Building a Character Matrix

Jen here – 

Interested in understanding how we take morphological data from extinct animals and use them to infer an evolutionary history? These trees can be used as a framework to test different macroevolutionary questions regarding species distribution, paleoecology, rates of change, and so much more! We hope to set the stage to explain how each step is done! First things first, constructing a character matrix. 

Before really diving into anything specific, I would suggest you think a little about evolution, phylogeny, and all the basic terminology that goes into this field. I would recommend that you work through The Compleat Cladist: A Primer of Phylogenetic Procedures. This is effectively a workbook that walks you through terms, concepts, and more!

This isn’t meant to be an exhaustive guide but rather set you up to explore the program and generate a test character matrix!

Step 1: Learn about your study group

This will involve a LOT of reading and diving into the history of the animals you are interested in. In some instances this is easy, in others it is very difficult! I won’t dwell on this too much but it’s easy to forget where to begin. I would start by using Google Scholar to research your group of interest plus evolution, morphology, phylogeny. Then you will probably have to head to the library armed with a list of literature that is much older than you to really begin your deep dive. Remember that ideas change through time, so starting at the beginning is really valuable to learn how ideas have changed!

What is important is that you also learn about homology and work to understand the homologous elements of your critters. Homology is simply similarity due to inheritance from a common ancestor. The understanding and evaluation of homology may be different depending on the group you are looking at. For example, echinoderms have been considered this way for a while now and there are several schemes. One takes into account the body as a whole and how the elements are connected, the other takes a more specific approach looking at specific plates around the mouth. These are not mutually exclusive schemes but can be used in concert with one another. Another good thing to remember is that some people like to think they are more correct than others – who’s to say, really. Just make sure you do your own homework to form your own opinions and ideas. 

Step 2: Organize your information

There are several ways to do this, you could simply store information in Excel or Google Sheets or you could use a program designed for curating character data. I have used Mesquite for this. Mesquite is freely available software that is 

“…modular, extendible software for evolutionary biology, designed to help biologists organize and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Because it is modular, the analyses available depend on the modules installed.”

You can easily describe your characters, add new taxa, remove taxa, import or draw a tree and see how characters change across different tree topologies. 

Here is the barebones starting place. I set up a new file and said I wanted three taxa and three characters. Now I can go in and start editing things!

 

There is a side tool bar where you can easily start to modify the matrix. So you can change the taxon names, add taxa, change characters, add characters, delete whatever you want, and a lot more that I haven’t really messed around with! I suggest that if you are a first time user, you spend some time with your fake matrix messing around. Once you get a sizable dataset in here, it’s best you don’t make any mistakes! Figure out where you may go awry and troubleshoot ahead of time.

Here is my edited matrix where I’ve added in three taxa and three characters. Notice at the bottom where it shows a character and the different states that are available. So when you edit the matrix you can use numbers or the character state – numbers are easier!

 

An easier way to import your characters and the different states is to use the State Names Editor Window.  This shows you the list of your characters and all the different states it can have – you can easily edit these and it’s a nice way to organize the characters since in the character matrix the text is slanted and kind of hard to read.

Character matrix with the character list on the far left column and the states spanning the rest. The states can be whatever you want – which is where bias can slip in so don’t forget to refer back to your knowledge base and understanding of homology.

 

The functionality of Mesquite extends quite beyond this. If you are looking for tutorials or to push the limits of the program here is some further reading:

Step 3: Export your matrix for analysis

Extensive export options via Mesquite!

File > Export will give you a series of options to export your file, don’t forget to also regular SAVE your file so that you can revisit your matrix to easily add to it! Most programs that infer phylogenies require a NEXUS file. This type of file has your matrix and often a bit more information about what you want in the analysis or information about the characters. I would suggest using your favorite plain text editor and exporting a few different types so you can see how they are structured and why certain programs may want different files and different information!

 

Counting Deep Sea Sediments

Adriane here–

As paleontologists and paleoceanographers, sometimes the analyses we do involve complex equations, time-consuming geochemistry, or large amounts of computational time running models. But every now and then, we gather data using a method that is simple and fast. Today, I want to talk about one such method that I use quite often in my research. These data are called biogenic counts.

In previous posts, I’ve written about the deep-sea sediments I use in my research, such as sampling the cores we drilled from the Tasman Sea, and processing these samples once they are back in the lab. Each sample, which is stored in a small vial and represents 2 cm of the core (or 10 cubic cm of material), contain pieces of hard parts of plankton and animals, as well as minerals. These minerals and biogenic pieces, then, can tell us about our oceans and the life it held millions of years ago.

Biogenic count data is just that: I dump the sediment samples onto a tray and count the number of ‘things’ that are in that sample to determine the percentage of each ‘thing’ there. ‘Things’ in the sediment fall into a couple different categories: benthic foraminifera (foraminifera that live on the bottom of the seafloor), planktic foraminifera (foraminifera that float in the upper part of the water column in the open ocean), echinoderm spines (the hard parts of things like star fish and sea urchins), foraminifera fragments (pieces of foraminifera shell that are broken), sponge spicules (the hard parts of sponges that look like spiked glass), and I also make note of any minerals that are found in the sample. In one day, I do about 10 samples, which doesn’t seem like much but adds up everyday!

Below I’ll go  over the exact steps I take when performing biogenic counts:

A) An image of one of my jarred samples. B) The microsplitter used to split samples. Notice that the sample being poured in is split between the two cups on either side.

First, I take the jarred sediment and split the sample using a micro-splitter. A micro-splitter is a tiny contraption that equally ‘splits’ the sediment into two holders. Because each sample contains tens, maybe even hundreds of thousands of particles, there’s no way we could count all of that! So instead, splitting the sample down to a reasonable number of particles allows us to more accurately and quickly count the number of particles in each sample, which we can then use to get a percent of each ‘thing’ (e.g., benthic foraminifera, fragment, echinoderm piece) in each sample.

Generally, I try to split the sample until about 300 particles remain in one of the cups. This can take splitting the sample anywhere between 3-9 times, depending on how much sediment is in each sample to begin with. Once I have the ~300 particles, I then sprinkle them evenly onto a picking tray (a metal tray with a grid on it). I then count the number of each ‘thing’ on the picking tray. I keep count of each ‘thing’ using a counter, which makes the process very fast and easy!

An image of my picking tray with the sample sprinkled on it. Some of the major components, or ‘things’, in the sediment are labeled. Most of them are planktic foraminifera, which can be very small or larger. There are a few benthic foraminifera, several fragments, and only one piece of an echinoderm spine. Generally, planktic foraminifera are most common in these samples.

Once I have this information, I then put them into a spreadsheet to plot the data. One thing I haven’t mentioned yet is, why we do this and gather the biogenic count data. It’s actually very useful! We can use the percentages of each ‘thing’ in the sediment to calculate the ratio of planktic to benthic foraminifera. This tells us something about dissolution, or if the bottom waters were corrosive and dissolved the fossils, as benthic foraminifera are a bit more resistant to this corrosion than planktic foraminifera. I also calculate the planktic fragmentation index, which is another ratio which also indicates dissolution (the more dissolved a foraminifera is, the easier it is to fragment).

Thus, the biogenic count data is a quick but extremely useful method to determine the percent of each ‘thing’ in a sample, which can be used to infer something about the corrosive nature of bottom waters, which in turn can tell us something about ocean circulation from millions of years ago!

 

 

 

Curating a Personal Fossil Collection

Cam here –

Cretaceous Fossils from Mississippi (Part 1)

Fossil collecting can be fun and a rewarding experience. It helps us get a perspective of how rich and diverse the fossil record is. Some of us make personal collections of the fossils we find. Collections typically start with fossils and other rocks mixed together with little to no record of where the specimens you collected came from. My way of collecting fossils has changed over the years as simply piling rocks on my bed headrest to buying drawers and cabinets to store the specimens and keeping a record of them by creating a log book and keeping label cards with every specimen in each drawer. There are many different ways to curate your collection. At the end of the day, it is all up to you.

Fossil Collections (Part 3), (Echinodermata, Blastoidea), (Row 2)

When creating a collection or collecting fossils, you want to make sure you know exactly where that fossil came from. Location is probably more valuable than the fossil itself. You can’t always rely on your memory. What I have done is printed out labels and write information down with a black ink pen. There are about 30 labels on each sheet so I have a good amount. I write additional information on the back such as the date, coordinates (if accessible) and more recently the drawer name in which that specimen is stored. It is OK not to have information about your specimen. You can always leave the location section with a question mark or “Unavailable”. Make sure you fill it out the card with information to the best of your abilities.  

Filled in label

Finding things to store your specimens in depends on how delicate and how large the specimens are. Large to small boxes with padding are good things to have. You can find these boxes at hobby shops and arts and crafts stores. Clear jewelry and bead bags are also very useful as well. With all of these boxes and bags combined I keep most specimens in cabinets and drawers. I label each drawer sometimes by location, age, phyla, or by fossil content. It is all up to you. The majority of my drawers are ClearView desk organizer drawers. You can find these at a Walmart in the craft sections and craft stores.

Organizing a collection can be fun but it can also take up space. Make sure you do have room and not stack things too much on top of each other. I have had almost half of my collection collapse on me for doing that. Have fun with it!

Labeled ClearView drawers

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.

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.

International Ocean Discovery Program Early Career Workshop

Adriane here-

Earlier this year before the world went into lock down, I had the opportunity to participate in an early career researcher (ECR) workshop through the International Ocean Discovery Program (IODP). The workshop was focused on how to write a scientific drilling proposal with colleagues and friends.

The workshop was held at Lamont-Doherty Earth Observatory in Palisades New York, just north of New York City. At Lamont, scientists and staff manage U.S. scientific support services for IODP, the major collaborative program which, among several other things, allows scientists to live and work at sea for two months drilling and studying sediment cores. The workshop was specifically for early career researchers, which is loosely defined as a researcher who has gained their Ph.D. but has not achieved tenure (that critical phase in a professor’s career where they receive a permanent residence at their college or university).

The Gary C. Comer building on Lamont’s campus, where the IODP ECR workshop was held.

This workshop, which first ran a few years back, was conceived between Time Scavengers’ own Dr. Andrew Fraass and his close colleague, Dr. Chris Lowery. They, along with their colleagues, built the workshop and it has run every 2-3 years since its conception. What is so neat about the workshop is that it is also run and organized by other ECRs, with the help of more senior scientists.

The first day of the workshop focused on introducing the attendees to aspects of IODP. These included presentations on the past and future of scientific ocean drilling and the IODP proposal writing process. We also did participant introductions, where we stood up and had 1 minute to talk about ourselves, our research, etc. using only images on one slide. We, the participants, were also broken out into groups later in the day by themes we identified ourselves as (for example, I indicated I was in the Biosphere group because I work with fossil and am interested in evolutionary questions). From these breakout groups, we then identified 5 places in the Pacific Ocean we would like to target for drilling. Later that night, the workshop organizers held a networking reception for us at a nearby building on campus. The networking event was incredibly cool (they fed us dinner, and it was really great food) and useful (I had the opportunity to meet and speak with other ECRs who have similar interests as myself).

My introductory slide. The upper left box contained our image, name, and association; the upper right box contained a research image (I cheated and included two) and our research interests in three words or less, the bottom left box contained our research expertise and any contact information, the bottom right box contained a mediocre skill we have (again I cheated and used this to plug this website).

The second day of the workshop, we arrived and discussed how to obtain data for a drilling proposal. Just to give some insight into what goes into a drilling proposal, this is a 15+ page document in which scientists write out their hypotheses, where they want to drill on the seafloor, preliminary data that says something to support the hypotheses outlined, and what we call site survey data. Site surveys are when scientists take smaller ships out with an apparatus pulled behind the ship. These apparatuses use sonar to map the features of the bottom of the seafloor, but also the properties of the sediment below the seafloor. The changing densities of the different sediments appear as ‘reflectors’, allowing an MRI-like preliminary investigation of the sediments in which the scientists want to drill into. An entire presentation was dedicated to obtaining older site survey data. We also heard presentations about the different drill ships and drilling platforms implemented by IODP. The second part of the day was again spent working in groups. This time, however, we split ourselves into different groups depending on what area of the Pacific Ocean we were interested in working on. I put myself with the group interested in drilling the southeast Pacific, off the southern coast of New Zealand. Here, we began to come up with hypotheses for our proposals and begin to write those down.

Example of a seismic image from a seismic site survey. The very strong, prominent lines in here are called ‘reflectors’. This image shows the location of a proposed drill location, named SATL-56A. From this seismic image, we can interpret that the top layers of ocean sediments are very flat. The seafloor, which is recognized based on its more ‘spotty’ appearance and lack of horizontal lines, is very prominent here (the top of which is indicated by the green reflector line). These images are essential to include in a drilling proposal so everyone has an idea about what might be expected when drilling.

The third and fourth days of the workshop included limited presentations, with more time dedicated to letting the groups work on their proposals. One of the main outcomes of the workshop is to have participants walk away with an idea of how to write a drilling proposal, but also to have the basic groundwork in place for a proposal with a group of people who share similar interests. So ample time was given for the participants to refine their hypotheses, find some preliminary data about their drilling locations from online databases, and build a presentation to present to the entire workshop. On the afternoon of the fourth day, the teams presented their ideas to everyone, including more senior scientists who have submitted drilling proposals in the past and have worked on panels to evaluate others’ drilling proposals.

All in all, this was a great workshop that really allowed for folks to learn more about the IODP program, where and how to find important resources, and how to begin writing these major drilling proposals. These events are particularly important for scientists from marginalized backgrounds and first-generation scientists. For me (a first-generation scientist), making connections with others is sometimes very difficult, as I have terrible imposter syndrome (when you feel like you don’t belong in a community and that you will be found out as an imposter) and am hyper aware that I was raised quite differently than most of my peers. Being in such a setting, with other scientists, forced to work together, is terrifying but also good because I had the opportunity to talk to and work with people I would not normally work with. For example, I had wonderful discussions with microbiologists and professors whose work focuses more on tectonics, people from two research areas which I hardly interacted with previously.

Interning at a Paleontology Lab

Haley here –

A Busycon coactatum, or Turnip Whelk, specimen.

I recently started interning with Dr. Sarah Sheffield (one of Time Scavenger’s collaborators and USF professor) at the University of South Florida (USF)! As a high school senior, this has been an extremely influential experience to me. With Dr. Sheffield, I have been learning how to catalog fossils, and I have been slowly (but surely!) entering the USF collections to an online database (MyFossil). Along with learning how to photograph and catalog fossils, I have been able to learn about graduate and undergraduate research, sit in on a college level course, learn about fossil identification and photography (1), and meet some amazing people.

I was able to have this internship experience through a class called Executive Internship that is offered to seniors at the high school I attend. This class spends the first nine weeks teaching career skills like writing a resume and cover letter, interview etiquette, and effective communication. Throughout the first nine weeks, we are encouraged to research various career paths that interest us and speak with people working in those careers. By the end of the nine weeks, we are expected to have secured an internship. The school partners with various businesses (such as the Florida Aquarium) in order to ensure that students have options. Some students use these connections, while others choose to intern with businesses they have been to before or reach out to family and friends for suggestions. Others -like myself- email everyone they can think of to see what they would think about having a high school intern. I was fortunate enough that one of the people I reached out to suggested that I speak with Dr. Sheffield, and I was even more fortunate that Dr. Sheffield found a project that she wanted to start and was willing to allow me to help. After everyone has secured an internship and we have completed the first nine weeks of class, all of the interns are given permission to sign out of school instead of attending Executive Internship class. In exchange for essentially leaving a class before school ends, all of the interns are required to record an average of five hours per week in our internship and complete a weekly log. Other than the hour requirement and log, internship schedules and tasks vary for each student.

I can not say when I first became interested in paleontology and geology, but this internship experience has only helped my interest grow. When trying to explain why I wanted to study those fields, my mom helpfully explained that I had “always been a rock girl” which sums it up pretty well. From family trips to North Carolina when I was in elementary school, I became fascinated by the variety of gems and minerals you could find. As I took more science classes, I learned about crystal structures and how various formations occur. In a public speaking class, I was able to pick any topic I wanted and ended up falling into a rabbit hole of the history and changes of paleo-illustration. I think part of what draws me to these fields is how seamlessly they integrate with so many other fields. From chemistry and biology, to history or art, there are so many aspects of paleontology and geology that can combine with other fields. In any case, there is always something new to learn and something to dig deeper into that can reveal so much. This is only highlighted by my experience sitting in on Dr. Sheffield’s class. The class addresses the evolution of life on Earth, but reaches implications of what we truly define as Homo sapiens, the history of paleontology in the United States, biomechanics (how organisms move), and much more.

Bryozoan encrusting on a Busycon carica (Knobbed Whelk) specimen.

When I started my internship, I was unsure what to expect. I am a high schooler, and I was going to be working with a college professor to begin a new project. I was excited to learn, but I can say that I definitely did not expect to come home and tell my parents that I wished there were more Anadara (2) specimens because they were the most fun to photograph. I learned the conventional lighting angles to use for fossil photography, how to measure various shells, and the information needed to catalog fossils. Properly labeled fossils soon became a valued commodity after some specimens only had labels like “bivalve”, “east coast”, or “recent” specimens. To catalog the specimens, I have been using the MyFossil database. It is an extraordinary website that allows museums and researchers to share their specimens so that they are available world-wide. It is amazing to know that I can catalog a specimen and see it appear online next to a trilobite specimen from China and a shark tooth from California. MyFossil has an important feature that allows specimens with detailed information (classification, dimensions, geochronology, and locality) to be marked research grade. This allows MyFossil to function as both a free online museum and as a valuable tool to researchers.

Learning how to catalog fossils entails learning about fossils just from exposure. I have learned about the variety of features of shells and how they function for each species. In order to revise some entries to make them research grade, I have used a website called Macrostrat. By looking up geochronology based on lithostratigraphy or formation, I have begun to recognize the common  rock units of various sites in Florida. I have been able to learn more about fossil features by asking how to denote various characteristics like boring. A notable specimen of snail had a bryozoan encrusting (3). By cataloging fossils and asking about them as I do, I have learned much more than what I expected to learn from the cataloging labels.

This internship has been a great learning experience. I was admittedly unsure of what I wanted to do in college, other than the fact that I wanted to do something with geology and fossils. Interning has allowed me to learn, discuss projects with others, and see the sheer variety of research within the USF School of Geosciences. This, paired with everyone’s enthusiasm for their research, has helped me see the kind of environment that I want to be a part of. It has been an opportunity that has allowed me to gain a better understanding of the college experience, and it has allowed me to have hands-on research experience in the field that I love. I look forward to expanding what I have learned even more through the rest of my internship!

A First to Remember

Hello, it’s Lisette, a geology student who’s had the honor to take multiple classes with Dr. Sheffield!

I would like to talk about my summer undergraduate research experience through the Leadership Alliance at the Department of Earth and Planetary Sciences at Brown University. The program itself is called the Summer Research – Early Identification Program, and it was the first REU that I’ve ever applied to, and it really was a summer to remember! By the end of this article, I hope to convey why the Leadership Alliance is an amazing program that professors should encourage undergraduate students, especially those from underrepresented minorities, who have an interest in research to apply!

Scenery around Brown University.

So, what is the program exactly? The SR-EIP serves as an opportunity for undergraduate students to conduct research at an academic institution and receive career mentoring simultaneously in order to curtail the shortage of underrepresented minority groups earning PhDs. During my first week in the program, I attended various seminars that stressed the importance of diversity in STEM as well as coached us on the leadership skills necessary to advance in any field one pursues. We met and learned the stories of some truly amazing women in the STEM field, including Dr. Medeva Ghee, the executive director of the Leadership Alliance. She told us about how she was the first woman to intern at a company she applied for during her undergraduate career and how this spurred her drive to make science a more inclusive discipline for everyone. These workshops would continue throughout my stay at Brown twice a week during group meetings and after weekly dinners. My particular favorite was the one where a group of graduate students and professors at Brown discussed their afflictions of imposter syndrome because it was such a relief to know I wasn’t the only one who felt that way.

On the first day, I met the professor who was going to guide me on my first research experience, Dr. Mustard, as well as the graduate student who was there to support me: Alyssa Pascuzzo. They were monumental during my summer because they offered endless support and encouragement. Dr. Mustard continually checked up on my progress and was always excited to hear about the new skills I had learned. We also had weekly meetings where we would go over scientific articles about the polar caps of Mars and he would teach me more about the world of academia, including how to make the most out of conferences and the various paths one can take to land a career in research.

Presenting at my first research conference.

In tandem, I cannot overstate how important and motivational Alyssa Pascuzzo was throughout the summer and beyond! Every single day she was there with me, guiding me throughout the research process but still allowing me the freedom to choose my own project and how to go about it. She taught me how to use ArcGIS and MATLAB and showed me resources on how to become more proficient at both. I really appreciated how she would take the time to send me even more scientific articles about what I was studying and made sure to go over them afterwards for clarity and understanding. She also served as a grounding friend in a completely new environment and was always there for advice and encouragement. She helped me create my first research poster and stayed late to help me practice my presentation for the Leadership Alliance National Symposium. Even now, longer after summer has passed, she still serves as an exceptional mentor. And I think that’s what makes the Leadership Alliance such a great program for underrepresented students: it truly fosters a sense of community and belonging in those just starting their path in the intimidating yet exciting world of research. You have the opportunity to make so many long-lasting connections with people both inside and outside of your field of interest, and all of the members are open and thrilled to help you make the most of your experience.

If you know any undergraduate student (or are one yourself!) who has expressed interest in research, I sincerely hope you encourage them to apply for the Leadership Alliance. Their program covers a wide range of research areas (including humanities and social sciences through the Leadership Alliance Mellon Initiative) and builds a strong network of mentors that one has for life. We can aid in the diversification of the research workforce together!

 

Plankton Photo Shoot Part III: Creating Plates

Adriane here-

This post is the third and final in a series I’ve written about taking scanning electron microscope images of my fossil plankton (‘Plankton Photo Shoot‘) and how I process those images in photo editing software (‘Plankton Photo Shoot II: Creating the Perfect Image‘). Here, I will show you all the purpose of these images and the editing process, and how these are useful to other scientists in my field!

Now that all my SEM images are cleaned up (meaning, the background is removed, the edges of every images are cleaned up, and each file is saved as a high-quality PNG file), it’s time to create plates! I’m not talking about dinner plates that you would eat off of; rather, when we talk about plates in paleontology, we mean a page of high-quality fossil images that showcase the features of our fossils.

A plate of vertebrate fossils, specifically those from an ancient penguin species. This is the plate caption: “FIGURE A5. Undescribed vertebrae and ribs referred to Kupoupou stilwelli n. gen. et sp. 1-7, vertebrae, NMNZ S.47339; and 9 and 10, ribs, NMNZ S.47339. 8, an incomplete vertebra, is part of NMNZ S.47302, associated with the larger Chatham Island form. Scale bar is equal to 10 mm.” This plate has a white background, as do most plates that showcase bones (the darker bone colors stand out better against white backgrounds). Image from Blokland et al. 2019.

Plates are published in scientific journals as part of journal articles, and usually include a scale bar (so others know how large or small the fossil is), a number or letter beside each image on each plate, and a description underneath the plate with each image’s genus and species name. Plates can also contain other important features to help other scientists identify the specimens, such as arrows and labels pointing out specific parts of the fossil. For my dissertation, I had to create plates of my fossil plankton to show other scientists how I was identifying each species, and they will be used as a reference for others so they too can identify species. In total, I created 29 plates of fossil foraminifera for my dissertation!

The first thing I do when I create a new plate is to create the template. I create all my plates in Adobe Illustrator, and I always give my plates a black background. I also go ahead and add a bit of white space below the plate, and a text box within the white bit, so I can create the plate caption as I add images. Below is an image of the template, with the black background and white space for the caption.

A screenshot of Adobe Illustrator with my blank plate template.

Next, I add in numbers where the fossil images will go. I like to create plates that have 5 rows and 5 columns, so a total of 25 images. Putting in the numbers before the images helps me align everything on the template, and it makes creating the caption that will go under the plate much easier. For example, when I add the image next to 1, I then add in the fossil information right in the caption.

Screenshot of the template with numbers added.

Now for the fun part: adding in the fossil images! All of my images are stored in separate file folders on my desktop, and each are labeled with the species name and the section from where it came within a drilled sediment cores. I just open the folder, grab the cropped image that I want, and plop in onto my template. I also plop in the original image file along with the cropped images. I do this because the original image has a scale bar, the information that tells people how large (or in my case, small) the fossil is.

The template in the background, with the cropped fossil image (left) and the original SEM image (right). Notice the scale bar in the original image at the bottom (100 microns, or um).

Because the original image and cropped images are the same size, all I need to do is trace the scale bar with a white line, delete the original images, then place the scale bar underneath the cropped image.

I trace the scale bar from the original image so it is just a white bar, and place that under the cropped fossil image. I also rotate the cropped image.

Once I have the cropped image and scale bar on the template, I then re-scale them (or just make them smaller) to fit beside the appropriate number on the template. I then go ahead and add in the image’s genus and species, and location information below in the white space.

The cropped image and scale bar are re-sized together to keep them at the same proportion. The image is then placed beside the appropriate number, and the location information is added into the caption at the bottom of the template.

I do this 24 more times to create a full plate of foraminifera images!

A screenshot of the final plate, with the complete caption underneath. I can then save just the template and fossil images as a PNG file, insert them into a document, then copy and paste the caption underneath of the image.

This process is tedious, and it is very detail-oriented, but it was one of my favorite things to create during my dissertation! There’s nothing I love more than flipping through pages and pages of my printed plates containing foraminifera images to admire the diversity of shapes and sizes. The beauty of the foraminifera are on full display, and it’s sometimes still hard to believe that all the wonderful shells are created by single-celled protists!

 

Writing a large NSF grant

Andy here –

Writing grants is a big part of doing science. While some science can be done with just a clever idea and data that already exists, it’s more common that we have to go do something. We might need to travel to collect some samples, so we’d need to pay for the train, flights, gas for a car, or even just food. We could need to do some chemistry, which costs money for reagents, time on thousands-or-million-or ten’s of dollar machines, or just beakers! We could also just need to pay our salary while we spend time identifying little tiny fossils, or we could want to pay a student to do it. That last bit is important: Science is a career, and for some folks, they need to bring in grants or they don’t get paid.

How we write grants is not something we talk much about, outside of the occasional (well-earned) whining on social media. It’s a lot of work, and getting them is tough. Here’s a little feeling of what it’s like to write a large grant.

The first thing is to have an idea. Now, not just any idea works. You’ve got to have an idea that: A. you think is exciting, B. others think is exciting, and C. everybody agrees is important. A ‘fishing expedition’, where you might get something neat but you’ve got no clear hypothesis to test, doesn’t work. Even just having a clear hypothesis isn’t enough. You really need to have an idea that has some important impacts for your field and usually society.

I mostly work with science that’s under the purview of the National Science Foundation (NSF) (or in the UK, National Environmental Research Council, NERC). Some of my friends work with grants from US Environmental Protection Agency or the US Department of Energy, or work for the US Geological Survey. What you work on sometimes governs the types of grants for which you can apply, how they are formatted, and the amount of money. To get a grant from the NSF you have to first have an idea that fits one of their ‘Calls for Submission’. My last grant was under the call: EarthCube Science-Enabling Data Capabilities

The most important part of the grant is a 15 page proposal. The proposal lays out the idea. It then supports it with specific language about how we’re going to accomplish that idea, including timelines, deliverables, and back-up plans of what we’re going to do if something doesn’t work. These documents usually need multiple sections, tables of locations, maps, graphs, theoretical diagrams, and a lot of times there’s even unpublished data which supports the hypothesis but just isn’t enough to publish yet. There are also lists of who is going to work on the grant, all of the referenced papers, explanations of how we’re going to coordinate so that we’re getting the maximum amount of science progress out of the money. Usually these things end up being extremely densely written with sub-sub-sub-headings. Ours wasn’t to specifically do science, it was to augment the capabilities in a few systems that existed, so that somebody could come later and do science. Since we’re creating this new thing, I’m hoping that it’s going to be us, since we’ve ostensibly got the jump on everybody, but the goal of open science is to make the data work for all of us. 

The proposal is only the fun part though, planning out how you’re going to do all the science. We also have to prepare a detailed budget that accounts for every dollar we’re asking for, and then a separate document that justifies why we’re spending it. Ours was 5 or so pages. We also had to write a list of all our collaborators for the last 5 years, supply our 5 most relevant papers and then 5 others, where we work, ‘synergistic activities’ (which is a fancy way of saying outreach or community-service type of activities). We had to prepare a 2 page summary of how we’re going to make our data publicly available (this was really easy for us since that’s the whole point of our grant). If there’s more than one person from the same institution proposing this idea, then they all need to list their collaborators, their papers, and so on. Then, if we’re working with another institution, they have to do all of that as well. Each University submits their own budget, justification, all of the co-principal investigators (folks proposing this work) have to list their collaborators, papers, and on.

For our grant, I’m the “Lead Principal Investigator” which means that I’m quote-unquote in-charge. It also means that I’m most liable if this thing fails, which would mean that I’m far less likely to get another grant any time soon (I should point out that I’m only able to be in charge of this because I’m affiliated with the Academy of Natural Sciences of Drexel University in Philadelphia as well as the University of Bristol). The grant primarily includes the University of Wisconsin and Texas A&M University, so they had to do their own budgets, and all of that. There’s also work being done at the a few other universities, a non-profit, and a programming company. Those folks just had contracts they had to draw up, but they were budgeted for on the primary universities budgets. All of those contracts had to be submitted alongside the grant.

Still not done though! We also had to get letters from everybody tangentially involved that was mentioned in the grant. So, we mentioned that we’d invite two other scientists who are experienced in similar things to one of the workshops we’re going to have. We had to have a letter from each of those people, as well as anybody else involved, which meant quite a few others.

Then, once you’re all done with that, the Grants Certification and Authorization office has to approve all of the information you’ve put in, and check your math on the budgeting. Sometimes that office requires weeks of lead time, so not only do you have to do all of the above, you have to do it early! Even more confusing, different institution’s grants offices work completely different, which can get very frustrating if you move around constantly, like many early career academics. Finally, and this part is a little sad, they get to push the button and submit. And then the other primary institutions do that too.

There’s a whole, long, parallel story about how proposals are reviewed and then how they decide on to whom to give money.

All of this is in the hopes that you are one of the one out of five proposals funded. They also usually cut your budget, even if they fund you. If you don’t get funding, you get 3 descriptions about why your ideas wasn’t good enough to fund. All in all, the above is several months worth of work, so it’s basically a high-risk/high-reward process. Even if you do have an amazing idea (like we did!), there’s a low probability of success on the first try (we only succeeded on our second try).