Squishy Clockwork Biobot Could Dose You With Drugs From the Inside

Photo: Sau Yin Chin. Soft and 3D-printed micromachines can be implanted in the body to deliver doses of a chemo drug.

When Swiss watchmakers invented the Geneva drive, a two-geared mechanism that produces precise ticks forward, they probably never imagined that bioengineers would one day craft a 15-millimeter version out of squishy hydrogel. But then, they weren’t trying to make a biocompatible micromachine that could be implanted in the body to deliver doses of drugs.

This strange new biobot comes from the lab of Samuel Sia, a professor of biomedical engineering at Columbia University, in New York City. It uses neither battery nor wires, and can be controlled from outside the body to deliver a dose on command. It’s a gadget well suited for this new era of personalized medicine, Sia tells IEEE Spectrum. “Doctors want to see how the patient is doing and then modify the therapy accordingly,” he says.

He has already tested the gizmo in lab mice with bone cancer, with exciting results that were published today in the journal Science Robotics. More on that experiment later.

Photos: Sau Yin Chin The researchers constructed their Geneva device layer by layer, in a process that took about 30 minutes.

Sia’s team first had to invent a type of 3D printing to fabricate their tiny Geneva drive and several other soft micromachines. They came up with a fabricator that lays down layers of a hydrogel to produce rubbery solid shapes. While human hands are required to put the pieces together, Sia says those assembly steps could be automated. And it’s pretty quick, as is: The whole process of printing and assembling one Geneva drive takes less than 30 minutes. Today’s typical 3D printers would take several hours to construct a similar device, Sia says, and most can’t handle soft materials like hydrogel.

Here’s the part that runs like clockwork! The squishy Geneva drive clicks forward when an external magnet moves a simple gear, which is just a rubbery piece with embedded iron nanoparticles (the black curved piece in the video below). With each click, one of six chambers lines up with a hole and a dose of medicine flows out. In the video, a magnet (the silver disk) keeps the device running continuously to demonstrate the mechanism, but in clinical use, a doctor could apply a magnet only when a dose is required.

You may be wondering: Could someone’s implanted micromachine be triggered accidentally by an external magnet or by a malicious person with fiendish magnetic powers? In other words, is the X-Men’s Magneto a risk factor? “Somebody walking by with a magnet won’t trigger it, but there are some cases where it’s not ideal,” Sia says. His lab is working on other ways to wirelessly drive the mechanism, including an ultrasound technique.

The hardest part of the design process was getting the material right, Sia says. Very flexible and soft materials are compatible with the body’s soft innards, unlike rigid silicon or metal devices. “But if your material is collapsing like jello, it’s hard to make robots out of it,” he says. “It has to be stiff enough to work like a tiny implantable machine.”

Image: Sau Yin Chin The pieces of the Geneva device were each printed in soft hydrogel.

The next step was in vivo.
Sia’s team wanted to see if their devices would work inside the body, with all the complications of chemistry and anatomy. Some mice with bone cancer received implanted devices that were loaded up with a chemo drug; other mice received typical chemotherapy, which floods the whole body with a toxic drug. When the team compared the effects of the device’s localized and periodic delivery of the drug to those of the typical treatment, the results were impressive. The bionic mice’s tumors grew slower, more tumor cells died off, and fewer cells elsewhere in the body suffered peripheral damage.

Photos: Sau Yin Chin Fluorescent imaging shows a chemo-delivering device inside a lab mouse.

The clinical possibilities seem obvious—oncologists could deliver more targeted and concentrated doses of powerful chemo drugs, and Sia imagines other uses, like regulating the release of hormones. But the drug delivery device is really just a proof of concept, he says. He’s not rushing out to form a startup: “We have to do the cost-benefit analysis to see if this is really a commercializable device,” he says.

He is bullish, however, on the medical potential of tiny squishy robots in general. Soft and mobile little bots could one day act as internal repair crews, doing a doctor’s work from the inside. (For more on this, check out IEEE Spectrum’s article on medical microbots.) Sia says his fabrication platform is capable of turning out a wide variety of devices. “I’m confident that we’ll find something useful,” he says.

Sia won’t say exactly what types of devices his lab is now experimenting with, except to say that they’re looking at implanted devices that move. Here’s my guess: It’s a tiny squishy micromachine that resembles a cuckoo clock.

ORIGINAL: IEEE Spectrum
By Eliza Strickland
4 Jan 2017

Here Is the World's First Engine Driven by Nothing But Evaporation. An engine with living parts

Bioengineers invent a way to harvest energy from water evaporating at room temperature. It's an engine with living parts.

Joe Turner Lin

It might not look like much, but this plastic box is a fully functioning engine—and one that does something no other engine has ever done before. Pulling energy seemingly out of thin air, it harvests power from the ambient evaporation of room-temperature water. No kidding.

A team of bioengineers led by Ozgur Sahin at Columbia University have just created the world's first evaporation-driven engine, which they report today in the journal Nature Communications. Using nothing more than a puddle of resting water, the engine, which measures less than four inches on each side, can power LED lights and even drive a miniature car. Better yet, Sahin says, the engine costs less than $5 to build.

"This is a very, very impressive breakthrough," says Peter Fratzl, a biomaterial researcher at the Max-Planck Institute of Colloids and Interfaces in Potsdam, Germany who was not involved in the research. "The engine is essentially harvesting useful amounts of energy from the infinitely small and naturally occurring gradients [in temperature] near the surface of water. These tiny temperature gradients exist everywhere, even in some of the most remote places on Earth."

An engine with living parts

To understand how the engine works, it helps to understand unique material behind it.

The key to Sahin's astonishing new invention is a new material that Sahin calls HYDRAs (short for hygroscopy-driven artificial muscles). HYDRAs are essentially thin, muscle-like plastic bands that contract and expand with tiny changes in humidity. A pinky finger-length HYDRA band can cycle through contraction and expansion more than a million times with only a slight, and almost negligible, degradation of the material. "And HYDRAs change shape in really quite a dramatic way: they can almost quadruple in length," Sahin says.

Figure 2: Hygroscopy-driven artificial muscles.
From Scaling up nanoscale water-driven energy conversion into evaporation-driven engines and generators
Xi Chen,
Davis Goodnight,
Zhenghan Gao,
Ahmet H. Cavusoglu,
Nina Sabharwal,
Michael DeLay,
Adam Driks
& Ozgur Sahin Nature Communications 6,Article number:7346

doi:10.1038/ncomms8346

Xi Chen

The idea for the HYDRA material came to Sahin more than half a decade ago, when he came across an unusual find in nature. While studying the physical properties of micro-organisms with advanced imaging techniques, he discovered that the spore of the very common grass bacillus bacteria responds in a strange way to tiny amounts of moisture. Although the dormant spore has almost no metabolic activity and does no physical work, its outer shell can soak up and exude ambient levels of evaporated water—expanding and shrinking while doing so.

"The spores stay very rigid as they expand and contract in response to humidity," Sahin says. "That rigidity means their movements come with a whole lot of energy."

Add caption

After many experiments, Sahin found a way he could mimic the spore's unique response. To make HYDRAs, he actually paints the spores onto plastic strips using a laboratory glue. By painting dormant spores in altering patches on both sides of a single strip, the pulsating spores cause the plastic to flex and release in a single direction in response to moisture—just like a spring expanding and contracting.

While a material made of living creatures may sound like it should have a short lifespan, Fratzl says that, in fact, HYDRAs are "likely to last for a very, very long time," he says. "In nature, it's absolutely critical that these spores survive from decades to even hundreds of years in dormancy, all while responding to outside humidity in this dramatic way without breaking down."
The inner workings

How do you go from spores on strips to a working engine? 
The engine is placed over a puddle of room-temperature water, creating a small enclosure. As the water on the surface naturally evaporates, the inside of the engine becomes slightly more humid. This triggers strips of HYDRAs to expand as they soak up some of the new-found humidity. Collectively, these HYDRAs pull on a cord which is attached to a small electromagnetic generator, transforming the cord's movement into energy. The HYDRAs also pull open a set of four shutters on top of the engine, releasing the humid air. With the shutters open, humidity inside the engine drops. This causes the HYDRAs to shed their water-vapor and contract, which pulls the shutters back closed. And the process repeats, just like an engine's cycle.

Sahin has found that the engine works at room temperature (around 70 degrees Fahrenheit) with water that's at a wide range of temperatures—from 60 to 90 degrees F. Because water naturally evaporates faster at higher temperatures, hotter water works best.

• With 60-degree (15.5°C) water, the engine will open and close its shutters once every 40 seconds. 
• At 70 degrees (21.1°C), it does so every 20 seconds. 
• At 90 degrees (32.2°C), it's every 10.

Sahin also created a second engine with his HYDRAs—this one a turbine-style creation that uses the motion of bending HYDRAs to spin a wheel. Placed on top of a miniature car, the entire device slowly ekes forward—again, powered by nothing but evaporating water.

More than a toy
On average, each pull of the engine creates roughly 50 microwatts. That's a tiny amount of energy, but it's enough to generate light with an LED by harvesting the energy of a puddle of water that's doing nothing but existing at room temperature. Sahin also says that the materials used to make the engine are extremely cheap. Even including the HYRDAs, he says it should cost less than $5 to put together.

There is plenty of room for improvement, too. For one thing, he says, each HYDRA band uses just 1 percent of energy potential of the bacteria spores. A HYDRA-like material that could make better use of the spores would radically increase usefulness of the device. In fact, Sahin says he already developed another material that could tap into one-third of the spores' energy potential, but it proved an absolute nightmare to finagle that material into a long-lasting engine.

For now, the evaporation engine is just a proof of concept meant to show that this unique type of energy generation really can be accomplished. Whether future devices will ever be able to compete with other renewable energy sources, such as wind or solar energy collection, may be a question that won't even be answerable for decades. But the promise is there, he says. Just consider the way the planet works: "The power in wind on a global scale primarily comes from evaporation," he says, "so there's more power to be had here than there is in the wind."


ORIGINAL: Popular Mechanics
By William Herkewitz

Single-Molecule Bioelectronics

Over the past several decades, a variety of imaging techniques have enabled a wide range of studies of the structure, function, and dynamics of molecules at the single-molecule level. However, popular fluorescent single-molecule techniques generally cannot directly resolve temporal changes that occur on sub-millisecond timescales, as imaging times must accommodate the relatively slow rate of photon emission from single fluorophores.

In contrast, non-optical techniques that offer direct transduction to ion or electron flux can enable studies of dynamic single-molecule processes on microsecond or nanosecond timescales. Although electronic single-molecule sensors produce larger signals than fluorescent techniques, they are still weak signals, and it is critical to minimize any measurement noise. Towards this end we are designing compact, low-noise, highly parallel, high-speed sensing platforms which combine new direct electronic single-molecule sensors with state-of-the-art semiconductor systems.

For example, a nanopore sensor is a single nanoscale hole in a thin insulating membrane which separates two aqueous solutions. When a target molecule (such as a strand of DNA) passes through a nanopore, it changes the ionic conductance of the pore, which can be measured as an electrical current. Due to the much higher mobility of small dissolved ions compared to larger analyte molecules, nanopores can produce millions of output ions for each individual molecule measured. 

We recently designed a high-speed nanopore sensing system which combines thin solid-state nanopores with custom low-noise CMOS preamplifiers in a millimeter-scale platform. The low parasitic capacitance of this system allowed us to measure nanopore signals as brief as 1 microsecond, more than 10 times faster than common arrangements based on commercial patch clamp amplifiers.

In addition, we are developing high-speed single-molecule sensors based on chemically functionalized carbon nanotube field-effect transistors. We electrochemically oxidize a carbon nanotube, creating a single point defect which dominates its electronic transport. A probe molecule can be covalently attached to this defect, and the binding of a target molecule to the probe modulates the electron transport through the nanotube. By electrically monitoring the conductance of the nanotube, we can observe single-molecule binding kinetics at very high bandwidth.

Related Publications

• J. K. Rosenstein, M. Wanunu, C. A. Merchant, M. Drndic, and K. L. Shepard, "Integrated nanopore sensing platform with sub-microsecond temporal resolution," doi:10.1038/nmeth.1932, March 18, 2012.
• S. Sorgenfrei, C.-Y. Chiu, M. Johnston, C. Nuckolls, and K. L. Shepard, "Debye Screening in Single-Molecule Carbon Nanotube Field-Effect Sensors," Nano Letters 11(9), pp. 3739-3743, 2011.
• Jacob Rosenstein, Sebastian Sorgenfrei, and K. L. Shepard, "Noise and Bandwidth Performance of Single-Molecule Biosensors," 2011 Custom Integrated Circuits Conference
• S. Sorgenfrei, C-Y Chiu, R. Gonzalez, Y.-J. Yu, P. Kim, C. Nuckolls, and K. L. Shepard, "Label-free single-molecule detection of DNA hybridization kinetics with a carbon nanotube field-effect transistor," Nature Nanotechnology 6, pp. 126-132, 2011.

ORIGINAL: Columbia University

First brain map of speech units could aid mind-reading

Video: How speech sounds activate the brain

"He moistened his lips uneasily." It sounds like a cheap romance novel, but this line is actually lifted from quite a different type of prose: a neuroscience study.

Along with other sentences, including "Have you got enough blankets?" and "And what eyes they were", it was used to build the first map of how the brain processes the building blocks of speech – distinct units of sound known as phonemes.

The map reveals that the brain devotes distinct areas to processing different types of phonemes. It might one day help efforts to read off what someone is hearing from a brain scan.

"If you could see the brain of someone who is listening to speech, there is a rapid activation of different areas, each responding specifically to a particular feature the speaker is producing," says Nima Mesgarani, an electrical engineer at Columbia University in New York City.

Snakes on a brain

To build the map, Mesgarani's team turned to a group of volunteers who already had electrodes implanted in their brains as part of an unrelated treatment for epilepsy. The invasive electrodes sit directly on the surface of the brain, providing a unique and detailed view of neural activity.

The researchers got the volunteers to listen to hundreds of snippets of speech taken from a database designed to provide an efficient way to cycle through a wide variety of phonemes, while monitoring the signals from the electrodes. As well as those already mentioned, sentences ran the gamut from "It had gone like clockwork" to "Junior, what on Earth's the matter with you?" to "Nobody likes snakes".

This showed that there are distinct areas in a brain region called the superior temporal gyrus that are dedicated to different types of sounds – the STG is already known to be involved in filtering incoming sound.

One cluster of neurons responded only to consonants, while another responded only to vowels. These two areas then appeared to divide into even smaller groups. For example, some of the consonant neurons responded only to fricatives – sounds that force air through a narrow channel, like the s sound at the beginning of "scientist". Others responded only to plosives – sounds that block airflow, like the b in "brain".

Other scientists have used neural activity in attempts to recreate what people are looking at or capture people's thoughts in the form of their inner voice.

Mystery of meaning

Mesgarani thinks that the phoneme map may make it easier to figure out what someone is hearing from nothing but brain signals. He has tried to do this before by analysing neural responses to sound in ferrets and in people. The map should make relating the brain activity to specific sounds much easier.

Sophie Scott at the Institute of Cognitive Neuroscience at University College London cautions that the way we hear language is more complicated than just lining up different phonemes. Sounds change in subtle ways when they come together, so the brain must analyse the sequence as a whole.

"I think it's a shame that they haven't taken a more realistic approach to what we know actually happens when people listen to speech," Scott said. "Information isn't located at the level of the segments, it's actually extending over the sequence."

Mesgarani agrees that how the brain turns phonemes into meaning is still unknown. "How the brain takes these basic units, and puts them together to form sub-word and words, and ultimately meaning, remains a mystery," he says. He hopes the phoneme map will one day help answer this question, too.

Journal reference: Science, DOI: 10.1126/science.1245994

ORIGINAL: New Scientist
by Aviva Rutkin
19:00 30 January 2014

Biology's Coefficient

 

JOEL E. COHEN. Laboratory of PopulationsRockefeller University & Columbia University

Joel Cohen uses the tools of mathematics to deconstruct questions of life.

New York, New York© THE ROCKEFELLAR UNIVERSITY

In 1992, Joel Cohen received a phone call from a journalist at Discover magazine. The journalist asked Cohen, a professor of populations at Rockefeller University with doctorates in applied mathematics and public health, “How many people can the Earth hold?” Cohen replied honestly: “I said to him, ‘I don’t know. I’ll try to find out for you.’ I said to myself, ‘This is your business. You’re supposed to know! What’s the matter with you?’”

Cohen spent the next six weeks reading studies that estimated Earth’s human carrying capacity based on a variety of data, from water and land use to food production to mineral availability to energy. “The more I dug, the more fascinated I became that everybody had an answer, but none of the answers agreed,” says Cohen. “They were all based on different assumptions. . . . The substance just was not there.”

Cohen became so irritated with the answers available that he spent the next four and a half years compiling more than 60 studies and developing mathematical models of the planet’s human carrying capacity. The book and Science paper he ultimately published on the topic concluded that Earth’s human carrying capacity is dynamic, uncertain, and shaped by the interactions of populations, economics, the environment, and cultures. The ecological notion of carrying capacity, while excellent for describing antelope populations on the plains, is not a useful tool for thinking about the challenges facing humans.

“Mathematical thought is the railroad over which we carry the freight of scientific discoveries. And I’ve wanted to help lay a few additional tracks.”

New York's Green Roofs Are Crawling With Fungi

Microscopic photo of an arbuscular mycorrhizal fungus courtesy of the USDA's Agricultural Research Service. USDA

Demand for green roofs might plummet if they became known as "fungal roofs." But that is what they are, at least in New York – and contrary to what it may sound like, it's not a bad thing.

The world just became a little more aware of the hidden-but-teeming biomass of green roofs thanks to the intrepid work of researchers from Barnard College, Columbia University, Fordham and the University of Colorado. Recently, these guys found themselves wondering if the gardens in the sky might support different kinds of life than the stuff at dog-pee level. It's a realm into which few scientific minds have tread. While green roofs as heat-island dampeners and rainwater-runoff plugs have been widely discussed, the extent to which they serve as urban "biodiversity reservoirs" (in the researchers' words) is something of a mystery.

So in the summer of 2011, the team set out to test the soil composition of 10 green roofs stationed at recreation centers throughout the five boroughs:

(Map courtesy of Jeremy Law at Columbia University)

Using soil corers, they hunted for fungi, because fungal communities play a key role in a roof garden's health and longevity. For comparison's sake, they also took samples from five city parks near some of the roofs, including Central Park and the High Line. A little magic from "[i]nductively coupled plasma atomic emission spectroscopy" at Alabama's Auburn University Soil Testing Laboratory, as well as a dollop of phospholipid fatty-acid extraction and Illumina-dye sequencing, and they had their results, which were published this month in the journal PLOS ONE.

So what were the conclusions? 

For one, these sun-kissed carpets of gray goldenrod and smooth blue aster are absolutely crawling with fungi. The researchers logged an average of 109 types of fungi per roof, such as Glomus, Acaulospora, Rhizophagus and Funneliformis, suggesting that green roofs can indeed contribute to urban biodiversity. As they explained:

We found that green roofs supported a diverse fungal community, with numerous taxa belonging to fungal groups capable of surviving in disturbed and polluted habitats. Across roofs, there was significant biogeographical clustering of fungal communities, indicating that community assembly of roof microbes across the greater New York City area is locally variable. Green roof fungal communities were compositionally distinct from city parks and only 54% of the green roof taxa were also found in the park soils.

In other words, the roofs are home to fungi not typically given to squelching around in normal parkland. They also seem to be better for growing stuff you might, you know, put in your mouth: While the soil in New York's parks showed a greater biomass of microbes, it also tested higher for heavy metals, a scourge of urban gardens that can be unhealthy if consumed in larger quantities.

Here's a comparison the researchers put together illustrating how the roofs stacked up against the parks, in terms of the abundance of fungal phyla:

Needless to say, this is hardly the first news of green roofs supporting life. The elevated gardens are routinely patrolled by insects and in some cases much larger fauna. In Australia, for instance, the Adelaide Zoo maintains several grassy roofs that are designed as homes for urban plants and wildlife, like reptiles, insects and bats.

And an immense green roof in the U.K., mounted on a wastewater treatment facility near Brighton, attracts seagulls and crows that pluck at its quaking grass in search of food. To fight those hungry birds, the roof's overseers have released even more animals over the roof – ferocious goshawks, a golden eagle and even a great horned owl.


ORIGINAL: Atlantic Cities

John Metcalfe
Mar 13, 2013

David Benjamin and the future of architecture

ORIGINAL: Azure
Elizabeth Pagliacolo

March 11, 2011

This creation of a new system of biofuel – with 80% less carbon emissions than petroleum fuel – involves design at multiple scales simultaneously, from DNA with a radius of about a billionth of a meter to the planet with a circumference of 40 million meters. (Nathan Smith, Bio Oil Workshop, Columbia GSAPP. Images are from Columbia’s Architecture Bio-Synthesis Project and Bio Oil Workshop

As biological technologies become more available, Do-It-Yourself inventors may engineer algae to create car grilles and catalytic converters that suck carbon from the air as you drive. (Nathan Smith, Bio Oil Workshop, Columbia GSAPP). Images are from Columbia’s Architecture Bio-Synthesis Project and Bio Oil Workshop

As it becomes possible to design cells as tiny, self-replicating computers, new forms of data processing and storage may emerge, such as embedding computing invisibly in our lakes and reservoirs. Cloud computing will become river computing. (Mike Robitz, Architecture Bio-Synthesis Class, Columbia GSAPP). Images are from Columbia’s Architecture Bio-Synthesis Project and Bio Oil Workshop

The co-founder of The Living, David Benjamin is blazing a trail in bringing synthetic biology to architecture.

Along with his partner at The Living, architect Soo-in Yang, Benjamin has already created paradigm-shifting projects, such as
Living Light, an interactive canopy in Seoul that reacts to air quality; and

Living Light (Seoul, 2009) from D B on Vimeo.

Amphibious Architecture, which communicates the level of pollution in New York’s Hudson River.

Amphibious Architecture (New York, 2009) from David Benjamin on Vimeo.

These projects entice people to participate in their environments in new ways, while making them aware of how they’re constantly changing.

At the Conversations in Design symposium hosted by the Interior Design Show in January, Benjamin spoke on the theme of crowd-sourcing as it applies to his firm’s projects as well as those by his students at Columbia University. Benjamin and his colleagues at Columbia developed a framework for students to share architectural tools, and he’s also created a new class exploring synthetic biology in architecture – a subject he’s been immersed in since participating in the National Science Foundation–funded Synthetics Aesthetics Project.

Azure sat down with Benjamin to discuss the brave new future of green architecture.

Why architecture needs to go beyond the blank page

In my teaching at Columbia Graduate School of Architecture, Planning and Preservation, I emphasize collaboration and open source design. This challenges the model of the architect as solitary genius and also the notion that each building has to be a one-off.

In the C-BIP [Columbia Building Intelligence Project] Studio that I teach with Scott Marble and Laura Kurgan, we created a framework for students to work individually to design a database of small-scale building elements, and then work in teams to combine a selection of elements into larger building designs. The teams start with modules of re-usable design intelligence rather than with a blank page, and they pick up where previous studios left off, rather than re-creating everything.

How synthetic biology can solve many persistent problems

Synthetic biology is a radical form of genetic modification. It is a new approach to designing new biological systems not found in nature. And some people say that in the near future, this technology will be the way we make everything, from medicines to fuels to buildings.

One example that is now being commercialized is a new anti-malaria drug. Synthetic biologists designed a way to combine 12 sequences of DNA never found together before and to create a new strain of yeast that could essentially churn out the anti-malaria medicine in a laboratory – without the use of the rare sweet wormwood plant. The new medicine is more pure and ten times cheaper than the old medicine, which means it could save millions of lives.

From the beginning, synthetic biology has been based on a framework from the field of electrical engineering. The idea is that if synthetic biology can develop a catalog of standardized biological parts – like transistors and capacitors in electrical engineering – then there can be a division of labor. Some people will be able to work on making new parts while other people will be able to work on combining the parts into devices and systems. This will allow for the creation of new medicines or new fuels or new building materials without starting from scratch.

This has some clear similarities with our database of building elements, but it potentially involves a wider spectrum of participants. The framework of synthetic biology may allow non-specialists – like architects, artists, computer scientists – to design new biological systems without learning all the details of molecular behavior. Just as non-specialists now combine electrical parts to make electrical circuits, soon they might be able to combine biological parts to make new organisms that perform specific functions. As biological technologies become less expensive and more domesticated, this may lead to an explosion of innovation similar to advances in computers after the domestication of digital technologies in the ‘70s and ‘80s. We may be at a transformative moment now, like the days of Apple Computer tinkering in the garage.

How synthetic biology can inform architecture

But so far, very few architects are working in this area. I am the only architect among six pairs of scientist-designer collaborators in the Synthetic Aesthetics Project, which involves conducting joint research (with funding from the National Science Foundation in the U.S. and the Engineering and Physical Science Research Council in the U.K.) with plant biologist Fernan Federici in the Jim Haseloff Lab at the University of Cambridge, U.K. We are experimenting with synthetic biology and architecture in a real lab with all of the standard safety protocols.

Then at Columbia, we are creating an advanced architecture design studio to teach architecture students to conduct experiments and design with biology. This is part of a new lab I am starting at the School which will conduct long-term research on the intersection of architecture, synthetic biology, and computation. We have just started to work with a software company to develop new computational tools for architecture and synthetic biology.

Why we need to re-think “nature”

We definitely have to be careful with this technology for designing new living systems, but it’s not unprecedented from a philosophical view. First, people have been manipulating nature for thousands of years. Second, the technology’s already out there and the best way to deal with the risks is probably to increase awareness and knowledge, rather than outlawing it, which would just push malicious projects underground. Third, what’s most crucial for me – and this relates to Amphibious Architecture [developed by Benjamin and Yang at the Living Architecture Lab at Columbia, in collaboration with Natalie Jeremijenko] – is that the “do nothing” approach is not always the safest approach. In New York, the rivers have been damaged by years of pollution and development, and some public agencies say it’s best to do nothing at this point. But it’s actually better to remediate and experiment in order to re-engineer a viable eco-system, to re-introduce species, to build special reefs and piles so mussels and oysters can grow. In the case of synthetic biology, there are many urgent problems that the new science might be able to address. I’m not blindly faithful in technology, but I think at this point the benefits of synthetic biology far outweigh the risks.

How we will one day grow our buildings

Some of the first applications of synthetic biology and architecture may involve high-performance materials like carbon-sequestering concrete and self-healing silicone. But in the future, architects may be able to program the DNA of a seed so that it grows into a building. Then, instead of architects designing plans and sections, instead of bringing all of the construction materials from the factory to the site, architects might be able to design rules for growth and differentiation and material performance. And the new biological machine – the living building – might be able to use the nutrients of the land and the natural ecosystem to do both the factory manufacturing and the site construction.

In some ways, it’s tempting to wait until the technology becomes more advanced before we get involved as architects. But if we wait too long, there’s a risk in that too. Architects should help think about the frameworks and the protocols and the potential applications of synthetic biology. Architects should engage in the discussion about risks and utopian visions and design tools before these things get frozen and the design palette gets limited.

The thing that ties it all together for me is this sinking feeling I have that we’re at this crucial moment where we know what the stakes are, and what we need to do, but we aren’t acting. We’re still not acting intelligently about the crisis of climate change. Of course, a large part of our response as architects must be to aggressively use all of our known and existing strategies to increase the environmental performance of buildings. But I also think some architects should be searching for radical new strategies that might change our idea of what’s possible. Some experiments may fail, but some crazy ideas – like combining architecture and synthetic biology and growing buildings – may eventually change how we think about architecture, and how we live, work, and come together in cities.

Bats a Source of MERS?

ORIGINAL: The Scientist
By Kate Yandell

August 23, 2013

A fragment of viral RNA isolated from an Egyptian tomb bat matches viral RNA isolated from the first human victim of the novel coronavirus.

MERS coronavirus. NIAID

Researchers may have found a source for the first reported human case of Middle East respiratory syndrome (MERS), which is caused by a coronavirus that has infected more than 100 people in the region and killed 49. A sequence fragment derived from an Egyptian tomb bat matches viral RNA isolated from a Saudi Arabian man who died from the virus in June 2012, according to a report published this week in Emerging Infectious Diseases.

The 182-nucleotide fragment was found in a fecal sample from a bat of the species Taphozous perforatus, which was captured within 7.5 miles of the victim’s home. The bat-derived sequence was identical to the corresponding section of viral RNA isolated from the victim.

But some researchers note that the short stretch of nucleotides is not enough to establish that the bat- and human-derived viruses are one and the same. Marion Koopmans, an epidemiologist at the National Institute for Public Health and the Environment in the Netherlands, told ScienceNOW that the findings indicate that bats are a reservoir of the virus. However, she added, the RNA snippet comes from a relatively non-variable region of the viral genome.

“There’s still potential for it to be relatively distant if we had the complete genome,” Andrew Rambaut, who studies molecular evolution at the University of Edinburgh, told The Canadian Press.

The RNA fragment was likely so short because the bat samples thawed after being opened in customs en route to study coauthor Ian Lipkin’s virology lab at Columbia University. Lipkin noted that while bats may play a role in human MERS, there are likely other missing links in the chain of transmission.

“There have been so many cases of MERS described in the Middle East where we cannot make a direct link with bats,” he told ScienceNOW. “So there is likely to be an intermediate host.”

Some MERS victims have reported contact with camels, which appear to be susceptible to the virus, implicating the animals as potential disease transmitters.

Extracted Oil And Gas Wastewater Causing Earthquakes?

ORIGINAL: The Energy Colective

Joseph Romm

March 29, 2013

A 2011 magnitude 5.7 quake in OK, linked to wastewater injection, buckled US Highway 62. (Credit: John Leeman)

After pulling massive amounts of fossil fuels out of the Earth’s crust so we can burn it up into our atmosphere, we have a good sense of where the stuff goes. Our oceans. A global greenhouse. Our lungs. But what happens to the ground formerly occupied by those fossil fuels?

It’s becoming increasingly clear that oil and gas extraction processes are actually weakening the structural integrity of the Earth’s crust just enough to cause more frequent earthquakes, in places not used to them.

Oklahoma, for instance, is not known for earthquakes. Yet the central U.S. has seen an elevenfold jump in recent years, including the Sooner State’s largest earthquake on record. This 5.7-magnitude quake occurred on November 6, 2011 near Prague, Oklahoma. And research published yesterday in Geology from the University of Oklahoma, Columbia University, and the U.S. Geological Survey has made a direct connection to the disposal of wastewater from conventional oil production:

A new study in the journal Geology is the latest to tie a string of unusual earthquakes, in this case, in central Oklahoma, to the injection of wastewater deep underground. Researchers now say that the magnitude 5.7 earthquake near Prague, Okla., on Nov. 6, 2011, may also be the largest ever linked to wastewater injection. Felt as far away as Milwaukee, more than 800 miles away, the quake — the biggest ever recorded in Oklahoma — destroyed 14 homes, buckled a federal highway and left two people injured. Small earthquakes continue to be recorded in the area.

The recent boom in U.S. energy production has produced massive amounts of wastewater. The water is used both in hydrofracking, which cracks open rocks to release natural gas, and in coaxing petroleum out of conventional oil wells. In both cases, the brine and chemical-laced water has to be disposed of, often by injecting it back underground elsewhere, where it has the potential to trigger earthquakes. The water linked to the Prague quakes was a byproduct of oil extraction at one set of oil wells, and was pumped into another set of depleted oil wells targeted for waste storage.

As Climate Progress has written before, this practice of disposing chemical-laced water generated during the extraction of oil and gas has far-reaching effects. Drillers have been doing this for more than a decade, and the researchers note that the Oklahoma quake did not actually require very much wastewater. In fact, because we have been doing this for so long, the built-up pressure in the Earth’s crust changes the criteria of how quakes happen. The study’s abstract notes:

Significantly, this case indicates that decades-long lags between the commencement of fluid injection and the onset of induced earthquakes are possible, and modifies our common criteria for fluid-induced events.

So we could be paying for more than a decade of wastewater injection and fracking for quite some time with earthquakes. There’s not much more room 9,000 feet down. Wellhead records indicate that pressure in these areas underground increased by a factor of ten from 2001 to 2006.

Fracking usually receives more attention for seismic activity than wastewater injection. Ohio banned fracking “to stop the ground from shaking.” But it’s the whole process of drilling (oil and gas), fracking, and then disposal that contributes to the problem.

A tanker truck prepares to leave OH Water plant that removes metals and chemicals from fracking wastewater. (Photo: Scott Galvin)

Can we stop doing this? Recycling the wastewater is cheaper, and more and more gas companies have started contracting out to do just that. But as Ohio Department of Natural Resources officials note, it’s hard to track where this water goes because it is not regulated. This is rather important because the water is laced with toxic metals, dangerous chemicals, and radium. Recycling companies say the waste ends up in landfills.

So the two options are to either inject it back down in the ground where it lubricates fault lines enough to cause earthquakes in Oklahoma and Ohio, or hope that radium doesn’t leak out of landfills.

Renewable fuels sound better and better the more we learn about enhanced drilling for unconventional oil and gas.

Authored by:

Joseph Romm

Joe Romm is a Fellow at American Progress and is the editor of Climate Progress, which New York Times columnist Tom Friedman called "the indispensable blog" and Time magazine named one of the 25 "Best Blogs of 2010." In 2009, Rolling Stone put Romm #88 on its list of 100 "people who are reinventing America." Time named him a "Hero of the Environment″ and “The Web’s most influential ...

Rafael Yuste y el Brain Activity Map (Podcast)

ORIGINAL: Naukas

Luis Quevedo

18 marzo, 2013

En la sexta entrega de Ideómica hablamos con el reputado neurocientífico de la Columbia University, Rafael Yuste. Él es uno de las cinco mentes detrás del reciente anuncio por parte de Barak Obama del lanzamiento de un mega proyecto de investigación en neurociencia: el Brain Activity Map o Mapa de Actividad Cerebral.

*Si no te funciona el reproductor Flash, aquí tienes un link directo al podcast.

¿En qué consiste este proyecto que los expertos comparan en dimensión y ambición al Proyecto Genoma Humano? Rafael nos cuenta en detalle el qué, cómo y cuándo de esta nueva aventura neurocientífica.

Si acabas de llegar a ideómica, te recomiendo que le eches una ojeada al Porqué de este proyecto y, si te apetece, síguenos en Twitter y Facebook.

La próxima conversación en el podcast de las ideas será con el físico valenciano afincado en el MIT, Roberto Sanchís Ojeda. Con él hemos hablado de la búsqueda de planetas extrasolares con el telescopio Kepler, de la ciencia y la vida de un científico en España y Estados Unidos y mucho más.

Quiero recordarte que todo lo que hacemos, el podcast de Ideómica y el de La ciencia de los viernes: Probeta en Nueva York, lo hacemos por amor al arte. Al arte y a la ciencia, claro. Si te ha gustado, compártelo, tuitea, cuelga en facebook, lo que te apetezca. nuestra única ambición es que, tal vez, hayas pasado un buen rato escuchándolo y con mucha más suerte todavía, te hayas encontrado con alguna idea nueva por el camino.

Gracias.

Sigue a Rafa en Twitter o visita su página web aquí.

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