Genome Compiler is released!

Genome Compiler‘s first public release just came out, as announced by Omri Drory, the founder and CEO of Genome Compiler. It’s a software tool for designing and debugging synthetic DNA, and ordering it, too! Haven’t played around with it yet but I’m excited to (update later after I try it out). Everyone is starting to make big, visible steps towards making synthetic biology more accessible, modular, and highly functional. Hopefully this will lead to many more awesome developments.

Advertisements

Tuna carry Fukushima radiation to California

A study released today by scientists Daniel Madigan and Nicholas Fisher cite findings from 15 bluefin tuna caught off of San Diego — 10 times more radioactive cesium than fish from previous years. These fish likely migrated from the waters near Japan, where bluefin tuna are known to spawn, the same area that was affected by the Fukushima nuclear reactor meltdown last year, which released radioactive materials into the water. The idea itself is already enough to fuel some worries, as fish is well-known for transmitting toxins in the water to the humans who like to eat them (think of all of the seafood watch mercury scares). However, the levels are just below the Japanese government’s safety limits, and probably don’t pose any threat to humans, though the scientists do not make any advising comment either way. The fact that the fish were found all the way across the ocean with traces from the nuclear reaction is a large cause of concern, though.

New Scientist article by Sara Reardon

The levels might not be high enough to harm you if you tucked into a tuna sandwich, but some tuna are still carrying radioactive caesium from the leak at the Fukushima Daiichi plant last March. Researchers hope that similarly low levels of radiation in turtles, sea birds and sharks will allow the migration patterns of little-studied species to be tracked.

Daniel Madigan, a marine biologist at Stanford University in California, was already studying how Pacific bluefin tuna (Thunnus orientalis) migrate across the Pacific Ocean when the Japanese tsunami put a new twist on his experiment.

The leak at the Fukushima Daiichi reactor released caesium isotopes into the Pacific, and fish can pick up the radioactive material from the water they swim in and from the food they eat.

Juvenile tuna can take between one and four months to swim the 9000 kilometres from Japan to California. The researchers measured caesium isotopes in young tuna caught off the coast of San Diego, and found detectable levels of caesium-134 in 15 fish. The isotope could not be detected in fish that were caught before 2011.

Because caesium-134 has a half-life of two years, Madigan expects that researchers will be able to find it in the long-lived fish for some time to come. Tuna migration patterns are well known, he says, but the radiation may be useful in tracking other species such as salmon sharks (Lamna ditropis). If these sharks behave as researchers suspect they do, the migratory males would carry Fukushima radiation, but the stationary females would not.

——

My first reaction: think beyond bluefin tuna to basic ecology and food chains — there are probably a bunch of marine species that have absorbed the radiation, that are being eaten by larger fish and organisms, which are then eaten by larger ones, and so on. Who knows how high the levels are in the smaller fish that get eaten by the tuna? Don’t we eat some of those species, too? Also, from a bioaccumulation standpoint, cesium gets magnified in biological organisms, meaning that the predator can contain higher concentrations than the prey. Not only this, but many of them are probably migratory, just like Pacific bluefin tuna.

Although, add in these quotes from the authors as mentioned in a Washington Post article about the finding:

“Much will depend on the concentration in the prey fish, which in turn is ultimately dependent on the water concentration. If concentrations in water will eventually decline, as we would expect, due to dilution and dispersion, then concentrations in living organisms will eventually decline as well.” – Nicholas Fisher

“However, certain small fish around Japan showed very high levels after the accident. If certain larger predators happen to feed on these prey, higher levels than we observed may be possible.” – Daniel Madigan

An NPR article dismisses the hype around fear of food, and states that the cesium levels found are not any more cause for panic than the already-existent levels of radiation in seafood from past nuclear testing and naturally occurring radiation:

“So the question is, how much more radiation did these particular tuna fish contain? The answer is: A trivial amount. In fact, radiation from the cesium is 30 times less than the radiation that’s already in the fish naturally in the form of potassium-40, according to the research paper. And the natural polonium-210 packs a radiation dose 200 times larger than the dose from the cesium.”

Confused? This is definitely a problem that I run into often with scientific journalism, coloring the results when communicating scientific findings. If you’re not sure what to believe, the solid solution is always to go straight back to the source and make a decision yourself. Even then, be wary, because authors have their own bias about why they’re conducting their research and what they say with their findings, despite the emphasis on just relaying the facts and making sound conclusions from those. It’s always going to be like this on some level, as we are human and all have our own opinions.

Thankfully, the authors of the study made their article open access (open source scientific knowledge, something to be discussed later), and you can read it in its entirety here.

Fig. 1A of the article shows the migration pattern of the bluefin and yellowfin tuna, as well as uptake and decay patterns of cesium from the water over the growth period.

I don’t think there’s a huge need for panic and re-evaluation of the bluefin tuna stock and how you choose or buy your sushi, based on this study. As argued in the NPR article, the authors themselves say:

“Total radiocesium concentrations of post-Fukushima PBFT [Pacific bluefin tuna] were approximately thirty times less than concentrations of naturally occurring 40K [potassium-40] in post-Fukushima PBFT and YFT [yellowfin tuna] and pre-Fukushima PBFT. […] Thus, even though 2011 PBFT showed a 10-fold increase in radiocesium concentrations, 134Cs [cesium-134] and 137Cs [cesium-137] would still likely provide low doses of radioactivity relative to naturally occurring radionuclides, particularly 210Po [potassium-210] and 40K.”

But, again, we should be conscious of the ecological footprint from the data, and the methods used in this study demonstrate how capable we are of detecting radioactive substances in seafood and marine organisms — especially ones that migrate long distances and are affected by growth and radioactive decay rates. The levels (“<<1% of total radiocesium released into Japanese waters”), while small, is “a conservative estimate based on one species”. The authors suggest further studies on turtles, sharks, and seabirds that feed and live near the affected areas, that are also migratory:

“However, the presence of Fukushima-derived radiocesium in all 2011 PBFT individuals reported here suggests that study of other HMS [highly migratory species] is warranted. Our results demonstrate that Fukushima-derived radionuclides in animal tissues can serve as tracers of both migration origin (presence or absence of 134Cs) and potentially, timing (using 134Cs:137Cs ratios) in mobile marine mammals, providing valuable complementary movement data to extensive tagging programs in the Pacific.”

If anything, further data would help us understand how radioactive materials move throughout the ecosystem, and the rate at which they are transported, disappear, or are magnified. The study outlines a detailed way to track this using cesium-134 levels and cesium-134:cesium-137 ratios.

Kio Stark at Kickstarter

“Don’t Go Back to School is a handbook based on over 80 interviews with people who have successfully taught themselves a wide variety of skills and subjects outside of school. Some of them are dropouts, some of them went to college, and some even went to grad school, but they all have in common an obsessive passion for the learning that they do independently. The book shares their secrets and strategies, so that anyone with curiosity and a desire to learn can find out how to do it without heading back to class.”

Last night, I got to hear Kio Stark speak at Kickstarter’s headquarters. Kio launched a Kickstarter project last fall, for a nonfiction book called Don’t Go Back to School: A handbook for learning anything. It’s about learning, education, and getting where you need to go without going to (or going back to) traditional school, such as college or grad school. The book hasn’t been finished yet, though you can head to her website to see how you can get a copy if you weren’t a Kickstarter backer. I was interested to hear what she found through interviews for her book, and to hear more about the ideas in the book, but the talk turned out to be centered more on stranger interactions and social dynamics in cities, which was just as fascinating. I think in a lot of ways, while the two topics seemed separate at first, the conversation really brought it all together.

Kio teaches at NYU’s Interactive Telecommunications Program (check out cool stuff from their Spring Show 2012!), where she leads classes in stranger interactions and intimacy and technology, and thinks about how humans relate to their technology and to each other through technology. It might be ironic to think of such a book coming from a grad school professor, but for what it’s worth, ITP definitely doesn’t work like regular grad school, and Kio herself dropped out of a Yale graduate program. I think her personal history and teaching position also just shows that everyone finds their own way to do their own thing, an idea that underlies her book.

Her talk at Kickstarter was sort of a crash course in what she teaches at ITP. She got us thinking about how cities are full of strangers, and how all of those interactions affect us, in person and online. It’s a very relevant concept for crowdfunding platforms like Kickstarter, where strangers often come together and help each other out, whether for personal material gain (rewards) or altruism, or that blurry middle ground where your friend is making something awesome and you want to help your friend out and also get a bit of the awesome. It’s a relevant idea for New York City, which is a liberal island in itself full of a constant interchange of ideas and very social-media-connected people (though Kio pointed out that being a liberal island is often actually very limiting and paints a skewed picture of what the world is or can be). It’s a big idea for the internet overall, which thrives on stranger interactions, and interactions with people you know that wouldn’t otherwise be possible without the internet. She got us thinking about anonymity versus accountability, such as how the culture has moved from using avatars and screen names to connecting all of your various social media accounts, and allowing openness with your name, identity, and personal details.

Interactions with strangers also facilitate learning, particularly on the internet. It’s fairly clear that while it was possible to self-learn and motivate personal education before the internet, it’s been completely revolutionized and entirely accessible with the internet — Wikipedia, open textbooks, Quora, even the Facebook posts that pop up on your feed with current events news articles. People want to share and show what they know, and in doing that, whether as a side or directed effect, they’re helping other people learn.

Overall, all of this thinking just emphasizes that there’s plenty out there to learn, in school or out of school, but doing it out of school opens up a wide variety of methods, on top of the range of topics. Kio received a range of responses from people who have built their own businesses, people who are engaging in biohacking, people who are trying to homeschool their kids, people who studied one thing in school and realized that there was so much more about other things that they wanted to learn. Humans are innately curious, and while school might have developed to nourish and encourage that curiosity, it’s become pretty clear that by trying to meet the needs of everyone as a collective, individual creativity and curiosity suffers. How do we fix the school system to still be a system, but still work for everyone? As more and more people turn to finding their own methods and paths, it makes you wonder — is it even possible?

(Side note: Kio lives with Bre Pettis in Brooklyn with their daughter. Bre is one of the founders of NYC Resistor and MakerBot…speaking of DIY)

The Vertical Forest

“More and more people believe that access to a garden, and to gardening, is a basic human need. But is the answer a traditional house and garden or should we be looking at gardens in the sky?”

Dubbed “Flower Towers” by the Financial Times, these fluffy green buildings designed by architect Stefano Boeri are currently rising in Milan. Photos show that the skeletons of the buildings are up, an intricate maze of balconies and jutting gardens designed to insulate the building, counter air pollution and support reforestation, work towards sustainability, and maintain biodiversity and a functioning ecosystem, all suspended 110 meters into the air. These microclimates ideally would maintain their own energy and water usage and recycling, including using repurposed grey water from the building to feed the plants.

The floor layout with plumbing detail makes the building look like an Escher piece. 900 trees of varying heights and structural types will be used to make a diverse wall, both for the biology of the building and for coating the sides of the buildings more fully. The finished product, which when flattened, is equivalent to 15,000 square meters of land and 10,000 square meters of forest, and is intended to counteract the growth of Milan’s rapid urban expansion.

Eco-cities coming of age?

NYU ITP Spring Show 2012

My roommate, a graduate student at NYU’s Interactive Telecommunications Program (and computer science / engineering / robots / circuitry / electronics / art&design extraordinaire, and overall awesome person), invited me to the ITP Spring Show this year, where ITP students display and demo their projects from classes, independent research, and theses. It’s a two-day showcase, spread out among the classrooms and lab spaces of the ITP floor within NYU’s Tisch School of the Arts. The students are all intensely innovative and creative, but also skilled in the technical background needed to carry out their ideas, and most importantly, very interested in how to connect to people and how to use technology creatively (ITP has proclaimed itself the “Center for the Recently Possible”). The show happens twice a year, at the end of the fall and spring terms.

There were many, many favorites, but here’s a small sampling:

Descriptive Camera, by Matt Richardson

“The Descriptive Camera works a lot like a regular camera—point it at subject and press the shutter button to capture the scene. However, instead of producing an image, this prototype outputs a text description of the scene. Modern digital cameras capture gobs of parsable metadata about photos such as the camera’s settings, the location of the photo, the date, and time, but they don’t output any information about the content of the photo. The Descriptive Camera only outputs the metadata about the content.

“As we amass an incredible amount of photos, it becomes increasingly difficult to manage our collections. Imagine if descriptive metadata about each photo could be appended to the image on the fly—information about who is in each photo, what they’re doing, and their environment could become incredibly useful in being able to search, filter, and cross-reference our photo collections. Of course, we don’t yet have the technology that makes this a practical proposition, but the Descriptive Camera explores these possibilities.”

Cool new way to approach photography, especially as all of your photographs become digitized and trapped onto your spare hard drives. Even analog photos that get printed on film get digitized, as if to save them in some way that seems more permanent to us (even if it isn’t). The camera works by sending the image to workers who have signed up for Amazon’s Mechanical Turk system, which feeds Human Intelligent Tasks (HITs) to other people over the internet, for a fee. The people who get these tasks send back a short descriptive text about the image. The Descriptive Camera makes it a fascinating study in what we see in images that don’t come with any context, and how people choose to tell stories or color what they see with their personal viewpoints.

Here are some descriptions collected from the show, as posted to Matt’s blog:

A thoughtful gentleman in a pink and baby blue plaid shirt stands next to a lovely woman who appears to be impersonating an orangutan.

A woman in a black top looks terrified by the gentleman in a grey shirt who seems to be telling a story about an enormous fish he once caught.

A woman in a black tank top stands in the foreground. Behind her, it appears as though there is a beard convention taking place.

Two men are fighting over the honor of this lady with bangs who is standing the background. She actually looks really excited about this fight. DRAAAAAAMA!

Added bonus: NPR’s Wait Wait…Don’t Tell Me show featured the Descriptive Camera in a recent limerick.

Chairish, Rocking Chair for Two, by Annelie Berner

The Design for Digital Fabrication class produced some great pieces on display made with laser cutters and 3D printers. This shareable chair was whimsical, functional, and beautiful — sit down with a friend and sway in unison on the carefully cut wood frame, which was made on a CNC router.

Rehuddle, by Philip Groman and Robbie Tilton

Rehuddle is a very simple conference-call site that makes it ridiculously easy to set up group calls. You can invite friends through calls, texts, or emails, and you even get those iconic little Turntable.fm avatars.

“Our target audience is small creative businesses that cannot afford expensive phone systems and are looking for a free, easy and fun solution. Our secondary target market is for anyone looking to speak and share information with two or more people.” – Project Description

BurritoBot, by Marko Manriquez

Laser cutting and 3D printing come together to yield…the evasive perfect burrito. The evasive perfect 3D printed burrito.

“Burritob0t is a platform for rapid prototyping and tracing the source of food in our lives to reveal hidden issues revolving around fast food: labor practices; environmental consequences; nutritional values. Mexican fast food is emblematic of the assembly line, mass produced era of modern consumables – appropriating the authenticity of the ethnic food sensibility it purports to embody while masquerading as an edible like substance.  Because the burrito is a mass market consumable, it lends easily as a way for examining and stimulating discussion on various aspects of the food industry including: how and where our food is grown, methods of production, environmental impact, cultural appropriation and perhaps most importantly – what our food means to us. By parodying the humble burrito’s ingredients and methods of production we can shed light on these exogenous factors and interconnected systems surrounding the simple burrito.”

Galapagos, by Ann Chen and Danne Woo

This is a typeface designed with the help of genetic algorithms. As someone who has worked on evolutionary biology and spent a lot of time looking at these sort of patterns and trees, it was particularly cool to see how people found them both beautiful and inspirational for design, especially as the principles of evolution and feedback were incorporated into each iteration of a font:

“User Scenario: We will have the program set up on an iPad. User approaches iPad, directions on how to begin generating typeface will be clearly presented. When user generates first evolution of the typeface, they have the option of either printing and saving what they’ve created or creating another generation. The characteristics of the next font generation (color, shapes, size, etc.) can be determined by the user depending on how long they hover over each example. The longer they hover over one, the higher ranked that letter’s characteristics will be and the more likely the next generation will look like that character. User saves the print and can email print to themselves.”

Dinosaur Treasures, by Anh Ly and Ji Hyun Lee

Who doesn’t love digging around in a sandbox? Let’s be real. This highly interactive piece encouraged the curious to pretend to be an archaeologist and hunt for dinosaur fossils…yep.

One part that seemed to capture everyone’s interest was how the sensors could tell how deep you were digging — the idea of depth adding a new element to your interactive, 3D space archaeology adventure. The sensors could tell where you were digging and how far down you were going, and dinosaurs (and lobsters) would pop up accordingly. I thought it would be pretty awesome to have an underwater deep-sea explorer version of this, like putting on a suit and floating around in a pool that gets magnified into a giant ocean? And whales and squids come at you? Is that too crazy?

Call Your Sequencer, by Byung Han Lim and Dong Ik Shin

This seemed complicated from far away, but you’re quickly drawn in by the visual/audial mix going on, and a bunch of very concentrated people staring at the screen, bobbing their heads, and poking their cell phones. A group of users calls up a phone number, each on their own cell phone. Once you get into the system, your number shows up on the grid, a whole row of cubes to yourself as your own personal 8-step music sequencer — within the 8-member-maximum band. You can control your beat and rhythm, which cycles automatically, by pressing numbers on your own phone’s keypad, which turns the steps on and off and animates (or stills) the corresponding cube. Once you get more comfortable, you can mix in the ability to change the pitch and instrument with the pound and star keys, and the flashing colors synching with your inner dial-pad-music-genius.

Caren Alpert’s electron microscope photos of food

Caren Alpert asks a good question with her series, terra cibus: what’s in our food? The project is a collection of electron microscope images of different foods, from shrimp tails (pictured) to chocolate cake to vegetables. In some cases you can clearly see the differences in texture, uniformity, composition, some beautiful and foreign, some just as you might have expected.

“Photographs taken with electron microscopes have seized my interest because of their mystery and simultaneous familiarity. This medium deconstructs, abstracts, and reveals the ordinary in a riveting way. The closer the lens got, the more I saw food – and consumers of food – as part of a larger eco-system.”

– Caren Alpert, terra cibus artist statement

Check out the gallery at http://carenalpertfineart.com/gallery.html.

Bike Share NYC

Bike shares are finally coming to New York, in July 2012! While NYC is pretty infamous for its unbicycleable streets, many are hoping that bike shares will help make more room for bikers…and safer for all who share the road. The bikes in New York will be sponsored by Citi ($41 million deal), and you can sign up for an annual membership ($95) or shorter, more occasional usage ($9.95 for a day or $25 for a week). The idea is that you can pick up a bike at a station, and return it to any other station — get where you need to go, get some exercise, don’t need to rely on taxis or the subway, and good for trips that are too long for a walk. The best part for many is that you don’t need to worry about maintenance or storage, two things hard to come by around here. Also, the system will use Spotcycle, a mobile app that tracks and updates information on bike availability and locations.

However, there have been a few concerns, mostly about the cost and time constraints. The NYC bicycle share will be a privately sponsored system, meaning that the bikes will be decked out in Citi blue (looking like these), and there is no taxpayer money going into the program. While the NYC Department of Transportation (DOT) and bike share program worked to get community input on where to put the stations, the pricing scheme that was recently unveiled was quite surprising. Andrea Bernstein sums it up well with her charts, comparing pricing systems and time limits across major bike share cities. A beginning chunk of the first 30-45 minutes of each ride is free with a one-day, seven-day, or year pass, but after you pass that grace period, the fee starts counting with the time, and it comes out fairly expensive. The justification is that most New Yorkers won’t be needing a bike over 45 minutes, because apparently 54% of trips we take are less than 2 miles, so we won’t need to frequent this hazy zone where fees start popping up. However, NYC is big, and the bulk of its residents live in the outer boroughs. Once you start heading out of Manhattan, or even north into the Upper East and West sides, where there aren’t even any planned stations yet, you run into some problems. The program hopes to expand to these areas, as well as further out neighborhoods of Brooklyn like Park Slope and Crown Heights — but at that point, a bike commute to work in midtown can take much more than 45 minutes.

NYC Bike Share general information

Comparison charts between cities and discussion by Andrea Bernstein

NYC bike station map (current plan, to be updated)