Easy enough for kids and amateur scientists to use, you might say DNA barcoding is inherently democratic.
In 2008, I happened to see an intriguing news story about two New York City high school girls who had used a new DNA-based identification method to determine if their neighborhood sushi restaurants were selling mislabeled fish. That was my first encounter with the technique known as DNA barcoding. Since then, I have helped hundreds of amateur scientists use barcoding to question the identity of everything from 'heirloom' oranges to 'beef' meatballs to the diversity of Alaskan plants.
The idea of identifying species through a very short genetic sequence, rather like the manner in which a supermarket barcode identifies products, was first proposed in a 2003 paper by Dr. Paul Hebert, a researcher at the University of Guelph in Ontario, Canada. The beauty of barcoding is that even non-specialists can obtain barcodes from tiny amounts of tissue and conclusively identify a species. Compare this to standard taxonomic identification, which requires intact specimens (often impossible in situations where you want to know the identity of foodstuffs) and an expert able to distinguish subtle anatomical differences between closely-related species using morphological features like the shape and color of the organism's parts. As The New York Times put it in their article about the abovementioned 'SushiGate' kids:
"What may be most impressive about the experiment is the ease with which the students accomplished it. Although the testing technique is at the forefront of research, the fact that anyone can take advantage of it by sending samples off to a laboratory meant the kind of investigative tools once restricted to Ph.D.'s and crime labs can move into the hands of curious diners and amateur scientists everywhere."
Readers of GeneWatch are probably more aware than most of the astounding rate at which DNA science in general is progressing. What they may not know is that there is a growing movement to democratize the technology, to put it into the hands of the public for the greater good. Professional scientists like myself have been inspired to found open, public-serving laboratories that are accessible to anyone who wants to pursue a safe and useful project. Genspace, which I co-founded and direct, is a nonprofit community biolab located in Brooklyn, NY. We provide workspace, access to equipment, and mentorship in the biosciences. Genspace offers adult education courses, free public events such as open barcoding nights, low-cost lab space for inventors, and is a place for students to work on projects for science competitions. One of the best uses of community labs is the kind of DIY investigation that can tell you more about your environment, health, or food. Is that goat cheese made with cow's milk? Bring it in and we'll teach you to barcode it. Want to know if your soy milk is Roundup Ready? We can teach you to determine that too, it's an even simpler protocol than barcoding. We want everyone to become more literate in the biosciences in order to join the discussion about them from a position of knowledge as opposed to forming opinions based on ignorance and fear. And I strongly feel that the best way to learn is hands-on in the lab.
Barcoding is a regular activity at Genspace. It's a great way for amateurs to participate in real science. Although the DNA barcodes of most common species have been deposited into public databases, most of the millions of species on earth have not been barcoded yet. This gives the student or citizen scientist an opportunity to contribute to the growing public database of DNA barcodes. Genspace first began teaching barcoding as part of Cold Spring Harbor Laboratory's 2011-2012 Urban Barcode Project, a science competition for high school students. Genspace worked closely with their Harlem DNA Lab and acted as its satellite site in Brooklyn for teacher training and open lab hours to mentor students in barcoding, a relationship that continues today.
Our newest barcoding project focuses on the importance of identifying organisms to help monitor the biological effects of global climate change. Accelerating habitat destruction is particularly evident in the Alaskan landscape, where glaciers recede practically before our eyes and environmentalists attempt to preserve species diversity in the face of opposing economic interests. In Genspace's Alaska Barcode Project, we invite the general public to monthly open nights where we teach them to barcode plant samples collected from remote locations in interior Alaska. The goal is twofold: to create a baseline survey of plants in particular areas such as the Skolai Valley in Wrangell-St. Elias National Park, and to add new identifying barcodes to the Barcode of Life Database to empower future amateur scientists to conduct similar surveys.
Part of the DNA sequence of the chloroplast gene rbcL has been designated as one of the two barcode regions for plants (the matK gene is the other region but is not used at Genspace). Barcoding a specimen starts with extracting its DNA. You only need a small piece, the diameter of a pencil eraser, to get plenty of DNA for barcoding. In a tiny plastic tube, the sample is mixed with a few drops of a solution that disrupts the cellular structure and then ground into a paste using a little plastic pestle. The DNA is then absorbed onto silica, which is washed with salt-containing buffers until all other cellular components are gone. The clean DNA is eluted off the silica with water and the barcoding region amplified using a procedure called polymerase chain reaction (PCR). The amplification is necessary to get enough material in the tube to send out for sequencing.
PCR is a standard lab technique that has become mostly automated. Prepackaged mixtures of enzymes and reaction components such as the PCR primers that target the barcoding region can be bought cheaply in bulk. All one has to do is add a minute quantity of your DNA to the PCR mix and stick it into a preprogrammed machine. What comes out is ready to be sent off for sequencing at a fee-for-service facility doing hundreds of sequencing reactions daily. The total cost for the whole procedure can be less than $20 per sample.
Our barcoding nights have been very popular. They educate people and make them more informed about cutting-edge science. There is also a social component to the project where participants often engage in discussions about the promise and the repercussions of the technology.
It wasn't that long ago that major scientific contributions were made by curious amateurs, and science itself was less of a profession and more of a hobby. The popularity of our barcoding nights might be predictive of the resurgence of such citizen science, where a diverse cross-section of the general population are enthusiastic participants in scientific inquiry. It's empowering to be able to use the latest breakthroughs to answer questions of importance to you. I can think of no better use of my time than to continue to facilitate this empowerment through my work at Genspace. And please do stop by and barcode something if you are in the neighborhood!
Ellen Jorgensen, PhD, is co-founder and President of Genspace, where she spearheads the Urban Barcode Project and other programs. She was an invited speaker at TEDGlobal 2012. Reprinted with permission from GeneWatch (Nov/Dec. 2013), a bimonthly publication of the Council for Responsible Genetics and America's first and only magazine dedicated to monitoring biotechnology's social, ethical, and environmental consequences.
Photo by Col Ford and Natasha de Vere, licensed under Creative Commons.
Arctic Cod may hold the key to a more efficient method for storing blood.
Maintaining an adequate supply of blood has always been a challenge for hospitals. While refrigeration and freezing can provide a blood bank with reserves, the limited shelf life of blood and the additives used for preservation have made blood storage far from efficient, and reliance on new donors perpetual. But a new study conducted by scientists at the University of Warwick has demonstrated that nature might have a solution.
Summarized by Peter Dunn-Warwick for Futurity and first published in the journal Nature Communications, the study took a closer look at the antifreeze properties of fish that live in sub-freezing waters such as the arctic cod. Scientists isolated the specific proteins that prohibit freezing in fish blood, and were able to mimic the properties of those proteins in a polymer alcohol that can be added to human blood for efficient storage. Matthew Gibson of the University of Warwick summed up the multiple benefits of using polymer alcohol in freezing blood: “Firstly, it reduces the growth of ice crystals during thawing, secondly it reduces the need for organic solvents, and crucially, it reduces the time between defrosting and having transfusion-ready blood by eliminating the need to remove solvent.”
Although further testing is needed, scientists are hopeful that polymer alcohol will not only enhance blood storage techniques, but also bolster treatments for certain cancers and neurological ailments.
Photo by NOAA Photo Library, licensed under Creative Commons.
New advancements in EEG technology allow the average consumer to unleash their inner Jedi via headset.
The ability to influence objects with sheer brain power has typically been designated to the realm of science fiction, but new advancements in EEG technology allow the average consumer to gain insight into the inner workings of their mind via headset. EEG, which stands for electroencephalography, is a tool used in neuroscience to pick up patterns in the brain’s electrical activity, such as those that occur while sleeping or during epileptic seizures. EEGs have been used in hospitals to detect epilepsy and monitor the activity caused by other brain conditions, but recent efforts have been made to pair affordable EEG headsets with products such as computer programs, cell phones, toys, and video games in order to develop mental control and relaxation. Many of these products are being offered within an open source model, allowing users to further develop and experiment with EEG technology at home.
Amy Standen of KQED Science reports that NeuroSky’s MindWave Mobile EEG headset costs only around $100 and is powered by a single AAA battery. Paired with the Puzzlebox Orbit Brain-Controlled Helicopter (priced at $89), the headset measures attention levels by requiring users to clear their thoughts and focus their concentration to power the helicopter while infrared signals on the gadget guide its flight. Richard and Erica Warp combined their knowledge of composing and neuroscience to develop another use for EEG headsets, the NeuroDisco computer program. The program composes music based on the brainwaves read from sixteen sensors placed around the scalp—the more focused you are, the more pleasant the notes produced.
This type of instant feedback allows users to understand how the brain influences certain results and subsequently alter their way of thinking to achieve change. As Adam Gazzaley of the University of California-San Francisco tells Standen, EEG programs may even help those diagnosed with ADHD. “Instead of being given a box of pills, they put an EEG cap on and they play a video game that looks at how they pay attention to relevant information, how they ignore information, how they sustain attention, how they deal with multiple tasks,” Gazzaley suggests. Then, devices such as the brain-controlled helicopter could provide an entertaining method of developing focus and mental relaxation. The affordability of EEG headsets will hopefully lead to further innovative uses of its potential and the continuing effort to bring such technology out of the hospital and into the hands of the everyday consumer.
Photo by David Huerta, licensed under Creative Commons.
The Oru Kayak aims to sustainably and affordably reconnect urbanites with the natural world around them.
The collapsible boat marketed to urbanites is not a new idea. But one California inventor and entrepreneur might have found the perfect combination of efficiency, sustainability, and affordability with his improvement on the collapsible kayak, reports Pat Joseph in the Summer 2013 issue of California.
Inspired by origami, Oru Kayak founder Anton Willis has successfully developed an all- plastic boat that’s fully recyclable, extremely durable, and able to be folded into its carrying case that can be stored in a closet or under the bed. It can withstand the folding/unfolding process up to 20,000 times, but most importantly, it actually works, and has been positioned as the ideal water vehicle for the urban dweller who’s interested in exploring their city’s waterways. And while Willis doesn’t recommend it for the weekend warrior, the Oru Kayak is even durable enough to handle the choppy waters of San Francisco Bay, demonstrating that it’s capable of handling pretty much any scenario an urban boater might come across:
As Joseph explains in his article, the Oru Kayak represents a new breed of collapsible boats as it’s lighter than comparable boats (it’s just about 25 pounds), more compact, and cheaper (the boat alone sells for $1,095). A successful Kickstarter campaign in 2012 got the ball rolling in a big way, proving that there was hungry market for Willis’ idea.
But the physical attributes of the boat only tell part of the story as far as Willis is concerned. From a philosophical perspective, this boat represents another extension of the mission at the heart of every project Willis has taken on; that is, his heartfelt desire to help urban people reconnect with the natural surroundings that are so easy for urbanites to miss or take for granted. His company’s product tester, Roberto Gutierrez, summed up Willis’ drive by saying, “For Anton, it’s not so much about selling stuff; it’s about getting people in boats and exploring the world around them. If selling Oru Kayaks can accomplish that, I think he’s happy.”
Photo of New York City from the Hudson River; courtesy of the Oru Kayak user gallery.
Scientific analysis of ancient Roman concrete suggests it was stronger, more durable, and more environmentally sound than modern concrete.
The simple fact that we can still visit the buildings and monuments of the ancient Romans illustrates that they knew what they were doing when it came to developing long-lasting building materials. Many historians even credit the Romans with inventing what we call concrete through their use of a very simple process:
But as Conservation reports in its Fall 2013 issue, it’s only recently that scientists have broken down the structure, chemical composition, and mechanical properties of ancient Roman concrete to the point of being able to glean useful information for contemporary concrete production.
Researchers from the University of California, Berkeley, summarized their findings in the Journal of the American Ceramic Society, and found the ancient Roman combination of limestone, volcanic ash, and seawater required far less heat (which means far less fuel) for solidification than modern concrete does. This suggests that contemporary application of the ancient Roman method may yield stronger, more durable concrete with a much smaller environmental footprint.
Image courtesy isawnyu, licensed under Creative Commons.
The April launch of the Digital Public Library of America brings the knowledge-sharing we love about local libraries to the internet.
This article originally appeared at Shareable.
Public libraries exist to ensure that people have free and open access to information. The Digital Public Library of America (DPLA), which launched in April, aims to provide that same access to information and materials, in the digital realm.
A project several years in the making, there are three facets to the DPLA: it’s an open portal that provides access to a variety of resources including documents, photographs, historic artifacts, film footage, art and other culturally significant materials; it's a tech platform for people to build upon (think apps that reveal geotagged materials); and it's an innovation and advocacy organization that works to make, and keep, content openly available to the public.
Launching with over two million materials from museums, libraries, schools, cultural centers and more, the DPLA is just getting started. The grand vision is to have the library be an ever-growing hub for librarians, students, teachers, artists, developers, historians and anyone else who is interested in seeing, learning about, using, repurposing, expanding and sharing materials.
John Palfrey, president of the Board of Directors of the DPLA sees the library as a symbol of the networked age. As he put it, “The most exciting idea is that we cannot begin to imagine the extraordinary things that librarians and their many partners can accomplish with this open platform and such extraordinarily rich materials...We will create new knowledge together and make accessible, free to all, information that people need in order to thrive in a democracy.”
Harnessing the power of collaborative
learning and DIY science, California’s
Maker Faire aims to combat throwaway culture by giving young people the tools
and inspiration to invent.
This article originally appeared at Shareable.
Since 2006, Maker Faire has
provided a space for inventors, tinkerers, builders, crafters, and
wannabe-scientists to showcase their creations with the intent of encouraging
others to dabble in inventing something themselves. With large-scale kinetic
sculptures racing and roaming the grounds, science experiments with electronics
and activities like clothing and apparel re-purposing stations on site,
participants are encouraged to touch, ask questions, and take what they learn
into their own workshops for some fun experimentation outside of the Maker
Faires' big top.
Sherry Huss, vice president of Maker Media, doesn't look the role of a
lab-coat wearing mad scientist that one might expect to be a Maker Faire organizer.
There are no beakers popping up and bubbling over in her office. She wears no
tool belt as she navigates the work spaces of Maker Media's headquarters in Sonoma County, California.
Yet, as anyone who has attended a Maker Faire may believe, Huss has the stuff
that genius is made of. Every year, she meets with her small planning team and
formulates the clever uses of time and space for what is referred to in their
tag line as “The Greatest Show and Tell on Earth.”
“We do it the old fashioned way,
with post-it notes and lay them out. And it somehow always magically works
out,” says Huss. “You have to get your head into it because everything that is
happening on site is intentional. There are very few things that just come
together,” she added.
And what comes together for
roughly 100,000 visitors after months of tireless planning is quite brilliant.
In addition to seeing a nearly
40 percent increase in new exhibitors each year, the contagious spirit of Maker
Faire continues to spread from the Maker's Bay Area headquarters to the rest of
the world. With annual events in San Mateo and New York, and
over 100 mini-Faires or satellite events internationally (including Rome, UK and a rotating country Maker Faire Africa, among others),
Maker Faire has an accessible, inclusive vibe that leads many to start
tinkering with or concocting projects of their own.
“Making is all over. It’s not
just the Bay Area,” says Huss. “We don't own the license on it...there are
Space is free for makers, and
event organizers only charge a small fee if an exhibitor plans to offer items
for sale. Maker is also careful with the selection process, focusing on
non-commercial exhibitors and ensuring that all of Maker Faire's inventive
action is family-friendly and safe. Especially with so much
up-close-and-personal, hands-on DIY participation.
“People are there showing their
projects and sharing how they made them,” says Huss. “Our goal is to make
Makers. People who come to the Faire get the confidence to become a Maker.””
Based on feedback from previous
years' attendees, demos and hands-on craft projects and exchanging ideas have
been the biggest draw. Naturally, organizers continue to foster the
collaborative learning that happens at the annual events that span two days. This
year's theme is Maker Spaces, which is sure to be a huge hit among DIY
enthusiasts. Similar to model homes and the nifty kitchen design displays at
big box stores, Maker Faire will showcase these Maker Spaces to plant seeds of
empowerment in the minds of aspiring makers from all walks of life. What
defines these spaces, however, is not simply the presence of tools and a simple
tool bench, but the act of making itself.
“Just look at Mister Jalopy, chronicling the decline
of the work bench in the garage,” says Huss. “Garages now are mostly just
storage places. They used to have a work bench. The toaster broke, you didn't
get a new one; you took it out and fixed it. I am hoping that this movement
will swing it back that way.”
Although the days of dad
tinkering with old radios and small appliances on his work bench in the garage
were often solitary escapes, the makers and fixers of today tend to have a more
collaborative focus. In addition to crews of several hundred helping hands,
sponsors and organizations collaborate to ensure that the festivities go on
without a hitch. In Detroit,
they collaborated with The Henry Ford
Museum and Research Center. In Kansas
City, they had help from the Kauffman Foundation. Portland partnered with the Oregon Museum of Science and Industry.
Huss isn't directly involved in
programming for all of the Faires outside of New York and the Bay Area, but she
provides training opportunities for those interested in setting up their own
events, ensuring that the infectious Maker spirit spreads to the garages and
minds of the aspiring tinkerer in all of us. After all, Maker is not just a
one-time event. More than anything, Maker is a way of life that brings together
communities in a too-often competitive culture, and encourages--above all
else--collaboration, innovation, and fun.
“I think there is a lot of
(interest) with continuing education and the Maker Space community,” says Huss.
“Like the old grange where people came together; usually around food. It is so
cool for people to come together to make things,” she concludes.
Image by Bridgette
Vanderlaan, Maker Faire.