate in a never-ending cycle of growth, decay and renewal. By crossing the boundaries of art, biology, technology and agriculture, Burr Raty offers spaces of liberation that incite new living habits by means of alternative cultural arrangements, which propose circular economy models such as the one based on fluid bio-transaction and pleasure. Speaking of and practicing boundary crossing, especially the idea of bodily fluids’ ecological entanglements, is crucial in today’s increased fear of touching and physical isolation due to COVID19’s hygiene theatre.
During this workshop-performance, registered participants will join the online audience from various remote locations. They will be asked to answer a number of questions reflecting their relation with bodily fluids from a variety of perspectives – personal, scientific or philosophical – and will be invited to test and give feedback on a series of special Beauty Kit (BK) transpersonal and gender neutral skin and care lines that will be delivered via mail to their homes. Finally, they will be encouraged to inquire on the product’s formulas and agro-cultural technology employed in this project.
The workshop-performance will take place on October 29 [2020] 3:00-5:00 pm [presumably this is on Eastern Daylight Time]
I believe “Fiends Institute for Research in Mathematical Science” should be “Fields Institute for Research in Mathematical Science.”
Isabel Burr Raty currently runs a mobile Farm that harvests human female erotic juices to manufacture Para-pharmaceutical bio-products with them, that will evolve into an Eco-erogenous Village of entanglements, where every-BODY will harvest each other.
We are looking for participants to take part in this unique online/distributed workshop-performance
Beauty Kit – eco-erogenous para-pharmaceutics
On Oct 29, 2020,
3:00-5:00 pm EDT
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How many types of female ejaculations do you know about? Can a brain orgasm be transformed into a source of renewable energy? Can the orgasmic body be a territory for sustainable agricultural development? Could engaging in and speaking of bodily fluids and intimate relations help us overcome current fears of the unknown and the microscopic and open up a new culture of care and sharing, mutual aid and solidarity?
These are some (but not all!) of the questions that this workshop/performance seeks to explore.
The joint participation of the online public is very important. Pointing out gaps in scientific perspectives about the body’s orgasmic agency, she exposes allopathic and ancestral perspectives on the faculty of sexual fluids to replace the components of beauty and wellbeing products that we find in the market. An invited audience of participants is warmly welcome to test the BK transpersonal and gender neutral skin and care lines that they will receive via the post to their homes, as well as to inquire on the product’s formulas and agro-cultural technology employed in this project.
To run this workshop, we are looking for volunteers to:
1. Participate in the workshop/performance remotely online
2. Try some Beauty Kit (BK) products
3. Engage in a public discussion with Burr Raty and the general audience
4. Agree to make themselves visible, as avatars, as themselves, as masked characters or by wearing a color that gives them pleasure
This is an inclusive workshop which seeks to address intimate, scientific and political topics with respect and care.
If you wish to be part of this experience, please, send us your intent to participate: RSVP to the workshop by Oct 15, 2020 by sending an email to artscisalon@gmail.com with a couple of sentences explaining why you are interested in being part of it.
We will ask you to provide a home address where we can send you the material.
We care about your privacy and we will do anything we can to respect your preferences. If you live in Toronto, arrangements can be made for physically distanced pickup.
This workshop is performative and participants are encouraged to impersonate their alter-ego, to play their avatar, to wear a costume etc…
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ABOUT ISABEL BURR RATY
Isabel Burr Raty is an independent filmmaker, artist, teacher and sexual Kunfu coach exploring the interstices between the organic and the artificial, between the unlicensed knowledge of minority groups and the official facts. In so doing, she aims to dig up chapters left out of history books, blur the limits between fiction/reality and re-think the memory of the future.
In her artistic work she interweaves performance and new media installation proposing hybrid narratives and bio-autonomy practices that invite the public to queer production understandings and embody SF in real time, such as the Beauty Kit Farm.
Isabel teaches Media art history in École de Recherche Graphique and is researcher in WAB IV nadine Brussels. In 2018 she was granted a bio-art & design deal by the AFK (Amsterdams Fonds voor de Kunst), which partnered her to: The Waag, Mediamatic and Prof. Toby Kiers (VU Amsterdam).
Burr Raty has shown her works and collaborations internationally, in venues such as: KVS (Royal Flemish Theater), Beursschouwburg, Constant_V, ZSeene Art Lab, Limal (Brussels); Palais de Tokyo Paris, ISEA Hong Kong and Cultivamos Cultura Portugal; presented her work in festivals and conferences such as: Enter Through The Void, Exit Through The Giftshop, Campo Victoria, Ghent (BE), Ecofutures at Queen Mary’s University London (GB), FEMeeting (PT), Taboo Transgression Transcendence in Art and Science (GR/AU), Human Enhancement Clinic at Border Sessions (NL), Science Friction at the Aki Institute in Enchede University (NL) and FACTT at Humbolt University Berlin (DE); and given workshops at the University of the Arts Berlin (DE) and Rampa Lab Ljubljana (SI).
Beauty Kit is part of Boundary-Crossings: Multiscalar Entanglements in Art, Science and Society, a public Outreach program supported by the Fiends [sic; Fields] Institute for Research in Mathematical Science
Boundary Crossings is a series exploring how the notion of boundaries can be transcended and dissolved in the arts and the humanities, the biological and the mathematical sciences, as well as human geography and political economy. Boundaries are used to establish delimitations among disciplines; to discriminate between the human and the non-human (body and technologies, body and bacteria); and to indicate physical and/or artificial boundaries, separating geographical areas and nation states.
This event is curated by ArtSci Salon with support from Sensorium: Centre for Digital Arts and Technology, York University
I believe this or something like it is what you’ll be receiving,
I’m not sure how mathematics relates to Beauty Kit but it is definitely boundary-crossing.
There seems to have been some lively debate among biologists about matters most of us treat as invisible: naming, establishing, and classifying categories. These activities can become quite visible when learning a new language, e.g., French which divides nouns into two genders or German which classifies nouns with any of three genders.
A July 26, 2020 essay by Stephen Garnett (Professor of Conservation and Sustainable Livelihoods, Charles Darwin University, Australia), Les Christidis (Professor, Southern Cross University, Australia), Richard L. Pyle (Associate lecturer, University of Hawaii, US), and Scott Thomson (Research associate, Universidade de São Paulo, Brazil) for The Conversation (also on phys.org but published July 27, 2020) describes a very heated debate over taxonomy,
Taxonomy, or the naming of species, is the foundation of modern biology. It might sound like a fairly straightforward exercise, but in fact it’s complicated and often controversial.
Why? Because there’s no one agreed list of all the world’s species. Competing lists exist for organisms such as mammals and birds, while other less well-known groups have none. And there are more than 30 definitions of what constitutes a species [emphasis mine]. This can make life difficult for biodiversity researchers and those working in areas such as conservation, biosecurity and regulation of the wildlife trade.
In the past few years, a public debate erupted among global taxonomists, including those who authored and contributed to this article, about whether the rules of taxonomy should be changed. Strongly worded ripostes were exchanged. A comparison to Stalin [emphasis mine] was floated.
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Here’s how it started,
In May 2017 two of the authors, Stephen Garnett and Les Christidis, published an article in Nature. They argued taxonomy needed rules around what should be called a species, because currently there are none. They wrote:
” … for a discipline aiming to impose order on the natural world, taxonomy (the classification of complex organisms) is remarkably anarchic […] There is reasonable agreement among taxonomists that a species should represent a distinct evolutionary lineage. But there is none about how a lineage should be defined.
‘Species’ are often created or dismissed arbitrarily, according to the individual taxonomist’s adherence to one of at least 30 definitions. Crucially, there is no global oversight of taxonomic decisions — researchers can ‘split or lump’ species with no consideration of the consequences.”
Garnett and Christidis proposed that any changes to the taxonomy of complex organisms be overseen by the highest body in the global governance of biology, the International Union of Biological Sciences (IUBS), which would “restrict […] freedom of taxonomic action.”
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… critics rejected the description of taxonomy as “anarchic”. In fact, they argued there are detailed rules around the naming of species administered by groups such as the International Commission on Zoological Nomenclature and the International Code of Nomenclature for algae, fungi, and plants. For 125 years, the codes have been almost universally adopted by scientists.
So in March 2018, 183 researchers – led by Scott Thomson and Richard Pyle – wrote an animated response to the Nature article, published in PLoS Biology [PLoS is Public Library of Science; it is an open access journal].
They wrote that Garnett and Christidis’ IUBS proposal was “flawed in terms of scientific integrity […] but is also untenable in practice”. They argued:
“Through taxonomic research, our understanding of biodiversity and classifications of living organisms will continue to progress. Any system that restricts such progress runs counter to basic scientific principles, which rely on peer review and subsequent acceptance or rejection by the community, rather than third-party regulation.”
In a separate paper, another group of taxonomists accused Garnett and Christidis of trying to suppress freedom of scientific thought, likening them to Stalin’s science advisor Trofim Lysenko.
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The various parties did come together,
We hope by 2030, a scientific debate that began with claims of anarchy might lead to a clear governance system – and finally, the world’s first endorsed global list of species.
Understanding the concept of zero—I still remember climbing that mountain, so to speak. It took the teacher quite a while to convince me that representing ‘nothing’ as a zero was worthwhile. In fact, it took the combined efforts of both my parents and the teacher to convince me to use zeroes as I was prepared to go without. The battle is long since over and I have learned to embrace zero.
I don’t think bees have to be convinced but they too may have a concept of zero. More about that later, here’s the latest abut bees and math from an October 10, 2019 news item on phys.org,
Start thinking about numbers and they can become large very quickly. The diameter of the universe is about 8.8×1023 km and the largest known number—googolplex, 1010100—outranks it enormously. Although that colossal concept was dreamt up by brilliant mathematicians, we’re still pretty limited when it comes to assessing quantities at a glance. ‘Humans have a threshold limit for instantly processing one to four elements accurately’, says Adrian Dyer from RMIT University, Australia; and it seems that we are not alone. Scarlett Howard from RMIT and the Université de Toulouse, France, explains that guppies, angelfish and even honeybees are capable of distinguishing between quantities of three and four, although the trusty insects come unstuck at finer differences; they fail to differentiate between four and five, which made her wonder. According to Howard, honeybees are quite accomplished mathematicians. ‘Recently, honeybees were shown to learn the rules of “less than” and “greater than” and apply these rules to evaluate numbers from zero to six’, she says. Maybe numeracy wasn’t the bees’ problem; was it how the question was posed? The duo publishes their discovery that bees can discriminate between four and five if the training procedure is correct in Journal of Experimental Biology.
Dyer explains that when animals are trained to distinguish between colours and objects, some training procedures simply reward the animals when they make the correct decision. In the case of the honeybees that could distinguish three from four, they received a sip of super-sweet sugar water when they made the correct selection but just a taste of plain water when they got it wrong. However, Dyer, Howard and colleagues Aurore Avarguès-Weber, Jair Garcia and Andrew Greentree knew there was an alternative strategy. This time, the bees would be given a bitter-tasting sip of quinine-flavoured water when they got the answer wrong. Would the unpleasant flavour help the honeybees to focus better and improve their maths?
‘[The] honeybees were very cooperative, especially when I was providing sugar rewards’, says Howard, who moved to France each April to take advantage the northern summer during the Australian winter, when bees are dormant. Training the bees to enter a Y-shaped maze, Howard presented the insects with a choice; a card featuring four shapes in one arm and a card featuring a different number of shapes (ranging from one to 10) in the other. During the first series of training sessions, Howard rewarded the bees with a sugary sip when they alighted correctly before the card with four shapes, in contrast to a sip of water when they selected the wrong card. However, when Howard trained a second set of bees she reproved them with a bitter-tasting sip of quinine when they chose incorrectly, rewarding the insects with sugar when they selected the card with four shapes. Once the bees had learned to pick out the card with four shapes, Howard tested whether they could distinguish the card with four shapes when offered a choice between it and cards with eight, seven, six or – the most challenging comparison – five shapes.
Not surprisingly, the bees that had only been rewarded during training struggled; they couldn’t even differentiate between four and eight shapes. However, when Howard tested the honeybees that had been trained more rigorously – receiving a quinine reprimand – their performance was considerably better, consistently picking the card with four shapes when offered a choice between it and cards with seven or eight shapes. Even more impressively, the bees succeeded when offered the more subtle choice between four and five shapes.
So, it seems that honeybees are better mathematicians than had been credited. Unlocking their ability was simply a matter of asking the question in the right way and Howard is now keen to find out just how far counting bees can go.
I’ll get to the link to and citation for the paper in a minute but first, I found more about bees and math (including zero) in this February 7, 2019 article by Jason Daley for The Smithsonian (Note: Links have been removed),
Bees are impressive creatures, powering entire ecosystems via pollination and making sweet honey at the same time, one of the most incredible substances in nature. But it turns out the little striped insects are also quite clever. A new study suggests that, despite having tiny brains, bees understand the mathematical concepts of addition and subtraction.
To test the numeracy of the arthropods, researchers set up unique Y-shaped math mazes for the bees to navigate, according to Nicola Davis at the The Guardian. Because the insects can’t read, and schooling them to recognize abstract symbols like plus and minus signs would be incredibly difficult, the researchers used color to indicate addition or subtraction. …
Fourteen bees spent between four and seven hours completing 100 trips through the mazes during training exercises with the shapes and numbers chosen at random. All of the bees appeared to learn the concept. Then, the bees were tested 10 times each using two addition and two subtraction scenarios that had not been part of the training runs. The little buzzers got the correct answer between 64 and 72 percent of the time, better than would be expected by chance.
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Last year, the same team of researchers published a paper suggesting that bees could understand the concept of zero, which puts them in an elite club of mathematically-minded animals that, at a minimum, have the ability to perceive higher and lower numbers in different groups. Animals with this ability include frogs, lions, spiders, crows, chicken chicks, some fish and other species. And these are not the only higher-level skills that bees appear to possess. A 2010 study that Dyer [Adrian Dyer of RMIT University in Australia] also participated in suggests that bees can remember human faces using the same mechanisms as people. Bees also use a complex type of movement called the waggle dance to communicate geographical information to one other, another sophisticated ability packed into a brain the size of a sesame seed.
If researchers could figure out how bees perform so many complicated tasks with such a limited number of neurons, the research could have implications for both biology and technology, such as machine learning. …
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Then again, maybe the honey makers are getting more credit than they deserve. Clint Perry, who studies invertebrate intelligence at the Bee Sensory and Behavioral Ecology Lab at Queen Mary University of London tells George Dvorsky at Gizmodo that he’s not convinced by the research, and he had similar qualms about the study that suggested bees can understand the concept of zero. He says the bees may not be adding and subtracting, but rather are simply looking for an image that most closely matches the initial one they see, associating it with the sugar reward. …
If you have the time and the interest, definitely check out Daley’s article.
Here’s a link to and a citation for the latest paper about honeybees and math,
I’ve already written about October 2019 science and art/science events in Canada (see my Sept. 26, 2019 posting), but more event notices for Octoberhave come my way. These events are all art/science (or sciart as it’s sometimes called).
… on the future of life forms … a two-night (Oct./Nov.) discussion in Toronto, Canada
Here’s more from the ArtSci Salon’s October 3, 2019 announcement (received via email)
“…now they were perfecting a pigoon that could grow five or six kidneys at a time. Such a host animal could be reaped of its extra kidneys; then, rather than being destroyed, it could keep on living and grow more organs, much as a lobster could grow another claw to replace a missing one. That would be less wasteful, as it took a lot of food and care to grow a pigoon. A great deal of investment money had gone into OrganInc Farms…” (Margaret Atwood – Oryx & Crake 2003)
In Oryx and Crake Margaret Atwood describes a not-too-distant future where humans have perfected the art of fabricating and modifying a variety of creatures to improve and prolongue their own lives and wellbeing.
As Atwood has stated in various occasions, this is not science fiction.
It is in fact already happening. New forms of life appear not only as the product of lab fabrication or gene editing, but also as the result of toxic pollutants and climate change induced adaptation.
what to make of them?
how to cope with a world where extinction, adaptation and mutation risk to make traditional categories and taxonomies obsolete?
or not?
Join us to this two-parts series to discuss the ethics and implications of these transformations with artists, scientists and bioethicists.
this is a “double date”! Please, note the two dates please, RSVP here https://bit.ly/2AH1Pe8
Part 1 Thursday, October 17, 6:00-8:00 pm The Fields Institute for Research in Mathematical Sciences
Altered Inheritance: extinction, recreation or transformation? a dialogue and discussion on the implications of genome editing on humans and other organisms
with Francoise Baylis – Research Professor, Bioethicist, Dalhousie University
Karen Maxwell – Dept. of Biochemistry, Maxwell Lab, University of Toronto
emergent artists from OCADU [Ontario College of Art and Design University] and YorkU [York University, Toronto]
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Part 2 Thursday, November 21, 6:00-8:00 pm The Fields Institute for Research in Mathematical Sciences
Classifying the new? why do we classify? what is it good for? what is the limit of taxonomy and classification in a transforming world?
with Richard Pell – Centre for PostNatural History, Pittsburgh, PA
Laurence Packer – Mellitologist, Professor of biology and environmental studies, York University
Stefan Herda – earth science artist
Cole Swanson – artist and educator (Art Foundation and Visual and Digital Arts, Humber college)
Anna Marie O’Brien – Frederickson, Rochman, and Sinton labs, University of Toronto
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BIOS
Françoise Baylis is University Research Professor at Dalhousie University. She is a member of the Order of Canada and the Order of Nova Scotia, as well as a fellow of the Royal Society of Canada and of the Canadian Academy of Health Sciences. Baylis was one of the organizers of, and a key participant in, the 2015 International Summit on Human Gene Editing. She is a member of the WHO expert advisory committee on Developing Global Standards for Governance and Oversight of Human Genome Editing. Her new book “Altered Inheritance. CRISPR and the Ethics of Human Genome Editing” is published by Harvard University Press
Karen Maxwell is a research professor in the dept of biochemistry at the university of toronto, where she runs the Maxwell Lab. Among other topics, the lab’s three branches “Anti-CRISPR”, “Phage morons” and “Anti-Phage defences” study the interplay of phages with their bacterial hosts, with a focus on phage mediated bacterial virulence mechanisms and inhibitors of anti-phage bacterial defenses.
Richard Pell works at the intersections of science, engineering, and culture. He has worked in a variety of electronic media from documentary video to robotics to bioart to museum exhibition. He is the founder and director of the Center for PostNatural History (CPNH), an organization dedicated to the collection and exposition of life-forms that have been intentionally and heritably altered through domestication, selective breeding, tissue culture or genetic engineering. The CPNH operates a permanent museum in Pittsburgh, Pennsylvania, and produces traveling exhibitions that have appeared in science and art museums throughout Europe and the United States, including being the subject of a major exhibition at the Wellcome Collection in London.
Laurence Packer is a mellitologist, ie a scholar whose main subject of study is wild bees. his research primarily involves the systematics of the bee subfamily Xeromelissinae – an obscure, but fascinating group of bees, restricted to the New World south of central Mexico. he has also expended considerable energy leading the global campaign to barcode the bees of the world. his work is concerned with promulgating the importance of bees: for genetic reasons, it seems that bees are more extinction prone than are almost all other organisms
Stefan Herda‘s practice explores our troubling relationship to the natural world through drawing, sculpture and video. Inspired by the earth sciences, Herda’s work navigates the space between truth and fiction. His material and process-based investigations fuse elements of authenticity, façade, the natural and the manufactured together. He received his BAH from the University of Guelph in 2010. His work in both sculpture and video has been included in exhibitions nationally and has been featured by CBC Arts and Daily VICE. Recently, Stefan has held solo shows at Patel Projects (Toronto) and Wil Kucey Gallery (Toronto), participated in group shows such as Cultivars: Possible Worlds at InterAccess (Toronto) and was featured as one of 12 artists in the Cabinet Project at the University of Toronto
Cole Swanson is an artist and educator based in Toronto, Canada. He has exhibited in solo and group exhibitions across Canada and throughout international venues in North America, South America, Europe, and Asia. At the heart of recent work is a cross-disciplinary exploration of materials and their sociocultural and biological histories. Embedded within art media and commonplace resources are complex relations between nature and culture, humans and other agents, consumers and the consumed. Swanson has engaged in a broad material practice using sound, installation, painting, and sculpture to explore interspecies relationships.
Anna Marie O’Brien is a post doc in the Frederickson, Rochman, and Sinton labs at University of Toronto, working on duckweeds, microbes, urban contaminants, and phenotypes.her PhD work was at Davis, with thesis advisors Dr. Jeffrey Ross-Ibarra and Dr. Sharon Strauss. she also collaborated closely with Dr. Ruairidh Sawers at LANGEBIO-CINVESTAV in Guanajuato, Mexico.
The first highlighted speaker, Françoise Baylis, has been mentioned here twice before, in a May 17, 2019 posting (scroll down to the ‘Global plea for moratorium on heritable genome editing’ subheading) and in an April 26, 2019 posting (scroll down to the ‘Finally’ subheading, the second paragraph). Both postings touch on the topic of CRISPR (clustered regularly interspaced short palindromic repeats) and germline editing (genetic editing that will affect all of your descendents).
Cartooney in New Westminster (near Vancouver, Canada) starting October 18, 2019
I like physics but I love cartoons Stephen Hawking
There you have it from one of the 20th/early 21st century’s most famous physicists. The quote is the opening line for the New Westminster (near Vancouver, Canada) New Media Gallery’s latest event webpage, Cartooney,
The impact of animated cartoons has been profound. In the early 20th century, we began exploiting the possibilities of the animated frame. The seven artists in this exhibition don’t create cartoons, they deconstruct those that already exist; from Looney Tunes, to The Simpsons to Charlie Brown. They exploit this potent material to reveal the inner and outer workings of our human world. The original cartoon is ever-present, haunting us with suggestive content.
The artists in this exhibition reframe our world. Here we are asked to consider the laws, systems and iconographies of the cartoon world while drawing parallels with our human world; physical laws, the laws of gravitation, matter + light, the physics of motion, and societal psychologies & behaviours. We are presented with fascinating catalogues and overlaying systems of symbolic language. The purposeful demolition of expectation in these works, mirrors the instabilities and dreams of modern life. They remind us that the pervasive medium of the cartoon can reflect and influence how we navigate the world. If there is a paradox here, it might be that dismantling a cartoon can throw open the doors of perception.
Artist Andy Holden becomes a cartoon avatar in Laws of Motion in a Cartoon Landscape.
Photograph By contributed [downloaded from https://www.newwestrecord.ca/entertainment/what-can-cartoons-tell-us-about-the-state-of-the-universe-find-out-in-new-west-1.23969740]
An Oct. 7, 2019 article in the New Westminster Record provides a few more details about the show,
The New Westminster New Media Gallery’s next exhibition is exploring the impact of animated cartoons.
Cartooney opens at the gallery on Friday, Oct. 18 and runs until Dec. 8 [2019], then again from Jan. 7 to Feb. 2 [2020].
Artist Kevin McCoy, one-half of the duo of Jennifer and Kevin McCoy, will be on hand for an artist talk on opening night, Friday, Oct. 18. The talk will run from 6:30 to 7:30 p.m., with a reception and open exhibition from 7:30 to 9 p.m.
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Laws of Motion in a Cartoon Landscape, by Andy Holden (U.K.):
In his two-channel audiovisual installation, 57 minutes long, Holden becomes a cartoon avatar, giving both a lecture on cartoons and a cartoon lecture, describing how our world is best now understood as a cartoon. The project incorporates Greek philosophy, Stephen Hawking, critical theory, physics, art, the financial crisis and Donald Trump, while adapting 10 laws of cartoon physics to create a theory of the world and a prophetic glimpse of the world we live in.
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CB-MMXVIII (I’ve been thinking of giving sleeping lessons), by Patten (U.K.):
In this multi-screen audiovisual installation, the artist duo Patten subjects Charlie Brown to all the digital stresses, distortions and manipulations available in 2018, testing his plasticity.
“Sampled texts from philosophy, science and critical theory criss-cross the screens and are linked with scrolling images related to the natural world, DNA, systems, multiples; all serving to influence our reading of the cartoon character and the texts,” says the release. The ambient soundtrack is a dramatically slowed down Linus and Lucy theme.
You can find the New Westminster New Media Gallery on the third floor at the Anvil Centre, 777 Columbia St. See www.newmediagallery.ca for more details.
Collisions Festival: Invasive Systems in Vancouver, November 2019
Curiosity Collider, a Vancouver-based not-for-profit organization, will be hosting its inaugural art-science Collisions Festival: Invasive Systems at the VIVO Media Arts Centre from November 8 to 10, 2019. The festival features an art-science exhibition showcasing independent works and collaborative works by artist/scientist pairs, a hands-on DNA sonification workshop, an opening reception with performances, and guided discussions and tours.
Curated by Curiosity Collider’s Creative Director Char Hoyt, the theme of the festival focuses on the “invasive systems” that surround us – from technology and infections, to pollution and invasive species. “We want to create a space to explore the influence of the invasive aspects of our world on our inner and outer lives” said Char. “We will examine our observations from both scientific and artistic perspectives- are these influences beneficial, inevitable, or preventable?” Attendees can anticipate a deep dive into the delicate and complicated nature of how both living and inanimate things redefine our lives and environments – through visual art, multimedia installations, and interactive experiences.
“I am not a scientist and do not come from a family of scientists, but I have always appreciated knowing how things work, how things are connected and how things evolve – collaboration between art and science feel natural to me,” said Vancouver artist Dzee Lousie. “Both artists and scientists are curious, perform experiments and are driven by questions.” Dzee’s work Crossing, an interactive puzzle painting that examines how microbial colonies can impact our behaviours and processes in our body, is the result of a collaboration with UBC PhD candidate Linda Horianopoulos. “As scientists, we often want people to take notice of our work and engage with it. I think that art attracts people to do exactly that,” said Linda.
The sculptural work Invasion by Prince George artist Twyla Exner explores the remnants of technology. “My artworks propose hybrids of technological structures and living organisms. They take form as abandoned technologies that have sprouted with new life, clever artificialities that imitate nature, or biotechnological fixtures of the not-so-distant future,” Twyla shared. Like Dzee, she feels that artists and scientists share the sense of curiosity, experimentation, and creative problem solving. “Both art and science have the ability to tell stories and shape how people see and interpret the world around them.”
The festival is hosted in collaboration with the VIVO Media Arts Centre (2625 Kaslo Street, Vancouver, BC V5M 3G9). It will open on the evening of November 8th, with a reception and a live performance by local sound artist Edzi’u, during which her sculptural installation Moose are Life will be brought to life. On Saturday, artist Laara Cerman will co-host a DNA sonification workshop with scientist Scott Pownall. Their work Flora’s Song No. 1 in C Major – a hand-cranked music box that plays a tune created from the DNA of local invasive plants – will be on exhibit during the festival. The festival will also include tours by the curator at 3:30pm and guided discussions at 4pm on both Saturday and Sunday. Visit https://collisionsfestival2019.eventbrite.ca for festival tickets and http://bit.ly/collisionsfestival2019 for festival information.
Other participating artists and collaborating scientists include: Christian Dahlberg (Photography/ Painting / New Media Artist), Chris Dunnett (Multidisciplinary Artist), Garth Covernton (PhD Candidate, University of Victoria), Joanne Hastie (Artist / Mechanical Engineer), Kathryn Wadel (Interdisciplinary Mixed Media Artist), and Katrina Vera Wong (Artist / Writer / Editor).
Curiosity Collider and VIVO Media Arts Centre gratefully acknowledge the support of BC Arts Council, Canada Council for the Arts, City of Vancouver, Metro Vancouver Regional Cultural Project Grants Program, UBC Faculty of Science, and our printing sponsor Jukebox, for making Collisions Festival: Invasive Systems possible.
About Curiosity Collider Art-Science Foundation
Curiosity Collider Art-Science Foundation is a Vancouver based non-profit organization that is committed to providing opportunities for artists whose work expresses scientific concepts and scientists who collaborate with artists. We challenge the perception and experience of science in our culture, break down the walls between art and science, and engage our growing community to bringing life to the concepts that describe our world.
Are you curious about data sonification? Wondering how music theory and DNA sequences could converge to create a work of art and science? Join us to explore more!
In this DNA sonification workshop, participants will learn the process of DNA barcoding of invasive plant species, and how to sonify DNA sequences with basic music theory and MIDI freeware. Participants will also get hands-on experience in amplying specific genetic regions in plants through polymerase chain reaction (PCR), a step necessary in preparing samples for DNA barcoding.
This workshop will be led by artist Laara Cerman and scientist Scott Pownall, whose art-science collaborative work “Flora’s Song No. 1 in C Major” will be on exhibit during Collisions Festival: Invasive Systems. Laara and Scott will also share their process of working together, and how decisions were made to arrive at their collaborative work of art and science.
We acknowledge that Collisions Festival and its events take place on the traditional, ancestral, unceded territories of the xwməθkwəy̓əm (Musqueam), Skwxwú7mesh (Squamish), Stó:lō and Səl̓ílwətaʔ/Selilwitulh (Tsleil- Waututh) Nations. We are grateful for the opportunity to live and work on this land.
I asked the Curiosity Collider folks (@CCollider on Twitter) if you needed to bring any equipment or have any knowledge of music. The answer was: no, you don’t need to bring anything (unless you want to) and you don’t need to know about music.
Uncorked at Science World at TELUS World of Science in Vancouver on November 14, 2019
This is not a cheap night out. An October 10, 2019 article by Lindsay William-Ross for the Daily Hive website gives you reasons to go anyway (Note: Links have been removed),
A new wine-themed event will have Vancouverites swirling with nerdy glee. Uncorked: A Celebration of the Science of Wine is an evening of sipping and learning that will bring together world-renown winemakers, chefs, and science experts for an unforgettable event.
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Participating wineries are:
Mission Hill Family Estate CedarCreek Estate Winery CheckMate Artisanal Winery Martin’s Lane Winery Road 13 Vineyards
The wines will be paired with bites from Chef Patrick Gayler from Mission Hill’s Terrace Restaurant and Chef Neil Taylor from CedarCreek’s new Home Block Restaurant.
Programming for the evening includes seminars on the science of blending wine, the science of aging wine, the role of technology at modern vineyards, and the science of soil and terroir.
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Proceeds from Uncorked will support Science World’s On the Road program, which last year brought live science performances to 41,500 students throughout B.C. who otherwise might not have had a chance to visit TELUS World of Science.
Tickets are $89 and can be purchased here. You may also want to reserve some money for the silent auction. Don’t forget, it’s November 14, 2019 from 7 pm to 10 pm at Science World in Vancouver. You can find directions and a map here.
… 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.
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. …
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 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 TechSample 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.
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.
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.
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.”
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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
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?
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.
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.
