The Sound of Science: towards robust monitoring of the optic and acoustic environments

Posted: December 15th, 2012 | Author: csoeder | Filed under: atlanta, Bioregionalism, Tools | No Comments »

There is a companion article at TopOc which takes a more detailed look at the science of environmental sound and light

If you look up at the sky, and it seems to glow orange and drown out the stars, you’re looking at light pollution.


This is a satellite composite map, showing the light released by humans, color coded by activity. Urbanization in particular has brightened the surface of the Earth over the last century or so. Light has lways been our friend, so it may sound odd to speak of it as a pollutant, but remember: pollutants are things that jam the workings of an ecosystem. And light is an important environmental regulator. A recent review highlights ‘well known’, ‘catastrophic consequences’ of light pollution:

“the deaths of migratory birds around tall lighted structures, and those of hatchling sea turtles disoriented by lights on their natal beaches. The more subtle influences of artificial night lighting on the behavior and community ecology of species are less well recognized, and constitute a new focus for research in ecology and a pressing conservation challenge.”

If you’ve dealt with a headache while Atlanta traffic squonked outside, you know what a nuisance urban noise pollution can be. It’s also a recognized occupational hazard. Moreover, the impact of human sounds on the environment are just now being recognized: robins and frogs are shifting their calls to communicate around or through traffic noise, and songbirds have begun to rebroadcast human sounds, chirping in ringtones.

Considering the scale and significance of human influence on the sonic and optic environments, there is a great deal we could learn from widespread ecological monitoring of sound and light. The review cited earlier reccomends: “measurements of light disturbance should be included routinely as part of enviromental monitoring protocols”. Monitoring of sonic ecology has thusfar been fairly transient and concentrated on localized and/or urban settings (eg, here and here)

At ArkFab, we’ve been thinking about how to develop and deploy an inexpensive infrastructure to monitor these environmental variables. The proposed system would involve a number of sensors placed in a wide variety of settings (urban, suburban, rural, etc) in geographically diverse regions. The sensors would consist of a small microphone and photodetector (and perhaps other inexpensive detectors, such as a thermometer for temperature measurements) in a weatherproof housing. Data would be stored, via a microcontroller circuit board, on USB sticks for easy retrieval and large data storage. The familiarity and small size and cost of a USB stick would mean that the disk drive could be easily replaced when full and mailed through the post office to a central site for data retrieval and processing. These low-power units would also be equipped with a solar panel for longer battery life.

Retrieving information from a geographically dispersed sensor array will require a nonlocal approach, and citizen science seems to be the best solution. Citizen science is the involvement of people outside of the mainstream scientific community in participatory research. A canonical example is that of SETI@Home, a distributed computing project which used spare computational power (ie, screensaver time) to analyze radiotelescope data.  The success of the SETI@Home project has led to an explosion of distributed computation projects, such as running malaria and climate predictions, protein folding and artificial intelligence simulations, and numerical explorations of famous unsolved mathematical problems. Protein folding further involved citizen science with the success of FoldIt, a puzzle game in which players add the finishing touches to protein-folding simulations (the last few steps are apparently more economical to do with a human brain than with a computer.) Citizen science has also been successfully used to monitor populations of insects, mammals, plants, and birds. In fact, this sort of distributed measurement philosophy has been explored, implemented, and advocated in studying urban noise pollution:

“…involvement of citizens is key. [...] In geography and urban planning there is a trend towards support for such participation. Under the flag of participatory GIS and participatory mapping new methodologies are being researched to better support the participation and involvement of citizens in projects that are typically tackled using geographical information systems (GIS), such as the mapping of spatial phenomena or land use and urban planning.”

Interested volunteers and science hobbyists already keep home weather stations; this enthusiasm could be tapped for sound and light monitoring. Indeed, there already exists a program which uses volunteers’ cell phones to record data about urban sound levels. Another group of potential citizen scientists are schoolchildren- the sensors could be given to schools as low cost educational kits, and possibly even designed to be assembled at the schools themselves, providing education in electronics and computer science as well as in ecology. There is already a strong precedent of student participation in citizen science. Remote areas are could be monitored by hikers and sight-seers, who often have an interest in the condition of the natural areas they visit. One place to start might be the Appalachian Trail, which is seasonally visited by hikers with a pre-established community which could be tapped into. Indeed, this community participates in monitoring mammal populations; participant and David Helms, participant and Natural Bridge Appalachian Trail Club president remarks:

“The Appalachian Trail was built and is still maintained by volunteers. Using volunteers is the way the world works on the trail.”


The ArkFab Earthship Breaks Ground – Great News from the GTech Green Phoenix Project!

Posted: July 10th, 2012 | Author: csoeder | Filed under: ArkFab Vertical Farm, atlanta, Food Production, Green Phoenix | Tags: , , , , , | No Comments »

ArkFab’s Earthship

Green Phoenix, an ArkFab umbrella project operating out of Georgia Tech, continues to develop innovative urban food production. They’re putting out a call for volunteers to help with construction:

Peachtree Creek

The project has broken ground and we are proceeding on multiple fronts.  We are currently excavating around the site to put in the greenhouse, acquiring pallets for our composting bins, and getting the final designs for our black soldier fly larvae (the fish food).

We have located hundreds of tires for the rammed earth tire wall which we are using as the thermal mass to keep our mushroom facility cool in the summer.

Basically, we are building an earthship which will house the mushroom growing facility. The tire walls are part of the earthship. We need help with everything – pulling tires, constructing the earthship, constructing the aquaponics part, composting, etc. We have some job openings as well, but we need some massive volunteer events first.

We need your help!​

Atlanta Memorial Park, Peachtree Creek between Northside Drive and Moores Mill

Time: The next 3 Saturdays – 7/14, 7/21, and 7/28 from 8am to 5pm

Details: We have located hundreds of tires in Peachtree Creek and we need help pulling the tires from the creek and loading them onto trucks.

Please come out and help!!

Please RSVP by emailing Steve Van Ginkel at

Source: Green Phoenix


CO2 Trouble: Arkfab’s First Feature Length Report

Posted: September 16th, 2011 | Author: csoeder | Filed under: atlanta, Political | Tags: , , , , , , , , | No Comments »

A companion article at TopOc discusses the importance of correct documentation and an unexpected observation I made while crunching numbers for this research.

The first feature-length report from the ArkFab Collective is now out as a downloadable booklet! “CO2 Trouble: Ocean Acidification, Dr. Everett, and Congressional Science Standards” is available for download and sharing HERE.

As I have written in previous posts, environmental issues are downplayed in the political sphere with scientifically questionable but mediafuzzy talking points. I found this to be the case with Dr. Everett’s 2010 congressional testimony arguing that ‘there is not aproblem with increased acidification’. I have been writing about my research on the subject at TopOc; CO2 Trouble is the final report of my findings. It has been designed to be a fairly short (less than 30 pages, including images, appendicies, etc.) and accessible read. Suffice to say, Dr. Everett’s testimony doesn’t stand up to scientific scrutiny.

One thing that this project brought up in my mind was about the institution of peer review: how does it function for this project specifically, and in a DIY/citizen science setting in general? In my case, the subject is not necessarily well-suited for the classical peer-reviewed literature, but outside of that arena, validation becomes hazy. There is a very real danger of slipping into what journalist Olivia Koski calls “Think Tank Scholarship”:

Public policy makers increasingly rely on the research of think tank scholars to guide their policy decisions. But who checks the accuracy of think tank scholar research? Unlike academic journal publishing, which follows a rigorous system of peer review and editorial oversight, think tanks publish opinion pieces without regard to the peer review process. Their policy publications are based not on pure academics, but on a complex interaction between academic, political, and economic interests. In Washington, there is no time to focus on the academic details.

Koski wrote that in 2007; in the years since, the think tanks have become even more crass in their tactics and have been joined by their DIY equivalent, Blog Science.

On the other hand, my experiences in trying to gather informal and community-based peer review left me hopeful for the future of democratic science networking. There are resources like ResearchBlogging for connecting science bloggers, where much of this report was field-tested. I am already experimenting with using ResearchBlogging to present original research. I also found that the experts I contacted with my questions were helpful and encouraging. Online communities have provided a forum for a lot of great discussions!

One final observation is about this networking of individual scientists, a prerequisite for science generally but for DIY and citizen science as well. Antiscience can sometimes have the effect of impeding research, as when a lab is flooded with nontrivial FOIA requests. I brushed against a bit of its erosive influence in the writing of this report: more than once, I had correspondence delayed because I was mistaken for a climate ‘skeptic’!

Stay tuned for more updates – coming up is an austere, printer-friendly version, a zine version, press information, and more. And be sure to check out the report, which contains unreleased material. Velociraptors figure prominently. (Really!)

Announcing ArkFab’s First Working Paper : Thermodynamics and Poker

Posted: July 1st, 2011 | Author: csoeder | Filed under: Uncategorized | Tags: , , , , | 1 Comment »

There’s a more technically oriented discussion at TopOc

The current version of the paper can be found here.

I’m releasing the work I’ve done thusfar on a fun problem. A while back, I got the idea to investigate how the entropy of a poker tournament evolves with time. In thermodynamics, entropy is a measure of how ‘spread out’ energy is amongst the states available to it. When the energy in a system is concentrated in one place (like a hot cup of coffee in a cold room), the entropy of the system is low. When the energy is spread out (a few hours later, both the room and the coffee are the same temperature) the entropy of the system is high.  Although originally defined for distributions of physical energy, entropy can be defined more generally to study arbitrary distributions – for example the distribution of capital, in the form of chips, between players in a poker tournament.

Just by looking at the formal structure of the game, you can tell some things about how entropy behaves. For example, it is formally required that entropy falls to zero with time. On the one hand, this is a fancy way of saying, ‘one person will eventually win the tournament’; on the other hand, it is interesting to consider that this is the exact opposite of what happens in the physical, thermodynamic world. The entropy of a closed thermodynamic system necessarily increases with time: hot coffee in a cold room will cool down, but warm coffee in a warm room will never heat up. However, the entropy of a closed poker table necessarily decreases. It has a second law of thermodynamics that runs in the opposite direction from ours.

But the natural and artificial worlds which complexity theory studies shows us that there are often interesting system-level properties not immediately obvious from a formal description of its subsystem. Simply conducting thought experiments is not necessarily enough; an ounce of real-world data is worth a pound of theory.

It was somewhat difficult getting access to the data I needed. Although online gaming sites keep records of their tournaments and provide them on request to participants, they strictly do not share them with non-participants. This has been a roadblock for others who wish to study tournament data as well. Next, I tried citizen science. Citizen science is the involvement of people outside of the mainstream scientific community in participatory research. It has been successfully used, for example, in monitoring animal populations, and folding proteins. Given the seemingly low commitment  (a few minutes to request a tournament history and forward the email), I assumed that I could get copies of tournament histories volunteered by the players themselves.

Reality was a bit different, and the mixed reactions I saw made me think about the way in which I think about and communicate science. I am used to a world in which people love to show each other the numbers they’ve been crunching, but a lot of people don’t live in that world. A common response I encountered was, What’s in it for me? It is an interesting question, how do we justify a decentralized, volunteer-based science infrastructure to prospective volunteers? A closely related issue, I think, was what I saw as widespread devaluing of pure research and misunderstanding of why people do it. I often encountered the question, What do you expect to find? Well, I don’t really know. If I knew what I was goingto see, I’d be a lot less interested in looking, right? It’s entirely possible that I’d find nothing, but also possible that I’d find something cool if I looked at it right. Communicating through these hurdles seems nontrivial.

On the other hand, I did get some interest, and a handful of tournament histories. My sample size is still too small to make definite claims, but it has still given some interesting results, and perhaps insights into how the system responds to perturbations. I have also had the opportunity to have some interesting conversations (for example, is entropy properly normalized by multiplication, or by addition?). I’ll let you know if there are any updates! And if you have any tournament histories you’d like to share, let me know by emailing ThermoPoker(at)

Tragic News

Posted: June 10th, 2011 | Author: csoeder | Filed under: atlanta | No Comments »

Liam Rattray, who founded the ArkFab project, died on May 30. A drunk driver hit his motorcycle, throwing him into oncoming traffic. The whole story is here.

It was a weekend in may, 2007, and a chain of events catapulted me from Carrboro, NC to Greenville, SC, building a community radio station. The night I arrived I soldered audio cables, painted walls, and met Liam. He was an easily excited, highly stimulated fellow, enthusiastic about everything. We had sleeping quarters in a high school gym, but we barely slept that night for talking and scheming. He was an
incurable shutterbug, snapping pictures of the weedridden playground, an eerie Stephen King landscape in the hot afternoon light.

Over the next few years, I saw him occasionally, this collage of hikinks, soldering LFO circuits, watching TED talks and dreaming about
viruses, looking for him at 5am in Chapel Hill. Last October I showed up in Atlanta to work on our projects with him.

He had a lot of friends and he was on the edge of amazing, unbelievable things. We will all miss him. His memorial site is here.

Ocean Acidification: A Short Video

Posted: May 10th, 2011 | Author: csoeder | Filed under: Uncategorized | Tags: , , , | No Comments »

At a local community center, ArkFab gives a short talk and chemistry demonstration about the environmental chemistry of carbon dioxide.

The Political Economy of Antiscience

Posted: May 3rd, 2011 | Author: csoeder | Filed under: Political | No Comments »

When it became clear that CFCs, a class of halocarbon refrigerant, were degrading the layer of ozone which protects us from ultraviolet radiation, the industries manufacturing the halocarbons began to turn their gears:

‘Launch a public relations campaign disputing the evidence … Find and pay a respected scientist to argue persuasively against the threat … Trumpet discredited scientific studies and myths supporting your point of view as scientific fact … Point to the substantial scientific uncertainty, and the certainty of economic loss if immediate action is taken … Use data from a local area to support your views, and ignore the global evidence … Disparage scientists, saying they are playing up uncertain predictions of doom in order to get research funding … Disparage environmentalists, claiming they are hyping environmental problems in order to further their ideological goals … Dr. Fred Singer… Claim that more research is needed before action should be taken.’

Does this sound familiar? It should – it follows the template of all sorts of campaigns to discredit economically inconvenient science. The same gears turned when we learned that industrial pollution was causing acid rain. And the tobacco industry spun them again, with a cynical PR campaign to sell ‘doubt’ about the health effects of smoking as a ‘product’ in its own right.

And then of course there’s climate change.

Antiscience is the opposite of science. It’s negative science. It complains about the things we don’t know as though they invalidate the things we do know – but it makes no attempt to answer these ‘unanswered questions’. While antiscientists whine about the deficiencies in climate models, scientists work to improve those models.

It’s easy to see the appeal of antiscience, when a captain of industry, or the politicians they support, are faced with evidence that their actions are degrading the environment. There’s profit motive to be sure, but on top of that there are all manner of psychological effects, from cognitive dissonance to outright denial.

And then of course there’s the Dunning-Krueger effect.

There are, certainly, plenty of different flavors of antiscience, tangentially or unrelated to environmental issues- creation ‘science’ is the most obvious example- but these may themselves carry political capital because they align the politician with their constituents, to the detriment of educational standards. And there is plenty of overlap between antisciences. Phillip Johnson, architect of the cryptocreationist Santorum Amendment, also denies the connection between HIV and AIDS, claiming that “the chance of ending up as an AIDS case if you avoid homosexual and drug behavior is less than the chance of being struck by lightning.” Jonathan Wells, author of a number of creation ‘science’ books, is also an HIV denier. And Guillermo Gonzalez, posterchild of the Intelligent Design movement, is also a climate change ‘skeptic’.

The radiative properties of carbon dioxide are fairly straightforward, and yet a cottage industry has developed around their dismissal. The same crew is now turning its sights on ocean acidification. In addition to absorbing and re-radiating infrared, CO2 is acidic, and is altering the chemistry of the world’s oceans, to the detriment of aquatic ecosystems – and yet, policymakers have been hearing that ocean acidification is no problem. ArkFab scientists have been analyzing one such piece of testimony – the final report will be issued soon [UPDATE: This report can be found here]. Unsurprisingly, ocean acidification ‘skepticism’ is as scientifically vacuous as its climatological counterpart.

A recent modeling study found that the outlook would have been bleak had we not banned CFC usage. The Montreal Protocols were a rare happy ending in the environmental arena: industry threw their PR weight, but at the end of the day our need for a livable world overrode their profit interest. We are now faced with threats at least as pressing – and we are losing precious time.

So what can you do?

  • Put the ‘democracy’ in representative democracy - call your representatives! Tell them you’re concerned about environmental issues and the quality of the scientific advice they are getting.
  • Get informed! Check out the resources below.
  • Evaluate your lifestyle - what sort of environmental impact does it have? How much oil must be burned to transport your food? How much toxicity does the manufacture of your computer create? How can you act to eliminate those impacts?


Resources for politicised science:

If you have suggestions for more, please comment :)

Experimental Flat-Panel Photobioreactor

Posted: April 29th, 2011 | Author: arkfab | Filed under: ArkFab Vertical Farm, atlanta | Tags: , , , , , , , , | 2 Comments »

With funding from the Center for Biologically Inspired Design I designed and built an open source experimental algae photobioreactor. Open Source Hardware plans will be released when I complete the research report. This is a 2 gallon experimental algae photobioreactor built from 1/8 inch cast acrylic cut on a laser cutter at the Georgia Tech Invention Studio. The lighting is provided by a 13.8 watt LED array that irradiates the culture at 465nm and 650 nm- the absorbence band for photosystems I and II. A water jacket is built into the reactor to cool or heat the cultures and modulate the incoming light frequency for experiments. A 2 CFM air pump provides CO2 rich air to the culture through the sparger at the bottom of the tank.

The objective of this research is to analyze the systems benefits of integrating fungi and algae cultivation. CO2 enriched air from the fungi incubator should increase algal growth while moderating the incubator’s relative humidity. If a prototype outdoor algae reactor were incorporated into the ArkFab project algae from the reactor could be used as an alternative to unsustainable ocean mined fish feed. Tilapia like to eat algae! Future uses may include growing high-value astaxanthin and measuring the metabolic rates of photosystems I and II in various algae strains.

I’ll provide an update as soon as my spirulina strain comes in.

How to grow gourmet mushrooms in your back yard

Posted: April 17th, 2011 | Author: arkfab | Filed under: Food Production | Tags: , , , , , , , | 5 Comments »

On February 20th this year I seeded a 20ft. garden bed mulched with 30lbs of wheat straw with two quarts of Pleurotus ostreatus (Oyster) mushroom spawn. Less than 8 weeks later on April 13th I harvested my first flush of mushrooms, about three ounces. This is how I did it with some notes on you too can easily incorporate tasty mushrooms into your home garden.

Catherine and I found a little Pleurotus ostreatus mushroom growing on a round of tulip poplar in a park down the road from where I live. This was in December, so the strain is probably a cold tolerant variety. I returned to this round in March and discovered a few more oyster mushrooms.

I gathered a native oyster mushroom from a local park and brought it into sterile culture in my home laboratory then expanded it on 400 grams of pasteurized rye berries mixed with a couple grams of gypsum in two quart jars. This previous post explains my process in greater depth. If you would like to seed your own garden with mushrooms buy an oyster mushroom strain suitable to your current season. If its cool outside get a cool variety, if its summer get a warm or tropical variety. I recommend Mushroom Mountain’s mushroom spawn for folk living in the Southeast as they tend to sell season-specific spawn that is expanded from native cultivars. Paul Stamets recommends using straw-based or sawdust-based spawn for outdoor cultivation, because insects like to eat grain-based spawn, but I think that the insects are doing us a favor by spreading the mushroom mycelium around our yards to possibly find other suitable habitats to grow and fruit. Use what is available and convenient. Don’t become paralyzed if you don’t think you have the perfect equipment and supplies. Fungi are alive and want to grow. Perfection is often the opposite of the good.

I established my mushroom bed right in with my vegetable beds. As the plants grow they create a little microclimate for the mushrooms. In the morning, dew collects in this microclimate providing baby mushrooms with much needed moisture during dry days. These plants can also provide shade if you are planting in a sunny area. Our yard is shaded by huge white oaks, so we already have lots of shade. Mushroom gardening is perfect for those of you without sunny yards for tomatoes! We started by sheet mulching our beds and amending them as we usually do. You can simply add a layer of fresh dry wheat straw, bought from your local hardware or garden supply store, to your existing bed or shady area.

1. Mulch your garden bed with 4 inches of dry wheat straw.

2. Crumble your mushroom spawn and be careful not to squash the individual grains if using grain spawn. Older spawn is difficult to crumble, so use fresh spawn!
3. Spread your spawn over the top of your straw in one continuous sheet. This allows the mycelia to coalesce into a single mat which can then penetrate into the straw below. My friend Nicole helped me establish this bed.
4. We then covered the spawn layer with another layer of straw about 3 inches deep.
5. This is the most important step: THOROUGHLY soak the 7 inch deep straw mulch with a hose for about two hours. You can use a sprinkler to do the job for you, but I did it by hand. For the next week you will need to thoroughly water for an hour or so every day, until the mycelia becomes established in the straw bed. Over the weeks, take a peak beneath the surface straw to see your mycelia running. Don’t let your bed dry out as this will harm your little mushries.
6. After the 8th week Ryan found mushrooms!
7. The mushrooms pop up between the vegetables and will probably fruit every few weeks depending on weather for the next year.
8. I interplanted the mushroom bed with garlic, kolrahbi, collards, arugula, and sweet peas.
9. My polyculture garden bed provides me with a complete meal, greens, mushrooms, and acorn bread from the white oaks overhead- if I were so inclined to harvest and process them!

SPORE v2… for post-disaster recovery?

Posted: March 30th, 2011 | Author: arkfab | Filed under: ArkFab Vertical Farm | 1 Comment »

Once we’ve built SPORE v2 we will be able to begin considering the application of similar kinds of systems to post-disaster recover scenarios, but I can’t help myself from considering the possibility right now after hearing what has happened in Japan. The three 40′ ISO shipping containers that house SPORE v2 can be stocked with the relief supplies to get people back on their feet and the necessary equipment to kick-start an economic recovery by producing food locally and cleaning contaminated soils. Take, for example, Hurricane Katrina, the hurricane created a massive surge of toxic flood waters that contaminated the soil around New Orleans, making it dangerous to grow food. I imagine the same is true for many parts of the Japanese provinces hit by the March 11 tsunami. SPORE v2 contains a 360 sq. ft spawn laboratory, 640 sq. ft. of environmental control chambers, and two 360 sq. ft. greenhouse nurseries. Once installed and running at full capacity this vertical farming facility can pump out 3/4 of a ton of mushroom substrate and 160lbs of edible protein-laden mushrooms every two weeks and numerous baby plant starts. This mushroom substrate can go far to bioremediate toxic soils and provide the necessary non-toxic organic substrate for reestablishing vegetable beds. Some mushrooms are even known to bioaccumulate radiation and may provide a biological option for cleaning up radioactivity.