Behind the Headlines: Methane and the Global Climate

     I posted two articles in the past week that appeared to contradict one another. The first article is about how Arctic Ocean methane does not reach the atmosphere and how methane seeps play an enormous role in marine life and global climate. Titles are important. They are crucial when trying to gain click-through rates to the web page so sponsors will keep advertising and writers can get paid. Now these titles sound controversial but are not what you think in reality. Read the articles and go past the headlines. Here is the pit of each peach, respectively, because it turns out that they might be related.
      From the first article, we know that methane gas is released from the seabed and increases the concentration of methane during the summer months. However, there is very little movement in the Arctic Ocean during the summer. An important term to introduce here is stratification. Stratification is a process where the layers and bodies of the ocean mix ingredients. In the picture below, fluids of varying densities will layer themselves in a column. We've seen this in elementary science class.

      If we take a stirring rod and attempt to mix these fluids, we may find that some mix better than others. We know that oil in water won't mix but will break up into bubbles of oil until we stop stirring. During the summer months, the Arctic Ocean is density layered and very little gas exchange occurs. Methane may be released but it will not enter the atmosphere until the conditions change and the waters begin mixing again through temperature (thermocline), density (pycnocline), oxygenation (chemocline), or salinity (halocline) variations brought on by the changing of seasons or weather events.

      About a week later, the second article was released and it sounded a bit ominous. However, we are finding out how important these hydrothermal vents are to the biosphere of the ocean. We do know that methane is 25% more potent as a greenhouse gas than carbon dioxide. That is why scientists and ecologists have been concerned about methane releases into the atmosphere. 

carbon dioxide

methane

      Then a fascinating result arose from studying the ecosystem of the methane seeps. The life forms that surround these vents consume a whopping 90% of the methane released! But there is a problem. These vents release more than methane and are being considered by mining companies as possible drill sites for copper, zinc, gold, lead, and silver. Drilling would destroy these habitats as we are beginning to learn how much methane they are withholding from the atmosphere.

Source: geology.com

A word on mentors...

    I don't think I can express the importance of women in science as role models for future aspiring scientists. Women are well-known in communication roles and have been gaining more traction in the science and technology fields. However, these two particular women have played a large role in the way I perceive and present research. They have both been wonderful role models in my time at Roanoke College.

     Dr. Kelly Anderson took me on as a research student in her computational chemistry lab. While we were waiting for further instruction from Dr. Siepmann on which projects we should be investigating, she gave me free reign to look through several papers and I designed a project. I ran two research projects that summer. The first one that I developed was to investigate some of the conformations of carboxylic acids and the role that they played in the formation of cloud condensation nuclei. My intent was to eventually match the findings in the research papers through geometry and energies of a cluster containing water, a carboxylic acid, and a base. We also wanted to see which changes had greater effect: temperature or pressure. The second project was to look back through a high school student's research project to make sure it was accurate. That one dealt with classical nucleation theory of a droplet of all the same molecules. 

Thank you Dr. Anderson for teaching me to trust myself.

     I worked with Dr. Erin Hackett at Coastal Carolina University two summers ago on a risky project. The only reason that it was risky is that we were not sure that we would attain the results that we set out to find. This project was a test to see if we could use seeding particles that are natural to an oyster larvae's environment to measure optical flow. In other words, I got to play with a class IV laser. I also designed the experiment to give us the most accuracy with the least influence from the equipment. What we found is that the nutrients in ocean salt that are used for aquariums can be used as a seeding particle and where as effective as the brown algae that the larvae feed upon. In summary, we use the particles of ocean salt to track flow of fluid while we use high speed cameras to record the motion of the larvae in the turbulent system. The data collected from an up-scaled version of the experiment is in the plan to be processed while waiting for a better camera before continuing with the project. She is conducting several experiments with undergraduate and graduate students. She is an excellent organizer and communicator. I was the first person to take part in this exchange program between Roanoke College and CCU. I can happily say that we are on our third exchange student coming up this summer!

Dr. Matthew Fleenor (Roanoke College Physics), Dio Beck (2nd exchange student), Dr Erin Hackett (CCU), and me!

Evaluation of Natural Tracers in Optical Flow Measurements: Part I

   There has been a few requests for more information about the research project that I worked on over the summer. The research that I worked on was a preliminary project for an up-scaled research experiment that will take place around June of next year. Since I have to present the research problem for my Independent Research class tomorrow morning, I figured that now is the perfect time to give everyone a more extensive discourse. 

http://www.vims.edu/newsandevents/topstories/archives/2011/oyster_reef_global.php

  Since 1980, the world's oyster reefs have witnessed a decrease in functionality by 85%. The Chesapeake Bay reef is considered functionally extinct. There are three basic reasons why: over-harvesting, disease, and habitat destruction. 

  But why are oysters important? They are filter feeders. They ingest phytoplankton, including algae. This reduces the incidence of unwanted algal blooms, keeps dissolved chemicals in the bay in check, and fixes nitrogen. They also provide habitat for bay life and serve an important role in the food web. 

ian.umces.edu/imagelibrary/displayimage-70-7044.html

     In response to human consumption, oyster aquaculture farms were introduced. There is quite a bit of controversy over their environmental impact versus their ability for economic sustainability. 

    However, the restoration of the Chesapeake Bay and other oyster reefs have taken a more central role in environmental sustainability. The two challenges facing natural restoration efforts have been engineering an alternative substrate to repair the habitat and the fact that we do not have a clear understanding of how larvae transport themselves. 

    Here, I will address the transport issue. We do know that oyster larvae respond to light, chemical cues, and fluid motion. We also know that larvae transport are controlled by the flow. Flow can be defined as currents, waves, or turbulence. Turbulence is the chaotic and rotational flow of a fluid. The only control that oyster larvae have in the umbonal stage of development is through a body part called the vellum. The vellum allows the larvae to float when open and can be withdrawn to allow the larvae to sink. The vellum, in the picture below, is the hair-like projection.

http://www.marinrodandgunclub.com/Oyster%20Habitat01.htm

el.erdc.usace.army.mil

      

   We want to measure fluid flow accurately without impacting oyster larvae behavior during the experiment. However, the standard seeding particle we use for particle image velocimetry measurements are glass hollow spheres which are not natural in reefs. The idea here is to see if we can use an algae, found in aquaculture farming, to feed oysters as a natural or biotic tracer. More information about the Isochrysis galbana can be found here. In the next post, I will talk about the equipment and the flow measurement technique used to capture the images.

 

Summer Research Talk

  So we have finally nailed down the presentation day/time/place. Honestly, I can't wait to do it. I can't wait to show everyone what I learned. So, here are the details...

Tuesday, October 21st

7:00 PM

Massengill Auditorium, Roanoke College

I will talk about oyster larvae and reefs

I will talk about seeding particles, manufactured and natural.

I will talk about how flow is measured through optical experiments.

I will talk about turbulence as pertaining to the experiment and the implications for future research.

I hope to see you there!

Response to: Atlantic Ocean key to global-warming pause.

  Now, before everyone goes off the deep end and right into the arms of climate change denial, there are a few key components mentioned in the article which I am sure no one read all the way to the end.

   "Tung says that his results show that global warming hasn’t halted. Comparing the long-term warming trend to a grand staircase, in which rapid rises are interspersed with plateaus, “we are now on the flat part of the staircase,” he says."

  In spite of this development, this is not deterring climatologists and their original assumptions about global warming. If anything, they are skeptical of the study until someone else can confirm the findings presented. Scientific research is not only about ground-breaking research but the confirmation of those original thoughts by several other agencies. Science must be repeatable and it is in this process that we can rely on newer models. 

  But what principle, exactly, are the models based on? Well, you will be surprised at how simple the concept is, called the Energy Balance Budget which is based on the Laws of Thermodynamics. 

Energy into system = Energy out of System

The graphic from NASA below should help clarify what this means. 

All the values are in Watts-area and described as an energy flux, starting from the left of the infographic we can see how much the energy flux is received by the sun and how much is absorbed and reflected. As we move to the right of the graphic, we can see how much energy the surface of the Earth emits versus absorption by back radiation or reflection from greenhouse gases. Plus, there is the transfer of energy by conduction, convection, and evapotranspiration. Even then, this is an oversimplification of all the processes that occur and the balance is very delicate within so many degrees. 
  So what is a Watt? It is a unit of power based on the International System of Units. Yes, I know how much Americans love SI units. All we need to know is that we are looking at power over a specific area. In this case, averaged over the surface of the Earth for the past 10 years. 
  This is what makes studying the climate so interesting, it is taking into account all the natural processes and interactions that not only happen between land-air and sea-air but even between molecules and that is what makes modeling very challenging, yet rewarding. 

Research Update: Revisiting the Purpose

  Hell Week was a couple of weeks ago which did not turn out as bad as originally thought. We only had one, fifteen-hour day to contend with. We realized when we received the veligers for the experiment that we had accidentally killed our algae population by adding in more saltwater to replace what we had used for experiments. None of my resources said that there was a specific process in which the saltwater had to go through in order to be sterilized. As far as I know, it involves killing bacteria with UV radiation. Therefore, oops.
  As it turns out, we may not have needed it at all. Reflecting back on the tracer particle experiments in the beaker, we had to open the f-stop on the camera in order for the Insight program to be able to "see" the particles. This overexposed the salt in the saltwater but gave us much better vectors during processing. However, we also realized the Instant Ocean did not completely dissolve in the water as expected. I am still not sure why at this point, so I will have to hunt down the answers on that but I have a few hunches.
  Now we are returning to the beaker experiments to see if we can use the salt in the saltwater as the tracer particles themselves rather than the saltwater and PIV particles. In addition, my partner and I are building the analysis code for the beaker experiments.
  There is a good chance we will not have enough time to investigate and analyze the data from the veligers in the big tank. However, there are a few observations that we made. The first one is that in order to see the velum of the larvae open and close, we would need a better high speed camera with a smaller chipset. We could see the veligers and distinguish them from the rest of the particles in the water, especially the salt. Particles sizes were at 10 microns, including the veligers. Using the LED light located under the tank, we brought the brightness up to about 90% and had to adjust our delta T, PIV timing, etc., to be able to record data the fell under the 15% error range we were looking for.
  Another piece of good news is that the veligers did float and sink just like the literature review stated. Those sets of papers used infrared lasers to track the particle movements because there would be a lessened effect on behavior than the Nd:YAG laser. This did turn out to be true. They could not get away from the laser path fast enough or the LED light. However, when the turbulent grid was cycling, they moved with the pattern of the flow in spite of the laser and they did perform their normal behaviors. It appeared that after the initial freak out, the veligers got used to their new environment pretty quickly.

  One of the drawbacks with this technique on studying veliger behavior in turbulence is that during the processing phase of the data gathered, the veliger movements may or may not show up as bad vectors. We still need the flow of the tank minus the veliger movements but we also need the larvae movements to understand their behavior better. Post processing generally wipes out the bad vector data by smoothing the vectors out so we have a vector field map that is useful to analyze. The key would be to use the Processing data, not the analyzed file folder data, to determine movement and behavior of the larvae, mathematically by giving them their own vector field map and creating a different set of code to analyze that movement which is not in the scope of this project for this summer. What we will have to report is which tracer particle is used best for the system that keeps the veligers in an environment similar to those of their natural habitat. 

Below are some preliminary graphs of the data we are analyzing from the beaker experiments at the two different speeds that were examined and the type of particles used. Once the results are centered and translated from pixels to centimeters, it should be easy to see that the results should be similar for any particle we use and we should be able to use the particle that is more conducive to the study in future work. 

Graph of the center line of U Bar flow

Graph of the center line of V Bar flow

Graph of the center line of the Vortex flow

  

Research update: Isochrysis galbana

from dtplankton.com

  

  Meet the brown algae that we are using in our experiment! We were concerned that the pigment given by chloroplasts in standard green algae would not be picked up by the PIV laser. Preliminary tests this afternoon show that the Isochrysis galbana (I. galbana) may be used in place of the 10 micron glass spheres! This algae is about 10 microns also. The low reflectivity of the algae meant that we had to open up the f-stop and increase the laser power to be able to accurately track these guys. One factor that we have noticed is that Instant Ocean doesn't completely dissolve in water but has a higher rate of reflectivity than the algae. So, we are working on making sure that any overexposure from the salt does not affect the study. 

  However, this made me curious as to why we obtained this particular set of algae versus the standard green algae. Come to find out that the accessory brown pigment is from an organic compound called fucoxanthin. Fucoxanthin is under heavy investigation based on a few other preliminary studies that point to this compound as a possible substance for human use in aiding with weight loss, as an anticancer agent, and an anti-inflammatory agent. These are only preliminary studies, so don't go running out looking to buy up the market on I. galbana. 

  Another factor, and one that is more prevalent to our experiment, is that these little guys are high in lipids and help sustain the diet of our oyster larvae (veligers). Why does this matter? It matters because we want to keep the veligers alive during the experiment and it would be optimal to recreate the veligers environment as much as possible. 

  One of the major issues in the scientific process is developing a plan of study for the experiment that not only gives optimal measurements but can also more closely replicate the natural environment of the living creatures involved. Experiments must be repeatable. Hence why we have a lab notebook to keep track of changes in the experimental set up. We try to keep this information in multiple places, if possible. Good science is repetitive science. 

  Remember when the first studies were released at the possibility of Higgs-Boson being proven? There was a mistake in some of the calculations. You can be sure that anyone who researches Higgs-Boson particles was reading that paper intently and trying to make sure that it was accurate, precise, and truthful to the best of our knowledge and instrumentation. This is what we aim for in the scientific community. Breakthroughs are nice but solid science must win out at the end of the day.