supplemental materials part ii lab manual extract l. a. hyatt

Supplemental Materials

Part II

Lab Manual Extract

L. A. Hyatt

Instructor notes on lab manual:

We require students to purchase a handbook for writing in Biology for our introductory course sequence. We have

used both K. Kinsely, A Student Handbook for Writing in Biology (Sinauer Associates, Sunderland, MA, ed. 2, 2005) and

J.A. Pechenik, A Short Guide to Writing about Biology (Pearson Education, New York, ed. 5, 2007). This book is

referred to throughout as “your Biology writing manual.” We also use Microsoft Excel to help students organize,

record and display their data; any spreadsheet and graphing program you and your students are comfortable with

would be appropriate.

Hyatt, L.A. 2012 Supplementary Materials Part II

Personal Plants: An Introduction Question: How do we use experiments to investigate scientific questions? Concepts: Experimental Design Plants and Seeds This week, you will be given a set of seeds and a question that you are assigned to explore. Your lab group's job this week is to plan an experiment that will allow you to test your hypothesized answer to that question. As we proceed through the semester, you will do various things with your personal plants in addition to this experiment. Creativity (not mindless destructiveness) will be rewarded. You will have nearly unlimited access to the greenhouse to tend to your plants during the semester. What makes a good experiment? For our purposes, a good experiment only changes one factor. The factor we manipulate is called the independent variable. For instance, if we were testing the hypothesis that hummingbirds were flocking to my hummingbird feeders because they were getting calories from the solution I put in the feeders, a good experiment would change the calorie content of the solution in the feeders. A experiment changing the calorie content, the location AND the appearance of the feeders all at once would be hard to interpret. The factor should be related to the hypothesis. In the example above, my hypothesis concerns hummingbirds and calories, not feeder appearance. Manipulating the appearance of the feeder will not tell me anything about whether or not my hypothesis is supported. You should be able to put a number on the factor you manipulate. In the hummingbird example, if I decided to add "more" sugar to my hummingbird feeders, I would need to know exactly HOW MUCH I added and how much was in there originally. Otherwise, I (and other scientists) would not be able to change it in the same way again. The response to the manipulated factor is quantifiable. The way we measure the response to the manipulated factor is to monitor the value of one or more dependent variables. In the hummingbird case, we might measure hummingbird visits per hour, or duration of hummingbird visits. In your experiment, there are many different dependent variables possible to measure. You need to select at least three that you will be measuring in your experiment; some on an ongoing basis, some as a final, destructive measurement. Be able to describe why you think your independent variable will impact your dependent variable. You perform your manipulation on more than one individual. Biology is a messy, noisy process. There is a lot of variability in biological processes, and in order to take that into consideration, we need to run our experiment on more than one individual at a time. This is called replication. At least one unit of your experiment does not experience any manipulation at all. We need "baseline" information in order to compare the effects of our manipulation to something. This is called an experimental control.


Write down your question and the plants you will be using: Come up with an hypothesis and a prediction related to your question: Hypothesis (an A because B statement): Prediction (an if C then D statement): From your prediction, what is/are your independent variable(s)? What are your dependent variables? How are you going to manipulate your independent variable(s)? How are you going to measure your dependent variables?


Draw a diagram that represents your experiment. Make sure that it meets all the criteria listed on the previous page: 1. One factor 2. Hypothesis-related 3. Quantifiable Independent Variable 4. Quantifiable Dependent Variable 5. Replication 6. Control

Your assignment for next week is to describe your experimental design in the form of a "Methods" section in a scientific paper. See the relevant section in your Biology writing manual. This should be one page or less. Some tips:

1. Write in the third person passive and past tense. This means "Seeds were planted" NOT first person active "I planted seeds". Write as if the whole thing has already been completed, even though some of this will take place in the future.

2. When you write the name of the species in your methods section, italicize or underline it: Alliaria petiolata. If you want to abbreviate thereafter, shorten the genus name: A. petiolata.

3. Give appropriate details (numbers of pots, numbers of seeds, date of planting, pot size) and omit inappropriate details (tape color, label coding). Appropriate details might impact the outcome of the experiment if someone else were doing it to replicate, inappropriate details would not.

4. Be sure to include the independent and anticipated dependent variables. Give enough details about the units of your independent variable to help the reader understand what you plan to do, even if it has yet to be implemented.

5. Read your methods section out loud. Does it make sense? Does one sentence flow into the next? Is it organized into paragraphs with topic sentences followed by supporting details? Use what you've learned in your writing classes here.


Personal Plant Notebook For this project, you are required to get and maintain a personal plant notebook that remains in the lab at all times. In this notebook, you should record all notes and data on your personal plant, as well as copies of all completed assignments that have been returned to you. This notebook should never leave the lab or greenhouse. If you need information from that notebook to complete an assignment, copy the information into another format and take it home with you. Everything you learn about your personal plant should eventually get entered into this lab notebook. You will start using your lab notebook this week. To begin, transfer everything on the previous page to your notebook. Planting your personal plant seeds Many of you have probably not planted something since putting bean seeds in paper cups for Mother's Day presents during elementary school; have no fear, it's still just about as simple, although you need to consider the species you'll be planting. Fill your pots with moistened soil from the bucket (your lab instructor will show you how) and label the pots with your name (and your plant species). Plant seeds in each of your pots as your experimental design requires You should plant your seeds 2-3 times their thickness. Thus, if you're planting a bean seed, you need to plant it about an inch deep. If you're planting a tiny basil seed, you need to place it on the soil and sprinkle it gently with a little soil. Do not pack the soil into your pots or over the top of your seeds; remember that the plant needs to grow its way out of the soil you put on top. You are expected to visit your pots at least every other day during the week and initially record in your notebook when and how many seeds germinated. Because seeds can get dislodged and seedlings can get squashed when being watered too aggressively, we will be subirrigating your plants for the first couple of weeks; they'll be watered from above once they've gotten established. Use your notebook to record the dates and times of your visits and your observations. As the semester proceeds, the kind of information you record may change; plant height, leaf number, stem thickness or other parameters may turn out to be important to record, depending on your experiment. At the end of the semester, it is likely that you will want to harvest, dry and weigh your plants to estimate their total biomass. This will kill the plant, and if you want to place it in the garden, or take it home with you, you may want to harvest only a subset of your plants. Further, you may have more than one plant in a pot. In order to estimate variability in your plant's response to your treatments, you'll need to harvest more than one and to harvest them individually. You will hear more about this later.


Week Due for Personal Plant Project General Assignment Information

1 Blank Notebook (10)

You will be recording information and observations about your personal plant in this notebook throughout the semester; it is essential that you have this available on the first day and that you leave it in lab all the time.

2 Methods Draft (10)

For this assignment, you are to describe of your experimental design in the form of a scientific paper's Methods section (see your writing manual). This work will eventually become the methods section of your final personal plant paper. It may change during the course of the semester, but this is your opportunity to get everything you did down on paper. You will receive further instruction on how to write a good Methods section during lab time.

3 Annotated Bibliography of

Scientific Paper (10)

See the lab manual for directions on how to write an annotated bibliography entry. You will be searching for a paper about the question you are investigating and/or the species you're working with. You are also expected to be keeping a daily log about your personal plants.

4 Introduction Draft (10)

For this assignment, you are to write a draft introduction to the scientific paper based on your personal plant work. Your Biology writing manual will provide important assistance. You may wish to cite the scientific paper that you found last week in your introduction. Remember that, in general, introductions to scientific papers start broad (what's the big question?) and end narrow (how are you going to seek an answer). Use the papers you read last week as models.

5 Graph and t-test of a feature of

your plant (10)

Take an appropriate measurement of plants from your two different treatments. Make a graph that shows the average readings for plants in your two treatments, conduct a t-test to compare them, and then interpret your findings. You will be doing similar work for lab as well.

6 Revision of Methods & Intro Due

(10)

You will now be revising your methods and introduction section based on comments provided to you earlier on in the semester, your experience with scientific writing from your annotated bibliography, and what you now know about how your experiment is coming along. You will be asked to fill out a checklist before handing in your revision to make sure that your writing covers all the bases.

7 Pollination/Dispersal Syndromes

(10)

Do some research on your plant's background. How are your plant's flowers pollinated? Are its flowers single sexed or hermaphroditic? What is the main pollinating agent for your plant? How are its seeds encased in fruits? How do those fruits get broken apart and seeds distributed in nature?

8 Systematics and biogeography of

your plant (10)

Do some research to investigate how your plant fits into the big picture of life – what Kingdom, Division, Subclass, Order, Family, Genus and Species is your plant in? For each hierarchical level, name a plant that shares that level but none of the levels below. Some of this information may be appropriate to add to either your Introduction or your Methods section of your final paper. You will also discover where your plant evolved, geographically speaking

9 Secondary Compounds of your

plant and its relatives (10)

What kinds of defense mechanisms do members of your plant's family employ? How do these work?

10 Results and Discussion Draft (20)

Now that your experiment is complete or nearly so, now is the time to summarize the results. You'll be making figures, calculating statistics, and crafting sentences that clearly summarize your main findings. You'll also be submitting an outline of the main topics you will cover in your discussion.

11 Your final PP paper (25) and discussion of your findings

You will now put all of your work together into one large document and discuss your major findings with the rest of the members of your lab. You are also expected to provide a summary of how your paper changed from its original draft.


Personal Plant Project: Annotated Bibliographies

Select one of the papers listed on the experiment assignment sheet you received at the beginning of the semester and placed in your personal plant notebook. Each member of your group should select a different paper. Your assignment for next week is to create an annotated bibliography entry for that paper. A bibliography is a list of sources (books, journals, websites, periodicals, etc.) one has used for researching a topic. A bibliography usually just includes the bibliographic information (i.e., the author, title, publisher, etc.). In contrast, an annotated bibliography includes a list of sources in proper citation format AND a summary and/or evaluation or each source. Why write an annotated bibliography? It will help you learn a lot more about your topic. Just collecting sources for a bibliography is useful, but when you have to write annotations for each source, you're forced to read each source more carefully. You begin to read more critically instead of just collecting information. Your annotation needs to answer the question "What is this paper about?" You cannot just cut and paste the abstract to get this job done. Your annotated bibliography needs to address the following points in one page, using paragraph form: Summarize: What is the question being asked? What methods were used to answer the question? What did the authors find to be their main result? Evaluate: How is this paper related to your investigation? How would it contribute to either your introduction or your discussion? How might you use it to support or reexamine your findings? Begin your annotated bibliography by providing its citation in proper format. Refer to the citation system your instructor prefers. Do not cut and paste the http: link that your search engine provides. You will have to rearrange the information on the experimental design sheet into the proper order.


Personal Plant Project: Writing an Introduction Your personal plant assignment for this week is to write a draft of an introduction to your final paper. How can you do that when you haven't even done the experiment yet?? It may well be the best time to do it. Your mind is not clouded by what your data is telling you and you can think clearly about the bigger questions. When writing the introduction to a scientific paper it is useful to keep an inverted triangle in mind. Your introduction begins broadly, addressing the general principle that you're investigating. Subsequent sentences and paragraphs narrow down the particular resources you're manipulating and why those might be important, the species you're using to ask those questions and why they might be important, and then finally the particular questions you're aiming to ask, and how you're going to investigate them (in general). You never write an introduction out of thin air. You have background information from your initial assignment, you can look up issues in your text book, you can search the library for books and articles. You've already written an annotated bibliography that forced you to focus on the relevance of a particular reference; use it! Your introduction is also a guide to the organization of the rest of your paper. Each question your introduction poses should be answered in the same order in the methods (how did you do it?) and results (what did you find out?) sections. You may change your organization in later drafts, but use this opportunity to organize your thinking and your data collection. Your introduction will be graded on a 10-point basis. See your Biology writing manual.


Part II: Comparing Midstream Treatment Effects To give you some practice in measurement and analysis, you will be measuring the effects of your treatments through quantitative dependent variables. Given the design of your experiment, you should make a prediction about what kind of effects you might see on your plants. Before you begin to take your measurements make sure that your group has worked out:

1. What is your independent variable? 2. What kind of replication are you planning? 3. What do you predict you will see and what is your rationale? 4. How are you going to control all other factors?

Your homework for this week is to construct a graph, conduct a statistical test to determine whether you saw the differences you expected, and to explain in words what you expected and saw.


Personal Plant Project: Graphs and Statistical Tests. "A picture is worth a thousand words" Scientists use graphs to show results of observations or experiments in a visual way. Although it is really easy to use software to make graphs, it is also really easy for software to generate graphs that make absolutely no sense and lead the reader to make a misleading or incorrect conclusion about your data. Thus, you have to use that thing between your ears before making a graph! The first question you want to ask yourself when making a graph is: What is the question I want this graph to answer? Your question will often take the form of "In what way does x influence y?" In scientific jargon, we refer to x, the influencER as the independent variable. Likewise, we refer to y, the influencED as the dependent variable. We're often implying, in graphs, that the independent variable, which we control, is responsible for changes we see in the dependent variable, which we measure {this is not always the case!}. In graphs, we usually show the independent variable on the horizontal x-axis and the dependent variable on the vertical y-axis. Sometimes the independent variable only takes on two values: treatment applied and treatment not applied. Other times, we use a range of independent variables: low, medium and high, for instance. These are CATEGORICAL values. In other cases, often when we are making observations, rather than undertaking experiments, we have MANY different values of the independent variable: salinity ranges from 0 to 500 parts per million and we may have single observations of a dependent variable at many different salinities. In this case, we consider the independent variable to be CONTINUOUS. So, you need to compose the question you want the graph to answer in such a way that you know how your graph is constructed – what are the y- and x- axes showing? The second question you need to ask yourself is: What is the answer my data provides to this question? You need to look at your dependent variable measurements to answer this question. In all likelihood, you have measured values of your dependent variable for more than one value of your independent variable. For example, you may have asked the question "how does light availability influence leaf number?" This might have led you to count the number of leaves on 6 plants growing in the sun and leaf number for 6 plants growing in the shade. What if your data looked something like this:

What kinds of trends are visible to you with the data in this format? It is difficult to see any kind of trend with all your numbers jumbled up.

Plant # Light Leaf # 1 Shade 9 2 Sun 11 3 Shade 5 4 Shade 8 5 Sun 12 6 Shade 9 7 Shade 8 8 Shade 10 9 Sun 11 10 Sun 12 11 Sun 13 12 Sun 14


How about rearranging the data in a table with one column for each value of the independent variable?:

Do you see any trends now? It is nearly always extremely useful to rearrange your data to help you visualize what it's telling you. How could you put the trend this table shows into words? You might say that "there appear to be more leaves on sun plants than shade plants". Your graph, then, should send this message loud and clear. This brings us to our third question: How can I show this most effectively? There are two ways you could show these data in a graph. One mumbles your message, and the other shouts it:

Which do you think sends the message more effectively? The left hand graph shows all the data we have, but the independent variable is not clear (unless you look at the legend). It's also very busy, containing 12 bars and two different styles. This is just hard to look at. Think back to our discussion about the question your graph seeks to answer. Our Independent variable here is light conditions, so that is what belongs on the x-axis, not plant number. The right-hand panel shows that very well. Another virtue of the right-hand graph is that each bar summarizes the information about 6 plants. This takes our rearrangement of the data to the next level by coming up with a single number that highlights the essential differences between sun and shade leaves. In this case, I've chosen to show an average for each category. An average is calculated by adding up all the leaf numbers for all plants in each category and dividing them by the number of plants on which I counted leaf number. I could have shown a sum, or a maximum or a minimum, but in general, an average expresses differences between groups of individuals most effectively. What are those little hats on the bars? Those hats also summarize information shown on the left hand graph in a much more effective way. The hats are referred to as error bars; they show the amount of variation among individuals that I measured. If the stems on the hats are really long, that means that there is a lot of variability. If the stems are really short, that means that there isn't much variability. There are several different numbers you can calculate to show this variation; the graph above shows something called standard error, but it's slightly easier to calculate variance or standard deviation. They all obey the property of having large values when variation is high.

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Educated graph consumers can also use the size of those hats to "guesstimate" whether or not the differences in dependent variables between the two independent variable groups are real and likely to be repeatable, or whether the observed differences just happened at random and could come out differently in another sample. Notice: I have yet to turn on a computer or run any kind of program. All this is happening on pencil and paper (and maybe calculator). The next question you need to ask yourself is: How certain am I that the answer to my question is real and repeatable? This question of certainty requires the use of statistics. As scientists, we can never prove a hypothesis to be absolutely true. This is the glory AND the agony of science. We are only ever able to obtain evidence that refutes a hypothesis, we cannot ever prove it. For this reason, science is always changing and hypotheses are altered all the time. Likewise, statistics can only quantify our certainty about an answer, but we can never be 100% certain. There are two main kinds of statistical tests you may get to carry out this semester and they are closely related to each other. They are t-tests and ANOVA tests. Although they use different mathematical procedures, they both come up with a P value, which represents the probability that the average value of a dependent variable is the same across groups. T-tests compare two groups and ANOVA tests compare more than one group. For a t-test, if the P value is really small (less than 0.05), the probability that our two groups have the same average value is very small; we may say that the two groups are "statistically significantly different" and we would be likely to get a similar outcome if we conducted a similar experiment at another time. If the P value is larger (more than 0.05), the probability that our two groups have the same average value is quite high; we might say that the two groups are "not statistically significantly different". The same holds for an ANOVA test. Once you've sketched out your question, your trend, your desired graph structure, and your statistical test, you can fire up the computer to make those dreams come true. Your lab instructor may show you how to use a computer program to accomplish what you want. Just as for the labs you conducted today, your assignment is to measure the chlorophyll content of plants in your experiment and to report your findings as a graph, test them with a statistical test, and then explain them in words.


Personal Plant Project: Revising This week's personal plant assignment is to revise the sections of the paper you've already written (the Methods and the Introduction). Revising does not mean correct the grammar and spelling mistakes that were pointed out to you, although that's an important last step. To revise your paper sections, follow the following steps:

1. Read your instructor's comments. Carefully. If you don't understand any words, see your instructor for a translation.

2. Put into words why your original drafts did not get full points. What was missing? Is the language you're using appropriate? Did you use the inverted triangle structure?

3. Outline your original writing; what does each paragraph say and is it summarized in the first sentence? It might be in the last sentence of the paragraph; check there!

4. Examine your original outline and make a new, more desirable one. 5. Rewrite the section based on your new outline, spell- and grammar-checking along the way. 6. Read your section OUT LOUD. Does it make sense? (for figurative bonus points, read it out loud to a

friend who will tell you when you stop making sense). Change it so that it makes more sense 7. Read your section OUT LOUD AGAIN. New problems might crop up; be willing to repeat this several

times. For full (10-point) credit, your revision must be substantial and make improvements to the document. Don’t forget how to do this! For full credit, your final paper must be introduced by a short statement outlining the modifications you made to the drafts of the various sections of your paper before the final version and how they improved the effectiveness of your writing.


Personal Plant Project: Pollination and Dispersal Syndromes Now that we've taken a look at flowers and fruits in a wide variety of species, this week's personal plant assignment is to take a look at how YOUR plant reproduces. Instead of writing a paper, this week, you need to make up a one-page fact sheet about your plant's sex life.

• Determine what your plant's flowers look like. Are they perfect? Monoecious? Dioecious? Complete? Incomplete? A picture might help you tell this story.

• Determine how your plant and its relatives are pollinated. Wind? Insects? What kind of floral traits does

your plant have that enhances pollination? What do some common pollinators look like? Does it have any particular outcrossing mechanism?

• Determine what your plant's fruits and seeds look like. What's the average seed mass and its variation (hint:

you calculated this a long time ago)? How many seeds occur in each fruit? How variable is it? Is your fruit superior? Inferior? Dry? Indehiscent? How many ovules does it have and how many seeds can it set?

• In nature, how do you suspect that the fruits might leave the parent plant? Are there any particular fruit

traits that might send the fruits and seeds to any particular location? Or predispose them to be eaten by a particular disperser?

A well-executed fact sheet is worth 10 points. You may use pictures and text, but only one side of a page (no fonts less than 10 point, please). Ask for help if you need it.


Personal Plant Project: Systematics and Biogeography This week's personal plant assignment is designed to help you figure out where your plant fits in with other plants, evolutionarily speaking. As discussed in class, plants are classified into nesting, mutually exclusive boxes that group closely related plants in similar boxes. In an ideal classification system, all members of a particular box include all descendents of a shared ancestor. The biggest organism box for plants is the Kingdom: Plantae. The Plant Kingdom is subdivided into smaller units called Subclasses. We're interested in the major divisions called the Anthophyta, the flowering plants but other divisions include the Coniferophyta (conifers), the Pterophyta (ferns) and the Ginkophyta (the ginkgos). The division Anthophyta is divided into two smaller units called classes: the Magnoliopsida (the dicots) and the Liliopsida (the monocots). Each class is subdivided into subclasses. Magnoliopsida

• Magnoliidae • Hamamelidae • Caryophyllidae • Dilleniidae • Rosidae • Asteridae

Liliopsida

• Alismatidae • Arecidae • Zingiberidae • Liliidae

Each subclass is divided into Orders and the Orders are divided into Families. These are too numerous to list here. You were given the genus and species name of your plant the first week of class. Your homework is to use any resources at your disposal (plants.usda.gov is a great place to start) to figure out what Class, Subclass, Order and Family your plant is in. For each level (Class, Subclass, Order and Family), name a plant that shares that group but none of the lower-level groups. For example, my plant is Alliaria petiolata. It is in the Family Brassicaceae, Order Capparales, Subclass Dilleniidae and Class Magnoliopsida. Another plant in the Brassicaceae family is Brassica oleracea, otherwise known as broccoli. It's a different genus, but the same family. Another plant in the Capparales order is Caparis spinosa, otherwise known as caper. It's a different family (Capparaceae) but the same order. Another plant in the Dilleniidae subclass is Vaccinium angustifolium, otherwise known as blueberry. It's a different order (Ericales) but the same subclass. Finally, another plant in the Magnoliopsida class is Pylostyles thurberi, otherwise known as Thurber's stemsucker. It's in a different subclass (Rosidae) but the same class.


Personal Plant Project: Secondary Compounds As you learned when you investigated your plant's systematics, plants and all living things are categorized and classified into mutually exclusive, nesting layers of organization. Ideally, all members of one particular level of organization share a common ancestor. Because all members of a genus, or family, or order, or class all share common ancestry, they share common evolutionarily-derived traits. We can often use these traits to help us to make good guesses as to which group a plant belongs. Your job this week is twofold. Answer each part with a brief paragraph, citing your sources in Name, Year format as described in you Biology writing manual. NO WEBPAGE CITATIONS PERMITTED, except for figures. While you may seek information using the web, back it up with a published paper source. Part I: Determine what chemical traits are shared by your plant and its close relatives. What do these chemical compounds do to the organisms they're directed towards and how else might we use them? Part II: Determine some of your plant's better-known relatives – are they in the same genus? Family? Order? Why are they better known or important? Why are they interesting botanically, horticulturally or agriculturally?

supplemental materials part ii lab manual extract l. a. hyatt

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