Open Science

Open Bio Workshops: Report from Dhaka, Bangladesh

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by Alex Yang, Sihinta Shembil & Adeline Seah

It’s Citizen Science, Baby!

Science isn’t the personal dominion of boffins in lab coats shaking Erlenmeyer flasks. Loads of people get involved with science. Science is about methods and mathematics and many other things. But, it begins with a thought, a hypothesis, observation, and the collection of each careful minute observation into the usefulness of organised data.

This might start in the lab if you’re intent on scrutinising the playful bumping around of molecules under the microscope. Or, it might be amateur birders noting the first arrival of the season of an elegant migratory bird, astronomers noting a hitherto unnamed speck in the vast canvas of the sky, or even volunteers washing and documenting broken old, very, very, very old pots in the archaeology lab.

You might be a schoolkid, homemaker, plumber, accountant, cyclist, or that government bureaucrat nobody likes. It doesn’t matter. Everyone can get involved. It’s not called citizen science for nothing. Are you a citizen? Yes? It’s your science!

Just as science has biology, citizen science has DIY bio, which, let’s be honest, sounds like a terribly awkward name. It also flies by another name: biohacking. That’s kind of scary, isn’t it? But it’s really just regular ol’ science! We don’t want to be stopped and interrogated by the authorities everywhere we go, so, let’s call it something nice.

So… (apologies to our dearest DIY bio friends), we’ll call it open bio in this article! (I swear to anything sacred, it’s Adeline’s idea)* And, it happens all over the world.

* yes it’s me, DIY Bio is a horrible term, Open refers to a lot more: open source, access, inclusion, diversity, open to new ideas, possibilities etc.. ~Adeline

 

Open Bio in Dhaka, Bangladesh

Citizen science and open bio are open to all and sundry, for sure. However, nobody does awesome work without some knowledge, right? Science must begin with education.

Originally intending to go to Bangladesh to see wildlife, Adeline ended up spending a wonderful week in Dhaka with the Tech Academy (Thank you, Marc!). The Hackteria connection to Shams Jaber led to Open bio workshops and discussions in Dhaka early this year, with the aim of sharing about tools and resources to “take” biology education and research out of academic institutions, and of course, to do the usual spiel about wildlife and using bio for good e.g. investigating pollution, conservation etc.

At BRAC talking about Biohacking, Citizen Science and Biodiversity research and conservation
Bringing Computer Science and Life Science students together for a hands on workshop at IUB,

Sihinta (now with the newly formed Biobot group) reports with such wonderful gusto that it’s best read unedited:

As a lover of biology and a dedicated student in biotechnology, I truly respected the key point of the “Bio-hacking” workshops: the importance of reaching out to the public about what we know in science, also known as citizen science. Open Bio gives a platform where people of varying ages, different educational backgrounds and diverse goals come together and learn with one another. It’s a fun and interactive way of learning, and meeting new people.

The Open Bio workshops in Dhaka consisted of teachers, students and children as young as four. The main activity with the kids was isolating DNA from strawberries. We all mashed strawberries, while sneakily eating a few, and mixed it with drops of detergent and alcohol to collect some long stringy white clumps, the DNA!

Promon Khan, researcher at BRAC University, guided the children with DNA extraction. His experience with bio-hacking was fruitful and enjoyable, and he mentioned “young minds never fail to surprise me when I see them learning something no matter if that’s a rhyme or DNA extraction!”

Shahreena Rahman, biotechnology student at North South University and high-school teacher, will apply what she learned in a few hours of the workshop to her teaching techniques: “I’m looking forward to showing my students what I do in my high-tech labs by using these bio hacks in my classroom. Thanks to Adeline Seah and The Tech Academy, now more people outside of labs can carry on with their experiments to satisfy their curious minds.”

Sheikh Saqif Ahmed, president of BRAC University Natural Science Club, anchored the Bio-Hacking workshop held at BRAC University. In regards to his experience he mentioned “I did have fun and learned a lot about citizen science and the importance of availability of science to the general public. We were also introduced to kids who are eligible in coding and making electronic gadgets.”

As for me, the two workshops I attended left me with a new goal: to gain the ability to break down intricate bio-knowledge filled with jargon and clearly communicate it with people in an easy and entertaining manner.

I believe Bangladesh is filled with bright minds who are willing to work ardently for their education and career. Open Bio and citizen science can utilize the potential of the youth, and it’s a perfect introduction to science for many. For this reason, The Tech Academy and BRAC University Natural Science Club are already planning to form a six month introductory biology curriculum for children and beginners. In the near future, they also wish to commence research projects where children can directly participate.

Thanks to the Open Bio workshops held in Dhaka, new paths towards science are being paved.

 

Last day in Dhaka, Feb 11, just happened to be the UN International Day of Women a& Girls in Science, so some of us met up at Jatra Biroti again to hang out, talk science & Open Bio in Bangladesh!

 

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Taxonomic Vandals aren’t Scientists

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A Few Bad Scientists are Threatening to Topple Taxonomy by Benjamin Jones from the Smithsonian.com:

“The goal of taxonomic vandalism is often self-aggrandizement. Even in such an unglamorous field, there is prestige and reward—and with them, the temptation to misbehave. “If you name a new species, there’s some notoriety to it,” Thomson says. “You get these people that decide that they just want to name everything, so they can go down in history as having named hundreds and hundreds of species.”

Taxonomic vandalism isn’t a new problem. “Decisions about how to partition life are as much a concern of politics and ethics as of biology,” two Australian biologists wrote in a June editorial in the journal Nature on how taxonomy’s lack of oversight threatens conservation. They argued that the field needs a new system, by which the rules that govern species names are legally enforceable: “We contend that the scientific community’s failure to govern taxonomy … damages the credibility of science and is expensive to society.”

How does this happen?

The rules for naming a new animal taxon are governed by the ICZN, while the International Association for Plant Taxonomy (IAPT) governs plants. And while the ICZN requires that names be published, as defined by the commission’s official Code, “publishing” doesn’t actually require peer-review.

That definition leaves room for what few would call science: self-publishing. “You can print something in your basement and publish it and everyone in the world that follows the Code is bound to accept whatever it is you published, regardless of how you did so,” Doug Yanega, a Commissioner at the ICZN, told me. “No other field of science, other than taxonomy, is subject to allowing people to self-publish.”

Thomson agrees. “It’s just become too easy to publish,” he says.

Why not? When the Code was written, the technologies that allow for self-publishing simply didn’t exist. “The Code isn’t written under the assumption that people would deliberately try to deceive others,” Yanega says. But then came the advance of desktop computing and printing, and with it, the potential for deception.

Moreover, the ICZN has no actual legal recourse against those who generate names using illegitimate or unethical science. That’s because the Code, which was last updated in 1999, was written to maintain academic freedom, Yanega says. As the Code reads: “nomenclatural rules are tools that are designed to provide the maximum stability compatible with taxonomic freedom.”

Who cares?

.”..most branches of taxonomy aren’t impacted as heavily as herpetology, where many prominent vandals operate. That’s because herpetology is home to thousands of undescribed species, so there’s plenty of low hanging fruit for vandals to pick. Moreover, “herpetology maybe does attract more interesting characters than other branches of science,” says Wüster. “Reptiles are kind of pariahs of the animal world”—as are some of the people who study them, it would appear.”

 

Why should you care?

If you want to protect wildlife: “Confusion created by parallel nomenclature complicates any process that depends on unambiguous species names, such as assigning conservation statuses like “Endangered” or “Threatened.” As the authors write in the Nature editorial, how a species is classified by taxonomists influences how threatened it appears, and thus how much conservation funding it’s likely to receive. As the authors of the editorial write: “Vagueness is not compatible with conservation.”

But in particular:

“Imagine, if you will, getting bit by an African spitting cobra. These reptiles are bad news for several reasons: First, they spit, shooting a potent cocktail of nerve toxins directly into their victims’ eyes. But they also chomp down, using their fangs to deliver a nasty bite that can lead to respiratory failure, paralysis, and occasionally even death.

Before you go rushing to the hospital in search of antivenin, you’re going to want to look up exactly what kind of snake you’re dealing with. But the results are confusing. According to the official record of species names, governed by the International Commission of Zoological Nomenclature (ICZN), the snake belongs to the genus Spracklandus. What you don’t know is that almost no taxonomists use that name. Instead, most researchers use the unofficial name that pops up in Wikipedia and most scientific journal articles: Afronaja.

This might sound like semantics. But for you, it could mean the difference between life and death. “If you walk in [to the hospital] and say the snake that bit you is called Spracklandus, you might not get the right antivenin,” says Scott Thomson, a herpetologist and taxonomist at Brazil’s Museum of Zoology at the University of São Paulo. After all, “the doctor is not a herpetologist … he’s a medical person trying to save your life.”

Taxonomic vandalism can have disastrous consequences for wildlife conservation—but it could also impact human health. Shown here, an African spitting cobra poised to strike. (Greatstock / Alamy)

What does this have to do with Open Science?

Open Science / citizen science is meant to encourage individuals everywhere to learn about science, be part of scientific research, and share their results freely. Taxonomy vandals are not scientists and shouldn’t be seen as citizen scientists; their self-publications that aren’t peer reviewed do not promote critical thinking and furthering our understanding of the world.

Microbial March for the Free Movement of Cultures – Thurs 9 March @ ArtScience Museum

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“Microbial March” is a living fermentation lab that invites everyone to come and learn about the art and science of food fermentation and to reconnect with their bodies and their environment through microbes.

Fermentation – a metabolic process that converts sugar to acids, gases, and alcohols by using microbial cultures (so-called “fermentation starter cultures”) – has been known as a traditional food making technique since the Neolithic Age.

After a short introductory talk about microbes + fermentation and their social, environmental, and health impacts, lab visitors will be invited to engage in a collaborative hands-on making of various cultured foods and drinks.

Everyone is welcomed to bring and share fermentation ingredients, starter cultures, as well as traditional fermentation wisdom and recipes known in their country, neighborhood or family. Along with the exchange of various cultures, both in the literal and metaphorical sense, we will discuss various fermentation-related issues as well as the globally growing inter-cultural tensions.
The event is co-organized by the FabCafe Singapore, The Singapore Eco Film Festival and the Fermentation GutHub group.

Time: 730 to 930 pm

Venue: ArtScience Museum

Program:

#1 Fermented Discussion & Speculation
Introduced by Adeline Seah (The Singapore Eco Film Festival), Markéta Dolejšová (Fermentation GutHub) & Philip Johns (Yale-NUS College)

#2 (Starter) Culture Exchange
There will be milk kefir grains from New Zealand; various yeasts from USA; kombucha SCOBYs from Singapore; and some random surprise starters + everyone is invited to bring samples of fermentation cultures, foods, drinks, recipes, ideas etc.

#3 Make Your Own Jar (Hands-on Workshop)
Collaborative hands-on fermentation: Basic vegetable pickling + yogurt & milk kefir making + kombucha brewing etc.

We will experiment with different teas and sugar levels (kombucha), salt ratios (veggies), additional ingredients (e.g. mango in kefir). The finished jars can stay in Fab Café to sit and ferment (there will be a follow-up tasting session in 2 weeks – exact date TBC). Everyone is also welcomed to bring her/his jars home of course!

#4. Fermented Dancefloor & Late Night Fermentation Vibes (**Free Movement of Cultures**)
Playlist under construction -> add your ideas here: http://bit.ly/2lYI0cT

Entry is free —> BYOjars, foods, cultures, and other friends

 

For more info and updates: https://www.facebook.com/events/1275463755881579/

 

500womenscientists: Working to Empower Women in Science

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One of the newest organizations we’re excited about, the mission of 500 Women Scientists
is to promote a diverse and inclusive scientific community that brings progressive science-based solutions to local and global challenges.

What we love especially are their values, many that we share. We list theirs here and are working on ours (coming soon!):

  • Recognizing that science touches the lives of every person on this planet;
  • Advocating for a strong role of science in society;
  • Identifying and acknowledging structural inequities and biases in science;
  • Pushing for equality and standing up to inequality, discrimination, and aggression;
  • Pushing to develop and strengthen access for traditionally underrepresented groups to fully participate in and become leaders in science;
  • Supporting the education and careers of all scientists;
  • Enhancing scientific mentorship and encouraging an atmosphere of collaboration;
  • Stepping outside of our research disciplines to communicate our science and engage with the public;
  • Using the language and wonder of science to bridge the divides that separate societies and to enhance global diplomacy.

Check out the interview with Maryam Zaringhalam, a molecular biologist who describes herself as “floating at the intersection of art x science x society x advocacy x STEMinism”. She talks about her various interests and activities, and her insights as an Iranian-American on the recent travel ban. Great read!

 

Join in Panthera’s New Project to Protect Big Cats Around the World

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From the Zooniverse folks:

Just launched, Camera CATalogue is a new website from Zooniverse and Panthera that allows citizen scientists like you to protect big cats by simply looking at and identifying photos of wildlife!

Panthera works in 50 countries around the globe to protect big cats and their vast landscapes. Motion-activated camera traps are used to count cats and their prey species, identify where they live, and determine how conservation efforts are helping to protect these animals.

These cameras produce thousands of images of fascinating animals, from the iconic leopard and rhino to the lesser-known aardwolf and civet. While certainly high-tech, these cameras do not distinguish between animal species. That is why we need your help to identify the big cats and other wildlife in these photos.

Log onto the Camera CATalogue now and help identify the amazing wildlife in these camera trap images. It’s a fun way to spend a few minutes (or a few hours), test and improve your animal knowledge (who knew what a gemsbok was?!) and support efforts to better protect leopards, other wildlife and their landscapes…without ever leaving your chair!

 

 

Citizen Science @ Bern

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Some familiar faces from Europe, cool “meeting” Hackteria friends 🙂

biodesign for the real world

What is biohacking?

Hackteria members were invited to the Swiss Citizen Science Network’s meeting “Biohacking meets Citizen Science” in Bern at Dialog Science and Society (Stiftung Science et Cité).

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bern 1

In the style of hackteria workshops, we started the morning hands-on.We set up the room as a temporary/mobile open source DIY bio-lab. During the round of self-introductions, we assembled gel-trays for electrophoresis. People were mainly from the German speaking parts of Switzerland, and Geneva’s Bioscope was represented – with educators, artists, biotechnologists, geologist, botanist…history of science – it was a nice atmosphere.

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To use some of the generic lab equipment, we decided to extract some DNA from the participants and run a genomic PCR on the serotonin transporter. This was inspired by some protocols from the Science Bar Incubator in Tokyo.

Also, genotyping ourselves is a great starting point for a range of discussions on gene <> phenotype  (can we tell…

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