The Taproot is the podcast that digs beneath the surface to understand how scientific publications are created. In each episode, we take a paper from the plant biology literature and talk about the story behind the science with one of the authors.
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S6E5: Transforming plants and the culture of publishing
Tuesday, January 24, 2023 ⢠Duration 43:54
In this episode, we speak with Yunde Zhao, a Professor of Cell and Developmental Biology at the University of California San Diego. Yunde earned his Bachelors in Biochemistry from East China University of Science and Technology, received a Ph.D. in Biochemistry
from the University of Michigan, and did his postdoctoral training in plant genetics at the Salk Institute, where he was a Howard Hughes Medical Institute Fellow of the Life Sciences Research Foundation. In January 2022, Yunde started his appointment as the
Editor-in-Chief of Plant Physiology, one of the oldest plant journals.
We discuss a recent paper from Yundeâs lab describing a fast and non-invasive method for monitoring plant transformations, and talk about the transformations that are needed in the publishing world. We also address a recent controversy about diversity among some newly appointed Plant Physiology editors.
Show Notes:
#DiversifyPlantSci
https://rdale1.shinyapps.io/diversifyplantsci/
Plant Physiology Synbio Initiative https://academic.oup.com/plphys/article/190/1/180/6613939
Pandemic-related effects on publishing are gendered:
https://www.nature.com/articles/d41586-020-01294-9
https://elifesciences.org/articles/76559
Paper: https://pubmed.ncbi.nlm.nih.gov/33024566/
He, Zhang, Sun, Zhan, and Zhao. A reporter for noninvasively monitoring gene expression and plant transformation. (2020). Horticulture Research 19:152.
Twitter Handles:
Liz Haswell Twitter @ehaswell
Ivan Baxter Twitter @baxtertwi
Yunde Zhao Twitter @YundeZhao
Taproot S6E4: Can We Force Academic Structures to be Inclusive?
Tuesday, January 17, 2023 ⢠Duration 42:22
In this episode, we speak with Jason Williams, Assistant Director of Inclusion and Research Readiness at the DNA Learning Center at Cold Spring Harbor Laboratory. Jason is also lead for CyVerse Education, Outreach, and Training â the U.S. National Cyberinfrastructure for Life Science. Jason received his B.S. in Biology from SUNY Stonybrook in 2004, then worked as a technician in several labs at Cold Spring Harbor, and then transitioned to multiple roles in the DNA Learning Center In 2009.
We discuss an article Jason and colleagues recently published in Science, entitled âAchieving STEM diversity: Fix the classrooms. Outdated teaching methods amount to discriminationâ. We also talk about the nuance and complexities around improving diversity, equity and inclusion in STEM education, in planning conferences, and in running scientific societies. Have a listen!
Show Notes:
Paper: J. Handelsman, S. Elgin, M. Estrada, S. Hays, T. Johnson, S. Miller, V. Mingo, C. Schaffer, and J. Williams. (2022). Science 376:1057-1059.
https://pubmed.ncbi.nlm.nih.gov/35653460/
Twitter Handles
Liz Haswell Twitter @ehaswell
Ivan Baxter Twitter @baxtertwi
Jason Williams Twitter @JasonWilliamsNY
S5E0: Season 5 Teaser
Tuesday, September 15, 2020 ⢠Duration 02:07
It has been quite a few months since our last episode! We intended to have a new season out by now, but as you might imagine, a few things got in the way. We are, however, back to working on topics and guests for Season 5 so stay tuned for new episodes this Fall!
In the meantime, we want to hear from you! Tell us how you're navigating these chaotic and unusual times. Or... if what you're doing can't really be characterized as navigating, tell us about that instead!
Let us know how you're trying to work right now, how you're navigating the next step in your career, or how the renewed attention on systemic racism in science and the world around us has affected you.
We're planning on playing a few of these in every episode. So tell us a little bit about yourself by recording a short voicemail on your phone and email it to us at Tapoot@Plantae.org.
We look forward to hearing from you!
Be sure to listen to our previous seasons while you wait and stay tuned
How to listen, download and subscribe to The Taproot podcast.
Questions, feedback, suggestions? Contact us at taproot@plantae.org.
Follow us on Twitter
@TaprootPodcast
@ehaswell
@baxtertwi
S4E8: Convergent Evolution of Caffeine and Divergent Careers
Tuesday, February 18, 2020 ⢠Duration 32:13
In the final episode of Season 4, we talk with Todd Barkman, Professor of Biology at Western Michigan University. Todd earned his PhD in Botany at the University of Texas at Austin with Beryl Simpson, and went on to a postdoc position at Penn State with Claude dePamphilis. He started his lab at Western Michigan in 2000, where his group studies the systematics and evolution of plants, as well as the molecular evolution of biosynthetic pathways.
We talk with Todd about his labâs publication, âConvergent evolution of caffeine in plants by co-option of exapted ancestral enzymesâ which was published in PNAS in 2016. Todd tells us the story behind the paper, how flowering plants evolved to make caffeine, and how he became interested in this topic.
Todd describes what it is like to work at an âR2, or Research 2â institution such as Western Michigan, where it is important to succeed as both an instructor and as a researcher, and where resources for the latter are modest compared to âR1â institutions. We talk about the pros and cons of this environment, and how to accomplish research goals with limited funds and time. Todd talks about the importance and limitations of collaborations and closes with advice and encouragement for early career scientists considering a career at an R2 or R3 institution. He also advocates for a less deliberate and more open-ended style of experimental planning, and acknowledges the power of serendipity in his work.
Huang, R., OâDonnell, A. J., Barboline, J. J., & Barkman, T. J. (2016). Convergent evolution of caffeine in plants by co-option of exapted ancestral enzymes. Proceedings of the National Academy of Sciences, 113(38), 10613-10618.
Taproot S4E1: Identifying the Principle Components: Gender Dimorphism in Flowers and Consciously Building a Happy and Rewarding Career in Science http://bit.ly/38QivyY
Todd's email: todd.barkman@wmich.edu
Twitter Handles
@ehaswell
@baxtertwi
@taprootpodcast
S4E7: Milestone-Based Decision-Making In and Out of the Lab
Tuesday, February 4, 2020 ⢠Duration 39:19
This episode, we continue our discussions about cultivating a career with guest Kelly Gillespie, Nursery Solutions Lead at Bayer Crop Science. Kelly got her bachelor's degree at Knox College, a small liberal arts college in Illinois. She then moved on to do a PhD with Lisa Ainsworth at the University of Illinois. She did a short postdoc with Dick Sayre at the Danforth Center before moving to Monsanto, where she has worked for 9 years, staying with the company through the merger with Bayer.
We talk with Kelly about her publication, âGreater antioxidant and respiratory metabolism in fieldâgrown soybean exposed to elevated ozone under both ambient and elevated CO2â, which was published in 2011 in Plant Cell & Environment. She talks about what it was like to work at the USDA Free Air Concentration Enrichment (FACE) site, the teamwork that was needed to collect her data, and how this experience taught her to work in highly collaborative environments.
Kelly also shares her career journey and the factors she considered when choosing to make the transition from academia to industry. Kelly emphasizes a âmilestone-basedâ approach, where each decision is broken into small steps and evaluated at checkpoints along the way. She talks about what it takes to succeed in a science career in industry, what might be familiar and what might be surprising to someone with an academic background, and emphasizes the value of making connections with other professionals.
SHOW NOTES:
Gillespie, K. M., Xu, F., Richter, K. T., Mcgrath, J. M., Markelz, R. C., Ort, D. R., ... & Ainsworth, E. A. (2012). Greater antioxidant and respiratory metabolism in fieldâgrown soybean exposed to elevated O3 under both ambient and elevated CO2. Plant, Cell & Environment, 35(1), 169-184.
Join ASPB http://bit.ly/PCASPBMembership
Plantae Webinar: Ask Me Anything: Plant Science Careers in Industry http://bit.ly/IndustryCareer_Seminar
The Awesomest Seven Year Postdoc http://bit.ly/2Os6mbp
Plantae Webinar: Prioritization and Work / Life Balance: Do Less, Work Better http://bit.ly/2vMYrit
Plantae Mentoring Center - Sign up to be a mentor or mentee http://bit.ly/395XWOT
Kellyâs LinkedIn Profile http://bit.ly/3b8bVWh
Twitter Handles
@kmgillespie
@ehaswell
@baxtertwi
@taprootpodcast
S4E6: Staying Afloat - Time Management in a Sea of Obligations
Tuesday, January 21, 2020 ⢠Duration 44:54
Our guest for this episode is Dr. Holly Bik. Holly obtained her PhD in Molecular Phylogenetics at the University of Southampton, working with John Lambshead at the Natural History Museum of London in conjunction with the UK National Oceanography Center. She completed postdoctoral appointments with Dr. Kelley Thomas at the University of New Hampshire and Dr. Jonathan Eisen at UC Davis before starting her faculty position.
In addition to her research, Holly is invested in science communication. She serves as an associate editor for the popular marine blog Deep-Sea News and maintains an active presence on Twitter (@hollybik). Holly has co-authored a number of peer-reviewed articles on the use of social media and online tools in academia, including âAn Introduction to Social Media for Scientistsâ in PLoS Biology and âTen Simple Rules for Effective Online Outreachâ in PLoS Computational Biology.
In this episode, we discuss the first paper to come out of Hollyâs lab at UC Riverside , entitled âNematode-associated microbial taxa do not correlate with host phylogeny, geographic region or feeding morphology in marine sediment habitatsâ (Schuelke et al., 2018). Holly elaborates on the unexpected results from this paper and talks about the many challenges associated with collecting and analyzing marine sediments.
In addition to the technical aspects of this paper, we also talk about time management and how Holly set aside time to write a draft in one week. She tells us about her 6-month-long personal work/life balance experiment in time-tracking and shares what she learned from this experience. We discuss the concept of Deep Work and why she continues to fill out weekly review worksheets to help manage stress and productivity.
At the time of this recording, Holly was in the process of moving her lab from UC Riverside to The University of Georgia where she is currently an Assistant Professor in the Department of Marine Sciences. We talk about the process of moving and the factors Holly considered when making this important career decision.
Holly explains that it's important for early career researchers to understand how long things take, and also be okay with the fact that some things are just going to take way longer than you expect.
SHOW NOTES:
Paper:
Schuelke, T., Pereira, T. J., Hardy, S. M., & Bik, H. M. (2018). Nematodeâassociated microbial taxa do not correlate with host phylogeny, geographic region or feeding morphology in marine sediment habitats. Molecular Ecology, 27(8), 1930-1951.
A few of Hollyâs Twitter threads:
Data-driven time management
https://twitter.com/hollybik/status/1133750210331496450
Concept of âdeep workâ
https://twitter.com/hollybik/status/1133751166091685888?s=20
Work life balance:
https://twitter.com/hollybik/status/1133751739599876106?s=20
The Monday Motivator - weekly emails that provides positive energy, good vibes, and a productivity tip from the National Center of Faculty Development and Diversity
Cal Newport (author of Deep Work) https://www.calnewport.com/about/
@hollybik
@ehaswell
@baxtertwi
@taprootpodcast
S4E5: Navigating Experimental and Situational Panic
Tuesday, January 7, 2020 ⢠Duration 37:41
In this episode, we talk with Laura Klasek who is a Plant Biology Ph.D. Candidate at the University of California, Davis about her research and experiences as a graduate student.
Laura received her undergraduate degree from Hendrix College, where she double-majored in Biology and English with a creative writing focus. She was a 2018-2019 ASPB Conviron Scholar, is currently serving as a Plantae Community Network Leader for the Student Space Network, and is an Early Career Representative for the ASPB Plant Biology Program committee.
For her dissertation, Laura is examining how the photosynthetic apparatus of the chloroplast develops. She is specifically interested in how proteins are targeted and folded within the chloroplast to facilitate improvements in how efficiently plants use light, water, and nutrients.
Laura began her graduate studies in 2014 with Dr. Kentaro Inoue. In August 2016 - two weeks before Lauraâs qualifying exams - Dr. Inoue tragically died in a traffic accident. The sudden loss of her advisor at a time when many graduate students already question whether to continue forced Laura to actively make difficult decisions about her career in a stressful and unexpected environment.
In this episode, Laura shares how she navigated her situation with honesty. We discuss graduate student agency and how options are not unlimited. We talk about how it is important to work through the panic when our experiments and careers do not go as planned and how to decide if something is salvageable or if it is time to walk away. Finally, Laura suggests ways in which graduate programs and universities might help students by having systems already in place that provide support when faculty are sick, moving, or otherwise suddenly unavailable to mentor and to provide financial stability.
SHOW NOTES:
View From the Trenches - Advice if your PhD Advisor Unexpectedly Dies by Laura Klasek
Hope is not a Strategy - Designing an IDP for a graduate program by Laura Klasek
Plantae Webinar with Katie Murphy and Laura Klasek
All aboard the mentor-ship: making and using an Individual Development Plan
Follow on Twitter
@EBibliophile
@ehaswell
@baxtertwi
@taprootpodcast
S4E4: Graduate Interviews Demystified
Tuesday, December 10, 2019 ⢠Duration 34:52
In the previous episode, we talked with Dr. Scott Barolo about his research and shared tips for completing written graduate school applications. In this episode, we go to the next step, following up with Scott to discuss what to do once youâve made it to the interviews.
Scott shares tips for how to excel at interviews and offers advice for prospective students to help them make their own evaluations during the process. We talk about how interviews work both ways--you are interviewing the school as much as they are interviewing you--and how to ask the right questions to determine if a particular university, lab or program is the right fit. We leave students with a list of questions to ask that will help them gain a better understanding of lab culture, possibilities, and expectations.
Whether you are a prospective student, a faculty member involved in admissions, or just want more insight into a process that can be pretty opaque--this episode is for you!
A transcript for this episode generously provided by Joe Stormer can be found here: https://bit.ly/3ubuCSu
SHOW NOTES:
Barolo Lab website: https://www.barololab.net/
Should you go to grad school? (Via Plantae) https://plantae.org/blog/should-you-go-to-grad-school-from-science-careers/
Plantae Mentoring Center
https://jobs.plantae.org/ementor/index.cfm
@sbarolo
@ehaswell
@baxtertwi
@taprootpodcast
S4E3: How to mastermind experimental designs and and your graduate applications
Tuesday, August 27, 2019 ⢠Duration 39:10
In this episode, we talk with Dr. Scott Barolo about how he made a popular board game into a teaching tool, and we start a two-part discussion about the grad school application process.
Scott gained his BSc at Penn State University and his Ph.D. in biology at the University of California, San Diego. He was then a postdoctoral fellow at the same university and started his lab in 2003 at the University of Michigan Medical School. Scottâs lab studies transcriptional pathways, repressors, and enhancers in Drosophila melanogaster. He has been the director of the graduate training Program in Biological Sciences (PIBS) since 2012. He is also a co-founder of the â9 Reply Guysâ - inspired by #MeTooSTEM - where he humorously categorizes unconstructive Twitter behavior of men/women into 9 types.
In this episode, we discuss a publication with Amy Strom, who was then an undergraduate student, titled âUsing the Game of Mastermind to Teach, Practice, and Discuss Scientific Reasoning Skillsâ, published in PLOS One in 2011. We discuss how he âforcedâ his students to play this codebreaker game and how it helped them think about good experimental design, hypothesis testing, and biases.
This paper helped provide some insight into aspects of scientific design that are often not explicitly explained to trainees. In the same vein, we ask Scott to describe the process of applying to graduate school. We talk about the advantages of taking off a couple of years first and getting lab experience to see if graduate school is a good fit. We get into a time machine and recall our own applications and how not to randomly apply to universities and programs.
Scott says when he evaluates large stacks of applications, being an overachiever is great but the applications he remembers are from people who are different in some way. He recommends students to âshow a bit of themselvesâ in personal statements. They should not be afraid to share some of their out-of-academia interests either!
The conversation was so great we decided to split the episode into two sections so look out for the continuation in our next episode where Scott demystifies the interview process!
A transcript for this episode generously provided by Joe Stormer can be found here: https://bit.ly/3do5FNM
SHOW NOTES:
Strom, A.R. and Barolo, S., 2011. Using the game of mastermind to teach, practice, and discuss scientific reasoning skills. PLoS biology, 9(1), p.e1000578.
https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1000578
Barolo Lab website: https://www.barololab.net/
Should you go to grad school? (Via Plantae) https://plantae.org/blog/should-you-go-to-grad-school-from-science-careers/
Twitter link to 9 reply guys introduction: https://twitter.com/sbarolo/status/1036685010869407744
Twitter:
@9replyguys
@sbarolo
@ehaswell
@baxtertwi
@taprootpodcast
#TaprootTuesday
S4E2: The GRExit and how we choose who goes to grad school
Tuesday, August 20, 2019 ⢠Duration 35:31
In this episode, we talk with Dr. Zen Faulkes about the graduate application process, what program directors are looking for and how hard it is (or indeed impossible) it is to have unbiased selection system.
Zen gained a B.A., Psychology at the University of Lethbridge in 1989 and a Ph.D. at the University of Victoria about sand crab digging behaviour in 1996. He was a postdoctoral researcher at McGill University until 1999, and then he was a postdoc at the University of Melbourne until 2001. He is currently a Professor at the University of Texas Rio Grande Valley. Zen writes the âBetter Postersâ blog, which dispenses advice on how to improve the posters we present at meetings.
In this episode, we discuss his publication, âResolving authorship disputes by mediation and arbitrationâ in Research Integrity and Peer Review, and also his letter in Science titled â#GRExit's unintended consequencesâ. As graduate program coordinator, he talks about the pros and cons of GREs. Whilst universities are looking for âsuccessfulâ people we have a chat about how we could define âsuccessâ to begin. Are assessments really consistent and reliable? Hm.
We talk through the whole graduate application process step-by-step from both the applicantâs and recruiterâs point of views. We chat about how to structure personal statements and what to expect during interviews but also keeping in mind that everyone is different and perhaps more introverted students might feel at a disadvantage.
Zen recommends students to ask program directors what competitive applications look like - they are very likely to give straight answers. While it is good to have a high GPA for a masters program, students really should get to know what the requirements and expectations are for different programs. Zen says, âIf you inspire to go to graduate school, you have to be proactive thinking about what your opportunities are.â
We leave students with a final piece of advice: every semester get to know one professor slightly better so at least you have a few people who know more about you. Asking for advice from professors and program directors can make graduate school application a whole lot smoother!
A transcript for this episode generously provided by Joe Stormer can be found here: https://bit.ly/3bpBjb5
SHOW NOTES:
Faulkes, Z., 2018. Resolving authorship disputes by mediation and arbitration. Research integrity and peer review, 3(1), p.12.
https://researchintegrityjournal.biomedcentral.com/articles/10.1186/s41073-018-0057-z
GRE exit - does not predict âsuccessâ - Letter in Science
https://science.sciencemag.org/content/363/6425/356.2
Better posters site
http://betterposters.blogspot.com/
Blog:
https://neurodojo.blogspot.com
Free pdf: https://faculty.utrgv.edu/zen.faulkes/Presentation_tips.pdf
Twitter:
@DoctorZen
@ehaswell
@baxtertwi
@taprootpodcast
#TaprootTuesday
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