Prepared by Beth & Bart De Stasio December, 2002 with help from Jeff Clark.
Contents
Part I: A Few Notes
Part II: Glossary of Terms
In order of use in the paper
In alphabetical order
Part III: Discussion Questions (no answers)
The audience for the McInnes paper is intended to be practioners of ecology, in particular ecologists who work at the level of populations through ecosystems. The journal, Ecology, in which this paper was published is avidly read by this group of scientists. It is the top journal in this field.
Remember that many terms that we use in common language, such as community, have very specific meaning to scientists in this particular branch of ecology. Thus you cannot assume that you know or understand the meaning of the terms. You are urged to look through this glossary and find those terms for which you were unaware of their specific meanings. We apologize if we insult the intelligence of any of you, but scientific literacy and interest varies widely.
How scientific papers are written: Usually the methods are written first - what one actually did, then the figures are prepared from the data and the prose sections of the results are written around the figures. From there one could write either the introduction or the discussion, though usually the introduction is done next as this includes a significant, if compact, literature review which will inform the writing of the discussion. The last two things to be done will be the abstract and title, where much care is given to delivering the maximum information in a minimum of words. Why? (see next section)
How scientific papers are read (by scientists): Scientists scan article titles in print or on-line journals. Many subscribe to services that send only the table of contents of the journal. Thus the title is an extremely important mini-abstract. You might have your students bring in copies of tables of contents from different journals in the library and compare science titles to those from other disciplines.
When the scientist finds a title of interest, she or he will look to see whether the authors are known and then will read the abstract. Many scientists stop at this point. There are too many papers published to read everything of interest, but by reading the abstracts, scientists keep abreast of new discoveries and the general direction of more than just their own special field of inquiry.
If, by reading the abstract, the scientist realizes this paper is an important one for her research, she will retrieve the entire paper. If the paper is in her area of expertise, she will look first at the figures, and perhaps the prose of the results and next at the discussion. If the paper is more peripheral, she may read the whole thing straight through. If she is only interested in one particular method or technological application, only part of the methods section may be read.
Because scientists rather rarely read published papers straight through, you will find a fair bit of redundancy in them. See if you can find examples in this paper.
Ethics of science: Once scientific research is published, the authors are obligated to supply the data, methods, and allow access to specimens or reagents free of charge to other scientists.
Data: please remember that the word data is a plural noun. Datum is singular. So you should say "the data are complete" or, "the data show that moose prefer balsam fir."
The footnote: The manuscript was sent to an editor of this journal in 1990. The editor sent it out for peer review by three scientists (internationally, national borders mean little in science) who made comments on the science itself (methods, approach, data analysis), the interpretation (the discussion), and the context (introduction, were they cited?). The reviewers gave written, anonymous reviews to the editor that include a judgment concerning publishability. The editor can then: 1. publish the paper as it is, 2. tell the authors that the manuscript needs more work or that more data are needed before publishing and that the authors may resubmit the manuscript (after addressing issues raised in the reviews) or, 3. reject the paper outright. In this case, we can see that the manuscript was revised in some way based on the reviews (you can tell that also by the politic acknowledgements at the end) and was resubmitted and accepted 18 months after the initial submission.
Order of authors, is there significance to the order?: You bet!! The first author, Pamela McInnes, probably did all the work and wrote multiple drafts of the manuscript. This is her graduate work and it formed the bulk of her PhD thesis (listed in the literature cited section). Dr. McInnes did her work in the laboratory of Dr. Cohen at U. Minnesota. Dr. Cohen is thus the anchor, or last, author. Drs. Naiman and Pastor run their own research groups and were collaborators on this project. Note that the voucher specimens were deposited with Dr. Pastor. All authors would have commented on and revised the manuscript and, perhaps, the data analysis.
See also power point slides for pictures of many of the different species of organisms discussed in the paper and the separate glossary of statistical terminology.
INTRODUCTION
Herbivore: An animal that feeds exclusively on plant material, as opposed to carnivore (meat eater, like a lion) or omnivore (eats both, like a bear). Herbivores include about half of the insect species, many mammals (mice to elephants), few birds (geese, swans), mollusks, turtles, and aquatic invertebrates such as copepods and rotifers.
Structure of vegetation: Relative abundance of trees, shrubs, and grasses in a particular area as well as the physical structure (size and shape) of these plants.
Biomass: weight of living material, usually expressed as dry weight per unit area (e.g. kg/hectare after removal of all water).
Production of vegetation: The amount of the sun's energy captured and used to make new plant material per unit time (energy used for basic metabolism is not counted). Usually measured as the change in biomass per year (or other time unit). Measured indirectly by McInnes as change in stem diameter per year.
Species Composition: A list of all species of organisms in a particular area at a particular time, usually limited to one group (e.g. herbivores, trees). It does not include relative abundance of each species.
Browsing (vs. grazing): Browsers eat leaves and twigs of woody plants - things growing above ground level such as shrubs. Grazers eat grasses, sedges, and other low-growing vegetation. In both cases, neither type of herb ivory is true predation in that only part of the whole organism (the vegetation) is eaten. Browsing and grazing is rarely lethal (to a plant) in the short term, but may have long-term effects on survival and reproduction of the plant, though browsing is rarely predictably lethal. Because effects of partial predation are not necessarily predictable, the effects of browsing are the crux of this investigation. There are other ways in which animals use plants as food, such as eating fruits, seeds, roots, or sap; boring holes in woody tissue; or leaf mining.
Ecosystem: A conceptual grouping of organisms in a defined area and the many factors that affect their survival, growth, and reproduction. These factors include soil type, climate (temperature, rainfall, amount of sunlight) and presence of other organisms (competitors, predators, symbionts, food sources). Typical ecosystems include: desert, forests (rain, boreal, deciduous), open ocean, coral reef, tundra, savanna.
Community: A collection of populations of organisms of different species that interact in some way and that live in a common area. It is the interaction between the populations (predation, competition, symbiosis, scavenging) that is of interest.
Scientific names of organisms: Genus name is first and is capitalized. Species name is next. Scientific names are given for specificity - the snow geese in Michigan may be a different species than those in Scandinavia and may behave differently.
Availability of nitrogen: nitrogen is a basic nutrient needed by all plants to build plant material (particularly proteins). Other basic nutrients include carbon and phosphorus. Terrestrial ecosystems are nitrogen-limited that is, if more useable nitrogen is added to the soil, more plant biomass is produced. Nitrogen in several forms (manure, nitrate fertilizer) is added by farmers to increase crop yields (biomass again!).
Exclosure: a region of an ecosystem that has been made physically unavailable to a particular species (e.g. moose) by an investigator, or an airport manager….
Boreal plant species: Species which live at northern latitudes where precipitation is low, though snowfall is heavy, temperature range is large, and growing season is short and are adapted to living where water is often frozen and sunlight is in shorter supply. Evergreens are well adapted with water-conserving needles, the ability to use photosynthesis in early spring, and the ability to shed snow.
Soil Types (From Table 1): These terms are formed from a mixture of Greek and Latin prefixes and suffixes.
METHODS SECTION
Disturbance history: natural disturbances include fire, flood, wind, and pest damage. Human-induced disturbances include road building and other 'development.'
Canopy gaps: areas in a forest where sunlight reaches the ground due to a lack of tall trees.
Soil nutrient availability: a measure of the amount of nutrients (nitrogen, phosphorus, etc.) and whether they are in chemical forms that can be used by plants (ammonia, NH3 and nitrate, NO3 rather than nitrogen, N2).
Edge effects: the transition zone between two communities where there is a mixture of species from each bordering community. The structure at the edge is very different from that in either community. Think of the edge of a forest with all the shrubs and younger plants. You don't see that kind of under story throughout the forest.
Voucher specimens: accepted practice it to deposit examples of each species in collections that can be made available to others.
Basal diameter: the cross-sectional dimension of a stem or tree trunk at the bases, or ground level, as opposed to dbh (diameter at breast height).
RESULTS SECTION
Production efficiency: A measure of how efficiently the plants convert the energy of the sun and the soil nutrients into biomass. In this paper it is calculated as the ratio of mean yearly production to standing biomass (the biomass at one point in time). Yearly production is less than standing biomass, thus these figures are less than one.
Nutrient content of litter: subsamples of leaf fall were ground up and chemically analyzed for the amount of carbon and nitrogen. These values are expressed as a percent of dry weight (1% nitrogen, 47% carbon).
Senescence: aging and death, in this case it refers to the fall die back of the herbs and how the mass of the herbs decreases as they dry and shrivel. The drying and shriveling lead to loss of more than just water - cell walls are broken and plant material is leaches into the soil. Other material is translocated into the roots, stored for use in the next growing season.
DISCUSSION SECTION
Apical dominance of the terminal bud: Many plants grow up from a main stem (top point or apex). This top, terminal bud produces chemicals (plant hormones) that inhibit growth at lower buds. If this top is removed, upward growth at many lower buds occurs. Note how trees that have been cut at the top along roadsides (under power lines) look.
Density dependent effects on production: The amount of a particular type of plant (or other species) affects production of new plant material, often because of shading or limited nutrient availability. Thus a sapling on Main Hall Green may grow at its maximum rate, while a sapling in a forest is in direct competition with established trees for light, water, and nutrients. There is also increased risk of disease spread with increased density.
Apical dominance of the terminal bud: Many plants grow up from a main stem (top point or apex). This top, terminal bud produces chemicals (plant hormones) that inhibit growth at lower buds. If this top is removed, upward growth at many lower buds occurs. Note how trees that have been cut at the top along roadsides (under power lines) look.
Availability of nitrogen: nitrogen is a basic nutrient needed by all plants to build plant material (particularly proteins). Other basic nutrients include carbon and phosphorus. Terrestrial ecosystems are nitrogen-limited that is, if more useable nitrogen is added to the soil, more plant biomass is produced. Nitrogen in several forms (manure, nitrate fertilizer) is added by farmers to increase crop yields (biomass again!).
Basal diameter: the cross-sectional dimension of a stem or tree trunk at the bases, or ground level, as opposed to dbh (diameter at breast height).
Biomass: weight of living material, usually expressed as dry weight per unit area (e.g. kg/hectare after removal of all water).
Boreal plant species: Species which live at northern latitudes where precipitation is low, though snowfall is heavy, temperature range is large, and growing season is short and are adapted to living where water is often frozen and sunlight is in shorter supply. Evergreens are well adapted with water-conserving needles, the ability to use photosynthesis in early spring, and the ability to shed snow.
Browsing (vs. grazing): Browsers eat leaves and twigs of woody plants - things growing above ground level such as shrubs. Grazers eat grasses, sedges, and other low-growing vegetation. In both cases, neither type of herb ivory is true predation in that only part of the whole organism (the vegetation) is eaten. Browsing and grazing is rarely lethal (to a plant) in the short term, but may have long-term effects on survival and reproduction of the plant, though browsing is rarely predictably lethal. Because effects of partial predation are not necessarily predictable, the effects of browsing are the crux of this investigation. There are other ways in which animals use plants as food, such as eating fruits, seeds, roots, or sap; boring holes in woody tissue; or leaf mining.
Canopy gaps: areas in a forest where sunlight reaches the ground due to a lack of tall trees.
Community: A collection of populations of organisms of different species that interact in some way and that live in a common area. It is the interaction between the populations (predation, competition, symbiosis, scavenging) that is of interest.
Density dependent effects on production: The amount of a particular type of plant (or other species) affects production of new plant material, often because of shading or limited nutrient availability. Thus a sapling on Main Hall Green may grow at its maximum rate, while a sapling in a forest is in direct competition with established trees for light, water, and nutrients. There is also increased risk of disease spread with increased density.
Disturbance history: natural disturbances include fire, flood, wind, and pest damage. Human-induced disturbances include road building and other 'development.'
Ecosystem: A conceptual grouping of organisms in a defined area and the many factors that affect their survival, growth, and reproduction. These factors include soil type, climate (temperature, rainfall, amount of sunlight) and presence of other organisms (competitors, predators, symbionts, food sources). Typical ecosystems include: desert, forests (rain, boreal, deciduous), open ocean, coral reef, tundra, savanna.
Edge effects: the transition zone between two communities where there is a mixture of species from each bordering community. The structure at the edge is very different from that in either community. Think of the edge of a forest with all the shrubs and younger plants. You don't see that kind of under story throughout the forest.
Exclosure: a region of an ecosystem that has been made physically unavailable to a particular species (e.g. moose) by an investigator, or an airport manager….
Herbivore: An animal that feeds exclusively on plant material, as opposed to carnivore (meat eater, like a lion) or omnivore (eats both, like a bear). Herbivores include about half of the insect species, many mammals (mice to elephants), few birds (geese, swans), mollusks, turtles, and aquatic invertebrates such as copepods and rotifers.
Nutrient content of litter: subsamples of leaf fall were ground up and chemically analyzed for the amount of carbon and nitrogen. These values are expressed as a percent of dry weight (1% nitrogen, 47% carbon).
Production efficiency: A measure of how efficiently the plants convert the energy of the sun and the soil nutrients into biomass. In this paper it is calculated as the ratio of mean yearly production to standing biomass (the biomass at one point in time). Yearly production is less than standing biomass, thus these figures are less than one.
Production of vegetation: The amount of the sun's energy captured and used to make new plant material per unit time (energy used for basic metabolism is not counted). Usually measured as the change in biomass per year (or other time unit). Measured indirectly by McInnes as change in stem diameter per year.
Scientific names of organisms: Genus name is first and is capitalized. Species name is next. Scientific names are given for specificity - the snow geese in Michigan may be a different species than those in Scandinavia and may behave differently.
Senescence: aging and death, in this case it refers to the fall die back of the herbs and how the mass of the herbs decreases as they dry and shrivel. The drying and shriveling lead to loss of more than just water - cell walls are broken and plant material is leaches into the soil. Other material is translocated into the roots, stored for use in the next growing season.
Soil nutrient availability: a measure of the amount of nutrients (nitrogen, phosphorus, etc.) and whether they are in chemical forms that can be used by plants (ammonia, NH3 and nitrate, NO3 rather than nitrogen, N2).
Soil Types (From Table 1): These terms are formed from a mixture of Greek and Latin prefixes and suffixes.
Species Composition: A list of all species of organisms in a particular area at a particular time, usually limited to one group (e.g. herbivores, trees). It does not include relative abundance of each species.
Structure of vegetation: Relative abundance of trees, shrubs, and grasses in a particular area as well as the physical structure (size and shape) of these plants.
Voucher specimens: accepted practice it to deposit examples of each species in collections that can be made available to others.
TITLE
What is the purpose of this long title?
INTRODUCTION
What is the purpose of the introduction?
Where can you find the scientific questions this work seeks to address?
Is there a hypothesis that forms the basis of the investigation?
What does Figure 1 say?
Does it help to see these interactions in the form of a drawing? Why? Compare the interactions of this figure with that of Bishop's poem "The Moose" or to interactions described by Leopold. What are the relative strengths and weaknesses of each type of description? Why might McInnes and Pastor have chosen to use this diagram as the first figure of the paper?
If Figure 1 reflects the real interactions in this ecosystem, what happens if the moose population increases significantly?
STUDY SITE
What kind of information is given in this section? Why?
Why are there so many references cited in this section?
Why is it important to include Figure 2?
METHODS
Why do the authors use as much as 2 1/2 pages to describe the methods of their work? No other artist of author we studied in Freshman Studies provided such information; why not?
Table 1 is referred to in this section. Are there important or relevant differences between the four exclosure sites? What are they? Why might they be relevant to the results or interpretation of the results?
Why are measures of tree, shrub, and herb heights relevant?
RESULTS
Using one or two of the figures or tables from this section, imagine what the raw data would look like. Create an imaginary page from the lab notebook that would correspond to the data in the table or figure. What measurement s needed to be taken? How many times? How much work is represented by the data presented in this table or figure? What kind of data analysis was done to create the figure or table?
Why do the authors need to use statistical analyses? Why do they report P-values?
Where do the authors use replicates? Why? Are the four study sites replicates?
Compare the sets of figures 3-5. What is the message of these figures? Would it have been misleading to show simply the "overall" average production figures (the last bars in each graph)? Why or why not?
DISCUSSION
Which type(s) of plant (tree, shrub, herb) is most affected by moose browsing? What data from the results section support this interpretation? How are these data summarized in the discussion section?
So what? Why should we care about litter production in areas browsed by moose?
What are the long-term consequences of moose browsing? What would you expect the boreal ecosystem to look like after another 20-50 years?
What suggestion for moose population management do the authors make implicit? Why do they need to make this suggestion?
Locate several unsubstantiated claims (or hypotheses) that the authors use to explain differences in results between the four study sites. Why is it appropriate that these claims are found in the discussion section? What purpose might they serve? Or, how does the inclusion of these statements fit with what you know about the process of science ("the scientific method").
ABSTRACT
What is the structure of this section? What is its purpose?
General Questions
Find examples of redundancy in this paper. Why do you think the authors chose to repeat some information multiple times?
Both the Leopold text and the McInnes paper are studied in Freshman Studies as examples of "science." In what way are these works similar? In what ways do they diverge? Do you think both illustrate scientific investigation? Why or why not?
In what way do you think the Leopold text might have been an important precursor to the McInnes paper?
Based on these two works, what do you think science is? How is it done? Is it always easy to tell science from non-science? Compare these answers to those for other academic disciplines such as social science, humanities, or fine arts.
31 December 2002