Today I hooked up a ps3eye w/ an inverted lens and attempted to calculate its magnification factor. I also made some commits to the github repo for the project (the code’s currently in processing but that will be changing over the next month).

iPhone 4 pixel size

(via prometheus.med.utah.edu/~bwjones/2010/06/apple-retina-display/)

• iPhone1: ~176 x 223μm
• iPhone 3G: ~176μm x 223μm

• iPhone 4G: ~78μm x 102μm

• 326 pixel per inch (960×640)

ps3 eye inverted lens resolution

iphone 4 screen magnified by PS3eye w/ inverted lens

• 3088 x 2312 uM = 3.088 x 2.312 mm
• 640 x 480 pixels
• 326 ppi

• 4.25 x 3.18 cm

• 4.25 cm / .03088 cm = 137.63

• 3.18 cm / .02312 cm = 137.63

so magnification ~137x ?

Synthetic Aesthetics is an upcoming program designed to bring 6 synthetic biologists and 6 designers together in a month-long mutually beneficial collaboration. The goal is to to bring together synthetic biologists, social scientists, designers, artists, and other creative practitioners, to explore existing and potential collaborations between synthetic biology and the creative professions.

I have been thinking recently about the design principles of the Arduino microcontroller prototyping platform and wishing for something similar for synthetic biology: a cheap, physical platform designed to help non-experts prototype and play with microbial genetic devices. So I submitted a proposal hoping to find a designer interested in collaborating. Here it is:

The tools of biotechnology are sometimes ready-made and often disposable.  As synthetic biology improves modularization, abstraction, measurement, and design techniques for biological systems, how will the craft of biotechnology change, and what new forms of craft will develop?  How will the character of a biotechnology design studio differ and evolve from that of a contemporary lab space?  As more individuals appropriate synthetic biology techniques for reasons besides research, such as art, tinkering, and play, how will their tools and workspaces evolve?

How can existing synthetic biology tools and techniques themselves be modularized, simplified, and accelerated to make them more accessible to non-experts, such as artists, designers, and tinkerers?

I would like to explore this question with a designer by prototyping hardware platforms that support simpler and faster interaction loops with bacterial genetic devices, facilitating play. I would like to investigate and apply the design principles exemplified in design of the popular Arduino microcontroller to contemporary synthetic biology tasks, such as basic biological part assembly, transformation, and measurement, and develop plausible physical prototypes that make those tasks easier and faster for non-engineers. Additionally, I would like to explore with the designer how the inputs (media, lyophilized cells, DNA, water, other feedstocks, antibiotics) and outputs (cells, growth rate, fluorescence measurements) to this synthetic biology prototyping platform could be modularized and made more user-friendly.

Secondarily, I would like to use the experience gained from developing the prototypes as the basis of several real-world mock-ups of what biotechnology studios of 2020 might look like. These renditions would explore contemporary assumptions about the priorities of biotechnology.  What does the practice and tool-chain of synthetic biology look like when tinkering and play, or art, or brewing, etc, are prioritized over research? What would a radically-sustainable, zero-waste lab look like? Or one constructed solely from rapid-prototyped equipment? How would a microfluidic-arduino and its associated ecosystem of add-ons, users, and code fit in?  Or a standard biological part trading card game?

At the end of the project, I would like to have primarily developed a physical prototype (a conceptually powerful, plausibly-working prototype) of something akin to a synthetic biology arduino, along with consistent designs of its inputs and outputs. Secondarily, I would like to have developed scenes and images representing several future contexts in which this platform would play a role. The tangible manifestations of these potential futures – of synthetic biology and of non-institutional science – will enhance contemporary discourse on the subject and inspire reflection about the path from today to their potential realization.

ucam development 25 Feb 2010 from mac cowell on Vimeo.

I’ve been fascinated by bioluminescence from the first time I saw pictures of deep-sea angler fish. Since then, I’ve seen dozens of live bioluminescent creatures at the Boston aquarium and cultured E. coli expressing the LuxCDABE operon from Vibrio fischeri in Tom Knight’s lab.

It surprisingly easy to grow bioluminescent microbes. I’ve found a couple of undergraduate-level protocols online for isolating marine Vibrio species from fresh squid. I’m currently in the middle of my second attempt at isolation. These are my notes so far. I’ve adapted this Basic Protocol for Isolating Bioluminescent microbes for use in my kitchen.

I’m using food-grade agar I got from a food-hacking friend, powdered chocolate jello (I ran out of powdered agar), Baking Soda instead of CaCO3 (chalk), and canned tuna water instead of powdered LB broth (hope it doesn’t have preservatives in it).

13 Jan 2010

18:30 Got fresh, “uncleaned” squid from New Deal Fish Market in Union Square: $2.50

18:55: got 1L gatorade

Added 1/2 teaspoon of sea salt to the empty gatorade bottle

22:00 cut squid head in 1/2, added to tap water in gatorade bottle

14 Jan 2010

22:00 It GLOWS! wow!

took pictures with ad-hoc cardboard camera frame; cutting gatorade bottle in half (squid now in what resembles a petri dish with 8-inch tall walls)

Added 15 mL of Jeff’s Food-Grade agar to 450 mL of water; not enough? Still liquid. (only have a 15 mL falcon tube, not a scale).

Boiling the agar liquid in a water bath. Will add Jiffy CornMeal to supplement.

22:25 agar solution at 175 C. Cools to a mildly viscous liquid.

22:30 adding 15 mL chocolate JELLO

How many grams is 15 mL of agar powder? 0.34 g / cm^3 (http://www.wolframalpha.com/input/?i=15+mL+Agar) 15 mL ~ 5g.

How about Jello? 1.1 g / cm^3 (http://www.wolframalpha.com/input/?i=15+mL+Jello) 15 mL ~ 17g

Most LB plate protocols call for 15 grams of agar powder / Liter. I started with 5g (15 mL) in 450 mL of water. So I was 2/3 short.

It turns out 15 mL Jello + 15 mL agar in 450 mL boiling water solidifies into something approximating an agar plate. I’m adding 2.5 mL more Jello to thicken it a bit.

Other ingredients of recommended for Luminescent Agar plates (per 450 mL H2O):

• 2.5 g CaCO3 (NaHCO3 is 2.173 g/cm3; and I’m going to substitute it. Added ~ 1g)
• 5 g Glycerol (left it at sprout)
• 15 g NaCl (2.165 g/cm3, added 4 mL; ~ 8.66 g)
• 4 g “dehydrated Nutrient Broth” (I’m using a teaspoon of liquid from a can of tuna)

0:00 15 Jan 2010 Poured “Luminescent Chocolate Agar”

0:30 poked bright blue bioluminescent patches on the squid carcass with a toothpick and streaked them out on the choco-agar.

Later that summer, I read Steven Levy’s “Hackers: The Heros of the Computer Revolution.”

Now I’ve started to see an analogy between the tools used by nascent biotech hackers today and the computer hackers of the late ’70s.

The upshot of improvements in diagnostic kit technology are more than just clinical: cheaper, faster, broader ways of interrogating the natural world will be a boon to everyone interested in understanding it. In particular, I believe the amateur / non-institutional biotechnology community requires easy, low-cost methods for asking questions and getting answers about biological systems, and my intuition tells me a lot of those methods will be based on diagnostic kit technology. To me, the impact of future diagnostic kit technology on amateur biotechnologists will be roughly analogous to the impact microcomputer kits had on the “amateur computer scientists” of the late 1970′s and early ’80s.

One of the first things we looked at was the trending terms on twitter; Specifically, for every day over the last 6 months. I made some fun aggregate visualizations of this with whiskerplots using topfunky’s sparklines gem in ruby: here’s the top 100 trends, and here’s the top 2000. (here’s the code.)

8 twitter trends from 1-jan-2009 to 5-jun-2009

That was all weeks ago, though. Today is a happy day for the WEP because today, we published our first report: Iranian Election and Twitter: The First Eighteen Days. I only contributed a little bit to some of the early twitter stats (I’ll write more about them later) – David Fisher and others were the real hard workers.

From June 7 – 26, we recorded 2,024,166 tweets about the election in Iran, and we found out some pretty interesting things. Guess how many of those 2 million tweets were retweets! Go check out the report to find out (pdf).

Iranian Election and Twitter: The First Eighteen Days

sampling sites from The Marine Viromes of Four Oceanic Regions - we can do a better job of mapping than this!

Then I’d like to do something a little more abstract. The first thing that comes to mind is distorting the map so that one of the dimensions of the data, such as read density (base pairs/ km^sq), is constant for each pixel. This would expand the map in areas that had been sampled and shrink it in areas that were not sampled. I actually think read density is a pretty boring thing to graph (at least until there are tens of thousands of samples), but I think this technique would be a neat way to represent something like a diversity metric for each sample. These kind of visualizations are called “cartograms.”

(Note: these are just some basic ideas. It might be the case that all density representations, such as heatmaps or the distortions I mentioned above, are inappropriate for representing sparse samples across a large area. Nonetheless, the first step is to get some data and start experimenting.)

In this cartogram “the sizes of states are proportional to the frequency of their appearance in news stories.” From Diffusion-based method for producing density-equalizing maps by Michael T. Gastner and M. E. J. Newman.

a tab-delimited example of a basic metagenomic dataset for constructing a map:

sample_id   lat lon sequence_id 16s_sequence    suspected_species
000001  32.131341   98.231332   0001    agcctagcacgga...    Bacillus subtillis
000001  32.131341   98.231332   0002    agcgtaggttgac...    Acinetobacter baylyi

I would be happy just with 10,000 entries in a single text file in a format similar to the one above (but note that lat/lon are identical for all sequences in a given sample). It would be even better if there were more dimensions of data. Here are some other potential columns:

• taxonomy (calculate a diversity metric from each sample from this? what else can we do with a taxonomy?)
• pathogenicity
• auto- or heterotrophic
• other metabolic information?
• GO terms, or something like them at an organismal level
• URL canonical species description in ncbi
• ? Please make suggestions in the comments.

Synthesizing such a dataset (as a large plaintext file or as a database) will require aggregating a variety of other datasets. I have no idea where to begin with them. If I know a particular species (Acinetobacer baylyi, for instance), is there a single entry point for deriving all this information in NCBI?

existing metagenomics datasets

I spent a couple of hours reading metagenomic papers and browsing around for datasets. Here’s a quick list of interesting resources. My naive first look didn’t turn up anything similar to the basic plaintext example above.

MEGAN – Metagenome Analysis Software & sample data

Methods for comparative metagenomics (introducing MEGAN) (paper)

UniFrac software & sample data (Look for the datasets they used to construct the phylogeny trees)

UniFrac paper (paper)

The Marine Viromes of Four Oceanic Regions (paper)

Data from Marine Viromes study (and more!)

ncbi metagenomics book soil chapter (Waseca County Farm Soil)

16s rDNA identified from Waseca County Farm Soil dataset (in ncbi’s nt database)

CAMERA: A Community Resource for Metagenomics (their webview of the datafiles looks interesting; the datafiles themselves are just fasta)

CAMERA: Surface Water Marine Microbial Community Gene Expression project

inspirational infographics:

Travel-time Maps by Chris Lightfoot & Tom Steinberg

Center for Mathematical Modeling infographics by Juan Pablo De Gregorio

• Temperature Gradient Gel Electrophoresis (TGGE) and Denaturing Gradient Gel Electrophoresis (DGGE)

DGGE of small ribosomal subunit coding genes was first described by Gerard Muyzer, while he was Post-doc at Leiden University, and has become a widely used technique in microbial ecology. PCR amplification of DNA extracted from mixed microbial communities with PCR primers specific for 16S rRNA gene fragments of Bacteria and Archaea, and 18S rRNA gene fragments of Eukaryotes results in mixtures of PCR products. Because these amplicons all have the same length, they cannot be separated from each other by agarose gel electrophoresis. However, sequence variations (i.e. differences in GC content and distribution) between different microbial rRNAs result in different denaturation properties of these DNA molecules. Hence, DGGE banding patterns can be used to visualize variations in microbial genetic diversity and provide a rough estimate of the richness and abundance of predominant microbial community members.

Solid-phase PCR (Polony PCR) is also intriguing: Dilute and spread the DNAs across a surface and use solid-phase PCR to amplify individual DNAs into polonies. Pick polonies and have them sequenced.

• In situ localized amplification and contact replication of many individual DNA molecules

“We describe a method to clone and amplify DNA by performing the polymerase chain reaction (PCR) in a thin polyacrylamide film poured on a glass microscope slide. The polyacrylamide matrix retards the diffusion of the linear DNA molecules so that the amplification products remain localized near their respective templates. At the end of the reaction, a number of PCR colonies, or ‘polonies’, have formed, each one grown from a single template molecule. As many as 5 million clones can be amplified in parallel on a single slide. If an Acrydite modification is included at the 5[prime] end of one of the primers, the amplified DNA will be covalently attached to the polyacrylamide matrix, allowing further enzymatic manipulations to be performed on all clones simul-taneously. We describe techniques to make replicas of these polony slides, and high throughput sequencing protocols for this technology.”

• More info: Solid phase DNA amplification: characterisation of primer attachment and amplification mechanisms
  

Lastly, I could just give up on the idea of a heterologous PCR product and instead design primers specific to a particular rDNA or other gene of interest. Instead of exploring the space of all rDNAs present in the sample’s metagenome, I would be testing for the presence of a particular DNA. Much less exciting, if you ask me.

I’m reading about Unit Tests and Zope and Test Driven Development. I am going to read the wikipedia page on each of the concepts and probably some other pages elsewhere on the web. I want to be able to highlight the one or two most valuable snippets from each page and use those together as a the history entry.

When I go to my history list, I don’t really care about the list of pages I visited, I care about what I was looking for and why I went there.

I want task- and concept-centric history lists.

notes: Generalize the concept of a content consumption stream, a content history. What if it magically existed for all the books and papers I read in college. Would each page be an entry? Each paragraph? Each book or article? That wouldn’t be as useful as some kind of… distillation of the key concepts:

• acting as pointer to help me find my way back to content surrounding main article (a bookmark)
• and as a stand-alone distillation or note of the record

In the pilot program, hundreds of participants will sign up at bioweathermap.org, gather in a “FlashLab” event, receive a sampling kit (probably something like a Q-tip and a test tube), and disperse throughout the local region to sample a particular type object, such as cross-walk buttons. The participants will then return their samples to the BioWeatherMap group for analysis.

Once several hundred samples have been collected and prepared, the BioWeatherMap group will purchase a single DNA sequencing run on a high-throughput DNA sequencer for all the samples at once, with each sample receiving about 1500 “reads”. The preparation step isolates and amplifies a small, species-specific region of DNA from the genome of each sample. For each sample, then, up to 1500 unique species could be identified (or the same specie could be identified 1500 times). By leveraging economies of scale, the BioWeatherMap group will be able to provide 1500 reads at the most economical cost.

The BioWeatherMap project is the first example of a new kind of distributed, participatory, bite-size science. It will demonstrate to participants that research doesn’t require a Ph.D. The data they generate will be fascinating – literal BioWeatherMaps: maps of time-series of microbial population flows overlaid on a Google Earth view of the city.

The first Flashlab event should be happening sometime this summer (2009).

In the meantime, I want to figure out how to do a smaller-scale version of the same thing – direct sequencing of a short, species-specific genomic DNA sequence for microbial species identification – in a cheap, garage-friendly way. I want to do Garage Metagenomics. (DNA Barcoding is the same concept but for Eukaryotic organisms).

I’ve started looking through the metagenomics literature(links to fulltext library) for simple protocols that could be adapted to a basic garage lab. I’m planning on outsourcing the actual sequencing ($50-$100?), but doing the rest of the sample preparation myself: isolating and purifying genomic DNA and doing PCR to amplify the species-specific DNA barcode, probably a 16s or 18s ribosomal subunit gene.

Check back soon for more info on my progress and please leave a comment if you would like to help out or do some Garage Metagenomics of your own.