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Fold@Home: Aid in COVID-19 Research from Home
Image via Folding@Home
By Nathan Levinzon, Neurobiology, Physiology, and Behavior ‘23
Author’s Note: The purpose of this article is to introduce and inform the UC Davis scientific community of Folding@Home; a distributed computing project that allows individuals and researchers to donate computing resources from their computers towards COVID-19 research.
Keywords: COVID-19, Folding@Home, Distributed Computing
Reports of localized viral pneumonia cases in the Chinese city of Wuhan began in December 2019, initially amounting to little concern for humanity. Since then, the world has drastically changed as a result of COVID-19. As of September 16, 2020, almost thirty million cases of COVID-19 have been confirmed across the globe, claiming the lives of close to one million individuals. In California alone, there have been seven hundred seventy thousand cases with close to twenty three thousand deaths as of September 28th [1]. Millions of individuals are currently under a government-mandated shelter-in-place order, forcing the lives of many to come to a standstill. In a statement made by UC Davis Chancellor May in March of this year, “much of [UC Davis’] research is ramping down, but when it comes to the coronavirus, our efforts continue apace” [2]. One such effort taking place at UC Davis is called Folding@Home (FAH), and it allows researchers to study the mechanisms of COVID-19 with nothing but a computer.
FAH originated as a project to study how protein structures interact with their environment. Currently, some proteins of particular interest to FAH are the constituents of the virus that causes COVID-19. Like other coronaviruses, SARS-CoV-2 has four types of proteins: the spike, envelope, membrane, and nucleocapsid proteins. Many copies of the spike protein protrude from the surface of the virus, where they wait to encounter Angiotensin-Converting Enzyme 2 (ACE2) on the surface of human cells [3]. In order to develop therapeutic antibodies or small molecules for the treatment of COVID-19, scientists need to better understand the structure of the viral spike protein and how it binds to the human enzymes required for viral entry into the cells. Before the spike proteins on SARS-CoV-2 can function, they must first take on a particular structure, known as a ‘conformation’, through a process known as “protein folding.” As a result of the many factors that impact protein folding, like electrostatic interaction, especially the electrostatic interactions between amino acids and their environment, research into therapeutics against COVID-19 first necessitates intensive computation in order to resolve protein structure [4]. Only after the proteins of SARS-CoV-2 are understood can the hunt for a cure begin.
FAH is able to study the complex phenomena of protein folding thanks to the computational power of distributed computing. A distributed computing project is a piece of software that allows volunteers to “donate” computing time from the Central Processing Units (CPUs) and Graphics Processing Units (GPUs) located in their personal computers towards solving problems that require significant computing power, like protein folding. In essence, FAH uses a personal computer’s computational resources while the computer is idle to perform calculations involving protein folding. This donated computing power is what forms the “nodes” within a greater cluster of other computers in a process known as “cluster computing.” FAH uses the cluster’s resources to run complex biophysical computer simulations in order to understand the complexities and outcomes of protein folding [5]. In this way, FAH brings together citizen scientists who volunteer to run simulations of protein dynamics on their personal computers.
Studying protein folding via distributed computing has humble beginnings but has grown into a technology that has the potential to research even the most elusive proteins. First, established protein conformations are used by FAH as starting points for a set of simulation trajectories through a technique called ‘adaptive sampling.’ The theory behind adaptive sampling goes as follows: If a protein folds through the states A to B to C, researchers can calculate the length of the transition time between A and C by simulating the A to B transition and the B to C transition [6]. First, a computer simulates the initial conditions of a protein many times to determine the sample space of protein conformations. As the simulations discover more conformations, a Markov state model (MSM) is created and used to find the most dominant of protein conformations. The MSM represents a master equation framework: meaning that, in theory, the complete dynamics of a protein can be described using a single MSM [7]. The MSM method significantly increases the efficiency of simulation as it avoids unnecessary computation and allows for the statistical aggregation of short, independent simulation trajectories [8]. The amount of time it takes to construct an MSM is inversely proportional to the number of parallel simulations running, i.e., the number of CPUs and GPUs available [9]. At the end of computation, an aggregate final model of all the sample states is generated. This final model is able to illustrate folding events and dynamics of the protein, which researchers can use to study and discover potential binding sites for novel therapeutic compounds.
The power of FAH’s distributed computing in the hunt for a cure to COVID-19 grows with each computer on FAH’s network.ch citizen scientist who donates the power of their idle computer. Currently, pharmaceutical research in COVID-19 has been hindered by the fact that there are no obvious drug binding sites on the surface of the SARS-CoV-2 virus. This makes developing therapeutic remedies for COVID-19 a long, expensive process of ‘check and guess.’ However, there is promise: in the past, FAH’s simulations have captured motions in the proteins of the Ebola virus that create a potentially druggable site not otherwise observable[10]. Using the same methodology as they did for Ebola, FAH has now found similar events in the spike protein of SARS-CoV-2 and hopes to use this result and future results to one day produce a life-saving treatment for COVID-19. By downloading Folding@Home and selecting to contribute to “Any Disease”, anyone can help provide FAH-affiliated researchers with the computational power required to tackle this worldwide epidemic. For more information, refer to https://foldingathome.org/start-folding/.
References
- Smith, M., White, J., Collins, K., McCann, A., & Wu, J. (2020, June 28). Tracking Every Coronavirus Case in the U.S.: Full Map. The New York Times. https://www.nytimes.com/interactive/2020/us/coronavirus-us-cases.html
- May, G. S. (2020, March 20). Update on Our Response to COVID-19. UC Davis Leadership. https://leadership.ucdavis.edu/news/messages/chancellor-messages/update-on-our-response-to-covid19-march-20
- Astuti, I., & Ysrafil. (2020). Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): An overview of viral structure and host response. Diabetes & Metabolic Syndrome: Clinical Research & Reviews. https://doi.org/10.1016/j.dsx.2020.04.020
- Sarah Everts. (2017, July 31). Protein folding: Much more intricate than we thought | July 31, 2017 Issue – Vol. 95 Issue 31 | Chemical & Engineering News. Cen.Acs.Org. https://cen.acs.org/articles/95/i31/Protein-folding-Much-intricate-thought.html
- About – Folding@home. (n.d.). Folding@Home. Retrieved June 28, 2020, from https://foldingathome.org/about/
- Bowman, G. R., Voelz, V. A., & Pande, V. S. (2011). Taming the complexity of protein folding. Current Opinion in Structural Biology, 21(1), 4–11. https://doi.org/10.1016/j.sbi.2010.10.006
- Husic, B. E., & Pande, V. S. (2018). Markov State Models: From an Art to a Science. Journal of the American Chemical Society, 140(7), 2386–2396. https://doi.org/10.1021/jacs.7b12191
- Sengupta, U., Carballo-Pacheco, M., & Strodel, B. (2019). Automated Markov state models for molecular dynamics simulations of aggregation and self-assembly. The Journal of Chemical Physics, 150(11), 115101. https://doi.org/10.1063/1.5083915
- Stone, J. E., Phillips, J. C., Freddolino, P. L., Hardy, D. J., Trabuco, L. G., & Schulten, K. (2007). Accelerating molecular modeling applications with graphics processors. Journal of Computational Chemistry, 28(16), 2618–2640. https://doi.org/10.1002/jcc.20829
- Cruz, M. A., Frederick, T. E., Singh, S., Vithani, N., Zimmerman, M. I., Porter, J. R., Moeder, K. E., Amarasinghe, G. K., & Bowman, G. R. (2020). Discovery of a cryptic allosteric site in Ebola’s ‘undruggable’ VP35 protein using simulations and experiments. https://doi.org/10.1101/2020.02.09.940510
Will This Pandemic Unite Us Against Climate Change?
By Pilar Ceniceroz, Environmental Science and Management ‘21
Author’s Note: I originally wrote this piece for a UWP104E assignment. However, the topic remains relevant to people all around the world. In the past, it has been hard to visualize our individual impacts on the environment. COVID-19 has become a great example of how behavioral changes can drastically transform our surroundings. I would like my readers to understand the power of unity in the face of what might be the next global crisis, climate change.
Introduction
After the World Health Organization (WHO) declared a global health emergency on January 30th 2020, the world has seen extreme changes as the daily lifestyle of almost everyone in the world has been rapidly altered [1]. The ongoing effort to slow the spread of the virus while sheltering-in-place has not been without sacrifice—countless people lost their jobs, most cannot physically go to school, and everyday activities have been significantly modified. However, this halt of “business as usual” has fascinating impacts on the environment. Stay-at-home orders shut down production in industrial facilities and power plants and minimized personal vehicle use [2]. With a major decrease in economic activity, highly polluted cities around the world are now seeing clearer skies. The seemingly dull, repetitive routine of quarantine life has allowed the environment to flourish.While consequences of COVID-19 include global economic devastation, the environment has seen both indirect positive and negative impacts as a result of stay-at-home orders and the declining economy. Regions with COVID-19 restrictions experienced a decrease in air and water pollution. These restrictions included a stop to nonessential work and travel as well as closing of restaurants and bars. Concurrently, the amount of single use products has significantly increased to limit the spread of the virus. Decreasing air pollution is a major milestone for our modern world, however, as the world returns to normal life, pollution levels will follow. Although a short term decrease in greenhouse gas (GHG) emissions is not a sustainable way to support the environment, communities around the globe have witnessed the instantaneous impacts of our everyday habits on the environment due to COVID-19.
Drop in Atmospheric and Water Pollution
Today, 91% of the world population lives in places where poor air quality exceeds the permissible limits set by the WHO [2]. Air quality is an important contributor to human health and living in an area with poor air quality can exacerbate the symptoms of COVID-19. According to the 2016 WHO report, air pollution contributes to 8% of total deaths in the world [2]. Countries that normally struggle with unhealthy air, such as China, USA, Italy, and Spain, have since seen clearer skies for the first time in decades after taking aggressive measures to slow the spread of the virus. There has been a dramatic decrease in the amount of CO2, NO2, and particulate matter emitted in China with the halt of industrial operations with the decrease in demand for coal and crude oil (see fig. 1) [3].
Changes in nitrogen dioxide emission levels in China from before and after lockdown.
Fig. 1. Zambrano-Monserrate, Manuel A., et al. “Indirect Effects of COVID-19 on the Environment.” Science of The Total Environment, vol. 728, 20 Apr. 2020, p. 138813., doi:10.1016/j.scitotenv.2020.138813.
Since this same time last year, air pollution levels have dropped 50% in New York [1]. There has been a 25% decrease in air pollution since the start of this year in China, one of the largest manufacturing countries [1]. The closing of factories contributed to a 40% reduction in coal usage at one of China’s largest power plants [1]. The average coal consumption of power plants has reached its lowest point in the past four years [3]. Clearly, the outbreak has improved short term air quality and has contributed to reducing global carbon emissions. Fewer flights and social distancing guidelines have reduced carbon emissions as well as other forms of pollution. Tourism significantly decreased worldwide, and beaches around the world have been cleaned up. For example, citizens of Venice, Italy were amazed to see crystalline waters and healthy fish in their canals [1].
Comparison of air quality in some of the biggest cities around the world before the COVID-19 pandemic and while the lockdown.
Fig. 2. Saadat, Saeida., et al. “Environmental Perspective of COVID-19.” Science of The Total Environment, vol. 728, 22 April 2020, p. 138870., doi:10.1016/j.scitptenv.2020.139815.
Increased Single Use Plastics
In order to completely analyze the impact of COVID-19 on environmental health, the negative impacts on the environment from the virus are equally as important as the positive effects. Although travel restrictions have led to less pollution caused by tourism, the amount of single use plastics and medical equipment has significantly increased waste around the world. In the USA, there has been a significant increase in the amount of single-use personal protective equipment, such as masks and gloves [1].
Imagine the amount of trash created when millions of people use one or a couple of masks daily, single use gloves and hand sanitizers. With a population of eleven million people, the city of Wuhan produced an average of 200 tons of clinical trash on any single day in February 2020, compared to their previous average of fifty tons per day [1]. This number is four times the amount the city’s only dedicated facility can incinerate per day [1].
The demand for plastics has increased as consumers move to online purchasing. Shelter-in-place guidelines established in most countries have driven consumers to increase their demand for online orders and home delivery [2].The increasing demand for shipping and packaging greatly increases the amount of waste produced as well as GHG emissions with increased activity in supply lines. Out of concern of spreading the virus through the plastic surfaces in recycling centers, some cities stopped their recycling programs in the U.S. [2]. Additionally, in some of these cities, citizens are not allowed to use reusable bags at grocery stores. Similarly, some European cities have seen restrictions within waste management. Italy has prohibited infected residents from sorting their personal household waste [2]. Industries have repealed the disposable bag bans, many have switched to single-use packaging, and online food ordering has increased in popularity [2]. The consumption of single use plastics has skyrocketed to limit transmission [1, 3]. Suspension of sustainable waste management practices potentially escalate environmental pollution.
Medical wastes generated during COVID-19 pandemic in the environment.
Fig. 3. Saadat, Saeida., et al. “Environmental Perspective of COVID-19.” Science of The Total Environment, vol. 728, 22 April 2020, p. 138870., doi:10.1016/j.scitptenv.2020.139815.
Where Do We Go From Here?
Over the last few months, people were enamoured by the modern-day pollution that vanished before their eyes. Strict stay-at-home orders decreased the amount of air and water pollution in otherwise unhealthy cities. Contrarily, the considerable increase in single use plastics may have a lasting negative impact on the environment. Although these outcomes may be hard to compare in magnitude, they help put into perspective the larger picture. Short term change is not a sustainable way to clean up the environment especially when it occurs alongside economic devastation. Before the pandemic, individual action against climate change felt like an abstract idea, out of reach due to its lack of immediacy. Now, the world has seen changes to our environment from worldwide behavior. Visible skies and vibrant waterways are distinguishable changes that are legitimate grounds to build momentum and take action for a healthier future. Although the pandemic may not have a drastic impact on the future of the environment itself due to conflicting effects, it can instigate discussion to improve personal actions that impact the environment. Long-term structural change and individual behavior changes are critical in combating environmental pollution. Moving forward, it is imperative that the unification of collective conscious behavior be a driving force to combat climate change. If neglected, climate change is likely to take many lives in the future, portraying this pandemic as a minor devastation. Let the urgency of our united global response to COVID-19 influence our future response to the next global crisis; climate change.
References
[1] Saadat, Saeida., et al. “Environmental Perspective of COVID-19.” Science of The Total Environment, vol. 728, 22 April 2020, p. 138870., doi:10.1016/j.scitptenv.2020.139815.
[3] Wang, Qiang, and Min Su. “A Preliminary Assessment of the Impact of COVID-19 on Environment – A Case Study of China.” Science of The Total Environment, vol. 728, 22 Apr. 2020, p. 138915., doi:10.1016/j.scitotenv.2020.138915.
[2] Zambrano-Monserrate, Manuel A., et al. “Indirect Effects of COVID-19 on the Environment.” Science of The Total Environment, vol. 728, 20 Apr. 2020, p. 138813., doi:10.1016/j.scitotenv.2020.138813.
The Parable of the Passenger Pigeon: How Colonizers’ Words Killed the World’s Largest Bird Population
By Jenna Turpin, Wildlife, Fish, and Conservation Biology ‘22
Author’s Note: I started this piece as an assignment for my undergraduate expository writing class under the guidance of my supportive professor Hillary Cheramie. Hillary urged me to take my writing beyond her course. In May, I had the wonderful opportunity to share this research at the 2020 UC Davis Annual Undergraduate Research Conference. I want to continue to share my work through publication. I wrote this piece with the intention of inspiring both students and teachers. From this paper, students can learn the parable of the passenger pigeon and teachers can come to understand why teaching about the passenger pigeon matters.
I learned of the passenger pigeon during my first week of college at UC Davis. One of my professors, Dr. Kelt, explained a brief history of the passenger pigeon to my first-year wildlife ecology and conservation class. The lesson was about wildlife-human interactions and the destruction humans can execute on the environment. The passenger pigeon’s story shook me to my core. It was a disturbing portrayal of how people sometimes negatively shape ecosystems. For me, it reinforced all of the reasons I decided to study wildlife conservation. I want people who read this piece to feel the emotions I felt when I first took in the parable of the passenger pigeon and come to the belief that humans have a responsibility to conserve species through management, policy, and education. The more people who hear this parable, the more people who hold sympathy for our wildlife. It should be built into schools’ science and history curriculums. A greater understanding of the passenger pigeon will save future species from extinction.
Abstract
Genre is the literary process through which people collectively communicate about a topic. Applied to a species, genre helps us understand how society communicates about that animal. Species’ genres change over time as different people interact with them. This influences human-wildlife interactions and thus plays a critical role in determining the fate of that species. In the passenger pigeon’s (Ectopistes migratorius) prime, it was the most abundant bird species in existence but went extinct. The dynamics of human-wildlife interactions over time defined the progression of the passenger pigeon’s recorded history. These interactions varied based on how the dominant people in North America thought about the bird and the genre surrounding its existence. The parable of the passenger pigeon is a poignant example of why genre matters in preserving species and how this can go wrong. The analysis of the historical evolution of the passenger pigeon’s genre showed that the European colonization of North America is why these birds went extinct. I conducted a survey that showed that the passenger pigeon’s genre is fading among young people. Failing to spread the parable of the passenger pigeon is a threat to every currently endangered species and their respective genres.
Introduction
The passenger pigeon (Ectopistes migratorius) lived in North America and was described as having a “small head and neck, long tail, and beautiful plumage” [1]. In its prime, it had the largest population size of any bird species at the time but went extinct due to overexploitation and habitat loss caused by European settlers [1]. The dynamics of human-wildlife interactions over time defined the progression of the passenger pigeon’s recorded history.
These interactions varied based on how the dominant people in North America thought about the bird and the genre surrounding its existence. Genre refers to “repeating rhetorical situations” to aid human interaction. In other words, it is the collection of how people refer to a specific topic. The definition of genre can be applied broadly. Genres are dynamic and develop over time, as people face new situations to apply them to. Every species has its own genre surrounding its existence. People participate in many genres on a daily basis, even if they do not know it. Genre is a “social action,” people shape genres and genres shape people [2]. The way groups of people collectively feel about anything is communicated through language. Thus, looking at the way people talked about passenger pigeons explains the processes that led to their downfall. The passenger pigeon is an effective ambassador for teaching youth about conservation because of the population’ rapid decline.
Historical Evolution
Indigenous People
The passenger pigeon’s parable begins with Indigenous people who lived within the range of the bird, mostly covering only the Eastern half of America [1]. These Indigenous people were the first humans to interact with the passenger pigeon and create its genre. Simon Pokagon, a Potawatomi tribe member was interviewed about seeing them in flight: “When a young man I have stood for hours admiring the movements of these birds. I have seen them fly in unbroken lines from the horizon…” [3]. Under Indigenous peoples’ care, the passenger pigeon numbers rose beginning in the years 100 to 900 C.E. [4]. This was because Indigenous people and passenger pigeons had a well-balanced relationship that allowed both populations to thrive.
Indigenous people carefully interacted with the passenger pigeon because it was an important game bird to them, second only to the wild turkey [1]. The passenger pigeon was a staple food of the Seneca, who named the bird jah’gowa, meaning “big bread” [4]. Tribes followed specific procedures for hunting the birds. Almost all tribes had a strict policy—based in both religion and biology—against taking nesting adult passenger pigeons. This strategic wildlife management policy promoted chick survival by allowing parents to care for their young. The Sioux and the Iroquois League were among those known to enforce their rules on other hunters. Instead of hunting the birds during this time, they often used nests as an opportunity to closely observe the bird. Individual tribes also had additional policies. For the Ho Chunks, hunting of the passenger pigeon could only happen if the chief held a feast. When the birds returned in spring, they offered much needed seasonal food. Before the Seneca began the hunt, they monitored the nests until the chicks were two to three weeks old. The Seneca even went as far as managing the habitat of the passenger pigeon, for instance they did not allow the cutting of any tree a “chief” pigeon nested in [4]. Chief Pokagon of the Potawatomi tribe credits strategies such as this for not only allowing the pigeon to maintain its numbers but actually increasing them [1]. By thinking about the needs of the pigeons and adjusting behaviors to accommodate those needs rather than freely hunting them, the population was able to continue on as a reliable food resource for the tribes that used them.
Furthermore, the connection between the two species went beyond the typical predator and prey relationship. To many Indigenous people, the pigeons were not just food, they were a being. Passenger pigeons were included in the religion of some tribes through stories, song, and dance [1]. The Seneca believed that the pigeon gave its body to create their children. The passenger pigeon was so important to the Seneca that they termed albino ones “chief of all pigeons” and strictly forbade hunting them. The Cherokee and the Neutrals told similar stories of the bird as a guide to avoid starvation. The Seneca and the Iroquois opened their Maple Festival every year with a dance song about the bird. The Cherokee Green Corn Festival featured a dance mimicking a pigeon hawk in pursuit of a pigeon [4]. The pigeons held value in the lives of the people who benefited from them.
European Arrival
The Europeans recorded their first passenger pigeon on July 1, 1534 [1]. Right away, colonizers of every walk of life made note of the massive number of pigeons Indigenous people had maintained. The average European enjoyed the sight, “…I was perfectly amazed to behold the air filled and the sun obscured by millions of pigeons…” [1]. Many accounts told the narrative of an undiminishable population. Schorger, a professional ornithologist confirmed this notion, stating that “no other species of bird, to the best of our knowledge, ever approached the passenger pigeon in numbers” [1]. More ornithologists like Alexander Wilson took records, “In the autumn of 1813…I observed the pigeons flying from northeast to southwest, in greater numbers than I thought I had ever seen them before…The light of the noon day was obscured as by an eclipse” [5]. Even Leopold described them as a “biological storm” that used the resources of the land to their advantage [6].
While everyone knew the birds to be copious, not everyone understood the science behind it. Ornithologists knew that the pigeons could thrive because they had ample food and habitat when the Europeans arrived. However, for the vast majority of Europeans who were not trained in biology, the flock of birds blocking out the sky was frightening and unexplainable. This is where the genre began to separate itself from Indigenous peoples’ understanding of the bird. Europeans constructed urban legends in an effort to explain what was unknown to them. When only one acorn was found in pigeons’ crop (food storage pouch), Europeans predicted death and sickness. The evidence they saw supported their beliefs, “It is a common observation in some parts of this state, that when the Pigeons continue with us all the winter, we shall have a sickly summer and autumn” [1].
Diminishing
As colonizers made themselves more at home in North America, they encroached on passenger pigeon habitat and depleted their numbers. The colonizers did not take wildlife management into consideration while hunting. Instead, they killed far more than they took and failed to leave young and nesting birds alone [1]. Extinction seemed entirely impossible, they did not see a need to ensure the next generation of pigeons could continue, it was understood as a given. To compound this, the birds were generally not thought of highly in European cultures. The passenger pigeon was merely a thing to exploit rather than a being to feel for. They began to disappear from the places humans occupied, retreating into what wilderness remained [3].
People began to notice that the passenger pigeon populations were fading. Some states, like Ohio, actively avoided policies to protect the species, claiming “the passenger pigeon needs no protection. Wonderfully prolific, having the vast forests of the North as its breeding grounds, travelling hundreds of miles in search of food, it is here to-day, and elsewhere to-morrow, and no ordinary destruction can lessen them or be missed from the myriad that are yearly produced” [1]. Other states, particularly Wisconsin, wrote laws to protect the species: “It shall be unlawful for any person or persons to use any gun or guns or firearms, or in any manner to main, kill, destroy, or disturb any wild pigeon or pigeons at or within three miles of the place or places where they are gathered for the purpose of brooding their young, known as pigeon nestings”. Laws along these lines were enacted in several states but no efforts were made to actually enforce them. Much of this was due to pushback by settlers to the laws. Farmers in particular protested any enforcement, worrying that allowing the pigeons to thrive would mean crop destruction [1]. To them, the pigeons were pests to get rid of, not preserve.
Gone
The last passenger pigeon, named Martha, was a resident of the Cincinnati Zoo up until her passing on September 1, 1914. She was named after First Lady Martha Washington and was housed with her companion named George. The pair never produced fertile eggs, the zoo’s captive breeding effort was too late to save the population [1]. The end of the species “removed more individual birds than did all the other 129 [previously recorded bird] extinctions put together”. They went extinct because of introduced species, chains of extinction, overexploitation, and habitat loss—all four of these were human-driven factors. Captive breeding, regulating hunting, and habitat protection could have saved them. However, these efforts were seldom made and not done early enough in the population’s decline [3]. The passenger pigeon was lost because of the genre Europeans created for it during the time it was still around.
The majority of non-indigenous Americans only appreciated the passenger pigeon and shifted their genre once they were no longer around. People now found a soft spot for the birds in their memories, “Alas, the pigeons and the frosty morning hunts and the delectable pigeon-pie are gone, no more return”. Artists incorporated these fond memories into their paintings, poems, and music. Monuments were erected around the United States inscribed with laments such as “this species became extinct through the avarice and thoughtlessness of Man” and “the conservationist’s voice was heard too late” [3]. People regretted the fact that future generations would not get to see the bird in the sky so they attempted to etch the passenger pigeon into everyone’s minds [6].
Making an effort to remember the passenger pigeon is important because the species’ story functions as a lesson and a guide for the future. However, in the past decade, the passenger pigeon is being forgotten. Many high school students are not taught about the population’s time on Earth and why they are now gone, as shown by a case study in Pennsylvania [7]. If people are no longer talking about it then the same mistake will be made again. At the same time, there are also organizations, like the Project Passenger Pigeon founded in 2014, working to tell the parable “through a documentary film, a new book, their website, social media, curricula, and a wide range of exhibits and programming for people of all ages” [8]. However, a small group of thoughtful individuals will not be enough to save the next species from human destruction if the story of the passenger pigeon does not make it into enough of the right hands.
Experiment
Over the period of one month during March 2019, I surveyed teenagers regarding their passenger pigeon knowledge. At the time of the survey, the teenagers were high school or college students in the United States. The overall purpose of my survey was to investigate if young people are talking about the passenger pigeon in contemporary society. Of the fifty-one responses, three (6%) subjects spoke about the passenger pigeon accurately. Furthermore, eight (16%) subjects believed to know the true story of the passenger pigeon, all of those eight falsely stated that the passenger pigeon was used to carry messages. Eight (16%) subjects even claimed to have seen a live passenger pigeon since 2000.
My survey found that very few teenagers have heard the parable of the passenger pigeon’s extinction. This group of people has gone through a large amount of schooling in their lives so far without being taught about the passenger pigeon despite its intertwining with significant historical events. The convenient fact about passenger pigeons is that they feel familiar to people since most have seen today’s common pigeon, the rock dove. It is easy for the uninitiated to imagine what a passenger pigeon was like based off of what they know about rock doves. The parable of the passenger pigeons can be taught in any classroom—science, history, art, and more.
The experiment shows that the genre is not being passed on. This is exactly why the way contemporary society talks about this species and its genre matters. Education that advocates for proper wildlife management and policy is the key to saving species from extinction.
Conclusion
The passenger pigeon species went from the world’s largest bird population to complete extinction, due to mistreatment from European colonizers. My survey of high school teenagers shows that people are not learning from this parable. This species makes itself an ideal candidate because of the rapid severity of its decline. It is increasingly important that we care about our environment before it is too late to take action. The clock is ticking, the passenger pigeon told us so. If we can learn to mourn a bird we never met, we will not have the opportunity to mourn the birds we know.
Works Cited
- Schorger, A.W. The Passenger Pigeon: Its Natural History and Extinction. Wisconsin, University of Wisconsin Press, 1955.
- Dirk, Kerry. “Navigating Genres”. Writing Spaces: Readings on Writing, edited by Charles Lowe and Pavel Zemliansky, vol. 1, Parlor Press, 2010.
- Avery, Mark. A Message from Martha. London, Bloomsbury Publishing, 2014.
- Greenberg, Joel. A Feathered River Across the Sky: The Passenger Pigeon’s Flight to Extinction. New York, Bloomsbury USA, 2014.
- Wilson, Alexander. Wilson’s American Ornithology. Boston, Otis Broader and Company, 1853.
- Leopold, Aldo. A Sand County Almanac. New York, Oxford University Press, 1954.
- Soll, David. “Resurrecting the Story of the Passenger Pigeon in Pennsylvania.” Pennsylvania History: A Journal of Mid-Atlantic Studies, vol. 79, no. 4, 2012, pp. 507–519. JSTOR, www.jstor.org/stable/10.5325/pennhistory.79.4.0507.
- Project Passenger Pigeon. The Chicago Academy of Sciences and its Peggy Notebaert Nature Museum, 2012, passengerpigeon.org. Accessed 19 February 2019.
Watercolor Bird Series
By Daphne Crum, Genetics & Genomics ’23
In this bird series I have painted a Northern Cardinal (Cardinalis cardinalis), a Song Sparrow (Melospiza melodia), and a Pine Warbler (Setophaga pinus). These three birds were painted as gifts for members of my family, each one personalized to match the region of the U.S. where they live. While I have yet to narrow down my all-time favorite species, all birds collectively make the top of my favorite-animals list. I have been keeping a life list for bird-watching since I was in 8th grade, with 80 species and counting! There is something so unexplainably whimsical about birds that has captivated me for as long as I can remember. Birds have stolen our hearts for hundreds of years, inspiring artists and scientists alike with their power of flight, their feather variety, their intricate language of chirps and song, and their differing social dynamics. Capturing the vivacity that birds emanate is a huge challenge for me when it comes to finding the perfect medium to paint or draw in, the angles at which to position the birds in my art, and the body language that should be portrayed. I am inspired by artists who can successfully capture a bird’s personality through their work, and I strive to do the same.
Yosemite Valley
By Ryan Lazzareschi, Computer Science ’21
At the end of the tunnel, I saw an opportunity I couldn’t miss. As the sun rose in the distance, the perfect composition of Yosemite Valley presented itself. The granite cliffs of El Capitan stretch thousands of feet down on the left with Bridalveil Falls set against the Cathedral Rocks on the right, and Half Dome barely peeking through off in the distance covered with a layer of snow.
Lower Yosemite Falls
By Ryan Lazzareschi, Computer Science ’21
Taking inspiration from the timeless black and white style of Ansel Adams, Yosemite Falls exemplifies the true beauty of Mother Nature. Lower Yosemite Falls as pictured (above, below, etc), comes crashing down 320 feet, making up only a fraction of the 2400 foot Yosemite Falls.
Yosemite Toad Painting
By Daphne Crum, Genetics & Genomics ’23
This piece is a watercolor painting depicting a Yosemite Toad. When I first arrived in Davis I knew I wanted to find clubs and organizations that would provide opportunities for me to do a bit of scientific illustration. When I became a member of the Society for Conservation Biology Chapter at UC Davis, I was ecstatic to learn that their Education and Outreach Committee was already looking for artists in the community to provide visuals for their video about Dr. Leslie Roche and her research on the Yosemite Toad (Anaxyrus canorus). I was more than happy to spend a weekend during the 2019 Fall Quarter to paint and submit a piece for their project! Watercolors are a great medium to use for painting animals because you can layer with varying color intensities to illustrate different textures in their skin. Being able to artistically interpret the significance of scientific research is something I have always wanted to dive into, and it would be such an honor to continue working with other lab groups and researchers on campus who are in need of hand-drawn or hand-painted visuals to pair with their publications.
Parity
By Emily Donnelly, Neurobiology, Physiology, and Behavior, ’21
Macro image of a brightly colored flower in the Arboretum of UC Davis main campus
This photograph is unique for many reasons including the fact that it was taken here on the UC Davis campus in a flower garden by the Environmental Horticulture buildings. This was originally taken for a photography class here at Davis: SAS 40, which focuses on bridging science and art and emphasizes the balance of chaos and order seen in nature. This particular flower captured my attention because even though it is asymmetric, to the human eye it looks perfect. The intense reds and full body of the flower reflect the natural beauty that often goes unappreciated in nature. While photographing, I framed the image in such a way that the center position of the flower draws you into it. A full blossoming flower such as this often symbolizes growth and prosperity which is something that so many students and people alike strive for. So although this is just an image of a flower, it has deeper symbolic meanings depending on the viewer.
This image was taken April 12, 2018 here at UC Davis.
The camera used is a Canon 60D with an 18-200mm lens.
Natural Beauty
By Emily Donnelly, Neurobiology, Physiology, and Behavior, ’21
View of Yosemite’s famous Half Dome from Glacier Point
This spectacular image was taken from the ledge of Glacier Point trail in Yosemite National Park, overlooking the iconic 8,844 foot tall half-dome granite rock, which is such a historical and symbolic part of this natural landscape. The rugged rock formations that make this terrain so beautiful were formed 65 million years ago and then were shaped by glaciers that moved through the landscape, creating the sheer rock faces and wide valleys and lakes that we see today. I chose to take this photograph in black and grey rather than color to allow the natural textures and composition of nature to be delicately exposed. This allows the viewer to focus on the details of nature and true depth of the image, however a camera lens comes nowhere near close to capturing the true beauty of this breathtaking landmark.
This was taken August 19, 2019 when I went to visit Yosemite for the first time with my family. The camera used is a Canon 60D with an 18-200mm lens.
In the future I hope to visit Yosemite many more times as it is truly the most beautiful place I have been.
Potential Methods of Life Detection on Ocean Worlds
By Ana Menchaca, Biochemistry and Molecular Biology ‘20
Author’s Note: As a biochemistry major who is interested in pursuing astrobiology research, I initially wrote this literature review for an assignment in my Writing in Biology course. Methods of life detection and what we know about life is a field in which we still have much to discover and explore, given Earth as our only example, and I hope to be involved in this exploration myself in the future.
Abstract
Ocean worlds, such as Enceladus, Saturn’s largest moon, provide intriguing environments and the potential for life as we continue to explore the Solar System. Organic compounds have been discovered in plumes erupting from the moon during flybys and point towards the presence of amino acids and other precursors of life. The data collected from these flybys, in turn, has been used to calculate the theoretical amounts of amino acids present in the oceans of Enceladus. While this data is intriguing, it relies on a limited definition of life, based on organisms and macromolecules that have only been observed on Earth. Other methods, including using nucleic acids or nanopores for detection, have been proposed. Nucleic acids utilize binding to identify a broad spectrum of compounds, while nanopores utilize the measurement of ionic flow. These alternative methods allow for a broader spectrum of compound detection than terran-based methods, creating the potential to detect unfamiliar kinds of life. Research into more holistic detection should continue.
Keywords: astrobiology, life detection, planetary exploration, biosignatures
Introduction
The search for life elsewhere in the Solar System is becoming increasingly relevant, and more importantly, feasible. Icy moons, such as Europa, Titan, and Enceladus, have been identified as holding the greatest potential for extraterrestrial life within the Solar System [1]. Europa and Enceladus, with seas below icy crusts, have geysers with unidentified fluctuations, along with evidence of tidal warming and geologic activity [2]. The Cassini spacecraft identified these geysers on Enceladus during flyby in 2006, spouting from four specific fractures on the surface of the moon [3]. Analysis of the vapors produced show that they mainly consist of water, along with CO2, N2, CO, CH4, salts, other organic compounds, and silica particulates [3, 4]. This points towards evidence of hydrothermal activity, the movement of heated water, which has the potential to provide necessary energy for life [4]. Additionally, the discovery of volatile aliphatic hydrocarbons in these plumes potentially indicate some degree of organic evolution within the seas of Enceladus [4].
However, there is no consensus yet on how to detect and identify life [1, 2]. Some scientists propose looking for life based on the shared ancestry hypothesis, which proposes all life shares the same genetic ancestry [2]. Others propose there is a potential for extraterrestrial life to present variations from terran life that we may neither be able to recognize nor detect with our current methods of biochemical detection [5]. Experimentally, the potential for nucleic acids based on different backbones has already been identified [5]. Here, we examine the range of proposed methods for identifying extraterrestrial life.
Proposed theories and methods based on current knowledge of life
Collection of amino acids
Current data collected from Enceladus’ plumes presents organic compounds that provide potential evidence of amino acid synthesis taking place in the oceans of the moon. Steel et al. used the thermal flux at the moon’s South Polar Terrain (SPT) to predict the hydrogen produced by hydrothermal activity. The predicted rates of production ranged between 0.63 and 33.8 mol/s of H2, and from there, amino acid production rates were estimated to be between 8.4 and 449.4 mmol/s [4]. Annual biomass production was also modelled in these calculations and estimated at 4 · 104 to 2 · 106 kg/year, compared to 1014 kg/year on Earth. These estimates, however, are dependent on the environment being an abiotic, steady state ocean; the actual production rates could be different if there is life present in Enceladus’ ocean [4].
While this limits our predictions of Enceladus’ true environment, it still provides a basis that can be extrapolated for use in the design of modules to be sent out. One such module that has been proposed is the Enceladus Organic Analyzer, which is designed to analyze amino acids through chain length variations [3]. To properly collect and analyze the amino acids proposed to be in Enceladus’ oceans, there are several requirements. The sample must be collected from the subsurface ocean with minimal degradation, isomerization, racimerization, and contamination of biological molecules and amino acids [3]. A collection chamber made of aluminum has been modeled, designed to reduce the thermal heating caused by collection of samples, in order to best preserve them. If the moon contains bacteria as postulated, this design will lyse and kill collected cells through either heat or shock but release their more stable chemical components for analysis [3]. This depends highly upon current knowledge as a starting place, focusing with a limited scope on amino acid and cell identification. Another such method using cell identification is digital holographic microscopy.
Digital holographic microscopy
The development and improvements of microscopy, while beneficial, depend heavily on the assumption that life in the same form as terran cells will be found. Investigators propose digital holographic microscopy (DHM) as a more efficient alternative over traditional light microscopy [1]. This technology produces a 100-fold improvement in the depth of field and is able to monitor both intensity and phase of images. However, even with the increase in resolution, differentiation of cells and cell-shaped structures is difficult, even before taking into account potential differences in extraterrestrial life. Refraction, an emerging field, was able to differentiate experimentally between crystalline structures and cells in the study’s Arctic samples. While the technology can be miniaturized and discriminate between cells and minerals, it depends highly on actual capture of a sufficient number of cells from plumes. This experimental data was obtained using dye-less techniques, which still function in the context of organisms without DNA or RNA, and refraction with the potential to differentiate structures [1]. DHM is both useful for detection of cells based on collected data and for the potential discovery of organisms without nucleic acids as we know them.
Expanding outside the current knowledge of life
Detection using nucleic acids
Other experiments and proposals, while not explicitly targeting life outside the current perceptions, propose a more holistic collection of data. This carries the potential of identifying life outside our current scope, as opposed to focusing directly on known amino acids and cells. Using a broader concept of nucleic acids as a means of detection and identification is one such method.
Oligonucleotides, through forming secondary and tertiary structures, have specificity and affinity to a wide variety of molecules, both organic and inorganic [2]. Even at a length of only 15 base pairs and within complex mixtures, these molecules can bind to what is being analyzed, or the analytes. Systematic evolution of ligands by exponential enrichment (SELEX) is a process that can identify oligonucleotides that bind very specifically to analytes. However, this method proposes the use of low affinity and low specificity nucleic acids that are typically discarded in this process. Unlike antibodies, this method requires no prior knowledge of the surface attributes or the three-dimensional structure of the molecule that is being bound. Through accumulating a wide range of binding sequences and statistical analysis, a vast number of compounds can be collected and environmental variations identified. Additionally, this method posits that the optimal means of capturing sequences is through proximity ligation assay (PLA), a technique currently used in scientific fields. PLA purifies the binding species based on ligation and amplification, producing a lower background than sieving, which separates based on size. It is also capable of capturing a vast range of sequences and structures, including inorganic, organic, or polymeric molecules [2], and thus is more capable of providing holistic results.
Nanopore-based sensing
Nanopore-based sensing, presented as an alternative to current methods, detects and analyzes genetic information carriers in watery systems without making assumptions about its chemical composition [5]. This system relies upon the restrictions placed on these sorts of compounds within watery systems, as the repeating charge of backbones keeps polymer strands from folding and favors solubility in water. A nanopore is a hole with a diameter of a few nanometers, surrounded by an insulating membrane within two chambers containing an electrolyte solution. Due to its diameter, only single-stranded DNA can pass through the nanopore, allowing for slow movement and characteristic signals that produce data clearly distinguishable from other molecular data. This method can detect and analyze molecules by measuring the ionic flow across the membrane. While biological nanopores are able to detect and resolve individual terran bases, nonbiological, solid-state nanopores provide the same function, avoiding the limitations of detecting terran molecules that may be present in biological nanopores. Graphene, with its crystalline form, can have its membrane adjusted to only accommodate one nucleotide at a time or can be sculpted to produce varying sizes of nanopores. This could allow for the detection of other polymers with chemical and sterical properties that vary from currently known polymers. This approach has the potential to analyze a broad range of molecules without any assumptions regarding the external structure’s outside charge and linearity. Few identified nonbiological polymers are structured this way, so any data picked up by nanopores would be significant [5].
There are, however, limitations to this approach. Nucleic acids have high electroporation speeds, making it necessary to find methods of slowing these speeds down for accuracy [5]. Electroporation uses an electrical charge to make the cell membrane more permeable. Potential methods include control through physical factors, such as temperature, salinity, and viscosity. Conditions of collection on other planets also pose the problem of extreme dilution of the target molecules, which depends on a large number of variables [5].
Conclusion
Radiation and stability are major concerns in moving forward with any sort of data collection from extraterrestrial worlds. Mechanisms and samples are potentially open to the detrimental effects of extreme vacuum and solar radiation [5]. These problems should be addressed in conjunction with the technology actually being used for analysis to produce the most beneficial results. Some of these issues have been addressed to some extent, such as using microfluidics for collection because they are unaffected by the vacuum of space due to their own internal surface tension [3]. However, these problems need to be explored further in all cases to ensure that each method can function in uncontrolled or non-terran environments.
The presented data indicates potential for the existence of amino acids in these environments. Even though prediction and detection of these amino acids seems a logical step forward, the development of further, broader technology for life detection should also be pursued. Current knowledge is limited by the qualities of terran life; while that is a well-supported starting point, methods that leave open the potential of deviation from this point may allow for the detection of otherwise overlooked forms of life. Moving forward, it seems only logical to combine these methods that can detect both the known and the unknown, allowing scientists to gather the widest possible array of data in future missions, especially on promising worlds like Enceladus.
References
- Bedrossian M, Lindensmith C, Nadeau JL. 2016. Digital Holographic Microscopy, a Method for Detection of Microorganisms in Plume Samples from Enceladus and Other Icy Worlds. Astrobiology 17(9):913–925.
- Johnson SS, Anslyn EV, Graham HV, Mahaffy PR, Ellington AD. 2018. Fingerprinting Non-Terran Biosignatures. Astrobiology 18(7):915–922.
- Mathies RA, Razu ME, Kim J, Stockton AM, Turin P, Butterworth A. 2016. Feasibility of Detecting Bioorganic Compounds in Enceladus Plumes with the Enceladus Organic Analyzer. Astrobiology 17(9):902–912.
- Steel EL, Davila A, Mckay CP. 2017. Abiotic and Biotic Formation of Amino Acids in the Enceladus Ocean. Astrobiology 17(9):862–875.
- Rezzonico F. 2014. Nanopore-Based Instruments as Biosensors for Future Planetary Missions. Astrobiology 14(4):344–351.