Now you are (almost!) ready to read your scientific article!

Now you are (almost!) ready to read your scientific article! This powerpoint will help you prepare to read a scientific article, specifically for the purpose of writing a Natural Inquirer article. Note: This powerpoint is heavy on text, and is longer than previous powerpoint sessions. Be prepared! You may want to divide it into two sessions.

EFFECT OF CLIMATE FLUCTUATIONS ON LONG-TERM VEGETATION DYNAMICS IN CAROLINA BAY WETLANDS Chrissa L. Stroh1,4, Diane De Steven2, and Glenn R. Guntenspergen3 1Master of Environmental Studies Program The College of Charleston Charleston, South Carolina, USA 29424 2USDA Forest Service–Southern Research Station Center for Bottomland Hardwoods Research Stoneville, Mississippi, USA 38776 3U.S. Geological Survey–Patuxent Wildlife Research Center Laurel, Maryland, USA 20706 E-mail: glenn_gtenspergen@usgs.gov Abstract: Carolina bays and similar depression wetlands of the U.S. Southeastern Coastal Plain have hydrologic regimes that are driven primarily by rainfall. Therefore, climate fluctuations such as drought cycles have the potential to shape lonterm vegetation dynamics. Models suggest two potential longterm responses to hydrologic fluctuations, either cyclic change maintaining open emergent vegetation, or directional succession toward forest vegetation. In seven Carolina bay wetlands on the Savannah River Site, South Carolina, we assessed hydrologic variation and vegetation response over a 15-year period spanning two drought and reinundation cycles. Changes in pond stage (water depth) were monitored biweekly to monthly each year from 1989–2003. Vegetation composition was sampled in three years (1989, 1993, and 2003) and analyzed in relation to changes in hydrologic conditions. Multi-year droughts occurred prior to the 1989 and 2003 sampling years, whereas 1993 coincided with a wet period. Wetland plant species generally maintained dominance after both wet and dry conditions, but the abundances of different plant growth forms and species indicator categories shifted over the 15-year period. Decreased hydroperiods and water depths during droughts led to increased cover of grass, upland, and woody species, particularly at he shallower wetland margins. Conversely, reinundation and longer hydroperiods resulted in expansion of aquatic and emergent species and reduced the cover of flood-intolerant woody and upland species. These semi-permanent Upper Coastal Plain bays generally exhibited cyclicvegetation dynamics in response to climate fluctuation, with wet periods favoring dominance by herbaceous species. Large basin morphology and deep ponding, paired with surrounding upland forest dominated by floodintolerant pines, were features contributing to persistence of herbaceous vegetation. Drought cycles may promote directional succession to forest in bays that are smaller, shallower, or colonized by floodtolerant hardwoods. Key Words: depressional wetlands, drought cycles, hydrologic regime, succession INTRODUCTION The hydrologic regimes of depressional wetlands determine their ecological character. Because depression hydrology is driven mainly by rainfall and evapotranspiration, these First, let’s learn how to read any scientific article! (Don’t read this one yet, it’s just an illustration!) EFFECT OF CLIMATE FLUCTUATIONS ON LONG-TERM VEGETATION DYNAMICS IN CAROLINA BAY WETLANDS Chrissa L. Stroh1,4, Diane De Steven2, and Glenn R. Guntenspergen3 Abstract: Carolina bays and similar depression wetlands of the U.S. Southeastern Coastal Plain have hydrologic regimes that are driven primarily by rainfall. Therefore, climate fluctuations such as drought cycles have the potential to shape long-term vegetation dynamics. Models suggest two potential long-term responses to hydrologic fluctuations, either cyclic change maintaining open emergent vegetation, or directional succession toward forest vegetation. In seven Carolina bay wetlands on the Savannah River Site, South Carolina, we assessed hydrologic variation and vegetation response over a 15-year period spanning two drought and reinundation cycles. Changes in pond stage (water depth) were monitored biweekly to monthly each year from 1989–2003. Vegetation composition was sampled in three years (1989, 1993, and 2003) and analyzed in relation to changes in hydrologic conditions. Multi-year droughts occurred prior to the 1989 and 2003 sampling years, whereas 1993 coincided with a wet period…

Reading a Scientific Article • When reading a scientific article in preparation for rewriting it, you must first read the article for overall comprehension. • To comprehend the article you must understand the main points of each major article section. • A brief introduction to the typical major article sections follows on the next slide. More detail will come later.

Introduction: Provides background about the problem. Leads to the research question. States the research question. Method: Outlines the methods used to answer the research question. Should include information about the variables studied (and their definitions), time frames and design of data collection, and type of analysis (data handling: summary, comparisons, etc.). Findings: Gives the results of the analysis. Discussion or Implications: Discusses the findings in light of the original problem. Provides possible implications, the “so what” of the findings in light of the original problem.

As you read the article…. • You can check your comprehension by trying to explain, in general terms, the article’s “story” to someone else. (Try it when you are ready!) • Following comprehension, you can begin to place your understanding into a context for learning. You must first comprehend before you can develop a learning tool. • Okay, let’s learn about scientific articles and how to read them.

Anatomy Of a Scientific Paper This information is from http://www.biochem.arizona.edu/classes/bioc568/papers.htm#organization Organization of a scientific paper In most scientific journals, scientific papers follow a standard format. They are divided into several sections, and each section serves a specific purpose in the paper. We first describe the standard format, then some variations on that format. A paper begins with a short Summary or Abstract. Generally, it gives a brief background to the topic; describes concisely the major findings of the paper; and relates these findings to the field of study. As will be seen, this logical order is also that of the paper as a whole. Abstracts generally include information from all four of the paper’s major sections. Always read the abstract before reading the paper. The abstract gives you an overview of all of the article’s sections, and provides a short introduction to the entire article.

EFFECT OF CLIMATE FLUCTUATIONS ON LONG-TERM VEGETATION DYNAMICS IN CAROLINA BAY WETLANDS Chrissa L. Stroh1,4, Diane De Steven2, and Glenn R. Guntenspergen3 1Master of Environmental Studies Program The College of Charleston Charleston, South Carolina, USA 29424 2USDA Forest Service–Southern Research Station Center for Bottomland Hardwoods Research Stoneville, Mississippi, USA 38776 3U.S. Geological Survey–Patuxent Wildlife Research Center Laurel, Maryland, USA 20706 E-mail: glenn_gtenspergen@usgs.gov Abstract: Carolina bays and similar depression wetlands of the U.S. Southeastern Coastal Plain have hydrologic regimes that are driven primarily by rainfall. Therefore, climate fluctuations such as drought cycles have the potential to shape lonterm vegetation dynamics. Models suggest two potential longterm responses to hydrologic fluctuations, either cyclic change maintaining open emergent vegetation, or directional succession toward forest vegetation. In seven Carolina bay wetlands on the Savannah River Site, South Carolina, we assessed hydrologic variation and vegetation response over a 15-year period spanning two drought and reinundation cycles. Changes in pond stage (water depth) were monitored biweekly to monthly each year from 1989–2003. Vegetation composition was sampled in three years (1989, 1993, and 2003) and analyzed in relation to changes in hydrologic conditions. Multi-year droughts occurred prior to the 1989 and 2003 sampling years, whereas 1993 coincided with a wet period. Wetland plant species generally maintained dominance after both wet and dry conditions, but the abundances of different plant growth forms and species indicator categories shifted over the 15-year period. Decreased hydroperiods and water depths during droughts led to increased cover of grass, upland, and woody species, particularly at he shallower wetland margins. Conversely, reinundation and longer hydroperiods resulted in expansion of aquatic and emergent species and reduced the cover of flood-intolerant woody and upland species. These semi-permanent Upper Coastal Plain bays generally exhibited cyclicvegetation dynamics in response to climate fluctuation, with wet periods favoring dominance by herbaceous species. Large basin morphology and deep ponding, paired with surrounding upland forest dominated by floodintolerant pines, were features contributing to persistence of herbaceous vegetation. Drought cycles may promote directional succession to forest in bays that are smaller, shallower, or colonized by floodtolerant hardwoods. Key Words: depressional wetlands, drought cycles, hydrologic regime, succession INTRODUCTION The hydrologic regimes of depressional wetlands determine their ecological character. Because depression hydrology is driven mainly by rainfall and evapotranspiration, these EFFECT OF CLIMATE FLUCTUATIONS ON LONG-TERM VEGETATION DYNAMICS IN CAROLINA BAY WETLANDS Chrissa L. Stroh1,4, Diane De Steven2, and Glenn R. Guntenspergen3 Abstract:Carolina bays and similar depression wetlands of the U.S. Southeastern Coastal Plain have hydrologic regimes that are driven primarily by rainfall. Therefore, climate fluctuations such as drought cycles have the potential to shape long-term vegetation dynamics. Models suggest two potential longterm responses to hydrologic fluctuations, either cyclic change maintaining open emergent vegetation, or directional succession toward forest vegetation.In seven Carolina bay wetlands on the Savannah River Site, South Carolina, we assessed hydrologic variation and vegetation response over a 15-year period spanning two drought and reinundation cycles. Changes in pond stage (water depth) were monitored biweekly to monthly each year from 1989–2003. Vegetation composition was sampled in three years (1989, 1993, and 2003) and analyzed in relation to changes in hydrologic conditions.Multi-year droughts occurred prior to the 1989 and 2003 sampling years, whereas 1993 coincided with a wet period. Wetland plant species generally maintained dominance after both wet and dry conditions, but the abundances of different plant growth forms and species indicator categories shifted over the 15-year period. Decreased hydroperiods and water depths during droughts led to increased cover of grass, upland, and woody species, particularly at the shallower wetland margins. Conversely, reinundation and longer hydroperiods resulted in expansion of aquatic and emergent species and reduced the cover of flood-intolerant woody and upland species. These semi-permanent Upper Coastal Plain bays generally exhibited cyclic vegetation dynamics in response to climate fluctuation, with wet periods favoring dominance by herbaceous species. Large basin morphology and deep ponding, paired with surrounding upland forest dominated by floodintolerant pines, were features contributing to persistence of herbaceous vegetation.Drought cycles may promote directional succession to forest in bays that are smaller, shallower, or colonized by flood tolerant hardwoods. In the abstract above, the introduction is abstracted in green, methods in orange, findings in blue, discussion (implications) in purple. The proportion of the abstract allocated to each section will vary according to the article. Read this abstract. Do you have a fair understanding of the problem and what was done to address it? You may want to do a little internet searching or other research to fully understand the abstract.

The next section of the paper is the Introduction. In many journals this section is not given a title. As its name implies, this section presents the background knowledge necessary for the reader to understand why the findings of the paper are an advance on the knowledge in the field. Typically, the Introduction describes first the accepted state of knowledge in a specialized field; then it focuses more specifically on a particular aspect, usually describing a finding or set of findings that led directly to the work described in the paper. If the authors are testing a hypothesis, the source of that hypothesis is spelled out, findings are given with which it is consistent, and one or more predictions are given. In some papers, one or several major conclusions of the paper are presented at the end of this section, so that the reader knows the major answers to the questions just posed. Papers more descriptive or comparative in nature may begin with an introduction to an area which interests the authors, or the need for a broader database. Often, the research problem or questions are stated at the end of the introduction. Look for these specific statements or ones from which you can determine the research question(s). Middle school students are learning to identify research questions and this is one of their science education standards, therefore it is crucial that you understand the research question or questions addressed in the paper and can clearly state them. See example on the next slide.

USDA Forest Service Gen. Tech. Rep. PSW-GTR-184. 2002. 741 Phytophthora ramorum and Sudden OakDeath in California: II. Transmission andSurvival Jennifer M. Davidson,2 David M. Rizzo,3 Matteo Garbelotto,4 Steven Tjosvold,5 and Garey W. Slaughter3 Abstract would be placed here. For the purposes of this exercise, we will just read the Introduction now. The Introduction is on this slide and the next one. Introduction The newly described Phytophthora ramorum canker disease of oak (Sudden Oak Death Syndrome) threatens millions of acres of California woodlands where coast live oak (Quercus agrifolia), tanoak (Lithocarpus densiflorus), or black oak (Quercus kelloggii) are dominant species (Garbelotto and others 2001, McPherson and others 2000). An important step in controlling this disease involves understanding how it is spread, both on a small scale between oak trees in an infected area, and over a larger scale from infected to uninfected woodlands. Transmission consists of spore production, movement of spores, and infection of a new individual. Knowledge of the necessary conditions for each of these steps may help us establish barriers to the spread of infection within a single park or between geographically separated host plant ranges such as the Coastal mountains and the Sierra Nevada of California.

Introduction Continued… Phytophthora species generally reproduce through both dormant (resting) spores, as well as rapidly produced fruiting bodies (sporangia) that contain swimming spores (zoospores). Dormant spores may either be sexual (oospores) or asexual (chlamydospores) (Erwin and Ribeiro 1996). The production of sporangia generally requires very high humidity, and therefore, will be strongly affected by seasonal temperatures and rainfall (Duniway 1983). Survival of all spore types will also be affected by temperature and moisture (Duniway 1983). In addition, production and viability of spores may differ on each host species. Once produced on or within the host plant, spores may spread via rain, soil, stream water, or movement of the infected plant itself. Movement of plant material may include infected nursery stock, firewood, or timber. Transport of soil containing propagules may occur on shoes of hikers, tires of trucks and mountain bikes, or the feet of animals. Movement of spores in stream water may allow for long-distance transport, depending on viability of spores in water, and the potential of spores to move from stream water to the susceptible parts of host plants (Hansen and others 2000). Rain splash has been shown to move Phytophthora spores of other species over several meters (Ristaino and Gumpertz 2000), making this a potentially effective means of local transport, especially for spores requiring moisture for production and survival. The mode of transmission for P. ramorum among California oaks is complicated by the presence of many other host plant species in the forest. Currently, the host list includes 10 non-oak plant species in five plant families (Rizzo and others 2002). These other hosts may serves as sources of inoculum and act as infectious links among oak trees. In addition, nursery stock of host plant species, such as rhododendron, can serve as vectors of disease when moved for landscaping. In this paper, we provide data on the types of spores produced by P. ramorum under laboratory and natural host plant conditions. We also document the seasonality of spore production in recovery from rainwater, soil, and stream water. Finally, we use survival of zoospores and chlamydospores in the laboratory in water, and on dry and moist filter paper to simulate viability of spores in stream water, and under moisture extremes on solid substrates, such as litter or soil.

The next section of most papers is the Materials and Methods. In some journals this section is the last one. Its purpose is to describe the materials used in the experiments and the methods by which the experiments were carried out. In principle, this description should be detailed enough to allow other researchers to replicate the work. In practice, these descriptions are often highly compressed, and they often refer back to previous papers by the authors. One of the Natural Inquirer’s goals is to help students learn the scientific process. Therefore, this section of the paper is important. Although a Natural Inquirer article rarely describes the statistical or other analysis in detail, the general aspects of the methodology are presented. Middle school students should be learning about variables, observation techniques, data collection and recording, and simple analyses. As you read the methods section, look for the general story of how the variables were defined, the data collected, and the general type of analysis used. This includes what the variables were and how they were defined (and quantified, measured, or identified); and how, when, and where data were collected. A sample Methods section follows on the next slide.

Methods Movement of Spores During the isolation of P. ramorum from 93 oak and tanoak trees, field observations of the position of cankers on trees and the location of infected trees with respect to topography were used to gain insight into the mechanisms of spore movement, whether above ground, moved in soil, or carried by rain runoff or streams. Location of infection on 20 bay trees and 6 rhododendron bushes also was noted. Recovery of spores was attempted from rainwater, soil, litter, and stream water in a time series spanning the winter rains and the drying summer months. Rainwater Raintraps were used to collect rainwater in a coast live oak woodland at Fairfield Osborn Preserve in Sonoma Co. Both coast live oak and bay trees were infected with P. ramorum at this site. Raintraps consisted of a 165 cm by 75 cm vinyl sheet stretched over a pvc frame and folded into a funnel with a 4 liter collecting jar at the bottom. Traps were set up on February 2, 2001 and used to collect rainfall through winter, and for one unusually late rain on June 27-28. Two traps were placed 0.5 m in front of cankers on each of 7 oak trees, for a total of 14 traps. Previous isolations confirmed that the cankers were caused by P. ramorum infection. Two “distant” traps were placed at a distance of 5 m from all infected oak trees. Four additional “distant” traps were installed on March 15, 2001. Although separated from infected oaks, “distant” traps still were under the forest canopy, which consisted mainly of bay trees. Rain water was collected at approximately 2-day intervals during a storm event. Rainwater was stored overnight at 4-5 °C to allow spores to settle. One liter of water was suctioned off of the bottom of containers and filtered through a Millipore 3 ì cellulose esterase filter to capture all spore types. The filter was then cut into strips and placed filtrate side down on selective medium plates. After 7 days, strips were removed, and colonies of P. ramorum were counted. Soil Beginning in March, 2001, soil and litter were collected on a monthly basis from around the base of 15 diseased oak trees at the Fairfield Osborn Preserve to test for the presence of P. ramorum. Previous isolations confirmed that all trees were infected by P. ramorum. At the base of each tree on the infected side, soil was collected in zip-lock bags from three separate spots and pooled to equal 500 g. Litter was collected at three spots to fill one-fourth the volume of a gallon zip-lock bag. A green d’anjou pear was pressed into the soil or litter in each sample so that one-third of the pear was immersed, and diH20 was added to the sample until one-half of the pear was immersed in water. Samples were allowed to sit for 6 days at 18-23 °C. Pears were then removed, washed, and monitored for signs of Phytophthora lesions. Tissue from likely lesions was plated on PARP selective medium to verify P. ramorum presence.

The third section is usually Results or Findings. This section describes the experiments and the reasons they were done. Generally, the logic of the Results section follows directly from that of the Introduction. That is, the Introduction poses the questions addressed in the early part of Results. Beyond this point, the organization of Results differs from one paper to another. In some papers, the results are presented without extensive discussion, which is reserved for the following section. This is appropriate when the data in the early parts do not need to be interpreted extensively to understand why the later experiments were done. In other papers, results are given, and then they are interpreted, perhaps taken together with other findings not in the paper, so as to give the logical basis for later experiments. In a Natural Inquirer article, the “Results” section typically presents the results of the analysis only. Interpretation is reserved for the following section. This is true even if the scientific article being rewritten uses a different format.

The example below and all examples from this article are not reproduced in their entirety. This article resulted in the Natural Inquirer article “Moving Spore-adically” from the Invasive Species edition. Results Movement of Spores Field Observations Observations suggest that spores of P. ramorum were aerially dispersed. Of the 93 oak and tanoak trees from which P. ramorum was isolated, none had cankers below the root crown. Cankers on one tanoak were as high as 20 m. Of the six rhododendrons sampled, all infection was in the leaves or stems. Of 20 bays sampled, all successful isolation was from leaves, although lesions were present on some terminal twigs. Infections on oaks were observed from sea level to 800 m and at all elevational positions on hillsides ranging from valleys to ridgetops. Infection did not strictly follow water courses. Raintraps Rainwater contained viable spores of P. ramorum (fig. 1). At some point during the sampling period, P. ramorum was recovered from rain captured in traps placed at all seven of the coast live oaks. This rainwater was a combination of throughfall rain, drip from the canopy, and splash from the trunk. Propagule counts were low, but present in rainwater from these traps at each of the collection periods except for the brief summer storm in late June (0.5 inches rainfall). Spore counts were variable from tree to tree, and ranged from 0.25-7 spores per liter in positive samples from traps placed at the oak trees. Of the six “distant” traps placed under the forest canopy but 5 m away from infected oak trees, two were positive for P. ramorum during the sampling period. Soil and litter also contained viable propagules of P. ramorum. During March, 3 of 15 soil samples and 1 of 15 litter samples tested positive. During April, no soil samples tested positive, and only 1 of 15 litter samples tested positive. During May, no litter samples tested positive, and only 1 of 15 soil samples tested positive. The positive May sample was from the same tree as the positive April sample. In June and July, all samples were negative.

The fourth section is the Discussion or Implications. This section serves several purposes. First, the data in the paper are interpreted; that is, they are analyzed to show what the authors believe the data show. Any limitations to the interpretations should be acknowledged, and fact should clearly be separated from speculation. Second, the findings of the paper are related to other findings in the field. This serves to show how the findings contribute to knowledge, or correct the errors of previous work. As stated, some of these logical arguments are often found in the Results when it is necessary to clarify why later experiments were carried out. Although you might argue that in this case the discussion material should be presented in the Introduction, more often you cannot grasp its significance until the first part of Results is given. In a Natural Inquirer article, this section varies widely. Because some topics are controversial or at least debatable, stay close to the article’s text and resist the urge to insert personal opinion. In the Natural Inquirer, this section is now always identified as “Discussion.” Although most environmental education guidelines suggest an “action” component, it is usually unwise to suggest an action in a Natural Inquirer article. Remember, the Natural Inquirer presents science. Students should be left to determine on their own how they will use their new information. (More on this later in the course!)

Discussion Current data suggest that P. ramorum, the causal agent of “sudden oak death,” may have been introduced to northern California approximately a decade ago (Garbelotto and others 2001, Garbelotto and others 2002, McPherson and others 2000). Today, the range of the pathogen covers over 600 km, from Big Sur into southern Oregon. This rate of spread surpasses that of Chestnut Blight in the early part of the 20th century (Anagnostakis 1987). Our data on transmission and survival of P. ramorum provide preliminary insight into the mechanisms underlying this remarkable spread. The rapid production of spores on foliar hosts, such as bay and rhododendron, may be key to the spread of P. ramorum within a locality, and perhaps between different geographic locations. P. ramorum produced sporangia on moistened leaves of both bay and rhododendron, the two foliar hosts tested. Chlamydospores were also noted on infected bay leaves. In addition, we have observed chlamydospores on infected rhododendron leaves in moist chambers for other experiments. While rhododendrons are not major components of most California forests, bay trees are dominant species in many coast live oak forest types. Consistent with laboratory results on spore production, evidence from the field suggests that inoculum from bay trees may be very important in vectoring P. ramorum to oaks. Swiecki and Bernhardt (2001) found a significant association between infected oaks and the presence of bay trees. Rainwater traps in this study placed 5 m from infected oaks contained viable spores that may have come from overstory infected bay trees. Furthermore, we often observe an increase in Phytophthora-like leaf spots on bays growing within oak infection centers. To further investigate the importance of bay as an inoculum source, studies are underway to determine temperature requirements for sporangia production on bay leaves, the viability of P. ramorum in leaves attached to trees or fallen in litter, and the distance spores can travel from bay leaves. The negative results of spore production on oak bark cankers or in bleeding sap require further investigation. Rapid contamination of oak cankers by fungal species may have prevented sporulation of P. ramorum. In addition, the seasonal state of the bark may not have been conducive to spore production at the time of the test (Brasier and Kirk 2001). However, successful amplification of P. ramorum DNA from bleeding sap (Garbelotto and others 2002), suggests the presence of propagules and underscores the need for additional isolation attempts from sap. Viable spores of P. ramorum were shown to be carried in rainwater, soil, litter, and stream water. The presence of diseased oaks at all elevations on hillsides and the above-ground nature of the disease suggest wind-blown rain or rain splash as a common mechanism for movement of spores. The abundance of viable propagules exhibited a distinct seasonality, peaking in March and early April of 2001, a low rainfall year. Production of sporangia by other Phytophthora species depends on high moisture levels (Duniway 1983). Hence, the presence of moisture from rain on infected plant tissue is probably necessary for production of spores that eventually end up in soil, litter, or stream water. Generally increasing levels of inoculum in rainwater in early April, and the lack of spores in the isolated, 2-day June rain, may suggest that a time of prolonged moisture is needed for inoculum buildup. Warming temperatures in early April during the period of consistent rainfall may also have contributed to the peak in spore production. Failure to recover P. ramorum from soil and litter in the summer months may indicate that seasonal drying is sufficient to reduce viability of spores in these substrates.

Finally, papers usually have a short Acknowledgements section, in which various contributions of other workers are recognized, followed by a Reference list giving references to papers and other works cited in the text. Papers also contain several Figures and Tables. These contain data described in the paper. The figures and tables also have legends, whose purpose is to give details of the particular experiment or experiments shown there. Typically, if a procedure is used only once in a paper, these details are described in Materials and Methods, and the Figure or Table legend refers back to that description. If a procedure is used repeatedly, however, a general description is given in Materials and Methods, and the details for a particular experiment are given in the Table or Figure legend. Middle school students should be learning how to read and construct tables and figures. The figures and tables given in a scientific paper must often be simplified. It is important, however, to identify and ultimately use the educational potential offered by an article’s figures and tables.

Here is figure 1 from the article you’ve been examining. Note that both the X and Y axis are labeled, and the figure has a caption. Figure 1. Mean number of P. ramorum spores per liter of rainwater (+ standard error) for storms occurring from February through June, 2001 at the Fairfield Osborn Preserve, Sonoma Co. Means were based on the average from two collecting traps at each of seven coast live oak trees.

Variations on the organization of a paper In most scientific journals, the above format is followed. Occasionally, the Results and Discussion are combined, in cases in which the data need extensive discussion to allow the reader to follow the train of logic developed in the course of the research. As stated, in some journals, Materials and Methods follows the Discussion. In certain older papers, the Summary is given at the end of the paper. Regardless of the organizational variations in a scientific paper, the Natural Inquirer ALWAYS follows the described format (Introduction, Method, Findings, Discussion). If you need a refresher, examine a Natural Inquirer article. This is done for one important reason: Reading scientific papers is difficult. If students understand the organization of a paper, they can more easily read and comprehend. If every Natural Inquirer article is organized similarly, students will have more success in comprehension. Think about reading a newspaper. You know its organization and this facilitates your comprehension. This is the reason one of the Natural Inquirer’s criteria for selecting a scientific paper is that it follows the standard format exactly, or so closely that as you rewrite, you can easily organize your writing into the standard sections.

You are now familiar with the anatomy of a scientific paper. Now, how should such a paper be read? Before we begin, there is one thing you should know: You will read your scientific paper many times before you begin writing! The first few times you read, therefore, do not worry about writing. The following information is from http://hampshire.edu/~apmNS/design/RESOURCES/HOW_READ.html How to Read a Scientific Research Paper— a four-step guide Ann McNeal, School of Natural Science, Hampshire College, Amherst MA 01002

Reading research papers ("primary articles") is partly a matter of experience and skill, and partly learning the specific vocabulary of a field. First of all, DON'T PANIC! If you approach it step by step, even an impossible-looking paper can be understood. Begin by following these steps….

Skim. Skim the paper quickly, noting basics like headings, figures and the like. This takes just a few minutes. You're not trying to understand it yet, but just to get an overview. • 2. Vocabulary. Go through the paper word by word and line by line, underlining or highlighting every word and phrase you don't understand. Don't worry if there are a lot places with underlining; you're still not trying to make sense of the article. After skimming the paper and noting words and phrases you do not understand, it is helpful to read the paper again, noting the things that you DO understand. You may underline or highlight the text, then write a clarifying note in the margin. In the “Introduction,” for example, restate the problem and the research question(s) in the margin or in your notebook. In the “Methods” section, restate pieces of the method, paragraph by paragraph. Over the next few “readings” of the paper, your task is to identify what you do and do not understand about the research.

Now you have several things you might do with these vocabulary and concept questions, depending upon the kind of question each is. You can: Look up simple words and phrases. Often the question is simply vocabulary--what's a lateral malleolus, or a christa, or the semilunar valve. A medical or biological dictionary is a good place to look for definitions. A textbook of physiology or anatomy may be a good source, because it gives more complete explanations. Your ordinary shelf dictionary may not be a good source, because the definitions may not be precise enough or may not reflect the way in which scientists use a word (for example "efficiency" has a common definition, but the physical definition is much more restricted.) • Sources for environmental words or phrases: • One of the best sources for environmental information is G.Tyler Miller’s (2007) book Environmental Science and Living in the Environment (2006). The cost is about $123 but well worth the investment. I use this book virtually every time I write an article. • Search web sites (with .edu and .gov extensions if possible) for clarification. Be sure to triangulate. That is, search more than one source and critically compare. • Science dictionaries and student science dictionaries.

(This is an older edition.)

In reading science to write Natural Inquirer articles, it is appropriate to use a regular dictionary if needed. It is important to understand a word’s meaning, regardless of whether it is a scientific or a non-scientific term. A regular dictionary will also come in handy when you want to simplify a word for your written article, and when you need to use diacritical marks. More on that later! In some instances, you may eventually need to contact the scientist who did the research, or a scientist in the same field of study. While this is acceptable, it is best to do as much self-directed research in advance as possible. That way, if you must contact a scientist with a question, your question will be well-informed and you will get more from the scientist’s explanation. In addition, the scientist will appreciate your basic understanding of terms and concepts, and the effort you made to understand his or her research. Greg Aplet, from the Wilderness Benefits edition

The two tips given below are critical strategies for understanding a scientific paper and identifying major concepts for inclusion in a Natural Inquirer article. Note that while you may not use the scientific word or phrase in your rewritten article (opting for a simpler term), you must understand what is being presented in the scientific article. Get an understanding from the context in which an unknown word or phrase is used. Often words that are used to describe the procedures used in an experiment can be understood from the context, and may be very specific to the paper you are reading. Examples are the "lithium-free control group" in a rat experiment or the "carotene extraction procedure" in a biochemical experiment. Of course, you should be careful when deciding that you understand a word from its context, because it might not mean what you think. Flag this phrase as belonging to one of the major concepts of the paper--it's bigger than a vocabulary question. For example, a paper about diet and cancer might refer to "risk reduction," which you would need to understand in context and in some depth.

The first two strategies, which we have just covered, are 1) skim and 2) vocabulary. Now, let’s focus on comprehension. 3. Comprehension, section by section. Deal with all the words and phrases, although a few technical terms in the Methods section might remain. Now go back and read the whole paper, section by section, for comprehension. In the Introduction, note how the context is set. What larger question is this a part of? The author should summarize and comment on previous research, and you should distinguish between previous research and the actual current study. What is the hypothesis or question being addressed in the paper? In the Methods, try to get a clear picture of what was done at each step. What was actually measured? It is a good idea to make an outline and/or sketch of the procedures and instruments. Keep notes of your questions; some of them may be simply technical, but others may point to more fundamental considerations that you will use for reflection and criticism below.

In Results look carefully at the figures and tables, as they are the heart of most papers. A scientist will often read the figures and tables before deciding whether it is worthwhile to read the rest of the article! What does it mean to "understand" a figure? You understand a figure when you can redraw it and explain it in plain English words. The Discussion contains the conclusions that the author would like to draw from the data. In some papers, this section has a lot of interpretation and is very important. In any case, this is usually where the author reflects on the work and its meaning in relation to other findings and to the field in general. Note that you have not yet begun to rewrite the article. The goal at this point is to clearly understand what you are reading. Understanding a scientific article, especially when you are not an expert in the discipline, is hard work. It takes perseverance. Remember, take it one step at a time.

4. Reflection and criticism. After you understand the article and can summarize it, then you can return to broader questions and draw your own conclusions. It is very useful to keep track of your questions as you go along, returning to see whether they have been answered. Often, the simple questions may contain the seeds of very deep thoughts about the work--for example, "Why did the authors use a questionnaire at the end of the month to find out about premenstrual tension? Wouldn't subjects forget or have trouble recalling?" Such questioning will help you develop meaningful Reflection Questions. By now, you should be able to tell a friend or colleague about this research, including information from all four sections. At this point, you are ready to begin thinking about how to rewrite the article for a middle school audience. But BEFORE you do that, there is one more important step in this process…..

Go through your article at least one more time. This time, however, you must do so with the following in mind: • What is it like to be an adolescent? Put yourself into an adolescent’s frame of reference and their stage of development. To be successful at writing for adolescents, you must try to think like you did when you were 13, but with the knowledge and wisdom you currently possess. What would be interesting about this article to a 13 year old? What information can connect this article to their everyday life? • What science education standards can educators address through this article? Write them down as you identify them. • In particular, what science process and science content standards may be addressed through this article? Note that some of them may not be obvious. • How can critical thinking be encouraged through the presentation of this article? What are some who, what, when, where, how, and why questions? You must now read your article with all of the above in mind. This is difficult to do and will require practice. Tips for success include…..

Tips for Success • Use a different color pen and write in the margins of the paper (or in your notebook) when you identify a relevant word, phrase, sentence, or idea. • In the Introduction, identify the problem and research question(s). State them simply in your own words. • In the Methods section, identify the steps taken by the scientists. What were the variables studied? Which was the dependent variable and what were the independent variables? How were they measured? Was technology used? How were the data collected? Where did the study occur? Etc….. • In the Findings section, identify the findings at the most simplistic level. • In the Discussion section, look for the relevance of the findings in relation to the original problem or question(s). At this point, it should be clear that many if not most scientific articles will be too complex to present all of the information in the article. To address this problem…..

…recognize that there are numerous “storylines” embedded in most scientific articles. Some articles may clearly state only one storyline, but this is rare. You must decide on ONE (only ONE) storyline on which to focus. If you choose more than one, realize that you are doubling or tripling the complexity of the reading and comprehension task. This is not advisable. If your article is part of a journal, the storyline you choose should fit the broad theme of the journal. If your article is a stand-alone monograph, you have more freedom to choose. Once you have selected a storyline, resist the urge to put non-relevant information into your text, regardless of how important you think it is. If the article is too complex, students will lose interest or be unable to comprehend.

A key to a successful Natural Inquirer article is its adherence to ONE STORYLINE. You must decide what to leave out as much as you decide what to put in. POP QUIZ: What is a key to a successful Natural Inquirer article?

Other things to consider as you read your article again….. • Look for opportunities to introduce Number Crunches, maps, map reading, geography skills, and Reflection Questions. • Look for opportunities to help students relate to their own experience. These can all be noted in the margin of your paper or in your notebook. • Remember to integrate the variety of disciplines discussed earlier, including language arts, math, geography, social studies, visual arts, etc. • In an article comparing the production of wood and steel doors, for example, energy was expressed in gigajoules. The following notes show how gigajoules were translated into a unit to which students could relate.

In this case, the question was how to represent gigajoules in a way that students could understand. Information about gigajoules was retrieved from various web sites. This led to research on kilowatts and calories, two units of measurement more familiar to students. Marginal notes were made right on the article. The next slide brings you a little closer. The following two slides show how gigajoules was represented in the final text.

From upcoming Energy Edition, “Which Do You A-door?” The amount of energy used in the manufacture of a steel door and a wood door was measured in gigajoules (gig uh julz) (table 3). One gigajoule is equal to about 278 kilowatt hours, or 238,000 nutritional calories. The joule is a member of the international system of units (SI), the modern form of the metric system. Table 3. Total amount of energy, measured in gigajoules (GJ), used in the manufacture of a wood door and a steel door. Total energy (GJ) Steel door 2.17 Wood door 0.10

From upcoming Energy Edition, “Which Do You A-Door?” continued…. Number Crunches {Sidebar} Let’s say that the average daily energy use in a home is 15 kilowatt hours (kWh). How many days will it take before the amount of energy used in that home is equal to the total amount of energy used to manufacture a steel door? How many days will it take to equal the amount of energy used to manufacture a wood door? While doing vigorous exercise such as running, an adult burns about 100 nutritional calories each hour. How many hours will it take to burn 1 gigajoule of energy? How many days of vigorous exercise will it take the adult to burn 1 gigajoule of energy? How many days of vigorous exercise will it take for the adult to burn the amount of energy used in the production of a steel door and a wood door? - end of Number Crunches - In this case, Number Crunches are used for four purposes: to help students understand the value of gigajoules, to show the integration of math with science, to give students practice in mathematics, and to relate gigajoules to the student’s everyday life.

You are now ready to read your scientific article. Remember the sections of a scientific paper relevant to the Natural Inquirer include: Introduction Methods Findings Discussion • First, skim your article all the way through. • Skim your article again, this time noting unfamiliar words, terms, and phrases. • Define unfamiliar words, terms, and phrases using Miller (2007), reliable web sites, science dictionaries, textbooks, regular dictionaries, etc. • Read your article again carefully, this time for initial comprehension and meaning. • Place newly defined words, phrases, and sentences into context. • Identify the major concepts of the paper.

Read your article again. This time note the problem and research question(s) from the Introduction; the general methods of data collection and analysis used from the Methods section; the findings from the Findings section; and any implications or other observations from the Discussion section. You can write this in the paper’s margins or on a separate sheet in your notebook. • During this same reading, begin to note educational opportunities, such as ideas for Thinking About Science, Thinking About the Environment, Number Crunches, sidebars, opportunities to relate the research to the students’ everyday lives. This can be done by highlighting and making marginal notes. • During this same reading, begin to note possible storylines. • Based on your notes from this reading, decide on one storyline. Write this down. (Note: The preferred storyline may or may not become clear immediately, even after your second or third reading.) • Read your article again, focusing on your chosen storyline. Highlight information that relates to the storyline, omit information not relevant to your chosen storyline. • You may need to give yourself time between readings. • As you read this time, keep the following in mind:

What is it like to be an adolescent? Put yourself into an adolescent’s frame of reference and their stage of development. To be successful at writing for adolescents, you must try to think like you did when you were 13, but with the knowledge and wisdom you currently possess. How can you connect the article to their everyday life? • What science process and science content standards may be addressed through this article? Note that some of them may not be obvious. This is particularly true for science process standards. • How can critical thinking be encouraged through the presentation of this article? • Make notes on each of the above points, either in the margin, on the back of the article pages, or in your notebook.

Continue the process of note taking relevant to your storyline until you are relatively certain of your story. • Remember that when you write, you will stay as close to the actual text as possible, but will write at a 7th grade level. • Why stay as close to the actual article text as possible? • According to Ann McNeal, Hampshire College: • There are many advantages to having students [sic] read primary literature (Epstein, 1972): • Articles have a vividness that is seldom found in a text, so students get excited by them. • Articles lend themselves to critical, analytical thinking. • Students feel smart and powerful when they read original sources. • Articles reveal the scientific process far better than secondary sources.

This is the end of session 10. (Finally!) Congratulations! • You should now have a scientific paper filled with highlighting, underlining, and margin notes; or a notebook filled with notes and ideas. • You know your storyline, and you know what to include and what to leave out. • You know what opportunities your article presents to connect 7th graders to the science, help teachers address educational standards, critical thinking skills, and to integrate other disciplines. • You understand most if not all of the scientific words, terms, and phrases in your article. • In Session 11, we’ll begin writing!

Now you are (almost!) ready to read your scientific article!