Beguiling Biology

Mutualistic pairs for an “Odd Couples” Valentine’s program at my work. (Why do so many of my big work projects revolve around Valentine’s programs?)

While humans have domesticated many other animals for their labor, the honeyguide remains entirely wild while electing to partner up with humans. Both humans and honeyguides have each developed specific calls to signal to one another that they are on the hunt, and these calls greatly increase the likelihood of success. According to this paper:

The production of this sound increased the probability of being guided by a honeyguide from about 33 to 66% and the overall probability of thus finding a bees’ nest from 17 to 54%, as compared with other animal or human sounds of similar amplitude.

That’s fucking bonkers, you guys!!! There are people out there who over the course of human history have created a sound to communicate with birds, and the birds themselves have a Human Call they use to communicate with us. There is no other wild animal you can just make noises at and immediately communicate that you want it to come help you!!!

What’s more, many scientists consider this relationship more exploitative on the honeyguide’s end than on our end! That’s unprecedented!! These birds have essentially negotiated a trade deal with humanity!!!! This is the stuff of fantasy movies, except it’s real.

Here’s an article from The Guardian about the broader implications of this kind of relationship with wild animals. It’s a good read:

*or at least what helped me when I was writing mine for a PhD in Cancer Biology in the US–so they may not apply to other fields and/or countries.

Firstly, what a PhD Dissertation and Defense process is like (for my program)

Always check your university’s graduate college’s dissertation formatting and guidelines. That should be your #1 rulebook to work off of. Download their formatting guide and read it thoroughly. Before turning in your dissertation, make sure you’ve addressed all the requirements. 

Get a sample from a previous student as reference, preferably one from your program, or even better, your lab. All dissertations are publicly available online at your university’s library (with the exception of those with embargoes). Always have an example on hand–you never know when it’ll come in handy for minor formatting details, or even references (if it’s a dissertation from your own lab). 

Familiarize yourself with whatever writing program you’re going to use, and if it can do any of the formatting automatically for you. For example, Microsoft Word can make a Table of Contents for you if you use their Automated Styles, and you can use the Navigation Pane to view all your sections at a glance (and jump instantly to that section). I highly recommend figuring out all the formatting before you start writing, as it may be really frustrating to go back and fix things (especially if you’re doing this on the due date). Scroll down to the end of this post for formatting resources. 

I think the ideal timeline is one month per chapter, give or take a few weeks depending on how much you have done beforehand and how much time you have per day to allocate to writing. There will be a lot of back-and-forth edits with your advisor, you may find out there are missing data that need analyzing/finalizing, etc. Your last month or so of writing may have to be dedicated 100% to your dissertation, so plan accordingly. I have heard many PhD’s tell me to even start a year out, because you may be busy your last couple of months with job interviews, or even starting your new job, etc. 

Export your images as .png if possible or your document will become too large. 

Use a citation manager, if you don’t have one already, such as Mendeley. 

Also have a way to keep track what each reference is about, especially for the Introduction as that may require some new additions (ie. things you learned in class or lab meeting but never actually had to chase down a primary reference for). You can use Excel, Word, or good ol’ fashioned printouts in subject binders–anything that helps you remember what the paper is about what. I ended up citing over 400 references in my dissertation–that was a lot of papers to keep track of!

As with any large writing project, make an outline first. This way you can better structure everything from a bird’s eye view, and make sure you’re not missing anything. Just like building a house, you need to set up the frames first before the drywall. The outline to my Introduction was 5 pages long before I even wrote the first complete sentence, and the outline also helped me not feel too overwhelmed with the task before me (likewise, I also started off each paragraph with a brief outline of the points I wanted to cover. It worked really well in getting rid of writer’s block)

Have a separate folder for each chapter, to keep things better organized and easier to manage. I didn’t put everything together in a single file until the very end. 

And always back up your files, or work entirely off a Cloud-based system, like Dropbox or Box (which your university may provide for free). There’s absolutely nothing worse than losing allll your hard work, especially your Dissertation! 

Set aside at least 1 hour before your Dissertation is due to your committee for last minute issues, like formatting, uploading, etc. 

If you’re in the Bio field, I highly recommend making your figures using Biorender.com. It honestly saved me so much time, and it took my dissertation and defense to a whole new level of professionalism. It’s free to use for students, though the paid student version ($35/mo) has more features. 

Links to other resources:

University of Michigan guide for using Microsoft Word for Dissertations

Dissertation templates (with build-in-instructions) from Duke University (scroll down to end of page) (thanks @conquerorwurm for this one)

Making an outline from Sacred Heart University

More about making an outline for Dissertations

Other tips on surviving this challenging time:

Write smart, not hard. Use your energy and creativity levels wisely. For example, I found out I was really great at synthesizing thoughts (and thus words on the document) in the morning, but not so much at night. So I did most of my writing in the morning, and then reserved evenings for making figures and adding references (aka things that required less brain-energy).

Take breaks! This is definitely a marathon, so please try not to push yourself too hard to prevent burning out. Here’s what my writing schedule looked like 1 week before my dissertation was due to my committee–you can see I worked hard, but I also had lots of breaks throughout the day to eat and/or recharge, and I tried to sleep 7-8 hrs/night. 

The moment you think you can’t do something alone, seek out a resource that will help you. There’s no time or energy to waste. Resources include: your advisor, another lab member, a university writing center, online tutorials, even other grad students on tumblr. No one else has written a dissertation on their own, so you shouldn’t have to either. 

Have a support system, like another fellow student going through something similar who you can talk to. It helps so much to not be lonely during this. 

Have something fun planned after you turn in your dissertation and after you defend to look forward to. Sometimes all that was left to get me through the tough and frustrating moments was the thought of all my plans post-defense: going to my favorite used bookstore, reading for fun again, relaxing and watching movies, and more. Small things, but oh so powerful to keep me going sometimes. 

You will get through this. I know it’s hard. I know how close to tears you are. But I also know you will survive. Remember all those tough times in the past? Like when you were studying for your qualifying exams? Or writing and re-writing that grant application for what seemed like the 500th time? Those were some tough times, but you got through them all. And so you will also get through this.

And lastly, but probably most importantly:

Do what works for you. You haven’t made it this far in your academic career without a solid understanding of your own working style, so stick to that. My advice is just what happened to work for me, personally, and thus may not apply to anyone else. 

08.16.20 // 49 pages and 290 references later (which aren’t part of the final page count), the Introduction to my Dissertation is DONE*!

I actually had a lot of fun writing this. I really like my field and my research project, so this was just 50 pages of me nerding out. 

> Congrats! You did it!! Celebrate, if you haven’t already.

> Here’s a secret: you have the same right to be there as everybody else. Imposter syndrome is real, especially when there are few others in your department that look like you. I need you to know that you got where you are out of grit and merit. Regardless of what resources you and your (male, white) classmates had before this point, you are all in the same place, and that is no accident. You are perfectly capable of success, even if someone has the audacity to tell you otherwise.

> Use all the help you can get. I was hesitant to get help or go to study sessions because it made me feel like I wasn’t smart enough to do the work on my own. But here’s another secret: the work is designed for you to need help/ work collaboratively. Email your TA! Go to office hours! Find/start a study group! Text the person who always talks in class (or better yet, set up a group chat). You already paid for these resources, you might as well use them

> Join societies/ clubs for women/women of color. Having women in you corner who get what you’re going through is invaluable. Especially if they are in your field! Listen to what they have to say, because a lot of the advice will be specific and you won’t be able to find it elsewhere. Plus, it helps to have a few friendly faces you can be yourself around

> Find your support circle. Not every friend you make will be in that circle, which is fine. Make sure you have a small number of people, both at school and at home, who support you and who you can talk freely with. Understand the difference between casual friends and those in your circle. That way you don’t end up oversharing with people who don’t really know you – and coming away feeling empty/awkward as a result

> Your mental health matters. Take time to process your emotions and seek help as soon as you need it. Psychology Today and Therapy for Black Girls are fantastic places to start looking for a therapist, and Loveland Foundation may be able to help you offset the cost if that’s one of your concerns. Even if you’re not seeking regular counselling, these can be great resources if you’re going through a rough patch. For a free option, look into your schools counselling services! (as a note: most if not all of these services will also offer online telehealth meetings)

the Golden Jellyfish of Lake Palau don’t sting! their bodies contain a symbiotic algae from which they get their energy, so they don’t need to actually eat.

instead, the jellyfish rise to the surface every morning and follow its path across the lake, providing their algae with sunlight!

Good morning,

When it comes to cell identification during a manual differential, it can be hard differentiating reactive (atypical) lymphocytes and monocytes.

The cell on the left is a reactive lymph that the experienced may not confuse with a monocyte. It has a round to oval nucleus with a fine chromatin pattern and a large, basophilic cytoplasm.

The middle cell, however, looks very similar to a monocyte, and by itself, without an actual monocyte for comparison in the same field, may trick some. It has an indented nucleus with a fine/lacy chromatin pattern, just like many typical monocytes do. The cytoplasm is a little less basophilic compared to the left cell and, if you stare at it long enough, can even have the sort of “ground glass” look that is very characteristic of a monocyte’s cytoplasm.

The cell on the right is a very typical monocyte. It has an oddly-shaped nucleus with a lacy chromatin pattern and a blue-gray, ground glass cytoplasm, as well as vacuoles.

For this particular patient, I knew that the cell on the right was a monocyte and not a reactive lymph because its cytoplasm was blue-gray and vacuolated. No other reactive lymph had these features. They all had more basophilic cytoplasms, especially around the edge of the cell and no vacuoles were present. But here’s the problem - reactive lymphocytes can be vacuolated and the cytoplasm of a monocyte can sometimes be more basophilic than blue-gray. It just wasn’t the case for THIS PATIENT. So what do you do if your patient has reactive lymphs and monocytes with similar cytoplasms and both are vacuolated? Try to find similarities between them to categorize them as two separate populations as I’ve done. For me, it was a basophilic cytoplasm and no vacuoles v.s a blue-gray cytoplasm with vacuoles. For another patient, it may be large sized cells with large azurophilic granules (reactive lymphs) vs. medium sized cells and no azurophilic granules (monocytes).