Same Data, Different Visual Forms: Data Visualization for Scientific Discovery – January 25th, 2018

Zan Armstrong, Freelance Data Visualization Engineer
Moss Landing Marine Labs Seminar Series - January 25th, 2018

Hosted by the Phycology Lab

MLML Seminar Room, 4pm

Open to the public

Zan Armstrong is a data visualization engineer and designer. Her work includes creating custom visualizations, both static and interactive, for analysts and scientists to enable them to make new discoveries in their data. She is most interested by identifying what characteristics of the data might be most analytically/scientifically important, and finding ways to reveal those characteristics visually. Zan also enjoys finding other ways to see familiar data that reveals a different perspective or illustrating situations in which the "obvious" understanding of the data is misleading or masks some deeper truth.

 

 

 

 

Same Data, Different Visual Forms: Data Visualization for Scientific Discovery

Picking the visual form for a data visualization is a decision about what part of our data we care most about. Should we highlight outliers? Focus on the densest parts of the data? Ignore numbers under a certain threshold? Look at values or differences? The right form depends on what we believe is most important to see. Zan Armstrong will describe the thought process behind data-driven design decisions from her work and share her 5 top recommendations for making more effective visualizations for scientific discovery (including code snippets in R and/or Python).

Watch Dr. Armstrong’s MLML seminar presentation below:

Bombs and blue marlin (Makaira nigricans) — confirmation of rapid growth and longevity – February 1st, 2018

Allen Andrews, NOAA's Pacific Islands Fisheries Science Center
Moss Landing Marine Labs Seminar Series - February 1st, 2018

Hosted by the Ichthyology Lab

MLML Seminar Room, 4pm

Open to the public

Allen Andrews joined the Life History Program of the Pacific Islands Fisheries Science Center in 2009.  He came to Hawaii from Moss Landing Marine Laboratories (MLML) in California where he operated the Age and Longevity Research Laboratory for 12 years.  He earned a M.S. degree in Marine Science from MLML in 1997 and in 2009 he finished a Ph.D. in Ichthyology and Fisheries Science at Rhodes University, South Africa.  His dissertation presented validated age and growth of the Patagonian toothfish (Chilean sea bass) and orange roughy. 

His area of expertise involves age estimation and validation of fishes and invertebrates using growth zone counting and radiochemical techniques (i.e. lead-radium dating) and bomb radiocarbon dating.  Recent works involved bomb radiocarbon dating of several shark species, the endangered white abalone, hawksbill sea turtle, and fishes of Indo-Pacific regions.  Allen's work with the Life History Program at NOAA Fisheries began with applying these techniques to dating opakapaka (Hawaiian pink snapper), and has continued with applications to other fishes of the Hawaiian Archipelago, as well as national and international collaborations on fishes and corals of the Gulf of Mexico, Great Barrier Reef, and Mediterranean. As an Affiliate Faculty member of the Oceanogrpahy Department and the Marine Biology Graduate Program at University of Hawaii, Manoa, Allen has fostered research with students involving deep-sea fishes and tropical snappers. Other interests are with photography, astronomy, and world travel. For more information please visit: “astrofish.me

 

Bombs and blue marlin (Makaira nigricans) — confirmation of rapid growth

Longevity of blue marlin (Makaira nigricans) remains unresolved. Use of fin spines and sagittal otoliths for age reading has led to unconfirmed longevity estimates of close to 20 years.  Age validation has been elusive because large individuals are rare and a technique that can be applied to the structures that provide estimates of age was absent. Use of otolith chemical signatures has been limited by sagittal otoliths that are very small—whole otolith mass of adult blue marlin can reach 10 mg for the largest fish. Recent advances in the detection limits of radiocarbon (14C) with accelerator mass spectrometry—coupled with recently acquired knowledge of marine bomb 14C signals spanning the tropical Pacific Ocean—have led to an opportunity to age blue marlin from small amounts of otolith material. In this study, otoliths from a recently collected 1245 lb. (565 kg) female blue marlin at 146 inches (3.71 m) lower jaw fork length were analyzed for 14C. Using a series of deductions in the bomb 14C dating method the age of this “grander” blue marlin was confirmed.

The economies of scale – effects of body size on cetacean foraging – February 8th, 2018

Danuta Wisniewska, Hopkins Marine Station
Moss Landing Marine Labs Seminar Series - February 8th, 2018

Hosted by the Vertebrate Ecology Lab

MLML Seminar Room, 4pm

Open to the public

Danuta Maria Wisniewska is a bioacoustician and foraging ecologist interested in how marine animals negotiate their surroundings and forage in their heterogeneous and rapidly changing habitats. Her research is centered on fine-scale empirical studies using multi-sensor biologging tags.  Danuta is an oceanographer turned biologist. After an undergrad in oceanography at University of Gdansk in Poland, she completed an Arctic Biology program at the University Centre in Svalbard, Norway. She then joined the Marine Bioacoustics Lab at Aarhus University, Denmark, where she worked on sensory ecology of echolocating toothed whales. After earning her PhD degree, she moved to the Section of Marine Mammal Research at Aarhus University, where she worked on the effects of anthropogenic noise on marine mammals. She is currently a postdoctoral fellow in Jeremy Goldbogen’s lab at Stanford University’s Hopkins Marine Station.

 

The economies of scale – effects of body size on cetacean foraging

Size dependence of metabolic rate, where smaller animals generally exhibit higher mass-specific  metabolism, is a major factor influencing how animals interact with their environment. Whilst large body size necessitates high absolute energy intake, it also grants low relative rates of energy use per unit body mass and, therefore, many physiological and ecological advantages. Such size-related functional constraints ultimately shape animal behavior, performance and life history. In this talk, I will discuss how these body size trade-offs affect foraging performance of cetaceans, from harbor porpoises to sperm whales and blue whales. I will focus on how biologging technology has enabled us to address this.

Watch Dr. Wisniewska’s MLML seminar presentation below:

How the Squid Lost Its Shell: An Adventure in Cephalopod Evolution and Science Communication – February 15th, 2018

Danna Staaf
Moss Landing Marine Labs Seminar Series - February 15th, 2018

Hosted by the Invertebrate Zoology and Molecular Ecology Lab

MLML Seminar Room, 4pm

Open to the public

Danna Staaf; Photo credit: R. Heywood

Danna Staaf fell in love with cephalopods at the age of ten. She began to keep them as pets in a home aquarium, learned to scuba dive in order to meet more of them in the wild, and eventually completed a Ph.D. on squid at Stanford University's Hopkins Marine Station. Her first book, Squid Empire: The Rise and Fall of the Cephalopods, was named one of the best science books of 2017 by NPR Science Friday. She lives in San Jose, California, and works as a freelance science writer and educator.

 

 

 

 

 

 

How the Squid Lost Its Shell: An Adventure in Cephalopod Evolution and Science Communication

Before there were mammals on land, there were dinosaurs. And before there were fish in the sea, there were cephalopods—the ancestors of modern squid and Earth’s first truly substantial animals. With dozens of tentacles and formidable shells, they presided over an ancient undersea empire. These mysterious, intelligent, and adaptable creatures are the heroes of an epic adventure spanning hundreds of millions of years, from the primordial ocean to the calamari on your dinner plate.

The story of squid evolution will be told interleaved with "the story behind the story": strategies, examples and practical tips for getting out the word about your favorite science, no matter how intricate or obscure.

Watch Dr. Staaf’s MLML seminar presentation below:

A single-cell view of microbial activity in the deep sea – February 22nd, 2018

Anne Dekas, Stanford University
Moss Landing Marine Labs Seminar Series - February 22nd, 2018

Hosted by the Biological Oceanography Lab

MLML Seminar Room, 4pm

Open to the public

Anne Dekas is an Assistant Professor at Stanford University in the Earth System Science Department studying the microbiology and biogeochemistry of the deep sea.  She is broadly interested in how microbial life affects the chemistry and climate of the planet, today and throughout time. Her research combines tools from molecular biology and isotope geochemistry to identify and quantify microbial metabolic capabilities, activity, and interactions, with a focus on understanding uncultured microorganisms in deep-sea water and sediment. Before joining the faculty at Stanford, she was a Lawrence Postdoctoral Fellow at Lawrence Livermore National Laboratory, where she investigated the carbon metabolic flexibility of pelagic marine archaea. She received a Ph.D. in Geobiology from the California Institute of Technology, where she studied nitrogen fixation, methane oxidation and sulfate reduction at deep-sea methane seeps. She received an A.B. in Earth and Planetary Sciences from Harvard University. Originally interested in space sciences, Dekas performed research at three NASA centers (Jet Propulsion Laboratory, Ames Research Center, and Goddard Space Flight Center ) before beginning her Ph.D., and she continues to be interested in the survival strategies of life in extreme environments.

 

A single-cell view of microbial activity in the deep sea

The deep sea is one of the largest habitats for microbial life on the planet: it covers nearly two thirds of our Earth’s surface and harbors approximately 70% of total marine microorganisms. The activity of microorganisms in the deep sea plays an essential role in biogeochemical cycling, including the production and consumption of greenhouse gases (e.g., CH4, CO2 and N2O), thereby affecting climate. Our knowledge of the diversity and activity of the microorganisms in the environment, including the deep sea, has expanded in recent years with the development of next generation sequencing (e.g., “-omics” methodologies). However, our understanding of trends in microbial activity as a function of phylotype and physicochemical parameters is still lacking, and particularly so in the deep ocean. Closing this gap in our knowledge will increase our understanding of greenhouse gas cycling in the marine environment, and will better equip us to predict the activity of microorganisms in a changing climate. To this end, my group is currently studying: (1) organic substrate utilization by pelagic marine Thaumarchaeota, (2) nitrogen fixation by anaerobic bacteria and archaea in marine sediments, and (3) methane oxidation by syntrophic archaea at methane seeps. In this presentation I will touch on each of these areas of exploration, as well as our recent methodological advances in the use of nanoscale secondary ion mass spectrometry (nanoSIMS) to quantify anabolic activity in uncultured microorganisms on the single-cell level.

Watch Dr. Dekas’ MLML seminar presentation below:

Public Engagement using the Marine Sciences – March 1st, 2018

Russell Arnott, University of Bath (UK)
Moss Landing Marine Labs Seminar Series - March 1st, 2018

Hosted by the Invertebrate Zoology and Molecular Ecology

MLML Seminar Room, 4pm

Open to the public

Having studied Oceanography at University of Southampton, Russell worked as a commercial oceanographer before becoming a high school Physics teacher. With a passion for public engagement, Russell left teaching to pursue science outreach as Education Consultant and Presenter for Incredible Oceans. Russell frequently performs at events across Europe including the Cheltenham Science Festival, Elderflower Fields Festival, Wilderness Festival, and Brighton Science Festival.

Russell joined the University of Bath in September 2016 to study phytoplankton morphology and its influence on turbulent interactions. As well as field data, the project involves empirical data gathering via mesocosm experiments leading to the production of 3D-printed scale models of phytoplankton cells.  You can follow him on twitter here.

 

Public Engagement using the Marine Sciences

As the role of the university within the local and global community evolves, being able to engage those in research outside of academia is becoming more important. Done correctly public engagement in the sciences can inspire and enthuse others in research areas / topics that they were previously unaware of while also providing the researcher with a plethora of benefits.

Watch Russell’s MLML seminar presentation below:

Observations of Intermittent Breaching at the Carmel River, CA – March 8th, 2018

Mara Orescanin, Naval Postgraduate School
Moss Landing Marine Labs Seminar Series - March 8th, 2018

Hosted by the Physical Oceanography Lab

MLML Seminar Room, 4pm

Open to the public

Dr. Mara M. Orescanin has been an Assistant Professor in the Department of Oceanography at the Naval Postgraduate School (NPS) since 2016.  Here, her research focuses on coastal physical oceanography relating to exchange between land and sea through rivers, inlets, marshes, and estuaries. She is currently supervising four Master’s students whose projects span ephemeral rivers using novel UAV imaging techniques, plume/wave hydrodynamics, as well as numerically modeling storm surge in small tidal inlet systems.  She believes in an hands-on approach to teaching and mentoring geared at stimulating active learning and has mentored students at all levels from middle school through graduate school.  Prof. Orescanin also teaches several classes to active duty naval METOC (meteorology and oceanography) officers at NPS including Nearshore Processes, Ocean Dynamics II: Waves and Instabilities, and Littoral Field Methods. 

Dr. Orescanin received her B.A. with distinction in physics from Carleton College, Northfield, MN, where she discovered her passion for teaching as well as engaging in research outdoors.  After her undergraduate degree, Dr. Orescanin received two M.Sc. degrees in 2009 from the University of Illinois, Urbana, IL, in geology and in theoretical and applied mechanics, where she studied both explosive multiphase flows from volcanoes and the flow of blood cells through small capillaries.  Here, she realized her passion for the beach, and completed her Ph. D. in 2015 through the Massachusetts Institute of Technology/Woods Hole Oceanographic Institution’s Joint Program in Oceanography, in the Department of Applied Ocean Sciences and Engineering.  She also has worked as a coastal engineer/consultant at the Woods Hole Group from 2014-2017 focusing on observations and numerical modeling of tidal marsh restoration projects.

Observations of Intermittent Breaching at the Carmel River, CA

Ephemeral rivers provide unpredictable transport from back lagoons to the coastal ocean critical to biological processes such as larval transport, and understanding the relative role of discharge, tides, and waves is critical to understanding the expected area of influence.  The Carmel River, in Carmel, CA, is well-known to seasonally breach, though the duration and timing of each breach is difficult to predict.  Observations of seven distinct breaches from December 2016 through January 2017 indicate that while river discharge is low, the combined effect of waves and tides is sufficient to reduce flow through the breach, allowing sediment to accumulate at the mouth and close off the river. 

Resolving the Food Paradox in the Sea – March 15th, 2018

Dr. Kelly Benoit-Bird, MBARI
Moss Landing Marine Labs Seminar Series - March 15th, 2018

Hosted by the Vertebrate Ecology Lab

MLML Seminar Room, 4pm

Open to the public

Dr. Kelly Benoit-Bird is a Senior Scientist at the Monterey Bay Aquarium Research Institute. She received a B.S. in Aquatic Ecology from Brown University in 1998 and a Ph.D. in Zoology from the University of Hawaii at Manoa 2003. She spent a year as Post-Doctoral Fellow at the Hawaii Institute of Marine Biology before joining the faculty of Oregon State University in 2004 where she served was a professor of Oceanography until 2016. Kelly is the recipient of a MacArthur Fellowship, a Fellow of the Acoustical Society of America, and an IEEE Oceanic Engineering Society Distinguished Lecturer. She recently served on the Scientific Steering Committee for the International Council for the Exploration of the Sea Symposium on Marine Ecosystem Acoustics, as an organizer for the National Academy of Sciences Kavli Frontiers of Science Symposium, and as Chief Scientist for an Office of Naval Research Basic Research Challenge. Her research explores the ecological role of spatial and temporal dynamics in pelagic marine ecosystems from the surface to the deep sea. Her collaborative, interdisciplinary approach to understanding ocean ecosystems combines acoustic technologies with other tools including optical sampling, animal tagging, and behavioral modeling. Her work is changing our understanding of how ocean animals including zooplankton, fish, squid, seabirds, and marine mammals make their living.

 

Resolving the Food Paradox in the Sea

The average concentrations of biota in the ocean are generally low, a critical problem for ocean consumers. When we examine the biology with new tools guided by the predators themselves, we find that instead of being relatively devoid of life, the ocean is peppered with narrow hot-spots of activity. From the surface ocean to the deep sea and animals ranging from plankton and fish to squid and whales, small patches of plenty have impacts on ecosystems disproportionate to their contribution to the total biomass. These small aggregations provide the key to solving experimentally demonstrated feeding paradoxes as well providing a mechanism for evolution in an apparently isotropic environment where there are no obvious barriers to gene flow, Hutchinson’s “Paradox of Plankton”.

Repelling sharks to save them…and us! – March 22nd, 2018

Ryan Kempster, University of Western Australia
Moss Landing Marine Labs Seminar Series - March 22nd, 2018

Hosted by the Environmental Biotechnology Lab

MLML Seminar Room, 4pm

Open to the public

Ryan is a researcher and co-founder of the shark conservation group Support Our Sharks. Ryan began his research career with a B.Sc. and M.Sc. in Marine Biology at Bangor University in the United Kingdom.  After completing his studies, Ryan travelled the world and was fortunate enough to gain experience working for a number of marine conservation organizations. He worked on a range of projects, including restoring mangrove forests in Thailand, surveying coral reefs in The Bahamas, monitoring fish populations in Fiji, and protecting sea turtle nests in Costa Rica. Despite having the opportunity to get up-close and personal with a diverse range of marine life, Ryan was always drawn to sharks.  In 2010, Ryan took his passion to the next level by completing a doctorate degree at the University of Western Australia, investigating the sensory biology of sharks.  His research in Australia focused on the sensory biology of sharks with the ultimate goal of refining and improving shark repellent devices to protect ocean users and reduce shark bycatch in commercial fisheries. 

Repelling sharks to save them...and us!

A detailed knowledge of the sensory biology of sharks is essential for understanding the way in which they interpret the world around them.  By understanding a shark’s senses, we may be able to develop non-lethal methods to manipulate their behavior and discourage negative interactions with humans.  Until recently, much of our understanding of the sensory biology of sharks was derived from early attempts by the US Navy to develop shark repellents to protect servicemen.  Although shark repellents have traditionally been used to reduce the risk of negative interactions with humans, they may also play an important role in reducing fisheries’ bycatch and, ultimately, in the protection of these ecologically and economically important species. Shark Biologist Dr. Ryan Kempster will reveal the history of shark repellent technologies and the latest insights from his own global research projects in the field. 

For more information, see: www.ryankempster.com; www.supportoursharks.com

The power of open data science: experience from the Ocean Health Index – April 5th, 2018

Dr. Julia Stewart Lowndes, UC Santa Barbara
Moss Landing Marine Labs Seminar Series - April 5th, 2018

Hosted by the Pacific Shark Research Center

MLML Seminar Room, 4pm

Open to the public

Dr. Julia Stewart Lowndes is a marine data scientist at the National Center for Ecological Analysis and Synthesis (NCEAS) at the University of California at Santa Barbara (UCSB). As Science Program Lead for the Ocean Health Index (OHI), she works to bridge marine science and resource management. Julia contributes to the science and open data science behind OHI assessments and also leads a training program internationally to enable independent groups to assess ocean health and inform policy in their own waters. Increasingly, she is teaching open data science trainings as an instructor with NCEAS, Software Carpentry (including at MBARI last December!), RLadies, and Mozilla Study Groups (eco-data-science).

Prior to joining the OHI team, Julia earned her Ph.D. at Stanford University’s Hopkins Marine Station in Pacific Grove, researching potential effects of the Humboldt squid in the California Current System on coastal fisheries in a changing climate. She collaborated closely with her PhD advisor Bill Gilly, as well as John Field, Steven Bograd, Elliott Hazen (NOAA), Bruce Robison and Steve Haddock (MBARI) and many others. She was also heavily involved in the Center for Ocean Solutions’ MARINE program.

You can follow her on twitter: @juliesquid

The power of open data science: experience from the Ocean Health Index

For the past four years, we have dramatically improved how we work with the Ocean Health Index by embracing open data science practices and tools. We now work in a way that is more reproducible, transparent, collaborative, and open, with more emphasis on communication. Because of this, more than 20 countries around the world are building off our science and our code for ocean management in their own jurisdictions.

We’re sharing our story in a recent publication in Nature Ecology & Evolution (Lowndes et al. 2017) because at the time we thought this transformation was intimidating, but we are living proof that it’s possible. By describing specific tools and how we incrementally began using them for the Ocean Health Index project, we hope to encourage others in the scientific community to do the same — so we can all produce better science in less time.