I just got back from my very first Congress on Gastrointestinal Function, a small meeting for researchers with a specific focus on the gastrointestinal tract, which is held every two years in Chicago, Illinois. The special session this year was on “Early Acquisition and Development of the Gut Microbiota: A Comparative Analysis”. The rest of the sessions opened up the broader topics of gut ecosystem surveillance and modulation, as well as new techniques and products with which to study the effect of microorganisms on hosts and vice versa. The research had a strong livestock animal focus, as well as a human health focus, but we also heard about a few studies using wild animals.
As I’ve previously discussed, conferences are a great way to interact with other scientists. Not only can you learn from similar work, but you can often gain insights into new ways to solve research problems inherent to your system by looking at what people in different fields are trying, something that you might otherwise miss just by combing relevant literature online. A meeting or workshop is also a great place to meet other similarly focused scientists to set up collaborators that span academia, government, non-profit, and industry sectors.
This year, I was excited for one of my abstracts to be accepted as a poster presentation, and honored to have the other upgraded from poster to talk! Stay tuned for details about both of those projects in the coming weeks, and be sure to check this meeting out in April, 2019.
In a recent post on The Rare Knowledgesphere, I mentioned that I when I tell people that I went to graduate school or explain what I do now, the replies can be overly modest or self-deprecating. Sometimes, people tell me that they don’t feel smart enough to make it through grad school or to dowhatIdo. Graduate school or other professional schools aren’t for everyone, but there is a big difference between not wanting to go and not feeling good enough to go. In my experience, people who think they can’t do it aren’t so much incapable as incapacitated by Imposter Syndrome. In my 9 total years of acquiring higher education, plus 2 years and counting of post-doctoral training, I find that when it comes to academic success, academic achievement frequently takes a backseat to having the right personality. In this post, I thought it would be helpful to describe some of those qualities that help set the most successful researchers apart.
Learning is a skill
Don’t get me wrong, you need to pass the graduate record examinations (GREs- general and subject) in order to be accepted, be able to understand the material once you are there, do well on exams, and maintain a certain grade point average (GPA). While grades and exam performance can be good metrics for intelligence, there are a lot of circumstances that could preclude someone from doing well, thus they aren’t the only metrics. Certainly you need a solid knowledge base in any subject in order to participate in it. But I don’t usually get asked by people I pass on the sidewalk to explain how 20 different enzymes react instantaneously when you consume a meal in order to alter your metabolism to maintain homeostasis. I am asked on a daily basis to assimilate new information, process it, and then apply it to my work. Whether it is learning a new skill (like learning to perform a laboratory technique or how to analyze data I have not worked with before), whether it is evaluating a proposed experiment and looking for flaws in the experimental design, or whether it is reviewing someone’s manuscript for validity and publish-ability, I need to be able to learn new things efficiently.
Learning is a skill, just like wood-working or weight-lifting: you need to start small and practice regularly. Learning a new skill, language, or activity challenges us. Not only can it broaden our view of the world, but continuing to learn throughout your adult life can improve health and cognitive function: essentially, the more you learn the better you become at learning. In addition to physically performing new tasks, reading is a great way to inform yourself while improving your reading comprehension skills, verbal IQ, and critical thinking so that you can assess the accuracy of the information. Scientific texts, even for those who are trained to read them, can be extremely difficult to fully comprehend. Articles are full of very technical language, explain new concepts, and often rely on a certain amount of knowledge inherent to the field. It’s tempting to read quickly, but in order to do this you efficiently it can help to be systematic and thorough.
You may not feel you are ready for graduate school, that you belong in grad school, or that you are ready to leave, but grad school isn’t the end point- it’s a learning experience to become a good researcher. Even once you leave, you never stop learning. Good graduate students don’t have to know everything, but they do need to know how to learn and how to search for answers.
Put on a happy face
You don’t need to love grad school, your work, or the process of research every second of every day, and you don’t need to pretend to, either. It can be difficult, and like with any job, there are good days and bad days. A hardy personality falls a close second to being able to learn new skills. The road through graduate school is arduous and different for everyone, and it takes a tough person to make it out of the labyrinth of Academia. Moreover, you are truly surrounded by your peers; everyone in graduate school has already maintained a high GPA, passed the GREs, gotten into grad school, etc. You are probably never going to be the smartest or most accomplished person in the room again, certainly not for a long time.
You need to be able to take criticism, and not just the constructive kind: not everyone maintains polite professionalization and at some point, someone will bluntly tell you that you don’t belong in graduate school. For me, this occurred about two years in, when I submitted my first manuscript. A reviewer mistook my statement that a certain type of photosynthetic, water-based bacteria were present in the rumen of moose (who acquire them by drinking swamp water) for saying that those bacteria normally lived in the rumen of the moose, and commented that the latter was incorrect, that I did not know what I was doing, and that I did not belong in science. To be sure, being able to deliver information in journal articles in an accurate manner is critical, and if a reviewer mistakes what you say in a manuscript, then you need to clarify your statements. If a journal article is found to be unsuitable for publication, the reviewer can recommend it be rejected and offer commentary on how to improve re-submissions. However, it is widely accepted to be inappropriate and unprofessional to make personal comments in a review. I was taken aback at how one misinterpreted sentence in a 5,000 word article could lead someone who had never met me to determine that I wasn’t suited for science.
In the end, I clarified that sentence, resubmitted, and the paper got accepted. Four years later, that article has been viewed over 6,500 times and several other papers have come out identifying bacteria of that type living in the gastrointestinal tract of animals. Research is a competitive field, and by its nature requires repetition and trouble-shooting. You need to be able to fail on a daily basis and still find the enthusiasm to learn from the results and try it again tomorrow.
Two heads are better than one
Working well with others is extremely important in graduate school (and really any work environment). In graduate school, other people can challenge you, help you reason through problems, identify holes in your logic, or add a perspective based on their personal experiences. In science, you can never be an expert in everything, and to be able to really answer a research question you need to be able to look at it from different angles, methods, or fields. Collaborations with other scientists allow you to bring a breadth of expertise and techniques to bear in projects, and can improve the quality of your research (1, 2, 3).
However, it can be difficult to wrangle so many researchers, especially when everyone is so busy and projects may span years. Emotional intelligence, the ability to empathize, has been found to contribute to academic intelligence and can foster interpersonal relationships and collaborations. When money, prestige, and ideas are on the line, the drive to be recognized for your work needs to be balanced with empathy in service to completing the experiments and disseminating the results. At some point in academia, personal conflict will jeopardize a project. As much as you have a right to recognition and reward for your hard work, you need to remember that other project members are due the same. That being said, as a graduate student you don’t always feel in a position to negotiate and may feel pressured to minimize your contribution or the thanks to which you are due. Settling on an order for authorship, or credit for contributions, is a conversation that needs to happen early, often throughout the project, and inclusively to acknowledge that you all worked hard for this.
Being able to juggle taking classes, teaching and grading, performing research, attending meetings, and all the other hundred things one must do in an academic day, takes a high degree of coordination. Your calendar is your friend: schedule everything from meetings to reminders about tasks. And using shared calendars really helps to schedule meetings or remind others. There are plenty of apps that are specific to laboratory scheduling needs to help coordinate meetings or assign tasks across multiple parties.
Even more important these days is digital organization: whether it be your email or your hard drive. You need to be able to confidently curate and store data or electronic materials so that you or someone else can find them, even years later. You never know when you will need to resurrect an old project or check on a method you once used, and without a solid paper trail you may not be able to locate or understand your digital breadcrumbs. Lab notebooks, protocols, data files, and knowledge need to be accessible to future members, and it is your responsibility to make them available and intelligible. There is nothing more frustrating than finding an unlabelled box of samples in a freezer and being unable to identify their owner or contents. While the Intellectual Property might be yours, if that research or your salary was paid by a university or governmental agency, you have a responsibility to make that information public at some point.
A high degree of organization can help you manage your time, keep track of your results, coordinate with others, and maintain a project schedule.
A spoonful of extra-curricular helps the biochemistry go down
Work-week expectations, course load, teaching load, research load, and financial compensation of graduate students vary by the nature of their appointment, by university policy, or even by department within a university.
Graduate Teaching Assistants are paid a stipend for providing undergraduate teaching and other miscellaneous help to the department (typically 20 hours per week), and may receive tuition compensation for the classes they take. Depending on the nature of the program, they may do research as well in order to write a thesis (masters) or dissertation (doctorate), or not do any research for their degree (non-thesis major). Graduate Research Assistants (GRAs) are hired strictly to perform research (again, usually 20 hours per week), for which they receive a stipend and/or tuition compensation, and also take classes. Most programs require GRAs to teach for one semester to gain the experience, and GRAs are almost exclusively performing research for a thesis/dissertation-based degree. Regardless of the type of appointment, there are a certain number of classes and hours of research which must be logged before a degree may be obtained. Between courses, teaching, and research, there is enormous pressure on graduate students to work more than 40 hours per week.
It might seem that immersing yourself in graduate school is the best way to be a good student. Or, maybe you are overwhelmed by the amount of work you are being asked to accomplish and feel pressured to spend 12 – 18 hours a day at it just to meet deadlines. Firstly, you are not lab equipment and should not be treated as such. As a student, as an employee, and as a person, you have rights in the workplace. It’s worth looking into university policy to see exactly what it required of you. Secondly, over-working yourself is a terrible way to be more productive, as I discussed in a previous post on work-life balance. To summarize that post, over-working yourself negatively affects your health, your cognitive function, and the quality of your work. On the other hand, taking regular breaks and vacation can help keep you focused and solve abstract problems.
In addition to helping you manage stress, having an active life outside of your program helps give you other experiences from which you can draw upon to aid your graduate work. For example, I worked for several years at a small-animal veterinary hospital before going to graduate school, at which I trained employees and had extensive interactions with customers. There, I gained the skills to manage others, simplify technical information, be very specific in my instructions, or maintain a professional demeanor in the face of emotional or chaotic events. My interests in painting and photography have improved the quality and presentation of graphical results, or visually document my experiments.
Learn to Type
Seriously. I spend most of my time at a computer: reading, writing, cut/pasting. If you can type as quickly as you can gather your thoughts,you’ll find that you are much more productive.
Today, the research team that I am a part of submitted a grant which I co-wrote with Dr. Tim Seipel, along with Dr. Fabian Menalled, Dr. Pat Carr, and Dr. Zach Miller. We submitted to the Organic Transitions Program (ORG) through the US Department of Agriculture’s (USDA) National Institute of Food and Agriculture (NIFA). The culmination of months of work, and some 12+ hour days this past week to meet today’s deadline, this grant will hopefully fund some very exciting work in agriculture!
Research relies on grant money to fund projects, regardless of the type of institution performing the research, though commercial research centers may partially self-fund projects. Most new research hires to universities will receive a “start-up package” which includes some funding for a few years to buy equipment, pay for a small, preliminary project, or temporarily hire a technician. Start-up funds are designed to hold a researcher over for a year or two until they may apply for and receive grant funding of their own. Sooner or later, everyone in academia writes a grant.
Grants may be available for application on a regular basis throughout the year, but some grant calls are specific to a topic and are made annually. These have one submission date during the year, and a large number of federal grants are due during in the first quarter of the year, a.k.a. Grant Season. University researchers find themselves incredibly pressed for time from January to March and will hole up in their office for days at a time to write complex grants. Despite the intention of starting your writing early, and taking the time to thoroughly discuss your project design with all your co-PDs well before you start writing to avoid having to rewrite it all again, most researchers can attest that these 20-30 pages grants can get written over from scratch 2 or 3 times, even before going through a dozen rounds of group editing.
The Bright Idea
Most large grants, providing several hundred thousand to over a million in funding over several years, require project teams with multiple primary researchers (called Principal Investigators or Project Directors) to oversee various aspects of research, in addition to other personnel (students, technicians, subcontractors). One researcher may conceptualize the project and approach other researchers (usually people they have worked with in the past, or new hires) to join the project. Project ideas may get mulled over for several years before they mature into full grant submissions, or go through multiple versions and submissions before they are perfected.
The grant I just co-wrote investigates the use of cover crops in Montana grain production. Briefly, cover crops are plant species which improve the soil quality but which you aren’t necessarily intending to eat or sell. They are grown in fields before or after the cash crop (ex. wheat) has been grown and harvested. Legumes like peas, beans, or alfalfa, are a popular choice because they fix nitrogen from its gaseous form in the atmosphere into a solid form in soil which other plants (like wheat) can use. Other popular cover crop plants are great at bio-remediation of contaminated soils, like those in the mustard family (1, 2, 3). Planting cover crops in an otherwise empty (fallow) field can out-compete weeds that may grow up later in the year, and they can prevent soil erosion from being blown or washed away (taking the nutrients with it). For our project, we wanted to know how different cover crop species affect the soil microbial diversity, reduce weeds, put nutrients back into soil, and improve the production of our crop.
We designed this project in conjunction with the Montana Organic Association, the Organic Advisory and Research Council, and Montana organic wheat farmers who wanted research done on specific cover crops that they might use, in order to create a portfolio of cover crops that each farmer could use in specific situations. As these organizations comprise producers from across the state, our research team was able to get perspective on which cover crops are being used already, what growing conditions they will and won’t work in (as much of Montana is extremely dry), and what production challenges growers face inherent to planting, managing, and harvesting different plant types.
Drafting Your Team
When you assemble a research team, you want to choose Project Directors who have different experiences and focuses and who will oversee different parts of the project. A well-crafted research team can bring their respective expertise to bear in designing a large and multi-faceted project. For our grant, I am the co-PD representing the microbial ecology and plant-microbe interaction facet, about a third of the scope of the grant. We will also be investigating these interactions under field settings, which requires a crop production and agroecology background, as well as expanding the MSU field days to include organic-specific workshops and webinars, which requires an extension specialty.
Because grant project teams are made up of researchers with their own projects and goals, in addition to providing valuable perspective they may also change the scope or design of your project. This can be extremely beneficial early on in the grant-writing phase, especially as you may not have considered the limitations of your study, or your goals are too unambitious or too lofty. For example, the cover crop species you want to test may not grow well under dry Montana conditions, do you have a back-up plan? However, as the submission deadline looms larger, changing the focus of your study can cost you precious writing time. Working in a research team requires a high degree of organization, a flair for communication, and an ability to work flexibly with others.
Identifying the research question
All grants center around a Project Narrative, and funding agencies will provide detailed instructions on how to format your project grant. Pay strict attention- in very competitive pools your grant can be flagged or rejected for not having the appropriate file names or section headers. The Narrative gives introductory background on your topic that details the research that has previously been published. Ideally, it also includes related studies that you and your team have published, and/or preliminary data from projects you are still working on. The aim is to provide a reasoned argument that you have correctly identified a problem, and that your project will fill in the knowledge gaps to work towards a solution. Grant panels are made up of researchers in a related field, but they may not be intimately aware of your type of research. So, you need to be very specific in explaining your reasoning for doing this study. If your justification seems weak, your project may be designated as “low priority” work and won’t get funded.
In our case, cover crops have been used by farmers already, but not much basic research has been done on the impacts of picking one species over another to plant. Thus, when cover crops fail, it may be unclear if it was because of unfavorable weather, because the previous crop influenced the soil in ways which were detrimental to your new crop, because you seeded your crop too sparsely and weeds were able to sneak in and out-compete, because you seeded too densely and your crop was competing with itself, or something else entirely.
You also need to identify the specific benefits of your project. Will you answer questions? Will you create a new product for research or commercial use? Will organic producers be able to use what you have learned to improve their farm production? Will you teach students? When you are identifying a need for knowledge and describing who or what will benefit from this study, you need to identify “stakeholders”. These are people who are interested in your work, not people who are directly financially invested. For us, our stakeholders are organic wheat farmers in Montana and the Northern Great Plains who want to integrate cover crops into their farming as an organic and sustainable way to improve crops and reduce environmental impact. Not only did our stakeholders directly inform our project design, but we will be working closely with them to host Field Day workshops, film informative webinars, and disseminate our results and recommendations to producers.
Crafting Your Experimental Plan
Once you have identified a problem or research question, you need to explain exactly how you will answer it. For experiments in the laboratory or field, you need to be incredibly specific about your design. How many samples will you take and when? Will you have biological replicates? Biological replicates are identical treatments on multiple individual organisms (like growing a single cover crop species in four different pots) to help you differentiate if the results you see are because of variation in how the individual grows or because of the treatment you used. Do you have technical replicates? Technical replication is when you analyze the same sample multiple times, like sequencing it twice to make sure that your technology creates reproducible results. Will you collect samples which will provide the right type of information to answer your question? Do your collection methods prevent sample deterioration, and how long will you keep your samples in case you need to repeat a test?
We then put each species into a bag to be dried and weighed.
We need to filter out the particles or they will clog the sprayer. Also pictured: Dr. Fabian Menalled.
The core sampler is used to collect soil from certain depths.
Climate change simulators.
In addition to describing exactly what you will do, you need to explain what might go wrong and how you will deal with that. This is called the Pitfalls and Limitations section. Because basic research needs to be done in controlled environments, your study may be limited by a “laboratory effect”: plants grown in a greenhouse will develop differently than they will in a field. Or, you might not be able to afford the gold-standard of data analysis (RNA sequencing of the transcriptome still costs hundreds of dollars per sample and we anticipate over 1,200 samples from this project) so you need to justify how other methods will still answer the question.
Even after explaining your research question in the Narrative and your design in the Methods sections, your grant-writing work is still far from complete. You will need to list all of the Equipment and research Facilities currently available to you to prove that your team can physically perform the experiment. If you will have graduate students, you need a Mentoring Plan to describe how the research team will train and develop the career of said student. If you will be working with people outside of the research team, you will need Letters of Support to show that your collaborators are aware of the project and have agreed to work with you, or that you have involved your stakeholders and they support your work. I was delighted by the enthusiasm shown towards this project by Montana organic producers and their willingness to write us letters of support with only a few days’ notice! You’ll also need a detailed timeline and plan for disseminating your results to make sure that you can meet project goals and inform your stakeholders.
Perhaps the most difficult accessory document is the Budget, for which you must price out almost all the items you will be spending money on. Salary, benefits (ex. health insurance), tuition assistance, travel to scientific conferences, journal publication costs, travel to your research locations, research materials (ex. seeds, collection tubes, gloves, etc.), cost to analyze samples (ex. cost of sequencing or soil nutrient chemical analysis) cost to produce webinars, and every other large item must be priced out for each year of the grant. The Budget Narrative goes along with that, where you explain why you are requesting the dollar amount for each category and show that you have priced them out properly. For large pieces of equipment, you may need to include quotes from companies, or for travel to scientific conferences you may need airline and hotel prices to justify the costs.
On top of what you need to complete the study, called Direct Costs, you also need to request money for Indirect Costs. This is overhead that is paid to the institution that you will be working at to pay for the electricity, water, heating, building space, building security, or other utilities that you will use, as well as for the administrative support staff at the institution. Since nearly all grants are submitted through an organization (like universities), instead of as an individual, the university will handle the money and do all the accounting for you. Indirect costs pay for vital research support, but they run between 10-44% of the dollar amount that you ask for depending on the type of grant and institution, potentially creating a hefty financial burden that dramatically reduces the available funding for the project. On a $100,000 grant, you may find yourself paying $44,000 of that directly to the university.
Draft Twice, Submit Once
The Budget is by far the most difficult piece to put together, because the amount of money you have available for different experiments will determine how many, how large, and how intensive they are. Often, specific methods or whole experiments are redesigned multiple times to fit within the financial constraints you have. If you factor in the experimental design changes that all your co-PDs are making on the fly, having to balance the budget and reconstruct your narrative on an hourly basis to reflect these changes, and the knowledge that some grants only fund 6-8 projects a year and if you miss this opportunity you may not have future salary to continue working at your job, it’s easy to see why so many researchers find Grant Season to be extremely stressful.
2016 started with a bang when I launched this site and joined Twitter for the first time! For the first quarter of the year, I was a post-doctoral researcher in the Yeoman Lab in the Department of Animal and Range Sciences at Montana State University. I was working on a total of eight grants, ranging from small fellowships to million dollar projects, both as a principal investigator and as a co-PI. I was also doing the bioinformatic analysis for multiple projects, totaling nearly 1,000 samples, as well as consulting with several graduate students about their own bioinformatic analyses.
In late spring, my position in the Yeoman lab concluded, and I began a post-doctoral position in the Menalled Lab in the Department of Land Resources and Environmental Sciences at MSU. This position gave me the opportunity to dramatically increase my skill-set and learn about plant-microbe interactions in agricultural fields. My main project over the summer was studying the effect of climate and other stresses on wheat production and soil microbial diversity, and this fall I have been investigating the legacy effects of these stressors on new plant growth and microbial communities. I have extracted the DNA from all of my Fort Ellis summer trial soil samples, and look forward to having new microbial data to work with in the new year. Based on the preliminary data, we are going to see some cool treatment effects!
Over the summer, I attended the American Society for Microbiology in Boston, MA in June, where I presented a poster on the microbial diversity in organic and conventional farm soil, and the Joint Annual Meeting for three different animal science professional societies in Salt Lake City, UT in July, where I gave my first two oral conference presentations. One was on the effect of a juniper-based diet on rumen bacteria in lambs, and the other was on the biogeography of the calf digestive system and how location-specific bacteria correlate to immune-factor expression.
Thanks to a lot of hard work from myself and many collaborators, a number of research projects were accepted for publication in scientific journals, including the microbial diversity of agricultural soils, in reindeer on a lichen diet, and in relation to high-fat diets in mice, it also included work on virulent strains of Streptococcus pyogenes, and a review chapter on the role of methanogens in human gastrointestinal disease.
A whopping thirteen manuscripts are still in review at scientific journals or are in preparation waiting to be submitted! Some of those are primarily my projects, and for others I added my skills to the work of other researchers. Editing all those is going to keep me plenty busy for the next few months. I’ll also be writing several more grants in early 2017, and writing a blog post about the Herculean task that can be.
I’ll be concluding my greenhouse study by March of 2017, just in time to prepare for another field season at Fort Ellis, on the aforementioned climate change study that is my main focus. In January, I’ll be spending time in the lab helping to process and sequence DNA from my 270 soil samples, and begin the long task of data quality assurance, processing, and analysis. I’m not worried, though, 270 samples isn’t the most I’ve worked with and bioinformatic analysis is my favorite part of the project!
This year, I am hoping to attend two conferences that I have never previously attended, and present data at both of them. The first will be the 2017 Congress on Gut Function in Chicago, IL in April, and the second will be the Ecological Society of America’s Annual Meeting in Portland, OR in August. Both conferences will give me the opportunity to showcase my work, network with researchers, and catch up with old friends.
If 2017 is anything like the past few years, it’s going to be full of new projects, new collaborators, new skills, and new opportunities for me, and I can’t wait! So much of what I’ve accomplished over the last year has been possible because of the hard work, enthusiasm, and creativity of my colleagues, students, friends, and family, and I continue to be grateful for their support. I’d also like to thank anyone who has been kind enough to read my posts throughout the last year; it’s been a pleasure putting my experiences into words for you and I appreciate the time and interest you put in. I look forward to sharing more science with you next year!
In the first installment of the work-life balance discussion, I discussed the different levels of employment for university faculty and gave general information on the different functions they performed on a daily basis. I also talked about how many of them work longer than 40 hours a week, including nights and weekends, and may even work summers without compensation. For example, in a 1994 report, the American Association of University Professors reported that professors worked 48-52 hours per week, and this had increased to 53 hours by 2005. Other sources over the past five years have reported more: 57 hours per week at a Canadian research institution, 50-60 hours per week in the UK. But like with anything, work quantity does not equate to quality.
All work and no play makes Jack a dull boy
For one thing, working long hours without sufficient weekly time off, or vacations, can significantly increase stress. And this stress can lead to all sorts of different mental and physical problems. Working long hours can interfere with our normal circadian rhythm– it can disrupt our sleep cycles, throw off our eating times and appetite, and make it difficult to exercise regularly. Longer hours have been directly correlated with incidence of hypertension and other cardiovascular problems (also reviewed here).
But for all that personal sacrifice, mounting evidence shows that a reduction in work hours is what promotes productivity, not a 24-hour work day. Reducing weekly hours increased productivity as employees were less likely to be absent from work due to poor health (reviewed here). Taking scheduled breaks instead of skipping them was also responsible for improving cognitive function in students. Even brief diversions were shown to improve focus and cognitive function. Besides giving us a rest from our current task, or engaging our attention with something novel, taking a break allows us to daydream. While this may seem like a waste of time, letting our minds wander activates different parts of our brain- including those involved in problem solving and creative thinking. If you’ve ever come up with a brilliant solution while doing mundane tasks, then you’ve experienced this. For my part, I tend to think of great ideas when I’m washing dishes or biking home. Daydreaming, or taking a break, also helps release dopamine, a chemical neurotransmitter involved in movement, emotions, motivation, and rewards. It’s very helpful in the creative process, as explained in a discussion of creativity in the shower.Restful thinking also seems to be involved with promoting divergent thinking, emotional connectivity, and reading comprehension.
Going on regular annual vacations was correlated with a lower risk for coronary heart disease: not only are vacations great for reducing stress, but they also provide opportunities for more exercise, mental downtime, and creative outlets. Mandatory time-off during nights and weekends for consultants resulted in a reported increase job performance, mental health, and attitude, though many said it was a struggle to enforce “time outs” from work in the beginning because they felt guilty about not working during their personal time. This was seen again in a study of Staples managers who did not take scheduled breaks out of guilt.
It’s this persistent feeling that you should be working at home, and that you could be doing more, which is largely reported by “driven” employees and workaholics. This feeling has lately been coined “tele-pressure“. It’s particularly invasive these days as you have access to work emails and other communications via smart phones, laptops, or tablets. In fact, by syncing many of these devices, your attention is compelled by multiple simultaneous electronic signals and vibrations whenever someone contacts you. It’s no wonder we can’t shut off at the end of the day. (And for the record, I wrote this on a Sunday evening.)
More important than knowing that taking regular breaks and vacations will help manage your stress and improve your productivity, is remembering that you are entitled to it. We have labor laws for a reason, and you are entitled to your nights, weekends, and your X number of weeks a year. You are entitled to stay home when you are sick, or whenever you feel like it. It’s your personal time, take it.
So, if you’re in academia, what do you do to unwind? Leave me some comments!
Scientific conferences are a great place to get your name out there, discuss research with colleagues, and meet other researchers with whom you might one day collaborate. It can be difficult to get noticed as a graduate student or post-doctoral researcher, especially if it’s your first time at a certain conference, if your poster time conflicts with more interesting events, or if you find yourself way at the back of a 1,000 poster hall. You need to be ready to introduce yourself and get your point across, and to do it in a memorable and concise way. There may be hundreds or even thousands of people in attendance, so you need to make a fast impression.
Though a bit outdated these days, I find business cards really handy. Not only can you quickly hand out all your information, but you can write notes on the back about what you discussed with someone so you can follow up with them later. It’s easy to leave a bag of them at your poster for people to take, too.
Not only is your poster or presentation’s content important, its visual appeal will help draw in people who are “browsing”. Make sure your font is large enough to read from 5-8 ft away, and that you have some color, but not enough to make text illegible. Bolding or bulleting take-home messages can also be really helpful. Make sure you can describe your poster in a variety of ways: in under 60 seconds to the person with a mild passing interest, and in-depth with the person that is curious about your methods or your other projects.
The most important thing to prepare, though, is yourself. You are representing yourself, your institution, and your science. Cleanliness, organization, and confidence make a huge difference when meeting new people, and will make you more approachable. Make eye contact, try to avoid filler words, and smile! I have watched posters get overwhelmingly passed by because the presenter was on their phone, or looked bored or annoyed. Making eye contact and saying hello to someone as they walk by is often enough to get them to slow down and ask you about your work.
When asking questions at other presentations, be sure to be polite; being demanding or rude is guaranteed to be met with disapproval from the rest of the audience. And go ahead and introduce yourself to other researchers, just be sure to keep it brief and don’t interrupt another meeting.
One more thing to consider at a conference is your behavior outside of your presentation. You are at a gathering of intellectuals who may one day be your boss, your colleague, your grant reviewer, or otherwise influential in your career. They may remember that they saw you talking loudly to a friend during a presentation, or that you got too drunk at the opening session. Conferences are often used as an excuse to take a concurrent vacation, especially for those in academia who generally can’t take a week off during the semester. But you should remember why you are there and act professionally, especially as a graduate student or post-doc, because you never know who’ll remember you in the future.
Microbiome studies do not usually employ culturing techniques, and many microorganisms are too recalcitrant to grow in the laboratory. Instead, presumptive identification is made using gene sequence comparisons to known species. The ribosome is an organelle found in all living cells (they are ubiquitous), and it is responsible for translating RNA into amino acid chains. The genes in DNA which encode the parts of the ribosome are great targets for identification-based sequencing. In particular, the small subunit of the ribosome (SSU rRNA) provides a good platform for current molecular methods, although the gene itself does not provide any information about the phenotypic functionality of the organism.
Prokaryotes, such as bacteria and archaea, have a 16S rRNA gene which is approximately 1,600 nucleotide base pairs in length. Eukaryotes, such as protozoa, fungi, plants, animals, etc., have an 18S rRNA gene which is up to 2,300 base pairs in length, depending on the kingdom. In both cases, the 16 or 18 refers to sedimentation rates, and the S stands for Svedberg Units, all-together it is a relative measure of weight and size. Thus, the 18S is larger than the 16S, and would sink faster in water. In both genes, there exist regions which are conserved (identical or near-identical) across taxa, and nine variable regions (V1-V9) . The variable regions are generally found on the exterior of the ribosome, where they are more exposed and prone to higher evolutionary rates. Since the outside of the ribosome is not integral to maintaining its structure, the variable regions are not under functional constraint and may evolve without destroying the ribosome. They provide a means for identification and classification through analysis [2-6]. The conserved areas are targets for primers, as a single primer can bind universally (to all or nearly-all) to its target taxa. The conserved regions are all on the internal structure of the ribosome, and too much change in the sequence will cause its 3D (tertiary) structure to change, thus it won’t be able to interact with the many components in the cell. Mutations or changes in the conserved regions often causes a non-functional ribosome and will kill the cell.
In addition to a small subunit, ribosomes also possess a large subunit (LSU rRNA), the 23S rRNA in prokaryotes, and the 28S rRNA in eukaryotes. Eukaryotes have an additional 5.8S subunit which is non-coding, and all small and large units of RNA have associated proteins which aid in structure and function. Taken together, this gives a combined 70S ribosome in prokaryotes, and a combined 80S ribosome rRNA in eukaryotes.
The way to study the rRNA gene is to sequence it. First, you need to extract the DNA from cells, and then you need to make millions of copies of the gene you want using Polymerase Chain Reaction (PCR). PCR and sequencing technology more or less work the same way as a cell would make copies of DNA for cell processes or division (mitosis). You take template DNA, building block nucleotides, and a polymerase enzyme which is responsible for reading the DNA sequence and making an identical copy, and with hours of troubleshooting get a billion copies! Many sequencing machines use nucleotides that have colored dyes attached, and when a nucleotide is added, that dye gets cut (cleaved) off, and the camera can catch and interpret that action. It then records each nucleotide being added to each separate DNA strand, and outputs the sequences for the microorganisms that were in your original sample!
The two main challenges facing high-throughput sequencing are in choosing a target for amplification, and being able to integrate the generated data into an increased understanding of the microbiome of the environment being studied. High-throughput sequencing can currently sequence thousands to millions of reads which are up to 600-1000 bases in length, depending on the platform. This has forced studies to choose which variable regions of the rRNA gene to amplify and sequence, and has opened up an arena for debate on which variable region to choose . And of course, the DNA analysis of all this data you’ve now created is quickly being recognized as the most difficult part- which is what I focused on during my post-doc in the Yeoman Lab. Stay tuned for a blog post on the wonderful world of bioinformatics!
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The “Women in Science” debate has been raging on in a variety of ways, from wondering why there aren’t more of us to whether or not a mixed-gender lab is too distractingly sexy. The amount of women in science, the pay gap, and career advancement potential varies wildly by country and research field. So does public opinion about whether or not there is an actual problem, what might be causing it, and what we might do about it. In 2011, women only earned about 18% of undergraduate computer science degrees, down from its peak of 37% in 1985. The percentage of women earning graduate-level degrees has been slowly increasing since 1970, with 28% of the masters degrees and 20% of the doctoral degrees (Ph.D ,s) being earned by women in 2011. Women make up roughly 41% of total STEM doctoral degrees earned; however, women only fill 24% of STEM jobs in the US, and only 25% of STEM managers are female. Universities are only slightly better, with 28% of tenure-track faculty positions being held by women in the US, but only 12% worldwide.
This debate isn’t just specific to science in academia, but a lack of diversity in the educational system can have interesting effects. First, a lack of female (or other demographic) role models means that female children are less likely to go into that field: if they don’t see anyone paving the way, then the idea that they might also become a physicist doesn’t occur to them or doesn’t sound like an attractive career. While boys and girls are taking math and science in equal numbers in grade school, this doesn’t translate into the same number of men and women in math or science undergraduate fields, where women only earn 18% of undergraduate computer science degrees, down from 37% in 1985, and only 11.5% of software developers are female. Part of this is the perception that men are better than women at math and science, even though women have been shown to be better at writing computer code than men, but only when reviewers did not know the coder was female. Science faculty, regardless of their own gender, were more likely to hire a male applicant over an identical female applicant, and offered them several thousand dollars more starting salary for the same position. The male applicant was perceived as more competent, more hirable, and more in need of mentoring than the identical female applicant.
Another problem is that women are less likely to have people sponsoring or advocating for them in the work place (available here and discussed here). People with sponsors were 30% more likely to be promoted or given raises. As of 2014, only 23% of Americans polled preferred a female boss, which is and has always been lower than the number of respondents preferring a male boss, which may account for the lack of support women find in climbing the ladder. Surprisingly, women were 13% more likely to want a male boss, which may be a reaction to fierce competition to become the “token woman” at a company or working group, as women or other minorities who advocate hiring another woman or minority are rated poorly. There is also the perception among women that a female boss is less likely to promote you over herself, as she doesn’t want competition, known as Queen Bee Syndrome. This too, has been refuted, as women are shown to be more likely to mentor and develop female employees lower down on the ladder (discussed here).
Finally, one of the reasons that women are not found in some fields or levels of management, which no one really wants to discuss, is the disparaging levels of sexism and harassment we may face. For female graduate students, post-docs, or new professionals, sexual harassment at work can increase attrition rates. Due to the close nature of the working relationship of graduates/post-docs with their advisors, many students feel they can’t report inappropriate behavior (of any nature) for fear of losing their position in the program. As a student, you need your advisor to approve everything, from the courses you have taken to manuscripts before publishing, and a poor relationship with your advisor can make it nearly impossible for you to complete your work. Tenured faculty who have been accused of harassment also seem to be acting with impunity, as it can be difficult, time-consuming, and costly to fire a tenure professor (in the absence of proven criminal activity). In field situations, sexual harassment can take on a more sinister tone, as you may be the only female in a group and depending on your abuser to keep you alive.
So what can we do about this? Because this isn’t just a woman’s issue. That’s what I discussed here because I have some expertise with being a woman, but in general, diversity in society is a hotly contested issue. It really shouldn’t be, increasing the diversity in a group can increase performance and improve decision making (discussed here). Having a diverse group of people (in terms of gender, race, sexuality, education, economic status, birth order, pets owned, places lived, live experiences learned from..) gives the group a wider range of previous experience to lean upon when solving problems. It’s why we evolved into a social society in the first place- it was better for survival.
The first step to solving our diversity issues is to let go of preconceived notions about yourself or others. Stop thinking about life-related obstacles to your career trajectory, such as whether you want kids or having to relocate your family, and stop assuming that others might be better or worse at their job because they have chosen a certain family dynamic. Stop thinking you might not get a job because of what the employer might thinking about women as bioinformaticians, and in turn stop stereotyping applicants based on your ideas of who they are and of what they are capable.
The second step is to be a role model, and to actively engage the next generations of computer scientists, astronauts, microbial ecologists, astrophysicists, and educators. As a woman in science, it’s important to me to encourage other women and girls in science, because I would not be here today without the positive female role models I have had. It’s important to support programs that encourage different minorities to achieve in fields where they are underrepresented, because it benefits all of us.
And the third step, perhaps the most difficult. is to have an open conversation about the difficulties and prejudices facing women, or anyone, in different science fields. Often people can fall back on stereotypes or be sexist or racist without realizing it, and it’s important to speak up and have a conversation with them to come to a better understanding of how to get along. When someone’s words or actions are creating a hostile work environment, tell them directly, as well as their supervisor or relevant reporting agency as needed. If we don’t address the problem on an individual basis, then individuals will never amend their actions. In addition, it’s important to validate the feelings of and listen to someone who has been the victim of harassment or a crime (of any nature), because it’s important to make them feel safe and believed. Often, victims of sexual harassment state that not having their reports believed or treating seriously by supervisors was worse than the harassment itself. And personally, I have plenty to do on a daily basis without having to deal with casual or institutional sexism. Working women are simply too busy quietly doing well at ours jobs to deal with men’s feelings about us.
As my current post-doctoral position winds down in the Yeoman Lab in the Department of Animal and Range Sciences, I am pleased to announce that I have accepted a post-doctoral position in the Menalled Lab in the Land Resources and Environmental Sciences Department! Dr. Menalled’s work focuses on agricultural weed ecology and management, particularly with respect to plant-plant interactions, changing climate (water and temperature changes), and now plant-microbe interactions!
I’ll primarily be working on a new two-year project that recently got funded through the USDA, entitled “Assessing the vulnerability and resiliency of integrated crop-livestock organic systems in water-limited environments under current and predicted climate scenarios”, but I’ll also be working collaboratively on several other similar projects in the lab.
My new responsibilities will include comparing agronomic performance and weed-crop-pathogen interactions between organic-tilled and organic-grazed systems, evaluating the impact of management and biophysical variables on soil microbial communities, and collaborating in modeling the long-term consequences of these interactions under current and predicted climate scenarios. It’ll mean a lot more field work, and a lot of new skills to learn! In fact, to help me study for my new job working with agricultural plants, my mentee and her friend made me flash cards:
In addition to my new skills, I’ll be integrating my background in microbial ecology and bioinformatics, in order to study agricultural ecosystems more holistically and measure plant-microbe interactions. In the same way that humans eat probiotics to promote a healthy gut microbiome, plants foster good relationships with specific soil microorganisms. The most exciting part is that I will act as an interdisciplinary bridge between the agroecology of the Menalled lab and the microbial ecology of the Yeoman lab, which will allow for more effective collaborations!
Encouraging girls to go into STEM fields is really important; studies show that female STEM high-school teachers and even online mentors increase the probability of female students following a STEM education. Moreover, any child benefits academically and psychologically from having positive role models in their life, especially when they were role models that they interacted with as opposed to celebrity role models. And the benefits don’t just extend to children, adults benefit from positive rolemodels, too. Certainly I have benefited from strong female role models in my life, from high school art teachers, to undergraduate lecturers, to family (happy birthday, Mom!).
This past fall I started putting my money where my mouth was- I started mentoring an elementary school-aged girl in Bozeman, MT through the Thrive Child Advancement Project (CAP). So far, we have mostly been making art projects and talking about archaeology. But we have been talking about trying to learn the Java programming language together!
There are lots of opportunities to mentor kids, either through CAP programs, Big Brother/Big Sister, Girls and Boy Scouts, etc., just a quick internet search brings up dozens of local options. For less of a time commitment, you can also volunteer for community workshops, like the Girls for a Change summit in Bozeman or the Girls-n-Science in Billings.