Please find all previous posts in pdf format, arranged by date:

what to expect: term papers

reading the primary scientific literature

how to critique

picking a topic

the role of citations and citation style

reading and writing about statistics

outlining and reverse outlining

thesis statements

using idea maps

transitions and flow

structuring your paper

anticipating counterarguments

sentence level revision

last minute checklist

Make sure you have done all of the following actions before handing in your term paper:

1. Use scientific names correctly.
Remember that all species names should be italicized. When you mention a species for the first time in your paper, list both the generic and specific names (e.g. Chrysoperla lucasina). When you talk about the same species again, use only the first initial of the generic name (e.g. C. lucasina) unless this makes things confusing. Never use the specific name alone.

Articles are not used with scientific names. Consider the following examples (McMillan 2001):

The most common lichen at both sampling sites was the Lecidea atrata.

Taxonomic groups or taxa above the level of genus are capitalized but not italicized (e.g. Chrysopidae).

Common names, including informal common names that are really taxon names with the ending removed, are not capitalized (e.g. chrysopids, green lacewings).

When one or more species you are discussing have yet to be formally described, after the generic name use sp. for a single species and spp. for two or more species (e.g. Chrysoperla sp.).

2. Match your in-text citations with your reference section.
Check to see whether you have cited all of the articles in your reference section. If not, remove the offenders.

3. Read your paper slowly out loud, or have a friend read it to you.
This is the easiest way to catch grammatical errors. This is also a good opportunity to check the flow of your paper. Flow can be greatly improved by varying the length of your sentences with a paragraph. For instance, if all of your sentences are short, your writing will seem choppy. If your sentences tend to be too long, well, your writing will either seem boring or will be confusing.

4. Format your paper one last time.
The term paper requirement is 12 point, double spaced, with 1-inch margins and page numbers.

Good luck! It’s been a long road, so enjoy your new scientific writing skills and revisit this blog whenever you need to. I’ll be posting pdf files of all of the blog posts, hopefully by the end of finals.

Science writing is known for its clear and concise prose. It is also known for being dry and boring. The contrasting impressions of science writing stem from the fact that good writing skills are often underdeveloped in scientists. You will need to learn to master these skills over several years of practice, but for now, you can work on making sure that your writing gets across your thesis by carefully revising for style.

For clarity, read carefully through your own work and make sure all of your sentences are unambiguous in meaning. This means that your sentences should meet the following criteria in the least:

1. Each sentence should have a subject and verb
The lack of subject and/or verb often occurs when you try to write in the passive voice. While many scientists do use passive voice in their writing, it is not a requirement in most circles or journals anymore. I would say that it would be much better if you can get across the same professional standpoint with an active voice. For example, the following sentences are much improved when rewritten in the active voice (McMillan 2001):

(Original) Territory size was found to vary with population density.
(Rewrite) Territory size varied with population density.

(Original) Nest destruction was caused primarily by raccoons, particularly late in the incubation period, when greater access to nests was afforded to them by lowered water levels.
(Rewrite) Raccoons caused most nest destruction, particularly late in the incubation period when lowered water levels allowed them greater access to nests.

2. Try not to use vague pronouns such as this, that, it, and which. Most sentences become confusing when you use these pronouns. For instance, it is unclear whether the following “this” refers to not being able to predict the number of adult males, or the daily variation in male density (McMillan 2001):

We could not predict the number of adult males likely to visit each breeding site because male density in the surrounding forest varied greatly from day to day. This is typical of most field studies on this species.

3. Because many terms used in science have specific scientific meanings that are slightly different from the colloquial sense, you must use these properly. Here are some examples (McMillan 2001):

Correlated, random, significant – all of these terms should be used in the statistical sense
Rate – a rate should be a measurement over a certain unit of time
i.e. and e.g.i.e. is the abbreviation for the latin phrase id est, or “that is”, whereas e.g. is short for exempli gratia, or “for example”
Varying vs. various – varying means that a measure is changing over time or with changing circumstances, while various means different
Fact, proof – there are very few scientific facts, most of what you think are facts would be classified as evidence or support for certain theories or hypotheses

For conciseness, you will be able to achieve quite a bit by doing just the following:

1. Do not hedge, and do not use modifiers such as very, quite, and rather. It is important that you are careful when drawing conclusions, but if your evidence is strong, you should make sure that is comes across as such. Take a look at the following example (Pechenik 2004):

(Original) This suggests the possibility that inductive interactions between cells may be required for the differentiation of nerve tissue.
(Rewrite) This suggests that inductive interactions are required for the differentiation of nerve tissue.

2. Replace the following wordy phrases with its concise alternative (from McMillan 2001; Knisely 2005):

A second point is that -> second
More often than not -> usually
It is apparent that -> apparently
At the present time -> now
In previous years -> previously
Owing to the fact that, due to the fact that, based on the fact that, in light of the fact that , on account of -> because
Despite the fact that, in spite of the fact that -> although, though
One of the problems -> one problem
In only a very small number of cases -> occasionally, rarely
In the possible event that -> if
So as to -> to
With regard to -> by, with
With the exception of -> except
With the result that -> so that
In a manner similar to -> like
Is dependent upon -> depends on
It is also worth pointing out that (omit)
Before concluding, another point is that (omit)
It is interesting to note that (omit)
In fact (omit)
Functions to, serves to (omit)

If you’ve been working on your structure and arguments, going through the list above should help with improving the readability of your paper. Finally, I’ll leave you with the following humorous list from Day and Gastel (2006):

The Ten Commandments of Good Writing

1. Each pronoun should agree with their antecedent.
2. Just between you and I, case is important.
3. A preposition is a poor word to end a sentence with.
4. Verbs has to agree with their subject.
5. Don’t use no double negatives.
6. Remember to never split an infinitive.
7. Avoid clichés like the plague.
8. Join clauses good, like a conjunction should.
9. Do not use hyperbole; not one writer in a million can use it effectively.
10. About sentence fragments.

Last week, I briefly mentioned that authors often address previous findings in the literature that demonstrate the opposite of the point they are trying to make. They do this because topics related to evolution tend to be contentious, so discussing both sides of an argument up front can make your point more compelling.

In order to use this strategy in your own writing, first try to find counterarguments that are already voiced and published, either within your sources or in articles that are written in response to the primary sources you are reading. The latter will typically have the word “response” or “comment” in their titles, e.g. Comment on “The latitudinal gradient in recent speciation and extinction rates of birds and mammals” (Seddon et al. 2008). Make notes of the reasoning that is being pointed out to you, so that you can build on it later.

Next, read through your own paper carefully and make sure you have your major points and supporting evidence clearly lined up, such as in your outline. Then try to come up you’re your own counterpoints by considering questions such as these (adapted from Hacker (2007)):

Could a reasonable person draw a different conclusion from the information you present?

Might a reader question any of your assumptions?

Could a reader offer an alternative explanation of this issue?

The first two questions are actually reflecting what potential flaws you might have in your argument. In the first case, imagine your reader going, “But doesn’t this mean A instead of B?” in response to your paper. If this seems possible, it means that your logic is not entirely sound. You may not be presenting enough information or you might be presenting what information you have ineffectively. You will have to go back and add more information from yours or other sources, or tweak the structure of your argument. In the second case, you probably need to do a better job at explaining the theoretical background of your thesis. In the third case, your reader might be saying “But this could also mean E rather than F.” after reading your paper, thereby presenting a true counterpoint.

Now, in order to address the counterpoints, consider the following tactics (from Hacker (2007)):

Explain why readers should consider a new perspective or question a piece of evidence

Qualify your position in light of contradictory evidence

Suggest a different interpretation of the counterevidence

For the first tactic, consider whether new theories or hypotheses been proposed recently, or have new techniques been developed that would allow more stringent hypothesis testing. Maybe your readers aren’t aware of new developments and need to be informed. For the second tactic, evaluate whether some of your explanations rely on specific conditions, or are only applicable in certain systems. You may be able to qualify your specific case, thereby justifying your explanation. For the last tactic, see if you can interpret the counterevidence according to your own logic and see if it makes sense.

Let’s look at an example of how this is accomplished in practice. The following is an excerpt from Tobias et al. (2008), with citations removed:

A second key issue raised by our data is that tropical lineages tend not to bifurcate but to proliferate. This makes sense because, as noted elsewhere, populations at low latitudes are typically sedentary and susceptible to subdivision by multiple barriers. By diverging concurrently, an ancestral Hypocnemis population generated six daughter species at a rate of 1.8 lineages per million years (Fig. 1). The sister-species method produced a low rate estimate of 0.2 lineages per million years for equatorial species, perhaps because it assumes that lineage splitting is sequential. Sequential splitting may approximate the situation at high latitudes, but it ignores the contribution of parallel speciation events in the tropics. Thus, methodological biases may in part explain why Weir and Schluter found lower diversification rates in tropical taxa, whereas analyses of net diversification rate produce the opposite result.

Next is an excerpt from Weir and Schluter (2008), a response to Tobias et al. (2008), again with citations removed:

Our method is most vulnerable to the assumption of a constant-rate birth-death process. Tobias et al.’s point that “tropical lineages tend not to bifurcate but to proliferate” is a special case of this more general rate problem. As we stated in, geological and climatic events likely concentrated speciation and extinction events in episodes. However, we find little evidence to support that tropical lineages are more prone to such bursts than temperate lineages. Indeed, it might be the case that the temperate zone has experienced the most recent series of bursts, namely in the Pleistocene. We also emphasized that our rate estimates apply only to recent time periods—that covered by the ages of most sister species. More even coverage of a longer temporal record (extending before 10 million years) would be needed to determine by how much our estimates based only on sister species would need to be revised.

The italicized portions indicate where each set of authors are addressing each others’ criticisms. You can see some questioning of assumptions from both parties, and qualifying of positions. Through such response papers as well as standard research papers, researchers make it a point to strengthen their position as much as possible and you should be practicing those skills in your term paper.

Let’s discuss how to effectively structure your term paper.

Term papers generally have 3 sections: an introduction, a body or discussion, and a conclusion. The different sections of your term paper should relate to each other in the following way.

The introduction is a prelude to the body or discussion of a term paper or any type of scientific paper. (Because of this, it is either written last, or rewritten after the discussion is finished; it is difficult to know how to start a story if you don’t know the end.) It should provide a general background to your topic, and contain a thesis statement towards the end. It should also briefly mention what evidence for your thesis you will be discussing later on. This means that specific details should be saved for the discussion. For instance, the following is an excerpt from an introduction from Klappert and Reinhold (2005), with the thesis statement in italics:

Two main processes, deleterious mutations and coevolutionary host parasite cycles, have been proposed to maintain genetic variance in [male] fitness. Here, we will address a third possible mechanism for the maintenance of genetic variance in fitness: migration between locally adapted populations. This hypothesis has only recently been examined in detail although it has been proposed as a possible mechanism for the maintenance of genetic variance in fitness before.

If individuals are genetically adapted to their local environmental conditions, and if migration occurs between populations that differ in their local adaptations, then migration can lead to the maintenance of genetic variance because it causes genes to occur in environments for which they are not adaptive. There is considerable evidence showing that local adaptation is widespread in plants and animals and local adaptation has even occurred in artificial selection experiments. In some of these studies, local adaptation was found to have a large effect on male mating success. Theoretically, the combined existence of local adaptation and migration between populations can thus cause the maintenance of genetic variance in fitness that is necessary for the good genes hypothesis, and females should benefit from choosing locally adapted males.

As you can see, the authors are planning to focus on the local adaptation hypothesis, to show that local adaptation, when females prefer locally adapted males, is a valid mechanism that could maintain male genetic variance, and in turn, female choice. They give you a glimpse of what kinds of evidence they might discuss later on. Most importantly, their thesis is very clear.

Your discussion should be closely tailored to match your thesis statement, and correspond to your introduction. If you are working from an outline, using headings from your outline can help make the structure of your discussion more transparent. From the example above, we can predict that the authors will probably go on to discuss examples of local adaptation from (1) plants and animals and (2) artificial selection experiments. They will then discuss specific cases, presumably from the examples they present, where local adaptation had a large effect on male mating success. They may also consider explanations as to why some studies found contradicting or negative evidence for the local adaptation hypothesis (Klappert and Reinhold 2005):

The observed preference of females for males from their own population may also indicate that male traits and female preferences have diverged for other reasons. In great reed warblers and great tits, where male traits probably did not differ between populations, resident females also seem to prefer native males over immigrants. Since these analytical studies were not focused on examining the effect of local adaptation on attractiveness, the difference in attractiveness between residents and migrants might, for example, also be explained by an increased migration tendency of less fit individuals. Experimental studies specifically aimed at testing the hypothesis that choice of locally adapted males contribute to the maintenance of female choice are therefore necessary.

In the end, you must show through careful discussion that you have thoroughly understood your topic. Based on the evidence you present in the discussion, you must then come to a strong conclusion. Conclusions typically summarize the thesis statement, the evidence, and then present the final verdict. Imagine that your reader just finished your term paper and asked you, “So what? What does this all mean? What next?” (McMillan 2001). Your conclusion should aim to answer those questions, by emphasizing the theoretical significance, pointing out the conflicts that need to be resolved, and indicating what further directions need to be taken.

Now that you have a framework for your term paper, how do you go about connecting those ideas from your outline or idea map into a well-written draft?

Think of writing a paragraph for each point or topic sentence, or make sure you already have one topic [sentence] per paragraph. Afterwards, within each paragraph, use transitional words or phrases to ensure your detail sentences lead the reader along a premeditated logical sequence that reinforces your topic sentence. (Imagine in your mind, your reader exclaiming, “Of course, that makes perfect sense!”, after reading each of your paragraphs.) For instance, let’s take a look at the following example from Hacker (2007), where she has italicized all transitions in an excerpt from Stephen Jay Gould’s, “Were Dinosaurs Dumb?”:

I don’t wish to deny that the flattened, miniscule head of largebodied Stegosaurus houses little brain from our subjective, top-heavy perspective, but I do wish to assert that we should not expect more of the beast. First of all, large animals have relatively smaller brains than related, small animals. The correlation of brain size with body size among kindred animals (all reptiles, all mammals, for example) is remarkably regular. As we move from small to large animals, from mice to elephants or small lizards to Komodo dragons, brain size increases, but not so fast as body size. In other words, bodies grow faster than brains, and large animals have low ratios of brain weight to body weight. In fact, brains grow only about two-thirds as fast as bodies. Since we have no reason to believe that large animals are consistently stupider than their smaller relatives, we must conclude that large animals require relatively less brain to do as well as smaller animals. If we do not recognize this relationship, we are likely to underestimate the mental power of very large animals, dinosaurs in particular.

In order to use transitions effectively, you will need to understand how your sentences within a given paragraph work together. Below is a list of common transitions you can use in order for your sentences to fulfill each function (from Hacker 2007).

  • To show addition – and, also, besides, further, furthermore, in addition, moreover, next, too, first, second
  • To give examples – for example, for instance, to illustrate, in fact, specifically
  • To compare – also, in the same manner, similarly, likewise
  • To contrast – but, however, on the other hand, in contrast, nevertheless, still, even though, on the contrary, yet, although
  • To summarize or conclude – in other words, in short, in summary, in conclusion, to sum up, that is, therefore
  • To show time – after, as, before, next, during, later, finally, meanwhile, since, then, when, while, immediately
  • To show place or direction – above, below, beyond, farther on, nearby, opposite, close, to the left
  • To indicate logical relationship – if, so, therefore, consequently, thus, as a result, for this reason, because, since

These transitions should also be placed between paragraphs in order for your draft as a whole to flow as well as that previous paragraph. If you remember that your term paper as a whole should make sense, more-or-less, with only your topic sentences, it is natural to try to make those topic sentences connect with each other through transitions. Let’s take at another example from Hacker (2007), which is an excerpt from Jonathan H. Alder’s “Little Green Lies”, with topic sentences marked by italics:

Consider aseptic packaging, the synthetic packaging for the “juice boxes” so many children bring to school with their lunch. One criticism of aseptic packaging is that it is nearly impossible to recycle, yet on almost every other count, aseptic packaging is environmentally preferable to the packaging alternatives. Not only do aseptic containers not require refrigeration to keep their contents from spoiling, but their manufacture requires less than one-10th the energy of making glass bottles.
What is true for juice boxes is also true for other forms of synthetic packaging. The use of polystyrene, which is commonly (and mistakenly) referred to as “Styrofoam,” can reduce food waste dramatically due to its insulating properties. (Thanks to these properties, polystyrene cups are much preferred over paper for that morning cup of coffee.) Polystyrene also requires significantly fewer resources to produce than its paper counterpart.

Hacker and I disagree on which sentence in the first paragraph is the topic sentence, but you can see that Alder is using transitions as well as the phrases “aseptic packaging” and “synthetic packaging” to sustain his argument between the paragraphs.

Read through your draft after you have added all the information you would like it to contain, and see if everything makes sense. If it doesn’t quite seem to, determine whether this is because you don’t have all the information you need to support your thesis (in which case you need to do more research and reading), or whether you haven’t quite structured your argument as well as you could have. In the latter case, adding transitions may help because this will force you to make your thought process explicit. For instance, you will have to determine whether you were trying to give an example, or were trying to compare or contrast ideas in order to use the appropriate transition

245W: Using idea maps

By now you should have something resembling a strong thesis or point of view about your topic. In order for your paper to be “successful”, it should be able to persuade your reader into seeing the validity of your point. Both outlines and idea maps are good tools for achieving this goal. Since we discussed outlines a few weeks ago, let’s look at idea maps this week.

Idea maps or mind maps are ways to visually represent your thought process in a non-hierarchical non-sequential manner. By thinking about the points you are trying to make in a non-sequential order, you can start organizing them into conceptually related or logically descending categories or clusters. By looking at things in a non-hierarchical way, you can create room to expand your thoughts and make your own connections instead of blindly following those of others. For instance, writers can easily fall into the trap of writing about sequential happenings. This would be the equivalent of writing a lab report methods or results section in the order in which you collected and analyzed your data, instead of organizing it by conceptually similar or hierarchically related parts. In a term paper, you might find yourself writing about a series of papers in the order in which you read them, instead of organizing the evidence from each paper into logical groups.

Let’s take a look at idea mapping in practice. I’m reading a paper on whether drumming in the wolf spider Hygrolycosa rubrofasciata is a sexually selected character (Parri et al. 2002). I’ll use the free software FreeMind (Müller et al. 2000-2008; available for download here) to build my idea map, but it is much easier to do it on a blank unruled piece of paper. Here are some of the points that I thought were interesting from the paper randomly linked to my main topic:

Figure 1. Start of an idea map with interesting points randomly linked to central topic.

Next I started organizing these points in a way that made more sense, and added some of my own questions. My points fell into more or less two groups. The first are associated with the question of sexual selection:

Figure 2. More developed idea map with points grouped into theoretically related clusters.

The second are associated with the organism, i.e. spiders, or more specifically wolf spiders:

Figure 3. The other side of Figure 2.

Either or even both of these encompassing ideas would be a great way to start a term paper. Because the idea map is based on only a single paper, the questions and points in the map are somewhat shallow. There are also a few points that I’ve neglected to follow up on because they don’t interest me as much as the others. Here’s my final idea map that I’ve made to resemble more of an outline:

Figure 4. Final idea map organized to resemble an outline for a term paper.

I hope it’s already apparent to you how useful idea maps can be. Just like an outline, it is easy to spot gaps and excesses in your ideas when you have a visual representation.


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