The (real) story of a Manuscript

Maha J. Cziesielski
Nov 4 · 6 min read

Every day an overwhelming number of papers are published. Rarely do we know how many rounds of drafts, reviews and rejections the final product has gone through. Rarely do we acknowledge the entire development of an article — from its beginning to its publication. This is the real story of a manuscript I drafted at the start of my PhD, and published after I finished.

Frodo knew good things happen when you leave your comfort zone. (Image Thomas Schweighofer)

I started in my lab as an intern. Fresh out of my Masters program, passionate about molecular biology, madly in love with lab work — I knew I wanted a PhD that would allow me to continue on this path. I received my PhD offer to work on the small sea Anemone Aiptasia, which acts as a model organism to corals at the end of 2014. Beginning of 2015 I began my research. My professor and I planned that my PhD would entail working on transcriptomic, proteomic and epigenetic mechanisms of heat stress response in cnidarians. The only problem was: I knew little to nothing of transcriptomics, proteomics or epigenetics.

Imposter syndrome is real, but it usually takes a bit of your childhood naivety to die off before it really hits you. Half way through 2016 I received my first data set: 32 transcriptomes and proteomes.

32 reminders that I am clueless.

32 reasons keeping me up at night.

All I wanted — all I needed — was one coral gene-protein-guide review. One place for me to find all the genes that have been worked on. One publication to rule them all; one publication to find information I needed, one publication to bring all the others together. I started going back in the literature early 2000, 1990, 1980s… 1920’s… 1800? With all the information I gathered, I wanted to provide a paper that would give those interested a place to learn about the story of this research field. I decided to write a review of 100 years of coral heat stress studies (and in the darkness bind them).

But just like Frodo: I was utterly unprepared for this quest.

A never ending story

“Facts — the one thing your review is full of — is the carbohydrate of your dish, but what is lacking is the spice” is how he started his review of the first draft of my first ever manuscript. “I’m afraid that I have to say that you lack narrative and you still have a long way to go before this review reaches publication-level quality” is how he ended it, shattering my confidence in my writing abilities.

In hind sight, my confidence was clearly not very high to begin with. I myself have by now given much harsher comments to my students and writers. If anything, postdoc X was being kind, because if I look back on that first draft … goodness it was appalling.

In my anger, fueled by my own lack of self-confidence and obvious inability to take criticism, I skipped postdoc X for the second draft. I sent it straight to my professor, who in no-time sent it back to me. He had little suggestions on how to fix it: the manuscript was beyond saving.

There was something fundamentally wrong with my writing: I did not know how to tell a story — let alone phrase a perspective. Draft after draft I fixed, changed, added, removed content. It got so bad, we named the manuscript ‘The never ending story’.

But as is so often with your own manuscript, I eventually couldn’t see the forest for the trees. I needed a fresh pair of eyes. At the end of 2017, another postdoc joined our lab. Postdoc S has been an incredible teacher to me and arguably saved me in my PhD, not just because he helped me get through this quest. I spent another couple of months rethinking the manuscript with postdoc S. Early 2018 we finally had a draft that warranted an attempt at publishing.

Don’t get caught in dark forests alone. (Image Rosie Fraser)

For the publication process is dark and full of terrors

Everyone always warned me that the first manuscript rejection is the worst, that reviewers shred you to pieces. So I was all set for another round of crying. To my surprise I didn’t. It may have been a rejection, but the reviewers had put effort into giving me constructive criticism.

Even though the reviewer’s comments were more than helpful, I couldn’t bear to work on it. It took me six months to not feel a creeping anxiety just looking at the file name.

Some of the major criticisms I received from the reviewers, besides the obvious lack in storytelling, was my use of colloquial language and a lack of vision. In essence: I needed to rewrite it all. Colloquial language I could fix, but vision? I was a mere PhD student, what perspectives was I supposed to have that would be of interest to anyone? Although I had little hope that anyone would care, I fleshed out and wrote down my perspectives that I developed over time thanks to numerous conferences and thought provoking conversations with great minds in my field.

Pick yourself up and try again

I got rejected two more times. In every round reviewers were critical, but helpful. I never felt horrible being reject because with every round I refined my own perspectives. I also learned to be confident in my work, able to disagree with reviewer’s comments in a respectful manner. Finally, the paper did go through in early 2019.

The never ending story found an end!

It takes a village

The people you work with, those with more experience or better language skills than you, can truly help you to hone your craft. Postdoc X and S took a lot of crap from me — literalistically and verbally — but they guided me through my PhD and helped me find my voice.

And then there are reviewers; they will always be critical. And rightfully so! Every round of rejection can ultimately make a manuscript better. I can confidently say that reviewers have helped my writing and shaped my perspectives. Take their comments as lessons and you’re sure to benefit.

Finally, there is the manuscript itself. There is more to a published article than meets the eye. We might not always be aware of the entire process, but every article has a hidden story. And often these carry more lessons learned than the final product can convey.


Cziesielski, M.J., Schmidt-Roach, S. and Aranda, M., 2019. The past, present and future of coral heat stress studies. Ecology and Evolution, 9 (17).

Reefs and Research

Anecdotes of a Ph.D. that decided to leave academia

Maha J. Cziesielski

Written by

Anecdotes of a PhD student in Molecular Marine Biology reporting the life in science and academia. Brazilian born; Berlin raised; Saudi based.

Reefs and Research

Anecdotes of a Ph.D. that decided to leave academia

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