updated January 2020

One of the central missions of the McEwan lab is to:

Create opportunities and guide students in the pursuit of their professional vision in the realm of scientific research, application and outreach.

Toward this end, the lab is committed to providing a healthy framework for student engagement. The pursuit of science can become an overwhelming experience and can create, or interact with, unhealthy patterns in the lives of students in the lab.  Destructive tendencies can flourish in the academic setting and it is our goal, as a lab community, to pursue science while also supporting the overall health and well-being of lab members.

Mental and physical health concerns.

If you are not feeling well, either physically or mentally, take the time off you need to seek out help and take care of yourself.  There are many resources at the University of Dayton that you can use and you should always feel free to take time off from the lab, miss a meeting, or otherwise disengage if you are ill or otherwise need to take care of yourself.  Please communicate with Dr. McEwan and other community members you might be working with if you cannot attend a lab activity where others are counting on your presence, or if you will be out for an extended period of time.

Personal emergencies.

You may be a member of the McEwan lab for an extended period and during this time it is possible that a life-altering situation or emergency will arise.  We have seen many different things arise in the lives of community members and it is critical that you take the time you need if such a situation arises in your own life.  Please communicate with Dr. McEwan if something happens that will require you to miss a lot of time in the lab.

Balance.

Scientists can be both ambitious and obsessive.  The pursuit of scientific knowledge is intoxicating at times and students can easily fall into a routine of working far more than is healthy.  If you are the kind of person who tends to push beyond your limits you can become a Growing Tree Academic and wind up personally destroyed in the pursuit of giving yourself to your project and to Science.  Many of our projects are bottomless, meaning that we can keep working forever and still have more to do.  This can lead to working far more hours that are healthy.  Thus, learning to set limits is an important goal.  For some, managing this comes naturally, while for others it can be extremely complicated.

I want to also note that what is an unhealthy level of work and commitment for some may be perfectly healthy for others.  Rarely are painters or musicians criticized for working obsessively, nor do we criticize the star athlete for working tirelessly on her craft – similarly, it is important that we are also accepting of the fact that for some people, Ecology is truly a labor of love and working “constantly” can be part of a healthy and happy life. If someone says “I don’t want to go to the Avengers movie because I am working on these figures” that does not mean they have a work-life balance issue, they might actually enjoy figure making more than the Avengers.  We encourage each person to find the balance that keeps them inspired, avoids burn-out, and keeps their project on track.

Work hours.

Science is a “product” driven enterprise.  The goal is the accumulation of knowledge and communication of that knowledge to the scientific community and the public.  Scientists approach the notion of work hours from a variety of different perspectives.  Some find success in setting up a “normal” 8-5 Monday through Friday work week, and come to campus during those hours and work, then do not work on the weekends.  Others work better from off campus at times and do not have as consistent hours. I have known successful scientists who wake up at 5:00 am every night and are super productive, and I have known successful scientists who did their best work between 10:00 pm and 2:00 am.

Dr. McEwan is normally on campus a lot during the semesters, but isn’t always in his office.  He also works from home a lot as he has found that focus is sometimes easier there away from distractions. Dr. McEwan works at least some most days, including weekends and holidays, also works at night often, but also will simply not come to campus some days and takes a lot of time for family when needed. That Dr. McEwan works on weekends does not indicate that you need to do so!  Your goal ultimately is to fine the working pattern that helps you be maximally productive and happy – nothing else really matters.

Email hours.

Email is the primary mode of communication in academia, science and in the McEwan Lab.  As a lab member you will be added to a list and there will be periodic communication over that list.   You must read your email to stay informed.  Further, you may also be involved in projects where Dr. McEwan is involved and those projects will likely prompt email communication.  Dr. McEwan may send emails at odd hours.  Late at night, early in the morning, during holidays, on weekends.  You should not take emails sent at odd times or days as an indication that you need to reply immediately.  You can manage emails in a professional fashion and should not answer emails during times where you normally would be on holiday or sleeping, etc.  Students are responsible for being responsible about when to read and reply to emails in a way that is healthy and productive for them as individuals.

Lab and field safety.

The Department of Biology has lab safety training that you should participate in if you are going to be working in the lab.  Let Dr. McEwan know so that can be scheduled.

Field trip safety is also an important concern for McEwan Lab members. Here are some safety rules:

• Transportation into the field is normally via the Department of Biology field vehicle (truck). Communicate with Dr. McEwan for safety rules and access.  Driver training is required.
• Do not go into the field alone. You should always have at least one person with you.
• Generally speaking if you are going into the field for terrestrial sampling you should wear tough closed toe shoes (boots), preferably water proof (think Gortex) and long pants.
  In the summer, pants preferably would be light, loose, and tough – ripstop nylon or something similar (think Army surplus!!).  Additionally, I personally like to wear light long-sleeved shirts.  Something that does not stick to you and that you can roll up or down sleeves. The main idea is to delete from your brain the thought of walking on lawns and trails, and insert the idea that your job as an environmental professional will often mean going perpendicular to the trail directly through briars, nettles, poison ivy, with swarms of biting flies, mosquitoes, etc.  If you have on shorts and sandals you will be sad and distracted and in pain, and therefore not able to do your job.
• Sunscreen, sun hats, insect repellant are often needed in a field situation. Protect yourself.

Commitment to Community & Inclusivity

Please read the stand-alone post on Inclusivity and use the online form to report issues that threaten our community.

Summary

(a) Ensuring that lab activities do not adversely impact the well-being of lab members is a critically important task and something we all take seriously and work on as a community.

(b) Undergraduate students often experience stressful times and mental health is a serious concern.  Many new studies indicate that stress and mental health are also serious concerns for graduate students.  In the McEwan Lab we will work to create an environment of support around mental health challenges.  Respect for work-life balance is fundamental to the McEwan Lab philosophy (LINK).

(c) Working in a research lab can be fun and the quest for scientific knowledge can be truly exhilarating.  Although we all experience pressure related to our lives as academics, we in the McEwan Lab seek to pursue answers to important scientific questions in a way that is mutually supportive and ultimately joyful.

(d) Students in the lab who experience challenges to their wellness are encouraged to seek out help.  Many resources exist at the University of Dayton which can be found by following this LINK.

Outside Reading

• College Student Mental Health Crisis (Psychology Today)
• Evidence for a Mental Health Crisis in Graduate Education (Nature)
• Work organization and mental health for PhD students

McEwan’s Mental Health LifeHack Lecture

Charybdis

Updated September 2019

 

Data collection practices

(a) If you are leading a project you must keep a field notebook in which you outline your observations and activities.  These are available in the McEwan lab.

data collection needs to be clean, legible to others, in pencil, on waterproof paper, with dates and data collector information on each sheet.  Data collected on paper in this fashion is timeless and superior to digital methods.

(c) When possible there should be uniformity in data collection system.  Preferably have the same person collect the same data in the same way for the whole project and deviate from that only if needed and with caution.

(d) QA/QC your data entry.  Errors are quite common in data collection and data entry.  You need to practice regular QA/QC.  Best is a quick scan of each sheet in the field (or lab) as the sheet is completed to see if anything absurd is written down (oak tree with 8900 cm DBH).  During data entry is a good time to catch mistakes. Then after data entry, depending on the number of sheets, it is useful to go back and re-check the entry.  Minimally, a random 10% sample of the data sheets and re-check with the entered data is needed.  If mistakes are found, then another random 10% sample (without replacement) is needed.

 

Precautions against the loss of data

Computers are only vaguely reliable instruments. 

You are required to assume that your computer, or the one you are using, will fail unexpectedly.

Examples of **unacceptable** reasons for losing data:

(a) my hard drive crashed!  (of course it did!)

(b) I was really busy getting ready for “x” so I didn’t back up the data

(c) there is only one computer with a microscope camera/software package/etc and so I saved everything there and didn’t back it up.

 

McEwan lab data management practices & data sharing

Here are some rules for working in the McEwan lab:

(a) Data ownership.

At the time of graduation, or the ending of any particular project, all data and other information associated with the project must be transferred to Dr. McEwan for curation, storage, publication or sharing.

Students may be entitled to authorship on subsequent publications; however, that is determined on an individual basis depending on the efforts of the students within the context of the overall project.

As Principle Investigator in the lab, and the person responsible to the University of Dayton, funding agencies, etc, Dr. McEwan is the ultimate owner of all data collected in the lab and reserves the right to make datasets publicly available and move forward with publishing or other uses pursuant to the code of ethics surrounding scientific information put forward by the Ecological Society of America.

(b) Everyone will use Excel to enter data and create CSV files and all analysis must be done in R.

(c) We will share data sets across the lab

(d) We will create data products (data sets) that are shared publicly

(e) Everyone will help out with analysis- share in a collaborative fashion

(f) Analysis of data sets will often be open to peers, and, in some instances, will take place live in front of the lab group.  This might feel scary at times if it is your data set, but this is the way we are moving forward

Process:

(a) Every new project in the lab should begin with the creation of a folder that is shared.  Dr. McEwan will create that folder and share it with the participants in the project.  If you are involved in a project and do not have a folder, let Dr. McEwan know via email or in person and he will create the folder.  All activities related to the project must take place within this shared folder.  The shared folder should have a logical sub-folder structure and can include “Literature”  “Analysis,” “Writing,” “Scripts,”  etc.

(b) Data products.  The first priority for any project, once data have been collected is to create data products for the project they are working on.  These data products will be shared in the Project Folder and consist of a written description of the methods,  data entered into the appropriate format for sharing and analysis in R, and explanatory text in the form of meta-data.

Features of a required data product

–  a journal-quality description of methods.  This may need to include images, etc.

–  a Final CSV folder that contains the perfectly cleaned and organized R-ready files

–  metadata for the CSV files

(c)  Projects will advance forward, following the completion of the data products, following normal processes including exploratory data analysis, final analyses and writing.  This could include writing a Thesis, a paper for publication, or preparing various presentations including posters and presentations.

(d) Once analyses are completed, the final, curated, annotated, scripts must be shared with Dr. McEwan.  These scripts may serve as the basis for future analyses.  To determine if you have met this lab requirement – Can a reasonably competent person, familiar with your project, reproduce your graphics and analyses in < 1 hr?

 

McEwan lab data archive

The McEwan lab seeks to publicly share all data collected in the lab through eCommons and the University of Dayton library. The idea is to store curated data set on the site in such a way that they are publicly available and have a citable DOI.  We will seek to publish the final, cleaned, csv files prior to publication and cite the data in the manuscripts we submit to journals.  This is a permanent archive freely available to all collaborators, agencies and other stakeholders.  Dr. McEwan will contact you about storing your data sets in the archive if appropriate.

LINK: https://ecommons.udayton.edu/mcewanlab/

 

 

Managing and Citing Scientific Literature

Updated June 2021

“A few months in the laboratory can save a few hours in the library.”  Frank Westheimer

 

Overview

Reading and managing scientific literature is one of the most important skills you need to develop.  Scientific literature is the foundation upon which all future work must be built.   Climbing to the top of the mountain of literature is a must for PhD students.  For Master’s students and undergraduates, you must engage the literature.  Reading the literature is a skill, and if you do not develop a commitment to developing that skill then that quality of your science will suffer.  In the McEwan lab all project leaders are required to commit to reading the literature and using that literature to bolster your science.

Mendeley

We use Mendeley as the literature management software in the McEwan Lab.  There is a lab account that you can sign into.  It has a web-based application and a downloadable desktop application including a plug-in.  I use the plug-in for some literature work on manuscripts, but the more important thing is that it serves as a repository.  LINK

The Salty Seven

Every project leader in the lab should find seven peer-reviewed scientific articles that apply to their project.  Use Google Scholar or Web of Science.  Then save PDFs of these articles and place them into a folder that you create in Mendeley.  These articles are then the basis for your work going forward.  Read them carefully.  Look at the figures.  Look at the literature they are citing.  Look at how they are “framing” the project in terms of ideas and concepts.  These papers can serve as a model for your project. What techniques to use, how to analyze data and how to frame up the science in the broader scientific conversation.

 

Creating a well-organized literature cited page in your manuscript.

 Proper citation of literature is a fundamental task of writing a manuscript for a Thesis, Dissertation or scientific publication.  In the McEwan lab we use Mendeley to manage literature and this does have a function to automatically create a literature cited page!  This makes things much easier.  However, the Mendeley library itself has errors that are propagated into the Literature Cited page.  Later in the process, you will need to de-couple from Mendeley and finalize your references, which will require you to be sure that the citations are complete and formatted consistently.  Journal copyeditors have some responsibility in getting your format correct once your article is accepted and prior to publication; however, it is important that the manuscript be edited carefully prior to submission.  If a reviewer turns to the references and finds something missing, or a very messy formatting situation, they may take a negative view of the work. You do not want this though popping up in a reviewer’s mind: “If the authors are sloppy and irresponsible with their references, maybe they are sloppy and irresponsible with the data collection too….hmmmm.” 

 Here are some McEwan Lab Best Practices to checking your references.

(a) Choose a format and stick with it.

 You need for your Reference Cited page to be consistent.  This means you need to select a format and then use the identical format for all citations.  If you have a journal that you are targeting from early on you can use that journal’s “Instruction to Authors” to figure out your format.  Mendeley might have something that matches precisely that format, or you can actually create your own format within Mendeley.  Alternatively, you can chose a Mendeley format that is close to the final format you need and edit from there.  Ultimately, your goal is consistency.      

(b) Make sure all the literature cited in the manuscript appears as an entry in the Literature Cited pages, and that all literature listed in the Literature Cited pages are also referenced in the manuscript.

The reference program you are using (eg, Mendeley) should help you with this, but still mistakes happen and especially if you are working with multiple co-authors you are almost guaranteed to end up with a mis-match between literature cited and Literature Cited.  My recommendation is to literally print out the manuscript, and the Literature Cite page and go through one-by-one with a marker and check off each manuscript citation.  There really is no substitute for this kind of screening process. Then if you find a reference in the text that is not in the Literature Cited you can fill it in, and if you find Literature Cited that is not in the text you can add it, or delete.

(c) Edit for consistent formatting

As you are working on your manuscript and approaching the later stages in the editing process it is good to begin scanning your Literature Cited for formatting mistakes.  There will often be many mistakes of consistency.  Here are some things to look for:

———————-

Author names and initials

You want these to be consistent.  Below are three different ways to list the author names and initials, fix this if you find it!

Borth, EB, Custer KW and McEwan RW (2018) Lethal effects of leaf leachate from the non-native invasive shrub Amur honeysuckle (Lonicera maackii) on a model aquatic organism (Hyalella azteca). Ecoscience 25: 189–197.

Borth, E.B., K.W. Custer & R.W. McEwan (2018) Lethal effects of leaf leachate from the non-native invasive shrub Amur honeysuckle (Lonicera maackii) on a model aquatic organism (Hyalella azteca). Ecoscience 25: 189–197.

Borth, E.B., Custer K.W., McEwan R.W. (2018) Lethal effects of leaf leachate from the non-native invasive shrub Amur honeysuckle (Lonicera maackii) on a model aquatic organism (Hyalella azteca). Ecoscience 25: 189–197.

———————-

Date

You want to be consistent in the way the date is displayed.  Each citation must be the same.  Below are three different ways to display date, this is no good.

Borth, EB, Custer KW and McEwan RW.  2018. Lethal effects of leaf leachate from the non-native invasive shrub Amur honeysuckle (Lonicera maackii) on a model aquatic organism (Hyalella azteca). Ecoscience 25: 189–197.

Borth, E.B., K.W. Custer & R.W. McEwan (2018) Lethal effects of leaf leachate from the non-native invasive shrub Amur honeysuckle (Lonicera maackii) on a model aquatic organism (Hyalella azteca). Ecoscience 25: 189–197.

Borth, E.B., Custer K.W., McEwan R.W. Lethal effects of leaf leachate from the non-native invasive shrub Amur honeysuckle (Lonicera maackii) on a model aquatic organism (Hyalella azteca). (2018). Ecoscience 25: 189–197.

———————-

Article title

Make sure the title is consistent and watch out for capitalization in particular.  For example, these are inconsistent.  This is bad.  Make all of your references the same.

Borth, E.B., K.W. Custer & R.W. McEwan (2018) Lethal effects of leaf leachate from the non-native invasive shrub Amur honeysuckle (Lonicera maackii) on a model aquatic organism (Hyalella azteca). Ecoscience 25: 189–197.

Borth, E.B., K.W. Custer & R.W. McEwan (2018) Lethal Effects of Leaf Leachate From the Non-native Invasive Shrub Amur Honeysuckle (Lonicera maackii) on a Model Aquatic Organism (Hyalella Azteca). Ecoscience 25: 189–197.

Borth, E.B., K.W. Custer & R.W. McEwan (2018) Lethal effects of leaf leachate from the non-native invasive shrub Amur honeysuckle (Lonicera maackii) on a model aquatic organism (Hyalella azteca). Ecoscience 25: 189–197.

———————-

Latin names are in italics

 See below.  The bottom one is incorrect.

Borth, E.B., K.W. Custer & R.W. McEwan (2018) Lethal effects of leaf leachate from the non-native invasive shrub Amur honeysuckle (Lonicera maackii) on a model aquatic organism (Hyalella azteca). Ecoscience 25: 189–197.

Borth, E.B., K.W. Custer & R.W. McEwan (2018) Lethal effects of leaf leachate from the non-native invasive shrub Amur honeysuckle (Lonicera maackii) on a model aquatic organism (Hyalella azteca). Ecoscience 25: 189–197.

​———————-

There should not be random stuff at the end of a citation

Let the Journal decide if they want to DOI at the end.  We just put the proper citation.  Don’t have stuff, like below in the top example in maroon, hanging out at the end.

Gregory, SV, Swanson, FJ, Mckee, WA, Kenneth, W, Swanson, J, Cummins, KW (1991). An Ecosystem Perspective of Riparian Zones Focus on links between land and water. BioScience, 41(8), 540–551. URL : http://www.jstor.org/stable/

vs.

Miller KE, Gorchov DL (2004). The invasive shrub, Lonicera maackii, reduces growth and fecundity of perennial forest herbs. Oecologia 139: 359-375.

​​———————-

All​ journal names should be treated identically and spelled out

You should not have some abbreviated, others not, not some italics, others not.  Three below are three different articles where the journal title has been treated differently each time.  Just spell out the title.  

Tank, JL, Rosi-Marshall EJ, Griffiths NA, Entrekin SA, Stephen ML (2010). A review of allochthonous organic matter dynamics and metabolism in streams. Journal of the North American Benthological Society 29: 118-146.

Vannote RL, Minshall GW, Cummins KW, Sedell JR, Cushing CE (1980). The river continuum concept. Can. J. Fish. Aquat. Sci. 37: 130-137.

Voshell Jr., J. R. 2002. A Guide to common Freshwater Invertebrates of North America.

Wallace, JB (1996). The Role of Macroinvertebrates in Stream Ecosystem Function. Annual Review of Entomology, 41(1), 115–139

​​———————-

Be consistent in whether you have “and”  “&” or “nothing” at the end of your author list. 

Below we have these treated three different ways.  It has to be the same.

Lenth, R., Singmann, H., & Love, J. (2018). Emmeans: Estimated marginal means, aka least-squares means. R package version, 1(1).

Lieurance D, Cipollini D (2012). Damage levels from arthropod herbivores on Lonicera maackii suggest enemy release in its introduced range. Biological Invasions, 14(4), 863–873.

Likens FH, Bormann, R. S. Pierce and W. A. Reiners, G. E. (1978). Recovery of a deforested ecosystem. Science 199: 492–496.