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Principles of Organization

Think of your dissertation or thesis in terms of macro organization.

Think of individual body paragraphs in terms of micro organization.

Both macro and micro follow the same basic principles of organization.

Here's the macro (paper-level) arrangement:

Here's the micro (paragraph-level) arrangement:

Compared, they match up like this:
Paper Paragraph
1.Thesis 1. Topic Sentence
2. Supporting Material 2. Supporting Material
3. Conclusion 3. Concluding Sentence

1. Both grab the reader's attention with a line that pertains directly to the topic.
*2. Both offer examples, evidence, and quotations to support the assertion already presented in # 1.

3. Both reaffirm in different words the assertion under discussion.

* A special consideration: In any persuasive/argumentative work, you should present your least important evidence first, saving your strongest point for last. Remember, in general, readers remember best what readers read last.

Transitions between paragraphs ensure that the reader makes a smooth connection between what has been said already and what is now being said. Place your transition at the beginning of the new paragraph. A transition can take one of three forms:

  1. a single word: "Furthermore"
  2. a short phrase: "In contrast to this pattern"
  3. a complete sentence: "A second pattern emerges when the temperature is lowered."

On occasion and if appropriate, a rhetorical question can serve as an effective transition: "Is this, then, the only effective approach that may be taken?"

Transition words indicate relationships. Here is a list of some possible relationships:

and, also, again, moreover, furthermore, then, in addition--etc.
but, yet, however, nevertheless, in contrast, conversely--etc.
because, accordingly, as a result, consequently--etc.
for example, for instance, namely--etc.
for one thing, first, second, last, finally--etc.
alternately, on the other hand--etc.

Rules for organizing the Master's thesis tend to be more flexible. Look for models in recently completed theses, usually available through your department or in the library.

The second example is a paper that comes from the plant sciences. Notice several key differences that characterize scientific publications. First, an abstract or summary usually precedes the introduction. Second, the section devoted to how the research was done is usually called "Materials and Method." (This particular example omits a literature review.)

Remember that different departments will have different organizational requirements.

Always consult your departmental rules and follow them exactly!


Underline (italicize) genus and species. Capitalize genus only.

Summarize paper's most important contents using past tense. Use present to suggest a general conclusion.



Label and begin on same page as Abstract. In longer paper or journal manuscript, start new page.

Spell out Colletotrichumonce, then abbreviate it when prededing speciews name.

For background, briefly review pertinent literature. Name-and-year method is used here to cite sources. Use persent tense to refer to established knowledge.

















Describe procedures in enough detail for others to repeat study.






Number figure even though only one is given. Identify important findings of gragh.


Interpret results or compare with other studies. Summarize results of statistical ...


Spores of the fungus Colletotrichum lindemuthianumwere germinated under different sucrose concentrations in the range 1 × 10-1 to 1 × 10-7 M. The formation of germ tubes with appressoria, as opposed to germ tubes only, decreased with increasing sucrose concentration. This finding may be significant in light of the leaching of sugars onto plant surfaces. Export of such substances may decrease the frequency of appressoria formation and reduce the likelihood of infection by parasitic fungi.


The fungus Colletotrichum lindemuthianum causes anthracnose, a disease of green beans (Phaseolus vulgaris). Once on the surface of a bean seedling or pod, a germinating spore of C. lindemuthianum typically forms a short germ tube that swells to form a spherical structure called an appressorium. The fungus then penetrates the host tissues from the appressorium. The morphology and roles of appressoria have been reviewed by Emmett and Parberry (1975). In laboratory experiments using etiolated hypocotyls of P. vulgaris sprayed with aqueous suspensions of spores of C. lindemuthianum, appressoria develop from most spores, usually on the ends of very short germ tubes (Skipp and Deverall 1974). Longer germ tubes (ones longer than about four times the average length of a spore) do not ever form appressoria and thus fail to penetrate the host tissue (Arnold and Lyons 1982).

In culture on agar media supplemented with sugars as carbon source, C. lindemuthianum spores produce germ tubes but no appressoria. However, spores suspended in distilled water do form appressoria (R. M. Arnold, pers. comm.) These observations suggested a need to determine the effect of nutrients in the culture medium on germination in this species. Arnold and Lyons (1982) showed that fewer appressoria are formed when spores of C. lindemuthianum are incubated in sucrose solutions. In this paper, I describe a more detailed study on the germination of this fungus under increasing concentrations of sucrose.


C. lindemuthianum was grown for 10 days on agar containing 35% bean juice. I made spore suspensions by flooding the petri plates with distilled water and gently rubbing the surface of the agar with a glass rod. The spores were washed by low-speed centrifugation in distilled water three times. Then they were mixed with serial dilutions of a stock sucrose solution (2 × 10-1 M) to give final sucrose concentrations in the range 1 × 10-1 to 1 × 10-7 M. I also prepared a control containing distilled water. A syringe was used to place 25-µ1 droplets of the spore suspensions in water or sucrose solutions on clean glass microscope slides. A cover glass was added to each and the slides were incubated in high humidity conditions for 24 h. After incubation, the preparations were examined microscopically. Spores in randomly selected fields of view wore classified according to germination morphology (appressorium or germ tube only.)


As shown in Figure 1, the proportion of spores that formed appressoria at the ends of germ tubes decreased with increasing sucrose concentration. Sucrose concentration did not significantly affect the proportion of spores that germinated in a treatment (X2 = 9.26, df =7, P > .05).


In this study, the mode of germination in C. lindemuthianum was affected by nutrient characteristics of the culture medium, with the production of germ tubes without appressoria occurring at high sucrose concentrations. This finding is in accord with data of Arnold and Lyons (1982). Appressoria formation is characteristic of the parasitic phase of the fungus, while germ tube formation without appressoria is associated with a saprobic or nonparasitic phase (Leach 1923).

In nature, sugars and other organic molecules leach onto plant surfaces (Godfrey 1976), presumably through stomata or other natural openings, in an apparently wasteful process. The findings reported in this paper suggest that, although these substances may encourage the growth of saprobic fungi, they may also make a potentially parasitic fungus grow only in a saprobic manner. Thus, the export of organic molecules to plant surfaces may have an adaptive value in helping to keep parasitic fungi outside plants.


I thank Dr. R. M. Arnold for his advice during all stages of the project, and Ms. Jennifer Arnold for critically reviewing the manuscript.


Arnold, R. M., and B. M. Lyons. 1982. Laboratory investigations using the anthracnose disease of beans. Am. Biol. Teach. 44:51-55. 

Emmett, R. W., and D. G. Parberry. 1975. Appressoria. Ann. Rev. Phytopathol. 13:147-167. 

Godfrey, B. E. S. 1976. Leachates from aerial parts of plants and their relation to plant surface microbial populations. Pages 433-439 in C. H. Dickinson and T. F. Preece, eds. Microbiology of aerial plant surfaces. Academic Press, London. 

Leach, J. G. 1923. The parasitism of Colletotrichum lindemuthianum. Minn. Agr. Exp. Sta. Tech. Bull. 14:1-44.

3.2.3 Clarity and Structure

Words are not meaningful unless they are meaningfully ordered; therefore, clarity is dependent on structure as well as words. The two main structural prerequisites for clarity are coherence and conciseness. Conciseness is also required to save space in journals and to save readers' time and effort.

Coherence. Coherence is the ordering of words into sentences, sentences into paragraphs, and so on, so that they develop a closely reasoned, logical, line of thought, both within and between units. Coherence is fundamental to clarify and makes the greatest demands on writers to think, write, and read clearly. Writers must formulate their ideas and then find the words and syntactic structures to express them so that they represent the conceptual structure of their thinking. This translation is very difficult, because there is no direct correspondence between thoughts and their formal expression in words.
The conventional sections of the paper establish the overall structure and so lay the ground for a coherent presentation. Once the line of development has been established for a section, the order of the paragraphs follows, and each paragraph contributes to the line of development. Therefore, much of the writing is focused on structuring paragraphs and the sentences in them.
The paragraph must have unify if it is to be coherent. A collection of sentences on different topics is not a paragraph; neither is a collection of sentences on one topic-the related sentences must be coherently ordered. That is, the sentences within the paragraph must be so ordered and structured that there is a line of thought that begins with the opening sentence and terminates with the last sentence of a paragraph. The paragraph may be variously developed. It has no prescribed shape except that which is prescribed by the structure of the message, but it must have an orderly structure.
In establishing order in a paragraph, the research scientist cannot depend on the topic sentence, the key structuring device recommended for much general writing. A topic sentence is a general statement that states the topic or subject of the paragraph and is developed by succeeding sentences. Instead of topic sentences, research scientists require a kind of organizing structure that allows the specific, detailed, and complex relationships found in scientific research to be developed into a logical line of thought. This can be accomplished to some extent, externally, by connectives, that is, transitional words or phrases. Scientists sometimes express the connections implicitly by structuring successive sentences so that their content and meaning expresses the relationship. Such implicit connections leave readers adrift or require them to supply connections from the context and structure alone. This is not conducive to clarity, since the reader's connection may only approximate the connection that the writer intended.

Carbohydrate loading on the High Performance Diet was developed in the United States based on studies by a team of Swedish physiologists. These studies show that the average concentration of glycogen stores is 1.75 g/100 ml with a normal diet. If this diet is then changed for 3 days to one of high fat and high protein, then the glycogen level drops to .6 g/100 ml. If the diet is modified again to include large amounts of carbohydrate for 3 days, then the glycogen stores will increase to 3.5 g/100 ml. If this carbohydrate phase is accompanied by strenuous exercise, then the glycogen level will rise to 4.7 g/100 ml. This is almost a three-fold increase in glycogen stores compared to a normal diet.

Figure 3.1. Paragraph illustrating coherence achieved by hook-and-eye linkage. Word (in oval) in one sentence linked to word (in rectangle) in preceding sentence.

Internal connections are more effective and important constructions for achieving coherence in scientific writing. A kind of hook-and-eye construction, in which one sentence is explicitly connected to the preceding sentence, clearly establishes the relation between the two sentences. This is accomplished by relating one sentence, often the beginning of it, to the preceding sentence by repeating a word or phrase from the preceding sentence, or by referring to a word directly or indirectly.

The example in Fig. 3.1 illustrates this kind of connection in an almost exaggerated form. Near the end of each sentence is a word (the eye), which is in the central line of development of the sentence. Near the beginning of the next sentence the same or a similar word (the hook) links the rest of the sentence to the preceding one and thus continues to develop the line of thought. The hook and eye need not be the same word (see Ex. 11.8), but they must be clearly and closely enough related that the link between them can be readily recognized.

Coherence at the sentence level, referred to as cohesion, requires the internal ordering of a sentence syntactically and meaningfully so that the parts clearly make the statement intended and the sentence forms part of the logical progression of the paragraph.

Coherence is also effected by consistency. A consistent point of view avoids distracting the reader from the main approach in the presentation. Consistency of form makes clear the coordinate character of the elements in a series or list, or the parallelism of concepts. Consistency in the titles of tables and figures, in footnotes, and in bibliographic references provides a formal order, which allows the various parts to emerge as ordered units, and thus contributes to clarity.