Lab 3 pre-lab (Fall)

This is the final lab in our introductory unit. You will participate in peer review of your scientific poster drafts and plan for your revisions before final submission. The skills and conceptual knowledge of the scientific method that you have developed in this unit will be utilized throughout the rest of our course. Many of the links and information in this unit are foundational and are also listed in our 123 Library so you can re-visit them throughout the semester. And do not worry...you will see the isopods again soon enough! This lab will also includes a special biodiversity activity we must complete before seasonal changes make finding organisms too difficult.
  • Introduction
  • Do you know enough?
  • What will we do in lab?
  • LABridge
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What is Peer-Review?

We have learned about the iterative process of scientific exploration, relying on past knowledge as ​a "jumping off point" for new research questions. This type of deductive reasoning requires a large body of scientific work to be made public and available, and that the work is both valid and reliable. That often entails the process of peer review by which scientists review and critique the work of other scientists and deem it acceptable or not. You have already done some research using peer-reviewed literature. Now we are asking what that process actually entails.
Researchers write up their work as a scientific paper or manuscript which they send off to an appropriate journal. Journals range from regional (like the Journal of the Kentucky Academy of Science) to global and highly regarded (like the journal Nature or Science). Once submitted, the manuscript is sent to 3-4 anonymous colleagues to serve as "reviewers." These scientists are usually working in the same field and have proven themselves to be quality researchers. Reviewers go through the manuscript, line by line, criticizing each decision and assertion. They then decide, along with the journal's editor, if the article is valid, credible, and relevant. The final decision can be one three:
  • Rejected: This article has too many flaws for publication.
  • Accept with revisions: There are significant flaws, but if they can be fixed it might be publishable.
  • Accepted: This article is valid and has merit, and will be published.
Most submissions are rejected; 70-95% depending on the journal. The figure in the sidebar shows some acceptance rates for popular ecology journals. Once rejected, projects are either revised and submitted to other journals or re-framed and organized into totally new questions and tests. With rejection rates this high, we can feel fairly certain that the papers that do get published are reliable and of high quality.
Instead of submitting your work to scientific journals, you will present it to your peers in class.
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Acceptance rates (right y-axis) for popular ecology journals. Click to enlarge.
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Top reasons papers are rejected from Khadilkar (2018), in "Rejection Blues."
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Watch the TedTalk. Be sure you understand how peer review works.
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Read over the peer review form you will use in lab. Be sure you know what to expect.
Important!!! You need to bring one color copy (8.5 x 11") of your poster to class with you next week to participate in peer review. If you are not sure how to do so, see the link below.
Special note: We will revisit this concept in our unit on biodiversity. However, by that time in the semester (late October) there will be much less biodiversity available on campus! So to ensure you get to participate in this activity, we are going to do data collection now, and discuss context and analysis later on.

Do you know enough about a bioblitz?

Cataloging and measuring biodiversity, the variety of life in the world or in a particular habitat or ecosystem, is an important part of many evolutionary and ecological studies, as well as conservation efforts. 
​Biodiversity has been linked to ecosystem function (the capacity of natural processes and components to provide goods and services that satisfy human needs), and predicting the evolution of diversity at the community level has led to many evolutionary models like island bio-geographical theory, which predicts immigration and extinction rates on islands vs. mainlands.
​In some cases scientists can not catalogue biodiversity fast enough to save it. Our flora and fauna are going extinct at an alarming rate, sometimes referred to as the Holocene extinction: 277 plant and animal species have gone extinct in the US since the 1700s alone. We will discuss these topics in later units. For now, let us focus on "how" one might catalogue all the species present in area. Scientist approach this from a rigorous sampling perspective, but the Bioblitz gives all of us a an opportunity to contribute!
A bioblitz is a communal, citizen-science, effort to record as many species within a designated location and time period as possible. Bioblitzes are great ways to engage the public to connect to their environment while generating useful data for science and conservation. They are also an excuse for naturalists, scientists, and curious members of the public to meet in person in the great outdoors, and they are a lot of fun!
We are going to run a quick BioBlitz of campus. Now, you are not all extreme naturalists of Western Kentucky flora and fauna, so we will use the iNaturalist App called "seek" for species identification. Please be sure you have downloaded it to your device. Do some practice before you come to lab to make sure you are familiar with the interface...just go outside and point & click! It is very intuitive but lab will go smoother if you practice first!
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Review the terms in bold.
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Download the seek app.
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Practice using seek.
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Current extinction rate. Click to view article.
In citizen science, the public participates voluntarily in the scientific process, addressing real-world problems in ways that may include formulating research questions, conducting scientific experiments, collecting and analyzing data, interpreting results, making new discoveries, developing technologies and applications, and solving complex problems.
-citizen.science.gov
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Citizen-scientists participating in a BioBlitz.
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We will use the seek app for our BioBlitz.

what will we do in lab and how will we do it?

Lab 3 contains two exercises:
  1. Peer Review- The final activity of our Introduction: You will trade your poster drafts with another group. Each group will use the poster peer review form to critique the poster and give the feedback back to the authors.
  2. Campus BioBlitz: You will conduct a BioBlitz on campus using the seek app to identify and log your sightings. We will use thee data in a later lab activity.
Important!!!
You need to bring one color copy of your poster (8.5 x 11") to class with you next week to participate in peer review. Printing help on campus.
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Cartoon by Nick D Kim, strange-matter.net.
If you feel confident with this material, click the bridge icon below and navigate to Blackboard to take the LABridge for this week. Be ready to be tested on this material before you go to the quiz, and make sure you have your Lab Notebook Guide ready to submit as well.
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Click here to get to WKU's blackboard to take your LABridge for this week.

Lab 3 Protocol (fall)

Following this lab you should be able to...
  • Provide useful feedback on scientific research.
  • Properly revise your work based on peer review.
  • Find various species in your natural environment.
  • Use the iNaturalist seek app to identify species.
Overview. In today's lab you will participate in peer review of your scientific poster drafts and plan for your revisions before final submission.
  1. ​Exercise I. Peer Review of Scientific Posters
  2. Exercise II. BioBlitz on Campus
  • Exercise I
  • Exercise II
  • Exercise III
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Exercise i. Peer review of Scientific Posters

Procedure.
  1. Partner up with another group and share the handout of your poster draft.
  2. Once you have another group's poster to review, get a Peer Review Form from your TA.
  3. You might also want someone to open the Poster Template. You can follow it along, like a checklist of what should be included in each section and how.
  4. Carefully review the other group's poster draft following the form and template.
  5. Complete the form and give it to the author's. Return the poster draft as well.
  6. Open your Lab Notebook Guide for Lab 3.
  7. Once you receive your feedback, discuss how you will deal with the critiques and questions from the peer review and complete the Notebook Guide.
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Click to download.

Bioblitz on campus

You do not have to be in a nature preserve or state park to witness a lot of biodiversity, and easy to use apps have made identifying what you see in nature fairly easy. Today we will use the seek app to identify and log the biodiversity on WKU's campus. We will come back to these data later on in our unit on biodiversity.
Procedure.
  1. First, identify who will do what in your group. Here's a list of basic needs throughout this activity:
    1. Using the seek app (directions below)
    2. Finding the latitude & longitude (directions in below)
    3. Recording each siting & coordinates 
    4. Looking for species to ID
  2. To use the app, first click the camera button. Allow it access your camera.
  3. Scan your area for a species to identify.
  4. Once you see something you want to identify, be sure it is in focus (the app will direct you).
  5. The app will take sometime to make an ID once your specimen is in the camera frame. You will see the ID change at the top, from class >> to family >> to genus >> and hopefully to species.
  6. Sometimes zooming in or changing your perspective or view will help.
  7. Once you have an ID to species (or as close as possible), click the camera button again to "log" the ID.
  8. You might be asked to double-check the ID for closely related taxa.
  9. Review the tips and commonly missed taxa below.
  10. You will be sampling outside for 30 minutes. Set your timer on your phone.
  11. Before you begin, you will need to collect one more piece of information for each sighting: the latitude and longitude. iPhone users can use the compass app and iPhone or Android users can use Google Maps (directions in sidebar).
  12. Minimally, you should work in a pair with one person managing the seek app and your partner recording the species ID and GPS coordinates on paper or on their phone.  
  13. Practice in the lab a couple of times.
  14. Head outside and document (log) as many species as possible using the app.
Tips
  • Plants are stationary and obvious. ID them, but look for other specimen as well.
  • Look for big and small organisms: lichens and fungi are easy to overlook but still valuable sightings.
  • Do not forget to look up, often.
  • Look closely at vegetation, especially flowering plants, for pollinators and other small insects.
  • Inspect things closely.
The images above were taken just seconds apart as seek was working to ID a black walnut tree. It started as ID-ing the class, then eventually made it to genus, and then species.

Coordinates

iPhone: Open "Maps." >> Tap the current location button on the top right. >> When the blue circle for your spot appears on the map, tap it. >> Swipe up from the bottom to view full details for your location and you'll see the Latitude and Longitude. Android
Android or tablet: Open the Google Maps app. >> Touch and hold an area of the map that isn't labeled to drop a red pin. >> In the search box, you can find the coordinates.

Troubleshooting the app

  • New species not showing under "My Observations: tab
    • Be sure "Location" is switched to ‘on’.
  • Not identifying species
    • Sometimes problematic cookies or cache files may cause issues on SEEK. Clearing your cache and browser history is a good first step to troubleshooting problems.
    • SEEK recommends, and supports, the latest versions of: Edge, Firefox, Chrome, or Safari.
  • Not working
    • ​Turn your phone off and back on
    • Offload and reload the app
Procedure.
After returning to lab:
  1. View all your sightings, which will be saved in the app, under "My Observations."
  2. Clicking on any observation will provide additional details.
  3. Open the BioBlitz Data Entry sheet that corresponds to your group.
  4. You'll see that after recording the species ID and latitude and longitude, you will need to look up some additional information. The seek app will give you the kingdom or other taxonomic information (e.g., insect, fungi, mammal, etc.) and it will also tell you if your species is native or introduced (i.e., exotic).
  5. You can ID other species with this app anytime you would like. The dates are saved so you will always be able tell "when" you saw "what."
  6. Complete your group's BioBlitz sheet.
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BioBlitz Data Entry GROUP 1.
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BioBlitz Data Entry GROUP 2.
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BioBlitz Data Entry GROUP 3.
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BioBlitz Data Entry GROUP 4.
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BioBlitz Data Entry GROUP 5.
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BioBlitz Data Entry GROUP 6.
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BioBlitz Data Entry GROUP 7.
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BioBlitz Data Entry GROUP 8.

Faculty Spotlight: Jarrett Johnson

Jarrett Johnson focuses on the biodiversity of amphibians in the context of evolutionary ecology, population genetics, and conservation. His lab uses field/laboratory experimentation and genetic tools to understand amphibian adaptation and speciation. Current projects include landscape genetics of several Kentucky amphibian species using “next-generation” sequencing and eDNA strategies. The goal is to provide data relevant to the conservation and management of amphibian populations while simultaneously improving understanding of evolution and ecology in general. You can visit his lab webpage HERE and two recent publications are available below.
​Students who are interested in his work should email [email protected].

​An integrative phylogenetic analysis of eastern Nearctic Leuctra (Plecoptera: Leuctridae)...
Demographic effects of phenological variation in natural populations of two pond-breeding salamanders...
Written and collated by Natalie Mountjoy & Steve Huskey
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