Getting Settled

The Paleantology project is getting settled. I’ve accepted a position at Southeastern Louisiana University. I’ve been meaning to write a little bit about academic job searching. Since I’m starting to prepare my lab documents, now seems like the time.

My search was a little different than other accounts we often hear in the Evolution, Ecology and Behavior space, in that I  always intended to end up at a primarily undergraduate institution (PUI) – a liberal arts school or small university without many graduate students.

By the time I leave for my job next month, I will have done a total of just shy of two years of postdoc. I started my postdoc with a six-week old toddler, who I am now watching eat yogurt at the coffee table. I will have to give up part of my NSF postdoc funding, but I found the job, and the place, and the school. I’m making the right choice.

Jeremy Yoder had a thread on Twitter this morning where he talked about the numbers behind his job search. I didn’t keep as detailed of notes as Jeremy did, but I probably applied to about 17 jobs, had phone interviews at 6, on-campus visits at 3, and received two offers. This reflects, very much, what Jeremy said about the number of applications sent being proportional to job openings. I’m an evolutionary biologist who uses computational methods to answer questions in statistical phylogenetics, particularly questions about how we incorporate fossil information into phylogenetic trees.

So I’m not applying to genomics jobs. I’m not applying to ecological physiology jobs. And my research might sound sort of esoteric. The number of jobs at primarily undergraduate institutions is already smaller than the number of R1 jobs (at least the years I applied). My interests put me in a smaller subset of those jobs.

On top of that, we have some tricky business. PUIs often write job ads that are a little broader than research schools, particularly big research schools. Big-name schools can rely on getting hundreds of applicants, even in specialized fields. Without the name recognition of big schools, PUIs may try to increase the depth of the applicant pool by making it wider. Many of the ads I applied to were something like “Faculty line in computational biology. May specialize in evolution, ecology, bioinformatics, genomics, ecoinformatics, cancer biology, neuroscience, or a combination thereof.” That’s a wide net being cast.

I applied to jobs for which I thought I would be a great fit, and never received a call. I applied to jobs where I thought I was a tangential fit, and had phone interviews. I had phone interviews that went awesome, only to see the seminar calendar get loaded up with genomics and neuroscience folks. And I get that – PUIs have smaller faculty rosters. Getting students into medical school is often a high priority. Having folks who can teach evolution, or bioinformatics, as well as a course in cancer genomics or neuroscience lets the department grow its course roster while increasing the number of courses about which the med school students will be excited. But I definitely did have moments, after everyone else in my house had gone to sleep, when I sat up wondering if there would ever be an opening for a theoretician who is passionate about working with students.

Next year would have been my last year of postdoc on my personal funding. I could probably scrounge some funds after. I would have hit the market harder, and maybe applied to some schools that weren’t PUI. I also would have applied to other postdoc fellowships, and jobs in industry. I have a skill set that would bring me success in industry. I have always known that card is in my back pocket. But I would have fought like hell to get a chance at the job I really want.

There is one other thing that I want to note about my PUI job search. Christie Bahlai wrote about her job search season, looking at the angle of challenges posed to people marginalized in science. And those challenges are real – having children so soon before moving for my postdoc, I was carrying some debt from medical and moving expenses that I was trying to pay down.

The money aspect can be pretty scary, and I’ve seen a smattering of comments to that effect from grad students and postdocs on Twitter. In my job search, with all three on-campus visits, I put less on my credit card than one conference, typically. You certainly can ask for a department to directly book flights, as opposed to reimbursing you. I did not have success with this, but I know others who have. Interview clothes don’t have to be the latest style. I bought everything I wore on clearance at Nordstrom Rack or TJ Maxx for under $100 dollars the first year. Due to post-baby weight loss, I had to buy some new things the second year – I spent about $15 on a plain, white button down to freshen up my skirt-blazer outfit. I bought a new pair of dark jeans, not for the interview, but I ended up wearing them on the interview.

Right, the baby. The first year I was on the market, I had to kick back a schedule for not having enough nursing breaks. It might be illegal for them to use info about my marital status or children in their hiring decisions, but they sure knew about it. On my second year on the market, I was never asked about children … because I volunteered it. The two schools I had on-campus visits at where in areas where I wasn’t familiar with the school systems and daycare. It’s info I needed. I will say that I was treated with nothing but respect when I asked about nursing accommodations, schools, etc. More respect than I’ve than been treated with at some workshops. I can’t promise that being honest about my kid didn’t hurt me (I don’t have that job where I had to push on the schedule, eh?). I can’t promise being honest wouldn’t hurt you. But I can say that I’m happy with my results. If being a mom cost me a job, that job probably would have eventually driven me out, anyway.

I read this piece out loud to my husband. He noted that I hadn’t mentioned him. And I didn’t know what he meant. And he said, “Well, the childcare.” On-campus PUI visits mean flying out one afternoon, being gone for a full day, and usually coming back the following afternoon. My husband works second shift, and had to rearrange his schedule on days I was gone so he could make the daycare drop-off and pick-up. He’s the best; I couldn’t do this without him. He did a lot of legwork to support me in this search. For us, this is a minor and annoying hardship. For someone without support, this can be a serious issue. If you’re reading this, and you’re on a search committee, do be aware that planning early early and being flexible with dates is really helpful with folks who are juggling these responsibilities.


The primarily undergraduate institution search is a little different than many of the job search we often hear about. I’ll follow up after the Evolution Meetings, where I will speak on Saturday (see event 8) about PUIs and why I chose that path, with a less personal essay and some nuts-and-bolts of these applications.


Edit0: Since I started writing, NSF announced they are ending the DDIG. The faculty position I have builds directly on the research I wrote my DDIG on. That award allowed me to be independent and establish my research program early. I am grateful for the opportunities afforded by that program, and I am saddened that others will not have this funding available to them.

Edit1: A couple of people have asked if I will publicly post job materials. My plan is not to do that, but if you want to see them, please do get in touch. I’m open to reconsidering this position, so if anyone thinks I’m wrong to not share, weigh in!

Edit2: A couple people have asked about bringing up nursing when scheduling an on-campus interview. I went with a simple:

I am presently still nursing an infant. I will need $X lactation breaks of $Y duration.

To push back on a schedule:

Thank you so much for sending this schedule. I have some concerns about the lactation breaks, which are scheduled for $X times. Would $Y alternative schedule be workable?

In my case, I just wanted a quick pump before my talk, so they slated me in an additional 20 minutes of prep time. No big deal.

End of the Semester!

This semester sure went by fast! Here, we have a couple wrap up statements from our two project undergraduates, Patrick Mendoza and Andre Flores. We were really lucky to have such great students working (project discussed here and here) with us this spring. In their words, here is what they learned, what more they hope to learn, and what is next for them.

Patrick Mendoza

One of the big takeaways from this semester will be the fact that biology is not as far removed from computing and statistics as I normally thought.  The biological sciences are an incredibly interdisciplinary branch of science that have many different areas and sub-disciplines.  I have learned that there are many ways to merge interests in math and computer science to complement biology, and particularly, phylogeny.

This past semester has been a great experience.  Working for April Wright and Walker Pett has been especially gratifying as that both are extremely knowledgeable and took time to distill complex concepts through exercises, lectures, and applied research.

I would like to spend more time understanding the root mathematical models and their derivation along with their correlation to applied phylogenetic analysis.  Not being a computer science major hasn’t been a hindrance, but it could help to learn more fundamentals.

This summer I will be attending an internship at the Boyce Thompson Institute in Ithaca as part of their Plant Genome Project.  Solanaceous crops have been genetically modified via CRISPR/Cas9 regarding leaf polarity.  I will be using in situ hybridizations and histology to detect modified genes in plant progeny.  I am looking forward to expanding my skillsets to include microscopic laboratory experiments.

Andre Flores

Although I generally felt proficient for my age in biological knowledge as I first the lab, I quickly realized I had considerably more advanced concepts to learn. The beginning was mostly a breeze as I refreshed my knowledge in phylogenetics, but concepts began to get harder afterward. Because I was taking a Genetics course concurrently, I found it easier to understand my lab work. In particular, it was much easier to grasp the concepts of DNA evolution. Since I had a better understanding of these molecular structures and their types of mutation, I was able to apply it to the models of evolution. The simplest of these was the Jukes Cantor substitution model, which was important to learn as both a basic model of evolution but also due to its importance in understanding statistical analysis.

When I first started to apply my programming skills as an analytical tool for biology, I had almost no clue how to summarize the data I was gathering. This started to change when I started learning about substitution models, as they explained mutation rates through methods in statistical probability. It was especially helpful when we worked through concepts and problems as a group while using the whiteboards, as it was much easier to grasp with relatively simpler material (like the JC model). Later on, I found it interesting to visualize the data using Tracer or the notebooks, especially as a visual learner. The same notebooks were also a great way to apply programming skills and try out new languages. Despite learning a considerable amount, I would still say I have much more to learn in statistical analysis before being confident in my abilities with it.

By far, the most trouble I had in the lab was trying to grasp understanding of the data. Although I learned how different models worked, I still had trouble understanding what to do with the data. The first time I ran scripts on Rev, I remember being basically clueless when I saw all the terms like “marginal” or “prior” followed by random numbers. While these were quickly explained to me, it was a lot to take in at once, so I had to do a lot of extra work refreshing my knowledge in stats before I could progress. Looking back, I think it would have been helpful for us to have spent more time learning about statistical terminology and their roles in affecting a data plot. Essentially, I would have liked to learn more about the stats/computing side of the lab. This would relate to a better understanding of my understanding on how to improve upon these models, but I luckily have the opportunity to continue learning these topics through the summer.

My summer plans are to continue learning under April and Will to hopefully prepare for presenting at SACNAS in October. I hope to learn a lot more about statistical analysis and be able to apply my knowledge to more datasets with better understanding. Being able to apply my new skills to more datasets is important because it is basically the most important point of what I hope to present over – providing data to support the efficiency of using Bayesian methods to study phylogeny. I plan to start immediately after finals week and be able to continue at least into July, from where I’m hoping to spend 4 weeks in Costa Rica at a conservation facility. I would spend half my time working hands-on with endangered species, then spend the other half in the jungle helping record data as a bioinformaticist. Afterward, I’ll likely pick right back up on studying molecular evolution, whether I continue the fall semester at Iowa State or not. Regardless, I would have a summer with a lot of valuable practice in the bioinformatics field.

Overall, I had a great experience learning alongside Pat in the Heath Lab. April and Will did an excellent job teaching us new material and were helpful in making sure we understood key concepts. Early on, I refreshed knowledge on basic biological processes that led to evolution, then transitioned into the computational methods used to analyze those biological processes. Although I still have a lot to learn, under April and Will’s guidance I hope to gather valuable experience continuing summer research as I build my biological skillset.

Start of the Semester!

Editor’s Note: Every semester, we bring on new undergraduate researchers to the project. We do a lot of basic-level training for computational biology. If you’d like to follow along at home, our schedule is here.

Andre Flores

I’m Andre, an undergraduate studying both Biology and Computer Science. I intend to pursue a medical degree in the future, hopefully incorporating bioinformatics to work in the fields relating to psychology and neuroscience. Working in the Heath Lab is my first experience working in a real research environment, an integral part of preparing my resume for graduate school. Furthermore, the lab is my first real opportunity for combined education and hands-on experience between my two drastically different areas of study. I’m hoping to learn a lot more programming skills and knowledge about phylogenetics, and the ways in which they can work together to study biology.

Pat Mendoza

I am a student majoring in Horticulture with an anticipated graduation in Spring ’18.  I’m coming to Ames after working in financial analysis for 13 years and with an existing BS in Mathematics, specializing in Statistics, from the University of California Irvine.  This semester I hope to expand on my skill sets as a programmer learning python and R as well as the application of statistics to further scientific research.  My interests are in mutualisms between plant and animal as well as mycorrhizae and phylogenies.  In the fall I will be applying to grad programs with the intent of pursuing a career in research.


SSB2017 Wrap Up

The Paleantology project was at the Society of Systematic Biologists standalone meeting this week. Below are the slides for my talk. If you want to try the model discussed, there is a use-case in the Total Evidence Dating RevBayes tutorial given by Tracy Heath, Walker (Will) Pett and myself. Feel free to get in touch with questions, or for help implementing the model with your own data.

Will and I have a couple students starting with us this week to elucidate aspects of the performance of the model discussed. Watch this space to get to know our students and their project!

Paleantology Goes to Sys Bio

Project PI April Wright (yours truly) and project sponsoring scientist Tracy Heath will be at the Society of Systematic Biologists standalone meeting Jan. 6 – 11 in Baton Rouge. Both of us will be involved in the RevBayes workshops over the weekend. My lightning talk will be Tuesday at 3:40. Watch this space for links to the finalized slides and tutorial materials.

And if you’re around, make sure to come say helleaux!

End of the Semester!

Editor’s Note: We’re finishing up our first semester of the Paleantology project! One big problem to managing big data is making sure you’re able to organize everything, and make that data accessible. I wrote a little about that here. Another issue is making sure data are entered without error. To that end, Krishna Gandikota joined the lab for the fall to learn more about programming. He worked on creating a software to automatically download and parse taxonomy information for the ants in our dataset. He’s leaving us for the University of Iowa biomedical engineering program. He worked with me on a piece of software to parse ant taxonomy information from AntWiki. Good luck in Iowa City, Krishna!

What does the software you worked on in the lab do?

The software that we created downloads taxonomy data for the ants in the fossil and molecular datasets. It reads a txt file containing the names of taxa, and converts them into urls for the AntWiki database. The urls are stored in a dictionary structure. Furthermore, it makes an http request to a URL and then uses Beautiful Soup and regular expressions to get specific information from the webpage. The last step of the program consists of writing out the new ant data to our ant taxonomy database.

What have you learned?

Initially I thought python could be used for writing normal code. Through this project, I learned that python has more capabilities for scripting and making http requests. The language is easy to handle and is much simpler than the other languages I have been exposed to. Overall my experience with the project as well as the language was beneficial.
What do you still need to learn?

The skills I need to develop include the ability to discern the structure of a function I want to create, including performance tuning. I need to learn how to code without making syntax errors. Memorizing the basic functions and syntaxes will make the coding process more efficient, and will come with more practice.