1. Read the claim above carefully. Think critically about the propositions set forth. You can read the excerpt in the sidebar for more context.
2. Search the literature for examples that support or refute this claim. Decide which position you will support.
3. Use terms like “vestigial” and “vestige," to search online databases for examples of articles in which biological structures are explicitly identified as vestigial.
4. Use the resources in our library (under "Scientific Literature & Citations"), if you need reminders on searching and citing the scientific literature. 
5. Record each of your sources in the Google Sheet in the side bar along with the requested details.​
6. Collect enough sources to build your scientific argument (five minimum). 
7. After collecting evidence, construct a scientific argument based on your evidence. Such arguments have three primary parts: a claim, evidence, and reasoning.
8. Review the figure in the sidebar. Your argument should include a paragraph for each of these sections. ​
9. Review the instructions and scoring guide in your Lab Notebook Guide under Exercise IV.

Content from: ​Turbek, S.P., Chock, T.M., Donahue, K., Havrilla, C.A., Oliverio, A.M., Polutchko, S.K., Shoemaker, L.G. and Vimercati, L. (2016), Scientific Writing Made Easy: A Step-by-Step Guide to Undergraduate Writing in the Biological Sciences. Bull Ecol Soc Am, 97: 417-426. https://doi.org/10.1002/bes2.1258

We have already explored scientific literature and the peer review process. For this project, your final product will be a scientific journal article. Many students fell nervous about this type of writing. Please don't! Although scientific writing can see a bit foreign and technical, once you gain experience by reading scientific literature and practicing the writing style, it is not overly difficult to master. This might be your first time writing in this style, and that is OK. This is meant to be a learning process. The step-by-step guide in the sidebar is from a journal article (Turbek et al., 2016) about undergraduates writing journal articles. Very meta. Please read it carefully. You may want to take notes.
​Let's put our current research in context.
To do that, you need some background. Stream A is an example of a stream located close to large agricultural area, with little to no riparian zone. Stream B is an example of a heavily-wooded stream, far-removed from agriculture or industry. Knowing what you now know about protists, bioindicators, and watersheds, what predictions might you make about these streams? How might your data help you test those predictions? Our key research question is: Do these streams have the same level of protist biodiversity?

• Exercise I
• Exercise II
• Exercise III

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Test your knowledge here.

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Using Protist Biodiversity to evaluate stream health

We will use statistics to draw more conclusions from these data next week. We will also begin our literature review and start preparing for your scientific manuscript. For now, take a look at your data and see if you can make any general conclusions so far.

​Procedure. Make some general conclusions

1. Review all your data.
2. Think about what your data may show in terms of the health of these two streams.
3. Discuss each of the three data tables with your group.
4. Complete your Lab Notebook Guide.
5. Complete and submit the exit slip in the sidebar.

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.

How to print a slide in PowerPoint

• 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.

Poster peer Review form

Acceptance rates (right y-axis) for popular ecology journals. Click to enlarge.

Top reasons papers are rejected from Khadilkar (2018), in "Rejection Blues."

Watch the TedTalk. Be sure you understand how peer review works.

Read over the peer review form you will use in lab. Be sure you know what to expect.

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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.

How to print a slide in PowerPoint

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.

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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!

Download seek @ App Store

 Get Seek on google play 

Review the terms in bold.

Download the seek app.

Practice using seek.

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

Citizen-scientists participating in a BioBlitz.

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.

How to print a slide in PowerPoint

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.

Click here to get to WKU's blackboard to take your LABridge for this week.

Materials for step 6 will be provided by your TA.

Fungi Lab
​

1. Examine the spores on the gill of a portabella mushroom. Using your mushroom from before, extract a single gill from under the cap. Place a drop of lactophenol cotton blue stain on a clean slide. Lay the mushroom gill on the droplet and cover with a cover slip. Examine under a compound microscope.
2. Examine the shelf fungi provided.
3. Examine the puffballs provided.
4. Examine the button mushrooms provided.

​

1. Yeasts. The term yeast is used to describe the numerous single-celled fungi (over 1500 species described to date). Yeasts undergo fermentation to produce energy and two byproducts often used by humans: ethanol and carbon dioxide. Ethanol is the type of alcohol found in beers, wines, and liquors. Yeast used in bread-making, digests sugars present and yields ethanol which evaporates into the air (the reason breads are so aromatic) and carbon dioxide. The carbon dioxide bubbles get trapped in the bread and create the pores we see in a slice of bread all while causing the bread to increase in volume, or rise. To quantify the ability of yeast to perform fermentation, you can gather the amount of CO2 produced by active yeast cells. Here you will trap the gas in an air-tight container as yeast cells undergo fermentation using different carbohydrates. As the yeast cells break down the sugars, they emit CO2 that fills the fermentation chamber. Follow the directions in the sidebar to determine the activity of yeast cells. 

Plant Lab
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1. Lastly, identifying plants and trees in an area can help with many aspects of understanding their evolution, ensuring their conservation, and determining their value. For someone that does not know the species in an area, a dichotomous key can be a very useful tool to identify them. Having built your own dichotomous keys in a previous lab exercise, you are now experts on how to use them. For the remainder of the lab, you will venture outside to locate and identify the 10 tagged trees around the building. List their commons names and scientific names here, keeping in mind that scientific names must be underlined since you can not write them in italics.

3

4.1

The introduction

• The Introduction sets the tone of the paper by providing relevant background information and clearly identifying the problem you plan to address.
  
• Think of your Introduction as the beginning of a funnel: Start wide to put your research into a broad context that someone outside of the field would understand, and then narrow the scope until you reach the specific question that you are trying to answer (Fig. 1; Schimel 2012). Clearly state the wider implications of your work for the field of study, or, if relevant, any societal impacts it may have, and provide enough background information that the reader can under-stand your topic.
  
• Perform a thorough sweep of the literature; however, do not parrot everything you find. Background information should only include material that is directly relevant to your research and fits into your story; it does not need to contain an entire history of the field of interest. Remember to include in- text citations in the format of (Author, year published) for each paper that you cite and avoid using the author’s name as the subject of the sentence:“Kilner et al. (2004) found that cowbird nestlings use host offspring to procure more food.”
• ​Upon narrowing the background information presented to arrive at the specific focus of your research, clearly state the problem that your paper addresses. The problem is also known as the knowledge gap, or a specific area of the literature that contains an unknown question or problem (e.g., it is unclear why cowbird nestlings tolerate host offspring when they must compete with host offspring for food) (refer to the section “Research how your work fits into existing literature”). The knowledge gap tends to be a small piece of a much larger field of study.
  
• Explicitly state how your work will contribute to filling that knowledge gap. This is a crucial section of your manuscript; your discussion and conclusion should all be aimed at answering the knowledge gap that you are trying to fill. In addition, the knowledge gap will drive your hypotheses and questions that you design your experiment to answer.
  
• Your hypothesis will often logically follow the identification of the knowledge gap (Table 1). Define the  hypotheses  you  wish  to  address,  state  the  approach  of  your  experiment,  and  provide  a  1–2  sentence overview of your experimental design, leaving the specific details for the methods section. 
  
• Here, you may also state your system, study organism, or study site, and provide justification for why you chose this particular system for your research. Is your system, study organism, or site a good representation of a more generalized pattern? Providing a brief outline of your project will allow your Introduction to segue smoothly into your Materials and Methods section.

title 1

title 2

Cichlid key taxonomy book.

Cichlid key app.

Cichlid tank.

Fish diagrams.

Magnifying glass.

Cichlid Tree: 

1. Hint: The basic shape is pictured here.

​Procedure.

1. Go back to our cichlid tank and spend 5 minutes (timed) recording observations in your manual.
2. Try to identify 5 species using the cichlid key. Record these in your Lab Notebook Guide.
3. Check your ID by using the cichlid ID app: Fish Companion.
4. Get your TA to check your identifications.
5. Complete your Lab Notebook Guide.
6. Clean up your station and check-out.

Lab 6 pre-lab.

Thus far, we have explored taxonomy and systematics in this unit. Both use evolutionary concepts to help us order the natural world for study and analysis, and to better understand and describe the relatedness of Earth's organisms. To conclude our unit on evolution, we will now explore the various types of evidence for evolution and further your understanding of the import principles and concepts that comprise the single, greatest, unifying theory in all of biology. ​

• Introduction
• Do you know enough?
• What we will do in lab?
• LABridge

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What does the theory of evolution entail?

Evolution is simply defined as change over time, that over the incredible expanse of time since the creation of Earth, approximately 4.56 billion years ago, the diversity of organisms on this planet has changed. You can compare it to a "null" version that would state that species are immutable and never-changing; that every species we see now has existed in same form since the beginning of geological time.

The theory of evolution comprises two simple tenants:

1. Species change over time.
2. Species are related by decent from a common ancestor.

Evolution usually occurs through a combination of two different processes: via natural selection (a deterministic process), or randomness (a processed guided only by chance). Evolution can occur exclusively via natural selection, or exclusively through randomness, when the process is mixed, we refer to it as stochastic. Let us use the extinction of the dinosaurs, the K–T extinction (i.e., Cretaceous–Tertiary extinction) as an example. A 10km asteroid hit Chicxlub, Mexico approximately 66 million years ago, killing off 75% of all life in existence. Among the few animal-survivors were the small mammals, who could regulate their own body temperature and had lower energetic needs, unlike the dominant reptiles of the time. Again, the asteroid impact was random, but the evolution (and subsequent radiation and speciation) of mammals across the planet, filling the now empty niches, was directed by natural selection. Remember the term for for this type of rapid speciation is adaptive radiation, as we explored with cichlids in Lab 4.
​Evolution via natural selection was first described by Darwin (see the sidebar) as "descent with modification" as organisms that descend from an ancestor are modified over time by their environments. It is often characterized by "survival of the fittest," meaning that individuals that are best fit to their environment are more likely to survive, reproduce, and pass on their traits. If these traits increase survivability and reproductive success, we characterize them as adaptive traits. Evolutionary fitness, therefore, can come as a result of physiological, morphological, and/or behavioral characteristics, if those characteristics are adaptive. Speciation, the evolution of new species, arises as organisms collect enough new adaptive traits, that they begin to separate from their original ancestral populations. The subsequent development of reproductive barriers then leads them to develop their own evolutionarily trajectories. 
As natural selection is a deterministic process (i.e., it occurs due to cause vs. chance alone) it allows for significant explanatory power, and even predictive ability. Darwin and Wallace, independently considered a strange orchid from Madagascar with and incredibly long "nectar spur" which houses nectar at the very bottom. Independently, they both proposed that due to natural selection, a moth must also exist in Madagascar with an equally long proboscis to reach the nectar. Twenty years later, naturalists discovered a giant hawkmoth with a footlong proboscis to feed on the flower's nectar. This phenomenon, when two species influence each other's evolution, is know as co-evolution.

Charles Darwin published his book "On the Origin of Species" in 1859. Because of this, he is often credited as the founder of natural selection However, Alfred Wallace (right), a contemporary and scientific competitor, also reached the same conclusions independently.

The star orchid and the co-evolved hawk moth (photographed by Robert Clark).

Click for link to article.

Be sure you understand the two primary tenants of evolution.

Know the bold-faced terms on this page and review the images and captions.

Read the short article on Darwin and Wallace's hawkmoth.

DO you know enough about the evidence for evolution?

Evidence for evolution can be biogeographical, structural, or genetic.​ The overwhelming evidence in support of evolution comes from many scientific subdisciplines, including paleontology, biogeography, comparative anatomy, comparative embryology, and molecular biology. Each has hypotheses, based on testable, objective data, supported by evolutionary evidence, and each provides testable and objective evidence in support of evolutionary hypotheses. Recall from Lab 2, that testing a single hypothesis, even with repetition, cannot lead to a theory; it can, however, add to theoretical development. Although it was first proposed by Darwin and Wallace, it is the hypotheses tested and supported by these subdisciplines have built the theory of evolution as we know it today. Each, in its own way, contributes to ideas of change over time and common ancestry.  Review the three examples below. We will explore others in lab.

Biogeographical

How and when species arise provides evidence for change over time.

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The study of the distribution of plants, animals and ecosystems across the Earth, and the causes of variation in their distribution, is called biogeography; think, where and why. Island biogeography has provided some of the strongest evidence for evolution as seen with Darwin's finches across the Galapagos Islands. Other examples include lizards in the Canary Islands and the unique flora and fauna of Madagascar.

Darwin's finches: The different environments on various Galapagos Islands exerted different evolutionary pressures leading to different adaptive traits in the finches that occupied them, eventually leading to new species of finches on each. This is also an example of adaptive radiation, similar to the cichlids in Lake Malawi.

Structural

Shared structural forms provide evidence of shared ancestry.

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Many sub-disciplines use structural similarities as evidence for evolution. Comparative embryology is a branch of biology that is related to the formation, growth, and development of embryo. It has bolstered evolutionary theory by showing all vertebrates develop similarly and therefore have a putative common ancestor. Understand that natural selection can only operate on what already exists, it does not re-start from scratch. 

Human embryos develop gill slits and post-anal tails. The million year old genetic "instruction manual" that we share with all vertebrates, having evolved from fish (the first), programs all vertebrate embryos in the same way. However, since these features are not needed for our survival after birth, they are lost during later stages of development.

MoleculAr

Shared genetics structures provides evidence of descent form a common ancestor.

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Our understanding of the molecular evidence for evolution has exploded in recent decades as techniques have been refined. As we understand the complete genomes of more and more taxa, it clear that all life is related. Comparative genomics compares genomic features (DNA sequence, genes, gene order, regulatory sequences, etc.) acorss taxa and provides a lot of evidence for shared evolutionary relationships.

The genetic similarity of other taxa compared to humans is above (click to enlarge). Each living thing on this planet is comprised of the same nucleotides and amino acids. This provides strong evidence for a shared common ancestor. Genomics is getting us closer to defining LUCA, the Last Universal Common Ancestor.

Review the three categories of evidence for evolution and the examples provided.

Watch the short YouTube videos under biogeography (on finches) and structure (on embryos).

The last YouTube video on LUCA is posted for you to watch if you are interested.

What will we do in lab & how will we do iT?

Lab 6 contains three exercises. Each one provides more more structural support for the theory of evolution from paleontology and comparative anatomy.

1. You will explore the fossil record by categorizing and ordering fossilized specimens.
2. You will investigate homologous and analogous vertebrate forelimbs as evidence for divergent and convergent evolution.
3. You will examine and measure skulls of close human relatives to produce a phylogeny. 

​https://online.ucpress.edu/abt/article-abstract/77/2/99/18751/Vestigial-Biological-StructuresA-Classroom?redirectedFrom=fulltext 

Review "it's just a theory"

*Please come to class with an open-mind. Evolution need not be a controversial or touchy subject. Evolution and faith are not mutually exclusive; they operate in entirely different areas of human experience and  and answer different questions.

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.

Click here to get to WKU's blackboard to take your LABridge for this week.

BIOL 123: Evolution Virtual Lab 

Objectives: Following this lab you should be able to…

• Describe the key mechanisms by which evolution occurs.
• Explain the evidence for evolution via the fossil record, DNA, and biogeography.
• Describe specific examples of evolution case studies, such as the evolution of birds, whales, and humans.
• Discuss and describe human evolution.

Overview

• Exercise I. You will complete a virtual lab through NOVA on evolution. It has three parts followed by construction of phylogenic trees. You will submit four pictures of you working through each exercise and the results of your tree construction in the post-lab.

• Exercise II. You will watch a 19-minute long movie called, Great Transitions: The Origin of Humans. You will create a table of human hominids mentioned in the movie along with important notes in the post-lab.

• Exercise III. You will watch a TedTalk of your choice on evolution. You will share your thoughts in a short essay reflection in the post-lab.​

ustrate the evolutionary relationships between Australopithecus and early Hominid fossils by comparing fossil evidence.
You will first need to create a coded character matrix from the character matrix below. Then construct a phylogenetic tree to illustrate the relationships among these taxa.
Submit a Word document with the following:

• Coded character Matrix (10 pts): Must be a table create in Word or pasted from Excel.
• Phylogeny (15 pts): The phylogeny can be a picture of your hand-drawn tree pasted into the word document or drawn using any other program or software you choose.  

Use the character matrix below for this exercise:



 LINK to document.
 
Images of these specimens can be found here:
Fossil Evidence in 3D: http://www.anth.ucsb.edu/projects/human/
Smithsonian Institutions 3D Fossil and Artifact Collection: http://humanorigins.si.edu/evidence/3d-collection
Bone Clones catalog: http://www.boneclones.com/catalog-fossil-hominids.htm 
 
Adapted from: Andrew J Petto, National Center for Science Education @ https://ncse.ngo/files/pub/evolution/a_garhi_lesson.pdf
Referneces:
Features for A garhi based on Asfaw and others, 1999
Asfaw B, White T, Lovejoy O, Latimer B, Simpson S, Suwa G. Australopithecus garhi: a new species of early hominid from Ethiopia. Science 1999; 284:629-5. Groves C. 1999. Australopithecus garhi: A New-Found Link? Reports of the National Center for Science Education 19(3): 10–13. http://ncse.com/rncse/19/3/australopithecus-garhi-new-found-link

Before you begin! Open the Evolution Post-Lab. 
Follow the directions in each exercise closely so you know what to put in your Post-Lab to receive full credit for this online activity.​

• Exercise I
• Exercise II
• Exercise III

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You will be completing an evolution virtual lab through NOVA LABS. You must complete four parts of this virtual lab.

1. Introduction to Evolution. Click the Introduction to evolution tab.Watch the video, answer the questions and take notes in the space they provide. The final screen is shown in the sidebar. Take a selfie next to this screen.
2. DNA and Evolution. Click the “CONTINUE” button to proceed to Exercise III. Again, watch the video, answer the questions and take notes in the space they provide. Take a selfie next to the final screen.
3. Evidence for Evolution. Click the “CONTINUE” button to proceed to the next activity. Again, watch the video, answer the questions and take notes in the space they provide. Take a selfie next to the final screen.
4. Play Game. This “game” will take you through construction of two groups of phylogenetic trees. When you get stuck, be sure to click the magnifying glass at the bottom right. You must complete the first and second “Missions.” Once you’ve completed both, take a selfie next to the final screen showing Mission 1 and Mission 2 as complete.

The final page looks like this. Note the continue button.

Final page for selfie showing completed Mission 1 & 2.

1. Watch this 19-minute long movie called, Great Transitions: The Origin of Humans.
2. Take notes throughout, paying close attention to: the name of each hominid discussed, the scientist who made the discovery, the age, and any related human characteristics. 
3. You will be asked to put all this information into a table in the post lab.

1. Please visit this page on Evolution Based TedTalks.  (https://www.ted.com/playlists/84/ancient_clues)
2. You will find 6 different TedTalks about evolution and the origin of humans. Please select one to watch based on your interests!
3. You will complete a reflection on your TedTalk in the post lab.

The mbuna cichlids of Lake Malawi: a model for rapid speciation and adaptive radiation 

​Figure 1 Representative mbuna body shapes and colour patterns: A, Genyochromis mento feeds mainly on fish scales, OBmorph female; B, Petrotilapia sp. ‘retrognathus’ combs edible material from between strands of filamentous algae, male; C,
Pseudotropheus ater, a member of the ‘elongatus’ group, is a cryptic species living in caves among rocks, male; D,
Pseudotropheus (Tropheops) sp. ‘red cheek’ feeds with its body at about 45, scraping algae close to the rock surface, male;
E, Pseudotropheus (Maylandia) zebra is an abundant generalist feeder on rocky shores, BB-morph male of a blue-dorsal race;
F, Melanochromis auratus is a roaming opportunist that feeds within the territories of other species, female; G, Labeotropheus
trewavasae has an underslung mouth allowing it to feed close to rock surfaces while holding its body almost parallel to the
substract, BB-morph male of a red-dorsal race; H, Cynotilapia sp. ‘mbamba’ – like many other zooplanktivores, males have a
bright ‘blaze’ on the dorsal fin and upper surface of the head, probably to attract females down from the water column,
male; I, Labidochromis caeruleus uses its narrow mouth to feed on tiny invertebrates among rocks, male of white race;
J, Melanochromis labrosus feeds on small animals which it suck from cracks between rocks, probably using its thickened lips
to help seal the crack, male. Edited from photographs by Ad Konings.

Faculty Spotlight: Phil Lienesch

Dr. Lienesch often uses fish keys in his research in the area of aquatic biology.  He has have two ongoing projects; one uses macroinvertebrate communities to assess stream health at water quality monitoring stations, and the other is examining commensalism between madtom catfish and the mussels whose shells the madtoms use as shelter. Recent fisheries projects focused on the life history characteristics of White Bass and Yellow Bass in Barren River Lake. He is also interested in how anthropogenic changes to the environment and the introduction of species affect native stream communities.
​
Use of Dead Mussel Shells by Madtom Catfishes in the Green River
Effects of a Whole-lake, Experimental Fertilization on Lake Trout in a Small Oligotrophic Arctic Lake

how can we best understand the scale of geological time?

The formation of our planet occurred 4.56 billion years ago. That's billion...with a B. Humans have an exceptionally difficult "time" understanding time at that large a scale. You may have seen some of these weird timeline facts floating around on the internet. They are great examples of how bad we are at time...

• The gap in time between Stegosaurus and the Tyrannosaurus Rex was bigger than between the Tyrannosaurus Rex and you.
  
• When the first pyramids where built whilst the wooly mammoth was still walking the earth.
• The universe is 13.8 billion years old: If we compressed that into a year, then the dinosaurs would be wiped out on 29 December, and modern humans would appear at 11:54pm.
  
• If you where to compress the entire history of earth into a single year, we would only appear on December the 31st at 11:00pm ( 0.004% of the earths history).

That fact that these facts are shocking highlights just how bad we are understanding long expanses of time; our lives are simply too short to comprehend 1000s of years, much less billions.

Geological time is the expansive time scale since the creation of Earth. To make it easier to conceptualize, scientists have divided into hierarchical sections and sub sections. Eons are the largest, which contain various eras (e.g., Paleozoic and Mesozoic), which comprise periods (e.g., Triassic, Jurassic) of time. Those periods can be further divided into early, middle, or late, or into specific epochs (e.g., our current Holocene epoch). Throughout geologic time their have several mass extinction events where 70-95% of taxa went extinct. These periods were essentially like hitting the "restart button" on all life on Earth. Some argue that we are currently in a mass extinction period, term the Holocene Extinction, because our current flora and fauna are going extinct at such an alarming rate.
We will discuss biodiversity loss more in later units. In this lab you will construct a timeline of life on earth, to scale, by converting time to linear measurements in the metric system. Without this sense of the grand scale of geologic time, it is impossible to understand evolution...our next unit.

-Weird timeline facts from: Blaze Press and Tom Chivers at Buzzfeed UK

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Watch the YouTube videos on geological time.

Know the categories of geological time and examples.

Review extinction events including the Holocene.

• Exercise I
• ppExercise II
• Exercise lll

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Test 1:

1. Record your hypothesis in your Lab Notebook Guide.
2. Place a piece of filter paper inside the dish to cover the bottom.
3. Obtain five pillbugs/sowbugs from your instructor and place them in the dish. 
4. Place the lid over the dish and leave it on the table for 3 minutes so the pillbugs/sowbugs can get acclimated to their new surroundings.
5. Place a lamp directly over the Petri dish, far above the glass and lay the shade cover over half of the dish and turn on the light.
6. Record the number of pillbugs/sowbugs in the light vs. dark locations every minute for the next 12 minutes in your data sheet. Record notes as you go in your Lab Notebook Guide.
7. Paste your Excel table into  your Lab Notebook Guide and record your conclusions.

Test 2:

1. Record your hypothesis in your Lab Notebook Guide.
2. Remove the shade cover from your Petri dish.
3. Open the lid and place 5 drops of water in one spot near the edge of the dish. *​Be careful! A little goes a long way, filter paper is extremely absorbent. If you moisten more than 50% alert your TA. 
4. Replace the glass lid (but not the shade).
5. In the table below, record the number of pillbugs/sowbugs in the dry vs. wet locations every minute for the next 12 minutes in your data sheet. Record notes as you go in your Lab Notebook Guide.
6. Paste your Excel table into your Lab Notebook Guide and record your conclusions.

Test 3:

1. Shake your Petri dish to redistribute the pillbugs/sowbugs.
2. Replace the shade cover over the side of the dish away from the wet side
3. In the table below, record the number of pillbugs/sowbugs in the dark/dry vs. light/wet locations every minute for the next 12 minutes. Record notes as you go in your Lab Notebook Guide.​
4. Paste your Excel table into your Lab Notebook Guide and record your conclusions.

Exercise II. Analysis

You’ve likely made statements using terms like “more, less, lower and higher” regarding your data thus far. That is a good place to start! However, now we must ask if the patterns we see in our data...

• ...are from chance alone (i.e., pillbugs/sowbugs just moved around regardless of environment) and match the null hypothesis = [fail to reject the null hypothesis]
• ...or if they are biologically relevant (i.e., related to pillbug/sowbug preferences) and match our hypothesis = [reject the null hypothesis]

​We term potentially relevant findings as significant- that is, differences, or patterns that are significantly different from those we would expect from chance alone, may be biologically important. We cannot know whether your results are significantly different from chance, without performing a statistical analysis on your data. We will use the Chi-Square Goodness of Fit analysis to reveal which stimulus is preferred, if any, by your pill bugs. This statistic compares your distribution of data (your OBSERVED DATA) to that of a distribution you might predict from randomness, or you null hypothesis (the EXPECTED DATA).

• If the null hypothesis cannot be rejected, your observed data will be close to the expected data.
• If the null hypothesis is to be rejected, your observed data will need to be very difference from chance alone.​

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write up your findings

Chi-square formula.

Chi-square table of critical values.

Exercsie iii. Poster Creation

The scientific poster is a form of scientific expression and one way researchers communicate their work with the wider scientific community, Most often, researchers will use the poster format as a way to put their preliminary research together and test the waters of scientific critique. Posters often come before presentations and manuscripts and they are presented at scientific conferences in large halls or rooms. Attendees wonder from poster to poster, get a 5 minute brief from the researcher and then a discussion begins. The appearance/content varies widely by field or lab, but they are often produced in PowerPoint and printed as 36" x 48" posters for display.

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Your Poster: Will be created in PowerPoint using a provided template.  We will print & display the 3 best, which will earn extra credit (TBD).
Lab Groups: You will work in your lab group. You must be an active participant in this assignment. You will be evaluating each other’s contributions via a peer evaluation form at the end of the term.
​Content: Specific directions on what to include in each section are available on the poster template and the evaluation measures are available in the rubric. 
Research: 
Formatting: You have a lot of leigh way!

• Colors: Your choice.
• Length: Variable section length. Typically, the results section takes up the most space, but include the least amount of text.
• Font: Use serif font (e.g., cambria or times), non sans serif (e.g., arial or calibri)
• Font size: You can go a bit smaller/ larger but stay close to these and be consistent within levels. Title: 80-100pt., Authors: 60pt., Sub-headings: 28-58pt., Body text: 24-32pt., Captions: 18pt.
• Tables & figures: Your design! Stay clean and readable. Tables get labeled (Table 1.) with titles that go above. Figures (diagrams, graphs) get labeled (Figure 1.) with captions that go below.
• Citations: 5 minimum, directions in template.
• Be creative and have fun with this.​ Examples below!

poster template

poster rubric

A preliminary study on habitat features and associated terrestrial isopod species

Learning from the environment: how predation changes the behavior of terrestrial Isopoda (Crustacea Oniscidea)

​Evolutionary adaptation of oniscidean isopods to terrestrial life: Structure, physiology and behavior ​

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Work with your group to create a poster draft over the next week. These must be submitted to Blackboard by ONR person in your group before we meet for lab. You will present your draft, informally, to class and get feedback. You will have another week to revise before submitting your final poster. Everyone in your groups must submit a final version.

• Exercise I
• Exercise II
• Exercise lll

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Introduce yourself to your lab group. Share a contact method that will work best for everyone and discuss general availability to work together outside of class. We will continue this process in Lab 2.

Exercsie I. Animal behavior experiement

The study of animal behavior is know as ethology. As discussed in your Pre-Lab, ethological theory has two primary components: 

1. Behavior traits can be inherited or learned. We refer to inherited or ingrained behavior traits as innate. Organisms are born with these behaviors and practice them (as instinctual) from birth. Learned behaviors are developed over time as a result of experience and exposure to various stimuli.
2. Behavior changes to achieve survival (i.e., it is adaptive). Behavioral traits follow the same patterns that govern other inheritable traits. Positive traits that increase fitness, an organisms ability to survive and reproduce, will be selected for, and increase across the population. Similarly, traits that make it possible for organism to learn behaviors would also be selected for if they are adaptive.

Simple Innate: Immediate post birth behavior is always innate, like sea turtles instinctively heading out to sea.

Complex Innate: Migration timing and location are ingrained in these migratory waterfowl.

Learned: Some primates, like this capuchin monkey, have learned to use tools like this stone to open nuts.

Kinesis is a simple innate behavior wherein individuals move rapidly or slowly in response to a stimulus. If you've ever flipped a rock and watched pillbugs scurry...you've witnessed positive kinesis! Today, we will focus on the innate behavior of taxis: Positive taxis refers to movement toward a stimuli, where negative taxis refers to movement away from a stimulus. There are many different types of taxis, but we will be studying the phototaxis and hydrotaxis of terrestrial isopods. Terrestrial isopods are arthropods. Although we call them "pillbugs" and "sowbugs," they are actually crustaceans that occur in moist, dark areas, such as: forest floors, leaf and grass piles, and under dead logs where they eat detritus. Knowing the ecology of terrestrial isopods, we can make predictions about how they might perform in the lab when exposed to different environments (e.g., light vs. dark or wet vs. dry). However, we do not know which stimulus affects them the most. Do they prefer dark/dry places over wet/light places, or vice versa? Today, you will conduct an experiment to answer that question. 

Different types of Taxis

• Phototaxis: Movement toward/away from light
• ​Hydrotaxis: Movement toward ot away from water
• Phonotaxis: Movement toward or away from sound
• Klinotaxis: Movement toward or away from a concentration gradient
• Gravitaxis: Movement against or with the force of gravity
• Thermotaxis: Movement toward or away from a temperature
• Chemotaxis: Movement toward or away from a chemical
• Rheotaxis: Movement toward or away from a current

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Materials: You will be provided with pillbugs & sowbugs and should use your phones to take photos as you go and time your tests.

Test chambers.

Direct your subjects.

Provides light.

Provides shade.

Provides water.

Dampen your filter paper

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Procedure.​
Notes: Our isopods are kept in a mixed community housing both pillbugs and sowbugs. For this lab, you can use either or a mix. ​ You can use the paint brushes to direct them into your testing chambers. Tests 1 and 2 can be completed simultaneously if directed by your TA.

Test 1:

1. Record your hypothesis in your Lab Notebook Guide.
2. Place a piece of filter paper inside the dish to cover the bottom.
3. Obtain five pillbugs/sowbugs from your instructor and place them in the dish. 
4. Place the lid over the dish and leave it on the table for 3 minutes so the pillbugs/sowbugs can get acclimated to their new surroundings.
5. Place a lamp directly over the Petri dish, far above the glass and lay the shade cover over half of the dish and turn on the light.
6. Record the number of pillbugs/sowbugs in the light vs. dark locations every minute for the next 12 minutes in your data sheet. Record notes as you go in your Lab Notebook Guide.
7. Paste your Excel table into  your Lab Notebook Guide and record your conclusions.

Test 2:

1. Record your hypothesis in your Lab Notebook Guide.
2. Remove the shade cover from your Petri dish.
3. Open the lid and place 5 drops of water in one spot near the edge of the dish. *​Be careful! A little goes a long way, filter paper is extremely absorbent. If you moisten more than 50% alert your TA. 
4. Replace the glass lid (but not the shade).
5. In the table below, record the number of pillbugs/sowbugs in the dry vs. wet locations every minute for the next 12 minutes in your data sheet. Record notes as you go in your Lab Notebook Guide.
6. Paste your Excel table into your Lab Notebook Guide and record your conclusions.

Test 3:

1. Shake your Petri dish to redistribute the pillbugs/sowbugs.
2. Replace the shade cover over the side of the dish away from the wet side
3. In the table below, record the number of pillbugs/sowbugs in the dark/dry vs. light/wet locations every minute for the next 12 minutes. Record notes as you go in your Lab Notebook Guide.​
4. Paste your Excel table into your Lab Notebook Guide and record your conclusions.

Handle the isopods with care: they cannot hurt you, they are pretty resilient but be careful. Ethical treatment of animal sin our care is our responsibility.

Click to download.

Click to open your data sheet in Excel.

Exercise II. Analysis

Procedure.

1. Now it's time to calculate the chi-square value for each test.
   
2. Open your datasheet in excel. Remember, you determined your observed and expected values last week. Review your Lab Notebook you submitted for Lab 1 if necessary.
   
3. Open the second tab in your Excel datasheet. The formula is in the sidebar and the tables in Excel will help you calculate it. You will have a single chi-square value (X^2) for each test, your "test statistic." Now that you have calculated your X^2 for each test, we need to put it in context. On its own, it tells us nothing! We need to compare our chi-square value to a "critical value" that is based on probability. To do that we need two things...
4. First, determine your: Degrees of Freedom (df). For this statistical test, the degrees of freedom = number of environmental choices – 1. For this experiment, df = 2.
5. Next, determine your: Alpha (α-level). For this experiment we will use the standard alpha = 0.05 ​ 5. Now, using the degrees of freedom and alpha, consult the table of critical values in the sidebar to determine our critical value to compare to our chi-square value. Record this in your Lab Notebook.
6. If your X^2 < Critical Value = ACCEPT Ho – No significant findings. If your X^2 ≥ Critical Value = REJECT Ho – Significant findings, potentially biologically relevant 
7. Add your findings to the Lab Notebook Guide under Exercise II. Click the "write up your findings" tab in for an example of how to write up your results depending on the outcome of your test. 
8. Lastly, write up your conclusions from each test in the Lab Notebook Guide.

write up your findings

Expected vs. observed distributions.

Options for your "observed" data.

Chi-square formula.

Chi-square table of critical values.

Exercsie iii. Poster Creation

The scientific poster is a form of scientific expression and one way researchers communicate their work with the wider scientific community, Most often, researchers will use the poster format as a way to put their preliminary research together and test the waters of scientific critique. Posters often come before presentations and manuscripts and they are presented at scientific conferences in large halls or rooms. Attendees wonder from poster to poster, get a 5 minute brief from the researcher and then a discussion begins. The appearance/content varies widely by field or lab, but they are often produced in PowerPoint and printed as 36" x 48" posters for display.

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Your Poster: Will be created in PowerPoint using a provided template.  We will print & display the 3 best, which will earn extra credit (TBD).
Lab Groups: You will work in your lab group. You must be an active participant in this assignment. You will be evaluating each other’s contributions via a peer evaluation form at the end of the term.
​Content: Specific directions on what to include in each section are available on the poster template and the evaluation measures are available in the rubric. 
Research: 
Formatting: You have a lot of leigh way!

• Colors: Your choice.
• Length: Variable section length. Typically, the results section takes up the most space, but include the least amount of text.
• Font: Use serif font (e.g., cambria or times), non sans serif (e.g., arial or calibri)
• Font size: You can go a bit smaller/ larger but stay close to these and be consistent within levels. Title: 80-100pt., Authors: 60pt., Sub-headings: 28-58pt., Body text: 24-32pt., Captions: 18pt.
• Tables & figures: Your design! Stay clean and readable. Tables get labeled (Table 1.) with titles that go above. Figures (diagrams, graphs) get labeled (Figure 1.) with captions that go below.
• Citations: 5 minimum, directions in template.
• Be creative and have fun with this.​ Examples below!

poster template

poster rubric

A preliminary study on habitat features and associated terrestrial isopod species

Learning from the environment: how predation changes the behavior of terrestrial Isopoda (Crustacea Oniscidea)

​Evolutionary adaptation of oniscidean isopods to terrestrial life: Structure, physiology and behavior ​

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Work with your group to create a poster draft over the next week. These must be submitted to Blackboard by ONR person in your group before we meet for lab. You will present your draft, informally, to class and get feedback. You will have another week to revise before submitting your final poster. Everyone in your groups must submit a final version.

• Introduction
• Do you know enough?
• What will we do in lab?
• LABridge

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Science as a way of knowing

Science is a systematic way to gain new information about the natural world. It requires testable questions, falsifiable hypotheses, and objective measurement and analysis.  Pursuit of scientific knowledge therefore requires a prescribed process, know as the scientific method. You have no doubt studied the steps of the scientific method many times. They can be described somewhat differently from source to source, but contain the same basic ideas. The figure at right contains six steps with cyclical components based on outcomes.​

​Descriptions of each step are provide below

Ask a question

Questions can arise from observations in the field, in the lab, from the scientific literature (e.g., scientific posters, presentations or papers), or from pre-existing data. In this class sometimes your question will be provided to you and other times you will get to decide what questions you want to investigate.

Conduct background research

This is a literature review process, in which researchers dig deep into what is already known about their topic of choice and what questions still remain. Often, the literature review helps to refine questions and direct hypothesis formation. Background research will be provided to you for in our first few labs but you will also do some research on your own in later lab activities.

Construct a hypothesis

A quality hypothesis must be objective, measurable and testable. It must include a prediction and potential rationale (examples) based in the literature or from previous work. You will do this often in BIOL 123.

Test with an experiment

There are various approaches to research design, based on your research question. These range from purely descriptive, to experimental designs, which involve manipulation of a variable or variables. Regardless of the method selected, the design should have clearly identified variables by type, and should be both valid and reliable. You will have varying levels of input on the experiments we conduct in lab.​

Analyze the data & draw conclusion

The methods used for analysis are largely based on the research design. In the biological sciences, analysis almost always involves the use of statistical tests and graphical representations of data. We will use several different types of statistics.

Communicate your results

This last step is essential. For our understanding of the natural world to grow, new research must be shared, so others can draw on what's known, to learn more. Results can be communicated through technical reports, presentations at conferences, scientific posters, and manuscripts which appear in scientific journals. You will create many of these products throughout BIOL 123

Common Misconceptions​. 
​Although the process appears fairly simple, there are several common misconceptions can that really limit your understanding of how science works:

• The method does begin by asking a question, but not one conjured from thin air. The ideas for what questions to ask come from observations in the scientific literature, or while working in the lab or field. 
• After forming your question, you do not go go directly experimentation. Is you question relevant? What potential mechanisms might explain your observation? These answers are found in the scientific literature: What do we already know about this topic? What else can be explained, refuted, or supported?
• The scientific method, although often pictured in a straight line, is never linear. It involves multiple iterations or cycles depending on the outcomes. 
• It is also never complete without disseminating or publishing results, because the goal is to move science forward with contributions.
• It never ends in the development of a theory and biological theories do not one day become laws.

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Review the figure of the scientific method. Be sure you know the general steps and what to do depending on the potential outcomes along the way.

Be sure you review the common misconceptions listed on this page. They will be revisited throughout this course.

Make sure you know what ethology is, how it's related to ecological and evolutionary theory, and at least one good example.

Do you know enough about experimental design?

Generating a quality hypothesis is the first step to a quality research design, but all hypotheses are not created equal. It is imperative that your hypothesis be testable, objectively measurable, specific, and falsifiable. It must be accompanied by a null hypothesis and generate a prediction. It should also contain at least one potential mechanism (i.e, the cause of your observation). Lets look at example using our famous white squirrels.

​The next step is to carefully design your test to best answer your question. This will sometimes involve controlled experiments or simple data collection and analysis in case of observational studies. First you need to identify your dependent variable(s), or DVs (the variable being tested), and independent variable(s), or IVs (the variable that may influence the test variable). Next you need to identify any confounding variables. These are variables that can effect your results if they are not eliminated or controlled for. Let's look at our example again.

White Squirrel Example
Hypothesis Creation
Observation + question: I seem to see a bunch of white squirrels on campus. I wonder if there are more here than in other areas? 

• ​Incomplete Hypothesis: There are more white squirrels here than in other places because they are being fed. ​
• Correct Hypotheis: White squirrel (S. carolinensis)  population abundance at WKU is higher than in other similar areas, like EKU, because they are being fed.​
  • Null Hypothesis: There is no difference in white squirrel abundance at WKU vs. EKU
  • Prediction: If I can compare the density of white squirrels on WKU campus to that of EKU, there would be significantly more on the WKU campus.​
  • Potential Mechanism: This article says it's because they are being fed Is that why? 

Experimental Design

• Dependent variable: The number of white squirrels ​
• Independent variable: Location (WKU vs. EKU)
• Confounding variables: Days spent counting white squirrels, season and weather of sampling days, sample scheme, sampling effort, etc.
• Assumptions: The forgage (e.g., nuts), trees, and predator populations would be roughly similar. We should also sample these things to, just to be certain. Otherwise we could not rule them out as reasons more squirrels our on WKU's campus.

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Do you know enough about analyzing your results?

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Be sure you know the characteristics of a quality hypothesis and associated concepts like the null, your prediction, and the potential mechanism.

Review the White Squirrel example and make sure you can follow the reasoning involved.

Know the key concepts involved in experimental design including: DV, IV, and confounding variables.

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

Lab 1 contains three exercises

1. ​Animal Behavior Experiment: You will be provided materials and isopod specimen to conduct environmental experiments. You will test the environmental preferences of pillbugs and sowbugs in wet vs. dry, light vs. dark, and dark/dry vs. light/wet conditions. Tests will be done in petri dishes, working with your lab group.
2. Data Analysis: You will collect data throughout your tests and analyze your data using the chi-square statistical test. You will create tables and figures (graphs) of your results.
3. Poster Preparation: You will be giving a template for a scientific poster and will use it to create one for your own experiment. You will present a draft version of your poster to the class in Lab 2. 

Watch the short You Tube video and read over these 15 Natural History Traits of terrestrial isopods (pillbugs & sowbugs). Please note...these little guys cannot hurt you. They do not bite or sting and are quite gregarious & fun to work with!

If you feel confident with this material, click the bridge icon below and navigate to Blackboard to take the LABridge for week 1.Be ready to tested on this material before you go to the quiz. It is a timed assessment. * ​Please note, there is no Lab Notebook assignment for LABridge 1.

Click here to get to WKU's blackboard to take your LABridge for this week.