Proposal

Proposal Guidelines and Rubric

BIOL/ENVS384 Fall 2020 Updated 20/09/20 Alejandrino 1

This document provides you with additional information (to those provided by Hofmann,
2016) for writing your proposals. Specifically, it details formatting guidelines and the rubric used
in grading. One important information you should keep in mind when using Hofmann (2016) for
examples. The examples used in the book are specifically short in length for the purpose of
illustrating points. In reality, proposal sections (with the exception of the Abstract), consists of
more than one paragraph.

The table below outlines the weight of each section of the proposal.
Item Weight (%)
Title 5
Abstract 10
Specific Aims 10
Background 20
Research Design 20
Significance 10
References 10
Format 10
Content 3
Organization 2
Total 100

The following text and tables are the rubrics that will be used for evaluating the
proposals. These may also help you in making sure all the instructions are followed. In terms of
grading, “10” means the specific criterion is met. A “5” means the specific criterion is not met. A
“0” means no attempt was made to address the criterion. Finally, a “-“ will indicate that the
criterion does not apply and will not be graded.

Title
The Title must be descriptive and informative. It should also be clear and concise. It
should contain the major expected result with respect to the overall objective. The Title should
identify the focus species, if there is one or two. The Title should also stick to the specifics of the
study i.e., do not make excessively broad statements. You can try to create a catchy Title to
attract the reader’s attention, but this can often result in a misleading statement. The author’s
name, their institution, and their institution’s address must appear below the Title in the
following format (without quotes).

• “Tawfiq, A., Whittier College, Whittier, California 90608”

Question Grade Total Grade:
Is it descriptive and informative?
Is it clear and concise?
Is the major expected result included?
Are the species identified and formatted correctly (if applicable)?
The Title should not be an excessively broad statement.
Is the author’s name included and formatted correctly?
Is the author’s institution included?

Proposal Guidelines and Rubric

BIOL/ENVS384 Fall 2020 Updated 20/09/20 Alejandrino 2

Is the institution’s address included?

Abstract
Follow the outline and guidelines provided by Hofmann (2016). The Abstract should
consist of a single paragraph, with about 250 to 500 words. For clarity, boldface the overall
objective.
Even though the Title and Abstract are the first and second components of a proposal,
write them last. Both of these summarizes the proposal and it is very difficult to write summaries
without first writing the details. Rather than spend several agonizing hours thinking and writing
these two components, finish the proposal and let these naturally surface.

Question Grade Total Grade:
Is the background or known provided?
Is the unknown or problem stated?
Is the objective identified?
Is the objective in boldface?
Is the general strategy indicated?
Is the Significance explained?
Is the Abstract a single paragraph?
Does the Abstract contain about 250 to 500 words?
There should not be any References.

Specific Aims
Again, follow the outline and guidelines provided by Hofmann (2016). Unlike the rest of
the proposal, the Specific Aims section should be in list form. However, within each aim, the
description should be in paragraph format. Each aim should be in boldface and hypotheses
should be italicized.
For students using this proposal for your Senior Seminar (either this semester or next),
you must have two (2) aims. If the paper you chose to write your proposal on only has one aim,
be sure to create another new aim. If you would like additional ideas or help, reach out to me and
we can discuss.

Question Grade Total Grade:
Are the Specific Aims separate from the Abstract?
Are the Specific Aims listed?
Is each aim in boldface?
Are the descriptions within each aim in paragraph format?
Are the preliminary results or rationale summarized?
Are the hypotheses italicized?
Are the approaches included?
Are the expected outcomes included?

Background
The Background of a proposal is similar to the Introduction of a Research Paper Report.
The idea is to provide information and to logically describe the purpose of the study. This is
where the context for the research is provided (general objective, specific purpose, known, and

Proposal Guidelines and Rubric

BIOL/ENVS384 Fall 2020 Updated 20/09/20 Alejandrino 3

unknown; Hofmann, 2016). For clarity, provide the hypotheses (italicized) and make sure it is
testable. “Testable” means that there is a way to gather data and the data can be analyzed. Each
aim makes up the subsections, so be sure to separate the aims (if more than one) with clear
labels. There is no need for a summary of the Background.

Question Grade Total Grade:
Is the general objective stated?
Is the specific purpose/aim provided?
Are the knowns detailed?
Are the unknowns specified?
Are the hypotheses italicized?
Are the hypotheses testable?
Is it clear how the aim will add to scientific knowledge?
Are the References effectively used?

Research Design
The Research Design of a proposal is similar to the Methods of a Research Paper Report.
This is where the details of the planned experimental procedures are explained. If a section has to
be the most important, it would be this one. This is because this section tells the reader or
reviewer whether the experiment is feasible and testable.
Please follow Hofmann’s (2016) outline as best as possible. Per subsection, restate the
aim and hypotheses. Explain the procedures of the experiment and how each procedure is
important for the experiment (e.g., “The salinity of each tide pool observed was measured using
a Vernier LabQuest 2 with a salinity probe. The salinity was measured in parts per thousand
(ppt) and it was collected to determine whether there was a relationship with the size of Lottia
gigantea, such that smaller individuals were associated with more saline conditions.”). Don’t
forget to address any experimental methods biases. Detail how the data will be calculated and
statistically analyzed (draw on your previous experiences from other classes; e.g., “A chi-
squared test was performed to examine whether the population of D. melanogaster deviated from
Hardy-Weinberg equilibrium during the course of the experiment. A significant difference in
allele frequency between the beginning and the end will show that at least one principle of
Hardy-Weinberg was violated.”). Be explicit on your expected results. Rather than describing
alternative strategies (Hofmann, 2016), discuss alternative hypotheses. In other words, if your
results are not as you expect, what might explain the discrepancy?

Question Grade Total Grade:
Is the aim restated?
Are the hypotheses restated?
Are the procedures provided?
Are the importance of the procedures explained?
Are the procedures sound and feasible?
Are biases identified and addressed?
Are all the equipment identified?
Are the use of the equipment detailed?
Are the independent variables identified?
Are the dependent variables identified (if applicable)?

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Are the data calculations described?
Is graphing of the data explained?
Are the graphs appropriate for the hypotheses?
Are the statistical analyses identified?
Are the statistical analyses appropriate for the hypotheses?

Significance
The last part of a proposal is the Impact and Significance section. As explained by
Hofmann (2016), the overall importance of the research to science and society should be
explicitly discussed. Additionally, it would not hurt to restate how the aim will add to scientific
knowledge.

Question Grade Total Grade:
Is the aim’s addition to scientific knowledge restated?
Is the importance to science clearly explained?
Is the importance to society clearly explained?

References
As with the research reports themselves, References can differ in format. For this course,
use the following guidelines. List References alphabetically, by the first author’s last name. If
two or more References have first authors with the same last name, alphabetize them according
to their first name’s initial. If an author or a group of authors have multiple publications,
organize them by year. If an author or a group of authors have multiple publications in a single
year, organize them by month, where the earlier publication has an “a” added to the date and the
later publication has a “b” added to the date, and so on. The References must have the “hanging”
paragraph format, as shown in the examples below. There must be 18-30 primary and peer-
reviewed References. Primary means the authors themselves conducted the research. Books,
reviews, communications, and commentaries are secondary References. This means that the
authors reviewed or summarized other people’s research. Peer-reviewed means other scientists
read the research and decided it was acceptable for publication. Make sure all the References are
cited in the text and vice versa. The References must be in APA format. Be sure to credit the first
10 authors by using their names. You can only use “et al.” starting with the 11th author. If you
would like additional information, you may want to visit Purdue University’s Online Writing
Lab
(https://owl.purdue.edu/owl/research_and_citation/apa_style/apa_formatting_and_style_guide/re
ference_list_basic_rules.html).

• Journal Article:
Weinrauch, A. M., & Blewett, T. A. (2019). Anoxia tolerance in the sea cucumbers

Parastichopus californicus and Cucumaria miniata reflects habitat use. Journal of
Experimental Marine Biology and Ecology, 520, 151203.

• Book:
Levinton, Jeffrey S. 2018. Marine Biology: Function, Diversity, Ecology 5th ed. Oxford

University Press.

Question Grade Total Grade:
Are there 18-30 primary and peer-reviewed References?

Proposal Guidelines and Rubric

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Are they listed alphabetically?
Are they in “hanging” paragraph format?
Are they in APA format?
Are the first 10 authors credited?
Are the References all cited in the text?

Format
Formatting sets the initial guidelines for proposals. There is a general pattern that most
proposals follow, but many deviates in various ways. The most important format to follow is the
one provided by the instructor, editor, or publisher (Hofmann, 2016).
For proposals written in this course, there is a maximum page limit of 13-20 pages. This
may seem like a lot, but it ensures sufficient information and detail. As with any writing
assignment, the best way to start is with an outline. This will help in being organized and staying
on task. However, this does not mean that the outline is inflexible. Making modifications may be
necessary, but try to stay focused. Tables, figures, and References are included in the page limit.
In this course, proposals must also adhere to the following format guidelines. Do not
include a cover page. Use single-spacing and paragraph formats (unless indicated otherwise, see
Hofmann, 2016). Use either Times or Times New Roman fonts. Use the 12-point font size and
use one-inch margins on all sides of the page. Always use page numbers. Submit the proposal
either as a Word, Pages, or GoogleDocs document so that the above items can be assessed. If
another document type (e.g. PDF) is submitted, points will be deducted because the correct
formatting cannot be assessed.
Use the appropriate measurement units where necessary. Science uses the metric system,
so make sure units are in meters, liters, or grams. Also use the correct species scientific names.
Binomial nomenclature is the two-word system that identifies the organism’s genus and species.
Below is the scientific name of the common fruit fly written in two acceptable forms. The genus
name is always capitalized, but the species name is never capitalized. The entire species name is
either italicized or underlined, but not both. When the species is first introduced, the full species’
scientific name must be used. Subsequent mention of the species can be shortened by
abbreviating the genus name e.g., D. melanogaster or D. melanogaster. All other scientific
nomenclature like phylum, class, order, and family only need to be capitalized, e.g. Mammalia.
If the common term is used, there is no need for capitalization, e.g. mammals.

• Drosophila melanogaster
• Drosophila melanogaster

In this course, we will use the APA in-text citations format (see below). If you would like
additional information, you may want to visit Purdue University’s Online Writing Lab
(https://owl.purdue.edu/owl/research_and_citation/apa_style/apa_formatting_and_style_guide/in
_text_citations_the_basics.html).

o One author
§ “Tawfiq (2020) found that…”
§ “According to Tawfiq (2020), the…”
§ “…was not a major factor (Tawfiq, 2020).”

o Two authors
§ “Medeiros and Garcí (2020) found that…”
§ “According to Medeiros and García (2020), the…”

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§ “…was not a major factor (Medeiros and García, 2020).”
o For three or more authors, “et al.” is used. It is Latin for “and others.”

§ “Zhou et al. (2020) found that…”
§ “According to Zhou et al. (2020), the…”
§ “…was not a major factor (Zhou et al., 2020).”

o For three or more authors, “and colleagues” or “and coauthors” can also be used.
§ “Zhou and colleagues (2020) found that…”
§ “Zhou and coauthors (2020) found that…”
§ “According to Zhou and colleagues (2020), the…”
§ “According to Zhou and coauthors (2020), the…”

Question Grade: Total Grade:
There should not be a cover page.
Is the proposal single-spaced?
Is it written in either Times or Times New Roman fonts?
Is it written using the 12-point font?
Does it have one-inch margins on all sides?
Does it have page numbers?
Is it submitted as a Word, Pages, or GoogleDocs document?
Are the appropriate measurement units used?
Are scientific names properly formatted?
Is the APA in-text citations format used?

Content
For this course, Content refers to two things: relevance and clarity. Make sure every
sentence and paragraph are relevant to the proposal itself. It they are not, make them relevant. If
they cannot be made relevant, remove them. Following these guidelines ensure clear and
effective communication. Avoid vague statements or provide explanations.

Question Grade Total Grade:
Are all the information relevant to the proposal?
Are all the References relevant to the proposal?
Is the proposal clear and easy to understand? (No excessive
grammar, punctuation, or spelling errors.)

Organization
As far as Organization, follow Hofmann’s (2016) outline. Similarly, each section must
have a natural flow and each paragraph must contain a single idea. This is where an outline is
most helpful. Check to make sure the paragraphs within each section are not jumping around two
or more different ideas. If multiple paragraphs can be united into a single, larger idea, create a
subsection but keep the paragraphs separate. Check to make sure each paragraph does not go off
in tangents. Are all the sentences that follow the topic sentence related to the topic sentence? If
not, move it where it fits better or remove it altogether. Do not worry about being repetitive;
repetition provides some clarity.

Question Grade Total Grade:

Proposal Guidelines and Rubric

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Does the overall proposal follow the most common standard?
Does each section have a logical flow?
Do paragraphs contain a single topic?

BIOL384

05/04/2018

The effects of pH on the prevalence of plankton off the Cabrillo Beach Coast

Abstract

The objective of this study is to determine the prevalence of plankton in the three
different areas at Cabrillo Beach and see if there is a correlation with the concentration of pH in
each area. We also want to determine if the three areas are statistically different from one another
regarding pH. We hypothesized that the prevalence of plankton, within the three different areas
off the coast of Cabrillo Beach will differ in concentrations of pH and abundance of plankton,
such that an area with a higher pH is correlated with a higher number of plankton present. A

pH

probe was used to obtain pH values for the three sampling areas of the beach. 60 μm nets were
used to captured plankton within these areas to determine their abundance. The results showed
that there is no significant difference between the three areas (A, B, C) regarding their respective
pH values (p= 0.0507). The results of this study also showed a general trend were a higher pH
value (more basic) was correlated with a higher number of plankton within a specific area. The
opposite was also evident, were a lower pH value (more acidic) was correlated with a lower
number of plankton observed. Overall, these results can potentially contribute to further
understand the effects of global climate change on the marine environment.

Introduction

Global climate change has shown to have extreme consequences for all ecosystems on
Earth, especially for marine ecosystems. Specifically, climate change has had various
implications on the habitats of several species leading to them having to adapt or migrate to
different areas that have more favorable conditions for them to thrive on (Levinton, 2018).
Global climate change is the result of an increase in CO2 production due to burning fossil fuels,
which also results in increasing the temperature of the earth (Levinton, 2018). Atmospheric
greenhouse gases trap some of the heat energy that would otherwise go into space, causing the
Earth to warm up. The consequential increase in global temperature can result in a surge of
physical and chemical changes in the marine environment (Harley et al., 2006).

According to researchers, the continuation of atmospheric CO2 uptake is expected to
decrease the pH of ocean water. This also means that the saturation of aragonite, calcite, and
other minerals for calcifying organisms changes along with pH (Harley et al., 2006). Decreasing
calcification rates in response to increased CO2 has been observed in species such as pteropod
mollusks and zooplankters (Harley et al. 2006). The chemical changes that have occurred due to
global warming are still unclear and that is why it is essential to further study the changes in pH
and how they may affect organisms such as plankton.

Few studies have focused how the pH of seawater affects the growth rate of
phytoplankton and the ecology of marine phytoplankton. Phytoplankton are photosynthetic
planktonic protists and are composed of single celled organisms. Zooplankton are non-
photosynthetic and have skeletal structures made out of chitin, cellulose and calcium. Studies
have shown that some species have maximum growth near equilibrium pH and others have a
range of pH, where growth rate is not affected by changes in pH (Hinga, 2002). Researchers
believe that the pH of seawater may limit the rate of primary production, growth, and total

abundance of phytoplankton (Hinga, 2002). Other studies on phytoplankton and zooplankton
show that the biomass and number of taxa tends to be less in acidic areas of water, with a pH
around 4.0 (Holopainen, 1992). pH levels have shown to increase during the summer and spring
while CO2 decreases because of phytoplankton production. They also determined that alkalinity
did not affect the concentrations of CO2. Overall primary productivity has shown to increase
during spring and summer, along with a decrease in pH levels with high CO2 concentrations (Shi
et al., 2017).

So far, it is not very well known if geographical barriers play a role in lowering pH levels
and this needs to be further studied. The main objective of this experiment is to determine the
prevalence of plankton in the three different areas at Cabrillo Beach and see if there is a
correlation with the concentration of pH in each area. We also want to determine if the three
areas being observed are statistically different from one another regarding pH. It is important
because these organisms are vital for other marine organisms to thrive and the effects of climate
change may alter their function and composition. Based on what we know so far, we hypothesize
that the prevalence of plankton within the different areas off the coast of Cabrillo Beach will be
different with differences in pH in the given area, with a decrease in pH, more acidic sea water,
will be correlated to a decrease in plankton. We also expect to see a difference in pH from the
three different areas at Cabrillo Beach, such that the three areas will be statistically different
from one another.

Materials and Methods

Samples that were used for this project were collected at Cabrillo Beach California.
Materials that were used for this experiment include, nets, a pH meter, and a microscope. To
examine the prevalence of plankton found in a given area, 60 μm nets were used in order to
obtain samples of seawater. Samples were obtained for three different areas that were indicated
in Fig 1. Because we will be collecting data on three different dates, we will have a total of nine
samples that will be examined for the duration of the project. The section, within each area,
where the samples were collected were kept the same throughout the project. When utilizing the
net, the number of strokes was also kept constant, 15 strokes/sample. Each sample was then
transferred into their designated glass bottles, each labeled A, B, C for the respective area. A pH
meter was also used to record the pH of the three areas (A, B, C) and three readings were
recorded per area on each day that data was collected. The probe was placed in the water near the
shallow part of the ocean, facilitating the recording of readings. The area of water where the
probe was placed within each sample site was also kept consistent.

A microscope was then used to see the abundance of any zooplankton and phytoplankton
present in each of our samples. To do this, a subsample from our sample in the glass bottle was
examined under the microscope. Once we counted the number of zooplankton and phytoplankton
for each sample we obtained the average of the totals and created a correlation graph, looking at
pH over the average of plankton found within each area. This type of graph was constructed,
using Excel to see the correlation between pH and the number of zooplankton and
phytoplankton. We then used an ANOVA test to determine if the pH values recorded for the
three areas over a specific period are statistically different from one another. A Bar graph
(histogram) was also created to illustrate this.

Results

pH

The first ANOVA analysis established if there was a difference in pH in one area (A, B
or C) over time. In area A the pH values for the three sampling dates were not significantly
different from each other (p= 0.0692). However, in areas B and C the pH values recorded
throughout the investigation indicated that the values were significantly different within each
area (p= 1.1137E-08 and p= 2.349E-05) (Table 1). The average pH values recorded for each
area also changed over time (Figure 1). The next ANOVA analysis was utilized to determine if
there is a significant difference between all three areas (A, B and C). The results showed that
there is no significant difference between the three groups regarding their respective pH values
(Table 1).

Plankton Abundance

Regarding the number of plankton, the results showed that all the three areas were
significantly different from one another based on the number of plankton that were accounted for
in the seawater samples (Table 1). For area A the number of plankton was significantly different
(p= 0.0190) based on the data collected over the four-week period. The number of plankton in
areas B & C were not significantly different over the four-week period (p= 0.2897, p=0.3852).

Correlation

During the weeks of sampling, the results showed that there was a correlation between
the number of phytoplankton and zooplankton and pH where an area with a lower pH is
correlated with a lower number of zooplankton and/or phytoplankton (Figure 2). From our data,
area A had the lowest pH (pH= 7.74) and the lowest number of phytoplankton and zooplankton
accounted for (n=0.833, Figure 2). In contrast, area C, had the highest pH (pH= 8.29) and had the
highest number of phytoplankton and zooplankton in that area (Figure 2).

Table 1. ANOVA Analysis for pH and number of plankton observed for each area. Three reading
were recorded each data collection day and then averaged.

Figure 1. Changes in pH over the four-week period of data collection from March 2nd, 2018 –
March 30th, 2018.

6.5

7

7.5

8

8.5

9

Day 1: March 2nd 2018 Day 2: March 16th 2018 Day 3: March 30th 2018

pH

pH Values over four week period

Area A Area B Area C

ANOVA Analyses

pH Number of Plankton

Area A p= 0.0692 p= 0.0190

Area B p= 1.1137E-08 p= 0.2897

Area C p= 2.349E-05 p= 0.3852

Area A, B
& C p= 0.0507 p= 0.3262

Figure 2. Correlation graph pH vs. number of Plankton observed. Average number of
phytoplankton and zooplankton observed correlated with the pH in areas A, B &C (R2 =
0.9348).

Discussion

The objective of this study was to investigate the prevalence of plankton in the three
different areas at Cabrillo Beach and determine the correlation between this and the
concentration of pH in a given area. With the presence of possible geographical barriers and
different compositions of the three areas, we hypothesized that the prevalence of plankton within
the three different areas off the coast of Cabrillo Beach will be different due to differences in pH.
We expect to see a lower pH in the area with less plankton and a higher pH in the area with the
most plankton accounted for. At the three testing areas at Cabrillo Beach, we found that the pH
values for these areas were not significantly different from each other. The number of plankton
found at the three sampling sites were also not significantly different from one another.

Overall our results indicate that there is a correlation between the pH value and number
of plankton found in one of the three areas analyzed in this study. The bay area at Cabrillo Beach
(Area A), had the lowest pH and also had the lowest number of plankton accounted for. In
contrast, Area C which encompass the tide pools at Cabrillo Beach had the highest pH value and
the highest number of plankton found within that area and was consistent with our hypothesis.
This trend is further supported by previous studies where, the biomass and number of
phytoplankton and zooplankton were low in acidic areas of water (Holopainen, 1992). They
found that the pH of the acidic pond was between 4.0-4.5 and the main pond had a pH of 6.1-6.6
during the same period of time. Their results showed that the biomass and number of taxa was
greater in the main pond than the acidic pond (Holopainen, 1992). This could further support our

R² = 0.9348

0

0.5

1

1.5

2

2.5

3

3.5

7.7 7.8 7.9 8 8.1 8.2 8.3 8.4

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pH

pH vs. Number of Plankton Observed

hypothesis that the less acidic the seawater is, the more number of organisms are found within
that area that cannot survive under those conditions.

Based on the statistical analysis, the differences between the three areas, in regard to pH,
the mean values for the three different sampling days were not statistically different indicating
that the means are considered to be equal. The same was seen for the number of plankton found
in the three areas, where there is no significant difference among the groups indicating that the
mean for each group is the same. It can further be inferred that the seawater between each area is
actually mixing to a certain extent, contradicting our hypothesis, despite the presence of
geographical barriers and the different compositions of each area studied.

For the second day of sampling, we had no access to a pH probe and therefore had to
resort to using pH strips, which could have made our results inaccurate for that day. An
estimation on the pH value was made based on the color of the strip, using the color guide
provided. For example, as a result, it was quite difficult to make an estimation between a pH
reading of 8.00-8.99 which could have skewed the data. Because of this inconsistency, our end
results in the statistical analyses could have been inconsistent to a certain extent. Our results also
showed that there was an increase in the pH over the span of four weeks. This could possibly
indicate that various temperature changes could have played a role in the change of pH and
possibly on the abundance of plankton. For future studies on this matter, temperature may be a
variable to possibly to look into.

To further investigate the effects of pH on the abundance of plankton in these areas,
analysis on salinity and CO2 levels can also be done to measure how these variables affect the
composition of sea water and as a result affect specific marine organisms. In a study conducted
by Shi, Li, et al., 2017, low levels of CO2 increased the pH and as a result increased in
phytoplankton. Their results showed that pH levels increased during the summer and spring
while CO2 decreased because of phytoplankton production (Shi, Li, et al., 2017). In conducting
some of these future studies, we may be able to have a greater understanding on the effects of
global climate change (temperature, pH and CO2 levels) to the marine environment. In turn
having more information on this matter may be useful for conservation efforts for some species
who are on the verge of extinction.

References

Harley, C. D., Randall Hughes, A. , Hultgren, K. M., Miner, B. G., Sorte, C. J., Thornber,
C. S., Rodriguez, L. F., Tomanek, L. and Williams, S. L. (2006). The impacts of
climate change in coastal marine systems. Ecology Letters, 9: 228-241.

Hinga, KR. (2002). Effects of pH on coastal marine phytoplankton. Marine Ecology-
progress Series. 238. 281-300.

Holopainen, I. (1991). The effects of low pH on planktonic communities. Case history of
a small forest pond in eastern Finland. Annales Zoologici Fennici, 28(2), 95-103.

Levinton S. Jeffrey. Marine Biology Function, Biodiversity, Ecology., 2018.

Shi X, Li S, Wei L, Qin B, Brookes JD. (2017). CO2 alters community composition of
freshwater phytoplankton: A microcosm experiment. Science of The Total
Environment. Volumes 607–608.2017 Pages 69-77.