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  • evanitallie

What does it mean to publish a paper?

It is almost the end of 2022, and I haven’t shared one of the biggest pieces of recent news, my first co-first author paper was accepted for publication in late October and corrected proofs were published in November. The paper is called Dorsal lip maturation and initial archenteron extension depend on Wnt11 family ligands, and it was published in the journal “Developmental Biology.”


Follow one of the links below for the paper. I suggest just watching a few movies and opening one or two immunofluorescence images in a new window.

Share Link: https://authors.elsevier.com/a/1g5%7Eh2mzTZVza (if you don't have Elsevier access!)


I’ve been looking forward to sharing this news in a blog post all year. The paper was submitted early January 2022, I spent six weeks in the spring in Boston working on revision experiments, and since moving to Durham I have zoomed with Chris Field (my co-first author) and spent time in the Durham County public library doing text and figure revisions. It has been a big part of my 2022.


But it’s much bigger than just 2022. The first discussions around the project were in late fall 2016. I don’t think you can work on something for so long and not question at some point why you are doing what you are doing; I certainly did. I struggled with why I cared so much about this work. I knew that I didn’t want a traditional academic career where first author papers are the most important thing. I really hoped, but I didn’t know for sure, that I didn’t care because I thought my worth was tied to whether or not I published this paper. Now that the paper is out in the world (officially the January 2023 issue!), I can consider with a little bit of hindsight what it means to me.


Learning to let go.

This paper taught me how to accept and embrace change. My early vision for the paper - which I held on to for a long time - was very different from the final paper. The last two thirds of the paper are image data - time lapse movies (see movie below of the bottom of a Xenopus laevis embryo that is undergoing gastrulation) and fixed immunofluorescence (all the credit to Chris!). My original vision was that there would be quantitative phospho-proteomics. The first imaging data came in very late February 2020. We had just enough to be excited about it before Covid-19 hit. The phospho-proteomics data was in fact useful to originally motivate the imaging, but we realized eventually that what we were seeing with the imaging was more exciting and publishable than the proteomics data. I was able to let go of the phospho-proteomics data, and the vision of the project that I had fought for so, so long.


Something similar happened for another part of the paper. I had spent a long time trying to understand a negative result (something wasn’t happening when I thought something should). Eventually it was obvious that the question was not easy to solve and didn’t really matter anyways. I stopped those experiments.


It often takes humility to let go of something you have fought hard for. It can feel like an acknowledgement of being wrong. But I think it’s more just a reality of life and definitely a reality of creating. I’m grateful for these two, among many, examples of the impact of letting go when you need to let go and being able to see another path.


Generate, Edit, Share, Revise.

Writing my thesis introduced me to the joy of drafting (writing) and receiving useful feedback. I did a major revision of one of my thesis chapters after feedback from my advisor, and my mother provided useful feedback on my introduction (and a lot of copy editing). It is rewarding to go from zero words to a complete draft, and it’s wonderful to know that someone cares enough about the work (or you, or both) to give thoughtful feedback. Once you get over the small heartbreak that is diving into editing, it is exciting to know that the writing is improving.


Working on “Dorsal lip maturation…” gave me the chance to use what I had learned from writing my thesis. In this case, there was both a lot of faster iteration feedback and the much slower formal feedback of peer-review. Chris and I were very much partners, and it was an important experience to learn to listen hard to her input, and to also communicate effectively when we disagreed. Some of my favorite memories are going through edits of the first draft together in their living room last December. The formal peer review process had its rather painful moments, but it definitely resulted in an improved paper. There was some unnecessarily mean critique, but it was also nice to hear that others in the field appreciated the work.


I take a lot of pride in how much I grew during graduate school to be someone who appreciates, seeks out, and is alert for constructive feedback. Once you value feedback, it motivates effective communication so that others can understand what you have done. This realization has radically changed my relationship to my professional life and to science.


The power of sense of place.

I’ve written before about the physicality of the experiments themselves for this paper - the sitting over a microscope and injecting tiny droplets into gorgeous embryos, but those experiments happened within a lab that was within a building that was in a specific location of Boston, and part of the experience of experiments has to do with that broader built environment. More than anywhere else, the lab was the physical constant of my Boston life. I lived at five different addresses in my nine plus years of graduate school, but by my first summer, the Systems Biology Department at HMS was the place I was consistently spending my time. Late summer before my eighth year started, I moved across the Charles River to Brookline and after seven years of bike community every day, switched to walking. The late fall and winter before Covid started, I spent a lot of time in lab, including on the weekends. Often, Chris and I would meet on Saturday mornings to do experiments. I would text her as I put my shoes on to say I was headed over, and then walk via the very close Dunkin’ Donuts for a second cup of coffee. I would always pay with cash and ask for change in quarters for the laundry machine in my apartment building.

A Dunkin' Donuts store front.
My beloved Dunkin' Donuts on Brookline Ave.

It was imagining a coffee and chocolate chip muffin from the same Dunkin’ Donuts that got me through more than a few nights spent in lab imaging embryos and collecting timepoints. I would stand in line with the construction workers and then walk back the HMS lab where I would eat leaning on the quad wall appreciating the early morning light on the marble. Starting in March 2020 through my defense in June 2021, I shifted to primarily work on a not-in-the-lab project. This was a good thing for many reasons, and I think that forced space from the physical lab was very useful for my mental health. However, because I continued to work some of the time on the “Dorsal lip” project, I did intermittently get to spend time in lab. This afforded me the luxury of being around people in a Covid-safe environment, it broke up my work-at-my-desk all day six days a week routine, and it kept me connected to a place that despite a lot of complexity, felt like home.


A sunrise with buildings in the foreground.
Sunrise out the window of the department kitchen.

I’m not sure if it is maturity or a lot of recent experience of change and transition, but I feel aware that it’s the constants - the trees you walk by on your commute, the sun rising out the window after a night in lab, knowing the cross-walk timing pattern - that you hold onto as memories just as much as the “special” moments.

Journey

One of the quotes in the front matter of my thesis is: “It is good to have an end to journey towards; but in the end, it is the journey that matters (Ursula K Le Guin)." It’s true, but it’s not entirely clear why. Maybe it’s that having an end provides the motivation so that we keep going, we “push through,” when things aren’t easy. [Of course, knowing when to turn around is a very important skill.] Challenging moments provide opportunities to problem solve and work as a team which is rewarding. When I think about “Dorsal lip maturation…” I think about planning out experiments on Chris’s office whiteboard to figure out how to find a path through revision demands, I think about rehashing and rehashing the Introduction to finally get it close to right, I think about painful Illustrator afternoons to make figures more interpretable which was 1000% worth the effort. I think about moments when it was hard, moments when it wasn’t clear what to do next but clear that something had to happen, I think about moments when we figured stuff out.

The two co-first authors, myself and Christine M. Field, PhD.

Problem solving together also strengthens interpersonal bonds. Chris and I were friends before we started working together but doing experiments side-by-side and writing and revising brought us even closer. When I left Boston for real in the middle of April, there was still a lot of work to be done. I worried that it would be hard to do now that I had uncoupled myself from Boston in yet another way. In fact, working on the paper and communicating with Chris about it provided continuity amidst my move to North Carolina and professional transition.


I’m proud of this paper. It might not be the hottest new thing in the field of developmental biology, but we contributed knowledge to the field and the movies and fixed immunofluorescence images are f*cking gorgeous. Mainly, I’m proud of how I navigated the journey, how I pivoted, how I was tough, how I allowed myself to grow and change. Parts of my graduate school experience weren’t easy, and the hardest parts were the periods where I questioned my instincts and my way of navigating through science and the world. These insecurities haunted me at times during the “Dorsal lip maturation...” journey. Now, with a bit of hindsight and perspective, I can see the difference between my insecurities and the truth. This paper doesn’t make me a valid scientist, it doesn’t change my worth as a person, what it is, is a permanent testament to an important journey.


Van Itallie ES, Field CM, Mitchison TJ, Kirschner MW. Dorsal lip maturation and initial archenteron extension depend on Wnt11 family ligands. Dev Biol. 2023 Jan;493:67-79. doi: 10.1016/j.ydbio.2022.10.013. Epub 2022 Nov 2. PMID: 36334838.



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