Bio 173 Fisheries Biology: Term Paper
Date: September 3, 2013 File: d:\B173-2013\B173_term_paper.wpd Summary You are to write a scientific term paper about a topic related to fisheries biology. Goal
Ron Coleman
The goal is for you to produce a term paper that illustrates that you have researched and thought in depth about a topic in fisheries biology. The term paper will tell me that you understand the important issues in a particular field and have identified the current cutting edge in that research. This paper is NOT an essay. I do not want you to explain a topic to me. I want you to discuss current research on a topic. If you find yourself including extensive background material then you are not doing the paper correctly. The paper is about the current research, not just about the phenomenon. For each of your source papers, tell me what the authors were trying to investigate, how they did their investigation, what they found and what it means. It is possible that you have never done this kind of paper before. If you are unclear about what you are doing, ask me about it. If you think that this is just like writing a typical term paper on some topic, then you are dead wrong. Most importantly, think of this as an opportunity to show me what you can do, not as something that you have to do. I want you to discover something and to share that discovery with me. Potential Topics I suggest you look at the following journals for inspiration: Science, Nature, Journal of Fish Biology, Canadian Journal of Fisheries and Aquatic Sciences, Transactions of the American Fisheries Society, California Fish and Game If you have a specific area of interest, I can suggest particular journals that you might look in. Potential topics might include the biology of particular fisheries species, historical fisheries analysis, current methods in fisheries, aquaculture, genetically-modified fishes, introduced fishes, etc. Be careful with anything historical: I do not want just a condensed version of one of the many analyses of past fisheries collapses. Source Material Our library has some of the journals mentioned above, and I have others in my personal collection. Your task is to find recent research. You may use online approaches (e.g., Google Scholar) to get copies of journal articles in pdf form, but do NOT cite websites, unless you are absolutely sure that they are primary literature (which will almost NEVER be the case; ask me). Mechanics You will use the primary literature, not secondary sources like newspapers, magazines, encyclopedias or the internet. I want you to read what the current researchers are writing, not what someone else wrote about what the researcher wrote. Your term paper will make use of a minimum of 5 papers from the primary literature. In writing the paper, you may need to cite some secondary literature as background material. So that I know that you know the difference between primary and secondary literature, in the Literature Cited section of your paper, you must put an asterisk in front of each paper you deem to be primary literature. By the first due date , you need to provide me with a typed (not hand-written) one page proposal for your paper. This proposal must include your name, the title, the full and proper citation of one paper from the
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Ron Coleman
primary literature that you intend to use and a brief description of your proposed paper (one paragraph) that cites that paper. See below for the proper way to format your citation. This proposal must not be hand-written. By the second due date, you must provide me with the cover page, the introduction and the analysis of one of your pieces of primary literature, along with the full and proper citation of any literature that you have cited. For the final due date, you will turn in the completed paper, which includes analyses of all of your primary literature, along with the checklist (see below). You are allowed (and encouraged) to turn this in before the final deadline. You will attach the previous draft (the one that I checked) to the back of your final paper, after the checklist. It should go without saying, but I will say it anyway, you cannot submit a term paper that you are submitting, have submitted, or will submit, for another course. You must have someone else read over your paper (to help you improve the writing) before you submit it. They must sign the checklist. You are to fill out the rest of the checklist, not them. Types of Literature In class, we will discuss the differences between the primary and secondary literature. The primary literature consists of the material published in journals (which are very distinct from magazines), written by the scientist doing the work and reviewed by scientific referees. Reviews or books (with rare exceptions) do NOT constitute the primary literature. Textbooks are NEVER primary literature. These are considered secondary literature. Magazines like Scientific American, Biosciences, American Scientist, Discovery or National Geographic are NOT primary literature. Gray literature is particularly common in fisheries and wildlife work; beware of it. The California Department of Fish and Game produces tons of it each year. Gray literature consists of circulars, bulletins, reports, technical reports, in-house documents and the like which are printed but do not undergo the typical scientific review process. These are used for internal purposes but because they have not undergone any external review, they are not considered scientifically valid. Nonetheless some gray literature is useful, but it must always be evaluated with a strong sense of caution. The title of the publication does not always tell you whether something is primary, secondary or gray literature. For example, the Bulletin of the Fisheries Research Board of Canada (now Canadian Journal of Fisheries and Aquatic Sciences) is the most highly regarded journal in fisheries research and is not a "bulletin" in the typical sense (which is why they changed the name a number of years ago). Similarly Transactions of the American Fisheries Society sounds like a list of Meeting minutes or some such thing but is in fact a respectable journal of basic fisheries research. By contrast, Fisheries Bulletin is exactly what it says it is: a bulletin of what is going on in fisheries and not a part of the primary literature. If a journal is titled Reviews in Evolution or something similar to that, you can be pretty sure that nothing in it is primary literature. For example, the journal Trends in Ecology and Evolution is NOT primary literature. That does not mean that you should not look at that journal for inspiration, but the papers in it are not primary literature (with rare exceptions). Sometimes the same issue of a journal will contain items that are primary literature and others that are secondary literature. For example, it is often the case for journals to have a review article in the front of each issue. The word “Review” at the top should be a strong hint that this is NOT primary literature. The journal Science, one of the most respected journals in science, often includes many news reports, etc. that are not primary literature, as well as substantial primary literature, in the same issue. If you are unsure as to whether a paper is primary literature or not, ask me about it. As a very simple litmus test: if a paper is really easy to understand, like it was written for non-scientists, the odds are high that it is NOT primary literature. Primary literature is densely written, often full of unexplained highly technical jargon. It is that stuff that you need to use for this term paper. Format The paper MUST BE TYPED -- I will not read handwritten papers under any circumstances.
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The paper must be double-spaced with pages numbered, starting with the cover page as page 1. It may be printed on one side of the page only or double-sided. This paper should be no more than, and not much less than, 11 pages (all inclusive) and must include a cover page with the title, your name and date. e.g., Regulating the Bluefin tuna harvest by Ron Coleman November 14, 2013 The Literature Cited goes on the last page, but that need not be a separate page, i.e., it can start right after the last bit of text. Write clearly and precisely. I am very unimpressed with spelling mistakes or grammatical mistakes. These kinds of mistakes will DRAMATICALLY affect the grading of your paper. Use a spelling checker program to check your writing and have a friend read it as well before turning it in. I expect a very high quality product. How to Cite Sources The purpose of citing material in a scientific document is to properly credit the work of others. A citation shows that the thought or information just presented is not that of the author of the current document, but rather comes from someone else and that person deserves the credit (or the blame). You do NOT cite what is regarded as general knowledge. But, and here is an important point to ponder, you should not be writing much general knowledge in your paper anyway. For example if you are writing a paper on the swimming biodynamics of tuna and you find yourself writing that tuna are fast moving fish that live in the ocean, then there is no need to cite anyone for that, but equally, there is no need to write the original sentence in the first place. We all know that tuna are fast moving fish that live in the ocean. Now if you want to tell me something specific, like tuna are the fastest swimming fish, clocked at over 50 miles per hour, you need a citation because I want to know who said that and then I can check it out myself if I do not believe it. The Literature Cited section The Literature Cited should contain ONLY citations to published work and must be set out consistently and professionally, paying attention to having complete information, the order of the information and the format of how that information is presented, e.g.: journal article: Galen, C., J.A. Shykoff and RC Plowright (1986) Consequences of stigma receptivity schedules for sexual selection in flowering plants. American Naturalist 127: 462-476. book chapter: Plowright, RC and C.M.S. Plowright (1987) Elitism in Social Insects: A Positive Feedback Model. Pp 413-436 in: Interindividual Behavioral Variability in Social Insects (Ed. R.L. Jeanne), Westview Press, Boulder, Colorado. book: Moyle, P.B., and J.J. Cech Jr. (1988) Fishes: An Introduction to Ichthyology (Second Edition). Prentice Hall, Englewood Cliffs, New Jersey. The references should be listed in alphabetical order of the last name of the first author. Notice the placement of the various pieces of information, such as the year. Notice that the issue number is not included, only the volume and the page numbers. Write out journal names in full.
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How Citations Appear in the text
Ron Coleman
The three citations listed above would appear in your text as, respectively, Galen et al. (1986), Plowright and Plowright (1987), and Moyle and Cech (1988). Note that citations to papers with more than two authors -- such as the first one above -- appear in your text as the first author followed by the words ‘et al.’ (Latin for "and others") but the full list of authors is given in your Literature Cited section. Notice that in the words ‘et al.’ there is no little dot after the word ‘et’ but there is a dot after the word ‘al.’. This is because ‘al.’ is an abbreviation, whereas ‘et’ is not. Unpublished work is referred to in the text either as "(A.J. Smith, unpublished data)" or "(J.G. Bloggs, personal communication)", depending on the context, but is not listed in the Literature Cited. DO NOT USE footnotes as a means to cite references. In fact, do not use footnotes at all. Most scientific journals do not allow them. Some journals use a numbering system when referring to references. DO NOT do that in this paper. Do not ask me whether you should use APA style or MLA style. The instructions are given above. If you ask me, I will be very unhappy that you have not read the instructions. Quotations It is almost never correct to use quotations in scientific writing. This is because in science we are interested in the ideas we get from others, not their exact words. If Jones said something interesting in 1992, then paraphrase what Jones said and give her credit. For example, the following might appear in your paper, The bluegill sunfish exhibits a diversity of reproductive styles (Jones 1992). You do not need to put the words in quotation marks because you are telling us that Jones wrote a paper on this topic. We now know that it was not you that first found out this exciting fact, but rather it was Jones and we know where to look to find more details. But, do NOT simply copy the text from Jones. You must paraphrase it. To simply copy it, whether you cite ir or not, is plagiarism, a serious academic offense. The only time you need to use quotations in science is when the actual exact words are very important. For example, Robert Trivers wrote a very famous definition of parental investment in 1972 and this one line is quoted extensively in the literature because each and every word is very precise and important. Long chunks of text Imagine you are writing a term paper on sea snakes and you want to make extensive use of Roberts (1999) paper on sea snakes. You do NOT do the following: Roberts (1999) wrote extensively on the ecology and reproduction of sea snakes. He found that most sea snakes are livebearers (Roberts 1999). Fourteen of 26 species are striped (Roberts 1999). They are found in all tropical oceans (Roberts 1999). You would do the following: Roberts (1999) wrote extensively on the ecology and reproduction of sea snakes. He found that most sea snakes are livebearers. Fourteen of 26 species are striped. They are found in all tropical oceans. There is no need to put "Roberts (1999)" everywhere because it is clear that all of this material is coming from Roberts' paper. The bottom line when citing material is as follows: you are trying to make sure that the reader knows who said what and where the reader can go to find more information. DO NOT QUOTE when writing in science.
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Check List
Ron Coleman
At the end of this document is a checklist that must be turned in with your final term paper. Do not ask me for a copy of the checklist when you turn in your paper. Doing so makes it clear that you did not USE the checklist in writing your paper and I will be very unhappy. Due Dates Sept 25, 1:00 pm: Proposal due Nov 4, 1:00pm: Part I due Nov 18, 1:00 pm: Final paper due Grading The paper will be graded out of 20 points. There is no late. The paper is due at 1pm. After that, even 5 minutes, the paper is worth 0. If the paper is less than 10 pages, that will be a loss of 4 points. Inappropriate literature will be a loss of 5 points at a minimum.
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Bio 173 [A sample introduction to a term paper]
Conflict and Cooperation: A review of biparental care
Ron Coleman
Biparental care is the name given to any situation where both parents (the male and the female) participate in parental care of the offspring. Biparental care is the norm in birds, is widespread in mammals and occurs sporadically in amphibians and fishes (Gross and Sargent, 1985). Biparental care is intriguing because it is a balance between cooperation and conflict between the two parents (Houston and Davies, 1985). In many cases, the longterm interests of the two partners are not aligned, e.g., when mating is only for a single reproductive event, and thus there may be conflict in terms of how much each parent is willing to invest in the offspring. And yet, if the parents do not cooperate to some extent, e.g., to protect the young, the offspring will perish and so some degree of cooperation is necessary. What factors influence this careful balance between cooperation and conflict? In this paper, I will examine five studies, from a diversity of taxa, which illustrate that the balance can be influenced by such things as availability of other partners, age of the offspring, number of offspring and even characteristics of the parents themselves (e.g., their relative sizes). Together these studies show that parents incorporate diverse information into their biparental investment decisions. Coleman (1993) examined biparental care in the convict cichlid (Archocentrus nigrofasciatus) using a manipulative laboratory experiment to see the effect of relative value on the balance of biparental investment. In this experiment, Coleman utilized 15 pairs of convict cichlids, which he bred in 15 different aquaria. The key to the experiment was that Coleman deliberately created pairs of particular size combinations.... [...and so on.] Notes: 1. The papers cited in the first paragraph are for background information. Some of them are secondary literature (e.g., reviews). These do not count in the three primary literature papers you are to utilize for this assignment. 2. Notice the underlined sentences at the end of the first paragraph. I have underlined them so that you will notice them – do not underline them in your paper. However, you should have roughly similar sentences in your paper at the end of the introduction providing a clear ROADMAP of where the paper is going and what it finds. 3. Do not describe the Methods in great detail but give enough information so that the reader has a good feeling for what was done, how many animals were used, whether it was a lab or field experiment, etc]
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Attach this Checklist to the back of your term paper Overall ___________________________ Printed name of proofreader
Author Proofreader
Ron Coleman
Name: _________________________________________
_________________________________ Signature of proofreader
___________ Date
_____ _____ There is a title page _____ _____ The pages are numbered, starting with the cover page as page 1 _____ _____ The paper is 11 pages in total (including the cover page) _____ _____ The paper is double-spaced _____ _____ You read your paper carefully for spelling and grammatical mistakes _____ _____ You have written a careful analysis of RESEARCH on a topic, not a description of a topic _____ _____ There are no quotations in the paper _____ _____ There is an introductory paragraph to introduce the topic _____ _____ There is a concluding paragraph at the end to bring the material together _____ _____ You have attached the draft (the one that I checked) to the back of this paper General Punctuation _____ _____ Every sentence ends with a period, exclamation point or question mark. _____ _____ Scientific names are written in italics, e.g., Lepomis macrochirus. _____ _____ The name of the Genus is capitalized and the specific epithet is NOT capitalized, e.g., Lepomis macrochirus, NOT Lepomis Macrochirus Citation of Literature In the body of the paper _____ _____ You used at least five pieces of primary literature _____ _____ You used "et al." when there are three or more authors _____ _____ You checked that "et al." is correctly written -- notice the "." after “al.” Do not put the words “et al.” in quotation marks in your paper. _____ _____ EVERY paper cited in the body of the paper is listed in the Literature Cited section Literature Cited section _____ _____ The papers are listed in alphabetical order by the last name of the first author _____ _____ You put an asterisk in front of each piece of primary literature in the Literature Cited section _____ _____ Papers with three or more authors have ALL authors listed fully in the Literature Cited section _____ _____ EVERY paper listed in the Literature Cited section is actually cited in the body of the paper
Note: All these things must be true or your grade will suffer severely. In addition, if you check these things off and they are not true, your grade will also suffer severely.
