Wednesday, May 17, 2017

First impression with Everglades National Park

My first visit in Everglades National Park! My impression with the park is first amazing beautiful flat ever-green sawgrasses. Yes, it is obviously true as the name suggests. Alligator, frogs, fish, grasses, birds and mosquitos, to name a few, I have seen all those in 5 minutes! What a beautiful ecosystem near highly populated Miami areas. However, after spending some times to read scientific papers about the region, I cannot help thinking of environmental disasters that have been happening and will happen in the near future.
Alligator vs. Crocodile, that was very confusing for me. But after I see this beautiful one I will  remember that an alligator live in freshwater and can be BIG!
I visited a research site in which super talented graduate students Ben Wilson, Shelby Servais, and Sean Charles, Drs. John Kominoski's and Tiffany Troxer's crew at Florida International University, have conducted a saltwater manipulation experiment. In essence, they have monthly added saltwater into brackish wetlands to examine the effect of higher salinity on ecosystem carbon and nutrient cycles for about two years. Compared to my research at Virginia Commonwealth University, this is higher salinity dosing experiment and brackish environment so that I would not be able to compare our results directly. However,  I have seen some similar results, suggesting negative effects of higher salinity on marsh production, soil stability, and nutrient export. Most striking observation of today is peat collapse. I have seen peat collapse frequently in my research site in VA, and it is usually found along a edge of wetlands where high energy events such as storms or tides weaken soil stability by erosion. But I found severe peat collapse in the middle of wetlands. I can't tell exactly how much soils have been lost, but at least 10 cm of soils seemed to be gone and most roots came out of soils.

Shelby and Ben covered their faces due to mosquitos

The definition of peat collapse. 
This is a huge regional and global problem. Sea level rise will bring more saltwater into fresher ecosystem. It will lead to an expansion of peat collapse upstream. Marshes are heavy carbon sinkers that can stabilize soil structure, and they are likely the last hope for us to fight against sea level rise. We really need to improve an understanding of marsh-saltwater-nutrient-soil interactions to predict future changes and to mitigate sea level rise. The marshes in the picture make me sad, but I feel good at the same time because I am fighting for something we all need to protect.

Thursday, April 13, 2017

Collecting soil samples in estuary and wetland

There are many methods to collect soil samples in different environments. One can collect soils in forests, estuaries, wetlands, and even deep ocean. I would like to share some methods I have used in estuaries and wetlands.

The box corer shown below is very light (~10 kg) and can be used in a small boat. Having a pulley can be useful if we collect many samples but mandatory at all.

Left: soil box corer which is made with PVC material. It's great for collecting a small amount of soil from shallow-to-mid water depths.
Right: Gigantic coring device. We can collect a huge amount of soil from the deep oceans.
Middle: soil samples that were sub-sampled from the box corer.

Coring device made with PVC pipe
I find that collecting soil samples in wetlands is a lot simpler but more difficult because there are  roots. The PVC coring device is simply made with 10cm diameter PVC pipe attached to a flange (handle). We also need a locking plug which creates a suction to prevent soils falling out of the pipe. 

Wednesday, April 5, 2017

DIY microcontroller recording temperature and float switch state for mesocosm experiment

It is extremely valuable to have environmental data in environmental science, of course! Monitoring or measuring device can be easily several hundreds or even thousands dollars. However, we can measure temperature, humidity, light, etc. (basic environmental and climatic data) with a fraction of commercial products' costs.  We can also monitor a state of experiments as well which is sometimes impossible to do because of either location, cost, or your time.

We are going to set up a mesocosm experiment to test the effect of salinity on soil and marsh geochemistry, including carbon and nutrient cycles. We will use eight large baths (about 10 feet diameter) holding soil samples, and four out of eight will simulate "high tide", while other four baths will simulate "low tide". The simulation will be run by a series of eight bilge pumps that will run by time (every 6  hours) to pump water from one side of four baths to another side.

Since the mesocosm facility locates at the Rice River center which is 40-minute away from our laboratory and we will visit only weekly, it would be great if I can make a microcontroller to monitor the status of pumping and water temperature.

I use Arduino microcontroller to accomplish two major tasks: temperature measurement (soil, air, and water) and water level (high or low water).

Total cost of this project is less than $40 if you have a sodering iron and SD card.

* Things needed
- Arduino board: Any model. I use Duemilanove which is very similar to most popular model, UNO
- SD card shield integrated with real time clock (DS1307): Find on Ebay ($4)
- Temperature probe (DS18B20): Find on Ebay ($2)
- Float switch (any type of float switch will work)
- Arduino power adapter: Find on Ebay ($2)
SD shield coming with RTC time clock
Float switch and temperature probe

* Building steps
1. Connect a temperature probes to Arduino board
- Red wire to 5 voltage
- Black wire to ground
- Yellow wire to 4.7 kohm resistor to Arduino digital pin# 2

2. This temperature probe can be wired ALL TOGETHER and use ONLY 1 DIGITAL PIN on Arduino. It is possible because each probe has its own "address". But you need to find out the address first to use the probe (Follow instruction below:)
- Download Arduino libraries ( Onewire.h, SD.h, Wire.h, SPI.h, RTClib.h
- Import the library (you may get an error message if you don't have or install all necessary libraries.)
- Run "Read_adress.ino" to find a unique "address" or identification number for each temperature probe (for example, one of mine is 0x28, 0x54, 0xAD, 0x2C, 0x06, 0x00, 0x00, 0x80)

3. Check Real time clock
- First, checking RTC  by running one of RTC examples which are listed in the example menu (find a model number matching your product). It will nicely print out current time in the following format:

2017/3/31 (Friday) 21:18:29

4. Check SD card datalog shield
- Format and insert SD card into a slot on the shield. Run a code provided by SD library (Find on the example menu). Decide a time interval for recording data (I used 10 min).

5. Float switch
- I connect float switch to Arduino digital pin# 3 with 10 kohm resistor.
- Test the switch by running any simple digital input example found on Google
I know that this picture is not really useful to learn a wiring  in this project. But it's very easy to find an instruction from any Arduino page. Just searching for each product name for Arduino.
6. Combine all codes and run Arduino
- As you can see temperature has been dropping over night in my house. I am going to add total three temperature probes.

I put the boards into a used container for some protection.

I use a wire connector and attach to the side of container. Wires coming from temperature probes and float switch will be connected to the screws.

The entire project took less than 6 hours from planning to assembling. But it will be used to monitor temperature and water level for several months or years as long as experiment is going.

Happy making!

Wednesday, March 29, 2017

Porewater samplers in wetland soils

Porewater in wetland soils has a tremendous information. Scientists can use porewater to know more about geochemical properties of soils, such as pH, salinity, conductivity, nutrients, etc.

But how do we collect porewater? Although there are many different types of samplers, I particularly like my design because it does not disturb soil environments at all when we collect samples.

Let's see how I make.

Things and materials used (for making one sampler):
1. PVC pipe
2. Two PVC pipe connectors (fitting)
3. One PVC pipe cap
4. Tubing
5. Two three-way stopcocks
6. Porex porous membrane pipe (nomial pore size: 20-40 um): I purchased Porex pipe from Interstate Inc.
7. One rubber stopper (cap)
8. PVC cutter, PVC cement, cork borer (or drill to make a hole on rubber stopper)

I can make any length of sampler to collect water from a different depth. But for this instruction, I will pretend to make a sample which has a target collecting depth at 10 cm below soil surface.

Cutting (see my note below):
1. Cut PVC pipe at a length of 35 (top) and 20 (bottom) cm
2. Cut porous membrane pipe at a length of 9 cm.
Top left to right: a sampler designed to collect porewater at 10, 25, and 50 cm below soil surface (Olivia De Meo note)

Assembling the pipe:
1. Using PVC cement and PVC connector, I connect the 35-cm PVC pipe to porex membrane pipe. Use enough PVC cement and even apply silicon gel when the cement is dry. The outer diameter of PVC and porex pipe is slightly (less than 1mm) different.
2. Attach another side of porex pipe to the 20-cm PVC pipe using the connector and PVC cement.
3. Put the bottom PVC cap on the another side of 20-cm pipe. I don't permanently attach the bottom piece because I want to retrieve a sampler out of soil to clean periodically.

Preparing a tubing:
1. Prepare a 80-cm and 25 cm long tubing
2. Using either a drill or cork borer, making two holes on a rubber stopper.
3. Put the two tubing through the stopper and leave 20-cm tubing above the stopper. (use hot water to ease the process)
4. Insert three-way stopcock (use hot water to ease the process)
5. Mark a stopcock with electrical tape to show which one is longer (sampling port) and short (air port)

To collect porewater, we need following items:
1. Nitrogen gas bag
2. Syringe
3. Sample tube
Picture showing porewater samplers installed in our experimental plots

How to collect sample:
1. Connect a syring and nitrogen bag into a long and short tubing stopcock, respectively.
2. Remove old water stored in a sampler by pulling water out using a syringe. This action will replace water volume with nitrogen gas. This is very important step because we don't want to inject oxygen into anoxic porewater sample. If we replace water with air (not nitrogen gas), it will spontaneously oxidize some ions (such as reduced sulfur, manganese, iron).
4. Disconnect both the syringe and the gas bag.
5. Wait about 30 min.
6. Do the step 1 again.
7. Collect sample.

Happy sampling!

Friday, January 30, 2015

Office name plate using Arduino Nano, LED backpacks (Adafruit)

My laboratory/office is located in the basement of Biology Department building which is difficult to find because there are many offices. I decided to make my name plate to be more visible using Arduino and LED packs.

- List of items
  1. Arduino Nano (Here)
  2. 4 character LED (Here)
  3. 8x8 LED matrix (Here)
  4. Power adapter
  5. Jumper wires
  6. Breadboard
  7. Potentiometer
I also used CNC router (from HackRVA) to carve my name and spaces for the LED matrix.
Matt, helping me to carve my first CNC project
Then, I connected Arduino Nano with the two LED backpacks.
Testing LEDs
 It turns out that the 8*8 LED backpack is way more powerful (or functional) than I originally thought because I can scroll a sentence (although I don't know how many characters I can use).

I use a potentiometer to control the display.
The window is not really clear transparent but still I can see my name and LED characters clearly.

I thank Aron, Matt, and other HackRVA members for helping me to build, learn, and do electronic work!

Wednesday, December 31, 2014

Arduino Duemilanove + GSM shield, trouble and solution

If you are a beginner in Arduino,  GSM shield, and have failed to use those for sending/receiving SMS, or calling/receiving a call, I can give you a bit of help. Maybe a lot depends on your previous skill level.

You will be able to find a lot of instructions for Arduino Uno + GSM shield. But for any reason, I could not find one good instruction explaining Duemilanove + GSM. Now, after I figure it out, it makes sense because Uno and Duemilanove are almost identical. However, although Arduino experts would understand this GSM instruction without a question, there are so many things which do not make sense to me at all, such as: (and I strongly believe that it is not just my fault as you can see below)
Figure 1. On the left (GSM shield), it clearly says that 'pins 0 & 1' are not connected! HOWEVER, when you connect the GSM shield onto Duemilanove, the GSM pins 0 & 1 are mounted onto the Duemilanove pins 0 & 1. As you can see in Figure 2!
Figure 2. See the bottom left side of picture (right above orange half circle). As you can see, I connect the GSM pins 0 & 1 with the Duemilanove pins 0 & 1. Why, why, and why the official instruction says "not connected"? I really want to know why they mentioned it. But I can confirm that you NEED to connect them. 
Also, there is one more weird instruction I found (please see Figure 3) below:
Figure 3. Check out the difference of TX/RX labels between pictures from the official website (left) and mine (right). Although left official picture says that Pin 2 = RX, actually, my shield Pin 2 is labeled as TX. 
In Figure 3, the pin 2 is actually labeled as GSM TX (not GSM RX as shown in the official website). I was extremely confused. But please ignore the difference. Just mount the GSM shield to Duemilanove.

I also had a problem with Sim card. I need to explain more about this problem. I don't have a phone using the same size of Sim card. I purchased Sim card from the Ebay and activated on AT&T GoPhone website. As soon as you activated the card (by adding Sim card number and IMEI number of the GSM shield), it automatically changed the Sim card Pin number!!Very annoying!!!!! At this point, only way you can add money to the card is by calling the company. However, you still need a phone using the Sim card to have a PIN number. I called three time, and all AT&T representatives ask me for finding a AT&T phone to get a PIN number. You may think we can receive the number by connecting the shield and Arduino to our computer. However, to run the Arduino 'ReceiveSMS.ino', we need to type 'pinnumber' which I didn't have.

So, what I recommend is simple: just go to AT&T store and explain that you need PIN number. I ended up replacing the SIM card.

Finally, I found that we need to type pin number in Arduino IDE (instruction). On the second line of the instruction, if you have PIN number (e.g., 1234), you need to remove quotation marks!!!!
So, instead of below
#define PINNUMBER ""
you need to type
#define PINNUMBER 1234

The PINNUMBER command line is the only line you need to change. I found some instructions to remove the pin number, but I don't know yet.

I hope this instruction help you.
Figure 4. This image shows another side of Figure 2. 

Wednesday, December 18, 2013

Scientific communication

Many agree with the expression 'A picture is worth than a thousand words' in scientific papers. I like a paper with a summarizing diagram at the end of discussion because it helps me understand main findings of the paper. But I wonder why I have not seen any scientific paper with a drawing, that's not just with boxes or arrows but with actual drawing. Even if we can add a drawing in a paper, I would be in big trouble because I cannot draw well yet all. 
Small pond with many cattails