Keeping up with the literature is almost always the first thing to fall by the wayside for all of us when we get busy. Usually this is because there are few overt short-term consequences of letting it slide. However, there are massive gains in stimulating ideas and experimental course correction that come with regular reading. Our lab also has quite a few new people and others trying to ramp up their background knowledge so I've been thinking about how to encourage everyone to maintain consistent reading habits. Some of the things we already do: We have a #recommended_reading channel in our lab Slack where I post things I think are of outstanding interest. I post several things here every day.We have a #365_papers Slack channel in which anyone can post what they're reading each day to help others discover helpful information. We do an in-depth journal club at least once per month.A new addition this week: I'm having an automated Slackbot message sent to the lab every week in the #365_papers channel asking what's something new they learned from a paper they read this week. I'm having this sent out in the very early afternoon on Fridays so that if they didn't get a chance to read something, they might be able to skim something as they wrap up loose ends for the week or make it a priority on their schedule for the upcoming week. When I did this last week, I posted two papers of particular interest I had read and wrote what I had learned. I've also seen on Twitter that Dr. Baucom's lab has a great summer reading challenge. It's a fantastic idea I'd like to try one day but we have a different ongoing summer challenge that I hope to post about in a few months! While I do want to increase the rate and efficiency with which everyone goes through papers, right now I'd like to focus on comprehension. To that end, I've assembled a short list of questions that are each geared towards a specific skill I'd like to emphasize. I'm hoping that using these as a worksheet at first might ensure a minimal depth of understanding for each paper. Hopefully the questions can eventually help each person develop a running critical internal dialogue as they ramp up their reading volume. While somewhat overlapping, this list is intentionally meant to be a bit different and more succinct than those I use to teach students about peer review and rigorous evaluation of papers. I hope my lab and perhaps yours finds these helpful. Literature reading comprehension worksheet:What are the hypotheses or goals of the study? What is the motivation for the work?In your own words, what is the take home message of this paper? i.e. what do you hope to remember about this work?List 3 things you learned that you didn’t know before. These can be about background, methods, or anything else.List something or a few things you didn’t understand about the paper (so you can follow up).What's the most important or interesting thing you saw in the supplemental data? Are the data presented in a manner that allow you to interpret them? Is any relevant information missing? Are images clear and/or quantified?If you look at the data alone, do you reach the same conclusions as the authors do? Do the data suggest an alternative explanation*? Suggest at least one orthogonal experiment not in the paper that might strengthen the results or might have been included instead.Does this paper make you think differently about your own project or experiments? If so, make note. What topic did this paper make you want to read more about?*Thanks to Arjun Raj for the suggestion on the second part of this question.
This morning I had the honor of speaking at the Kansas City March for Science. I was invited by an organizer, one of our fantastic graduate students, Cassi Johnson. It was a blustery day so the conditions weren't ideal, but it was good to see so many of our students out in force. I was tasked with giving a speech about the value of basic science and gave one that I hope achieved that goal. For those who couldn't attend, below is the text of the speech. Thanks so much to everyone who planned the march and those who came out to celebrate science!
With startup funds rapidly dwindling and major external grant funding elusive, this year has been arguably the hardest of my professional career. I don’t say it lightly given that other notable gut punches included switching graduate labs and starting over in a new field after 4+ years in a PhD program, the death of my father during my postdoc, and the birth of my son while finishing my final postdoc paper and going on the job market. While those challenges were emotionally wrenching, I've always dealt with personal hardship through renewed focus on work. But this past year, it felt like more intense work was not yielding improved results in any predictable way. It felt like things were no longer in my control. Success felt arbitrary.Three months into 2018, things are looking up. I got a score on an R01 equivalent grant, the ESI MIRA, that made my heart skip a beat (in the best way)—fingers crossed! The lab is making good progress and we will soon preprint and submit a couple of papers that I’m very excited to share. I was appointed to the board of directors to one of my favorite organizations, ASAPbio, and became the first early career researcher on the board of directors of the progressive journal, eLife. I attended the ASAPbio/HHMI/Wellcome trust meeting on peer review, where I spent time with several of my science heroes and made some fantastic new friends. I was also filmed for a course on experimental design on one of my favorite educational platforms, iBiology, partly because of some of the posts on this blog! In a truly thrilling development, I was recently asked to be a speaker at this year’s March for Science in my city. In my speech, I hope to highlight the importance of basic science research, the utility of model organisms, and convey my excitement for discovery. What an enormous honor and responsibility! All this is to say that I’m so proud of what the lab is doing and the way we’re doing it! And I've been lucky enough to spend some time with many inspiring people that share my passions. Despite a tough year, I know what a privilege it is to do this job and I take so much joy in the findings made by my lab. As always, it is the thoughtful and supportive people in life, Twitter, and New PI Slack that have been my lifeline. Here’s to all of you science warriors. Hang in there. We can do this!
I’ve been thinking about doing a year in review for the lab but it has been difficult to think about. It’s been quite a rough year. Last year I was very optimistic. We had gotten positive comments on a couple of declined NSF grants, we had just submitted 2 preprints, and I had both a new NSF grant and R01 under review. But some key grant rejections and difficulties had me reeling. Let’s see what went down in 2017:Our first preprint was submitted and then accepted for publication in mSphere. This was the first independent publication out of my lab, so it was a big milestone. Our second collaborative preprint was submitted for publication and received very reasonable comments. It is still in revision, but we decided to expand the story based on new results, so it might be a little while before it’s published.My R01 got triaged. This was only briefly upsetting. The reviewers trashed it, but they were right. There was lots of useful and constructive feedback for what I now think was a rather conceptually messy grant.Former undergraduate summer scholar, Brittany Jack, who became a research assistant in the lab was accepted to graduate school at our institution and also awarded the NSF Graduate Research Fellowship! She returned to the lab as a full time graduate student. Brittany is my first grad student!My research assistant, David Mueller, was accepted into medical school, a lifelong dream of his. Congrats David!We were awarded a small internal grant. Hurray!My NSF grant (our second investigator initiated proposal submission, third overall submission if you include the previous declined NSF CAREER) was scored with low priority and declined. This result hurt for a very long time as I thought we had a great chance and the reviews were positive. There was some disagreement on the panel about the impact of the work and we needed to better sell this point by rearranging and removing aims. Part of what made this so rough is that it was declined at a time when, despite submitting a grant per month on average, we had zero large external grants in the pipeline. I found out that not having the hope of a pending grant feels a lot worse than a rejected one. To avoid having this feeling ever again, I went on a grant writing frenzy and submitted an NSF CAREER, NIH DP2 (New Innovator), NIH R35 (ESI MIRA), NIH R01 within about 2.5 months.I learned my NSF CAREER got an improved score (medium priority, in the range where proposals were funded) but ultimately missed the funding line. This got revised for another investigator initiated proposal submission in November-fingers crossed!I was selected to be on eLife’s Early Career Advisory Group. This has been an amazing opportunity. It’s been wonderful working with the eLife folks to get support for initiatives important to me and other early career faculty. We submitted our third preprint and got excellent feedback from attendees of the ASCB annual meeting. We’re now making a few key revisions before choosing a journal (target for journal submission, January 2018). My postdoc Soumita Dutta, has completed her time with us. She is rejoining her husband who had to move across country a few months ago. In less than 2.5 years in our lab, Soumita published one paper and we are preparing her final paper for submission. This has turned into a really interesting story so keep an eye out for the preprint early next year. Soumita was my first postdoc and I’m thrilled to say she survived, enjoyed her productive time in the lab, and landed a second postdoc returning to her passion for host-pathogen interactions. There are a couple of other bits of good news/recognition that I’m really proud of, but these have yet to be publicly announced so I’ll post about them early next year. Stay tuned!Overall, I think my general feeling that it was a painful and difficult year came from the crushing pressure to get funding before things get dire. But going through all that’s happened, I’m proud of what we’ve accomplished and am cautiously optimistic about pending grants. Let’s hope that some of our hard work will pay off in 2018!
Hello again, world!Thanks to Authorea for generously setting up this new site for me on their platform! It allows me to assign DOIs for posts and improves data integration. I’m planning to post about our upcoming preprint in a few weeks so this was appealing. If you’re new to the blog, welcome! The older posts will still be archived on the lab website. As always, feel free to contact me via email or Twitter. Thanks to Liana Lareau for thinking up the great name (Preprint or perish) and tagline (Navigating the new academia) for the new blog and all my friends at New PI Slack for providing feedback on it. The title is meant to convey my strong support for preprints and that I feel relying exclusively upon dated information in the form of years-old finally published work is a good way to slow down one’s own scientific progress. The tagline about navigating the new academia is aspirational. I hope that we can constructively adapt to the shifting academic landscape in the face of low funding rates and changing needs of trainees. My blog has generally been about sharing small mentoring experiments (like this and this) that aim to raise the bar of what we expect from ourselves/our colleagues as well as improving the day to day realities for academics. I’ve also tried to provide some level of instruction for things most of us were forced to learn by osmosis (as here, here, and here). Together, I hope we can wade further away from the status quo for practices that are failing us in the current climate and find new ways to thrive. We can do better and we must try - for our sake and that of the next generation of scientists.