Chapter 2 How we work

2.1 Principles

Do ambitious research. Research always seems to take more time than it should, so spend your time on important questions. Think hard about what should be done, not only what can be done. Try not to let others define subfields and questions for you. Be deeply practical in evaluating your progress and choosing your next steps, but work toward lofty aims.

Learn fast and change direction when necessary. Research involves making mistakes, or at least doing things that seem really dumb in retrospect. Learn as much as possible from your failures. (Could you have found that bug earlier? Learned about that other technique earlier?) Do not shame yourself for them. Instead, admit them, and document this learning for yourself and others by talking about it or potentially adding some advice to the handbook. Note that failing is not the same thing as not having the result you wanted—it’s a good day when your hypothesis is not supported and you get to learn something about how the world works. Frequently reevaluate your approach and the direction of each project, and take initiative in doing this. Take initiative as a collaborator too.

Know your corner of the literature. It makes you much smarter and can save enormous time in the long run. It also makes it easier to spot good opportunities and unanswered questions. Knowing the history of work on your problem inside and out is a requirement for first authors. Develop a scientific reading habit if you don’t have one yet. As a general guideline, on average, graduate researchers and postdocs should be reading five papers a week, and skimming more.

Be open to collaboration, and respect your collaborators. Getting anything worthwhile done in research requires learning from others, including through papers, talks, and whiteboard time. Be proactive in thinking about who might have relevant expertise. Ask for help, give help, and carefully acknowledge the contributions of others. Clarify expectations when you start on a project: make agreements explicit (and for important things, in writing), with expectations and timelines, and be reliable. For instance, let your collaborators know when they can expect to hear from you with new results, drafts, etc. These principles hold for interactions inside and outside the lab. By default, you should think of yourself as a collaborator on every project in the lab, and remain engaged.

Communicate assertively. It’s nice to hear from other people that they’ve benefited from your analysis, timeliness, criticism, etc. Tell people whenever you can that you like what they’re doing. Consider emailing strangers when you like their paper or talk, and explain why. On the flip side, it’s frustrating to learn from a third party that someone is unhappy with something we said or did. Assertive communication means we give each other direct, constructive feedback if we think something isn’t right. You can trust me not to negatively describe your behavior to others without speaking to you first. More broadly, if you think something can be improved, speak up to the right people before complaining to others. Be constructive by criticizing the idea, analysis, or behavior, rather than the person. Communicating assertively and kindly usually takes practice.

Don’t be too narrow. Take time to play intellectually. Participate in departmental seminars, go to talks in other departments, meet with people who seem to be doing interesting things, and read exciting papers that might not be obviously related to your current projects. (Graduate researchers should aim to attend a departmental seminar and journal club each week.) Start journal clubs and groups that you wish existed and would make time for. Try to balance exploration with work on existing projects. I don’t know the right balance here, but it’s worth trying to figure it out.

Work hard but sustainably. Figure out sustainable habits for effective research. What is sustainable is personal: avoid blindly adopting others’ criteria. Focus on habits, such as working set hours each day, before benchmarks (e.g., “Publish”, “Get speaking invitation”, “Be famous!!!11!!” etc.). Resist the temptation to run from one deadline to the next, and think instead about how to make regular progress. (Do this especially if you’re (i) fresh out of undergrad, or (ii) have never done it before because you think you work best under pressure.) Aim for 40 hours of focused work per week. If you’re not happy with your progress or productivity, there’s no shame in asking for help or ideas from others, including your advisor. For what it’s worth, I do think it’s possible to do great research while having a life. (I’ve seen others do it… lolz) A great resource for sustainable habits is the National Center for Faculty Development and Diversity. They have online classes, weekly newsletters, and writing support groups. The University of Chicago has a subscription, so you should be able to get free access.

Be accountable. All work in the lab is collaborative, involving the blood, sweat, and tears (and hopes and dreams!) of multiple people, and often indirectly taxpayers. Respect all these contributions by being a reliable, involved scientist. Let collaborators know if your contributions will be delayed, if you think something should be done differently, or if you have concerns about quality. Always look for better hypotheses and approaches. Speak up if you see something that’s not right. Remember we’ll all be dead soon enough, and this is our opportunity to help others.

A contrasting time scale of research

Figure 2.1: A contrasting time scale of research

2.2 Work hours

I will not judge your progress based on the hours you keep in the lab: what matters most is that you make substantive progress on the lab’s goals. I encourage you to figure out how you work best. You thus have broad freedom to choose how you work, provided you communicate your plans to others and see the projects through. But because we’re human, and it’s nice to see other, non-digitized human faces regularly, aim to spend at least three days a week (for most of the workday) in lab. You don’t have to communicate your schedule with me in advance, as long as you’re around roughly this much and show up for meetings. Undergrads and out-of-state lab members will have different arrangements, of course.

Take vacations! Take good ones, show us the photos, and bring back tea, chocolate, and/or fine liquor. Try to use all your vacation time. You don’t need approval from anyone before you select dates, but please try to give collaborators advance notice and consider their schedules. Mark the days you plan to be away on the lab calendar.

Please stay home if you’re sick. You will be judged for this one.

Non-hourly, benefits-eligible employees (including graduate students) are entitled to various forms of parental, personal, and family leave, and I encourage you to take them if you need them. If you need other accommodations, please let me know.

2.3 Workspace

The lab space is supposed to help you work efficiently and happily: I want it to be a place where people can reliably go to get stuff done.

  • Keep the main room quiet. If others are present, have meetings (in person or via Skype) in an adjacent conference room.
  • Please feel free to customize your space. Adjust the location and height of your desk and file cabinet as you see fit. Let me know if you’d like a privacy screen, a fan or space heater, etc.
  • Check with others before bringing pets to work.
  • Consult others before making dramatic changes to the lighting or temperature.
  • Keep things clean. Wipe your desk. Wipe the kitchen counter. Do not wipe crumbs on the floor. Clean up spills. Gently encourage others to do the same. Bad habits kill mice.
  • To make the room easier to clean, avoid letting your stuff overflow past your desk. Don’t leave piles of stuff on the floor for more than a few days.
  • Please let me know if there are ways the space can be more comfortable, or if there are particular things (e.g., new computer or software) that would improve your work.
  • Lock the door if you leave and no one is in the lab.

2.4 Communication

Please limit the use of email for research questions and discussions. Use Asana instead—it makes things much easier to find in the long run, and it has no overeager spam filter. Asana is also the best tool for lab announcements and discussions.

I do not expect you to check email or Asana on weekends, vacations, sick days, or holidays. I’ll always try to respond to your communications within 24 h, excluding weekends, vacations, sick days, and holidays. In general, you should check email and Asana a few times a day and try to respond to urgent requests within an hour or two (M-F), but I expect urgent requests to be few and far between. They will probably have some warning (e.g., an impending paper or grant deadline).

If I’m in my office and the door is open, you’re welcome to come in to talk. If the door is closed, it means I’m working, and it’s best to communicate via Asana.

2.5 Weekly check-ins

Most weeks, you’ll meet individually with me to discuss research and occasionally other topics. The agendas of these meetings is largely up to you. However, I ask you to come prepared with slides, an updated summary, or notebook (Rmd, Jupyter, etc.) concisely describing progress since the last meeting. You can choose whichever format works best for you, but somehow, your notes should clearly state (i) what goals you had set last week for this week, (ii) your progress on each goal, and (iii) what you think comes next. (This structure is really helpful for me.) You should also be prepared to show system and unit tests, or some kind of validation, to convince me your research results are correct. The meeting is time to both dig into the weeds but also think about the big picture.

I’ll try to remind you of this, but one of my main goals for each meeting is to learn how I can best support you, during the meeting and after. If our relationship needs adjusting, please let me know. If you want to talk about career goals, that’s fine too. This is your time, but please be organized about it.

When I’m traveling, these weekly meetings may need to be rescheduled or occur over the phone. Please always feel free to request a meeting when I am traveling, unless I’m on vacation.

2.6 Lab meetings

We’ll meet weekly as a lab. Meetings start with various announcements of abstract deadlines, cool upcoming talks, new papers, etc., and then we briefly update one another on our research (roughly 1-5 min per person). The point of these updates is to practice describing our research and especially to keep each other involved in our work, which includes providing helpful suggestions. The rest of the meeting is usually dedicated to an in-depth presentation and discussion of one of our research projects or a discussion of a paper. Plan to present your research once per quarter and to lead at least one paper discussion per quarter. Pick papers at least a week in advance so people have time to read them. Everyone is expected to show up having read and critically thought about the paper. If someone is presenting, everyone else is expected to make helpful suggestions.

2.7 Daily “Standup”

We use a Slack app to do quick check-ins on a daily basis. In the morning, everyone receives a prompt to list the work they’re planning for the day. Everyone’s activities then appear at 10 AM Central for others to read. Checking in is optional and skipping the prompt is acceptable with or without explanation. We use this to start conversations, and to build the habit of formulating our intentions in advance.

2.8 Reproducible research

You have broad freedom in most aspects of how you work, but there are certain protocols we follow to keep our work reproducible, accessible, and organized.

Reproducible means that other researchers could use your notes and code to reconstruct your results precisely without guesswork or manual labor. All of the figures and results in any manuscript must be fully reproducible by executing one or a few scripts in a public github repository. It should also be easy to reproduce intermediate results during development. Basically, this means we use version control, git.

Accessible means that (i) all of your code, including small scripts, is maintained in a git repository that is regularly (e.g., daily) synced to the lab’s github account; (ii) all raw data and major results are stored on Midway projects/cobey (unless other arrangements are required by IRB); (iii) project management is visible to all lab members on Asana; and (iv) you regularly back up your laptop using an external hard drive and CrashPlan Pro.

Organized means that you keep your project files organized, use version control, document your code, include unit and system tests, use Asana and/or notebooks to record all decisions in your analysis from day to day and week to week, and you refactor code when it stinks. It also means you communicate progress promptly to collaborators in meetings and (for external collaborators) emails.

Specific suggestions are in Section 4.