The Highs and Lows of a Research Project

One of the enticing facts that drew me to UC Santa Barbara was that it was one of the top schools for research. It sounded interesting, but I didn’t have a great idea of what you actually do in research. When I imagined what a research project was like, I imagined a “grown-up” version of my fourth grade science fair project where I compared mung bean plant growth in sunlight and in shade. It wasn’t until I completed my own small research project that I learned how difficult but rewarding research actually is.

During the summer of 2016 I took EEMB 170: Biology of the Marine- Land Interface. This was the most challenging and the most fun science course of my undergraduate career so far. I experienced firsthand what it’s like to do fieldwork and conduct a research project. This class had lectures with set material that we had to learn, but in the labs I had the opportunity to be creative and learn independently by designing and conducting an independent research project. Compared to previous classes, I never felt as much responsibility for my learning than when I was working on the research project.

Soda Bottle on Clam Gun

Something as simple as a 2L soda bottle can become a cutting-edge research tool!

The final project was a research paper about some aspect of the beach food web. I wanted to study something I had no experience with, so I studied blood worm abundance and distribution. The experiment was conducted with a partner, while the analysis of the data was done individually. We would use clam gun to take a few cores at a site at different times for a few days, and count the number of blood worms found in each core, as well as the depth each blood worm was found. However, when we tried sampling the sites, we found that this project would be much harder to accomplish. I thought that sampling would be easy because we had planned it out well, but it required a lot more problem solving. I learned that the provided tools may not be enough, so I had to make my own. When we released the cores into a dish pan, the sand would crumble instead of holding the cylinder shape of the clam gun. The solution? Find a container the exact diameter of the clam gun. We would place the clam gun in the container, shake out the core into this container, and this would allow us to dig out the blood worms and note their location. We brainstormed different ideas, like cutting a PVC pipe, or shaping a sheet of plastic. I spent a few hours at the Home Depot trying out different cylinder-shaped items, but I couldn’t find anything that really worked. Luckily, I found that a 2-liter soda bottle is the perfect fit for a clam gun.

I asked many questions throughout this research project and I had the advice of two research professors, a graduate student, and a lab assistant to brainstorm with and answer all of my questions. I also had help from the members of the lab I intern. I thought research projects were more of a solo effort, only involving the researchers. It was a nice surprise to realize how collaborative the process really is, and the support was encouraging. I learned so much from asking questions, and this helped me the most when writing the paper. The hardest part was figuring out how to use Excel and how to understand my data. The most interesting part was reading about other research projects that people have done on blood worms. From one of the papers, I learned that blood worms have practical use as biological indicators for environmental management. I had no prior knowledge of or experience with blood worms, but after reading through many research papers, I ended up learning more about blood worms than I needed to write my paper.

Blood Worm

A sandy beach blood worm. It gets the red color because the molecule it uses to transport oxygen, known as hemoglobin, turns red in the presence of oxygen. Sound familiar? We have hemoglobin in our red blood cells!

I’ve learned that research is about repeatable results that can be clearly interpreted, so it was interesting to see how my partner and I drew different conclusions from the same data. I thought that we could neither prove nor deny our hypothesis, while she thought that our hypothesis was correct. I thought that data was made of solid facts, so there was only one way to understand it. It seems that data doesn’t always speak for itself, and that research projects won’t always have simple answers.

I hypothesized that blood worms burrow vertically into the sand when the tidal level rose. After sampling and analyzing the data, I didn’t have a definitive answer. It only led to more questions that led to ideas for future research, which I found to be exciting. I wondered how researchers find so many topics to research about. It seems that, while the purpose of a research project is to answer a question, it often leads to more questions. There’s always more to learn, and I think that’s something to look forward to.

My experience in this class, and especially with this research project, has validated my decision to pursue a science degree. I thoroughly enjoyed the learning and the challenges I faced in this class. Finishing this research project felt like more of an accomplishment than any success in a more traditional class setting.

An Introduction to Tidal Harmonic Analysis

You’re lying on the beach. You’re eyes are closed and the sun is warm. All is well. The oceans however, grow louder and louder, when suddenly a surge of water advances, and drenches you and all your belongings!

What may seem to be the ocean’s way at getting back at the humans who pollute its waters, is actually just the periodic ebb and flow of the ocean known as the tides.

In many aspects of oceanography, it is useful to separate data series such as temperature, velocity, pressure, etc… in terms of tidal and non-tidal components. For example, in my work for EUREKA, I am trying to evaluate changes in pressure (and relatedly sea level height) measured via a sensor placed on the ocean floor. I need to be able to discern changes in sea level height on the order of + 5 cm. This became a difficult proposition when I realized the sea level is constantly fluxuating on the order + 2 m multiple times a day!

If you are interested in the physical mechanisms that underlie the tides, I highly recommend the video below. For this post however, I will be focusing on the techniques oceanographers use to reduce tidal components of their data.

The Building Blocks:

Let’s acquaint ourselves with what a typical pressure signal looks like over a month long period. The blue line represents the pressure signal (measured in decibels) and the red line represents the average value of the signal over the month long period. The periodic nature of the graph easily implies a strong tidal component, although other periodic trends exist like wind forcing of the water due to a sea breeze, but no other periodic trends occur at the scale of tides in terms of consistency.

Graph 1

Our goal is to attempt to identify the tidal signal, and since it is periodic, it is a good idea to review our sines and cosines as they are useful in modeling periodic graphs.

Here is a simple sine function: y = sin(x) from 0 to 6 pi.

Graph 2

This graph is clearly periodic, but yet it doesn’t quite represent our pressure data. We can do better though! If we add some other periodic functions we will really start to see some resemblance between our pressure signal and the simple graph I created below.

Here y = sin(x) + cos(x) + sin(2x) + cos(2x) from 0 to 30 pi.

Graph 3

We can continue this process of adding up various sines and cosines until it resembles our pressure signal. In fact, mathematicians in the 18th and 19th century deduced that all periodic functions can be represented as the summation of sines and cosines.

Here is a link to a wonderful animation showing how even a couple sines and cosines can add up to look like a saw tooth!

http://bl.ocks.org/jinroh/7524988

Armed with the knowledge that any periodic function can be modeled as the summation of sines and cosines, we can in fact look at our pressure signal and determine what frequencies are present and the relative impact they have on the overall signal! Let’s not forget how powerful this tool is. Richard Feynman remarked, “It is easy to make a cake from a recipe; but can we write down the recipe if we are given the cake?” Joseph Fourier and his colleagues showed that we can have our cake, and determine its components too!

 

Breaking down the Tides, Constituent by Constituent:

If the moon orbited around the Earth in a perfect circle in the plane of the Earth’s equator and the sun were not present (A lot of assumptions!), a typical graph of a tidal signal may look like this:

Graph 4

The insight to be gained from looking at this graph is that the dynamics of our orbits with astronomical bodies influence the tides in a regular manner (i.e. at specific frequency). These specific frequencies are each given names. In the example above, it is called the M2 frequency. In the case where we now consider both the Moon and the Sun’s effects (S2) on our tides, our tidal graph may look like this:

Graph 5

Note the longer term periodic trend of the graph of about 2 weeks which corresponds with the alignment and mal-alignment of the sun and moon.

The M2, S2 and other frequencies are called constituents. They are further specified by the sum of various frequencies arising from planetary motion such as the rotation rate of the earth, the orbit of the moon around the earth and the earth around the sun, and periodicities in the location of lunar perigee, lunar orbital tilt, and the location of perihelion. (See References & Resources for additional info).

When analyzing the tidal components of our signal, anywhere from 5 – 60 constituents must be taken into account depending on the accuracy needed and the length of the raw data used. Once these tidal constituents are determined by methods of spectral analysis (See References & Resources), they are removed from the pressure signal, and a “de-tided” signal remains. This is called the harmonic method of tide analysis and was developed by Lord Kelvin and Sir George Darwin beginning in 1867. We can now evaluate the variations in pressure we care about with great precision!

The final product of de-tiding a pressure signal is shown below at Point Purisima (PUR). Note how small the variations in pressure are in the de-tided signal vs the raw pressure.

Graph 6

Graph 7

 

References & Resources

The Feynman Lectures on Physics: Volume 1 http://www.feynmanlectures.caltech.edu/I_50.html

What Physics Teachers Get Wrong about Tides!             PBS Digital Studios https://www.youtube.com/watch?v=pwChk4S99i4

Fourier Series Wikipedia https://en.wikipedia.org/wiki/Fourier_series

Harmonic Analysis and Prediction of Tides Stony Brook University http://www.math.stonybrook.edu/~tony/tides/harmonic.html

Classical tidal harmonic analysis including error estimates in MATLAB using T_TIDE (Pawloicz et. Al) 

Note: I use T_TIDE to de-tide my data.

http://www.omg.unb.ca/Oceano/fundy_tides/T_Tide_CompAndGeo.pdf

 

My summer experience

This summer so far has been a valuable learning experience in which I finally obtained some clarity on my future.

As an engineering student entering my fourth year, the concept of planning my next step after college is now starting to hit me hard. I have loved my 3 years of engineering classes up to this point. Although challenging, I never had any doubt once I took my first engineering class that this is what I wanted to do. However, I have taken courses covering such a wide breadth of engineering fields such that my specific career path has appeared very fuzzy in my mind.

This was my first time doing summer research, under AIM Photonics, and the cliché of “better late than never” has certainly held true thus far. Both the panels and especially the two dinners have greatly assisted in the processes of planning out my next chapter in my career. These events have given me some key lessons on how to be successful, including the main takeaways of the importance of communication, networking, and simply being easy to work with. From the industry dinner I learned that a master’s degree or higher is not a requirement if you want to be a leader in a company, which was a huge question that I had been itching to find the answer to.

At the very same dinner, I experienced the power of networking as I met one of the CAPSTONE project leaders from FLIR, and had a lengthy discussion that got me deeply interested in that project and the opportunities that it can bring me. Furthermore, my specific research project which is focused mainly on design has helped give me a glimpse into what I can expect if I enter an industry position.

I still have a few months to help clear up my vision for the next few years, but this summer has helped me tremendously in doing so.

Before you do research

Not many students really think about researching as an undergraduate because graduate school is something of a mysterious land that they have yet to even imagine exploring. However, it’s something I have considered pursuing since matriculating into UCSB but the thought itself is very scary. That is why undergraduate research is a step in the right direction because it allows for you to experience a small portion of what could be if you do decide to head toward this direction. But before you start research, I want to talk about a misconception I had previously about research.

Not all research experiences are the same. I came in thinking that I would immediately be in the lab designing and testing circuits and working side by side with my mentor; instead, I had papers upon papers to read. The big mistake I made there was thinking that research was going to be easy. The material that doctoral students had to understand and digest cannot be understood in a few weeks by undergrads. The reality of the situation was that I needed a strong physics base knowledge in electromagnetic fields to start comprehending the design parameters of my project. But like I said before, not all research experiences are the same. There are research projects where the majority of the job is spent testing samples because the project is nearing completion or the bulk of the work lies in repetitive tasks. These usually require less technical knowledge but more lab skill. For example, a friend of mine was looking at plants under a microscope to sort them for a professor. The research value gained from that was mainly the networking and exposure to the lab atmosphere. Each experience is valuable in its own respect and you have to make the best of it.

Learning from an Internship

Aim Photonics is my first internship where I do real research; I was surprised of the abilities and qualities that someone needs to have in order to explore new fields and discover new ways to make life easier by building new devices. I believe that is very difficult to do research because the people who are doing research are working in something that nobody worked before. Sometimes there are not a lot of reference or papers similar to what they are doing; therefore, there is a lot of fails every day in the labs. I am having a very good time working in my research cleaning and preparing silicon surfaces to grow III-V epitaxy with my mentor Dan Pennachio; I am learning a lot from him because he always helps me and explains things in a way that I can understand. Also, all the members of the Palmstrom’s group helps me by giving their opinion about my research and suggest me things to do to improve results.  Palmstrom’s lab is super interesting because is hard to believe that such technology can exist. I am performing several methods to clean the surface of the silicon and I am using several equipment to analyze how good the procedure is. Using these devices makes me to feel lucky because I am using apparatus of millions of dollars that not everybody can have the opportunity to use. Also, all members of the Palmstrom’s group motivated me to continue my education and I started to think that maybe I would like to become a research scientist.