Microbial 'omics


Lab Culture and Expectations

Table of Contents

The purpose of this document is to serve future members of our group about its professional inner dynamics, and offer a resource for its current members to remember the important professional things we care about.

Study hard what interests you the most, in the most undisciplined, irreverent, and original manner possible.
Richard Feynman

We let the following principles guide us when we think about who we are as a group, or whether something we are doing is worth our time. There is an intentional order to the list:

  • We try to study rigorously what excites us without cutting corners.

  • We strive to serve the community. This includes writing extensive tutorials, giving lectures or workshops, and responding to messages that are coming from our colleagues near and far. We assume that one of the best ways to spend our time is to make it easier for others to learn what they wish to learn from us.

  • We maintain a critical outlook. We are most critical of our own work, and geninunely try to first understand what others are trying to accomplish before being critical of theirs.

Group Culture

The purpose of this section is to establish best practices for our frequent endeavors and make suggestions.

Data analysis

The thing that doesn't fit is the thing that's the most interesting.
Richard Feynman
  • Reproducibility and transparency. Be prepared to redo everything from scratch yourself, and document everything in such a way that someone else inside or outside of our group can do it without needing you, too. Do your best to avoid ad hoc solutions, AWK one-liners, or anything you can’t clearly describe formally in a conventional methods section of a hypothetical manuscript.

  • Robustness. Make sure you have discussed the technical details of your work with at least one more person in the group. Even the most seemingly rudimentary analytical decisions can have profound impacts on your findings downstream, and others may be able to see what you have not. If you are going through someone else’s analysis, be as critical as you can while being considerate and compassionate.

  • Mindfulness. If something that should be working is not working, do not move on to trying another way to make it work without first letting others know. If you don’t have time or experience to take a look at the code, that’s OK –writing up an issue on GitHub, or sending a quick note to people who may have an idea about it would also be sufficient.

Writing

In a way, writing is all we do. We often understand better as we write, and sometimes we write just to understand.

  • Continuity. Everyone is expected to write something. It can be a research article, a piece of code, a blog post, or a tutorial. No day should go by without writing anything.

  • Clarity. Science is hard, science writing is harder, and reading science written by someone else is the hardest. Especially for those of us who are not native in English. We try to make our writing more accessible by avoiding lazy or vague sentences.

  • Meaning. We pay attention to words and statements. We avoid flashy but blank sentences or common but inaccurate statements (like “most microbes cannot be cultivated”). We avoid poorly-thought analogies or empty buzzwords (like microbial dark matter).

Group discussions

Reality must take precedence over public relations, for nature cannot be fooled.
Richard Feynman

Doing science in a social setting requires a delicate balance of things that often point to different directions. While the best science emerges from minds that defy all rules and boundaries, social environments are most functional when all members of a group recognize and observe common sense. So here are a couple of reminders for group discussions:

  • Efficiency. It is best if at any given time only one person is talking, especially during official lab meetings or spontaneous discussions in the lab. Getting excited is a part of our daily routine and the definition of our job, but starting multiple discussions at a given moment can be very inefficient since both parties will be missing out others’ ideas.

  • Criticism. It as our responsibility to be tough on ideas during group discussions yet it is not easy to criticize an idea while making sure that the owner of the idea does not feel as if they are not appreciated as a member. Ideas can be torn apart, thrown away, and improved. But it is not acceptible to not be careful to find the delicate balance. If you are delivering a criticism, please be mindful. If you are at the recieving end of it and you are upset with the mode of delivery, please speak up. If you are the observer of a tough situation, please consider taking action. That said, the absolute respect and compassion we expect from each other when we are among ourselves is a luxury that we may not expect from our colleagues elsewhere. Others will criticize us, and we must be welcoming of such external criticism, too. In addition we must be prepared that they can be harsh, and we must learn to respect those opinions regardless. But also we should be able to move on when it feels necessary without slowing down and without being cynical or dimissive of outside criticism.

  • Mindfulness. No one interrupts anyone else. Body language can be as interruptive as spoken words, so we should strive to encourage the speaker’s attempt to speak up their mind by making sure they are not dealing with our verbal or physical reactions. Delivering an idea is already hard enough and we can all do without additional stress. Some days are worse than others for each one of us. If you feel that it is one of those days, you should feel free to not attend to a group discussion.

Member Roles and Specifics

The purpose of this section is to clarify general expectations of our group.

Meren’s Promises

This list may not include some of my implicit promises. If you see a topic that needs to be covered in this section, please let me know.

  • My main role and responsibilty in this group is to keep everyone happy, productive, and funded. I promise to work with everyone to deliver this. If a member is systemmaticaly lacking either of them despite our best efforts, I also promise to do my best to help them find a better place. Throughout my career in science I saw many PhD students and post-docs lost years before they realized they were at the wrong place, and I am determined to not let that happen to anyone in our group.

  • Besides the group meetings, every member will at least have a 1-hour slot per week to have a private meeting with me. Unless I am traveling or sick. During the times of travel, I will do my best to meet you through Skype if you are willing.

  • You will be free to walk into my office anytime if you have a question. If I am coding or writing something that takes lots of concentration and should not be interrupted, I will close my door or will not come in to work at all. If my door is open, you are welcome to come in and ask me anything.

  • I will do my best to find exciting projects for each one of you, and involve you with outside projects that you may contribute based on your skill set and level of interest. That said, I promise to not enlist anyone for any project without first probing thier level of interest and availability.

  • I will do my best to make sure you have a high-end laptop, an external monitor, a pair of noise-cancelling headphones, an ergonomic keyboard, an ergonomic mouse, and an optional standing desk solution when you start in our group. And somewhere to sit, hopefully.

  • PhD students: you are my top priority. I will always have time for you, regardless of where I am. You can even interrupt me while I am having a meeting with someone. I would turn to my guest and be like “excuse me, emergency”. Seriously.

  • I will make sure that the lab has coffee, some semi-healthy snacks, and chocolate available at all times (and I expect you to let me know when our snack drawer shrinks and/or gets boring, and help me with what to select for the next order).

  • I am not a micro-manager, and I will never micro-manage anyone unless they specifically ask for it. That said, I will not be absent either: I promise to be around as much as I can, and make sure I attend to everyone’s needs as quickly as I can.

  • The synergy in the lab is more critical to me than our productivity. Threfore I will take everyone’s opinion into consideration before accepting a new member to the group (except rotation students, interns, and visiting scientists with short planned stays).

  • We will never grow into a very big group. This decision has advantages and disadvantages. If you are planning to join our group, I would like you to take a moment and consider the potential implications of this on your journey.

Wishes and Expectations

Many things in this section are open to discussion. We can modify them, or there can be exceptions. We just need to talk about them first. It is our best interest to avoid not delivering something from this list systemmatically and quietly.

  • Vacation is very important, and we must pay attention to beauties of life outside work as often as we can. You have university defaults in your pocket. But you can ask for more. Let me know about your plans ahead of time, so I have a chance to make suggestions and am prepared to protect you.

  • Regular attendence is critical for the group synergy and for the personal development of everyone. Each member represents a significant fraction of our group. For this reason alone, we aspire to be around regularly to maximize our time together. Family must come first and life events should take priority. As a guideline, we have agreed to be in the lab at least between 9:00am and 4:00pm every non-holiday week day. There are always exceptions and these times are not written on stone.

  • I expect you to follow and efficiently use the lab calendar, Slack, and Lab Fiesta.

  • Every member is expected to present when it is their turn during our lab meeting, and attend to each presentation to listen to others. We designate the person who is lined up to present the week after as our meeting scriber.

  • I expect you to reach out to me when you need help. Please remember that it is not your job to try to protect my time.

  • In addition to technical and intellectual difficulties, science life can have steep ups and downs. Even when you are excellent at what you are doing and on the right right track, doubts can be quite challenging to overcome. I wish you to let me know if you are going through a rough patch.

  • It is important for you to attend to talks at the university. Especially the departmental seminars and seminars by the Committee on Microbiology. Regardless whether you think it is relevant and worth for your time, especially if you are a PhD student. Even the talks that seem to be least relevant to you will play a role in your progress by helping you develop a broader vision. This will also make you a good citizen of our department.

  • You represent the lab and its members when you are at meetings inside and outside of the university. Make your fellow labmates proud with your excellence. It is OK to be critical, but doing it with absolute respect, accuracy, and compassion is key. You may not initially realize it, but science is a small world, our field is even smaller, and your social mistakes will linger much longer than you wish, and affect more people than just yourself. Assume that everything you will say about someone else will be heard by them sooner or later. I think the best strategy is to compliment people from their backs, and criticize them to their faces.

  • We absolutely denounce any form of discrimination, especially towards people who belong to minority groups and those who are not affiliated with so called ‘elite’ institutions. I hope that you will go out of your way to make them feel welcome, and be brave to raise your concerns if you witness a mistake. We will not tolerate racist or sexist inclinations of any kind.

  • I wish every Postdoc and PhD student to read at least 3 papers from other groups each week. It would contribute to everyone’s journey if you were to post the PDF to Slack, and include one- or two-sentence summary of why you were interested in that work and what you have learned.

  • We are a data-crunching lab. We can design new algorithms, implement new software, and have access to reasonable computational resources to run them. Most of our significant contributions include reanalyses of public datasets. I wish you to use this power. Find interesting research, bring it to the lab and share with others.

  • Become an expert of our own literature. I expect you to know everything the lab has published. Yes. Unfortunately this will require you to read all those papers in which Meren is the first or the last author until you fully understand them (especially those that were published in 2015 or after). Lucky for you, there aren’t many of them hahaha (starts sobbing).

  • Be aware of everyone else’s project. I expect you to be able to articulate in one sentence what each person is working on. If you don’t know what someone else is doing in the lab, meet with them for a dicussion. Those exchanges will not only help you to keep up-to-date with what is going on in the lab, but they will help others to figure out the best way to explain what they are doing.

  • You are welcome to take part in collaborations inside or outside of our institution. But if you are interested in collaborating with an outside group on a project, please ask me first. If someone is asking you to do something outside of the lab, tell them to ask me first. These are not only to protect you, but also to protect the lab and its intellectual mojo.

Thank you very much for everything.