synthetic aesthetics

SB 5.0

cagapakis — Tue, 14 Jun 2011 08:20:36 +0000

SB 5.0

I'm making my way up to SB 5.0 for what promises to be a great conference. If you're going too, come say hi and smell some cheeses during the poster session!

cagapakis Tue, 06/14/2011 - 04:20

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synthetic aesthetics

synthetic biology

Designer Bacteria

cagapakis — Fri, 11 Feb 2011 07:42:24 +0000

Designer Bacteria

Synthetic biologists work on designing living cells, but engineered bacteria don't usually come up when you think of "designer" things. This year however, a synthetic biology design is up for a Brit Insurance Design of the Year award, up against the Lanvin Spring collection, Angry Birds, and Rock Band 3! Designers Daisy Ginsberg and James King worked in collaboration with the 2009 Cambridge iGEM team (including awesome blogger Lab Rat) to imagine ways that people could use bacteria engineered to produce pigments in the future. Check out their video about the science and design of E. chromi:

cagapakis Fri, 02/11/2011 - 02:42

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Interesting... Unfortunately, the eejits will scream "IT'S UNNATURAL! ONLY DOG IS ALLOWED TO DO THAT SORT OF THING!" and completely present things out of context, while misrepresenting the facts.
Fortunately, this is in Britain, so there may not be actual death threats against participants (sigh).

So far have received no death threats!

Also no one has asked me to make any dogs go purple...

Purple bacteria are, in my opinion, slightly *more* natural than mobile-phone games, which is the competition that we are up against...

I'd love to see this, but the graphic doesn't open as a video for me. Is it being blocked by AdBlocker or something?

Here's the direct link to vimeo in case the embedded video isn't working for you: http://vimeo.com/19759432

Orange Liberation Front? Really? I guess I don't understand the second half of the video. I'm totally down with chromatic engineering of bacteria (seems like you a "You had me at hello" sort of situation), but I'm not sure why the timeline with the fantastical speculations is necessary.

A lot of those crazy ideas in the timeline (I think) were ideas that the iGEM students came up with during a workshop designed to make them think creatively about future implications of their work. It's easier to understand the possible short-term uses but difficult to imagine what the future will be like. Some of them can get silly perhaps, but it's a great exercise for any student and biological engineer.

can you guys make some retroviruses that implant glow in the dark or UV reactive pigment sequences into my dermal cells, please. that'd be cool. and i'm jealous. when i was at cambridge we weren't writing bio code.

Chemical Cartography

cagapakis — Sat, 13 Nov 2010 14:01:23 +0000

Chemical Cartography

Everything has a unique chemical signature. Every body, every place. When you smell home you're sensing all the chemical traces that make up the place you grew up. When you smell your mate, you're smelling the unique combination of their body and the microbiome of their skin.

The unique smell of a city is something that my Synthetic Aesthetics partner, Sissel Tolaas, has been interested in for a long time. Yesterday in her lab I got to smell her recreations of the smells of Paris--the corner bakery, dog poop on the sidewalk, old rusty cars, cigarettes and perfume, sun on the street after heavy rain.

She's analyzed the smells of several cities, creating scratch-and sniff maps of Mexico City, beautiful perfume bottles filled with the smell of Berlin neighborhoods, and smell profiles of cities as different as Vienna and Kansas City.

Yesterday I also learned via @bldgblog that DARPA is seeking proposals around a similar project, collecting and cataloging the normal chemical traces and smells of cities in order to be able to rapidly detect an airborne chemical attack. Sissel maps city smells to explore the boundaries we create in cities, to repackage and recontextualize the sometimes gross smells we encounter in our urban environments, to question the language we use to describe smells. She's quoted in a great Edible Geography article saying:

Challenging people to use their noses gives them new methods to approach theirâ¨ realities; it doesn't matter whether they smell a so-called bad or good smell. What countsâ¨ is that they rediscover their own surroundings in that very moment--be it other humanâ¨ beings, places, the city -- and start to approach it differently.

I'm curious about what the effect of the DARPA project will be. Will people become more aware of their smell environment when more fine-grained and technical information is available about the spatio-temporal distribution of chemicals in the city air? Will smell information become just another facet to organize our fear around? The data is likely to be fascinating either way, an "X-ray of the air" that we can use to better understand the air that we breath every day.

cagapakis Sat, 11/13/2010 - 09:01

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I think that dogs navigate by smell. That's why they want to stick their nose out the window when riding in a car.

wohoo-youre back to blogging :)

p.s. ill order some miracle fruits when im back home in germany- it was a great idea for the poster session (when life gives you lemons... ;) )

Hahaha nice pic in the first post... they should hire a K9 to help them categorize the smell. I'm curious how they do identify different smell, any idea? anyway if you need candida cures just leave me a pm.

Olfactory-like signaling in mammalian sperm

cagapakis — Sun, 26 Sep 2010 19:54:49 +0000

Olfactory-like signaling in mammalian sperm

So I was browsing the internet for info on G-protein coupled receptors and ended up finding some interesting facts about sperm. It turns out sperm don't just swim blindly, hoping to randomly bump into eggs. Instead, like bacteria, sperm can sense their chemical environment and adjust their swimming accordingly. Sperm have a sense of smell.

The (g-protein coupled) olfactory receptors in our noses that activate our sense of smell were discovered in 1991, an amazing discovery that earned the 2004 Nobel prize for physiology or medicine. The receptors sit on the surface of the cells up high in our nose, and smelly chemicals in the air we breath bounce around on them. When a molecule bounces onto the specialized receptor that recognizes it, the receptor turns on and activates the G-protein coupled to it, in this case G-olf. G-olf then goes on to activate a cascade of other proteins which end up opening protein channels in the cell's membrane, allowing ions to flow through. The ion flow changes the electrical potential of the cell and starts the electrical signal that will make it all the way to the brain--that is if the receptor is in your nose.

After the initial discovery in the nose, olfactory receptors kept showing up in all sorts of tissues--in the heart, in the spleen, in the prostate, and even in sperm. On the sperm cell, what the receptors are doing is a lot harder to figure out than in the nose, especially in a way that is meaningful to how sperm swim in their natural environment. In vitro studies of sperm in a test tube identified chemicals that can activate the sperm olfactory receptors and others that will block them, but the model of how the receptors are connected to the waves of calcium ions that control the swimming motion of sperm is full of question marks. Even the chemical that sperm swim towards in vitro has no apparent physiological significance, bourgeonal being a chemical common in perfumery for its lily of the valley scent. Understanding the biochemistry of the sperm olfactory receptors in their physiological context may some day have impacts in fertility treatments, in vitro fertilization technology, and perhaps even hormone-free contraceptives, although the authors of the review that introduced me to world of sperm olfaction cautiously note that:

such speculation may still be a long way from future drug development and subsequent clinical trials. It will be challenging to demonstrate efficiency and inoffensiveness of potential pharmaca as well as to discover suitable ways of drug application.

Olfactory receptors turning up in unexpected places can expand our understanding of the way that cells interact with their environment, whether it's how we navigate our smellscape or how sperm navigate to the egg. Findings like these also highlight the generalness of many of the proteins involved in cellular signaling and the flexibility of the olfactory receptors themselves--their general usefulness in sensing chemicals for all kinds of cells and the evolutionary conservation that allows even yeast to be engineered to have a sense of smell. So three cheers for olfaction and three cheers for all the G-protein coupled receptors!

cagapakis Sun, 09/26/2010 - 15:54

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one immediate application: lily-of-the-valley-scented birth control!

er, prophylactics.

thanks for the heads-up on this research! very cool stuff!

Fascinating research, but I really wonder why any woman would want birth control that *doesn't* switch off your periods - ill for a week or more each month, versus slightly reduced life expectancy. Not a difficult call.

If you went back far enough in evolutionary time, to our parent fishes and then far, far beyond, would human evolutionary history coincide with that of human gametes?

In other words, is it evolutionarily reasonable to say that we are eggs and sperm writ multicellular? Or, at least, that our earliest multicellular ancestors were? Or is that unresolved because the origin of sexual reproduction is unresolved?

In other other wordsâ¦ do sperm sensory features likely date back to the period when our ancestors were multicellular, or do they likely come afterwards, as an innovation specifically in the environment of navigating the body of the female? Or is it in-between, dating from the phase where, like modern fish, our reproduction didn't involve connective mating?

In any case, sperm sensation is apparently useful today, whether that's due to aiding the sperm's "host human" or (much more likely) out-competing the human's other sperm.

This is also the same way leukocytes (including neutrophils, macrophages and lymphocytes) migrate to sites of inflammation. Cells at inflammation sites release chemokines that interact with the GPCR of leukocytes and modify their cytoskeleton - making them move up the chemokine concentration gradient, towards the source of inflammation.
GPCRs are pretty badass! :)

G-Spot.

"So I was browsing the internet for info on G-protein coupled receptors"

I used to do that all the time; it's hard for single G-proteins to find an acceptable partner in the hustle and bustle of modern life, but then I found
www.sikapaga.com

Sure, there's a survey to fill out, and a fee to pay, but judging by the gushing testimonials, a lot of lonely G-proteins have found their ideal life partner this way....

G-protein coupled receptors and ended up finding some interesting facts about sperm. I loved all of these posts. A lot of these things we have, but I got some really great ideas.

Wireless Cellular Communication

cagapakis — Wed, 08 Sep 2010 09:40:33 +0000

Wireless Cellular Communication

Cells are constantly jibber jabbering, sending messages to each other to coordinate behavior, both within a population of single-celled organisms or between cells of an individual multicellular organism. Most of these signals are chemicals that float around in the liquid that surrounds the cells but there recently has been an increased appreciation for cells' sense of "smell"--how cells respond to chemicals that are present as gasses.

A brand new paper outlines the discovery of "olfaction" in a species of bacteria, Bacillus licheniformis. Trying to save space on a 96 well dish by putting different experiments side by side, the researchers accidentally discovered that even though each experimental strain was separated in its own plastic well, bacteria growing closer to wells that were producing gaseous ammonia were forming more pigment and more vigorous biofilms. As olfaction can be defined at its simplest as responding in some way to volatile chemicals, these bacteria seem to display olfaction, although the details of how the ammonia to biofilm response occurs have not yet been explored.

In higher organisms such as fungi, response to gasses has been better studied, allowing for the creation of genetic parts for synthetic biology that turn on in the presence of volatile acetaldehyde. When the DNA sequence responsible for sensing acetaldehyde from the fungus Aspergillus nidulans is engineered into cultured hamster cells, gene activation can be measured as a function of distance away from the source of acetaldehyde on a plate:

The acetaldehyde-smelling part can be used to activate any gene that the researcher wants, including genes that are required for the cell's survival. Such a strain would require an acetaldehyde producing strain nearby in order to survive, creating a synthetic ecosystem that communicates through the air!

Being able to listen in to cellular conversations and understanding all the ways that organisms can sense and interact with their environment is amazing and incredibly powerful for the synthetic biology toolbox. Like natural ecosystems, synthetic biological systems made up of multiple engineered strains or even species can create ecosystems that together can do much more than any one species alone.

cagapakis Wed, 09/08/2010 - 05:40

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So there's not just WiFi, but also WiO (pronunciation pungently obvious)?

(Incidentally, I came across this reference to your German blog partner: http://tiny.cc/qdf1d)

My heavens, that's fantastic discovery. So, we can conclude that we humans are again second.

Cyborg Noses

cagapakis — Mon, 06 Sep 2010 08:27:55 +0000

Cyborg Noses

A lot of synthetic biology is about getting biology to be more like electrical engineering, designing genetic "logic gates" to create a living circuit board. Beyond analogies, however, cells have many fascinating electrical properties--proteins that transfer electrons like wires, membranes that separate ions and create an electrical charge that drives the metabolism of the cell, channels through these membranes that open and close to activate an electro-biological response. Electrons are electrons whether they are in proteins or copper wires, and many scientists have designed ways to connect the soft and squishy electrical flows of living systems to the hard electricity of computers, creating hybrid cyborgs that play to the different but compatible strengths of cells and computers. One emergent application of such technology is in the design of chemical sensors, connecting the amazing ability of cells to sense and respond to very small changes in the environment to a human-readable output on a computer screen or even to a robot that can move and seek out the source of a chemical.

An amazing recent paper from a Japanese research group shows how such a cyborg nose could work. The team worked with frog eggs, large and hardy cells that are relatively easy to manipulate one at a time, placing them into a specially designed chamber where the electrical state of the cell could be measured by a computer while different solutions flowed across the surface of the cell. However, egg cells can't "smell" on their own, they need to be engineered with receptors that can sense and respond to chemicals in the solution. To accomplish this, the researchers engineered the egg cells to express the smell receptors from various insects on their surface. Mammalian smell receptors activate a cascade of signals inside the cell that are difficult to measure without biochemistry, but insect smell receptors are much simpler, opening a channel through the membrane that rapidly changes the electrical state of the cell. Since the electrical potential is constantly being measured by the special chamber, when the right chemical binds to the receptor and opens the channel, the computer "sees" the smell.

Once the computer sees the chemicals, that signal can be translated into any other mechanical system. In a simple but awesome demonstration of the ability to connect the chemical biosensor to robots, the egg cell chamber was mounted into the nose of a robotic mannequin head. When the chemical was sensed, the robot shook its head from side to side. The cells are highly sensitive, able to sense very small chemical concentrations, and highly specific, able to distinguish between similar molecules with a high tolerance for noise.

Cells don't have to be computers to be able to do amazing things with computers. Biology has unique and powerful skills, and biologically inspired and biologically integrated engineering has great potential for all kinds of new cyborgs.

cagapakis Mon, 09/06/2010 - 04:27

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electrical engineering

genetic engineering

olfaction

That insane I cant even begin to comprehend that a computer can "smell"

Smellscape

cagapakis — Wed, 04 Aug 2010 10:01:22 +0000

Smellscape

My Synthetic Aesthetics partner, Sissel Tolaas, is featured in the terrific current issue of the German interview magazine mono.kultur. Her work focuses on smell, exploring the unique smellscapes of different cities, creating provocative scents to show in art galleries, branded "logo" scents for Adidas, "Swedish" scents for Ikea, and therapeutic memory-triggering scents, part of the healing process for patients dealing with traumatic experiences. Until we have smell-o-vision, her work is almost aggressively analog--"beyond what is seen and heard to something indiscernible yet more immediately telling than anything else"; smells are impossible to show online, impossible to experience without a physical and emotional response. It is this response, this primitive communication and understanding through smell that she captures in her work. Interspersed between the pages of the fascinating interview where she discusses her inspirations, her intentions, and her process are blank pages coated with fancy scratch-and-sniff micro-bubbles of her scent creations. As you rub the pages between your fingers, the scents are released, almost like the perfume samples stinking up women's fashion magazines but much more powerful and evocative than any advertisement.

The 12 scents presented in the magazine are intended to provoke, to explore the smells of the human body in a context that allows them to be more than just "good" or "bad". Part of her 2006 exhibit at MIT's List Visual Arts Center the Fear of Smell--the Smell of Fear, the scents are chemically recreated versions of the smell of sweat produced by men suffering from extreme anxiety disorders in their most fearful situations. The sweat is collected in tiny underarm vacuum cleaners and shipped to Sissel's Berlin lab/studio for analysis and recreation. The scents can communicate fear, violence, aggression, but also a surprising complexity and passion. For Sissel, "Nothing stinks--only thinking makes it so!"

Nose training can teach us to look beyond just "good" or "bad" smells, to identify different components, to feel what is being communicated through smells, and she teaches classes around the world to get students to just this point:

I train them to relate to smells from the perspective of curiosity by saying 'listen, could this give you some information that you pass by or leave out because you were not used to seeing it as information'

Or to release it from certain stereotypes by abstracting it?

Of course. With sweat, it's the same -- they're difficult smells for a lot of people. If you see a person and smell his sweat up front, you back off. But if I position the same smell in an aesthetic displacement, you approach it differently: You come back and you're fascinated!

Experienced as blank pages in a beautifully designed magazine, the sweat smells almost good--musky, piney, deep scents that made my chest clench while reading. But it is the differences between the different pages that makes the experience so complex and interesting: Guy #10's cool, almost melon-scented overtones, Guy #6's cinnamon, Guy #9's seductiveness that made one gallery visitor "come every day for three months and kiss the wall up and down with different lipsticks." There is a lot of emotion lurking in the smells, enough to completely envelope and affect the magazine reader, enough that another gallery visitor, "a 90-year-old man started to cry in front of Guy #05."

These differences can communicate a lot about us to others, but we've all but eliminated this part of our life from our cultural experience--

We all dress smells: we spray on deodorant or use soap that smells the same on everyone. So we are all soldiers, or slaves, of certain scent systems...

People manipulate their olfactory identity and surroundings to establish or maintain their class identity--to fit in!..What is the meaning of 'clean'? What is the meaning of 'dirty'? What defines a 'good' smell? Who made these rules, anyway? They were made by the commercial world for white middle-class Europeans from a certain time and they've remained with us forever. But we are living in a global world where the definition of cleanliness and 'bad' and 'good' is completely different...

In the 21st century, the ideal society is presented as deodorised. The fantasy worlds created for us are totally odourless. They exist only in the domains of vision and sound.

What will the future hold for our smellscape? Will globalization completely deodorize our world, making everything smell of soap? Perhaps, but perhaps biology, with all its living smells, will be re-introduced into our lives. As we better understand how our bodies are made up of marvelously diverse communities of bacteria and human cells living in evolutionary harmony, and as synthetic biology pushes to replace many of our industrial processes with living systems, perhaps the definitions of "good" and "bad", "natural" and "synthetic" will begin to change too. Artwork that can provoke us to think about and reconsider how we've constructed our world, what we think of as "normal," can be tremendously powerful, can offer potential for radical change--"We must provoke one another to think differently. If we get to the moment of provocation, then there is hope."

cagapakis Wed, 08/04/2010 - 06:01

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Synthetic Aesthetics

cagapakis — Sun, 11 Jul 2010 06:23:01 +0000

Synthetic Aesthetics

I am thrilled to announce that I will be one of the Synthetic Aesthetics residents this fall. Synthetic Aesthetics is a new program run through Stanford and the University of Edinburgh and funded by the National Science Foundation and the UK's Engineering and Physical Sciences Research Council that asks the question "how would you design nature?":

Synthetic Biology is a new approach to engineering biology, generally defined as the application of engineering principles to the complexity of biology. Biology has become a new material for engineering. From biological circuits made from DNA to entire systems, synthetic biology is interested in making biology something that can be designed.

Traditional engineering disciplines have tackled design by working alongside designers and developing longstanding collaborations. Synthetic Aesthetics is a research project jointly run by the University of Edinburgh and Stanford University that aims to bring together synthetic biologists, social scientists, designers, artists, and other creative practitioners, to explore collaborations between synthetic biology and the creative professions. Interaction between these two broad fields has the potential to lead to new forms of engineering, new schools of art and design, a greater social scientific understanding of science and engineering, and new approaches to societal engagement with synthetic biology.

The complex intersections between science, engineering, technology, art, design, and social sciences highlighted by synthetic biology have fascinated me for a long time, and I am very excited to be able to explore these issues while working with Sissel Tolaas, an odor artist whose work focuses on how we communicate and interact with our environment through scent. I will of course be writing here and elsewhere about our project and that of the other residents, as we all try to figure out how we would design nature together.

cagapakis Sun, 07/11/2010 - 02:23

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Congratulations Christina!

Design and nature have a highly fraught intersection. You get biblical literalists straining to see perfect design in the violently dispassionate hodge-podge of nature, dreadlocked architects trying to make cities of the future look like Endor (good luck, homes), paleo-artists drafting pink and purple tyrannosaurs with zero consideration to the aesthetics of the living nature around them, those bad-ass german robotics guys making floaty air-penguins, Victorian-era diatom arrangements, and....

So on. It's war, I say! Have fun, but more importantly, fight to win.

That sounds great! I was tempted to apply myself, but I think they wanted people wit actual labs rather than just floating currently-jobless lab students for applications :) It sounded like a really awesome project though, so should be fun.

Congratulations, Christina. Sounds like a wonderful opportunity and a fascinating collaboration! We visit your blog from time to time and love your perspective. If you are interested in using film/television to express your team's findings, please get in touch... you can check out our team at www.compasslight.com

congrates christina...