Congratulations to Lola Holcomb, for passing the graduate comprehensive exam!! She now goes from being a PhD student to a PhD candidate, and for the next few years will focus on developing her own research designs and writing her thesis.
The exam was set by her PhD program in the Graduate School of Biomedical Sciences and Engineering, and involved writing a 6-page research proposal over the past two months, and on the day of, giving a 1-hour presentation and answering questions from her committee for up to two hours. The focus of the proposal and the presentation are a hypothetical experiment she designs on a topic that is similar to her existing research but not directly related. In that way, you can test a student’s ability to translate their existing knowledge and fact-finding skills to a totally new area and see how well they can reason through a new problem. The committee will ask students to explain their thought process, methods, and how they will assess the progress on the hypothetical project. It’s a long and arduous process, but Lola’s depth of knowledge and ability to problem-solve helped her pass with ease!
Today is the fifth and final day of the July 2022 MSE virtual symposium, which is focused on “MSE Education Practices and Curriculum Design”. Don’t worry, you still have time to register!
This session will feature three talks featuring educators who have brought sociology into their microbiome courses, and vice versa, and who have experience creating out-of-the-box curricula to engage students in learning while helping them to see themselves as scientists. Our hope is that attendees for this session learn from different perspectives how to creatively present microbiology courses which situate learning about the microbiome with learning about social and environmental systems.
Session 5: “MSE Education Practices and Curriculum Design”
Erin Eggleston, PhD, Assistant Professor of Biology, Middlebury College
Monica Trujillo, Ph.D., Associate Professor, of Biology Queensborough Community College, The City University of New York
Carla Bonilla, Ph.D., Assistant Professor, University of San Diego
Scope: Curriculum which blends disciplines is highly engaging, and can be used to teach complex concepts, and can help students combine their existing cultural and social identities with their growing researcher identity. However, creating an interdisciplinary curriculum can be challenging. This session frames educational conversations in MSE, and gives perspectives on creating courses that blend microbiome and social sciences for different levels of education.
Learning Objectives of Session: Attendees will 1) identify successes and barriers to entry for MSE curriculum at different education levels (K-12, UG, grad, general public), 2) Share ways in which we incorporate MSE in our curricula (i.e. assignments, class period, multi-day module, full course, etc.); 3) develop ideas for further curriculum design for their own courses.
Format of talks: Three 30-min lecture-style talks from education practitioners who have successfully built courses around MSE topics, including an outline of learning goals, approach to course, lessons learned/challenges, and more.
Format of breakout rooms: Each room creates a lesson plan outline, and each room has a designated topic area (e.g. human microbiome equity) to help audience members group by teaching discipline.
“Tiny Earth: Leveraging an instructor community to create antiracist curriculum in a research course”
Dr. Ally Hunter, PhD., Lecturer, iCONS Program & Postdoctoral Fellow, Center for Youth Engagement, University of Massachusetts, Amherst. Part of NSF Project RAISE (Reclaiming Access to Inquiry Science Education for Incarcerated Learners), and NSF Project INSITE (INtegrating STEM Into Transition Education for Incarcerated Youth).
Dr. Melissa Zwick, PhD., Associate Professor of Biology, Stockton University
“Science through storytelling: Using case study pedagogy as inclusive practice in undergraduate microbiology.”
Dr. Davida Smyth, Ph.D., Associate Professor of Molecular Microbiology at Texas A&M University in San Antonio
“Using wicked problems to CURE your teaching”
12:30 – 14:15 Introduction and Speakers
14:15 – 14:30 Break
14:30 – 16:00 Breakout room discussions based on skills development, in smaller groups
We are a week away from the fifth and final day of the July 2022 MSE virtual symposium, which is focused on “MSE Education Practices and Curriculum Design”. This session will feature three talks featuring educators who have brought sociology into their microbiome courses, and vice versa, and who have experience creating out-of-the-box curricula to engage students in learning while helping them to see themselves as scientists. Our hope is that attendees for this session learn from different perspectives how to creatively present microbiology courses which situate learning about the microbiome with learning about social and environmental systems.
Session 5: “MSE Education Practices and Curriculum Design”
Friday, July 22nd, 12:30 ~ 16:00 EST. Register for this session, which is free and will be held over Zoom.
Session leaders:
Erin Eggleston, PhD, Assistant Professor of Biology, Middlebury College
Monica Trujillo, Ph.D., Associate Professor, of Biology Queensborough Community College, The City University of New York
Carla Bonilla, Ph.D., Assistant Professor, University of San Diego
Scope: Curriculum which blends disciplines is highly engaging, and can be used to teach complex concepts, and can help students combine their existing cultural and social identities with their growing researcher identity. However, creating an interdisciplinary curriculum can be challenging. This session frames educational conversations in MSE, and gives perspectives on creating courses that blend microbiome and social sciences for different levels of education.
Learning Objectives of Session: Attendees will 1) identify successes and barriers to entry for MSE curriculum at different education levels (K-12, UG, grad, general public), 2) Share ways in which we incorporate MSE in our curricula (i.e. assignments, class period, multi-day module, full course, etc.); 3) develop ideas for further curriculum design for their own courses.
Format of talks: Three 30-min lecture-style talks from education practitioners who have successfully built courses around MSE topics, including an outline of learning goals, approach to course, lessons learned/challenges, and more.
Format of breakout rooms: Each room creates a lesson plan outline, and each room has a designated topic area (e.g. human microbiome equity) to help audience members group by teaching discipline.
“Tiny Earth: Leveraging an instructor community to create antiracist curriculum in a research course”
Dr. Ally Hunter, PhD., Lecturer, iCONS Program & Postdoctoral Fellow, Center for Youth Engagement, University of Massachusetts, Amherst. Part of NSF Project RAISE (Reclaiming Access to Inquiry Science Education for Incarcerated Learners), and NSF Project INSITE (INtegrating STEM Into Transition Education for Incarcerated Youth).
Dr. Melissa Zwick, PhD., Associate Professor of Biology, Stockton University
“Science through storytelling: Using case study pedagogy as inclusive practice in undergraduate microbiology.”
Dr. Davida Smyth, Ph.D., Associate Professor of Molecular Microbiology at Texas A&M University in San Antonio
“Using wicked problems to CURE your teaching”
12:30 – 14:15 Introduction and Speakers
14:15 – 14:30 Break
14:30 – 16:00 Breakout room discussions based on skills development, in smaller groups
The speaker lineup is set for the fifth (and final) day of the July 2022 MSE virtual symposium, which is focused on “MSE Education Practices and Curriculum Design”. This session will feature three talks featuring educators who have brought sociology into their microbiome courses, and vice versa, and who have experience creating out-of-the-box curricula to engage students in learning while helping them to see themselves as scientists. Our hope is that attendees for this session learn from different perspectives how to creatively present microbiology courses which situate learning about the microbiome with learning about social and environmental systems.
Erin Eggleston, PhD, Assistant Professor of Biology, Middlebury College
Monica Trujillo, Ph.D., Associate Professor, of Biology Queensborough Community College, The City University of New York
Carla Bonilla, Ph.D., Assistant Professor, University of San Diego
Scope: Curriculum which blends disciplines is highly engaging, and can be used to teach complex concepts, and can help students combine their existing cultural and social identities with their growing researcher identity. However, creating an interdisciplinary curriculum can be challenging. This session frames educational conversations in MSE, and gives perspectives on creating courses that blend microbiome and social sciences for different levels of education.
Learning Objectives of Session: Attendees will 1) identify successes and barriers to entry for MSE curriculum at different education levels (K-12, UG, grad, general public), 2) Share ways in which we incorporate MSE in our curricula (i.e. assignments, class period, multi-day module, full course, etc.); 3) develop ideas for further curriculum design for their own courses.
Format of talks: Three 30-min lecture-style talks from education practitioners who have successfully built courses around MSE topics, including an outline of learning goals, approach to course, lessons learned/challenges, and more.
Format of breakout rooms: Each room creates a lesson plan outline, and each room has a designated topic area (e.g. human microbiome equity) to help audience members group by teaching discipline.
“Tiny Earth, A Course-based Undergraduate Research Experience (CURE)”
Dr. Ally Hunter, PhD., Lecturer, iCONS Program & Postdoctoral Fellow, Center for Youth Engagement, University of Massachusetts, Amherst. Part of NSF Project RAISE (Reclaiming Access to Inquiry Science Education for Incarcerated Learners), and NSF Project INSITE (INtegrating STEM Into Transition Education for Incarcerated Youth).
Dr. Melissa Zwick, PhD., Associate Professor of Biology, Stockton University
“Science through storytelling: Using case study pedagogy as inclusive practice in undergraduate microbiology.”
Dr. Davida Smyth, Ph.D., Associate Professor of Molecular Microbiology at Texas A&M University in San Antonio
“Using wicked problems to CURE your teaching”
12:30 – 14:15 Introduction and Speakers
14:15 – 14:30 Break
14:30 – 16:00 Breakout room discussions based on skills development, in smaller groups
The symposium will convene researchers from different disciplines, foci, and geographic locations, and fosters in-depth conversations and research skills development. It is an ideal venue for training graduate students and incubating their burgeoning ideas. Thus, students in the class will attend the symposium, engage in conversations before and after attending sessions to reflect on how our perspectives changed, and create written assignments that will receive peer and instructor feedback. If the course is successful, I hope to add additional instructors and enrollment, we will expand the course and host it again each year we host the symposium.
I frequently receive requests for advice on choosing graduate programs, or to work in my lab, and have conversations with graduates who are struggling with program, department, or university policies which they were not aware of when they began. I decided to put those thoughts and conversations in one place, to create a non-exhaustive list of advice and considerations for choosing a graduate program. This will mostly be applicable to STEM programs, but some aspects will be universal.
Some of this will be discouraging, because graduate school is not a thing to be entered into lightly. But, I also believe that anyone can participate in science, and that many times when people think they couldn’t succeed in science, it’s not because they aren’t good enough, it’s more of a problem with an environment that selects for just one type of researcher.
Define your goal.
What do you want to do with your career and why do you need to go to graduate school to accomplish this?
I spend more time talking people out of graduate school, or into a lesser commitment, than I spend convincing people to go to graduate school, because there is an inflated sense of the need and prestige of having a graduate degree. And, many people assume they need a degree, or the highest degree available, to get the job they want.
When I was in 6th grade, I decided I was going to be a veterinarian because I wanted to help animals, and I refused to consider other career paths which felt like a lesser calling. Three weeks into my undergraduate degree in animal science, I realized that the reality of being a veterinarian is very different from its portrayal, and it wasn’t what I wanted at all. I had only thought I wanted it because I had gotten a very limited exposure to career choices prior to going to college. I see the same mistake with people considering, or in, graduate school. I don’t mean to disparage having a veterinary or graduate degree, I just mean that the way they are portrayed to prospective students is not always accurate. Do your homework before committing to those career paths.
More than that, when you receive career advice or look into career paths, the advice tends to focus on the highlights or major types of jobs and ignore the nuance of interdisciplinary or support-level careers. Not only does this mean that everyone in animal science thinks they can only be a veterinarian or a professor to be in the field, but the way that careers are portrayed makes students think that the only suitable use of their time, and justification for massive financial burden of higher education they incur, is to go for the career with the highest prestige – whether they want that or not. Unfortunately, when students realize they don’t have the grades and the accolades to make it into the career with the most prestige, which also has the most strict entry requirements, it means students are more likely to give up entirely, consider leaving their degree unfinished, and feel guilt or shame for having failed. But here’s something no one tells you up front: choosing a different job doesn’t mean you failed to be the boss, it means you chose a different job. A veterinary technician isn’t a failed veterinarian, and a laboratory technician isn’t a failed researcher, they are performing different functions in a setting which requires collaboration from various job types.
So, I’ll ask you again, like I ask all prospective graduate students: what do you want do with your life, and do you need graduate school to get you there? This question helps you focus on creating stepwise objectives to meet your goals. Maybe you need a specific degree, or a degree in a specific field, or don’t actually need a degree at all, maybe you need an internship or professional training, and those might require a specific order to the events. Do you want to travel for work or not? Do you want to have clear definition of your job responsibilities, or the flexibility to determine your own to-do list? Do you want to be at the bench, in the field, or at the keyboard and to be doing the research, or do you want to be writing proposals and papers, and administrating the research and the lab personnel? And, do you actually want to work alone or are you alright in a social environment? Spoiler alert, most jobs in science actually require daily socialization, communication, and presentation.
All of these aspects will determine the particulars of what you need out of a graduate program and the type of degree you get. It’ll also help you in the future when you need to decide if you have met your grad school goal and are ready to move to the next phase of your life.
You can probably outline your personal goals and constraints, but defining your professional goals will take some homework. I’ve previously described the academic ladder, with descriptions of responsibilities of students, post-doctoral researchers, adjuncts and researchers, and tenure-track faculty. I have also compiled some “science journeys” into a video. Professional research blogs can be a good way to learn about life in academia, although keep in mind many labs only post about their successes and not about their failures. You can also connect with faculty on campus, and most labs will take on undergraduate (or even high school) students to participate in research. If you aren’t sure if you would be interested in research, you can ask to shadow researchers in the lab, attend a few lab meetings, or otherwise participate in a voluntary and commitment-free capacity. There are also plenty of research opportunities off campus, as well.
Volunteering for Adventurers and Conservationists for Science, collecting water samples to look for microplastics. Photo: Lee Warren.
Define your limits.
Graduate programs can be demanding, and you may need to relocate to find the topic, project, and mentor who is right for you. Before you start applying everywhere and racking up application fees, think about your constraints, your limits, and what would be a “deal-breaker” for you. Defining your limits (especially if you have a lot of them) will feel like you are writing yourself out of the possibility of finding a graduate program that works for you. In reality, it will help you find an institution that matches your life better and will help you focus on what is really important to you. You don’t have to erase all other aspects of your life in order to be a scientist.
Often, you feel pressured to give up everything to go to graduate school or other professional degree programs. The perception is that because there are fewer available positions than applicants that you need to underbid everyone else and give up everything, essentially that you need to recruit the graduate program. You assume you have to relocate and out of your own pocket, you need to put family on hold, you need give up job benefits, and you will have to work all the time.
I’ve moved over 7,000 miles for academic jobs.
Some of that may be true, and you should think about what you are able to manage and what you can’t live without. Some of that is just perception cast by work-a-holic culture and you will be able to reject or negotiate aspects. Think of your list of limits as conditions your employer might need to meet in order to convince you to take the position.
Narrow down your interests.
What do you want to do day after day, failure after failure?
If you start to make a list of things you are interested in science and you start writing down all the cool things you saw on social media – stop right there. Science is cool, but most of the time is cool in retrospect after the work has been completed and narrative added in. Science is arduous, iterative, and requires a lot of process improvement and reflection, and that takes time and focus. You need to be able to work on the same thing day after day and maintain interest even if everything you do seems to fail everyday. Especially when you are trying to develop technical skills and analytical skills, you need to be able to focus and dive deep into your topic, and you can’t be distracted by every little thing you think is cool, otherwise you will never get anything done.
You don’t need to commit to your research interest for life, and you don’t need to have an incredibly narrow scope to your interests, but you should be able to identify a common theme or the aspect that draws you in. Which topic makes you ask “yes, and?” over and over. What cool science story made you look for a second similar story, and then a third?
Search for a program.
There are a few different types of graduate degrees available, and each have nuances about the requirements to get in, requirements to graduate, cost to you, salary and benefits to you, and approach for application and acceptance into the program. I recommend looking into programs first, to find a location and institution that best meets your personal and professional goals and limits, and then trying to find a mentor. Don’t underestimate the importance of geographic location, and the environmental and social climate you will find there. You might need to be close to family, or find a location with a job or program for a partner. And if you are used to sun, several years of overcast winters might lose their novelty.
Most people apply to multiple programs and it can take time to find the right match. If you end up applying to multiple programs at a single institution, you can ask them to waive additional application fees, something that is commonly done but not commonly advertised.
Masters of Professional Studies are designed to give you familiarity with research and build skills. MPS is not thesis-based and requires research participation but not your own research project, so it is often used for people who will be in research-adjacent jobs. Students are admitted to programs based on their GPA, exam, or other numeric qualifications, and during their first semester have to identify a research mentor and two other committee members to guide their curricula and career development. MPS students pay for their own tuition, and most program/university policies stipulate that they are not allowed salary for their research, although they usually can be paid summer research salary. MPS students are eligible for teaching assistantships, but few, if any research assistantships. Because you are categorized as students and not employees, you do not receive health insurance or other fringe benefits, but you are eligible for student health insurance plans. MPS are completed in 2 years, but can be completed over longer periods of time to accommodate working professionals.
Master of Science programs are thesis-based, and require research study in a project you co-lead. Applications may be accepted year-round or according to deadlines, depending on the program. Master’s programs are designed to last 2 -3 years (credit hour requirements make it almost impossible to accomplish in fewer than two years), and beware mentors or projects which assign you a PhD-level amount of work to accomplish in just two years. Finding funding for master’s programs can be tricky, as many universities prioritize PhD students in order to boost their Carnegie research rating, but master’s programs are needed for training the majoring of the research workforce. Typically, you are paid a salary for your master’s, including partial coverage of your health insurance, and full coverage of your tuition. Most programs do not cover full health insurance, or semester fees, both of which can cost a thousand dollars of more in each of the spring and fall semesters, but you might be able to negotiate these to be paid by your advisor. You are considered both a student and an employee, but most university policies make graduate students ineligible for university-based or even individual-based pre-tax retirement savings programs for employees, although you can configure a post-tax retirement savings plan on your own.
Doctorate of Science programs are dissertation-based and requires that you (more or less) lead a research study and have contributed significantly to the theory behind its design, or theory behind its analysis and interpretation. PhD programs are designed to take about 5 years in the US (3 years in many other countries which don’t require coursework). Credit hour requirements make it almost impossible to accomplish in fewer than 4 years in the US, and PhD time can vary between 4 – 9 years, depending on the research and other circumstances. Applications are accepted year-round for direct-to-lab admissions (see below), and once or twice a year to be considered for lab-rotation-based fellowships.
Thesis-based science programs have two paths to admission, which is not always common knowledge. You will always have to apply to the graduate college of a university and meet the qualifications set by the university, as well as the program/department. After passing initial qualification checks, the graduate school will forward applications to the department to review, and it is this step that offers two paths.
If graduate programs have a collective fund to support students (teaching or research assistantships), they might accept a certain number of students as a cohort based on their qualifications. The top number of applicants will have some sort of recruitment event in which you are shown the facilities, have a chance to talk to students and faculty, and are interviewed by the program admission committee. Applicants who are admitted as a cohort have salary provided for the first 1 – 2 years as they take classes and rotate through different research labs. At the end of rotations, you match with a lab that has money to continue funding your salary and your research. Most programs will not accept so many students to the cohort that they will be unable to find them funding to continue their graduate work.
However, because thesis-based study is a funded position, you might apply to a department as a “direct admission”. This means that you have already matched with an advisor during prior conversations, the advisor has already looked through your application, and that the advisor and the department have informally agreed to offer you a position. But, this method is entirely dependent on that advisor having funding to pay your salary, tuition, and your research costs. You need to start the conversation with a possible mentor 6 months or more before you want to begin, unless you are applying to an advertised position in their lab. Finding research funding takes 6 – 18 months because of the slow pace of federal funding review and allocation, so if your advisor needs to find funding it will take planing ahead of time. Direct admission can happen on a rolling basis, but you will still need to apply to, and meet the qualifications of, the graduate college. Because of the unpredictable nature of the funding, you can defer a direct admission offer for a year, as needed.
Interviewing and searching for a mentor.
Whether you are applying as part of a cohort or a direct admission, you will have some sort of interview. It might be a series of informal conversations with potential advisors, or a formal interview with a program admission committee. When you are going into a graduate program interview, it feels daunting, and it’s not until you advance your career enough to be on the interviewer side that you realize it is supposed to be a conversation and not a test.
The graduate interview is not really about proving your qualifications because you have already met that hurdle with your application. The interview is to match students to mentors, and to confirm your interest in research. By having conversations and interacting in real time (whether in person or via electronic chat), interviewers can assess your communication skills, and get a better idea of your goals and interests.
The graduate advising relationship is quite different from what you might have experienced with previous instructors or undergraduate advisors, so it’s important that your personal and professional goals line up with those of your advisor. It really helps if you actually get along. You’ll be working together for several years during your degree, and will maintain a mentoring relationship for a good portion of your early career after you graduate. As a member of their lab, you’ll be performing a lot of their research and representing them at conferences and other venues during presentations, collaborations, or future work. It’s important to your career and theirs that you are able to work well together.
Therefore, during your grad school interviews you should remember that you are interviewing them, as well. The interview is an opportunity for your future advisor and institution to impress you and convince you to take a position with them. This is your chance to ask them about the projects you might be doing, where former lab members are now, their expectations of you, and more. Many federal funding proposals require a detailed mentoring plan, so advisors already have an idea what your professional development might look like. Importantly, get an idea about the lab culture. Some advisors feel you should work nights and weekends and during all breaks, others feel that your contributions belong to the lab and you might not have as much access to your own intellectual property than you think. And, not every lab has made a commitment to equity and inclusion. Here’s the policy for the Ishaq Lab.
It’s also a great time to ask grad program coordinators about university policy, departmental expectations, and financial support opportunities which might affect you. Does the program provide some or all financial support for health insurance, tuition, salary, and student fees? If not, what opportunities are in place to secure these? Are you able to switch mentors if there is a professional or personal mismatch? Is childcare available for graduate students? What about time off for maternity leave, and is this paid or unpaid? Family or medical leave? What if you need to take a semester or a year off, can you get back into the program and would you lose your funding? How many papers will you need to publish, or scientific presentations to give, and will there be financial support for those costly endeavors? While no one would ask you to pay publication fees out of pocket, I have heard of researchers refusing to financially support grad student travel to conferences, despite many departments requiring students to present in order to obtain their graduate degree. Travel to scientific conferences can run to several thousand in travel and participation costs per trip, and one trip to a national-level conference could cost an entire month’s graduate student salary.
Adopt healthy habits.
If everything comes together and you’ve been accepted into a graduate program that works for you, congratulations!! I wish you the best on the next step of your journey. If you are looking for more advice for once you get there, check out my previous posts, including preparing yourself before you start by adopting good habits for organization and work-life balance.
A second course that I developed was accepted at the University of Maine! AVS 454-554 DNA Sequencing Data Analysis will be offered to undergraduate and graduate students starting Spring 2021.
AVS 454-554 teaches bioinformatics using DNA data. Starting with raw DNA sequencing data, students go through the process of quality assurance, statistical analysis, graphics design, as well as drafting a scientific manuscript. The course integrates research into teaching by using unpublished data, ideally data the students bring from their own research projects. Not only do students learn highly sought-after analytical and scientific writing skills, but it makes them active participants in research and their own learning. Most of the course time and skillset are focused on amplicon sequencing data, but we’ll also dabble with whole-genome, metagenomics, and metatranscriptomics.
Along with my Introduction to Animal Microbiomes course, I hope to get students interested in microbial ecology earlier in their studies, such that they have time to get involved with microbial ecology research in Maine in time for them to develop a Capstone research experience around it in their senior year. And what a coincidence, I’ll be teaching the Capstone courses for AVS (401 and 402) starting in fall 2020, as well.
This course is based on the precursor version, AVS 590, which I taught as a small, special topics version in the 2020 spring semester. And, even that is conceptually based on a lab section I taught at Montana State University in 2015 and 2016. DNA data analysis and I go way back.
Photo credit: Tom Rayner, Tenure Chasers
It can take several months to get course proposals approved, especially if you are proposing they meet general education requirements, are listed as required for a major degree, or have other levels to them. I started Sept 1, and the AVS faculty curriculum committee, the first step in the approval process, was meeting in early October. I didn’t have time to develop two course proposals in time, so I first proposed my data analysis course as a “special topics” version. These versions are offered selectively and are not counted the same way as an approved course. But, it gave me time to shore up my teaching materials, and teach several students who were graduating and couldn’t wait another year to learn these skills.
DNA sequencing data analysis is challenging to teach as well as to learn, but once over the learning curve, it can be extremely fun and rewarding. I’ve previously taught bioinformatics to undergraduates, and have or continue to publish with a number of them. In AVS 590 in the 2020 semester, there were 4 datasets being analyzed, and 3 of those led to manuscripts which are anticipated to be submitted to for review in scientific journals sometime this year!
