New job! Where I’m going and how I got here

Richmond, California’s Finances Remain Shaky
Richmond, CA from the air, showing the turbid waters of the SF Bay

Well folks, it finally happened. I found a permanent scientific job. On January 31st, I’ll be starting as an Environmental Scientist at the San Francisco Estuary Institute (SFEI), working on the Nutrient Management Strategy (NMS) program. NMS is a group trying to understand how nutrient supply in the San Francisco Bay works.

The SF Bay is an extremely nutrient-enriched environment (eutrophic) due to human pollution and natural factors, to the extent that if all other factors were equal, scientists would expect it to be a nasty green sludgy mess. Yet up to today, due to factors that are still debated, the SF Bay is in much better shape than it should be. It is not a dead zone, choked off by algal blooms and oxygen-starved in the way that other high-productivity regions such as parts of the Gulf of Mexico have become. Those factors may include the cloudiness (turbidity) of the Bay’s water limiting algae growth, naturally rapid tidal mixing with ocean water, and the influence of clams and other grazing animals keeping the populations of potentially harmful plankton suppressed.

However, there is also evidence that this resilience may be fading as water temperatures in the Bay increase and the ecology of the system changes with climate change. Oxygen levels are dropping and levels of harmful algae are rising, which endangers the health and livelihoods of millions of people in the SF Bay area who depend on a clean, ecologically functioning SF Bay. In my role at NMS, I will be assisting in processing and interpreting huge quantities of environmental data on temperature, dissolved oxygen, water flow, light levels, algae concentrations, and harmful algae toxins, to help figure out how the SF Bay works and how we can protect it. I will be assisting another scientist joining the team in deploying more sensors to monitor the Bay on a minute by minute basis, and also packaging the data to help create models which allow us to figure out the various moving parts that make it work.

In a way, this is oddly similar to the work I’ve done during my postdoc at Biosphere 2, where I’ve been growing giant clams in their 700,000 gallon ocean tank since May 2020. The clams are biological sensors have been recording the environment of the Biosphere 2 ocean through their shells and valve opening/closing activity, and I have had to decode their diaries through comparison with the environmental data we collect on light, pH, dissolved oxygen, chlorophyll and other measurements. The SF Bay is a site of enormously influential research which has been important to understand estuaries around the world, but it is still a mysterious body of water in many ways. NMS is trying to understand how all its complex pieces fit together, much like I’ve been doing at Biosphere 2, which is why I jumped at the opportunity to apply for the job.

I also am excited to get involved in this work because it’s immensely important for everyday people’s lives. The SF Bay provides millions of people with food, employment, recreation and overall well-being, and the science that NMS produces has real-world value for making policy and a concrete plan to keep the Bay healthy. It represents exactly the kind of science that I wanted to do since I first jumped into environmental biology as a 19-year-old at USC. At that time, I was interning at JPL studying historical trends in California rainfall data, so this new job represents a homecoming of sorts to California water science!

This job will be a bit of a change of pace from my present work as at first, because I’ll be part of a scientific team with a shared mission, unlike most of my prior research, where I came up with ideas, pitched them to my advisors and funders and then coordinated the projects to collect and analyze data. There will be more teamwork, and while academic publications will still be one of our products, we also will be writing reports for policymakers and stakeholders who are deciding on how to regulate nutrient levels in the Bay.

I also won’t be working with clams on an everyday basis! But as I mentioned before, clams do play a major role in the Bay in terms of filtering the water, and so it is likely we will need to understand the activities of the clams and other grazers to explain the trends in nutrients that we see. I didn’t start as a Clam Man, but my curiosity about clams meant that my attention kept being drawn to these enigmatic but influential creatures, and I expect that dynamic will continue. I am, and always will be, Dan the Clam Man.

I will continue to get my present clam projects out the door as publications, so there will be lots of clamsplaining in the future months as those get out the door. Regarding the Biosphere 2 clams, we still have four individuals of Tridacna derasa (the smooth giant clam) growing in the 700,000 gallon ocean tank, and intend to leave them as long-term research subjects and an exhibit for visitors to enjoy and learn about. We also have proposals in the work for new projects to expand on this work. I hope I can continue to visit in the coming decades and see our clams grow to be true giants, two feet in length! I also hope to acquire pet giant clams of my own, with names rather than specimen numbers, to be my friends rather than my research subjects.

I’ll be starting the new job remotely at the end of this month, to give myself time to tie off loose ends in Tucson, intending to move to the Bay Area by March. I will really miss Biosphere 2 and Tucson, but this isn’t the last they’ll see of me, because my collaborations with people here will continue into the future. I knew from the start as a postdoctoral researcher that my position would not be permanent, but it is still bittersweet to leave. I will miss hiking in the Sonoran desert, swimming in the Biosphere 2 ocean tank and also my advisor Diane Thompson and her lab here, full of people who have been a joy to work with.

But I am excited for this new chapter, because the postdoc life has been lately losing its luster for me. I’ve enjoyed being a postdoc for the freedom it entails, both in my research topics and the way I structure that work. But postdoc work is emotionally exhausting, as I have been a journeying academic contractor on “soft money”. My employment for the following year has always been contingent on the next grant coming through. Moving between different institutions on different continents has been a big weight on my family and my partner, who I miss greatly.

As a postdoc, while I’ve had fun and wouldn’t change anything about it, I have felt like a plane trying to take off in unfavorable weather. I could see the end of the runway approaching as my current funding ends in May, which was a scary feeling. I’m willing to hustle and fight for research funding, but not my basic income. Looking back, I have applied to around 45-50 academic positions (including postdocs) since finishing my PhD and got interviewed for less than ten percent of those, and received offers for two postdocs. When I got the offer from SFEI, which was itself a rigorous, multi-stage process over months, I cannot describe what a relief it was to clear out my “job applications” folder in my to-do list. This SFEI job will allow me to pursue marine science that helps the environment and people, in a more emotionally sustainable way.

I’m excited to start my next chapter and share with you all the discoveries our team makes about the SF Bay, while also continuing to clamsplain here on my own time. Keep an eye out for my Biosphere 2 studies, which will be rolling out over the next months as the data arrives!

Recent Science Communication!

At Biosphere 2, our science is essentially done in public. Every time I’m in the water checking on our clams and the sensors around them, I’m in view of the public and essentially an attraction for the public to watch. This is a really unique way to do science unlike any of my past experience, when I’ve been out in the field with a collaborator, or in the lab with a laboratory technician. I was initially intimidated by the idea of doing my science with an audience, but I’ve decided to lean into it as a huge opportunity. It is rare that the public gets to see all the steps going into our science; they usually only see the end of the story and not the whole journey leading up to that point. So recently I participated in two new ways of sharing my work while it’s in progress with the public.

The first was a collaboration with Mari Clevin, a videographer with the University of Arizona who made a really nice profile of my crazy clam journey. It was a lot of fun showing her around B2, trying to capture what it’s like to work here. It was fascinating seeing how all her footage and interviews came together into a video, and how she captured the key points of our conversation into a narrative!

The other scicomm event I participated in was a “Research Show and Tell” event run by the PAGES Early Career Network. Early Career Researchers include PhD students, postdoctoral researchers like me, and early career faculty. The ECN is intended to help us band together to share opportunities and plan events relevant to our interests. Among the North American regional representatives for the ECN, we saw a real need for more informal ways to share our research to an advanced audience of our peers. We’re all burned out from Zoom webinars, and on the other side Zoom coffee hours don’t typically provide much opportunity to share scientific content, so there’s a real need for events in the middle. So I was excited to share my research with a group of my peers, touring them around the Biosphere, showing them my clams via pre-recorded video and then having a Q and A to describe the work. It was a lot of fun and you can watch the whole hour-long event below!

Biosphere 2 Update!

A view from my parking spot at work

I am now several months into my postdoctoral fellowship at Biosphere 2 in Oracle, Arizona! I am working with Professor Diane Thompson on a project measuring the shell and body chemistry of giant clams in Biosphere 2’s huge reef tank. Our goal is to find better proxies (indirect ways of measuring) the symbiosis of these clams with the algae they farm within their bodies. The controlled, closely monitored conditions of the Biosphere 2 ocean tank represent the perfect balance between the real ocean and the more controlled environment of a lab. Using trace metals and isotopes in their shells and tissue, we can trace back the ways that clams record their own internal biology. Wild giant clams make chemical records via the growth lines in their shells, similar to tree rings. These have been the subject of many cool past studies, but there are aspects of the “language” they use to write their shell “diaries” that are poorly understood. Much like researchers used the Rosetta Stone to decode heiroglyphics, we are observing clams as they grow in order to better translate the shell diaries of their prehistoric ancestors. Doing so, we can better understand how their ancestors reacted during past periods of climate change, and identify similar bivalves in the fossil record which may have harbored symbionts.

A view of the ocean tank at Biosphere 2

I started my postdoc remotely in May. The following months were spent sheltering at home in Southern California with my mom, supervising the installation of a cohort of giant clams into the 700,000 gallon ocean tank over Zoom. It felt like a science fiction movie, watching technicians Katie Morgan and Franklin Lane from hundreds of miles away on my computer screen as they nurtured and installed the little clams in their new home. I felt like Mission Control back on earth, watching a group of space colonists work with strange alien creatures.

Some of the T. derasas in the Biosphere tank

But in August I was able to finally move to Tucson to meet these clams in person! We had three species in the first batch: Tridacna derasa, T. squamosa and T. maxima. Of the three, T. derasa (the smooth giant clam) has proven to be the most successful in the Biosphere 2 ocean tank. All of the derasa clams from May have survived and thrived, attaching themselves to the bottom with byssal threads and growing their shells, both very positive signs of clam health!

Some of our newer batch of T. derasa in the quarantine tank

So we have doubled down on T. derasa and installed 11 more individuals last week, sourced from Palauan clam farms via a reef supply company in Florida called ORA. They are currently in a shallow quarantine tank where we will monitor them for disease and unwanted hitchhikers before introducing them to the broader Biosphere tank.

The workers at Biosphere 2 are very creative problem solvers. Giant clams need intense amounts of light to sustain their symbiotic algae and create food for themselves, a quantity of light higher than is available in the current Biosphere tank. To provide a light supplement, the engineering team at Biosphere 2 constructed a floating lighting rig with hanging LED lighting, right over the lagoon where we have the clams!

The lighting rig glows with a blue light as the sun goes down outside the Biosphere

To make sure the clams have enough light, we installed a Li-Cor light sensor to measure the exact amount of photons (light particles) hitting the clams over the course of a day. The light is measured in units of micromoles of photons per meters squared per second. A mole is 6.02 * 1023 particles, and other clam experts like James Fatheree have suggested that the clams need light levels of at least 200 micromoles/m2s to make enough food for themselves. That’s 120,400,000,000,000,000,000,000 light particles we need to hit every square meter of their habitat every second. The clam channels as many of those photons as it can to its algae residing within tubes in its tissue. The symbionts use it in photosynthesis to make sugars, which they share with their host. A well lit giant clam is a happy, well-fed giant clam! But because the glass dome of Biosphere eats up some of the light, and plankton and floating particles in the seawater eat up another portion, we use the lights to make sure the clams have the boost they need to maintain their symbiosis like they would in the clear, shallow waters of a tropical coral reef.

The Li-Cor sensor floats above the clams, telling us how much light they’re getting

Much like a new dad might read parenting books to get ideas for baby care, I am always poring through the literature trying to figure out how to maximize the growth of these clams. Dr. Fatheree is kind of like Dr. Lipschitz from Rugrats, except unlike the suspect childcare advice in the show, this real-life giant clam advice is very valuable. Like human babies, these clams can be a challenge! The clams sometimes decide to move around and get themselves into trouble, requiring us to rescue them if they get trapped behind a rock or under a pile of sand. So I have had to do a fair amount of clam-herding during my time here.

We are growing the clams for science, and there will be data to collect. We will be monitoring data like the trace metal chemistry of the clams’ tissue and shells, the color of their mantles, and the pH, temperature and oxygen levels of their environment, all to relate together to make the best clam record of their environment possible. So far, I have been snorkeling in the tank every couple days maintaining their setup. Next week, I will dive in the Biosphere tank for the first time to collect data on their shell chemistry! I have other projects in the works to measure their valves opening and closing using magnetic sensors, and to measure their color changes through time through computational photography.

That brings me to what I’ve found to be the coolest part about Biosphere 2: the people. Something about this place attracts creative, brilliant, can-do people who solve problems on the fly and are always jumping into the next project. It has been a privilege to learn and pick up technical skills from them in the brief time I’ve been here. This place is really like a space colony out of The Expanse or Silent Running. There are endless valves, pipes, tanks, exchangers and other hardware needed to keep Biosphere 2 running. Getting to witness the technical competence behind the whimsical solutions the staff comes up with, like the floating light rig, has been the most exciting part of this job for me. Everyone has a deeply ingrained curiosity and passion for science that is inspiring to see; they are as interested in my clams as I am in their corals, tropical plants, and geochemical experiments. I would argue that the human team behind Biosphere 2 is a bigger treasure than the unique metal-and-glass structure they work under, and I look forward to seeing the results all of the collaborations we have in the works!