Scavenging the fossil record for clues to Earth's climate and life
Adriane, Jen, or another collaborator will post here biweekly to showcase what they did over the past week or so. The goal being to show what exactly goes into being a scientist. It’s not always fun field work or museum trips, often we are rummaging through data or staring into a microscope!
This summer a few members of the UMass Micropaleo Lab traveled to Texas for the first ever International Ocean Discovery Program-Past Antarctic Ice Sheet (IODP-PAIS) Antarctic School at Texas A&M University! This program allows scientists from all over the globe who research Antarctica to come together to study the marine sediment cores stored at the IODP Core Repository.
During our week at the repository, our mornings were filled with lectures and real-life activities led by geoscientists who have sailed on previous drilling cruises. We learned from them what shipboard life is like, how drill cores are taken, what problems can arise while drilling in Southern Ocean around Antarctica, and how to interpret the clues within the drill cores. To explore those clues, we were divided into mini-research teams and each given a core section from a prior expedition to analyze. Each afternoon we rotated among different core analysis stations: how to make and analyze microscopic smear slides, how to describe the macroscopic features of the core section, how to gather and interpret paleomagnetic and density data on the core sediment, how to scan core sections for key trace elements and improve your paleoenvironmental interpretations using element abundance data, and how to develop a timeframe for your core section (chronostratigraphy). Putting this all together, we were able to map a pattern of ice advance and retreat over where the drill core was taken. Since the core sections we were studying came from expeditions, we were able to double-check our data and interpretations against the published results and see how successful we were–my group was able to match the chronostratigraphy of the original study!
I was excited to learn so much and gain so many new friends at the Antarctic School, but my excitement was tempered by being the only woman of color in the program. I was ashamed to learn that an international program participant could not attend because they were not granted a U.S. visa in time: the American visa process is extremely biased, and as an international organization the IODP should use their agency to help all invited participants attend, regardless of their countries of origin. It is not enough to non-racist in today’s society–we must be actively anti-racist. I think international STEM research programs such as this one should hold spots specifically for students of color, students with disabilities, and other folks who are traditionally marginalized and underrepresented in STEM to attend. Programs like this are critical for early-career scientists to network with each other and the leading scientists in the field, and without holding doors open for marginalized students, how else will diversity in STEM increase?
Creating a poster for class, a workshop, or a professional conference can be a daunting task. No matter what I’m creating the poster for, I try to stick with a simple and clean background and then once the organizational structure is in place, start to fill it in. This usually results in huge changes as I progress through the content but that’s okay!
Before getting started on your poster there are a few major things you should think about:
What program do I want to make my poster in? Google Slides integrates well with Google Sheets (free), Microsoft Powerpoint is pretty easy to manipulate (not free), and Adobe Illustrator is excellent for really detailed work (not free). There are many other programs, such as Canva (free), that offer lots of integration for images, line drawings, and more.
Who is in your audience? This will help you tailor language, depth of content, and figure detail on your poster.
Are there poster requirements? Size can be dramatically different and it’s always easiest to start with the biggest poster allowed and cut it down if you don’t need the space.
Generally, I like to work with boxes. Boxes help keep the organization of the poster nice and tidy. A major title box at the top that includes your poster title, authors, affiliations, and abstract number (if relevant). I usually aim to have the title in 72 point font and then everything else is a bit less. Having your regular text between 18-24 point font is a pretty good range and headers somewhere in the 40s-50s.
The rest of the poster is subdivided into larger boxes for each part of your project. These generally include but are not limited to: Introduction, Methods, Results, Conclusions, and Acknowledgments. Obviously, science and other projects don’t fit neatly into these categories but it’s a good starting place and titles can always be changed! It often helps just to get something on the page and then you can modify things later.
It’s always good to make sure your poster can stand alone when you aren’t there to walk viewers through the content. This means I usually include introductory or background text to help set the stage for the reader and reduce the text throughout the rest of the poster. This means shorter text, phrases, or bullets through the methods and results to concisely walk the reader through your content. Full sentences can be useful for discussion, conclusions, and/or broad implications of your work but sometimes bullets are plenty! Once you get to creating, it should be clear how much or how little you need to say.
Don’t forget to include references and people who have helped you out in your acknowledgments section. If people are interested in how you phrased something they may want to look up a reference that dives more deeply into the content. You can use regular in-text citations on your poster or superscripts to keep it neat and tidy. It’s good to include funding, departmental (internal or external) equipment that helped with analyses, and anyone who helped you run the machines or gain access to specimens!
The other major thing about posters is color schemes. Sometimes your supervisor or department may urge you to use school colors, this is fine but make sure you are following brand/logo policies (because they are confusing and there are a lot of rules). I like to throw in a lot of color wherever I can. It may be because I work on fossils and they are gray and often dreary-looking but I do believe that if your poster is visually appealing at first glance it will draw people over to you!
Quick Tips and Tricks
Make sure to include your affiliation (organization or institution)
Include logos of institutions or funding that helped support your project
Use colors that you like but that also help draw people to your poster
Send it to your friends and co-authors to edit before finalizing it
Always save it as a pdf when you send it off to be printed
Sometimes printing can take long, make sure you have enough time
Have fun, posters are an excellent networking opportunity
If you click here you can go to a template Sarah and I made when we were teaching a summer course. You can save a copy of this template to your Google Drive to play around with the different elements.
Have you ever wished there were more scientists involved with politics or politicians who were more informed about science? I certainly have. So when an opportunity to travel to Capitol Hill to get training on how to meet with legislators about climate science- and to actually meet with their offices- presented itself I jumped on it. Policy proposals that impact science are happening around us all the time and the best way for scientists to help ensure that policies are backed by science and support the scientific process is for us to get involved. There are many different programs through various scientific societies that provide training to student scientists and early career researchers on how to communicate their work to policy makers. The specific program I participated in is called Climate Science Day and is coordinated by 12 different scientific societies. The training took place at American Association for the Advancement of Science (AAAS) in March 2019 and my participation was sponsored by the American Geophysical Union (AGU). The objective is to provide a non-partisan way for us to meet with congressional staff, begin building relationships with offices, and learn about some of the work that is currently being done on the Hill.
In total thirty five early career scientists participated and we were broken into teams of three based on geographic region. My teammates were Logan Brenner from Columbia University and Heather Sussman from SUNY-Albany, and our team leader was Lexi Shultz the Vice President of Public Affairs at AGU. Together we met with 7 congressional offices from Massachusetts and New York. To prepare us for the meetings we had a webinar and informational packet to go through in advance of the trip. These materials covered how Congress is structured, what the differences are between the Senate and the House of Representatives and how that impacts the work each side does, what the important committees relating to climate change are, and how to effectively communicate during meetings. They also emphasized the unified ask of “support, communicate, and use in policy discussions and decisions the scientific community’s consensus on climate science.” When we arrived in DC we had one day to attend a training at AAAS, meet our teammates, and prepare our materials for the next day’s congressional visits.
We had a limited time to prepare for our meetings. We all arrived the day before the meetings were to take place and attended a training at AAAS where we learned how to conduct a congressional visit, heard from a panel of staffers, and met our teammates and team leaders. To have a successful meeting you need to be knowledgeable about who you are talking to. Meetings rarely happen with the legislators themselves, instead they are usually with congressional staffers. The staffers are usually people with scientific backgrounds and occasionally they are themselves early career scientists interning as fellows sponsored by various professional organizations to learn more about the connections between science and policy. They are also very important to getting things done on Capitol Hill and are instrumental in carrying out the work that happens in the offices. Their time is extremely valuable and it is important to speak to them as though they are highly knowledgeable about these topics- because they are!- and to express your gratitude for their time. My three favorite staffers we met with were all fellows and had backgrounds in teaching, solar development, and marine biology!
The most valuable part of the training was the breakout sessions with our teams to decide what our specific asks were from each office and who would lead each meeting. Having a specific ask is very important as this is the action step you are hoping to convince your representative to take. The ask varies based on what you think your member of Congress is likely to want to do and what actions they have taken in the past. For members who are less engaged on climate issues asks should revolve around getting them to commit to becoming more involved. For us one of the offices we met with was of a Rep Katko (R-NY-24). We noticed in looking through the committees he was on that he was the only member of the New York delegation not on a specific environmental committee. We chose our ask for that office to be for him to join that committee. In the meeting at that office we spoke to his staffer about environmental issues that are a concern in his district, how climate change can exacerbate them, and how his work in joining this committee could benefit his constituents. For congressional members who are already active on climate issues we first thanked them for being leaders on such a pressing issue and then asked of them to go a bit farther, for instance by giving a floor speech on recent climate publications put out by government scientists such as the Fourth National Climate Assessment, or co-sponsoring a piece of upcoming environmental legislation. For members in our own local districts, we included in our asks invitations for them to come visit our research labs and perhaps do a public event with us to bring light to scientific work on global issues happening in their local districts and policy work they are doing to advance solutions.
On the day of the meetings we donned our business attire and convened on Capitol Hill. Logan and Heather each led two of the four meetings with the NY offices and I led the three meetings with MA offices. First up was Rep. Clark of MA’s 5th congressional district. It went very well and was the perfect meeting to ease us into the day. We met with a staffer who was a fellow with a background in education. She was eager to hear about our work and said Rep. Clark would likely be happy to complete our ask of giving a floor speech. One of the highlights of our day was meeting with Rep. Grace Meng (D-NY-6) who we requested join SEEC, the Sustainable Energy and Environment Coalition, chaired by Rep. Paul Tonko (D-NY-20) which is one of the most active and effective congressional committees on environmental matters. Later in the day we met with Rep. Tonko’s office and they mentioned that they had just received a call from Rep. Meng asking to join his committee! This was a huge win for us as it meant that Rep. Meng had already acted on our ask just an hour or so after meeting with her office. Another highlight of the day was meeting with the Legislative Assistant for Rep. Adriano Espaillat (D-NY-13). He was very interested in connections between social justice and climate change and how to improve the health and wellbeing of the people in his community, while providing them with good jobs, and working to combat climate change all at once. We ended the day at MA Senator Markey’s office where we met with two staffers who were fellows just out of graduate school- one was a marine biologist and the other worked on solar development and sustainability. We had a great conversation on scientists and scientific data that are being used to craft legislation for the Green New Deal.
The two days on Capitol Hill were a whirlwind of meeting new people and learning how scientists and policy makers can work together to make substantive change. If you want to get involved in communicating with your legislators, check with the scientific societies you are a member of to see if they have trainings coming up. You can also reach out on your own to your local legislators and offer your expertise and knowledge for policy work they are currently doing. In addition if you ever find yourself in Washington DC you can also ask for a meeting yourself if you would like to share your science and find ways your work and expertise can benefit their offices. With so much work needed in developing concrete actions that will help implement a global transition to a climate friendly world we will need everyone getting involved and offering to help in any way they can. You have so much to offer, so get out there and start making it happen!
This post is a follow-up to one I wrote previously called ‘Plankton Photo Shoot‘. In that post, I described how I take images of my fossil plankton using a scanning electron microscope, or SEM. But that was really just the first phase of taking images. In this post, I’ll talk a bit about what I do with the SEM images once I have them, and how I clean them up.
After I have SEM images, I save them to a few different folders. When taking images of fossil plankton, we usually take several pictures of the same specimen: one of the spiral side, the umbilical side (think of this as your back and front), and one of the side view of the specimen. After the images are organized into the appropriate folder that corresponds to the side of the plankton I took an image of, I then begin the editing process!
The first thing I do is open the image I want to work with in Adobe Photoshop. Once imported, I then use the ‘Quick Selection’ tool to draw an outline around the fossil. I do this so I can copy and past just the image of the fossil into a new document and cut out the background. One I have the fossil isolated, then the real fun begins!
The first thing I do with an isolated fossil image is to zoom into the image. The reason I do this is because I want to inspect the image to see how well the ‘Quick Selection’ tool worked. Sometimes, if an image does not have a lot of contrast, or the background looks the same color as the fossil, some of the background will be included in the selection. If this happens, I then use the Eraser tool to go around the outside edges of the image. This makes the image more crisp and defined!
This is what the image looks like after using the eraser tool on the edges of the image. You can’t tell too much, if any, of a difference, but it does help give the image a bit more definition! I also delete the white background before I save the image as a .PNG file type (.PNG files don’t have a background, which is great because then I can put the image against any color background I want to later).
And that’s it! I now have a beautiful fossil image that will be used later in a publication! Of course I have to repeat this process for each fossil (which, right now, I have over 200 to edit!). Stay tuned for Part III of Plankton Photo Shoot, where I’ll show you how these images will be displayed in a publication for other scientists!
A good portion of the FOSSIL Project team are in the UF College of Education and I’ve been trying to learn all that I can about studying learning in digital spaces. A recent grad, Dr. Lisa Lundgren, worked to determine who were the members of the myFOSSIL online community. She developed a taxonomic system to describe who was interacting on myFOSSIL. I’ve been a participant within the community since 2014 when it began so I have been really interested in her work. One of the primary goals of the project is to connect professional and amateur paleontologists. I wrote about her defense on my personal blog, which you can find by clicking here.
So, now that Lisa has produced a framework (Paleontological Identity Taxonomy (PIT), read more here) to begin examining and analyzing the community the education team is really diving into it. I was asked to join one of the projects they are working on to analyze a year’s worth of Twitter data. The idea being to explore who major contributors are on Twitter in relation to FOSSIL. Are there certain people that may catalyze interactions? How do these people fit into the taxonomic framework that has been previously established?
This project is using both qualitative and quantitative methods. In my normal work, I primarily use quantitative work to assess various things in my chosen fossil group. Diving into the qualitative work was a bit challenging at first but really interesting once I fully understood what I was doing. We were working to classify users within the FOSSIL Project’s Twitter community. This involved going through each person’s Twitter biography to determine how they fit into the PIT. Such as, in their bio do they identify as a scientist? What type of scientist? Or are they a member of the public? If they are a member of the public do they have an interest in fossils? I haven’t had much exposure to how different scientists study learning or communication so I’m really excited to be part of this project. Lisa will be presenting results at the upcoming 10th International Conference on Social Media & Society Conference in Toronto this summer.
As Time Scavengers continues to grow as a community, we need to make sure we understand how to analyze all of the data we have been collecting and if there are best practices for different types of questions we are asking! I have made valuable connections within the education team that have already shown to be beneficial as Adriane and I are teaming up with Lisa on a manuscript right now!
I’ve done a lot of stuff during my time here at UMass Amherst, probably too much stuff (including building this website with Jen and collaborators, which is definitely something I have no regrets about!). Because of the amount of teaching, outreach, and large research projects I’ve done and continue to do, my PhD, which is funded by my department for 4 years, will take an extra year. However, my funding runs out at the beginning of May 2019.
It’s not uncommon for a PhD degree to run over the 4 year mark; in fact, it’s really quite common. But how to sustain oneself for this extra time is the tricky part. There is money available to graduate students to support us in our final year(s) of our degree through fellowships and grants. These are often very competitive and hard to win, but totally worth applying for. So I decided to apply for a fellowship to fund the remainder of my time here at UMass.
The fellowship that I applied for is through the Cushman Foundation for Foraminiferal Research, an organization specifically for scientists who work with fossil plankton. The organization has been around for quite a while, and its members include professors, researchers, and students from all over the world. The Foundation is great because they have several grants and awards for students, to fund their research and travel to local, regional, and international meetings.
The Johanna M. Resig Foraminiferal Research Fellowship is named after its namesake, who was a life-long foraminiferal researcher and editor of one of the most prominent journals for foraminiferal research, the aptly-named Journal of Foraminiferal Research. Johanna was born in Los Angeles, California on May 27, 1932. She found her love for geology at the University of Southern California, where she received her Bachelor of Science in 1954 and her Master of Science in 1956. After graduation, Johanna went to work for the Allen Hancock Foundation. There, she studied foraminifera that live off the southern coast of California. In 1962, Johanna was awarded a Fullbright grant, a very prestigious award that gives money to scholars to study abroad for a few years. With this grant, Johanna continued her research at the Christian Albrechts University in Kiel, Germany. While in Germany, she earned her PhD in natural science in 1965. Once she had her doctorate, Dr. Resig began a professorship at the University of Hawai’i as a micropaleontologist in the Institute of Geophysics. She was the first woman recruited in the Hawai’i Institute of Geophysics, and remained the only one for several years. She was a professor at the university for over 40 years, where she published over 50 articles and book chapters on foraminifera. Dr. Resig published mainly on benthic foraminifera (those that live on the seafloor) as well as planktic foraminifera (those that float in the upper water column). She worked with sediments from all over the world, and also used the shells of foraminifera to construct geochemical records of our oceans. During her career, Dr. Resig described and named five new species of foraminifera and even a new Order! Dr. Resig was not only known for her research, but she was also a dedicated mentor and teacher at the University of Hawai’i. While there, she taught hundreds of undergraduate and graduate students in her courses, and mentored about a dozen graduate students. When Dr. Resig passed away on September 19, 2007, her family gave funds to the Cushman Foundation in her name, and thus the Johanna M. Resig Foraminiferal Research Fellowship was established.
Interestingly, my PhD advisor, Mark, worked with Dr. Resig during her career. They sailed together on a large drillship called the Glomar Challenger, which took sediment cores of the seafloor for scientists to study. During an expedition together to the western equatorial Pacific (called ‘Leg 130’), they were both micropaleontologists (scientists who use tiny fossils to interpret the age of the sediments and reconstruct the ancient ocean environments). Mark is a huge fan of country music, and he recalled that he loved to play country music on the ship while the scientists were working. One song he was particularly fond of, ‘All My Exes Live in Texas’ by George Strait, was deemed entirely comical by Johanna! Mark describes Johanna as a dedicated scientists, a wonderful micropaleontologist, and someone that was a joy to be around.
The fellowship named after Dr. Resig will support the remainder of my time as a PhD student at University of Massachusetts Amherst. The money will be used as stipend (which is a fancy academic word for income), but it can also be used for analyses and lab expenses and travel to conferences. One way in which I’ll use the money is to pay an undergraduate student to process sediment samples that I will use in my next research project. This way, I’ll get a jump-start on my next project, and a student will be earning money doing science. They will also learn more about the samples that are collected as part of scientific ocean drilling. It’s totally a win-win situation, and I feel that by using part of the fellowship to mentor and help the next generation of students, I am honoring Dr. Resig’s memory and her commitment to mentoring and advising.
I do a lot of research for my PhD, and some of that research is painstaking and tedious. But some aspects of research are just downright fun! Today I’m going to talk about one of my favorite parts of my research: taking very high-resolution and close-up images of my fossil plankton, foraminifera!
Because the fossils I work with are so small (about the size of a grain of sand), we need a very unique system to take high-quality and close-up images of them. To do this, people who take images of microfossils use scanning electron microscopes, or SEM for short. An SEM uses electrons reflected off the surface of the fossils to create an image. To do this, the interior of the SEM is a vacuum, and the fossils need to be coated with a conductive material. At our university, we use platinum to coat our fossils.
The first thing I do before I can take images of my fossils is to pick out specimens that I want to photograph. These are then placed onto a small, round piece of double-sided sticky tape. The fossils are so tiny, I can fit tens onto one small piece. This sticky piece is then placed onto a glass slide. We call the fossils, tape, and glass a ‘stub’. Once all the fossils are in place, I then put the stub into a coating machine. This machine coats all the fossils with a very thin layer of platinum while in the presence of xenon gas. The entire process is very quick (about 30 minutes at most). Once the specimens are coated, they’re ready for imaging in the SEM!
The SEM itself is a rather large contraption, but incredibly amazing! The entire machine is operated from a computer that sits on a desk beside the SEM, so everything is pretty self-contained and right there. The first thing I do after coating is to mount the stub on the stage within the SEM. This is simple: it involves taping the stub to a metal piece, which in turn fits snugly onto the stage element of the SEM.
Once in place, I then slide the door to the SEM shut and vent the machine. Venting means I push a button on the computer, which tells the machine to begin creating a vacuum inside its chamber. This process takes about ten minutes or so.
After the chamber inside the SEM is under vacuum, I can then begin the process of photographing my fossils! Everything from this point forward is operated using software on a desktop computer that talks to the SEM. Just like a camera, the images have to be focused before taking the actual picture. This can be either very easy, or very tedious. There are several factors to determining how the image looks on the screen: are the levels balanced, is there charging on the fossils that’s causing a disturbance, the distance of the stub fro’m the camera, etc. There are controls on the computer program that allow the user to make changes and adjustments as necessary.
I find that the best way to focus the image is to zoom in very close to the fossil I want to photography. In this case, ‘very close’ means zooming in more than 2,000 times or more, so I’m really getting up close and personal with the fossils! I use a technique where I select a small window of the entire image, and use the tools in the program to tweak and focus the image in that smaller box. This is a faster way to focus, and when I’m happy with the results, I can apply the changes made to the small area to the entire image.
Once the settings are adjusted and correct for my fossils, I can then get through taking images pretty quickly! Each image includes a scale bar to indicate the size of the fossil and the magnification, which is helpful and necessary to include with each fossil picture. For this project, I was very interested in taking close-up images of the surface of my specimens, and also taking a side-view of the shells (quite unfortunately, this means I had to break open some foraminifera shells once placed on the stub and before coating).
Once all the images are taken, I can then download them onto a thumb drive and work with them on my own computer. This involves using other photography programs such as Adobe Photoshop to crop the fossil images and place them onto a black background.
Although the process of taking SEM images of fossils is incredibly fun, it’s also vastly important for research. I will include images of all my fossils in a publication. This way, other researchers will know how I tell one species apart from another, and the different characteristics of each plankton species. Ideally, I’ll have pages and pages of fossil images, called plates, included with my publications!
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!
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!
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.
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!
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).
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!
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.
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.
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).
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!
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.
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!