DIY Christmas light pH probe

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I have been weighing the options of testing soil in the field vs. on the bench for parameters of interest. The parameters I am focusing on are soil ph, temperature, moisture, fertility, conductivity and organic content. Of these seven, only temperature and moisture must be collected in the field. I believe that the others can be more accurately determined in a bench-top environment. I am developing my hardware designs accordingly. The next steps for me are to track down materials to build this ph probe and figure out how to interface it with an arduino board and relay information back to the field science android app through bluetooth. I am also planning to have a conversation with Mike Deibel this week about using optical measurements for organic content and fertility tests (and possibly munsell color tests). I also have a back-burner interest in geophysical surveying techniques for archeological dig sights that is still very much in the research stage.

“Science in a Box” Soil Platform

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My current project is to develop a functional and consistent set of sensors and protocols to collect information about important soil parameters such as pH, fertility, conductivity, temperature, organic content, and moisture. In Iceland and Nicaragua, the approach was to construct a unified soil sensor platform using Arduino and Yoctopuce technology that takes readings in the field.



Screen Shot 2015-09-17 at 10.24.48 AMScreen Shot 2015-09-17 at 10.25.38 AM

The potential benefits of this approach are that every parameter of interest is collected in the field and immediately saved in .csv format on a nexus device. The downside is that it is not particularly easy (or in some cases, possible) to test every parameter in harsh environments accurately or without causing damage to the sensors.

With this in mind, I am planning to take a sightly different approach: a sensor for use in the field that measures parameters that must be collected in situ (such as temperature and moisture), supplemented by benchwork preformed in the evening to collect other relevant soil parameters. The evening benchwork would also have hardware and software components. For example LED/photometer sensors could be used to measure organic content and other optical sensors could be used to make observations about the color of the soil and its composition.

The next steps for me are:

  1. Learn more about the chemistry of soil fertility and ph and find a way to test them cheaply without using standard kits.
  2. Consider the hardware element. Look for cheap sensors that are compatible with Arduino boards and begin preliminary designs. I will probably build the temp/moisture sensor first since it most closely follows the paradigm of sensors that have already been developed as a part of this research.


How to Bird Survey

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My focus of this week has been on researching the best techniques for a bird nesting survey. Through many papers the way I think will work best with what we want to achieve is to use thermography to map nesting locations. This has been done in grassland birds as well as several others and there is likely enough literature to find the best and most successful techniques. The issue we are running into is what to use for the thermo-camera, because they are very expensive. We are not a large research institution so we will not be able to spend what they would. We also would need to especially test the cheaper options to see if they can actually detect relatively small birds. The other factor will be how to detect how far away the bird is and whether we will mount an aerial camera or from the ground. Looking into range finders will be key. Both options have major complications involved that we need to research further.

… and all the other things that need to be done

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My role is to support Kristin as she leads our group, mostly by being the “institutional memory” for this project since its’ inception in 2012. In the summer of 2013 we made our first trip to Iceland, thanks to the help and generosity of Kathleen Affholter (geology, Pellissippi State Community College). We returned to Iceland on our own in the summer of 2014, and to Nicaragua in December, 2014. On each of the trips we work with and as computer scientists, physicists, biologists, geologists, archeologists, agronomists, and cooks and bottle washers. So far I have been organizing lists, completing financial reports, and looking for funding.

And so they begin…

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September 7th, 2015 marked the beginning of our preparation for our trip to Iceland in the summer of 2016. Four alums to the project, Charlie, Tara, Deeksha, and myself, and four newcomers, Nic, Eamon, Erin, and Ben met in the Hopper lab in the new Center for Science and Technology, excited and eager to get started on the projects for next summer.

There’s lots to be done before we can go off to Iceland next summer. There are a number of projects that the members are working on, a summary is below with the name of the person/s working on them in parentheses:

  • Bird nesting site survey at Skalanes (Erin, Ben)
  • Field Science Android application development (Kristin, Charlie, Nic, Tara)
  • Soil Platform (Tara)
  • Environmental monitoring/sustainable energy (Erin)
  • Visualization Tool (Eamon, Deeksha)
  • Wet Lab work (Nic, Erin, Tara, Deeksha)
  • Data Model (Deeksha, Eamon, Everyone)
  • Archaeology site survey (?)
  • Archaeology species survey (?)

Archaeology Site Survey

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I’ve been doing research on the archaeology site survey project — trying to determine where the sites are at Skalanes, without having to excavate the site. I’ve determined that people do what’s called a ‘Geophysical Survey’ which is a non-destructive way to determine where their are sites.

There are differents methods:

  • Electrical Resistance
    • Using (usually) four metal probes stuck into the ground measuring electrical resistance. Many archaeological site characteristics will have different electrical resistance from their surroundings. For example, a stone wall structure might impede the flow of electricity, and organic materials in soil might conduct electricity more easily.
  • Electromagnetic Conductivity
    • Measuring the conductivity of the soil. A magnetic field is created underground by sending a current with a known frequency and magnitude. The currents spur a secondary current in underground conductors that is picked up by a receiving coil. Less sensitive than resistance meters.
  • Magnetometers
    • Measuring the gradient of the magnetic field of the Earth ( gradiometers), provides resolution of small near-surface occurrences. Magnetometers react very strongly to iron and steel, brick, burned soil, and many types of rock, and archaeological features composed of these materials are very detectable. It is often possible to detect disturbances in organic material.
  • Ground Penetrating Radar

Android, Android, oh yeah and some more Android

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The past week, I worked on a variety of things — setting up the wordpress, researching archaeology surveying techniques, and setting up our field science application with Android Studio.

In previous years, the IDE that we used for Android was Eclipse. As of earlier this year, Google is no longer supporting Eclipse as the Android IDE and has switched to Android Studio. Things are different in Android Studio and I’ve been working on trying to set up Seshat and get it working. I’ve been running into errors about gradles and builds and libraries, so I’m trying to figure out what’s going on there. I had it working, but realized that I needed to update the YoctoLib library, and when I did that things went down the drain again. Once I have it working I’m going to create a document that will explain what to do.

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