How to grad school: CV version control and Git

My personal goal for this academic year is to develop the good habits that I’ve been putting off. Possibly the most important of these habits is version control. Today as I was updating my CV, I realized this would be a good opportunity to make life easier for Future Me. It took a lot of searching the internet for bits and pieces of useful code, so I’ve compiled it into a nice document for future reference!

Before any of this you need to install Git and make it talk to GitHub. Jenny Bryan has great step-by-step instructions here, so I won’t go into that.

So, assuming that you have Git installed and talking to Github, let’s go!

*Note: These instructions are for Mac. Sorry, I’m not sure if it’s different for a PC.*

1. Make a new repository on Github.

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Give it a good name and click the “Initialize this repository with a README”. Create repository!

2. Clone repository.

Now that you’ve created a repo, click the “Clone or download” button and click the icon to copy the url to your clipboard.

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3. Open the command line.

Change your current working directory to where you want the cloned repo to go.

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4. Clone the repo.

git clone <URL>

Paste the GitHub repo URL after “git clone”.

5. Make sure everything is okay.

git status

This command let’s you check the current state of your repository and the files it contains. It should say: on branch master, your branch is up-to-date with ‘origin/master’, nothing to commit, working tree clean.

Double check that you’re still in the working directory that you want.

6. Update directory and check status.

Update your CV (gotta keep that up to date!). Once you’re done making changes to your local directory, you need to update your GitHub repo.

git status

Now that you’ve updated files, this command will show the status of files. The updated CV will appear under the heading “untracked files“.

*Note: Git doesn’t recognize file names with spaces.*

7. Add file and commit.

git add <FILE-NAME>

This adds your file to the staging area and it will be part of the next commit.

git status

Your file’s status is now under the heading “changes to be committed”.

git commit -m “your message”

“Commit” means that Git will take all the staged files and store them as a single unit under version control. Write yourself a useful message so that you’ll remember what you did. For example: “Updated date”, “fixed typos”, etc.

git log

This shows a history of commits. Use :wq to exit log.

8. Push to Github

git push

This updates the GitHub repo with the committed changes.

Congratulations! You did it!

Bonus: Pull from Github

If you make changes to Github but not your local directory, make a Git pull request.

git pull


How Not To Apply To Grad School

When it comes to grad school, I did it all wrong. I didn’t know that I didn’t know everything I needed to know.

I didn’t know that I should find a mentor and do an undergraduate thesis if I wanted to go to graduate school. Most of my friends were engineering or fine arts majors with no intentions of attending grad school. I didn’t know that I was doing it wrong.

When I applied to graduate school I didn’t know that I should directly contact the person I wanted to work with. I thought that applying to grad school was like applying to undergrad: just fill out the application and you’re done. I didn’t realize that the process actually takes months when done correctly. It wasn’t until right before I started my Master’s program that I learned I hadn’t even applied to the correct department. Because I hadn’t contacted faculty, I didn’t know that the website hadn’t been updated and the person I wanted to work with was no longer with that department. One of the first pieces of paperwork I had to submit as a graduate student was a change of concentration form: changing from paleontology (the concentration I wanted) to general biology (the one I didn’t). Because I hadn’t done my research, I was the only paleontologist in a department of microbiologists, ornithologists, and entomologists. On the bright side, my lack of planning introduced me to my current research (which I love).

My biggest mistake was thinking that I could do this alone. It never crossed my mind that I might be doing things wrong; I’m smart and capable, couldn’t I figure it out? Maybe I’m the only person to make this mistake, but I doubt it. Why don’t we let grad school hopefuls know what they’re getting themselves into? If I could have attended a session called “So You Want To Go To Grad School” as a sophomore or junior I wouldn’t have gone into my application blindly. I would have known to contact faculty. I would have known that becoming a full professor was not as simple as I had been led to believe. The graduate school process is hard enough, why not make the necessary information readily available? Sure, this information might be hidden somewhere on a university website, but why not just sit down undergraduates and tell them what’s what? My undergraduate university had resources for applying for industry jobs, but not for entering academia.

For me, it was Twitter that got my act together. If Caroline VanSickle hadn’t answered my question about the difference between a personal statement and a statement of purpose, applications would have been more difficult (I referred back to that tweet all 3 times I applied to grad school. Thanks, Caroline!). Twitter helped me to connect with fellow stressed graduate students and to ask experts questions. Twitter introduced me to my PhD advisor and supplied me with elusive pdfs. I cannot stress enough how helpful Twitter has been for me.

As many mistakes as I have made, I can’t complain too much. Despite not understanding the system, it still treated me fairly well. Even though I just threw an application into the fray without a faculty guide, I was still accepted into a graduate program straight out of undergrad. I learned from my experience and I don’t want others to have to jump through the same hoops I did.

How to become a botanist in 20 easy steps*!

So you want to be a botanist! Here’s how to do it in 20 easy steps*!

Step 1. Be a curious child. It’s helpful if you’re also raised in the country. Explore outside and be fascinated by nature.

Step 2. Love science. Love it madly and without reservation. Soak up everything you can and ask too many questions.

Step 3. Decide early on that you want to be a paleontologist when you grow up.

Step 4. Be told early on that you can’t actually be a paleontologist when you grow up.

Step 5. Reassess your life goals. Decide that science is still awesome and that you’ll decide on a career later.

Step 6. Take all of the science classes your high school offers and decide that you want to study something that people think is really hard, like brain surgery or rocket science.

Step 7. Graduate from high school and head to a really nice college.

Step 8. Major in environmental science and try to figure out what you really love.

Step 9. Have an eccentric geology professor who reminds you that you can actually be a paleontologist.

Step 10. Take an ecology class and realize that field work is one of your favorite things.

Step 11. Take a field botany course and realize that plants are pretty cool.

Step 12. Get a paleontology internship and be the only biologist among geologists. Extol the wonders of trees to them.

Step 13. Graduate from a really nice college and apply to graduate schools.

Step 14. Only get into one Master’s program. It’s your last choice but go anyway.

Step 15. Sit down with your advisor and be told that you’ll be doing paleoclimate with plant fossils.

Step 16. Start working on your thesis and really enjoy it.

Step 17. Finish up your thesis and start to hate it.

Step 18. Get another paleontology internship. Do more paleoclimate with plant fossils.

Step 19. Decide that you don’t hate your research anymore and apply to PhD programs.

Step 20. Visit a Pleistocene fossil site and realize that you’re more interested in the paleoecology and paleobotany than the mammoths.

Congratulations! You’re a botanist!

*Results may vary.

Baumgartner Florissant Intern

Substitute Teaching or: How I learned to stop worrying and love the chaos

Substitute teaching is a terrifying thing. There were many days that I covered classes that I had no background in and the lessons were a learning experience for me as well as my students. Even though I will not be substitute teaching again next school year (much to the sadness of some of my students), I must say that I enjoyed the experience. Oh goodness, was it a learning experience.

I learned the importance of rephrasing and synonyms. If I had a dollar for every time I had to define a part of speech I wouldn’t need to substitute teach, and I can’t tell you how many times I would answer a question, ask the student if they understood, only to be told no. Alright, back up, try again. I take pride in my ability to explain just about any concept (as long I understand it myself!) to just about everybody.

I gained a renewed appreciation of special education teachers. A few times while I was substitute teaching I covered special education resource rooms. I must admit I found these assignments overwhelming. The patience and abundant teaching methods that these teachers possess is astounding.

I learned the importance of asking questions. Lessons plans (like all written instructions) only tell you so much. It is always best to get insight from someone who knows first hand. For me, that meant asking the students how things were normally done. Most students are creatures of habit and were more than happy to tell me how things “should be done”.

I learned my limits. There are just some things I can’t do. Try as I might (no matter how many times I substitute taught it), I don’t know how to speak Spanish; I can’t even roll my R’s! Geometry lies outside of my wheelhouse as well; give me algebra, give me trigonometry, give calculus and I’ll be happy. And I don’t know how to teach the basics. When one of my students didn’t understand the relationship between addition and subtraction, and between multiplication and division I didn’t know how to help. I find it quite simple to break something down to the basics but I struggle to teach the basics themselves. Perhaps I’ve been in school too long and simply take them for granted.

I learned that students ask the best questions. Children ask the exciting questions such as “Why did mammoths have little tails but dinosaurs had big ones?” and “If dragons were real and lived with the dinosaurs, how would they be classified?”. And their enthusiasm is infectious.

I learned something new every day. Just as youth is wasted on the young, high school is wasted on high schoolers. I definitely appreciated high school more the second time. History class became so much more meaningful to me once I left the tiny Midwestern cornfield I grew up in. Shakespeare was funnier once I didn’t need all of the jokes explained to me. I had a chance to make a chalk mural and helped make (and eat) liquid nitrogen ice cream twice.

So if any of my former students are reading this, thanks for making this year so much fun. I’ll miss you guys next year!

So Nice They Named It Twice: Gorilla and Bison

I have a fascination with scientific names that have an identical (or nearly identical) genus and species epithet. So nice they named it twice! Here are somebrief introductions to some of these plants and animals. If you know of any more, feel free to include them in the comments and I will add them to my list.

Gorilla gorilla

Cross River gorilla, Limbe Wildlife Centre, Cameroon. Photo by Arend de Haas (CC BY-SA 3.0)

Gorilla gorilla is commonly known as the Western gorilla and is divided into 2 subspecies: western lowland gorillas and Cross River gorillas. They are critically endangered great apes endemic to western Africa. After chimpanzees and bonobos, gorillas are humans’ closest relatives. Unfortunately human activities including poaching, commercial logging, and civil wars are primarily to blame for the gorillas’ decline.

Gorillas live in groups of up to 20 individuals, with a dominant silverback male as well as several females and their offspring. Despite their immense size and fearsome teeth, their diet consists mainly of plant matter and invertebrates.

Bison bison

American bison. (Photos by Eadweard Muybridge, animation by Waugsberg)

There are only 2 living species of bison: the American bison (Bison bison) and the European bison (B. bonasus). Despite commonly being referred to as ‘buffalo’, bison are distantly related to buffalo. However, bison are very closely related to cattle and are sometimes bred and called ‘beefalo’. As recently as the Ice Age there were other species of bison (with very impressive horns) wandering the plains of North America and into Central Asia and Western Europe (B. antiquusB. latifronsB. occidentalisand B. priscus).

Until relatively recently, bison roamed across much of North America: from the Appalachian Mountains to eastern Oregon and from northern Mexico to Alaska. Unfortunately, as settlers spread across what would become the United States they took advantage of this abundant source of meat (as anyone who has played Oregon Trail knows). Today bison are restricted to isolated patches in the Rocky Mountains of the United States and Canada.

So Nice They Named it Twice: Fire Salamander and Llama

I have a fascination with scientific names that have an identical (or nearly identical) genus and species epithet. So nice they named it twice! Here are some brief introductions to some of these plants and animals. If you know of any more, feel free to include them in the comments and I will add them to my list.

Salamandra salamandra

Salamandra salamandra by Marek Szczepanek (CC BY-SA 3.0)

Salamandra salamandra is also known as the fire salamander. Salamanders hide in moss and dead wood. If you set fire to wood that has a salamander in it, it’s going to come crawling out. People came to the incorrect conclusion that the salamanders came from the flames rather than the wood, hence the name fire salamander.

Fire salamanders live in the deciduous forests of central and southern Europe eating insects, worms, and slugs. Adults weigh about 40 grams and can be 15-25 cm long.

Lama glama

A llama (Lama glama) in front of the Machu Picchu archeological site, Peru by Alexandre Buisse. (CC BY-SA 3.0)

Lama glama, or llama, falls into the nearly identical category. Llamas are South American camelids and domesticated llamas are raised for meat and wool around the world. Like all camelids llamas’ ancestors originated in North America and spread into South America and the Old World, before going extinct in North America.

Llamas are native to the Andes mountains and are well adapted to high elevations and cold temperatures. They grow to about 1.8 m tall and weight 130-200 kg. Llamas live in herds and are very territorial; llama guards can be used to protect other livestock from predators.

Plants Aren’t Boring, You Are

I dislike the assumption that plants are boring. When I mention people that I am a paleobotanist, or that I was looking forward to taking a botany class, I’m frequently met with confusion and disinterest. “Why would you study plants? They’re so boring?” “They don’t even move. Who cares?” “My study organism eats your study organism!” I’ve heard it all.

I must admit, I haven’t always been enamored by plants. I have always been curious and plants often were included in the long list of things that caught my interest, but the fascination went no further. As I grew older, my interest in ecology and paleontology led me to taking botany classes and I changed my tune.

My first reaction to my college botany classes was anger. Why hadn’t anyone told me that plants were so cool? This anger turned to frustration. Why wasn’t everyone interested in botany?

Botany is given a bad rap. In my experience, everyone can find something interesting about botany. From middle and high school students to grad school friends to strangers on planes, I will teach anyone who will listen. And people love it! (My go-to fact is telling people that oranges, pumpkins, and cucumbers are all berries.) Students who claim to dislike science and say it’s boring will wave their hands in the air to ask questions. Why do coconuts have milk? Are blackberries berries? How does a cactus work? How big can a Venus flytrap grow? Why does the top of that pine tree look so weird? Here in Michigan we find ourselves surrounded by trees and plants, and we think nothing of them. But when given the chance to learn more, we jump at the opportunity.

Chestnut and beech

I wish that more people could meet botanists. Instead of refrains reminding us that plants don’t move, we could have conversations about the amazing adaptations plants have to survive in unforgiving habitats. Instead of talking about how plants are defenseless, we could talk about the complex and deadly defenses plants have to herbivory. Instead of dismissing plants as boring, we could marvel at the diversity of extinct and extant plants.

Plants are not boring. Everything is interesting if you look hard enough.

How To Make It Plural

Everyone has that small linguistic pet peeve. For some, it’s the differentiation between well and good. For others, it’s the improper use of apostrophes. For me, it’s improper plurals in scientific jargon.


When most English speakers need to make a word plural, the first instinct is to just add an ‘s’ to the end; if one is femur, then two must be femurs. Nope. Of all of these linguistic sins, in my experience this one is the most common. To make the word ‘femur’ plural, you add an ‘a’ instead of an ‘s’ (and tweak the spelling a bit); one is a femur and two are femora. Besides, femora is just more fun to say!


Let’s stick with the osteological focus. Again, for most people their first instinct is to turn ‘radius’ into ‘radiuses’ in order to make it plural. Instead, take off the ‘us’ and add an ‘i’; one is a radius, two are radii. Radii is one of my favorite plural words and it’s just so much fun to say!


And the last osteological term: scapula. And again, don’t add an ‘s’, just add an ‘e’. That probably seems counterintuitive but one is a scapula and two are scapulae.


Genus is a tough one. Some people default to trying to simply add an ‘s’ but others seem to know thats not right and try something else. Others don’t change the word at all in order to make it plural. I’ve heard many variations but the most common are ‘genuses’ and ‘genii’. Genus doesn’t act like the other words in this list; the plural form of ‘genus’ is ‘genera’. So that’s it.

Femur -> Femora, Radius -> Radii, Scapula -> Scapulae, Genus -> Genera.

And if this is confusing, just do what I do: use a different word! I tell my students that synonyms are for when you can’t spell or pronounce the word that you actually want to use. But really, don’t let this scare you. When in doubt, just power through and act confident even if you don’t feel it.

I still listen to a lot of podcasts (Part 2)

My brother asked me when ‘soon’ is, so it must be time for more podcast suggestions!

If you’re looking for hours of podcasts, look no further than Science… sort of. They currently have more than 200 episodes, most of which are at least an hour in length. This podcast features a rotating cast of characters, drinking beer and talking about “science, things that are sort of science, and things that wish they were science”. I have done hours of data analysis while listening and I would often giggle to myself (My brother’s Christmas gift was inspired by this podcast). If you’re not interested in the science, you can at least be impressed by their beer choices!

Sawbones: A Marital Tour of Misguided Medicine has a bit of an unwieldy name, but it is a fantastic podcast. Dr. Sydnee McElroy and her husband Justin talk about the history of medicine. Sometimes it’s funny, sometimes it’s disgusting, but it’s always enlightening. Episodes are about 30 minutes long, so they’re easy to marathon (and I definitely have). If you have any interest in science or medicine, I highly recommend Sawbones!

If you like food and science, listen to Gastropod; I like to listen to it while I cook. Cynthia Graber and Nicola Twilley talk about the intersection between food and science. Topics range from the way that our cutlery influences flavor to apples varieties to the importance of entomophagy. Regular 45 minute episodes are interspersed with smaller ‘Bites’, so you don’t have to wait too long between episodes. Nicola and Cynthia are obviously passionate about the topic and I honestly wish the episodes were longer!

No Such Thing As A Fish isn’t quite like the other podcasts on this list, but I still think it deserves a place. This is a weekly trivia podcast that covers every topic under the sun, from why Scottish military men no longer wear kilts in battle to mouse lingerie to special editions of Chuck Norris films. I often bring up things that I have learned from the podcast in conversation. If you want to sound clever at parties, listen to No Such Thing As A Fish.

This is all for now, but I’m sure I’ll add more podcasts as I discover them. Happy listening!

2014 by the numbers

I love quantifying things, so here I go quantifying 2014 (I took the idea from Alex at The Lab and Field).


The roundtrip distance (in km) of my trip to Vancouver for the GSA Annual Meeting. (It would have been less if I hadn’t had to fly to Canada by way of Texas.)


The total number of page views on this blog! Thank you everyone for your interest!


The total number of followers on Twitter. Twitter has been my source for academic insight and I’ve had many great conversations with these people.


Page views for my most popular post this year: Video Game Paleontology: Piranha Plants, Yoshi, and the Fossil Record.


The number of people who backed my crowdfunding campaign to present at the GSA Annual Meeting in Vancouver. To be honest, I was surprised that strangers were willing to support my research financially. Crowdfunding was an eye-opening experience in many ways.


The number of posts on this blog. Abysmally low, but I’d like to think it shows quality over quantity.


The number of applications submitted this year.


The number of states I called home this year: Tennessee, Colorado, and Michigan.


The number of conferences I attended: North American Paleontological Convention (NAPC) in February and Geological Society of America Annual Meeting (GSA) in October.

Here’s to 2015 and a new set of numbers!