www.sciencemag.org/cgi/content/full/337/6103/1620/DC1
Supplementary Materials for
Personal Plants: Making Botany Meaningful by Experimentation
Laura A. Hyatt
*To whom correspondence should be addressed. E-mail: [email protected]
Published 28 September 2012, Science 337, 1620 (2012)
DOI: 10.1126/science.1215226
This PDF file includes
Materials and Methods
Supplemental Materials
Part I
Selected Personal Plant Prompts and Instructor Notes
L.A. Hyatt
General Instructor Notes:
It is a good idea to order seeds for these projects at least 6 weeks in advance of the term in which you wish to use
them. We have ordered seeds from a variety of seed companies, most recently Territorial Seed Company
(territorialseed.com) and Johnny’s Selected Seeds (johnnyseeds.com). Both of these companies carry seeds for all
the exercises described here.
These activities have been developed using six inch plastic round greenhouse pots and ProMix potting soil (with
some exceptions, see below). Pots are filled with premoistened growing mix, placed in trays and subirrigated until
seedlings are established. Subsequently, the trays are removed and plants are watered from above. The location of
pots/treatments on benches should be randomized, especially as plants get larger and may begin to shade plants
outside their pots. At least three replicates of each treatment are recommended; more are better if room is available;
it allows for other factors like disease or inattention by students.
Midstream measurements of plant height keep students engaged as the experiment is proceeding, but students must
keep track of WHICH individuals they measured each time. Given free rein, students often measure three
“random” plants each time. Some have devised a system to tag individual plants with colored wires for tracking
plants, instead of measuring each plant in the pot. When examining these data for the final report, encourage an
analysis of growth RATE (change over a unit of time). Multiple statistical tests of the effects of treatments on plant
size over time, although they provide good practice, are not advisable, statistically speaking; repeated measures
analyses are more appropriate analyses. Graphing the data by hand over time might make a good substitute
practice.
If you have the resources, other midstream measurements can be done in connection with classroom topics. We
sometimes measure chlorophyll using a handheld Minolta SPAD meter, or take a variety of photosynthetic
measurements using a Li-Cor 6400 Infrared Gas Analyzer. We also have a lab in which we measure water potential
using a pressure bomb; students have done some of these measurements on their personal plants, but plan for this
activity must be in place when planting experiments so that plants are available to be sacrificed.
Students generally count leaves and measure plant height as dependent variables. Leaf area is also a good variable to
consider. An easy way to measure leaf area is to use a flatbed scanner and NIH’s shareware program called ImageJ
(http://rsbweb.nih.gov/ij/index.html); make sure to use a reference ruler in the scanned images for interpretation.
Encourage students to harvest plants on an individual basis at the end of the experiment; multiple plants per pot, if
not all of them. Aboveground dry biomass and leaf area are both excellent indicators of plant performance. If
students place plants in individually labeled envelopes and put them in a 60◦C oven for at least 72 hours, they will be
sufficiently dry for good estimates of biomass. If they really want to keep their plants and use them for other
purposes, you may also encourage students to destructively measure some plants and get regression factors to
convert nondestructive measures into dry biomass estimates.
Depending on the design, analyses of data using block as a factor in an ANOVA test may be most appropriate; if
the instructor does not have expertise in the field, this may be where teaming up with a statistician might prove
fruitful.
Hyatt, L.A. 2012 Supplementary Materials Part I Page 2
Gardeners are often told not to plant carrots and dill next to each other. Why?
For centuries, gardeners have developed a great deal of common wisdom about how best to grow plants. The
sources of some of these ideas are not always well known; last semester, one student told me that his grandmother
always put egg whites on her plants because she said they grew better. She did this because her grandmother, and
her great grandmother had always done it. We conducted an experiment in the greenhouse last year and found
absolutely no effects of eggwhite addition on marigold growth in the greenhouse. This, of course, does not
necessarily mean that egg whites didn’t impact the grandmother’s plants in her garden with her soil, but we only had
one semester, one species, one environment; she had several generations of practice with a diverse array of garden
plants.
One of the common practices gardeners engage in throughout the world involves plant placement in the garden.
Some plants are said to do well together; eggplants and marigolds, beets and onions are common pairings. These
are called “Companion plants”. The mutual benefits of these plants may include insect repellant properties or
pollinator attraction.
At the same time, other plants are negatively recommended as pairs. Carrots (Daucus carota) and dill (Anethum
graveolens), are a plant pair to avoid, says the common wisdom. Both species are members of the plant family called
the Apiaceae. Other members of this family include coriander or cilantro, fennel, parsley and parsnips. Because of
their shared common ancestry, these are all smelly plants, and some produce compounds called furanocoumarins
that are toxic to insects or even people, in high enough doses. Might this biochemistry be the source of the noncompanion plants notion?
Activated carbon, which fish-lovers put in their aquarium filters, is very good at sopping up many toxic compounds
in soil. If we add it to the soil, plants still produce the furanocoumarins, but the chemicals don’t have any effects on
other plants because they are absorbed by the activated carbon.
Your job is to find out whether or not recommendation to avoid placing these carrots and dill together is due to the
effects of these furanocoumarins. You will be provided with several pots, activated carbon, soil, and carrot seeds.
Resources:
Toxicity of Angular Furanocoumarins to Swallowtail Butterflies: Escalation in a Coevolutionary Arms Race? May
Berenbaum; Paul Feeny Science, New Series, Vol. 212, No. 4497. (May 22, 1981), pp. 927-929.
Invasive Plants versus Their New and Old Neighbors: A Mechanism for Exotic Invasion Ragan M. Callaway; Erik
T. Aschehoug Science, New Series, Vol. 290, No. 5491. (Oct. 20, 2000), pp. 521-523.
Interactive Effects of Disturbance and Shade upon Colonization of Grassland: An Experiment with Anthriscus
sylvestris (L.) Hoffm., Conium maculatum L., Daucus carota L. and Heracleum sphondylium L.
J. Silvertown; M. Tremlett Functional Ecology, Vol. 3, No. 2. (1989), pp. 229-235.
Hyatt, L.A. 2012 Supplementary Materials Part I Page 3
Instructor notes on companion planting:
In mixed treatments, it is important to plant multiple individuals in mixed pots; at least four of each type. Initially, it
is difficult to tell the difference between the two plants, but Dill produces featherier leaves. It also makes
furanocoumarins while carrots do not, a fact that students should discover on their own through literature
investigations.
Students have difficulty with the concept that activated carbon does not prevent the production of
furanocoumarins; it merely reduces their effectiveness. Make sure to have some conversations on this matter.
You can purchase activated carbon in aquarium stores, but smaller pieces are more effective than larger ones; either
have students grind up the carbon with a mortar and pestle or purchase ground up activated carbon. We use five
grams per six-inch pot.
Activated carbon may also modify the availability of nutrients (Lau, J.A. et al. Inference of allelopathy is complicated
by effects of activated carbon on plant growth. New Phytol. 178 412-23 (2008)); you may wish to help students
explicitly add this layer of complexity to their study.
Hyatt, L.A. 2012 Supplementary Materials Part I Page 4
Should I invest in bone meal for fertilizing plants at my organic cucumber farm?
Farmers are bombarded with advertising from seed vendors, fertilizer manufacturers, pesticide and herbicide
makers, and a wide variety of other companies, seeking a piece of the farming “pie”. Organic farmers are not
excluded from this marketing barrage, either. Farming organically essentially means avoiding synthetic pesticides
and fertilizers, but there are plenty of naturally occurring products that are fair game for use in organic settings.
While plants get all the carbon they need from the atmosphere, provided they have enough light, they must get
water and other mineral nutrients (like nitrogen, phosphorus and potassium) through their roots in the soil. The
availability of these mineral nutrients can make a big difference for plants, influencing their growth and
reproduction capabilities.
Phosphorus is an important element for plant growth. It’s in DNA and RNA, important molecules in all living
things. Phosphorus is also a major component of ATP, an energy-shuttling molecule.
Phosphorus mainly comes from weathered rocks underneath the soil; it is in extremely limited supply in tropical
regions, less so in temperate regions. Phosphate miners extract phosphorus from underground and process it for
use in agricultural settings. It is also available naturally in the form of ground up animal bones, referred to as bone
meal. Plant flowering has been linked to phosphorus availability; plants with phosphorus deficiency do not flower,
but will flower when it is added.
Will adding bone meal make a difference for the productivity of cucumbers in your organic farm? Your assignment
is to design an experiment to investigate how phosphorus influences plant vigor, especially rooting and flowering.
You will be provided with potting soil, bone meal, a natural source of phosphate, and cucumber seeds (Cucumis
sativus). Read the label to figure out how much bone meal you need to mix in with your soil before planting the
seeds. The rest is up to you.
References:
The Effects of Phosphorus Deficiency on the Growth of Epilobium montanum L. D. Atkinson; A. W. Davison New
Phytologist, Vol. 70, No. 4. (Jul., 1971), pp. 789-797.
Phosphorus Acquisition and Use: Critical Adaptations by Plants for Securing a Nonrenewable Resource Carroll P.
Vance, Claudia Uhde-Stone, Deborah L. Allan New Phytologist, Vol. 157, No. 3, Special Issue: Soil Microbes and
Plant Production (Mar., 2003), pp. 423-447
Relationships between Seed Weight, Ash Content and Seedling Growth in Twenty-Four Species of Compositae M.
Fenner New Phytologist, Vol. 95, No. 4. (Dec., 1983), pp. 697-706.
Hyatt, L.A. 2012 Supplementary Materials Part I Page 5
Instructor notes on phosphorus:
The bioavailability of phosphorus from bone meal is dependent on fungal activity – if you carry this one out with
students, you may either wish to ensure that the potting soil you use has Glomus spores in it, or encourage an
experiment using bone meal and mycorrhizal spores in a two-way design.
The literature recommends adding 60 g of bone meal per 2 L of soil; encourage students to do the math to figure
out how much they should put in their soil before potting.
Make sure to get greenhouse cucumber seeds. (Diva at Johnny’s and Bella, Telegraph or Manny at Territorial).
Although they are more expensive, they’ll fare better indoors than field cucumbers might and will not need hand
pollination. Invest in some bamboo stakes, as well, for the twining vines. Students doing this project will need to
be scrupulous to keep their plants from taking over other experiments on the bench.
You do not need to plant more than one or two seeds per pot; the plants get large quickly.
Hyatt, L.A. 2012 Supplementary Materials Part I Page 6
My seed packet recommends sowing basil seeds at least 4-6 inches apart, but I can get more plants into
the garden by planting them closer. Should I ignore the directions?
Competition occurs when there is not enough of a particular resource to go around for the organisms that need it.
In the marketplace, businesses compete over customer dollars. In nature, animals often compete for food,
territories, or mates. Competition only occurs when the resources are in limited supply.
Plants respond to competition in different ways than animals do. While animals can move around and seek
resources elsewhere, plants cannot. They respond to their environment by growing differently. They may change
the size and shape of their roots, their leaves or their stems.
While water and soil nutrients can be depleted by plants using them, light is a funny resource to think about
competing for. It does not run out, yet plants can interfere with each other’s ability to obtain enough light to grow
and reproduce. Growing tall and skinny might help a plant escape from competition from others, but this might be
a costly tactic, since it takes calories to grow tall and skinny and renders them susceptible to being knocked over.
How do plants grow differently in response to competition? And does it matter if your objective is to get lots of
leaves for making pesto or a salad with basil? Your assignment is to design an experiment to investigate why we
might want to leave room between basil plants in a garden. You can grow basil seeds pretty close together – up to
50 plants in a 6 inch round pot.
You will be provided with pots, soil, and basil seeds (Ocimum basilicum). The rest is up to you. Be sure to include
replication, and to make your independent variable replicates as consistent as possible.
References:
Self-Thinning and Competition Intensity Over a Gradient of Nutrient Availability. E. C. Morris; P. J. Myerscough
The Journal of Ecology, Vol. 79, No. 4. (Dec., 1991), pp. 903-923.
Germination of the Light-Sensitive Seeds of Ocimum americanum Linn. C. K. Varshney New Phytologist, Vol. 67,
No. 1. (Jan., 1968), pp. 125-129.
How Competition for Light and Nutrients Affects Size Variability in Ipomoea Tricolor Populations. Jacob Weiner
Ecology, Vol. 67, No. 5. (Oct., 1986), pp. 1425-1427.
Hyatt, L.A. 2012 Supplementary Materials Part I Page 7
Instructor notes on plant density:
Students should use a range of densities and adjust replicate numbers. Many more pots of singletons are necessary
than of high density plantings. Encourage students to ensure that their higher density plantings have the same
numbers of plants. Students have used as many as 4 densities.
Because the number of plants involved varies by treatment (and thus variance), students may discover difficulties in
finding statistical differences between their treatments, even though they are visually obvious. To quantify size
distributions, some students have invented their own metrics that are very similar to coefficients of variance or Gini
coefficients. Having them come up with their own metric is far more meaningful than if you provide a
“professionally” invented statistic.
Some students may have heard about pinching apical meristems off basil plants, but are often not sure why they
might want to do this – They may wish to add this as a layer of their experiment.
Hyatt, L.A. 2012 Supplementary Materials Part I Page 8
Farmers often rotate legume and grain plants on the same farmland in successive years. Why?
Crop rotation is an important tool for many farmers. It is thought that planting the same crop year after year on the
same plot of land leads to decreased productivity. Because of this, farmers like to move their crops around, often
planting grain in a field one year and legumes or beans in that same field the next.
Why beans and grains and not some other combination? Nitrogen (N) is the key – it's in every single protein in
every living thing. The more N a plant has, the better it is at doing most of the jobs of being alive; that's why there's
so much N in plant fertilizers. Some members of the legume family (like beans) are known to produce nodules on
their roots that provide anaerobic (oxygen-free) environments. Some nitrogen fixing bacteria in the genus Rhizobium
can only fix nitrogen in anaerobic conditions and these nodules on legume roots are perfect hideaways for these
bacterial cells. The bacterial infection winds up "feeding" its legume host plant. Further, some of the N might also
leak out of the legume plants and fertilize the soil where they grow.
Corn, barley and other grains are well known to pull lots of nutrients out of the soil; they deplete soil quickly and
require a lot of fertilizers. They also are known to leave chemicals in the soil that can influence the performance of
crops that come after them.
How much of an effect could this possibly have in one pot in the course of a semester? Does it really matter
whether the first plant is a grain or a legume? Your assignment is to investigate how crop rotation between barley
and mung beans might influence barley growth.
You will be provided with barley (Hordeum vulgare) and mung bean (Vigna radiata) seeds and a number of pots. Your
first task is to create (at least ) two kinds of soil; one that has had mung beans growing in it, and one that has had
barley growing in it (what might a third kind be?). What are you going do with the plants once the soil has been
"created"? Consider that you will need time for both species to grow and want to be comparing the growth of
plants of the same chronological age. Remember to include replication in your plan and to quantify both your
independent and dependent variables. For the purposes of the rest of your personal plant work, two of you should
select barley, and two should select mung beans.
References:
Root and Shoot Interactions Between Barley and Field Beans When Intercropped M. P. L. D. Martin; R. W.
Snaydon The Journal of Applied Ecology, Vol. 19, No. 1. (Apr., 1982), pp. 263-272
Plant-Affecting Streptomycin-Sensitive Micro-Organisms in Barley Monoculture Soils. Stig Olsson; Sadhna
Alstrom New Phytologist, Vol. 133, No. 2. (Jun., 1996), pp. 245-252.
Influence of Plant Interactions on Vesicular-Arbuscular Mycorrhizal Infections. II. Crop Rotations and Residual
Effects of Non-Host Plants J. A. Ocampo; D. S. Hayman New Phytologist, Vol. 87, No. 2. (Feb., 1981), pp. 333343.
Hyatt, L.A. 2012 Supplementary Materials Part I Page 9
Instructor notes on crop rotation:
This experiment yields incredibly clear results, regardless of design. In response to this prompt, students have often
devised two-way experiments, with three soil types and two species, yielding six treatments that need, at minimum,
three replicates.
Ensure that students create at least two, if not three types of soil (planted in barley, planted in mung beans, planted
with nothing) and that the numbers of plants are consistent across the pots by species – this may require
overplanting and thinning over several weeks. Plant at least fifty seeds of each species.
The first crop should be harvested after about five weeks, carefully removing all surviving plants (just cutting them
at the soil surface may result in resprouting). Some very thorough students establish plant-less pots and treat them
the same as their planted pots for the first five weeks. Barley exudes alkaloids like hordenine and gramine that can
affect subsequent plant growth in interesting ways. Some bean seeds are pretreated with rhizobium spores; use your
judgment as to the use of these.
Hyatt, L.A. 2012 Supplementary Materials Part I Page 10
Is it worth paying extra for potting soil with mycorrhizal fungal spores in it?
Plants get all the carbon they need from the atmosphere, provided they have enough water and light, but they must
get other mineral nutrients (like nitrogen, phosphorus and potassium) through their roots in the soil.
Sometimes these mineral nutrients are hard to come by because they’re locked in organic (carbon-bound) forms or
complex molecules that plants can’t get at.
Fungi (we know them as yeast or mushrooms) mainly exist as tiny chains of cells called hyphae that live in between
soil particles. They and their spores are all around us all the time. Fungi are very good at breaking down organic
molecules and living tissues, extracting these useful mineral nutrients, sometimes at very high rates, often liberating
more of these minerals than they themselves need.
At least 75% of land plant species have developed ways to tap into this excess mineral supply using fungi, inviting
them to infect plant roots and exchanging photosynthesized sugar for these useful mineral compounds. In many
cases (especially forest trees and most orchids), the plants are utterly dependent on these fungi; they could not live
without them. These fungi also expand the “reach” of plants; sometimes even doubling the amount of soil surface
plants are able to exploit. These mutually beneficial relationships between plants and fungi are called mycorrhizae.
At our garden supply center, there are two kinds of potting soil; one with no ingredients added ($28), one with
mycorrhizal spores added ($30). I can also buy a pound of mycorrhizal spores for $20.
Your assignment: Design an experiment that will reveal the amount of growth improvement provided by these
mycorrhizal fungi – is it worth it to the host plants to share sugar in exchange for mineral nutrients? And is it worth
it to invest the extra money in spores or in potting soil containing fungi?
You will be provided with mycorrhizal fungi and chive seeds (Allium sp.). The mycorrhizae must be mixed in with
the soil at the time you plant the experiment; make sure that liquid draining out of pots with mycorrhizae in them
cannot mix with liquid draining out of non-mycorrhizae pots. The rest is up to you.
References:
Functional Compatibility in Arbuscular Mycorrhizas Measured as Hyphal P Transport to the Plant S. Ravnskov; I.
Jakobsen New Phytologist, Vol. 129, No. 4. (Apr., 1995), pp. 611-618.
Relationship between Root Growth of Flax (Linum usitatissimum) and Soil Water Potential E. I. Newman
New Phytologist, Vol. 65, No. 3. (Jul., 1966), pp. 273-283.
The Susceptibility of Roots to Infection by an Arbuscular Mycorrhizal Fungus in Relation to Age and Phosphorus
Supply F. Amijee, D. P. Stribley, P. W. Lane New Phytologist, Vol. 125, No. 3 (Nov., 1993), pp. 581-586.
Hyatt, L.A. 2012 Supplementary Materials Part I Page 11
Instructor notes on mycorrhizae:
Although chives are not very exciting to watch grow, they respond a great deal to the availability of mycorrhizae.
Consider that soilless mixes with and without Glomus spores are widely available – invest in a bale of Glomus-free soil
and keep it away from any other potting soil you may use. Potting soil with these spores are also common in the
marketplace, as well as potting soil with fungal suppressants in the form of bacteria (biofungicidal Bacillus subtilis).
Adding mycorrhizal granules will require that students calculate the volume of their pots, add the granules early in
the experiment, and keep the pots away from control pots, especially if subirrigation is used. We have not ventured
to compare the performance of plants growing in packaged mycorrhizal soil with plants growing in sporeless soil
with granules added.
If students are interested and microscopy expertise is available, it is possible to stain roots and look for
endomycorrhizae. Try http://invam.caf.wvu.edu/methods/mycorrhizae/staining.htm for a start.
Hyatt, L.A. 2012 Supplementary Materials Part I Page 12
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.
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.
Hyatt, L.A. 2012 Supplementary Materials Part II Page 2
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?
Hyatt, L.A. 2012 Supplementary Materials Part II Page 3
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.
Hyatt, L.A. 2012 Supplementary Materials Part II Page 4
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.
Hyatt, L.A. 2012 Supplementary Materials Part II Page 5
Week
Due for Personal Plant Project
1
Blank Notebook (10)
2
Methods Draft (10)
3
Annotated Bibliography of
Scientific Paper (10)
4
Introduction Draft (10)
5
Graph and t-test of a feature of
your plant (10)
6
Revision of Methods & Intro Due
(10)
7
Pollination/Dispersal Syndromes
(10)
8
Systematics and biogeography of
your plant (10)
9
Secondary Compounds of your
plant and its relatives (10)
10
Results and Discussion Draft (20)
11
Your final PP paper (25) and
discussion of your findings
General Assignment Information
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.
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.
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.
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.
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.
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.
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?
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
What kinds of defense mechanisms do members of your plant's family
employ? How do these work?
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.
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.
Hyatt, L.A. 2012 Supplementary Materials Part II Page 6
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.
Hyatt, L.A. 2012 Supplementary Materials Part II Page 7
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.
Hyatt, L.A. 2012 Supplementary Materials Part II Page 8
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.
2.
3.
4.
What is your independent variable?
What kind of replication are you planning?
What do you predict you will see and what is your rationale?
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.
Hyatt, L.A. 2012 Supplementary Materials Part II Page 9
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:
Plant #
1
2
3
4
5
6
7
8
9
10
11
12
Light
Shade
Sun
Shade
Shade
Sun
Shade
Shade
Shade
Sun
Sun
Sun
Sun
Leaf #
9
11
5
8
12
9
8
10
11
12
13
14
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.
Hyatt, L.A. 2012 Supplementary Materials Part II Page 10
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:
Sun
11
12
11
12
13
14
Shade
9
5
8
9
8
10
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:
Sun plants produce more
leaves than shade plants
Sun plants produce more
leaves than shade plants
16
Leaf Number
12
10
8
Sun
6
Shade
4
2
Leaf Number
14
16
14
12
10
8
6
4
2
0
Sun
Shade
0
1
2
3
4
5
6
Plant Treatment
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.
Hyatt, L.A. 2012 Supplementary Materials Part II Page 11
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.
Hyatt, L.A. 2012 Supplementary Materials Part II Page 12
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.
Hyatt, L.A. 2012 Supplementary Materials Part II Page 13
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.
Hyatt, L.A. 2012 Supplementary Materials Part II Page 14
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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.
Hyatt, L.A. 2012 Supplementary Materials Part II Page 16
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?
Hyatt, L.A. 2012 Supplementary Materials Part II Page 17