Understanding growth rings in geoduck clams and their historical environmental significance

North Pacific climate recorded in growth rings of geoduck clams: A new tool for paleoenvironmental reconstruction

Robert C. Francis, Nathan J. Mantua, Edward L. Miles, David L. Peterson

Summarized by Baron Hoffmeister

What data were used? Growth chronology (i.e growth patterns that accumulate over years in the shell of the organism, similar to tree rings) of geoduck clams (see figure 1) collected in Washington, USA were used to reconstruct sea-surface temperatures (SST) in the Strait of Juan de Fuca.  

This is an image of a geoduck. These are known to have life spans lasting over 165 years. From How Stuff Works.

Methods: This study used growth ring data in geoduck clams to determine how sea surface temperatures affected the shell growth (something called “accretion”) within these organisms over their life span. 

Results: Geoduck clams are a part of the class Bivalvia (i.e., a marine or freshwater mollusk that has its soft body compressed by a shell; this includes other organisms like snails and squids). These organisms produce their own shells, and the shells continue to grow as these organisms age (unlike organisms like mammals, who stop growing at a certain age). The shell accretion of these organisms can be observed under a microscope from samples of the shells. These are called growth lines and the spacing in between lines indicates how much new shell material the organism produced during a certain period of time (see figure 2). The growth lines of the geoduck clams found within Strait of Juan de Fuca correlated strongly with sea-surface temperatures. Researchers found that when the water was warmer, more growth was observed. This is common for a number of marine bivalves, and these proxy methods help construct a better understanding of sea surface temperatures from the past. 

The top panel is an SEM micrograph of the ring structure in a 163-year-old geoduck clam. An SEM is a scanning electron microscope that uses a focused beam of electrons that interact with the sample and produce signals that can be used to collect data about the surface composition and surface structures. The bottom panel shows the growth index (solid black line) with local air temperatures (dotted line) from 1896 to 1933. From 1900 to 1910, shell accretion correlated with warmer air temperatures.

 

Why is this study important? This study helps reconstruct environmental conditions and researchers can use this data in conjunction with other climate proxies to better understand how current climate patterns and ocean temperatures can affect marine ecosystems in the North Pacific basin.

The big picture: This study is important, not only for creating a more cohesive climate proxy database, but also indicating that shell accretion in specific marine organisms can provide important climatic data. Bivalves have a large geographic range and the data collected from these organisms through shell accretion studies can allow us to have a better understanding of historic climate conditions worldwide. 

Citation:

Francis, R. C., Mantua, N. J., Miles, E. L., & Peterson, D. L. (2004). North Pacific climate recorded in growth rings of geoduck clams: A new tool for paleoenvironmental reconstruction. Geophysical Research Letters, 31(6).

Data Management

Jen here – 

I started a job as a Research Museum Collection Manager in September and a large part of it is specimen based. I handle donations, reconcile loans, look for specimens for researchers, organize the collection, and manage other types of data. Now that my job has moved to largely remote I wanted to share some of the things my museum techs and I have been working on to keep our projects moving forward. 

When we think about museums we immediately think of the beautiful displays of mounted dinosaurs and ancient deep sea dioramas that transport you through time. However, there are many research museums that are essentially libraries of life (thanks, Adania for that phrasing). Similar to libraries with books, these institutions hold records of life on Earth and they are massive. At the University of Michigan Museum of Paleontology we have over 2 million invertebrates, 100 thousand vertebrates, and 50 thousand plants. Each of those specimens is tied to other records and data!

Specimen Database

Digital databases allow for the storage of data related to the specimen including location, time period, taxonomy, rock formation, collectors, and much more! Depending on the type of database the structures are slightly different but the overall goal is the same: create an easy way to explore the specimens, see what is on loan, where they are located in the collection, and if they are on display!

Databases, like regular software, get updates over time. The database I’m working in was started ~10 years ago and there have been a lot of updates since then so we are working to upgrade the way the data are organized. For example, now there are different fields that didn’t exist before so we are making sure the data are appropriately entered and then fixing these fields. We are also digitizing our card catalog to verify that the specimen data in the database matches the physical records. We have three card catalogs: Type specimens, Alphabetical taxonomic groups, and Numerical. I spend time scanning in these cards and my museum techs help transcribe and verify the data with our other records. 

Example of a card from the University of Michigan Museum of Paleontology invertebrate card catalog. Many are typed index cards with information on the specimen.

I have quite a few donations that have new specimens that need to be put into the database. To do this, I format the dataset and upload it to the database. Seems straightforward but it takes some time and isn’t the most fun task so I have a stockpile of them to get through while I continue my remote work.

Loan Invoices

One of the tasks we had started before the COVID-19 crisis was to digitize our loan documentation. We have documentation for specimens that we loan out to other institutions, for specimens we bring in to study, and any transfers that may occur. This information had not been digitized so our first step was to scan the paperwork and transcribe key information such as: Who were these specimens loaned to? How many specimens were loaned? Were specimen numbers listed? Where these specimens returned? 

We now have a large spreadsheet which now allows us to search this information rapidly. For example, when we are working in the collection sometimes we find specimens with paperwork or that are out of place. Now we can search the number, see if they were on loan, and make sure we close this loan as being returned. In some cases, we cannot find specimens so I have to reach out to colleagues at other institutions to see if they have a record that the loan was returned. Then it’s up to us to find the specimens in the collection and get them into their proper storage places.

Three-Dimensional Fossils

The last big project we are working on is to get new fossils ready for our online fossil repository: UM Online Repository of Fossils. This involves some on site work at the collection space and lots of post-processing of the fossils. We use a camera to image a fossil from many angles (photogrammetry) and then stitch the photos together to create a three-dimensional fossil. If you are interested in our protocol and set up please check out our website by clicking here. Most of this work has been done by me alone but I am working on ways to incorporate our museum techs into different aspects of the process that can be done at home, such as cleaning the output model and orienting the specimen for final display on the website. Check out our most recent invertebrate addition: Hexagonaria percarinatum.

Example of a species profile on UMORF! Click here to head to the page and explore the viewer.

Marie Boirot, Biologist & M.Sc. candidate in Palaeontology

What is your favorite part about being a scientist? My favorite part is discovering something no one ever discovered before. It is exciting to know you are the first person seeing what you see ! There is so much left for us to discover. Something we take for the absolute truth today may be proven inaccurate in ten years. Science is constantly evolving, so we will always have a job! Also, the scientific and academic background are really helpful to develop the critical mind and not fall for answers too simple to be true (conspiracy theory, yay!).

What do you do?
I am finishing my wildlife management master’s degree under the supervision of Richard Cloutier at the Palaeontology and Evolutionary Biology Lab (at the Université du Québec à Rimouski, in Québec, Canada). My project consists of scanning fossil fishes skulls to see what’s inside! I work with super cool fishes, the lungfishes, that still exist today and are closest relative to all terrestrial vertebrates (amphibians, reptiles, mammals and birds)!  My species are more than 380 million years old, that’s more than 130 million years BEFORE the first dinosaurs! I work on 3D-preserved skulls, which is relatively rare in fossils. I scanned them to see if their braincase was ossified or not, and their description helps untangle the relationships between fossil lungfishes !

How did you get interested in your current research project?
I met Richard during an undergraduate evolutionary biology class and he mentioned that he worked on lungfishes. I’m a big fan of lungfishes, particularly Neoceratodus, the Australian lungfish (it is too cute, it looks like it smiles all the time !) and I really enjoyed Richard’s class and way of teaching. As a joke, I told my brother that I would do a master with him (I wanted to do an oceanography master’s degree initially), but eventually I did ask Richard to join his lab! I followed my instinct rather than the thing I “was supposed to do” and I don’t regret it. He offered me several projects and I chose this one! I had never done palaeontology before, it is really challenging but so much fun to learn a whole new biology discipline.

What are your data and how do you obtain them? My material is five skulls of the lungfish Scaumenacia curta, endemic to the Escuminac Formation, in Miguasha, Québec, Canada, and one Pentlandia macroptera specimen, from the Orcadian Basin, in Scotland. I scanned the specimens with a micro-CT scan, which uses the same technology as a X-ray scanner at the hospital. Then I segmented on a computer my scans, which basically means I colored the interesting structures with a graphic tablet, and I extracted a 3D-model. For Scaumenacia, thanks to a peculiar preservation process called pyritization, I had enough information on the braincase to code for phylogenetic characters and add it to a matrix. The matrix is from Clement et al., 2016, and we modified it a little bit. It is really fun to do the process myself, from the enigmatic skull to a phylogeny including my data on the inside of this skull.

(Clement, A. M., Challands, T. J., Long, J. A., & Ahlberg, P. E. (2016). The cranial endocast of Dipnorhynchus sussmilchi (Sarcopterygii: Dipnoi) and the interrelationships of stem-group lungfishes. PeerJ, 4, e2539)

How did you learn about the palaeoVC? What did you take away from the conference? I learned about it during a lab meeting in January I think, and since I was finishing my results it was a wonderful opportunity to present them, even more with the coronavirus resulting in all physical conferences cancelled. I learned that it is possible to use palaeontology as an education tool for children and that it actually works! We often think fundamental science is “useless” in everyday life but it is really important to continue to expand our knowledge and more importantly to share it with non-scientist people! Also, the idea of a virtual international congress was really ahead of its time! Beside the corona crisis, the carbon impact of an international meeting is enormous, and we often don’t have time to see all the presentation we want. It is really clever to do this virtually.


How does the Coronavirus pandemic affect your research and academic life?
I finished writing the first complete draft of my thesis during the first two weeks of lockdown! All my social implications being cancelled, I had no other choice than write all day ! I did not have to go to the lab anymore so it did not stop me from working, even if I missed the university routine and separating work from home. I don’t have to complain, because many of my colleagues had to stop their researches because they did not have access to the equipment, and I can only imagine how frustrating it can be. Another meeting I was supposed to go to was cancelled, I am disappointed but it could have been much worse ! I could present here and it was a wonderful opportunity.

What advice do you have for aspiring scientists and other early career researchers?
My first advice would be: do not do that for anyone except yourself. Science and research can be really challenging and you have to have a motivation and desire to learn to get through an entire 2-3-4 years project. Do not do it to prove something to someone, but because you really want to try it. On the other hand, if you really want to try doing research, go for it and do not let anyone tell you you are not good enough ! Passion is the only fuel, and there is no feeling like seeing your first results, getting a R script to work, or presenting your research!

Follow Marie’s work through her lab’s Facebook Page, her ResearchGate, or contact her via email (marie.boirot@ uqar.ca).

Marie is one of three early career paleontologists who won for best presentation at the 2nd Palaeontological Virtual Congress in 2020. Read more about the Congress here!

Kailey McCain, Interdisciplinary Natural Sciences Undergraduate

Kailey hiking in the Nantahala National Forest in December, 2019.

Hello, my name is Kailey and I’m a Junior at the University of South Florida majoring in interdisciplinary natural sciences, with an emphasis on geology, chemistry, and biology. Most people are surprised by my degree, and I get a lot of questions about the interdisciplinary aspect. As a future scientist, I believe it is critical to have an interdisciplinary approach to solve problems. Sir Francis Bacon, developer of the scientific method, urged not only scientists, but all people, to remove the lens they look at problems through and take into consideration the myriad of perspectives. To me, my degree embodies that. 

Upon graduation I plan on pursuing a PhD in ecology and evolutionary biology and my research interests are centered around dissecting the effects anthropogenic factors, or human activity, have on disease prevalence and transmission. 

What is your favorite aspect about being a scientist?

Graphic explaining the difference between primary (original research) and secondary evidence (syntheses, summaries).

Growing up, I always had an insatiable curiosity about life and our world. That curiosity has ranged from why we have an atmosphere to how human activity has caused harm, not only to our climate, but to all of ecology. I found that studying natural sciences challenges me, but rewards me by answering those questions.

Another aspect of science I love is the community that being in the sciences gives you! As a young woman, it is incredibly motivating to see such a diverse set of individuals working towards one common goal: expanding the knowledge of humankind. Before I immersed myself into the community, it was hard to see myself as a scientist. This was due to a lack of representation of female scientists; however, now I know that I can be whoever I want and I hope to show other young girls that too.

As to how I got interested in science, I originally went into college as planning on pursuing medicine,  but after taking a history of life course through the Geosciences department, my whole trajectory changed. I suddenly found myself so excited for the lecture and I started asking questions that didn’t have concrete answers, and that captivated me. I always wanted to help people and the world, and becoming a research scientist seemed to fit that more so than anything else.

How does your research and education contribute to the understanding of climate change and to the betterment of society?

By studying the ways in which human activity affects wildlife diseases, scientists are able to predict what our future world will look like, attempt to change the trajectory of diseases, and protect some of the world’s most amazing ecosystems. I also think it’s important to expand on this catch all term “human activity”. This can include, but is not limited to, deforestation, climate change, light pollutants, and habitat fragmentation. All of these actions are intertwined in how we look at protecting the world’s ecosystems, while still allowing for human development.

3D scan of Gyrodes abyssinus, which is Late Cretaceous in age (~100-66 million years ago).

What are your data, and how do you obtain them?

I am currently working on a systematic review of all the meta-analyses (I’ll explain what this means below) on Toxoplasma gondii, which is a type of parasite that is predominantly found in cats and humans. The data collected for this study is not found in the field or even the lab, but in other scientific publications, which is why we call it a meta-analysis! My job is to find all studies that are relevant and point out potential positive correlations between the data for other researchers to explore further.

I am also currently interning at a 3D visualization lab scanning paleontological collections (fig. 2)! The purpose of 3D scanning is to digitize collections that can be shared to people all over the world.The softwares utilized are Geomagic Wrap and Zbrush.

What advice do you have for aspiring scientists?

My advice to aspiring scientists is to not give up! As an undergrad, is it incredibly difficult to remove this level of perfection we place on ourselves, but it is necessary. Everyone has messed up, everyone has failed a test, and no one is perfect. Your well being and mental health is more important than any grade. 

Another piece of advice is to always try. There have been countless opportunities that I could have had, but I was too scared of rejection. At the end of the day, rejection is a part of life (especially the academic life).

 

2nd Palaeontological Virtual Congress

This year was the second iteration of an entirely online conference, Palaeontological Virtual Congress, open to abstract submissions from anyone studying paleontological sciences. A broadly accessible conference as the digital means provides increased access to scientific content. There is flexibility with file format, presenters can be visible on camera augmented by images and slides edited into the video, upload their slides without an overlaying audio, or walk through their slides while providing audio narrative. 

Talks can be uploaded as recorded .mp4 and like files by the presenters prior to the conference and then the content is available for two weeks for attendees to view and comment on through the WordPress site. The organizers answered some questions for us on the event:

Who organized this event? The organising committee was formed by 10 people, with 3 professors (Carlos Martínez-Pérez, Evangelos Vlachos and Paolo Citton), 3 post-doc, and 4 pre-doc students. In the first iteration of the congress, it was expected there would be around 100 participants, and the final attendees were near 376. This year there was a total of 161 projects presented and 398 participants from 44 different countries.

Were there any issues with the COVID-19 crisis? This congress was first made having in mind only online mechanics, so the Corona crisis did not change how the congress work. But we have noticed an increase in the media exposure that this congress has achieved, and also, a biggest interaction in the participants during the congress and outside the congress. Specially, the congress has been very active in Twitter and the interactions with the palaeontological community in this social media has increased in this edition.

What do you take away from the congress? What did you especially like, and what would you do differently next time? We created this congress as an opportunity for those palaeontologists that do not have enough resources to go to most (or any) palaeontological congress. For that reason, the members of the organizing committee don’t take anything away from the congress… apart form stress! We are proud of the work we have done these two editions, and we are awfully glad of the way the palaeontological community has welcomed this congress, so we can say that that is our award.

Some of the aspect that we like the most about the congress are the video presentations and the virtual field trips. People can be highly creative when given the opportunity to present their work with the video presentations, and the virtual field trips are a nice way to expose interesting places that would not be known otherwise.

We are still struggling making the interactions between the participants as “natural” as possible. This edition, the comment section for the different works have been very active, and we have seen very interesting debates in some of them. This is a problem if you think that we have participants from all around the globe, and our time zones don’t match; but we are sure that we will be able to overcome this for the next edition.

Will there be a 3rd PalaeoVC? Yes, of course!  We want to rest for a bit, so it is most possible that we will have the 3rd edition by 2021, although we still cannot tell for sure about the dates.

Click here to read the Nature Ecology & Evolution paper on “Virtual conferences are the future” by Abel Barral.

This year, there was an Early Career Session to highlight the work of early career paleontologists. Time Scavengers team member, Jen Bauer, was invited to aid in judging the session and as a result the winners selected from this session will be promoted via Time Scavengers Meet the Scientist blog.

Congratulations to Marie, James, and Thomas! Follow the PalaeoVC tag on Time Scavengers to see their posts.

Follow the updates for future PalaeoVC events on their website, Twitter, or Facebook.

Anxiety in Academia

Andy here-

A few weeks ago an undergrad tweeted that their professor had told them they shouldn’t go to grad school if they were having anxiety attacks because they wouldn’t be able to handle it. I replied that it’s doable but difficult. I want to elaborate. I’m trying here to be as specific and open about my experiences as I can. The beginning of this post is a narrative about how my disorder has impacted my career and life, and the bottom is hopefully some helpful tips I’ve found over the years.

I was diagnosed in undergrad with a Generalized Anxiety Disorder, as well as Scholastic and Social Anxiety disorders. When I was diagnosed they said that in part it was because of life circumstances but also because “some people just have jumpier nervous systems”. I have a family history of extremely severe anxiety; mine is not as bad as that relative, though it has impacted my life and career. I’ve been on anti-anxiety drugs (SSRIs, which are also used to treat depression) twice, once in undergraduate and I just restarted them a few weeks ago. I’ve been in therapy and counseling twice, once in undergrad and then again starting soon.

Educational & Professional Life

I failed out of college when I was a freshman/sophomore. This was largely because I had never learned to actually work in high school because I could just coast through. I was advised as a college freshman, because I was good at science, to take the extremely accelerated track at the University of Wisconsin (UW). Taking Organic Chemistry as a freshman with no study skills is a bad idea. After failing out of college I took a few classes at a community college, worked a job where I was stuck in the back of a large room entirely by myself, and retreated into online gaming. Coming back from all that was difficult. I went from not socializing for a full year to being back in large 300 person lectures. The only reason that I ended up in graduate school was because my advisor at UW took a chance on me; my grades were below the minimum for admission. Months of therapy (talk and group) helped some. A part of this experience failing left me with intense impostor syndrome which amplifies aspects of the anxiety disorders (Impostor Syndrome in Graduate School)

I had my first migraine in graduate school. I had just given a presentation to my group that I had been really worried about, and got a migraine on the way home. It became a thing, a massive release of stress and then a migraine. The second one had me go to an Urgent Care facility and put on morphine because of the pain. Medication has helped, but also meditation. My anxiety and stress levels are linked, and so the migraines seem like they’re a manifestation of the anxiety.

One of the things about academia is that every new level brings an additional layer of stress. During my PhD things became more intense again. I never felt like I was accomplishing enough each day, even though I would get to work at 7 or 8 AM and then leave at 5 PM, working once I got home. I was working flat out during those days as well, trying to accomplish as much as I could. I couldn’t shut my brain off once I was trying to get to sleep, so I would be awake for hours. Susanna (my wife) eventually suggested that I stop working at 8, force myself to shut down and take time before going to sleep. I also started to meditate before bed, repeating the thought, “I got enough done today.” It helped. I also accomplished more during the day. Your brain needs downtime, just like the rest of you does.

One persistent feeling is that my accomplishments are not my own. This is a part of impostor syndrome, but it’s also a part of anxiety. I still cannot shake the feeling that the postdoc I had at the National Museum of Natural History was because the curator I worked for wanted a specific speciality and he was friends with my PhD advisor, it wasn’t because of me as a researcher. I know that’s not the case because I got another prestigious fellowship 10 days (Newton Royal Society) after I accepted the NMNH fellowship, one that I can’t figure out how to tie completely to another’s success or rank. I remember having thoughts, though, trying to figure out a way to make it not my victory, but something I got because of another person. My second postdoc I got because I had the specific skills in data analysis they wanted. I know that’s an aspect of me as a researcher, but it feels like luck. Something outside my control. My fellowship feels like it was because my postdoc supervisor is a part of the committee, but I know she was out of the room when they discussed my ranking and selection. I either feel that my accomplishments are because I knew somebody that thought I needed help or I was lucky.

Conferences & Meetings

Networking at meetings is tough. My social anxiety is strongest with people I perceive as ranking above me. As a graduate student, talking to prospective advisors was next to impossible. So is doing the talking with mid or senior level scientists as an Early Career Researcher. It means that my involvement in certain projects is behind where it would be if I were able to network better.

Being at meetings is also exhausting. My social anxiety is best explained in analogy to a chemical reaction. I can switch to a more extroverted person temporarily, it just takes a lot of energy. If you think about a chemical reaction, there’s a certain activation energy needed to promote the reaction. If the reaction is initiating a social interaction, for an extrovert it’s lower, in an introvert it’s higher. For me, a person with social anxiety, it’s higher still, because I can feel my fight-or-flight reaction start when I am meeting another person in a meeting context. Because a meeting is a sustained version, I haven’t come back from a meeting in years without catching some kind of cold. Being in therapy makes this even more apparent. After a first session describing previous issues, why I was seeking help, I was ‘keyed-up’ and having an anxiety attack for the next several hours. I was unable to even look my wife in the eye without having an anxiety/adrenaline response.

If it feels like I’m describing all of this in an over intellectualized way, I am. I’ve done this for years to try and take all the emotions I can out of thinking about this because it helps reduce my anxiety levels. Just writing about this is difficult.

Interviewing & Teaching

Having anxiety means that your self perception is off, at least for me. I almost always feel that job interviews go horribly. The worse I feel the better they seem to go. I was completely convinced that I had made multiple fatal mistakes during my most recent interview. I repeatedly went over all interactions in my head. I spent hours mulling over all the answers I had given. I worried over what exactly to send in my emails. A lot of that is normal. What isn’t normal is that I had a feeling of panic the entire time. Weeks of utter dread. I felt as if I had let down my family, that I was never going to get a job. I told everyone that there was no way that I got that job. I ended up seeking medical help because I thought that my anxiety was going to cost me another job after this.

The first question I received after my talk is a good example. I had just finished and my first question was about the underlying driver of one of the topics I’d talked about. I have spent the last two years working on this question and have supervised three MSc students on it. I 100% knew the answer to this question. As soon as the question was asked, my mind went blank. The answer I finally gave, in my memory, made no sense. I remember not even speaking in complete sentences, instead in phrases or just words. It actually took me a week or two after the interview to have the answer reappear in my head, it was like my mind decided to protect itself by temporarily hiding that information. It really did just pop right back in my head like it had never been gone. This phenomenon happened again after a trip to the doctor discussing my anxiety. I was biking, made a turn, and ended up biking towards an oncoming car because I could not figure out which lane I was supposed to be in. I’ve been living in the UK for nearly two years and commute via bike every day. It happened last week when my group was talking about minerals somebody asked me what the hardest mineral was other than diamond. It’s quartz, but I made a joke because I didn’t want to say that in case I was wrong. Of course it’s quartz, I know I’m not wrong, but I can’t trust my self-perception of my answers, so I hide behind humor.

I got that job. I had completely given up on it and spent two weeks after they told me I was their top candidate feeling like they had made some kind of mistake. I know that my interview can’t have gone as poorly as I feel like it has, simply because if it went as poorly as I think it did there’s no chance I would be their top candidate. I know some of my competition for that job, they are amazing scientists! That’s really the bottom line of having anxiety in academia. You will intellectually know what’s going on. You’re in a grad program, so you fully know that you’re a smart, hard working person (you are). You will, however, feel that someone has made a massive mistake. In graduate school, I knew that nothing hugely bad would come of having a conversation making small talk, but even right now, as I sit at my kitchen table, I can feel some amount of adrenaline building just thinking about it.

All this might sound like me teaching could be a problem. Because my inability is situational however, I can teach just fine. If I know I’m the most knowledgeable person in the room, all of this goes away. If I perceive I’m the top of the hierarchy or an equal, then I don’t have a problem. My issues also recede as I get used to a new person, or while I’m actively suppressing them. Finding the limits of your disease can help figure out where you can and can’t be at ease. Storing up that energy when you can is vital.

Anxiety can also be useful, with some huge caveats. I have figured out how to use it as a tool in certain situations. When trying to get a grant finished, for example, if I can ride the balance between being worried about getting it all done and devolving into a complete panic, I can be exceedingly productive. It’s hard on me, it means that I work really quickly but can miss important details, and it does not work well if I do it over too many days.

It’s also, lastly, important to recognize that a basic truism of academia: there are not enough jobs and we face constant rejection. The constant threat of the complete impossibility of winning this lottery will be felt constantly. I, my family, went through 5 years of instability with constant worry about where we were going to get a paycheck from in a year, two years, three years, in the future. Anxiety issues are going to make that worse. Having a family means there’s even more riding on everything, because it’s not just you, it’s dependents as well. It’s worth it, but go into all of this with thought. Consider support systems, make plans (that’s what we do well, right? Plan to deal with anything that happens?).

Managing Stress & Anxiety

I want to end this with some things that have worked for me to help manage stress and anxiety. I’ve culled these from discussions with therapists, reading, and talking with other people. I hope they help you as well.

Find somebody to talk to that you trust: I would not be in the same mental state if I didn’t have Susanna to talk things through with. If I’m feeling anxious about something, I talk things through with her. She’ll give me an honest but supportive take on whatever it is. She pushes me to find professional help when I need it. For somebody that finds asking for help to also cause anxiety, that’s important. I know this seems like me saying “oh, just find somebody you love. That’ll fix it.” but it doesn’t have to just be a spouse. Find a trusted friend to confide in, or a parent. A support structure is important in graduate school or academia for anybody, but it’s even more important for somebody with anxiety.

Many universities have counseling services that offer a certain number of sessions with student or credentialed therapists. That’s what I started with at UWisc. The University of Bristol even also has a free staff counseling service. Seeking professional help is incredibly helpful. If you are in graduate school, you should recognize that expertise is important. Just because it’s your head, doesn’t mean that you are the best person to think your way out of your issues. I’ve tried. It does not work, a professional can guide you through the process better than you can do yourself.

Stop working: It’s really easy to fall into the trap that getting more stuff done will solve anxiety problems. It won’t. You’ll get more done for a day, then your productivity will begin to drop off, and that’ll cause more anxiety. Having a firm time everyday that no-matter-what you will stop working lets you take space. You cannot work all the time and be productive. People that say they can are wrong and dangerous. It’s not healthy for you or the others around you. I play first person shooter video games (the modern Wolfenstein series is a favorite), it takes me out of the things that are worrying me at the moment and lets me focus on something external. It’s been an effective catharsis for me. Find something that works for you to distract you from constant barrage of thoughts about work.

I now have two kids, and I trained myself to have fairly intense guilt about working from home. While that’s not great at the moment because of the pandemic, it’s been an effective deterrent to working constantly.

Breathe: I meditated for 15-20 minutes before my PhD defense. I put on a specific song that helps calm or center me, closed my eyes, sat cross legged, and tried to clear my head. I’ve been doing this since therapy after my panic attack. It has helped. I have no idea if I’m even meditating correctly, but find something that works for you. You just need to create some mental space from yourself and your stressor.

Give yourself a break: Recognize that this is going to make graduate school harder. It’s going to make being an academic harder. You will feel the lows more than the highs, and academia comes with all sorts of lows. Rejection will feel sometimes like a gut punch, it’ll make you want to leave. Yes, everybody feels this, but you, a person with anxiety, does not have an accurate self perception of your personal successes. I’ve had several really prestigious positions, PI’d a large multi-institution NSF grant as a postdoc, published in Nature, Nature Ecology and Evolution, and a bunch of other really good journals. I just got a research heavy Assistant Professor position, picked from over >100 people. I constantly feel I will need to leave academia imminently because somebody is going to figure out that I’m not as good at something as I should be. I don’t even know what that thing is. You’re going to feel this too. It’s a part of us. Sit with that thought, identify it, and realize that it’s a feeling and it’s not true to what you intellectually know. But then recognize that it sucks to constantly feel like this. It just does! It’s not your fault.

Figure out your triggers: I mean this in both a positive and negative, find things that make your mental state less and more anxious. Figuring out how to calm yourself down is just as important as figuring out what might lead to more anxious feelings.

I listen to a lot of very fast music (the more I think about my disorders the more I realize it’s completely interwoven into every part of my life), which many people have told me would make them feel anxious. A good example is Animals as Leaders – Tempting Time or Daughters – The Hit. This is what I (used to) listen to when I work. It’s quick, layered, and helps clear out the rest of the thoughts that I have rattling around in my head. But the cacophony can make things worse, so sometimes I have other music (e.g., Imogene Heap) which I can use to calm down. For me it’s about finding that balance between using the anxiety as a tool to get things done and not over doing it.

Drugs: I recently went on Sertraline (Zoloft in the States). So far, it’s helping. It’s tough to say, as I got over the initial increase in anxiety the Covid-19 pandemic really gained speed, the UK went on lockdown, and I received my job offer. While it’s tough to say what’s going on for any of us emotionally, both I and Susanna think that the drugs are helping. Taking drugs isn’t a weakness. Some of us (hello!) literally have nervous systems that react stronger to our experiences. Getting help is important.

If you also suffer from Anxiety and want to talk with somebody who has made it through, please do reach out to me. I’m on twitter (@macromicropaleo) or via email (andy.fraass (atsymbol) gmail.com), or anywhere else you can find me. I’m more than happy to talk or write with anybody about my experiences, your experiences, or just to listen. If you want 5 minutes or several hours, please, really do reach out.

3D Visualization Undergraduate Internship

Hey everyone! It’s Kailey, an undergraduate student at the sunny University of South Florida.

The image shows a specimen, Gyrodes abyssinus, sitting on a mesh block with a scan via geomagic wrap on the screen in the background.

I wanted to take some time and share with you guys an amazing opportunity I was given earlier this year. As any ambitious college student will tell you, internships are extremely important when it comes to choosing a career path. Not only do they grant students hands-on experience in a particular field, but also general time and knowledge in the workforce. Good internships are hard to come by, which is why I was elated when I got the opportunity to intern at the 3D visualization lab at USF! 

And yes, the lab is as cool as it sounds.

For a place where complex research happens daily, the mission of the lab is rather simple: to harness 3D scanning equipment and data processing softwares. These technological tools have been a wonderful addition to the arts, the humanities, and STEM everywhere, as it has not only supported, but completely transformed, the research in these worlds. This dynamic lab embodies the philosophy of open access research and data sharing, meaning that scientists and researchers from all over the world are able to use its different collections and visit historical sites from the comfort of their homes and offices.

This image shows the Faros arm scanner extended.

My job at the lab was to scan and process some specimens from the department of geosciences’ paleontological collection. The first step in this process is to use a laser scanner and scan my object in various positions (figure 1) using the FaroArm scanner (figure 2). This bad boy has three different joints, making the scanner move around any object seamlessly. The FaroArm also has a probe with a laser, which is essentially taking a bunch of pictures of the object and overlays them. An important note is that these “various positions” need to be easily and manually connected in a software called Geomagic Wrap; therefore, every scan must seamlessly match up like a puzzle! This was probably the most difficult thing to learn, as you not only must think more spatially, but pay close attention to the small, yet distinguable,details, like contour lines and topography (figure 3). In some cases, these small details mean the most to research scientists by showing things like predation scarring and growth lines.

This image shows a close-up shot of the contour lines and topography on the 3D model.

Once the scan is connected and we have a 3D model, the file is switched to a different software called Zbrush. This is where the fun and creative aspects come in! Zbrush allows users to fill in any holes that appear in the scan and clean up any overlapping scan data. This happens when the scans aren’t matched up properly in Geomagic. Next, we paint texture onto the model using different pictures of the fossil. Then, voila, you have a bonafide 3D model (figure 4). The model shown in figure 4 is of Gyrodes abyssinus Morton, a mollusc from the Late Cretaceous. 

I completed a total of three data scans and processes, but was cut short due to the coronavirus pandemic. While my time at the lab was short, I learned so much in terms of technical skills and problem solving. However, the most notable thing I learned was just how interdisciplinary science and research operates at the university level. Networking with archeologists, geologists, anthropologists, and so many more opened my eyes to the different fields contributing to the research world. The experiences I gained at the 3D visualization lab will follow me through my entire academic career.

This is an image of the final 3D model of Gyrodes abyssinus with coloration and texture.

You can visit https://www.usf.edu/arts-sciences/labs/access3d/ for information on the 3D lab and visit https://sketchfab.com/access3d/collections/kailey-mccain-collection to view the rest of my collection.

How Climate Change Impacts the Mortality Rate of Latin American Frogs

An Interaction Between Climate Change and Infectious Disease Drove Widespread Amphibian Declines

by: Jeremy M. Cohen, David J. Civitello, Matthew D. Venesky, Taegan A. McMahon, Jason R. Rohr

Summarized by: Kailey McCain

What data were used? 

This study combined laboratory experiments, field data, and climate records together to support their hypothesis that amphibians have a higher mortality (death) rate when exposed to warmer temperatures, this is known as the “thermal mismatch hypothesis”

Methods: 

Atelopus zeteki or the Panamanian Golden Frog in their natural habitat.

The laboratory experiments consisted of a temperature gradient and a temperature shift experiment. Both experiments exposed an endangered captive frog, Atelopus zeteki or the Panamanian Golden Frog, to a disease causing fungus, Batrachochytrium dendrobatidis, and measured the rate of death. The temperature gradient gradient slowly increased the temperature, while the temperature shift experiment exposed the frog to the fungus at specific temperature units: 14°C, 17°C, 23°C, or 26°C.  

The data was then compared to field data collected from the International Union for Conservation of Nature red list database to observe a real time decline in a total of 66 species of frog. The geographical range for the field data was limited to Latin America and the rate of decline was compared to historic monthly climate data.

Results:  

The results of the temperature gradient and temperature shift experiments show that mortality increased when the infected frog was exposed to higher temperatures. However, it also shows that temperature did not affect the mortality rate of the control group, the non infected frogs. As for the field data collected, the results showed that the frogs’ decline could not be correlated to precipitation nor altitude, but climate change, the thermal mismatch hypothesis clearly  predicted an increased decline of the species.

Figure A represents the data collected for the temperature gradient experiment and shows a linear decline in survival time with an increase in temperature. Figure B represents the data collected for the temperature shift experiment and shows the different temperature units plotted by the proportion alive versus time. The graph indicates that the warmest temperature has the lowest survival rate.

Why is this study important? 

This study tackles two of the largest challenges facing the modern world: climate change and disease prevalence. Some believe these issues are falsely linked, but the evidence collected in this study shows a positive correlation between disease induced death and increased temperature, both in a laboratory environment and the outside world. 

The big picture: 

While this study was isolated in geographical terms, the data collected gives researchers a look into what the future might hold for the spread of diseases in a warming world. Alone, the rising temperatures were not found to increase the rate of mortality; however, when mixed with a pathogen, a deadly combination was created and increased the rate of mortality greatly.

Citation: full citation of paper 

Cohen, J. M., Civitello, D. J., Venesky, M. D., McMahon, T. A., & Rohr, J. R. (2019). An interaction between climate change and infectious disease drove widespread amphibian declines. Global Change Biology, 3, 927. https://doi-org.ezproxy.lib.usf.edu/10.1111/gcb.14489

Baron Hoffmeister, Environmental Scientist & Geologist

Baron in the Calhan Paint Mines in Calhan, CO.

Hey there! My name is Baron Hoffmeister and I am a graduating senior at the University of South Florida. I am pursuing a Bachelor’s degree in  Environmental science with a minor in geology. I have always been drawn to the outdoors, and extremely curious about nature and how things work. When I decided to attend college I knew that I wanted to study something related to science. I decided to pursue environmental science as I became extremely interested in climate change and resource management.  In my junior semester at USF, I went on my first geology field trip to Fort de Soto Park in St. Petersburg, Florida. This was for USF’s Sedimentary Environments course and the goal of the trip was to study common sedimentary structures associated with barrier island formations. On this field-trip, we explored the barrier islands that make up Fort de Soto park and in several locations took pound core samples and dug trenches. In figure 1 you can observe some of the pound core samples taken from various parts of Fort De Soto Park. This is one of many useful methods that sedimentologists use to understand depositional history within a small region. This hands-on field experience left an impact on me and I immediately fell in love with geology. I was so far along in my environmental science program that it didn’t make sense to switch majors, so I chose to pick up a minor in geology instead. Fortunately, the majority of the geology courses I have taken all allowed me to take trips and participate in fieldwork relating to the courses. Most importantly, each of my professors expresses such a profound passion for geology that it is infectious and this has been instrumental in my admiration for geology. 

Pound core samples from Fort De Soto Park in St. Petersburg, FL.

My favorite part about being a scientist is that it allows me to spend time outdoors learning about the environment and the process that takes place that shapes the world we live in. This has always driven my passion for science and has carried over into my personal life. Any opportunity that I can find to go and explore nature I jump at. Figure 2 is a photo from my last trip to Colorado where I had the chance to explore the Calhan Paint Mines and study the large clay deposits in this region. It was very cold and windy that day. I believe with the windchill the temperature that day was in single digits. There was also a brief snow shower that rolled through and covered the entire park in a fresh layer of snow while we were there. After living in Florida for the past five years it was nice to finally see some snow again! 

Currently, I am interning for a contract management group before I apply to graduate school for sedimentary geology to start in the Fall of 2021.  I am interested in studying sedimentary geology and its relation to paleoclimate. Specifically, I am interested in how past climates have affected the rates of sedimentation and carbon cycling. I want to use this information to understand how current climate change patterns affect carbon cycling and sedimentation throughout the world. Science communication is critical for sharing ideas, research, and for education, but it is also crucial for being a great scientist. That’s why I have decided to write for Time Scavengers. I am excited about this learning process and the opportunity to educate others about geology, and understanding climate change!

I would tell any aspiring scientist to work hard and pursue an education, even if it is through your own efforts and experience.

Geology of the Mount Rogers Formation and Virginia Creeper Trail

Mckenna here- This post will show you the geology of the Mount Rogers Formation and Virginia Creeper Trail on a recent field trip I took to Virginia!

Day 1

Image 1. Our professor leading us to a geology lookout point on the way to Abingdon to see an outcrop (visible rock formation).

On October 10th of 2019, my Mineralogy, Petrology, and Geochemistry class went on a 4 day field trip to Abingdon, Virginia. Imagine this: it’s October. You love fall but you’ve lived in Florida your whole life, and you finally get to wear all the winter clothes you bought for no apparent reason. Considering these facts, my excitement for the trip was through the roof. After a 14 hour ride in a van with 10 other people and frequent restroom stops (much to the dismay of my professor) we finally arrived in Abingdon, Virginia to the joys of leaves turning colors and a crisp feeling in the air. A van full of (mostly) Florida-born students  seeing fall leaves for what was probably the first time was a van full of amazement and pure excitement. It sounds silly, but it was really wholesome seeing how giddy everyone got just by seeing some colorful trees (me included). We got to our hotel and prepared for the next day spent in the field. 

Day 2

Image 2. Rhyolite at Mt. Rogers with visible high silica flow banding (lava flow)

We woke up early in the morning and were able to enjoy a delightful breakfast made by the hotel to kick start our day. I packed my lunch and snacks and put on layers of clothes to be ready for any weather. I put on my new wool socks from the outlet store and old hiking boots that seemed structurally sound at the time (important to note for later). On our way to Mount Rogers in Damascus, Virginia we happened to take a road conveniently coined “The Twist”. As a long term participant in unwillingly becoming motion sick in situations such as going down one of the curviest roads in Virginia, I wasn’t thrilled. Luckily, I knew mountain roads could be bad so I packed some Dramamine which I made sure I took every time we got in the van from then on. 

Once we got to Mount Rogers my friend and I immediately had to use the bathroom which in this case, was wherever you felt like the trees concealed you enough. They don’t really mention this too much for field trips/field camps but bring toilet paper!! It will make your life a lot easier. After this venture, we were soon on the hunt for rhyolite. Rhyolite is a type of rock that my professor has talked a lot about and I had heard from other students that it is mostly what you will be seeing on the Virginia trip. It is a type of igneous rock that has a very high silica content so it is considered felsic (which is usually light colored). Rhyolite is made up of the minerals quartz, and plagioclase with smaller amounts of hornblende and biotite

The upper part of the Mount Rogers Formation consists mostly of rhyolite which we have, thanks to the continental rifting that occurred around 750 mya. The volcanoes that were once present here erupted and the igneous rock formed from the lava flow. 

Figure 1. Formation of rift valley in Mt. Rogers (From Radford)

We used our rock hammers that you can see in Image 2 to break off bits of Rhyolite and observe them under our handheld lenses. Through these lenses, we could (almost) easily identify the minerals present in our rock samples. 

Stop after stop, we observed more rhyolite. It became quite easy to answer our professor’s questions as to what type of rock we were looking at; the answer was usually “Whitetop Rhyolite”. There were, however, different types of rocks as we descended down the side of the mountain: buzzard rock and cranberry gneiss.

Image 3. Buzzard rock
Image 4. Cranberry gneiss

 

 

 

 

 

 

 

 

After we were finished at our first destination, we drove off to Grayson Highlands State Park. Here we observed more outcrops of rhyolite with a new fun bonus: tiny horses. Apparently, these tiny horses were let loose here in the late 20th century to control the growth of brush in the park. Now, there are around 150 of them that live in the park and are considered wild. While the park discourages petting the horse, you are able to get a cool selfie with them!

Image 5. Selfie with tiny horse in Grayson Highlands State Park

At the state park , there were lots and lots of giant rocks to climb on which everyone seemed to enjoy doing. So, while climbing the rocks, we were also observing and identifying them so it was a great combination. I was taking the liberty to climb almost every rock I saw and everything was going great for the time being. At one rock, I decided I wanted some pictures, for the memories! Mid mini photo shoot, I realized that the sole of my hiking boot had come clean off. Luckily, TWO very prepared people in my class happened to have waterproof adhesive tape and offered for me to use it to fix my boots. I was so thankful (and impressed that they had it in the first place) for the tape and used it to wrap my sole back to my boot and reinforce my second one because I noticed that the sole was starting to come off. The taped boots almost got me through to the end of the second day but I had to do some careful, soleless walking to get back to the van. I was able to go to the store near our hotel to get some replacement boots for the third, and final day in the field. 

Image 6. Realization of broken boot
Image 7. The final product of taped boots

Day 3

Image 8. Shale sample taken from outcrop along the Virginia Creeper Trail

The last day in the field was spent at the Virginia Creeper Trail in Damascus, Virginia. This specific trail serves almost entirely as a 34 mile cycling trail; by almost entirely, I mean entirely a cycling trail with the exception of a class full of geology students. Our day consisted of identifying rock types in outcrops along the trail and receiving a wide range of looks from cyclists passing by as our lookouts at the front and back yelled out for us to get out of the way. We walked around 1.5 miles of the trail, all while taking notes and pictures while our professor and teaching assistants were explaining each outcrop. Once we reached a certain point, our professor informed us that they would be leaving to get the vans and we would be walking back the way we came plus a half mile or so and identifying each outcrop while counting our steps and noting our bearings. So we measured our strides and got into groups to commence the journey. The goal of this was to eventually be able to create a map of our own that indicated each outcrop type and where they were on the path we took. 

Image 9. Mudstone displaying “varves”, which are a seasonal bedding pattern that develops in high latitude lakes. The thicker deposits develop in the summer and the thinner ones develop in the winter (please ignore my nailpolish-it is not a good idea to paint your nails before a geology trip).

This all sounds relatively simple, right? The answer is well, not really. The entire venture took around 4 or 5 hours and honestly made some people a little grumpy. I was happy though, because among the rhyolites and basalts, we were also able to see some really cool sedimentary rocks. Along the way we saw some awesome shale (Image 8) which we were told had some fossils in it if you looked hard enough. Of course, being interested in sedimentary geology I would’ve stayed forever chipping away at the shale to find a fossil but we were quickly ushered along by one of our professors. Shale is a type of sedimentary rock that is formed from packed silt or clay and easily separates into sheets. This type of rock is formed under gentle pressure and heat which allows organic material to be preserved easier as opposed to igneous or metamorphic rocks. As we continued along the trail we also saw mudstones and sandstones, diamictites, and conglomerates. After reaching the end of our journey, my group might have gone a little overboard and recorded 51 different outcrops. The outcrops we recorded could be reduced to: basalt, rhyolite, diamictite, conglomerate, sandstone/mudstone, and shale. The last field day was now concluded with tired feet but happy hearts as we listened to Fleetwood Mac in the van on the way back to the hotel.

Image 10. Diamictite (type of conglomerate) with poorly sorted grains suspended in a clay matrix. This specific rock was likely created by glacial activity and/or volcanic activity.

Day 4

We had a very early morning, skipped the hotel breakfast (they put out fruit and pastries for us though), and piled into the vans for a long journey back to Tampa, Florida. This trip was everything I had hoped it would be and made me fall in love with geology even more than I already was! I hope to go on many more adventures like this in the future. 

Bonus images of cool finds:

Image 11. Swallowtail feldspar (basalt) contains epidote and quartz. Lava cooled very quickly which caused rapid crystallization
Image 12. Rhyolite with pyrite (fool’s gold) clasts visible under hand lens