This place in the Bay Area Stochastic Labs(not much information on them) was asking for applications to give $20k to Science, Art, Technology projects. I heard about it with about 24 hours before it was due but decided to write something up because I thought it would be a good exercise and a good way to put some of my thoughts down.
Here it is in all it's glory:
Bio (500 words)
My name is Dr. Josiah Zayner (really Dr.? yeah I know seems pretentious sorry) and I work as a research Scientist at NASA attempting to develop biotechnology for long-term space exploration and colonization. I started in on science and technology in my late teens. At the age of 19 I received a job with Motorola as a Network Engineer and Programmer for their iDEN cell phone network. In the early 2000s I was laid off when the tech bubble burst and I decided to goto college. I ended up with a B.A. in Plant Biology from Southern Illinois University and an M.S. in Cell and Molecular Biology from Appalachian State. For my Ph.D. I studied how light activated proteins function and how to develop them as optogenetic tools. I received my Ph.D. from the Department of Biochemistry and Molecular Biophysics at the University of Chicago in 2013 where I won the Best Thesis Award. I am currently(Till Dec. 2014) an Imagine Science Artist in Residence and a self-taught computer.microcontroller programmer and electrical engineer. I even wrote a slightly useful piece of software for firewall testing and network troubleshooting called IP Sorcery. Definitely, my claim to fame… No, no it was biotech’s first musical instrument, the Chromochord (http://www.scientificamerican.com/article/biotechs-first-musical-instrument-plays-proteins-like-piano-keys-slideshow/). Or even The ILIAD project (http://www.npr.org/blogs/health/2013/12/04/248854769/scientists-turn-to-the-crowd-in-quest-for-new-antibiotics?ft=1&f=1001). or maybe The Kglove?(http://doitourselfscience.blogspot.com/2014/05/the-kglove.html)
What project are you most known for?(500 words)
If I had to choose a single project that I am most well known for it would probably be The Chromochord. The Chromochord is a musical instrument that allows the musician to strum proteins quantum mechanically like they would strum a guitar. The basis of the instrument is s type of protein called Light-Oxygen-Voltage ((LOV) Pronounced Love) domains. These proteins respond to light by undergoing a quantum mechanical energy transition(from a singlet to triplet state) that changes their photo absorption properties. This can be measured spectroscopically. Once in this triplet state this “vibration” decays over time due somewhat to thermal energy. It is very analogous to strumming a guitar string and the kinetics can probably be modeled very similarly. The measured values from these fluctuations in excitation and decay can be used digitally to modulate MIDI notes on a computer. It basically works by the musician interacting with the protein using light by activating LEDs, the excitation of the protein is measured spectroscopically as it is excited or decays and then the computer sonifies this into whatever sound the musician wishes. For The Chromochord I wrote the software and built the hardware and synthetically created and purified the proteins. I have given a number of concerts, talks and demonstrations on The Chromochord.
More Information and media on The Chromochord can be found:
http://www.scientificamerican.com/article/biotechs-first-musical-instrument-plays-proteins-like-piano-keys-slideshow/
http://www.theverge.com/2013/9/5/4694324/biophysicist-uses-proteins-to-create-chromochord
http://en.wikipedia.org/wiki/Chromochord
https://www.youtube.com/watch?v=LJoFazIJ3w4
https://www.youtube.com/watch?v=jlp-k8tqVl0
What project are you most proud of?(500 words)
The project that I am most proud if would probably not be the conventional definition of a “project”. It is my Ph.D. Thesis. I remember the first journal article I wrote that my thesis would stem from (https://drive.google.com/file/d/0B_R75gIJvkFUeVAzZWxsRjJ3R28/edit?usp=sharing). I poured my heart into that article. All the beauty and pain and Science that was me at that point in time is in that article. The figures of the publication were painstakingly crafted to try and portray how much this work meant to me. My Science had become Art and I just wanted others to recognize that. Unfortunately, Science is a very critical and ego driven world. My paper suffered many blows by people who knew little about the Science behind the work. My life changed after that. Science to me was no longer about publishing in well respected journals or being famous or receiving a prestigious professorship and instead became about the beauty in the experiment. My Thesis work became about beauty and creativity, seeing and creating something that I was proud of and something that was beautiful regardless of what others thought of it. My Thesis is the most personal and insightful document into me and my life except instead of a narrative the descriptions are my experiments. Very few people will ever be able to read it and understand me that way because the key to unlock that insight is knowledge and knowledge is not something that can be bought.
My thesis can be found here: https://drive.google.com/file/d/0B_R75gIJvkFUWVAxNWVNTFRmX0E/edit?usp=sharing
Tell Us about your project(1000 Words)
The project I have been working to create is the first living rewritable hard drive. Using light activated gene expression of fluorescent proteins in engineered bacteria I plan to create a computer interface that allows the writing of data to wells of bacteria. The system will be comprised of three major parts: 1) Engineered DNA and Bacteria 2) Camera and Lighting System for Fluorescent Imaging 2) A Computer to Record Data and Interact with the Bacteria.
The Bacterial system will be composed of two plasmids: one will contain a blue light activated gene expression system that creates the Red Fluorescent Protein(RFP) that can be imaged, with a degradation tag, the other plasmid is a green light activated gene expression system that expresses the ClpA, ClpP and ClpX proteins that will degrade the RFP due to the degradation tag. The bacteria will be placed in a 384 well plate, 1 bit per well. When the bacteria express the RFP it will accumulate and will denote a 1. When there is no RFP or the RFP falls below a certain level due to degradation the value will be a 0. This allows 48 bytes of information storage. The camera, lighting and filter system will image the plate for processing on the computer. The computer will read the values and reconstruct the data just as if the data was stored on a hard drive or other media.
By exposing a well to blue light, the bacteria will be “written to” by expressing the RFP protein that can be imaged. By exposing a well to green light, the bacteria will be “erased” as the RFP is degraded.
The blue light system has been mostly created into a plasmid by Ohlendorf et al., only the tag needs to be added to the RFP. All the DNA sequences and primers have been designed and only need to ordered. The parts that need to be accomplished are: the ClpA and ClpX proteins need to deleted out of the bacterial genome, the green light system DNA needs to be ordered and cloned into a plasmid. The hardware and software need to be created. Because the lighting hardware will be very similar to The Chromochord I will base it off that, which should significantly ease the developmental process.
All Engineered Bacteria, Plasmids and DNA will be made available Open and Free to the community of biohackers and anyone else who wants them. All software and hardware schematics created will also be made Open and Free so others can create their own systems.
References
Ohlendorf et al. (2012) From Dusk till Dawn: One-Plasmid Systems forLight-Regulated Gene Expression
https://drive.google.com/file/d/0B_R75gIJvkFUaTVNN0NhVnFTN2s/edit?usp=sharing
Farrell et al. (2005) Cytoplasmic degradation of ssrA-tagged proteins
https://drive.google.com/file/d/0B_R75gIJvkFUUVNuNEpwZEk5M3M/edit?usp=sharing
How is your project Innovative(500 Words)
There has been very limited work done on biological rewritable systems. A publication by Jerome Bonnet in 2012 attempted to use recombination to create a rewritable system in bacteria. However, it suffered from from two major problems: 1) It is extremely noisy and requires precise tuning to achieve the rewritable nature of the system 2) It requires the addition of chemicals to switch the state of the system. This makes the system unusable as a living hard drive. As far as I know, there has not been any other work that attempts biological storing of information and rewriting.
Other working attempts to use DNA to store information is not a viable rewriting solution as we do not know how to manipulate DNA on the level of writing and rewriting yet in a living cell.
How does one define Innovative? Because some people think Yo is Innovative (http://valleywag.gawker.com/the-man-who-gave-yo-200-000-1593328826). I would rather describe this project as unique, interesting, inspiring and perhaps a little beautiful. No one has ever created something like this. People will be able to visualize the inner workings of the device and interact with it by writing to the living drive. Whatever people want to call it, I just think it is damn cool.
References
Bonnet et al. (2012) Rewritable digital data storage in live cells via engineered control of recombination directionality https://drive.google.com/file/d/0B_R75gIJvkFUM21KR1FRVnFmbk0/edit?usp=sharing
How do you plan to reach.build your audience or user base(500 words)
I plan to reach my audience and user base using many different mediums. I write actively for my personal blog about Science, Technology and Art (http://doitourselfscience.blogspot.com/) and would document the process. I am a member and teach classes at Biocurious in Sunnyvale and would do project demonstrations there. I am also an Artist in Residence for Imagine Science films, they would help me document and publicize the work once it is completed. I also currently run the only DIY Science online store(http://www.the-odin.com). The plasmids and bacteria will be available for free on the store from funding provided. I am heavily involved in the DIY Science and Art community online and could find opportunities through people I know to present this work in Chicago and New York city besides the Bay Area.
How do you plan to use the 20k grant(500 words)
https://docs.google.com/spreadsheets/d/19uG123bXLtnWZx9XBIl-dBqxOpGelS_SmYp8LC4RNvo/edit#gid=0
Item
Cost
Description
Travel
$300
2 Months Caltrain Pass and.or Gas to Berkeley
Genes and Primers
$3,000
DNA synthesis will be ordered from IDT
Reagents and Enzymes
$2,000
For, PCR, Gibson Cloning, Ligation, Restriction Digests
Computer Controlled Camera and accesories
$800
GoPro HERO3+ or Similar for Fluorescence Imaging
Light Filters
$300
Light Filters for Fluorescent Imaging
Hardware
$400
Microcontrollers, LEDs, Misc. Components
Laptop Computer for Art Installation and Other Displays
$1,100
Inspiron 15(for running Linux) ~$900 + Tax and Shipping
Living Expenses
$500
Food and Red Bull for Working Late Nights and Alcohol for trying to sleep after those late nights
Plasmid and Bacteria Distribution
$300
This would provide enough plasmid and bacteria to distribute it free to ~1000 people
Miscellaneous and Unforeseen Expenses
$1,300
Basic Molecular Biology Class
$1,000
Supplies to teach 3 free basic molecular biology classes
Total
$11,000
What are the greatest challenges to success(500 words)
The project is theoretically sound but still theoretical. The greatest challenges will definitely be in the DNA engineering because the green light system has not been tested yet in living bacteria. If the green light system works, I predict the chances of success being in the 75% or greater range. Even if the green light system does not work a “punch card” like memory storage design could be created from only the blue light system and plates, i.e. only writable once. The hardware and software required is fairly straightforward and will just require some time to sit down and write it.
How do you think your project will benefit from STOCHASTIC community(500 words)
As a Scientist I have not had the chance to develop many of the skills that surround presenting Art. Honestly, I would not know how to even begin to find a place to hold an Art installation or even how to hold one(I guess I could always search the internet). Further, because I enjoy the Science and Engineering part of projects some of them are less than aesthetically pleasing and use copious amounts of duct tape. I think that being around other Artist’s could help me out alot in the many aspects of Art that I have not experienced being primarily a Scientist and Engineer. FInally, groups of intelligent and creativity people often can give you an objective perspective of your work that cannot be reached otherwise.
Rough timeline
Money being deposited in my account being the start of Week 1
Week 1 will be the ordering of DNA and components.
Depending on when DNA arrives(1 - 2 weeks)
Weeks 1,2-4 to clone green light activated system
Weeks 1,2-4 to remove the ClpX and ClpA genes from bacteria
Weeks 4-8 to create hardware and software system
Obvious, this is an accelerated timeline and there are chances that this will likely take 3-4 months to complete.
What building event or service project do you plan to do
I plan to teach 3 Free Molecular Biology classes at either Biocurious, Counter Culture Labs or Berkeley Biolabs(or all three). The class will teach people how to amplify and clone synthetic DNA fragments into bacteria to create a unique organism.
Anything else
I just found out about this grant at ~10PM on July 2nd or the application would be of much higher quality and would not have been submitted so last minute. I thought this would be a great opportunity to work on a dream project I do not currently have the monies to fund.
Links to content
Designed Primers, Genes and DNA sequences for the project:
https://docs.google.com/document/d/1J8bKYXBEL6PBVcbqY5BSJE39OyL147cl_WGgtyidkuo/edit?usp=sharing
Link to answers in one file:
https://docs.google.com/document/d/1d9DqUobiqNxoqzDKEszqrJZQDAa0MDGotcy_Q3uEVIM/edit?usp=sharing
My blog:
http://doitourselfscience.blogspot.com/
