Biology Graduate Gazette December 2020

Letter from the Editor

Congratulations! We almost made it through 2020. It was a hectic semester with online classes, constant emails about COVID cases, and uncertainty about the future. I'm looking forward to seeing you all outside of the little Zoom box on my computer. But until then, hopefully this is a place where we can celebrate each others accomplishments and strengthen out community in these apocalyptic times. Good luck with the rest of the semester and I will "see" you in 2021!

~ Brianne Palmer, Ecology PhD student

How are you feeling?

We asked, and you answered.

BGSA sent out a survey to determine the graduate student climate and the results are in! We have shared these results with key faculty members and are working with them to improve student well-being. If you are a Masters student, please fill out this survey to help us understand the tradeoffs between health care and salary.

In general, you all are fairly happy, concerned about how COVID will impact your research and a timely graduation, and have many financial concerns. Now that we have this data, BGSA is leveraging it to force change at the department, college, and potentially university level.

We are also working on compiling resources to help students with the financial burdens and stress.

These data will also be shared with faculty to help improve the classes and prepare students for their research and future careers.

Thanks to Dillon Jones for putting these graphs together.


Master's Thesis Defenses

Joshua Miu, Alex Escobar, Allen Zheng, Kyle Gunther

Master's Proposals

Brandon Molina, Jaqueline Lara, Jasmine Chavez, Dillon Jones, Xavier Deogaygay, Amber Morey. Ashley Schumann, Gabriella Kalbach, Karl Koehler, Vanessa Van Duesen, Meena Murali

Other Accomplishments

Jessica Griffin passed her qualifying exam!

Brianne Palmer published her first dissertation chapter in Global Ecology and Conservation. She presented this work at ESA.

Amanda Alker and Theresa Burnham received the ARCS scholarship

Amanda Alker published her first first-author paper in Environmental Microbiology

Emma Tomaszewski had her article Landscape seroprevalence of three hemorrhagic disease-causing viruses in a wild cervid accepted in EcoHeatlth.

Ryan Hesse received honorable mention for best talk in Applied Ecology at the Western Society of Naturalists conference.

Did you or someone in your lab or cohort do something super cool that should be acknowledged? Email me! Let's celebrate all our accomplishments!

BGSA Quarterly Recap

This semester BGSA has been running virtually. Now that we are a recognized student association we are forging ahead on a variety of initiatives including: BGSA merch, a three-minute thesis event, virtual social events (possibly with food), undergraduate outreach, and developing resources on the website.

Ben Scott has been running a monthly seminar for undergraduates about getting into grad school and we have been working on developing a program to easily connected undergraduates with research labs.

We have representatives attending the department and college Diversity and Inclusion Committee meetings to improve the campus response to DEI issues. Resources about this are slowly being added to the website.

Amanda Alker has been attending weekly meetings with all the College of Science student groups and has been learning about all the resources available to BGSA. She is now the chair of COS research.

Brianne Palmer has been attending the Ecology faculty meetings and is working with the faculty on a plan to improve the salary of biology Masters students (fingers crossed).

If you have any ideas about what BGSA can do to improve the biology grad student environment better or if you are interested in helping out with any of our ongoing initiatives, please email sdsu.bgsa@gmail.com with “Subscribe” in the subject line to get on the email list and join the BGSA Discord.

BGSA Leadership

  • President: Amanda Alker
  • Treasurer: Greta Schmidt
  • Secretary: Leslie Johnson
  • Social Committee Chair: Dillon Jones
  • Ecology and DEI Chair: Brianne Palmer
  • Evolution and UG Outreach Chair: Ben Scott
  • CMB Chair: Jared Camillo

Pets are the Companions We All Deserve

During COVID quarantine, Niveditha Ramadoss starting aqua scaping and fish keeping. After several hours of binge watching aqua scaping tutorials on You Tube, she set up her first jungle themed five-gallon, self-sustainable, bio-orb which now houses a betta fish. The fish is named Beats and he is the first pet she has ever owned. Beats loves posing for photos and watching colorful cartoons on TV.


This semester MEBSA has hosted trivia, Loteria, and an ugly sweater party!

Currently, they are working on ways to engage with the greater community through virtual field trips. If you are interested in this type of science please email mebsa.cmil@gmail.com.

Jessica Griffin is developing a project to increase participation of community college students in the science. The program is in its early stages but the vision is to provide a paid position for a few summer interns to participate in a science project over the summer.

Cooking Delights

Sugar skull hand soap for Día de Los Muertos, chocolate Oreo brains, and pretzel zombie fingers by Jasmine Chavez. 

Sourdough Focaccia

This is the simple sourdough recipe I use when my starter is ripe but I don't want to go through the hassle of making a loaf of bread. Just make sure you have a happy starter and a little patience. ~ Brianne


50 - 100 g active starter

10g salt

430 g water

500 g flour (I used whole wheat)

3 tbsp. olive oil (divided) with extra for the drizzle

Cherry tomatoes and sesame seeds (optional)


  1. Mix the starter, salt, and water in a large bowl and stir to combine. Add the flour slowly and mix until incorporated
  2. Rest for 30 minutes then perform a "fold." Reach into the bowl and pull the bottom of the dough into the center. Turn the bowl in quarter turns and continue pulling 8-10 times.
  3. Drizzle with a little oil and rub to coat. Cover the bowl with a towel and leave to rise for 4-18 hours (I usually let it rise overnight on the counter)
  4. When dough has doubled in size, place 2 tbsp. of olive oil into a 9x13 inch pan
  5. Gently deflate the dough and scoop it into the pool of oil in the pan. Fold the dough like an envelope from top to bottom and side to side to make a rectangle. Flip the dough over so the seam is down.
  6. Rub the top of the dough with more oil and leave alone, uncovered for 4-6 hours (until puffy and nearly doubled)
  7. Heat oven to 425F. Rub hands with oil and then using your fingers, create dimples in the dough, slowly stretching the dough to fill the pan. Sprinkle with salt. Add tomatoes and sesame seeds (optional).
  8. Bake for 25 minutes. Let cool for 20 minutes before slicing.

Research SpotlighT

Jason Baer ~ CMB

The Rohwer lab recently deployed a Coral Ark offshore of San Diego for testing. The goal is to create a fully functioning "piece" of a coral reef ecosystem and move it up into the water column, where conditions are better for coral growth than on the degraded seafloor. Then, we can use it to reseed degraded reefs with coral and invertebrate larvae, attract fish, conserve biodiversity and test new conservation/restoration strategies. Travel restrictions right now have us confined to local testing, so for now we are using kelp and urchins as a proxy for the community dynamics we might see in the Caribbean. Once we're allowed to travel again, we will be heading to Puerto Rico and Curacao to get them into the water.

Ecological Finds

Nathan Smith ("Nature Nate") was exploring the Pahrump area of Nevada and was black-lighting for scorpions and found this specimen. After conferring with some specialists at the California Academy of Sciences, he decided to target a specific arroyo in an un-sampled valley next to Pahrump. There he found a specimen of the genus Paruroctonus which had never been found in that area and looks different from all the other species! He sent the specimen to the Academy and they confirmed that is it likely undescribed! Contact Nate if you have any ideas on what to name this potentially new species.
Marine ecologist, Erica Pollard, ventured onto land and started a garden and found amazing creatures. Her parsley became home to caterpillars named Big Onion and Benjamin. Benjamin is now a beautiful swallowtail butterfly. Much life cycle. Such science. WOW.

Creative Writing

The Man & the Moose

The story of a disabled moose and one very dumb human

by Ben Scott

I only spotted him because of the few cars that pulled over on the side of the road. He was a zoo attraction, surrounded by obnoxious tourists filming him on their phones as he ate his dinner. At first glance he appeared to be stoic, dismissive of the introducers that were beneath him. But then I saw his antlers. His left horn was broken, snapped and dangling down his check. I was stunned how the mightiest creature in the forest could look so, meek. So weak. I guess even the strongest amongst us falls down sometimes.

I began to feel increasing unease with the current predicament I found myself in. With my large camera I was signaling more and more tourists to come, like flies swarming a garbage can. With each new car that pulled over it signaled two more cars to stop, and slowly more gathered at the small roadside attraction. I felt disgusted at myself for contributing to his harassment, that I had turned this animal into a spectacle for snapchat. Eventually we hit an inflection point of parasites, which seemed to scare him enough that he retreated into the woods. My fellow carnival goers thought that was the end of the show, but I knew where he was going and moved to follow him. I cut the corner of the forest, scanning through the trees at each large fallen log that remotely resembled a moose. My eyes darted back and forth across the landscape and suddenly he was just there, watching me intensely from 50 feet away. I returned his gaze, and looked deep into his warm, piercing black eyes. I tried to maintain eye contact, but I could not help but stare at his injury. This giant, this king of the forest had been reduced to nothing. I am unsure if he received this injury from another bull or from a car, but he was defenseless. Without a second antler he cannot defend himself against other moose, nor any predators that may come his way. He has no hope of mating with a female if he cannot fight off other bull moose. If a pack of coyotes found him, that would likely be the end of his story. Yet he slowly made his way towards me, unfazed by my presence and exuding strength and power. I was still in his kingdom. I retreated behind a large fallen tree, as though it would offer me safety if this wounded warrior decided to show me just how tiny I truly was.

I followed him for a while, photographing him. We exited the forest, into the marshland and I watched him feed. I tried my best to maintain my distance but something about him was incredibly compelling. I connected with him and I could not fully comprehend why I felt this deep connection to him. Perhaps I too was proudly boasting my confidence with injuries that I could not hide. But to me he also symbolized the castration of nature. The loss of what makes the wilderness great, of humankind’s destruction of it. Here was the most powerful animal in the forest reduced to a shadow of his former self.

I felt a deep anger and sadness watching him, the personification of the untamable wild becoming docile. The animals of the wild attempt to stay away from our expanding concrete domains, but here was irrefutable proof that there was no escape. That blackhole of humanity would slowly pull in everything, and those that were lucky enough to remain beyond the event horizon would still be errerably transformed. Yet despite his injury he was so majestic, so proud. As I watched him in the marsh it seemed like he doubled in size. I was almost overwhelmed with his presence, the size of his muscles and the strength of his character. His life will never be easy again, but from my point of view he seemed unfazed. Every living thing in this world still has their own race to run, and disabilities do not give a free pass. Watching him was depressing and inspiring. A reminder that humans, while destructive and a natural disaster in their own right, are just a brief fleeting moment in the grand life of the world, and life, no matter how chaotic and unfair, finds a way.

My contemplation broke when he began to feed on some fireweed, a shot I had desperately wanted for weeks. I tried to get slightly closer, but now I lacked the safety of the trees. By now he had tolerated my presence for 10 minutes, and I suddenly had the predilection that I had overstayed my welcome. He was still 200 feet away when I began to move away, and then I saw movement out of the corner of my eye. A flash of 1200 pounds of brown muscle. I knew immediately the tables had turned, but without time to perceive what was happening my body moved on its own and I started to run. Just behind me was the false shelter of a large forest service map, the only thing in 600 meters that could offer me any protection.

I had taken three steps during this instinctual maneuver, still only halfway to my perceived protection when I turned my head to see a brown tsunami. He had reduced the distance between us instantly, and I glimpsed his overpowering stature as it pierced my tiny personal bubble. The moment I turned my head to look back, he abruptly turned 90 degrees and darted away, and I was stuck with my foot in my mouth and my cock in my hand with the realization that he could have killed me without any hesitation, and chose not to. He chose to change direction. He chose to be the bigger animal and leave me uninjured. Whether he was struck by the fear of becoming even more injured, or the same injury had instilled a sense of empathy, he chose to let me go.

It’s difficult to describe the emotions I felt after this interaction. Pity for the animal, anger at a world that has created so much unnecessary pain; anger at myself for pitying an animal that was still so capable; inspired by his ability to strive on. Life is funny, powerful, exhausting, overwhelming, and beautiful. It’s so easy to anthropomorphize an interaction with an animal, especially one that we see so much of ourselves in. So easy to draw meaning when none was there. From his perspective, I could have just been an annoying scavenger that was bothersome. Yet at the same time this feeling is palpable and indescribable. I think it is the conjunction of my sadness for him and my realization that I did in fact, almost die in the most stupidest of ways. That I did not give him the respect he deserved. I was no better than the road side viewers I so easily condemned. Had I gotten hurt, wildlife authorities would likely have to relocate him, or worse, euthanize him. He may have personified the perversion and loss of the wild, but I was the personification of the destruction that caused it.

Lilikoi, Like Rain

by Jason Baer

Grains of sand fall slowly against a backdrop of blue; my only reference of the passage of time. I watch them, captivated, as they fall to their final resting place on the seafloor, ordered by waves into neat ridgelines. Streams of light weave dancing patterns over my fingers as they drag in the pale dunes, and for a moment I feel like the subject of that moving light. I smile at the anthropocentrism: that familiar human inclination to believe everything revolves around me.

I look up. A reef rises up from my place in the sand like the gates of a cathedral. Fish congregate around sky-reaching towers decorated in swaying anemones, framing the entrance to a bustling atrium. Within the gates, avenues wind through the rocky columns like aisles in a nave, leaving clearings of sand where fish meet in quiet prayer. The clicks and clacks of the millions of crustaceans that live here form a chorus of voices, chanting psalms that harmonize in a rich and pervasive soundscape. The gates, a perfect duality of Gothic architecture and fractal geometry, are a gentle reminder: I’m pretty sure you’re not supposed to bring a spear gun into a place of worship.

I come here often, each time bearing different roles: sometimes a scientist, sometimes a parishioner. Today I take the role of hunter.

I kick off the bottom gently. My movements are slow, aimed at keeping my heart rate down: my breath will last longer that way. Already I’m feeling the high that accompanies a freedive, the euphoric calm that comes not from oxygen deprivation but from the buildup of carbon dioxide in my blood and lungs.

With a flick of my fin, the hunt carries me through the gates. To either side, fish shrink back under rocky outcroppings, hiding from my shadow, and shades of lilac light filter in through the fan corals like stained glass. Coris wrasses, decorated in electric purples, pinks and greens dart through the pale-yellow branches of Stylophora, one of the prominent hard corals on these reefs. A little damselfish, the size of my finger, throws itself at my mask, the impact on the glass reverberating through the water. A warning meant to keep me away from its small patch of farmed algae. It works. I make a quick right turn.

Around me, stone pillars encrusted with algae and coral vibrate slowly with the movement of invertebrates: bright blue worms, speckled crabs, and sluggish sea stars making their daily rounds for food. Filter feeders sway in the current, extending their leaf-like nets to feed on the plankton that pass them by, and I am reminded that no resource is wasted on this bustling reef. The work of animals and bacteria deep inside the reef probably help with that, I imagine, as they ceaselessly process the waste that trickles down from above. Every good congregation needs a recycling service.

Motion to the left. I raise my gun slowly, aiming at a shadow in between two outcroppings. Manani, a type of Tang fish. The pop reaches my ears a second later, but the end of the spear is disappointingly still. Lodged in sand, sans fish. I collect the spear, reload. My vision’s closing in, a little bit.

I return to the surface and take a breath. It’s been a little under two minutes, I think; feels like longer. I let my pulse settle, take a few breaths, and once again enter the cathedral, scouring the aisles until my lungs spasm and my body acquiesces to the limitations of its physiology. I do this until it feels like there is no pew unturned, no encrusted spire unmapped, until my mind burns in a haze of hypoxia and frustration. Up and down, up and down.

It’s getting late, still no fish. I decide to swim a bit further out. Below me, a school of thousands of glassfish, their movements perfectly coordinated, lie between me and the bottom. I push forward, and a hole opens in the mass of tiny fish, translucent bodies glinting in the fading sunlight like molten glass. I pass through the great glass donut. I am now hungrier than I was before, and the peace of the preceding hours is tinged with irritation.

I settle on the sloping bottom. On one side, high above me, the cathedral bustles as before; on the other, just deep and empty blue. I swim to the right, trying to keep my movements slow, my eyes trained on a blue background that reveals itself slightly more with each kick of my fin. Too soon, my vision starts to sway. The tightness in my chest comes, and then passes; I breathe out a few bubbles to trick my brain into thinking it’s almost over. I am deeper than before, and the hint of frustration spikes my heart rate, reducing my time at depth. My lungs begin to burn. A numbness starts in my fingertips and travels slowly up my arms, and I struggle to keep my eyes from looking up at the surface, the air a temptation I would not be able to resist. I remind myself of the goal. I am getting desperate.

Ahead of me, a flash of color materializes out of the blue. Uhu, a parrotfish. Frustration dissipates in a cloud of promise; my impending success pushing off the discomfort like a spark of flint in a dark room. I raise the gun slowly, plant my knee in the sand, line up the shot, fire.

Spear impales nothing. Uhu disappears behind a rock. I frown, grab the line, and kick off for the surface.

My ascent to the sky seems to pass in slow motion. The bubbles I exhale keep me company: in them, my reflection is clear and convex, eyes sparkling against a backdrop of blue. In those bubbles I see all the roles I have taken in coming here: the curious scientist, the loyal patron, the famished hunter. Those roles seem to melt, one into the other, until the purpose underlying each dissolves into nothingness: this was never about food, or science, or photographs, or exercise, or God. I was really only ever here to be here. I glance up at our destination, chest tightening again. Wind-whipped barrels at the churning surface act as prisms, sending rainbows down on a tower of bubbles, an unsuccessful fisherman, and an empty spear, trailing from the line below.

My head clears the surface, and in the wave of air that meets my lungs there is a hint of new perspective. I came here for food, and I am empty handed. I pushed my physiology to the brink and was met only with tingling palms and vision blurring at the edges. I am exhausted. But the experience wasn’t a failed one; what began as a hunt has simply become a pilgrimage. All this time I spent diving, only to arrive exactly where I began and realize the ‘up and down’ was all that mattered.

Fuck the destination. Sometimes the journey is just a journey.

I look to shore, see the clouds collecting over the lush forest, and my stomach growls again. Leaving the ocean poses as much of a challenge as the relinquishment of my ambition, but it’s a worthy cause. What awaits me on land is a welcome departure from the burden of purpose. Instead of Uhu, I will sustain myself on the mangoes and lilikoi that fall from the jungle trees, like rain.

Aboriginal burning practices: a solution to Australia’s catastrophic wildfires?

by Brianne Palmer (originally published here)

The cause of the 2019–20 “black summer” bushfires that swept across Australia—burning over 40 million acres and 3,000 homes and killing 33 people—can be found in Australia’s history, says Michael-Shawn Fletcher.

And a solution may also be found by looking back, he says: restoring the cultural burning practices of the aboriginal people who first settled the continent 65,000 years ago.

“We sit here with this feeble attempt to fight and battle and contain [fire] rather than embrace, and love and embed,” said Fletcher, a Wiradjuri man and associate professor of geography at the University of Melbourne. Fletcher painted the historical backdrop of the Australian bushfires in a recorded presentation released Oct. 16 during the Council for the Advancement of Science Writing’s New Horizons in Science briefing at the virtual ScienceWriters2020 conference.

When British colonists invaded Australia, a land that was home to many aboriginal peoples, in the late 1700s they brought an attitude of Western superiority, ideas of European land management, and a fear of fire. Unbeknownst to them, they had just settled on the most flammable continent.

Before the British, historical records indicate that Aboriginal peoples maintained the grassy and open landscape by frequent burning of the vegetation, which kept fire fuels low. “Humans are a fire organism,” Fletcher said.

These early Aboriginal Australians used fire as a tool to create reliable and safe environments in a highly unpredictable landscape. Fires created areas of refuge, cleared bush for easy transportation, and kept the landscape tidy. “It’s a lot like mowing the lawn in your garden. If you let your yard go three years without mowing, it’s going to look like an overgrown mess,” Fletcher explained in an interview after a live Q&A session with writers Oct. 20.

Aboriginal people who survived the decades of frontier massacres, infections, and mass poisonings inflicted by the British invaders were ripped away from their culture and from the land on which they relied. With the loss of Indigenous people from the landscape came a loss of cultural burning, Fletcher said. Soon shrubs and trees began colonizing the open spaces and adding more fuel for fires.

Now fire is treated as a threat by Australians. Fletcher pointed out the combative language used to describe people’s relationship with fire: with militaristic force, humans form brigades to extinguish and suppress fires. The element that was once humanity’s greatest tool became its enemy.

Reconnecting humans with nature can improve the land

Fletcher pointed out, during the interview, that when people force a division between nature and culture, biodiversity declines, as seen in Australia in the centuries since the British arrived. Aboriginal peoples, he said, believe that when we care for the land, it cares for us. According to Fletcher, when we remove people from the landscapes they have historically inhabited, we destroy the environment.

The solution is getting the right people managing landscapes, and Western scientists may not be the right people for the job, he said. Western science tends to segment fuel loads and biodiversity into separate areas of management. Indigenous management takes a more holistic approach.

Traditional cultural practices are beginning to gain wider support. Recently the Aboriginal Carbon Foundation has attracted government support and shown success in returning cultural burning to Australian landscapes in the tropical savannas. By burning throughout the dry season, Aboriginal people prevented large, catastrophic fires because there was less fuel to burn. This also increased biodiversity and reduced carbon loss. Similar practices are now being carried out across the continent.

Now, Fletcher and his team are working to connect cultural traditions with Western science to get the data about cultural burning into the hands of decision makers.

“The solution to this problem isn’t removing people,” he said. “It’s changing the way that people do things.”

All photos courtesy of Michael Shawn-Fletcher.


COVID Halloween decorations (video by Jasmine Chavez)

Brianne Palmer started a new experiment to determine how fire changes the soil microbial community which involves a lot of fun with a blow torch

Do you have something you want to submit?

Email me at brianne.r.palmer@gmail.com by March 1, 2020 for the next issue! As you can see, I will publish anything! Artwork! Writing! Memes! Accomplishments! Complaints!



Created with images by Megan Ellis - "untitled image" • TallGuyInc - "oceanside san diego pier" • Joel Vodell - "Ocean" • PublicDomainImages - "bull shot elk" • joakant - "fish underwater corals" • alicia3690 - "heart coral australia" • visavietnam - "fish aquarium sea" • Mariamichelle - "underwater coral reef"