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Book Review

Growing a Scientist: Undergraduate Research 2018, part 3

Each summer, the University of Rhode Island Graduate School of Oceanography (GSO) hosts undergraduate students from all over the country to participate in oceanographic research. These Summer Undergraduate Research Fellows (SURFOs) have not only been working with GSO scientists, but they have spent part of their time learning how to communicate this science to the public. Read on to find out what they have been up to, and why they everyone should be as excited as they are about their work.

Authors: Deborah Leopo, Mike Miller, Whitney Marshall, and Robert Lewis

Why am I spending an entire summer making gene copies of a hydrothermal vent snail?

By Deborah A. Lopo, University of California, Santa Cruz

SURFO Advisor: Dr. Roxanne Beinart

A brief history on biological communities in hydrothermal vents.

Before 1977, it was thought that the deep sea was a barren place devoid of life; that changed when scientists from Woods Hole Oceanographic Institution discovered hydrothermal vents for the first time. (Fig 1). Thousands of meters below the ocean surface, they found environments teeming with animals, and this discovery revolutionized the way scientists thought about undersea life!

Figure 1. Snails, mussels and clams form a rich biological community at hydrothermal vent sites in Lau Basin, Tonga. Photo Credit: Dr. Roxanne Beinart

Yet the discovery also inspired a lot of questions…what was allowing these organisms to survive without sunlight in extreme pressures, high acidity and warm temperatures? As it turns out, many vent organisms can form symbiotic relationships with bacteria to obtain the nutrients needed to survive in these stressful environments. A symbiotic relationship is an interaction between two organisms living closely with each other. Some of these interactions can offer positive, neutral or negative benefits.

Among the symbiotic vent organisms are a species of snails known as Alviniconcha; these snails harbor bacteria in their gill tissue. These species of snails are abundant in the Lau Basin vent fields by Tonga and have recently been described as a ‘cryptic species’.

Cryptic species are organisms that are physically indistinguishable from each other but are genetically differentmeaning they may look the same but are different from each other at the molecular level.

Detection of key differences in Alviniconcha spp.

Despite being described as a ‘cryptic’ species, two key differences have been detected in three species of Alviniconchafrom the Lau Basin, Tonga vent fields (Tahi Moana, ABE, and Tu’i Malila).  These key differences or morphological differences were noted in 1) the skin coloration of the snail (Fig 3) and 2) the patterns of spikes found on the thin outer coating of the shell, known as the periostracum(Fig 4). These morphological differences were first observed and documented by my mentor Dr. Roxanne Beinart. For my research project, I am testing these differences and seeing if they correspond to different species ofAlviniconcha.We think that they may and if our hypothesis is correct, it may be that these species do have distinguishing features after all!

Figure 3. Epithelial or skin coloration on two Alviniconcha species from the Lau Basin, Tonga vents. The snail on the left has a deep pink coloration than the snail on the right (light pink)

Figure 4. Pattern of spikes on two Alviniconcha species from the Lau Basin, Tonga vents. The pattern of spikes are separated into two categories 1) Alternating and 2) Uniform. Alternating has a big hair followed by three little hairs and then another big hair. In uniform, all hair lengths are the same.

Importance of making mt-Co1 gene copies of the snail Alviniconcha spp.:

To test our hypothesis, I made copies of the mt-Co1 gene. Genes are segments in DNA that help determine physical traits, for instance, the of our color eyes; whether they be blue, brown, green, etc. The mt-Co1 gene will help us identify what type of species of Alviniconchawe have in our samples. In the Lau Basin, there are three known species of Alviniconcha1) A. strummeri, 2) A. boucheti and 3) A. kojimai.  We hypothesize that A.bouchetiis light pink in skin coloration and that both A. strummeri and A. kojimai are dark pink in coloration. To distinguish A. strummerifrom A. kojimai, we then must refer to the patterns of the periostracal spines, uniform vs. alternating (Figure 5).

Figure 5. Dichotomous key of the three species of Alviniconcha (A. boucheti, A. strummeri and A. kojimai) found in the Lau Basin, Tonga. The key is separated by the morphological differences observed, 1) epidermal coloration and 2) patterns of periostracal spikes. We hypothesize that A. boucheti has a light pink coloration; for A. kojimai and A. strummeri suspect they correspond to either alternative or uniform periostrcal spikes.


Our studies have shown that our hypothesis is true! A. bouchetihas light pink coloration while both A. strummeriand A. kojimaiboth has dark pink coloration. To distinguish A. strummeriand A. kojimai, you will have to refer the spikes. Genetic testing shows that A. strummeri has uniform spikes while A. kojimaihas alternating. These findings are important because Alviniconcha is a dominant vent organism are susceptible to studies. Finding ways to tell them apart will allow for faster shipboard experiments.

Predicting Sea Level Change: Searching for a (Ne)edle in the Haystack

Michael Miller – University of St. Thomas

SURFO Advisor: Dr. Brice Loose

As of May 2018, climate studies have predicted the beloved floating city, Venice, to be completely underwater by the year 2100.Similar predictions have been made for coastal metropolises around the world, but exact dates for our large-scale flooding can fluctuate. Sea level projections have been difficult to interpret due to constantly changing rates of ocean heating and glacier melt. The variation in predicted sea level rise places a lot of strain on law-makers and city planners to develop infrastructure that will mitigate sea level rise in a timely manner. To prepare for the future, we need a better understanding of how quickly sea level is rising. One key to access this understanding lies in the water surrounding the most remote continent; Antarctica.

The continuous rise in our oceans is largely attributed to West Antarctic glaciers depositing over 100 billion tons of fresh water into the surrounding seas every year.2Sea level predictions depend on our ability to detect the volume of freshwater runoff from melting glaciers. Observing where and how quickly freshwater is flowing into the sea can help determine where the most problematic glaciers are, and how fast they melt each year relative to one another. To differentiate glacial meltwater from seawater, scientists have established methods of detecting variations in temperature, salinity, and dissolved oxygen concentration. While these methods are useful, relying on them can lead to biased results. For example, oxygen concentration can fluctuate daily as marine plants release it through photosynthesis and marine organisms extract it when they breathe.

A more accurate alternative, dissolved neon, has become a favorable indicator for glacial meltwater. Neon gas is trapped within tiny pockets of air inside glacial ice. As the ice forms, it starts as fluffy snow and is later compacted by several years of snowfall. As snow first accumulates, there is a lot of space in between grains. Over time, additional layers of snow compress the layers beneath it. Pressed by the added weight, the grains are pushed closer together. Scientists call this semi-compact glacial layer firn. After snow continues to further compress the firn, the added pressure causes the spaces between grains to be cut off forming tiny air bubbles.

Ice core diagram outlining the arrangement of an ice column and the formation of air bubbles within. Credit: Adventures on Ice Blog3

Neon is favorable because it is among the six noble gases on the periodic table. These gases contain a full electron shell, making them unable to bond with other atoms through biological or chemical processes.This means that the high levels of neon in glacial meltwater won’t change even if its surroundings do. However, in its current application, detecting dissolved neon is expensive and inefficient; current technology used to detect neon in seawater is limited to a small sample size. This could require collecting hundreds of individual seawater samples, costing about $500 to analyze. This quickly adds up.

Detecting neon in the lab is expensive because it amounts to searching for a needle (neon) in a haystack (air). Of the many gases that make up the air we breathe, only 0.0018% of it is neon. The device that searches for this needle is called a quadrupole mass spectrometer (QMS). To pinpoint neon, the QMS hits gas atoms with a stream of electrons altering the sample so that it only contains positively charged ions. The ions are then sent through an electric field generated from charged rods turning on and off at high speeds. Varying the amount of charge on the rods allows the electric field to separate ions based on their mass to charge ratio (m/z).

Particles with a larger m/z value are atomically “bulky,” and can’t turn as quickly as a particle with less mass. The relationship is similar to comparing the Titanic to a jet ski; if the Titanic wanted to turn, it would have to do so over a long period of time, while a jet ski can turn almost instantaneously. The electric field exploits the weaknesses of particles. Ions with a large m/z value are attracted to the rods and don’t have enough time to change direction before they collide with them. Ions with a small mass to charge ratio change paths so quickly that as the poles switch on and off, it is never allowed to keep a straight path and is neutralized. Only neon ions that contain the perfect m/z value can travel through the field and make it to the detector on the other side.

Quadrupole mass spectrometer system displaying the path of an ideal mass to charge ratio particle through the system. Credit: (Micek, 2008) (4).

To make neon a more viable option, I hope to modify the quadrupole mass spectrometer so that it can complete this process continuously underwater. Measuring neon at its source will allow for meltwater concentration to be calculated seamlessly at precise locations and times. However, subjecting a vacuum sealed device to harsh elements along with size and power restrictions greatly reduces the machine’s ability to detect neon alone. To help ensure that only neon is detected, a “getter” will be installed. A getter is a deposit of highly reactive metal, that when heated, combines with unwanted gases such as oxygen, nitrogen, and carbon dioxide. Eliminating common gases leaves the mass analyzer with a better chance to detect neon alone.

Developing and applying this new method of spectrometry will allow us to answer more accurately “Where?” and “How fast?” grounded Antarctic glaciers are melting.

Tourists walk on duckboards as seawater floods St. Mark’s Square in Venice. As rising ocean levels threaten our daily lives, how will we choose to respond? Credit: International business Times (5).

With this knowledge comes more stable predictions of global sea level rise. Although this research cannot slow glaciers that are already in a runaway state of melt directly, it can give us vital information on how our actions have drastically impacted the world. It might sound grim, but sometimes it takes a looming deadline to spur meaningful collaboration and implementation.


  • Walker, P. (2017, March 6). Venice will vanish underwater within a century if global warming is not stalled, climate change study warns.
  • Rasmussen, C. (2018, May 2). GRACE-FO: Cracking a Cold Case.
  • Nicewonder, M. (2015, September 5). Adventures on Ice. Retrieved from https://mindynicewonger.weebly.com/
  • Micek, C. (2008, December 8). Huygens Probe Gas Chromatography Mass Spectrometer. Retrieved from https://attic.gsfc.nasa.gov/huygensgcms/Mass_Spec_Intro.htm
  • Sim, D. (2015, December 30). Venice Carnival 2015: Revelers try to keep their costumes dry on flooded St Mark’s Square. Retrieved from https://www.ibtimes.co.uk/venice-carnival-2015-revellers-try-keep-their-costumes-dry-flooded-st-marks-square-1486241

Who’s at Fault for these California Earthquakes?

Whitney Marshall, Pennsylvania State University

SURFO Advisor: Dr. Matt Wei

The liquid mantle beneath earth’s crust causes the plates that make up earth’s surface to move in relation to one another. This motion causes the ground to crack and shift right under our feet. Some collide and form mountain ranges, others separate forming mid-ocean ridges, and some slide past one another causing faults. Faults occur all over the earth’s surface since earth’s crust is constantly moving.

Image 1: The movement of earth’s crust caused the ground to shift an change. The crust can be moving past one another (top image), apart from each other (middle image) or colliding with one another (bottom image) (D. 2016).

Earthquakes can occur at each of these points of contact between Earth’s crust. Earthquakes that occur along faults are often shallow rather than being deep within the crust; these shallow quakes result in noticeable ground changes along Earth’s surface. The earthquake can push Earth’s surface in any direction. There are multiple ways to study these earthquakes to understand their origin. However, my work revolves around a novel method to better understand faults, using satellite images that allows us to study the fault beneath an earthquake.

Image 2: There are many types of fault motion that can occur on land which can be caused by both convergent and transform plate boundaries. These changes in ground height can be either moving up, down or to the right or left (D. 2014).

In my project, we take satellite images from before an earthquake and after, and then overlay them to see how earth’s surface has changed. We then use these changes of arth’s surface to modelhe fault that lies beneath it. While other scientists have used satellite images in this way to look at faults, my project is unique because it applies the local geology to the fault model which hasn’t been done before. Earth’s crust is made up of many different layers, some rough and hard, others soft and moldable. Applying this information to the fault model improves the accuracy since it adds a wider range of realistic conditions to the model.

When we model out fault we get a plot that shows the direction and magnitude of motion along the fault plane. The disruption originates from a single location within the fault and send energy towards the surface, which we refer to as an earthquake. We can view the depth and direction where this disruption originated and better understand how the fault relates to the earthquake at hand..

In one area of focus for this project we will study a low magnitude earthquake in California that was caused by a slowly moving fault. This fault is moving horizontally with the right side sliding past the left.

Image 3: This fault, located near San Diego, CA and shows the ground motion by the amount of ground slip along the fault in color. The largest amount of ground slip is seen in red. The arrows show the direction that the ground is slipping within the fault.

Applying a layered geology improves the fault model. This can help researchers in the future to improve the accuracy of their respective fault models; this is important because continually improving fault models can tell us more accurately where the fault is located. We can say how long the fault is, how deep it is, the direction the fault is angled underneath Earth’s surface, and most importantly the type of motion within the fault that results in earthquakes. Knowing the fault behavior and location can help society to know where they shouldn’t reside to avoid the risks associated with fault areas.

Image 4: The plot is the same fault, after applying a layered geologic structure. As seen through the white circled areas, there is more data centered around the surface with more slip; more data means a more accurate representation of the fault. The model shows more detail which aligns with the slow creeping behavior of the fault and indicates the model is more accurate.

For example, California doesn’t allow houses to be built within a certain distance of a fault line. This research gives greater accuracy to the location of certain faults which can help local governments to decide where construction may occur, keeping more people out of possible harm’s way.


D. (2014, March 31). Fault geology stock vector. Illustration of ocean, geological – 39324668.

Retrieved from https://www.dreamstime.com/royalty-free-stock-photos-fault-geology-


D. (2016, August 10). Tectonic Plates. Plate Movement Stock Vector – Illustration of eruption,

deep: 75589302. Retrieved from https://www.dreamstime.com/stock-illustration-tectonic-



Battening down the hatches on our coastlines

Robert Lewis, University of Puerto Rico Mayaguez

SURFO Advisor: Dr. Amanda Babson

Close your eyes for a second and imagine the beach. The murmuring of the grass being jostled by a light sea breeze. The taste of salt deposited upon your tongue, and the sand in between your toes. The emerald water glides beneath bursts of golden light dancing in a reflected halo over the cresting waves. What else do you see?, perhaps a saltmarsh where grasses thrive on the confluence of fresh and saltwater. Do you hear that?, a piper plover scurries across the beach triumphantly with a fiddler crab in beak.

Do you feel the tide ebb back into the immenseness of the ocean?

With all these dazzling images, you may begin to imagine how this place we call the beach is actually an elaborate and dynamic ecosystem; home to many species of flora and fauna. In reality, these beautiful habitats are constantly changing from storms, seasons, and human interactions.

Inlet formed by Hurricane Sandy in Fire Island National Seashore.

While this ecosystem is dynamic by nature, climate change poses severe changes that threaten the coastal flora and fauna as well as our coveted coastal developments. Most importantly, our world must look to changing national policy with the hopes of reducing our contribution to climate change. However, significant damage has already been done and thus we must look into how we can anticipate and best prepare for future repercussions to our carbon usage.

When we think of climate change preparedness, we often first think of coastal hubs such as Miami or New York; how much flooding will occur, how high should first floor flood elevations be for future buildings, or what is the extent of damage that more intense hurricanes may incur. Yet, some of our greatest coastal treasure are not our cities but rather our coastal parks.

The existence of those beautiful habitats is threatened. Marsh grass is forced to retreat inland, barrier islands are breached by increased storm surge, and coastal monuments like Ellis Island need to be protected as well. The great news is that there has been research done for these coastal national parks to help them prepare for storm storm and sea level rise! Two studies in particular, one for all coastal parks led by University of Colorado at Boulder and the other led by the University of Rhode Island (URI) for three parks impacted by Hurricane Sandy, have sought to map out what storm surge in our coastal parks will be in the future. With higher sea level rise comes higher storm surge, coastal flooding caused by hurricanes. Thus these projections of future storm surge will help the National Park Service best protect these coastal lands.

The three coastal national parks that we focused on in this research.

Our research is a comparison of the similarities and differences in the methods and projections between these two studies. Both studies calculated what future storm surge would be with sea level rise at the year 2050. The program SLOSH (Sea, Lake, and Overland surges from Hurricanes) was used by both studies to make these storm surge projections. Some of the major differences that must be taken in consideration when comparing these two studies are listed below;

NOAA based program SLOSH for the New York basin. Fire Island National Seashore and Gateway National Recreation Area included.

The most significant difference exist in how each study performed their storm surge calculations. The Service Wide study used a simplified method of adding current storm surge to projected sea level rise whereas the Sandy Study combined projected sea level heights with calculated future storm surge in their projections.

Another difference between the two studies is the scope of how many parks were included in each one. The study produced by the NPS, the Service Wide study, was performed for all coastal national parks whereas the study produced by URI specifically focused on the three coastal parks most affected by the Superstorm Sandy. Those three parks, Gateway National Recreation Area, Fire Island and Assateague National Seashores, were covered by both studies. Lastly, the sea level rise projections used by each study differed slightly by several centimeters.

By comparing and contrasting these two studies,we can see the more computationally intensive method of combining storm surge with sea level rise done by the Sandy Study is more accurate than the simplified method used by the Service WideStudy.

In order to measure these differences, in our research we are making several different comparisons using the program arcgis. Arcgis, geographical information system, represents topographical features and phenomenon. Since both studies represented their projections through this program, arcgis map proved to be the best program to make the following comparisons;

The first comparison looks at the amount of area both studies project will be inundated in each park. We have found that both studies agree with each other about lands inundated at 93 percentile. Another comparison looks at the projections of inundation depth in each park. To best measure these differences of inundation depth, we divided each park into different regions; oceanside, bayside, and inland areas. With this done we then measured amount of difference greater than 1 foot in between both studies. Two findings that stood out from this comparison were that all three different parks had distinct values and that more dynamic values such as a oceanside area showed higher differences than less dynamic areas such as areas on the bayside of these parks.

Areas of inundation agreement in Fire Island National Seashore. Pink shading denotes all areas where both studies projected inundation.

The last comparision to be made, is looking at the inundation depths around coastal protection structures. These structures can range from a seawall, a sand fence, bulkhead, or a revetment. The purpose of comparing the inundation depths around these structures is to determine if the structures wills serve their original purpose or will be overtopped by storm surge.

Inundation depth differences in Fire Island National Seashore. Blue denotes areas where the Sandy Study projected deeper inundation depth differences. Areas shaded in red denote areas where the Servicewide Study projected deeper inundation depths.

We hope to generalize some of these findings to enable parks not included in both studies to be able to decide whether or not performing the combined storm surge and sea level rise modeling as done by the Sandy Study is necessary for the specific features of their park. Ideally stopping climate change is the aspiration we all have, however we must also work to prepare our coastal communities and lands for these changes to ensure their longevity.





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