Our Supercharge Experience: The Logan Lab

By Arie Dash, CSUMB Logan Lab


The Logan Lab is the Marine Environmental Physiology Lab at California State University, Monterey Bay (CSUMB). We are a mix of graduate and undergraduate students under the guidance of Dr. Cheryl Logan, and we’re focused on evaluating the physiological responses of marine fish and invertebrates to the current and predicted effects of climate change. Many of our projects rely on analyzing large environmental, physiological, or genomic datasets but most of us do not have formal training in data science.

Over time, we’ve developed several shared workflows, but our code, documentation, and data management practices have not always been optimal. Luckily, this challenge is not unique to our lab and we decided to undertake Openscapes’ 10-week Supercharge plan during the 2020 Fall semester to learn more about current open science best practices. We dedicated a number of our regularly scheduled weekly lab meetings to the Openscapes modules with different combinations of students taking the lead each time.

While we didn’t fully finish the 10-week plan, we made good progress in several areas. At the individual level, most of us started using GitHub to work collaboratively (no more emailing code back and forth!) and started intentionally organizing our files so that others, including our future selves, can more easily use them. We also found that collectively learning about the techniques was helpful when approaching concepts we weren’t familiar with, and as a result, our coding ability has increased tremendously!

The Logan Lab at California State University Monterey Bay (CSUMB)

As a lab, we wrote a formal code of conduct and created a lab-wide Github page. Most of our sessions were heavily discussion based, which was very helpful for getting everyone up to the same speed and learning about the topics, but we lacked time to actually implement all that we learned. As a result, while many of us made individual progress, most of the lab-wide goals like a shared GitHub page and a formalized onboarding and offboarding process still have work to be done.

In the current 2-month Champions Program, we are excited to learn more advanced techniques for what we’ve already implemented, discuss data management approaches with different CSU labs, and collaboratively implement more open science best practices. This will be an ongoing process, but we hope that by the end of the workshop we will be able to work more efficiently and collaboratively, and that we can further our lab goal of fostering a supportive and inclusive community approach to open science.

Dissonance in science communication: Taking an evidence-based approach to discussing climate science

By Jason Gonsalves, MLML Physical Oceanography Lab


You don’t have to be actively involved in the larger national discussion to know that climate change is an increasingly sensitive topic, even in 2021. As unbelievable as it may sound, the chances of someone in your social circle not being under the impression that global warming is happening are shockingly high. In a 2020 survey, an estimated 72% of Americans think global warming is happening right now. When adjusting to a more specific question, that same survey showed that only 57% of Americans believe global warming is occurring as a result of human activities.

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Microplastics in Monterey Bay

By Bri Sotkovsky, MLML Geological Oceanography Lab


What are microplastics?

Hi there! My name is Bri and for my graduate thesis work at Moss Landing Marine Labs I plan to focus on microplastics in the beach habitat, and how it may be affecting the health of Monterey Bay’s ecosystem. This blog will walk you through an overview of microplastics and why this research is important. “One study estimated there are 15 to 51 trillion microplastics particles floating on the surface of the oceans. A trillion is one thousand billion. A trillion seconds is nearly 32,000 years” (National Geographic).

Microplastics pollute many aquatic ecosystems, but due to their small size, they often find themselves exempt from regulations that attempt to maintain the health of said aquatic ecosystems. Micro, coming from the Greek prefix meaning small (less than 5 mm to be precise) and plastics, also derived from the Greek word ''plastikos'' meaning fit for moulding, can come from a wide range of products with varying levels of semi- or fully synthetic polymers (materials constituted of long molecular chains (macromolecules) and organic connections obtained through processing of natural products or through synthesis of primary materials from oil, gas, or coal).

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What climate change means for water management in California and what you can do to help

By Allie Margulies, SFSU Estuary & Ocean Science Center

Looking back on the past few years, it feels as though Californians have faced a climate related crisis almost every year, whether it’s related to floods, fires, or drought. Within the past decade, many of us have become increasingly aware of our water usage after experiencing one of the most extreme multi-year droughts on record from 2012 to 2016. Then, in 2017 we experienced a record-breaking flood year. Now we are officially in another drought (Figure 1). Personally, I know I have made many permanent changes to my daily life in order to save water, such as making more informed food choices and taking shorter showers. Unfortunately, our problem is likely to get worse.

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Climate Change and the Legacy of Moss Landing

By Erick Partida, MLML Chemical Oceanography Lab


One of the many points of pride that Moss Landing Marine Laboratories holds up is the legacy of our former director Dr. John H. Martin, and his formulation of the Iron Hypothesis. This hypothesis, and the experiments conducted to prove the hypothesis transformed our understanding of oceanography as well as our understanding of climate change and earth’s history.


John Martin’s Iron Hypothesis

Throughout the ocean, the growth of microscopic plants, or micro-algae in a particular region is controlled primarily by the availability of nutrients (things like nitrate and phosphate that are like food to a plant) within that region. These micro-algae are extremely important, not only for oxygen production but for the uptake of the greenhouse gas, CO2 from our atmosphere, and their eventual transfer of that carbon to the deep ocean. This process of removing greenhouse gases from the atmosphere is a vital component controlling the earth’s climate, and its function relies almost entirely on the availability of nutrients.

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The other pandemic: linking COVID-19 and climate change

By Grace Teranishi, MLML Ichthyology Lab

Salinas, CA (Summer 2020)

By now we’ve grown somewhat accustomed to the haze and the smell of smoke, the ash that dusts our cars, our patios, our coats. It’s August, night. My friends have invited me over to drink beer and observe the glare of the River Fire ebb and flow over the hills across the highway. Within the week they’ll receive an evacuation order.

With both COVID-19 and environmental crises to convulse the world, this past year has witnessed its fair share of fires—literal and figurative—disrupting homes, livelihoods, social norms, and mental stabilities. Unsurprisingly, we find increasing evidence of how one pandemic (COVID) interacts with and bears resemblance to another, even deadlier one: climate change.

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Recognizing individuals through repeated field encounters

By Kameron Strickland, MLML Ichthyology Lab & CSUMB Image Analysis Lab

Our pursuit for statistical power involves repeated trials and non-trivial sample sizes.  After hundreds of fish dissections or thousands of water samples, big data can become a big chore.  Once exciting field observations are converted to numbers, I find myself occasionally forgetting the amazing individuals we are fortunate enough to study.

I’ve enjoyed photographing both fish and birds for a few years.  Through repeat encounters, I’ve come to recognize specific individuals both on land and on sea.  If you have had the same experience, you will understand the excitement in recognizing these individuals time and time again.  Sexual dimorphism, unique behaviors, and physical markings are all indicators that can be used for identifications.  Here, I provide small anecdotes about some of the individuals I’ve met through my photography.


Scarred Kelp rockfish

I just logged my 400th dive in my SCUBA career.  A majority were around the Monterey Peninsula, most being in the Carmel Bay.  While studying microhabitat associations of Kelp rockfish in Carmel, I recorded more than 1,000 observations of the species.  Kelp rockfish display a wide range of color morphs and patchiness patterns, from a ghostly white to earthy greens and browns.  I recognized this specific individual across a few dives due to the distinct white scar its left side.  After an hour of deep depths and freezing temperatures, it was exciting to find this fish hanging around the same patches of kelp.  I’m not sure if the feeling was mutual!


Two Vermilion rockfish in Carmel, CA

Just across the bay live two large Vermilion rockfish.  The smaller of the two is much more orange, while the larger one has more complicated silver patches on its body.  These large, vibrant rockfish stand out from the other species on the reef.  When I dove nearly every day during the summer of 2018, I would see these individuals in almost the exact same places.  Because of their large size, I believe these two individuals could have easily outcompeted other rockfish for the best crevices along the rocky reef.  Since 2018, this kelp forest has turned into an urchin barren with only a few opportunistic Macrocystis and Nereocystis fronds remaining.  Yet the Vermilions remain – I just saw one of them last week!  It still feels as if these two fish purposefully come out to greet me on dives.


White-tailed kite

During runs, I’ve passed this White-tailed numerous times while it was perched on the same tree.  I’ve made it a mission to return with camera gear and try to photograph it, but have only succeeded twice.  Their bright red eyes have always fascinated me.  If my presence doesn’t scare it off, turkey vultures and crows seem to always chase it away.


Anna’s hummingbird in Moss Landing

I discovered this Anna’s hummingbird at a location I frequent weekly for shorebirds.  This individual favors flying back and forth between three perches.  It was shy when I first discovered it, not letting me approach very closely.  I began using my camera’s electronic shutter to shoot silently and minimize disturbance on its natural behavior.  After many weeks of returning to this individual, it has become more comfortable with my camera gear.  It now lets me move closer and will even return to me after flying away.  Over a the past few months, this bird has become a part of my weekly photographic routine; I like to think that I am a part of its week as well!


Pair of Eurasian collared doves in Moss Landing

Not far from the hummingbird I visit, two Eurasian collared doves that have claimed a tree as their own.  These two are inseparable.  Although I am no dove expert, I suspect they may be a breeding pair.  Since their tree is near the busy Moss Landing harbor, they sometimes have to other flying fauna.  In my opinion, these goofy doves have one of the most hilarious calls.  Unfortunately they are hesitant to drop down at eye level, which makes it difficult to capture photos.


Photographing wildlife is an enjoyable break from the hard science I feel is prioritized during grad school.  These small encounters have highlighted some of the interesting routines and personality traits of my subjects.  I hope you are able to recognize individuals across your scientific endeavors.  Happy research!

Where have all the abalone gone? The impacts of ocean acidification on abalone populations

By Kayla Roy, MLML Ichthyology Lab


When you think of sea food what do you think of? Do you picture a fish fillet, lobster bisque, or maybe fish and chips? These are some of the common seafood dishes you can find on the menu at your favorite seafood stop, but have you ever seen abalone steak on the menu? It used to be a common staple eaten up and down the California coast. Now abalone are almost impossible to find not only on the menu, but in the ocean. So why have these animals begun to vanish from our diet and seas? This is due to the many changing oceanic conditions including ocean acidification.

Abalone have disappeared from our diet because the oceans have become too acidic, which has greatly reduced their population size. Climate change, driven by human emissions of carbon dioxide mainly from fossil fuels, is changing Earth’s climate and altering ocean chemistry. One of these changes is ocean acidification, which is a process that makes the ocean more acidic because of an increase in carbon dioxide. Change in acidity impacts marine life like abalone by reducing population sizes through developmental deformities, shell dissolution, lowered reproductive success, and reduced survival. So why do we care about the impact of ocean acidification on abalone and their continued existence in our ocean? Besides their previous inclusion in our diets, abalone contribute to the ocean and to people in many ways.

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Earth’s Climate History

By Noelle Lewis, MLML Geological Oceanography Lab


How and why we study temperature changes in the past 540 million years

You may have heard the phrase that looking to the past can help us understand the present and predict the future; but you probably didn’t think it would be necessary to go back in time over 500 million years. Global Average Temperatures are increasing rapidly due to human greenhouse gas emissions. To understand what a warmer future will be like, we can compare warming today to warming in the past.

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MLML alumna Erin Loury ’11 featured in Diversity in Action magazine

During her tenure at MLML, alumna Erin Loury ’11 researched the impacts of marine protected areas (MPAs) on the trophic ecology of gopher rockfish. In the decade since she graduated, Erin has conducted research on fisheries throughout the world and now works as the Communications Director & Fisheries Biologist at the environmental consulting company FISHBIO.

Erin’s marine science career path is one of several highlighted in the latest issue of Diversity in Action magazine. Read the article here.