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Table of Contents

Landing page (this page)

  1. Intro from Dominic

  2. How to think about our lab

  3. How NOT to think about our lab

  4. Lab structure

  5. Starting in our lab: what are you expected to know?

 
Life and lab

  1. Expectations (of...)

    1. the PI

    2. all lab members

    3. Research support staff

    4. Graduate students and post-docs

    5. Undergraduate students

  2. Wellness

    1. Mental and physical health

    2. Personal emergencies

    3. Work-life integration

    4. Imposter syndrome

  3. Inclusivity

  4. Bullying/harassment and personal relationships

  5. Off-boarding (not completed yet)

Lab research

  1. Research philosophy

    1. Organismal vs. process focused research

  2. Working in the lab

    1. Work ethic

    2. Working hours, location

    3. Lab meetings

    4. Support letters

    5. Attending conferences

    6. Environmentally sustainable science

  3. Practices

    1. Prioritizing Experiments/Projects

    2. Reproducibility

    3. Collaborations

    4. Mistakes

    5. Project Management

    6. Literature search

    7. Writing

    8. Other research practices

  4. Policies

    1. Policy on non-dissertation or non-thesis research

    2. Funding policies

    3. Research integrity

    4. Conflicts of interest

    5. Competition

    6. Authorship policy

1 | A message from your PI*

Welcome to the Roach Brain Lab, where we use our brains to study the evolution of biodiversity. Dominic focuses on cockroaches, but your research project may have a different focus. Regardless of whether you study cockroaches or not, you are now a "roach brainiac" and you are a part of our community.

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My goals as a PI* are to build a diverse community, and have a synergistic academic relationship with each community.

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Indeed, we are more than a place where research happens, we are a lab community. As part of that community you have roles, rights, and responsibilities. The main rights you have are that you should be feel respected, and valued.  Read on to see more.

 

*PI stands for "principle investigator". The head of the lab is usually considered the PI because the overall direction of the lab's research is largely determined by their expertise, funding, and network. As a secondary (or higher order) investigator, you will have your own expertise, funding, and network. This should grow, in part, from your PI but will eventually be distinct.

2 | What our lab is

A physical space to...

  • feel safe and at home in

  • work on coursework in (study, complete assignments)

  • develop relationships with colleagues, and build collaborations

  • do your "roach brain lab" research in

An academic community to...

  • participate in

  • have a voice in

  • help grow

  • get support from

A research community to...

  • study macro-evolution

  • study biodiversity

  • study genomics and bioinformatics

  • integrate biodiversity science with other disciplines

3 | What our lab is NOT

  • Your literal home. There were some days where I treated my old lab as my home because I did not have any other place to go. There were some days where I had so much work to do that the lab felt like my home. It's OK if this happens from time-to-time but NOT long (or even medium) term. If you are making the lab your home that might suggest an unhealthy relationship.

  • A place primarily for socializing. We all talk to each other when we're in the lab. Science can feel isolating and we LOVE to get away from that to bond with our colleagues. This is normal. But if you notice it happening too often (or at inappropriate times) then this is problematic. You should feel comfortable asserting your privacy if you need time to yourself ("Hey! I would love to talk but I have trouble focusing and need to get something done. I would love to talk at lunch time?").

  • A place to work on non-lab research. You should feel comfortable doing course work, or any research Dominic advises you, on in the lab using lab resources. You can also do other research in the lab (i.e., maybe you're doing a lab rotation or have a personal project you're working on) but you should ask permission first. Lab resources are expensive and have specifically budgeted purposes. Often it will be totally fine to use them for other purposes, but sometimes not. Ask first and it will be all good.

  • A community to gate-keep. If you think a person in the lab is problematic, this is a great thing to talk about with Dominic (or the dept. chair, or another professor).

  • A community for "lurking" but not actively participating in. Since one of the lab's goals are to be "synergistic" we expect you to both grow and help others. If you are an undergraduate perhaps you feel you have nothing to contribute. But  that's not true. You can help by being a reliable research assistant, and coming to lab meetings. You can grow by asking questions, taking good notes, or working to improve your interpersonal skills (confidence, communication, emotional intelligence). If you are a graduate student you should be recruiting and advising undergraduate research assistants, offering to assist lab mates, participating in lab meetings, doing lab outreach, and any number of other activities. This is not an exhaustive list. If you need help defining your particular role in the lab, discuss this with Dominic.

  • A community to dominate. No one should be dominating the lab community (even your principle investigator). All people should have space to shine and participate.

  • A place to rely only on your PI. Dominic loves himself and his research, but it is not healthy to have your research entirely defined by your PI and you. As a graduate student you will have a committee, possibly a co-advisor, and hopefully coauthors. You should utilize those people as much as possible to expand your network and make your research robust.

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If any of these are problems that you don't feel able to deal with on your own then talk about them with Dominic in private.  If you don't feel comfortable talking about them with Dominic you can go to the dept. chair, school head, or any other professor (associate, or full professors preferred).

4 | Lab structure

  • Principle Investigator (PI)

    • Who do they act as advisor for? Graduate and (sometimes) undergraduate students.

    • Who do they act as mentor for? Post-docs, graduate students, and undergraduate students.

    • Who are they mentored/advised/evaluated by? Their department chairperson, other senior faculty, and higher administration.

    • Important notes:

      • Funding: PIs are the direct source of funds for most lab research. The ability of lab members to do research almost always depends on the PI's funding.

      • Lab management: The research conducted in the lab, the people in the lab, and the physical lab space (including machinery, supplies) all flow from the PI's research directions and funding.

    • Power: The PI is typically the most empowered member of the lab because they are responsible for hiring, managing lab funds, and determining the research direction of the lab.

  • Lab technician/manager

    • Who do they act as advisor for? No one.

    • Who do they act as mentor for? This is up to the lab tech. Anyone can ask them for mentorship but don't expect them to say yes.

    • Who are they mentored/advised/evaluated by? The PI.

    • Important notes:

      • Lab management: If a lab technician is working 50-100% of the time they likely are responsible for managing the day-to-day activities of the lab, as well as managing lab safety and supplies.

    • Power: Lab technicians may have special powers determined on a case-by-case basis. As the day-to-day manager of the lab, they will most-often have power to enforce lab safety protocols, scheduling of machinery/facilities, maintenance of the lab and purchasing of necessary equipment.

  • Post-doctoral researchers (post-docs)

    • Who do they act as advisor for? Usually, no one (but might vary).

    • Who do they act as mentor for? This is up to the post-doc but they are highly encouraged to. Take on mentees by request or by their own initiative.

    • Who are they mentored/advised/evaluated by? Always, the PI. Sometimes other faculty members.

    • Important notes:

      • Funding: Post-docs will often have their own funds. If they do, they are responsible for managing their funds. When their funding needs intersect with the lab's funds (e.g., they need to use lab equipment/supplies) they should consult with the PI or lab technician.

      • Lab management: As temporary, and somewhat independent researchers, post-docs have limited lab management duties/power.

    • Power: Although post-docs may be among the most experienced members of the lab they are often outside of the power-structure of the lab (particularly if they have independent funding).

  • Graduate students

    • Who do they act as advisor for? No one.

    • Who do they act as mentor for? Undergraduate assistants.

    • Who are they mentored/advised/evaluated by? Always, the PI. Sometimes a post-doc also.

    • Important notes:

      • Funding: If they have their own funding they likely are in charge of managing appropriations of their funds. However, in most cases their funding will come from the PI or another source.

      • Lab management: In the absence of the lab technician and the PI, graduate students are responsible for managing lab resources and space to the best of their ability. Purchases should be approved by the PI or lab technician, not a graduate student (unless they are using their own funding).

      • Power stemming from investment: Often graduate students will have the most invested in the operation of the lab. In other words, graduate students will often spend the highest amount of time in the lab and have the highest stakes of anyone in the lab. As such, this imbues them with an intangible power/importance in the lab.

    • Power: Graduate students have power over their undergraduate assistants and the resources directly relating to their own project (as given to them by the PI). Among graduate students, power typically descends by order of seniority. However, seniority can be ambiguous. If this is a problem, best to consult with another member of the lab.

  • Undergraduate students

    • Who do they act as advisor for? No one.

    • Who do they act as mentor for? Other undergraduates in the lab (with less seniority, usually).

    • Who are they mentored/advised/evaluated by? The PI is almost always the official advisor. However, undergraduate students will often have unofficial mentorship/advisement from other lab members. Both types are very important.

    • Important notes:

      • Sponsored research: Some undergraduates might be involved in the lab because they are working on a research project for course credit or another reason. If so, they might be viewed like "mini graduate students". However, often these projects will be offshoots of other lab projects. When that is the case they will usually be mentored directly by a more senior lab member. In all cases, the PI is the official advisor/mentor since they will be responsible for assessing the student's performance.

      • Funding: If they have their own funding they likely are in charge of managing appropriations of their funds. However, in most cases their funding will come from the PI or another source.

      • Lab management: Undergraduates should only utilize lab resources they have been trained/approved for by their direct supervisor and the PI.

    • Power: Undergraduates are the least empowered members of the lab. Yet, they are deserving of as much (if not more) respect and consideration as all other lab members.

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* What is the difference between mentoring and advising? Academic advising involves helping someone navigate a bureaucratic structure or system. For example, your academic advisor can tell you what your degree requirements are, or what to do if you fail a course. Mentoring is a broader and, in many ways, more important activity. Mentors provide guidance on how to achieve career, research, or other professional goals. Good mentors don't just give advice. They should should lead by example, be proactive about mentoring, provide opportunities for growth, and engage in meta-cognition about the mentor-ship process.

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*NOTE on power: It is important to consider who has what power in the lab. Power structure can determine conflicts of interest and potential abuses. If you have a complaint against someone higher than you on the power structure you may feel more comfortable contacting someone outside the power structure of your lab (i.e., a non-lab faculty member, or administrator).

5 | When you start, what are you expected to know?

When joining the lab as a grad student, I assume you have taken an undergraduate-level evolution course where you have covered micro-evolution and macro-evolution. The specific knowledge you should have of is going to vary depending on what kinds of projects you’re doing/interested in. Below is a list of what I think you should know before starting in the lab or in the first few months of being in the lab.

  1. General<< EVERYONE

    • Know how to use MSWord, MSExcel, Power point or the GoogleDocs equivalent

    • Be able to make a scatter-plot with a best fit line

    • Use a calendar app to keep a schedule

    • Back up everything on a cloud app (e.g., OneDrive)

    • Use a reference manager (e.g., EndNote, Mendeley)

  2. Microevolution<< EVERYONE

    • The four mechanisms of evolution

    • Speciation patterns and processes (allopatric, sympatric, parapatric and peripatric)

    • Species concepts (in particular the biological species concept, genetic species concept, morphological species concept and phylogenetic species concept)

      • Optional: knowledge of coalescent species concept or other genomic species concepts could be very useful if it pertains to your project

    • Homology (definitions)

  3. Macro-Evolution << 3.1. for EVERYONE, 3.2 and 3.3 only if your project is specifically in phylogenetics

    1. How to read phylogenies <<<this is the most important item to know in this document

    2. The definition of parsimony in relation to phylogenetics

    3. How a gene tree differs from a species tree

    4. Optional: maximum likelihood, Bayesian statistics, or evolutionary models

  4. Molecular biology << only if your project is in analyzing or collecting genetic data

    • Using micropipettes

      • Even if you know this, ASK Dominic when you’re using them. He will help you be better at it.

    • PCR (how it works and why it works)

    • Optonal: The basic structure of DNA and the process of DNA replication

  5. Bioinformatics<< only if your project is in analyzing or collecting genetic data

    • Alignments (homologizing genetic data)

      • You may not know this and learning it is fairly simple. Though you should have a solid understanding of what homology is, which can be a surprisingly complex topic

    • How to use a UNIX terminal (Mac or Ubuntu) or windows terminal

      • If you don’t know, do what everyone else does and just Google a “how to guide”

    • Optional: how to write a batch file (windows) or “for” loop (UNIX).

    • Optional: Coding in R or Python

    • Optional: Use ssh and FileZilla to access the lab computer

  6. Anatomy, physiology and behavior << Only if your project is about these things

    1. What is eusociality and what other types of social structures are there?

    2. Parental care in cockroaches (See Bell, Roth & Nalepa 2007 textbook)

    3. Termites lifecycle and social structure

    4. Optional: Wood feeding in cockroaches and termites (See Bell, Roth & Nalepa 2007 textbook)

    5. Optional: Nitrogen metabolism and Blattabacterium in cockroaches and termites (See Bell, Roth & Nalepa 2007 textbook)

    6. Optional: Basic cockroach anatomy (ask Dominic to share his textbook figures)

    7. Optional: What a transcriptome is and what kinds of things it can tell us

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