Publishing Scientific Research

Sarah here –

This post will focus on something that can be a little confusing if you’re not a researching scientist and that is how we publish our research!

So we’re going to start this with assuming that we already have a scientific study that has been written down. A paper generally follows this pattern: an introduction of what your study is about and why it matters, background information to help the reader learn a bit about the broader material that your study fits in with, methods and materials (i.e., how you did your study and what did you use to do it?), the results of your study, the discussion of your results (i.e., what do your results mean?), the conclusions (summary of your results and their meaning along with any future work that might rely on this specific paper), acknowledgments (i.e., thanking people who helped you collect data, supported you during this process with helpful comments, or anyone who helped pay for your research), and references (i.e., the other published papers that you cited in your article that helped explain related information or gave credibility to the types of methods you used, etc.

So, now that we have ourselves an awesome study, let’s get it published! Should be pretty straightforward, right? Well….not exactly. There are a lot of steps to publishing. Some papers can be published relatively quickly (a few months) whereas others can easily take longer!

Step One: Choose a journal

There are a bunch of journals that publish scientific papers. In general, you should choose a journal that requires peer-review (more on this process later). All reputable science journals require your paper to be read by a number of scientists (usually two or three) in your field to make sure your paper will be a good contribution to science. Second, you should choose a journal that publishes papers similar to the one you wrote. What that means is that not all journals publish the same things. Some journals specialize (e.g., The Journal of Paleontology publishes papers that focus on paleontology), whereas other journals, like Nature, will publish all types of science papers that they think their readers will find interesting. In my most recent publication, I chose the Journal of Paleontology. Once a journal is chosen, you have to format your paper to the journal standards using the correct font/font size, reference style, etc. Every journal has its own format and most journals won’t agree to read your paper unless it’s largely formatted correctly.

Step Two. Submit!

This takes place via an online platform and can take a little bit of time (an hour or two, usually). You upload: your text for the paper, any images you have for the paper, tables, data, and explanations of the data. You also upload a cover letter explaining to the editors of the journal why your paper belongs in their journal (e.g., this paper is of similar interest to readers that your other paper, published last year, was). You are often asked to suggest reviewers to read your paper. This is because you, the author, probably know more experts in your field (in my case, echinoderm paleontology and evolution) than the editors do. It really helps them when you can suggest a few reviewers (usually between two and four).

Step Three. Editor’s decision!

The editor will read your cover letter and your paper and decide if it’s a good fit for their journal. If it is a good fit, they will send your paper out to a few reviewers, specialists that can comment on the analyses you used, the validity of your conclusions, and whether it’s significant enough for publication.

Step Four. The reviews!

Peer reviewers have a set amount of time to read and comment on your paper (usually two weeks to a month). Peer reviewers are generally not paid for their work-it’s something called “academic service”. Usually, people who publish papers expect to review one or two papers for each one that they publish. The reviews will have a mixture of positive, neutral, and negative comments. They’re focused on strengthening your paper, so you might see comments on making certain sentences more straightforward, making images higher resolution so features can be seen, or comments that require more work (e.g., a reviewer might think you need to run different analyses to be considered for publication). Overall, comments should be helpful (not cruel) and they should be about the paper NOT the author (e.g., “this paragraph needs restructuring to make the point clearer”, as opposed to “the author didn’t write this paragraph clearly”).
Each peer reviewer will mark your paper as one of the following: “accepted with no revisions”; “accepted with minor revisions”; “accepted with major revisions”; “revise and resubmit”; and “not publishable in this journal”. Major revisions usually means running new analyses or rewriting large portions of text. Just because a paper isn’t accepted doesn’t make it bad, either. It may very well mean that the reviewers felt that it didn’t belong in that particular journal! Usually, the editor will take the decisions of the peer reviewers and make a final decision on whether the paper will be accepted.

My most recent paper was accepted with minor revisions-I had to rephrase some of my conclusions and reviewers had me strengthen some of my arguments by using data from other recently published papers. All in all, peer review is a very important step towards making your paper better!

This is a before and after look at one of my most recent peer-reviewed papers, published in Palaeontology. On the left is the paper that I submitted to the journal and on the right is the final, copyedited, and typeset version.

Step Five. Revising.

Very, very few papers are rated as “accepted without revisions”. Usually, reviewers point out a few things, at least, that could make your paper stronger. For most journals, you have to “respond” to these. Meaning, you take the comment by the reviewer and state that you agree with the change or disagree and provide your reasons why. In my personal papers, this could range from “this sentence isn’t clear-rewrite” and I would respond with “Yes, I see how this could be unclear. I’ve rephrased to XXX”. Or, a reviewer might say, “I disagree with this interpretation based on X. This should be revised to say Y”. I could respond with “I disagree with the reviewer’s interpretation and here’s the evidence to back up my claim”. I could amend the text in my paper to strengthen my argument and provide more evidence for my claim, too.

Step Six. Are we done yet? Well….no. Not yet.

Once you get the reviews and make all of the edits, you have to go back to step two: submit! Once you do this, the editor will determine if the changes you have made are sufficient or if it needs to go through a secondary round of peer review (in which case, please return to step four!) Once the editor has decided your paper is acceptable for publication, the editor will make sure your paper conforms to all journal standards and there are no glaring issues (e.g., you forgot to label your scale bar or forgot to put a reference for an in-text citation).

Step Seven. Proofs!

Copyeditors have the job to go through your paper line-by-line, word-by-word to make sure everything is grammatically correct, properly cited, and has no typos. They’ll send you a copy of your paper in the proper format-with all of the images set on the page, looking just how it will look printed in the journal or online. Your job is to go through the paper carefully to make sure you don’t see any extra mistakes or typos.

Step Eight. Celebrate!

Your paper will be published online very soon. Great work!

Preparing Samples for Stable Isotopic Measurements

Adriane here-

Recently, Andy and I have started to collaborate on a research project together. Well, the project is his, and I’ve agreed to do some lab analyses for him in exchange for being a co-author on the research paper. Being a co-author means that on a published journal article, I will have my name as one of the people who contributed to the science in the paper. My job for this project is to pick, weigh, and analyze foraminifera for stable isotope analyses. In this post, I’ll go over briefly how I do this!

Lucky for me, Andy had already picked the foraminifera he wanted to be analyzed from his sediment samples and put these into cardboard trays. Each tray is labeled so that it corresponds with the sediment sample from which it came, thus I know exactly which sample I’m working with. The first step is to take the cardboard tray and put it under the microscope. Using a paintbrush with water, I gently pick up the foraminifera specimens and place them in an aluminum tray. After I’ve filled up all 14 of my aluminum trays, I take these and weigh them on a microbalance, which is a fancy name for a scale that measures very small weights (in this case, micrograms). I want the samples to weigh between 180 to 220 micrograms, as this is the ideal mass needed to get a good measurement. After the samples are weighed, I then put them into a tall glass vial that is numbered. I have a spreadsheet on my computer where I keep track of which sample is in which vial.

The home-made device we use to pump helium into the vials and air out. We fill 10 vials at a time for about 4-5 minutes each.

After I have about 60-80 vials of weighed foraminifera, I can then begin the process of analyzing them for stable isotope measurements. In this case, we want to measure carbon and oxygen (see our ‘Isotopes‘ and ‘Carbon & Oxygen Isotopes‘ page for more details on what these data are used for). This process is a bit tedious and always makes me nervous, but it’s also kind of fun!

The acid is poured into a syringe with a needle, and then four drops of acid are inserted into each vial. It’s a very medical-like procedure for a geologic endeavor!

Analyzing foraminifera for stable isotopes means working with a mass spectrometer, a (very expensive) machine that, very simply put, measures the amount of carbon and oxygen that are within a gas. Notice that the mass spectrometer needs a gas, not a solid, to be able to take a measurement. This is where things get fun! The first step is to make sure all of the air is out of the glass vials. To work correctly, the mass spectrometer has helium constantly being pumped through it. No air is allowed into the system, as air contains oxygen, and oxygen is one of the elements we want to measure. If air gets into the mass spectrometer or into the vials, it’ll ruin the results of the analyses. To rid the vials of air, I put the vials on a contraption that continually pushes helium into the vials through one tube while letting air out of another small tube. I let the vials fill with helium for about 4 minutes each. After the vials are filled with helium, I then put acid into each vial. Four drops of 100% pure phosphoric acid is placed into each vial. This is done to turn the foraminifera, which are made of calcium carbonate, into gas (any acid placed on calcium carbonate, the material which seashells and foraminifera are made of, will cause them to dissolve). Because calcium carbonate is CaCO3, the resulting gas includes elements of both C (carbon) and O (oxygen).

Once all the vials are filled with acid, it’s then time to start the mass spectrometer! This is a very easy process considering the machine itself is complex and intimidating (well, at least to me). In short, I basically change the file names, make sure the machine knows how many samples its analyzing, and then I click the ‘Start’ button. Each sample takes ~12 minutes to analyze, so an entire run of 60 to 80 samples takes about 12 to 16 hours.

The last part of this process will be to take the results, put them into a spreadsheet, and give them to Andy. From there, Andy will have the hard but fun job of interpreting the data and writing the majority of the research paper (with help from us, when needed).

Learning New Methods

Maggie here-

One of my favorite parts of being a scientist is constantly learning about new ways to answer research questions that I have. I am a paleontologist, but in recent years, I have become very interested in how I can use geochemistry (looking at stable isotopes and trace elements) to address paleontological questions. Since this is a relatively new interest of mine, I have been taking classes in geochemistry, and this past semester I took an analytical geochemistry class to learn different methods that I can use to answer my own research questions. I want to share some of what that class was like because WOW, I’m still processing how awesome it was!

The Lab
Two years ago now, my department (Department of Earth and Planetary Sciences, University of Tennessee) moved into a new building that has not only lab space for faculty and graduate students, but has a research lab designated for undergraduate research. This lab has many different instruments (ion chromatograph, gas chromatograph, inductively-coupled plasma optical emission spectrometer) as well as equipment for bench experiments that is intended to provide undergraduates with research experience through classes and working with faculty members and graduate students. The class that I was a part of did consist of graduate students, but we got to be a part of the process of launching the use of this lab and continued to prepare this space for use by undergraduates. This lab space in and of itself is a unique space for undergraduates to explore the geosciences, but my experience using the lab and learning the methodology of the instrumentation available in the lab was very beneficial.

A gas chromotographer. These instruments are designed to separate and analyze compounds (substances with two or more elements).

Class Set Up
My favorite part of this class was how it was set up because it was so interactive. We spent the first half of the semester getting acquainted with the lab itself and learning the processes that are involved with setting up a lab like this and preparing for a safety inspection. We completed a chemical inventory, worked on developing a chemical hygiene plan, and discussed budgeting (everything from how much DI water costs to the basics of how much each standard is). While this seems pretty mundane, it was an interesting process to complete and to see how detailed the process of setting up a lab is.

Photo by Dr. Annette Engel.

The second half of the semester, each student in the class chose a method to research and teach the class to use. This was a two day lesson that we were each in charge of, the first day spent teaching the theory behind the method and how the equipment works, the second day was spent using that method to look at a quick in class experiment. This meant that not only did we each become the in-class expert on a method, but we had to be able to think about timing to stage each step of the process to using that method. Some of the methods we learned about include gas chromatography, ion chromatography, and inductively-coupled plasma optical emission spectrometry (ICP-OES).

Photo by Dr. Annette Engel.
In addition to learning the process of setting up a lab and learning all different methods, budgeting was also emphasized in this class. Our professor was very transparent with us about how much money was spent to set up the lab as well as how much our science cost to do. With every method, every student leader included a question for us to figure out how much it would cost to run a certain number of samples using that method. This really impressed upon all of us in the class that science does cost money and more importantly, time, and how that all needs to be thought about well before wanting to do any analyses.

The set up of this class ensured that not only did we learn how to use different methods, but that we learned how to run our own labs and understand the work that goes into the different analyses that we write about wanting to complete. Not only did I walk out of the lab this semester being able to complete many different geochemical analyses on my own, but with some idea of the complexities of running a lab!

Class Projects

Photo by Dr. Annette Engel.
I mentioned above that part of this class was to see the breadth of projects that could be completed using the equipment that already exists in the lab. The four other people who took this class with me and myself all have VERY different areas of research and our class projects reflected that. One person was looking at fluid inclusions in granites, someone else was looking at toxins in microbes, and I was looking at trace elements in different skeletal elements of sea urchins. Almost all of us used the ICP-OES because we were interested in trace elements, but for several of us, our samples required other methods that we discussed in class to prepare the samples to be run through the ICP-OES.

All of us in the class completed all of the prep work and ran our own samples regardless of the method that we chose. Yes, we had guidance from our professor and lab manager, but the project work was all very hands on and completed by us. This gave us each a chance to apply what we had learned in class, see just how long some of these methods take, and gave us an appreciation for juggling multiple people’s lab schedules! At the end of the day though, all of us walked out of the lab with useable data to complete our chosen research projects. And, for several of us, the work done for this class project either directly helps with the completion of analyses for our theses and dissertations or helped inform us if the method we used is useful for the question we want to address.

Personal Takeaways

This is the first time in Maggie’s science journey that she has had to wear a traditional white lab coat. Photo by Dr. Annette Engel.
I am going to be really honest here, at points this class was incredibly overwhelming to me-I don’t have a strong geochemistry background and I really didn’t know what I was expecting to see in the results of my research project. But I’m really glad that I took a chance on it because I did learn so much more than I thought I would. I feel more confident in my abilities to complete geochemical analyses on my own, I learned the capabilities of several different instruments and have ideas of how to use them in future research projects, and overcame some personal lab fears-using acid to break down solids into liquids is a little scary the first time you do it! But beyond the methods, this class really emphasized the process of setting up a lab for the first time and understanding how time and monetary budgets fit in to building labs and getting analyses run. I am glad that I challenged myself to learn new methods this semester and I encourage you all to step outside your comfort zone to see where you can stretch your research to!

Florida Association of Science Teachers

Jen here –

Here is a flyer from our workshop with the information for the institute that I am part of.

Part of my new job is as a postdoctoral associate at a newly developed institute: Thompson Institute for Earth Systems. This institute has a primary goal of helping translate the complex science done at the University of Florida as it relates to Floridians. This includes anything related to the environment and the primary Earth systems (life, land, water, air). Recently, the institute was awarded a large grant to pursue a project to get scientists into Florida classrooms. To help promote and share content we hosted a workshop at the annual Florida Association of Science Teachers (FAST).

My supervisor had submitted the proposal for this workshop but was also giving a lecture the day before on the larger project and suggested I run the workshop instead. The idea was to give a brief but useful content overview to the educators and then allow time for lesson plan development and questions. This was a surprisingly daunting task: I’m used to giving quick research talks on a very specific topic and here I was tasked with describing how global processes can affect Floridians.

Simplified diagram to show the processes of weathering and erosion. One of the major limiting nutrients is phosphorus, which is held within the rocks!

It took me an incredibly long amount of time to decide how I wanted to structure the talk. A colleague had suggested we play BINGO during the talk. I made BINGO cards for the teachers with terms that I would use during the content portion of the workshop. If someone got BINGO they would have to share the terms and describe how they are interconnected. One of the key points of the workshop was to exhibit how interconnected all of the spheres really are. The talk began with a direct issue here in Florida – sea level rise. NOAA has a sea level rise viewer where you can simulate what happens in a specific area when sea level rises. So I zoomed in to the area directly around where the conference was in Miami, Florida. The simulator starts at 0 and goes up to 6 feet, and unfortunately the average elevation in Florida is only just above 6 feet. I then walked the educators through the four basic spheres of Earth system and how we can visualize them here in Florida. This included how sea level rises, ocean circulation, erosion and weathering, cave and sinkhole (karst) features, greenhouse gases, and more!

The next portion of the workshop was designated to allow the teachers time to brainstorm ideas for a lesson or activity and to ask questions to content experts (the rest of our lab group and team was there in the room). There were some really great activities thought out and we were able to discuss ideas with the teachers for how we can better serve them as an academic institute. Overall, it was a great experience for me to share more information about Earth’s natural systems and foster discussions with educators.

Geological Society of America Meeting 2018

Adriane here-

The first slide of Jen’s GSA talk.

In early November, some of the Time Scavengers team (myself, Jen, Sarah, Maggie, and Kyle) attended the annual Geological Society of America Meeting. This year, the meeting was held in Indianapolis, Indiana; a nice midwestern city that was very walkable with lots of restaurant options (yes, I judge cities based on the quality of their food). In previous posts, we’ve talked about these annual (some being in Canada) and regional conferences and their importance. Here, I want to provide an update on some of the scientific and educational aspects of Time Scavengers that we presented at the meeting. As some of you may know, our site isn’t just an educational website; Jen and I are also using the site as a sort of experiment. Specifically, we want to know how we can best reach a broad audience using social media and social media advertising tools. I’ll tell you about our presentations, and the major findings from each one!

First, Jen gave a wonderful overview talk about the Time Scavengers site. She gave her talk in an educational session, which are not as well-attended as the science sessions in general. Her talk included the story as to how Time Scavengers began and the motivation behind the site, the reason for inviting collaborators to join us on the project, and the purpose of each part of the site (blogs and static informational pages). Since we were at a conference full of other geologists and avocational scientists, we also put out a call for anyone interested to contact us for collaboration (such as writing a blog post). Jen’s talk was well-attended and well-received! The room was packed, and several people took a picture of the contact information slide during Jen’s talk. We also received good feedback from people regarding the talk throughout the conference. The last part of the talk included to images of our posters that Sarah and I were to present later in the week. So having the overview talk first, before the posters were presented, set Sarah and I up quite well.

Sarah presenting her poster on image heavy vs. non-image heavy blogs that she has written.

Sarah was the first to present a poster on her blogs, in which she has used several large and high-quality images to explain the geology of a particular region (see her posts about Acadia National Park and the Bay of Fundy). She compared how these posts engaged readers compared to some of her other posts that were not so image-heavy. To compare these posts (lots of images vs. not so many images), she looked at the number of visitors to the site on the day each blog post was released, as well as the engagement rate of each post (engagement rate= number of interactions/number of people who see the post). Sarah concluded that over time, her image-heavy posts would gain more views and interactions than her posts with less images.

I was the next to present a poster later in the week. The data I presented was related to six advertisement campaigns Jen and I set up on Facebook. The purpose of paid advertisements are to gain a larger following on social media and to reach a wider audience. There are two main types of ads on Facebook: a paid ad, where you create an ad in the Facebook Business Manager site, and a boosted post. A boosted post is a post that is already on social media (that shows up on a page’s timeline), but you pay money for that post to be ‘broadcast’ to a larger audience outside of the page’s followers. Jen and I have experimented with both types of ads, and we have also experimented with using both static images in the ad and short slideshows.

Me and my poster, in which I presented data relating to the success of our social media ad campaigns.

To compare which ads did best, I looked at the number of engagements each ad received (clicks, reactions, shares) and the number of visitors to the site for the period for which the ads ran. I also calculated the engagement rate for each ad. It turns out that the ad with the highest engagement rate was the first ad (boosted post, static image), although this ad did not have the highest number of engagements. What was different about the first ad is that Jen and I shared it into several groups on Facebook (Women in Paleontology, etc.). The ad that gained the most engagements was a 6-second slideshow with images from the site (it was a paid ad). However, this ad had one of the lowest engagement rates, meaning although it was seen by a large number of people, not many of those who saw it interacted with the ad.

I then compared the number of new visitors to the site, the percentage of women and men, and percentage of site visitors by age group during the ad campaigns to the same variables for the entire site. The number of site visitors during ad campaigns didn’t increase substantially, and the percentage of women, men, and site visitors by age group remained relatively the same from the site total. This indicates that our ad campaigns aren’t doing a great job getting new people to visit the site. Instead, the site attracts an audience by releasing new blog posts and content. In our site user data (which shows us the number of visitors to the site on any given day), peaks in users occurs on days where we release new blog posts. So for the Time Scavengers site, maybe paid advertisements aren’t the way for us to build a larger community and reach more people.

To recap, all three of us who presented on Time Scavengers (Jen, Sarah, and I) had great conversations with other people who are also making educational content and work in the realm of science communication. All in all, GSA 2018 was a huge success in terms of sharing science, meeting new people, forming new collaborations, and learning about the cool new things our friends and colleagues have been working on!

 

Cooking with Foraminifera Part I

Adriane here-

Stirring a solution of tap water and Miramine for use in our experiment.

A lot of the research my lab and I do is related to understanding how the oceans worked in the past, the ocean’s response to climate perturbations, and understanding plankton evolution. Every now and then, we find the need to do a different type of research: testing a new or old method. This fall, my lab mate Serena, my advisor, Mark, and myself have developed a little experiment to see if boiling foraminifera in different solutions has any effect on their shells. Specifically, we’re interested to see if boiling affects the isotopic measurements of the shells. This has not been tested thoroughly before, which is surprising. In this post, I’ll talk about the first part of the experiment, and I’ll elaborate on the other part of this experiment in a subsequent post.

Our samples split into three different solutions. Notice how different the contents of each beaker look! This is because the sediment types we chose have very different colors.

You may be thinking ‘why on Earth would you boil foraminifera in the first place?” When we, scientists, get in sediment samples from deep sea sediment cores, sometimes the sediment is very hard or full of fine-grained sediments. These hard and/or fine-grained sediments have a tendency to not want to break down and release the foraminifera shells contained inside. To aid in breaking down tough sediments, we often turn to boiling the sediment in tap water or other solutions.

To begin the experiment, Serena and I chose four different sediment samples from different places around the world and of varying ages. We split each sample into quarters to be tested in our boiling experiment. We then chose three different solutions in which to boil our samples: tap water, Sparkleen (a mild detergent) mixed with tap water, and Miramine (an oily substance used as a emulsifier and corrosion inhibitor, but also good for breaking down rocks) mixed with tap water. Each quarter of the samples we chose were placed in these solutions in a beaker, which were then placed on a hot plate. The samples were brought to a slow boil and left for an hour.

Eight of our samples boiling on the hot plate. We place a piece of venting over the hot plate and beakers to keep the beakers from falling off the plates.

The fourth quarter from each sample was used as a control for which to compare everything else against (from here out I’ll call these the ‘control quarters’). The control quarters were simply rinsed over a screen using tap water. Doing this removes the small sediment particles, but holds back the foraminifera shells.

This is what one of samples that was boiled in Miramine looked like under the microscope! It’s hard to see here, but the rounded bits of sediment are actually foraminifera. The large chunk to the right is a piece of sediment.

After the samples were finished boiling, we then washed each one over a screen in our sink, just like we did with the control quarters. These were placed in an oven overnight at a very low temperature to dry. Once the samples were dried, Serena and I picked out three different species of foraminifera from each sample: a species that lived at the very top of the water column, a species that lived deeper in the water column, and a benthic foraminifera species that lived on the seafloor.

The last step was to put the species we had picked from each sample into a vial for further analysis. The next step will be to put these vials in our mass spectrometer, a device used to measure the isotopic signature from each sample. We’ll then compare the measurements from the boiled samples to the control quarter samples to determine if the isotopic measurements from foraminifera shells are affected by boiling!

Fun with Foraminifera

Audrey here-

This summer, I will graduate from with a bachelor’s degree in Geology, and then begin a Master’s program in Elementary Education. My favorite thing about being a Geology student was the fact that we had so many opportunities to learn in hands-on settings, from taking field trips to just getting to hold different rocks and fossils in the lab. As a future educator, this experience showed me exactly how important it is for science instruction to involve meaningful and tangible experiences for students, not just lectures. For the last few months, I have been working on an independent study project with two graduate students, Jen and Maggie. To combine my passion for education with my love of geology, we decided to assemble a set of resources that educators can use to effectively integrate fossils into the K-12 classroom as an educational tool.

Why foraminifera?

Paleontology education is a great way for students of all ages to learn about Geology. The use of fossils makes learning fun and hands-on. For many students, the thought of fossils brings to mind images of giant dinosaur skeletons. However, most of the fossils discovered by paleontologists are very small!

For frame of reference, we took photos of real foraminifera on a penny! Notice Abe’s nose!

Microfossils like foraminifera, or forams, have so many exciting uses for the scientific community. These planktonic marine organisms are usually the size of a grain of sand. They’re small, but mighty! Due to their small size, it can be difficult and expensive to effectively teach about forams in most classrooms. Typically, a microscope would be required to view them, but the cost of this technology is prohibitive for most school settings. Even if microscopes are present in the classroom, it can be difficult to be sure that all students are able to see and identify the specimen through the lens. In our lab, we have a set of enlarged plaster models of forams that are used to teach about the various foram morphologies (shell shapes). I think these models make great tools for teaching about microfossils, but first we needed to make them accessible for science classrooms.

Implementation

Here I, Audrey, am scanning some of the foraminifera models.

By using a 3D laser scanner, we were able to make digital 3D copies of our models. With access to 3D printing technology, anyone who has these digital files can print out their own set of foram models! All of the scans that we made are able to be accessed on an amazing website called myFOSSIL. This website is a platform for social paleontology, which means that anyone can share their 2D and 3D images of fossils. These images can also be accompanied by educational resources like lesson plans. The website is completely free to use, and you are not required to set up an account in order to view any of the fossil samples. Find our 3D fossils by clicking here!

Foraminifera in the classroom

To go along with our foram models, we created several lesson plans to guide educators through these resources. All of the lesson plans are written in order to be used with a variety of age groups. The subjects include introductory information about forams, an ecology lesson, and a high-school focused lesson on paleoclimatology. We even wrote one lesson that focuses more on English Language Arts (ELA) skills for younger students, by discussing science content, and diversity in science, through an ELA lens. The goal with these lessons is for each to be accessible to a wide range of ages and ability levels. For middle and high school students, there are a wide range of expectations for students to understand science concepts. These are outlined in the Next Generation Science Standards, and cover topics from earth science, to biology, and even engineering. These were a little easier to touch on in our lessons because 6-12 grade students have distinct and exciting milestones that they are expected to reach in their scientific development. However, for K-5 grade students, science classes are more about setting a foundation to build upon later. For this reason, elementary lessons about forams focus more on teaching students to think, research and communicate like a scientist would, using Common Core Standards as a framework. The amount of detail that each teacher decides to go into on science concepts can vary by age, ability, and other factors that we could talk about all day. However, having the opportunity to do hands-on activities with data and fossil models is a great opportunity, and a lasting experience. While high school classes might focus on more formal research projects, elementary classes could dress up like scientists to tell their classmates and parents about what they learned. There are so many possibilities!

Big Picture

As a science teacher in training, this project was tremendously helpful for me in thinking about the expectations that I might have for my future students and planning for the ways that I could differentiate these resources to be exciting and educational for students across all ages and abilities. I also think that using these lessons in any classroom would help other teachers to delve into the ways that we teach students to think of themselves. Some of our students are encouraged to pursue science from a very early age, others are not. With these resources, there are fewer barriers to accessing science education. On a large scale, this could be an amazing stepping stone for a future generation of scientists. On a small scale, I feel like I was able to better myself by working on this project, and I hope you enjoyed hearing about it.

Picking Foraminifera for Stable Isotope Analyses

Adriane here-

I am beginning to finish one of my dissertation chapters, which means I am starting on a new research project! But first, let me explain (for those who may not know) what a dissertation is: A dissertation is a compilation of three papers, or as we in academia call them, chapters. Each chapter is meant to eventually be published in a scientific journal, as each one is a separate research project or study. Some PhD programs may be different, but at my university, we usually have 3 chapters in our dissertations; in other words, in order to gain a PhD, we have to conduct 3 separate research projects.

Sea surface temperature map of the northwest Pacific Ocean (see inset map at top left). Here, the major ocean currents are labeled by white arrows. The Kuroshio Current flows along the eastern coast of Japan, where it meets the cold-water Oyashio Current. Around 35 degrees north, the Kuroshio Current flows into the Pacific Ocean, where it becomes the Kuroshio Current Extension. The three sites I’m working with are plotted on the map (Sites 1207, 1208, and 1209).

The new project that I am beginning is to reconstruct the ‘behavior’ of the Kuroshio Current Extension. This current, which I’ll call the KCE, is a western boundary current. Western boundary currents flow along the western edge of ocean basins. The KCE flows along the east coast of Japan, on the western side of the Pacific Ocean. Western boundary currents are quite important because they transport really warm waters from the equator northward to higher latitudes. This warm water that is transported towards the poles provides water vapor to the atmosphere. Thus, these currents, to some extent, control weather patterns (such as rain). But western boundary currents, and especially the KCE, are very important areas for wildlife as well. Where the KCE is forms what is called an ecotone. An ecotone is a region where two biological regions come into contact. Here, within the KCE, species that live in warm waters are able to mix with species that live in cooler waters. This makes for a very diverse (a lot of different species) area within the KCE. Even corals, who can only tolerate warmer waters, are found at their furthest poleward extent in the KCE region. And associated with corals and coral reefs are fish and their predators. So, the KCE region is an important region to local Japanese fisheries.

By now you might be wondering why all this background on the KCE matters. Because the area within the KCE is so important from a climate, biological, and economical perspective, it’s important to understand how the current will behave (shift to the north or south, increase or decrease transport capacity) under climate change. Right now, we have direct measurements of the KCE that indicate the current is beginning to slowly shift northward. But how much will the current shift? How will this affect the food chain in this region? To begin answering these questions, geoscientists often go back in time to investigate these systems during times of elevated global warmth. Thus, I will be reconstructing the sea surface temperature at three sites that cross the KCE during a more recent warm period in Earth’s history, called the mid-Pliocene Warm Period.

In 2001, there were three sites in the ocean that scientists collected sediment cores from. These three cores were collected to the north of, directly under, and to the south of the modern-day position of the KCE. I’m using sediment taken from the cores collected at these three sites to reconstruct the position of the current from 5 to 2.5 million years ago. But how will I do this?

When a specimen of Globigerinoides ruber or Globigerinoides obliquus is found from a sediment sample, it’s picked out with a paintbrush and some water and plopped into this labeled slide. The numbers at the top are the sample number.

To reconstruct sea surface temperatures, we need to measure stable isotopes of carbon and oxygen (read more about these two proxies on our ‘Isotopes’ page). Namely, oxygen is the most commonly used proxies to reconstruct temperature, and carbon is more commonly used to determine how productivity (or, more simply, how many nutrients were in the water column) through time. We measure isotopes of carbon and oxygen from the shells of planktic foraminifera.

This is one of the small weighing trays I use to weigh the specimens that are picked from the sediment samples. Each tray has a number associated with it (see sticker at bottom right).

The first step in this study is to ‘pick’ planktic foraminifera. This means that within each sediment sample within my 5-2.5 million year time interval, I sprinkle sediment into a tray and, with a paintbrush, literally pick out a certain species of foraminifera. The species that I’m using in this study is called Globigerinoides ruber. I just call them ‘rubers’ for short. This species of foraminifera is useful because it is still alive (extant) in today’s oceans, and because of that, scientists know exactly where this species likes to hang out in the water column. Rubers live in the upper part of the surface ocean, so they effectively record the conditions of the ocean’s surface, which is great!

Once I have picked out enough specimens from a sample (which ranges from 10 to 20), I weigh the specimens in an aluminum tray on a very sensitive scale. I need about 150 micro grams of rubers per sample for a good isotopic measurement.

After I have weighed the specimens, I then take my paintbrush and put them, one at a time, into a small plastic vial that is numbered. I also have a spreadsheet where I record all of the information, such as the number of specimens picked per sample, the empty weight of the aluminum tray, the weight of the tray and specimens (so that I can then calculate the weight of just the specimens), and the vial number that corresponds to each sample.

Plastic snap-top vials that each have a number. After the specimens are weighed in the aluminum trays, I then transfer them to these vials. I’ll mail these to another university, where the specimens will be analyzed.

I put the specimens in a vial with a very tight snap-cap because I will send all my samples to another university for isotopic measurements. We could do the measurements at my university, but the machine that we use to do this is not properly calibrated to make measurements off of foraminifera. But lucky for me, I have some awesome collaborators that do have machines that are finely tuned to take isotopic measurements from foraminifera!

Once vialed, the samples will be mailed off to the University of Missouri for isotopic measurements. It usually takes anywhere from 1-3 months for my collaborator there to run all my samples. When he is finished, I’ll receive a spreadsheet with the measurements. I’ll plot these data through time. Then, the fun part: I get to make interpretations about my data! I’ll use these data to track changes in the KCE through time, and also to correlate evolution and extinction events of planktic foraminifera to changes in sea surface temperature through time!

Creating a High-Resolution Biostratigraphy

Adriane here-

A sea surface temperature map of the northwest Pacific Ocean, with warmer colors representing warm waters, and cooler colors representing cooler waters. The white lines with arrows are the major ocean currents , with the Kuroshio Current flowing along the coast of Japan. The three deep sea sites I’m using in my research are plotted on the map (black dots).

For the past two years, I’ve been conducting research into planktic foraminifera (‘foram’) evolutionary events in the northwest Pacific Ocean, specifically across the western boundary current known as the Kuroshio Current Extension (which I’ll call the KCE from now on). This is a dynamic area of the ocean, and is unique in that forams from warm waters are able to mix and mingle with cold water forams. This mixing of warm and cool species may lead to evolution of new species, but this process is poorly understood. So, part of my dissertation is to determine how important these western boundary currents, specifically the Kuroshio Current Extension, is in the creation of new plankton species. In doing this study, I am also creating a way to tell time using planktic foraminiferal biostratigraphy. OK, those were a lot of big words, so let me explain:

Biostratigraphy is composed of two primary words: bio, meaning life, and stratigraphy, which is a branch of geology concerned with the relative order of rocks and putting time into the rock record. So in short, biostratigraphy is using life to put time into the rock record, or using fossils to tell time. In my case, I use planktic foraminifera to tell time (read more about how I do that here). Commonly in biostratigraphy, we (paleontologists) create zones, which are blocks of time that are constrained by the evolution and extinction events of animals or, in my case, plankton. In the northwest Pacific, there are currently no detailed planktic foram biostratigraphies. Part of my research is to fix this problem!

To conduct a biostratigraphy and thus look at plankton evolution and extinction events, I’m working with sediment that was taken from three sediment cores. These cores were drilled from the north, directly under, and to the south of the modern-day position of the KCE in the northwest Pacific Ocean. The sites go back in time to ~15 million years ago, which is quite young compared to the rest of Earth’s history (4.6 billion years!). Each site contains minerals that aligned to the Earth’s magnetic pole when they were deposited on the seafloor. The direction in which these minerals align were measured by other scientists when the cores were drilled. It turns out that each core records almost all of the Earth’s changes in its magnetic pole. This is important because other scientists through the decades have worked hard to date each of these magnetic reversals. Thus, I can use these ages to construct an age model for each of my sites (an age model is where I assign an age to a certain depth in the core where a magnetic reversal happened; what I end up with is a plot where I can calculate the age at any depth in the core). This age model is important because I can then use it to determine precisely when a foram species evolved or went extinct at any of my three sites.

One of my cardboard slides. Each box contains a different species of foraminifera. On the side of the cardboard box, in purple ink, is the identifying code that tells me where exactly in the world and in the sediment core this sample is located. Currently, I have 414 of these!

The first step was to determine at what resolution I wanted to look at foram evolutionary events. I went with 30,000 years, on average. This means that every extinction or evolutionary event has an error of plus or minus 30,000 years. This seems like a lot, but in reality, it’s pretty good! After determining the resolution I wanted, I then used my age model to determine where within each core I wanted to request sediment samples from. All of the cores I use are stored in a facility in College Station, TX (read more about it here), and any scientist can order samples from the facility for free (it’s awesome!). The samples arrived within 2 months after I ordered them.

After I had sorted, sieved, and dried each sample to obtain foraminifera, my samples were ready to be used! I started at the warmest site, the one located to the south of the KCE, in the youngest sample. I sprinkled sediment from the sample onto a tray, looked at the sample under the microscope, and picked out with a small paintbrush every species I could identify. These specimens were placed on a specimen slide (a rectangular cardboard slide with 60 boxes) that had a thin layer of glue over it. In this way, the specimens from each sample stay on the slide, and can be looked at by researchers for years to come. I also have slide maps, or pieces of paper with 60 boxes printed on it where I label what species is in each box on the glued specimen slide. Picking one sample takes anywhere from 30 minutes to an hour, depending on how many species are present in the sample.

This is a figure with all of the evolution and extinction events that happen at my three sites. Site 1207 is on the left; 1208 in the middle; and 1209 on the right. In the middle is the Geologic Time Scale, representing the last 15 million years of earth’s history. The other two sites (1207 and 1209) are also plotted along time, with oldest at the bottom and youngest at the top. The species names that are in red are extinctions; the names in blue are evolution events.

It’s important to note that I did not look at all the samples that I ordered from College Station, TX. Instead, I did a ‘preliminary pass’ through every 10th or so sample. When I found a sample where a species evolved or went extinct, I then looked at the sample between that one and the next, and repeated that process over and over until I had constrained the event to +/- 30,000 years. I then repeated this process for the other two sites.

Once I had all the data, I plotted it up into several figures and spreadsheets to see where all the evolution and extinction events are taking place. Then, I looked at when several species that are commonly used to define zones among sites (these species are used because they are resistant to dissolution when ocean waters become acidic, they are large and easy to identify, and they occur in high numbers in each sample) evolved or went extinct. It turns out that although the three sites I’m using are close together (they span about 5 degrees of latitude), an evolution or extinction event in one species happened at different times across cores! This is a really cool result, as it means changes in the position of the Kuroshio Current Extension could have caused a species to migrate away or not able to live in the area anymore!

In addition to constraining plankton evolutionary events, I was also able to create zones for use in biostratigraphy bound by these evolutionary events. This is the first study that will have constrained plankton evolutionary events in the northwest Pacific Ocean at a high resolution, and the first time mid-latitude planktic foraminifera zones are calibrated (directly plugged into) the Earth’s magnetic record! I hope to publish these results later this summer in a scientific journal!

Geologic Mapping on Mars

Rose here –

One of the famous first stories of modern geology involves the publishing of a geologic map of England by William Smith in 1815. This was one of the first geologic maps made by a geologist doing fieldwork, which often involves camping out in an area for a few days, weeks, or months to find out as much as possible about the area to be mapped. Geologists walk around the area to be mapped and take measurements of what types of rocks are there, how thick each layer is, whether they are tilted or faulted, etc. They may also take samples of the rocks to do chemical tests or look at them under a microscope. Field geologists look at the morphology (shape) of the landscape in order to map the locations of ridges, depressions, and other features and determine the processes that formed them.

Several students (I am on the far right) mapping the “Banana Canyon” area in southern Idaho at senior field camp, summer 2014. We spent a couple days roaming around this area, taking measurements and notes and figuring out what kind of rocks were here. Then we would go back to camp and use our measurements to make a cross-section showing the different layers of rocks and where faults or folds might have occurred. Our long sleeves, pants, and hats were so we didn’t get sunburned – it was actually pretty hot that day (and every day)!
My experiences in geology as an undergraduate major were largely field-based, going on many field trips to various places and taking notes and measurements at different locations. But how do you make a map when your field area is on average 140 million miles (225 million km) away from Earth? I had never considered studying geology in a field area anywhere other than Earth, but shortly after starting my master’s degree I had the opportunity to work with a team of collaborators to create a geologic map of a small region on Mars. Geologists can now create maps of planets, moons, and asteroids using high-resolution images from spacecraft orbiting Mars, Mercury, the Moon, and many other bodies in our solar system. I was excited to begin this project, but first I had to learn a whole new set of skills than what I had used in field camp as an undergrad.

There are several software programs scientists can use to make maps using images and other types of geospatial data. These software programs are collectively called Geographic Information Systems (GIS). GIS software is used in many different fields for different kinds of projects and analyses. For example, biologists might use GIS to make maps of where certain species of animals live in relation to cities, lakes, highways, etc. Geologists might use GIS to produce maps showing the location of certain types of rocks or geologic features.

For my master’s project, I used a mosaic (several images digitally “stitched” together) of images from the Mars Reconnaissance Orbiter’s (MRO) Context Camera (CTX). To identify a feature in these spacecraft images, it needs to be big enough to have at least two pixels across it each way (so a minimum 2×2 grid). CTX images of Mars have a resolution of 6 meters (m) per pixel, which means they can be used to find features about the size of a large room. When I upload these images into my GIS program, I can zoom in and out to see features better. When I find a feature that looks interesting, I can mark its location and shape by making a new “layer” and drawing on the image. I use different layers for different types of features, and each layer can be turned on and off so I can see where different features are in relation to each other.

Here I am doing a totally different kind of mapping! I am using the GIS software ArcMap from ESRI to map the locations of wrinkle ridges in my study area, a place called Aeolis Dorsa in the eastern hemisphere of Mars near the equator.
My first step in mapping was actually not mapping, but reading lots of previously published papers about the geology of my study area and about the particular type of feature I wanted to map. I am mapping a type of ridge on Mars called a wrinkle ridge. This ridge is formed by tectonic contraction and is found in layered igneous or sedimentary rock units. Once I had read as many papers as I could find on wrinkle ridges and made several tables summarizing the various types of information on them, I could finally start mapping. It took quite a while for my eyes to get used to looking at these images and to pick out the features I was looking for. However, wrinkle ridges have several common distinguishing characteristics, mentioned in many published papers, that I used to double-check my visual identification. When I had gone over my whole study area several times and marked any feature I thought could possibly be what I was looking for, I went over it again and narrowed down the number of features using my list of common characteristics. Learning to identify wrinkle ridges and other features visually is a good skill and I spent a great deal of time trying to do so. However, it is also important to make my results understandable and reproducible by other scientists. Thus I need to be able to clearly show how I identified a feature as either a wrinkle ridge or not. With my list of common characteristics, I decided how many of them would be required to determine if a feature is a wrinkle ridge, and within those determined to be wrinkle ridges I further divided them by how many characteristics they had into certainty levels: Certain, Probable, and Possible. This process allows my work to be reproduced or at least easily followed by any future scientists studying the same type of features.

I’ve been working on this project for about two years now and while it’s been a lot of hard work and tired eyes, it so rewarding to see my map finally coming together. While I’ve been mapping one type of feature, other scientists in my research group have been mapping different types of features and we are about to put them all together and make one complete map. When we have all our mapping together on one map, it will be published as an official United States Geological Survey (USGS) geologic map. Stay tuned!