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.
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!)
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)gmail.com
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.
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.
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.
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?
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.
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!
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.
The original hoophouse designs for the ArkFab farm have an estimated lifetime of only four years… and they don’t stack. I took the multistage bioconversion process from these first designs and incorporated it into a standard repurposed shipping container structure with an estimated lifetime of 10 years. This reduces the annual estimated depreciation expense for the facility by a few hundred dollars a year, increases the amount of material recycled in our structure, provides easier installation and relocation of the facility, and allows us to stack them to take up less precious real-estate. Plus, shipping containers look really cool. Additionally, the logistics and shipping industry is well familiar with how to move these containers around the globe, so as we continue to develop sustainable urban agriculture systems based on these containers we will be able to consider applying them in post-disaster recovery situations.
There is a companion article focussing on the technical details of this project over at TopologicOceans
At long last, second generation DIY spectro has arrived!
The spectrophotometer. Yes, that is an invisibility cloak. You can't see the stuff that's under it can you? Then that stuff is invisible!
If you recall, when last we left our humble spectrophotometer, it was a shambling mess of stone-age technology. Now, its a shambling mess of information-age technology!
The principle is the same: A light source is split into its component frequencies, which are passed through a sample, and a detector measures its intensity. The intensity at each frequency is compared between a blank sample and an analyte to calculate the absorption spectrum.
Much of the heavy lifting (motor control and sensor reading) is now done by an Arduino microcontroller with Python on the other end of the USB cable:
The great commuicator.
The microcontroller controls the motor assembly and sends sensor data to the computer for analysis. The guts of the machine look a bit different, too:
The moving parts of the machine. You can see the motor peeking out from below the flashlight, and the sensor in the background.
A subplot in William Gibson’s book Count Zero involves a collection of abstract art pieces, consisting of seemingly random scraps of material assembled into unsettling but delicately beautiful arrangements. Though it didn’t occur to me during development, the aesthetic stuck. But did I take the route I did simply because I enjoy gluing pieces of trash to other pieces of trash? (and oh how I enjoy it!) One commentor remarked:
‘the project seems like a spoof on all the meticulously documented, high-production-value projects out there. I mean, masking tape, not gaffer’s tape? A TP tube, not a hunk of PVC?’
I could have sat down and planned the whole device from start to finish, designing blueprints in AutoCAD and precisely manufacturing the parts out of high-quality materials. But I didn’t do that- because I planned from the beginning to fail.
When I was a kid, I tried to build a drum machine using sticks and rope and powered by a rock which would fall from my treehouse. I planned it out with pencil and paper, every part in its right place, the connections between parts simple and obvious. And I put it together.
And it didn’t work. Some considerations were minor, but together they built up; other considerations weren’t obvious until the whole thing had already failed. Reality refuses to follow our plans for it.
Instead of starting with a schematic derived from theory, my process was of building and then unbuilding scaffolding, combining already functional modules and tweaking their arrangement until their assembly was a new module. I encountered unforseen difficulties sequentially, and in the context of a previously functional machine, rather than all at once, without context. In a sense, I helped the machine evolve by adding just the right bit of aluminum here or rerouting a wire there, contingency by contingency. As engineer Henry Petroski once wrote, technologies ‘do not spring fully formed from the mind of some maker but, rather, become shaped and reshaped through the (principally negative) experience of their users’.
Though the ultimate goal is to have a standardized open source instrument without the evolutionary contingencies and analog fiddling, I suspect that DIY Spectro hasn’t seen the last of the functional kludges. Part of the appeal of open source instrumentation is that it democratizes science. Besides hobby and educational applications, low cost instruments have potential for third world communities. There are all kinds of environmentally and medically relevant colorimetric tests (eg, for oxygen demand, nitrate concentration, pH, glucose…) which low cost spectrophotometry could support. However, these communities may well lack access to the specific parts of a given hardware project, due to lack of funds for manufacture and transport, and inconsistent supply lines. And as time progresses the environmental, social, and economic costs of a manufacturing and transportation system dependant upon fossil fuels may well rise making current resources less sustainable and possibly inaccessible. However, all the while we have been digging up the world’s mineral wealth, we have been reburying parts of it, stored in the material and organization of discarded technology. The gear system in this model was pulled out of an old floppy drive- how many floppy drives are wasting away in dumpsters across the world? Already, the first world exports its technologic waste to the third world, where it is destroyed for its precious, though toxic, mineral wealth. It’s a sick example of structural ecological inequality. But careful reuse of prebuilt technology might actually sequester those toxins- if you don’t break open a module containing lead, you don’t put that lead into the environment. This approach could help developing and alternative communities.
Also its really fun to glue pieces of trash together.
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.
