Writing an Introduction for a Scientific Paper

Dr. Michelle Harris, Dr. Janet Batzli,

This section provides guidelines on how to construct a solid introduction to a scientific paper including background information, study question, biological rationale, hypothesis, and general approach. If the Introduction is done well, there should be no question in the reader’s mind why and on what basis you have posed a specific hypothesis.

Broad Question: based on an initial observation (e.g., “I see a lot of guppies close to the shore. Do guppies like living in shallow water?”). This observation of the natural world may inspire you to investigate background literature or your observation could be based on previous research by others or your own pilot study. Broad questions are not always included in your written text, but are essential for establishing the direction of your research.

Background Information: key issues, concepts, terminology, and definitions needed to understand the biological rationale for the experiment. It often includes a summary of findings from previous, relevant studies. Remember to cite references, be concise, and only include relevant information given your audience and your experimental design. Concisely summarized background information leads to the identification of specific scientific knowledge gaps that still exist. (e.g., “No studies to date have examined whether guppies do indeed spend more time in shallow water.”)

Testable Question: these questions are much more focused than the initial broad question, are specific to the knowledge gap identified, and can be addressed with data. (e.g., “Do guppies spend different amounts of time in water <1 meter deep as compared to their time in water that is >1 meter deep?”)

Biological Rationale: describes the purpose of your experiment distilling what is known and what is not known that defines the knowledge gap that you are addressing. The “BR” provides the logic for your hypothesis and experimental approach, describing the biological mechanism and assumptions that explain why your hypothesis should be true.

The biological rationale is based on your interpretation of the scientific literature, your personal observations, and the underlying assumptions you are making about how you think the system works. If you have written your biological rationale, your reader should see your hypothesis in your introduction section and say to themselves, “Of course, this hypothesis seems very logical based on the rationale presented.”

  • A thorough rationale defines your assumptions about the system that have not been revealed in scientific literature or from previous systematic observation. These assumptions drive the direction of your specific hypothesis or general predictions.
  • Defining the rationale is probably the most critical task for a writer, as it tells your reader why your research is biologically meaningful. It may help to think about the rationale as an answer to the questions—how is this investigation related to what we know, what assumptions am I making about what we don’t yet know, AND how will this experiment add to our knowledge? *There may or may not be broader implications for your study; be careful not to overstate these (see note on social justifications below).
  • Expect to spend time and mental effort on this. You may have to do considerable digging into the scientific literature to define how your experiment fits into what is already known and why it is relevant to pursue.
  • Be open to the possibility that as you work with and think about your data, you may develop a deeper, more accurate understanding of the experimental system. You may find the original rationale needs to be revised to reflect your new, more sophisticated understanding.
  • As you progress through Biocore and upper level biology courses, your rationale should become more focused and matched with the level of study e., cellular, biochemical, or physiological mechanisms that underlie the rationale. Achieving this type of understanding takes effort, but it will lead to better communication of your science.

***Special note on avoiding social justifications: You should not overemphasize the relevance of your experiment and the possible connections to large-scale processes. Be realistic and logical—do not overgeneralize or state grand implications that are not sensible given the structure of your experimental system. Not all science is easily applied to improving the human condition. Performing an investigation just for the sake of adding to our scientific knowledge (“pure or basic science”) is just as important as applied science. In fact, basic science often provides the foundation for applied studies.

Hypothesis / Predictions: specific prediction(s) that you will test during your experiment. For manipulative experiments, the hypothesis should include the independent variable (what you manipulate), the dependent variable(s) (what you measure), the organism or system, the direction of your results, and comparison to be made.



                      Hypothesis that Needs Work

(manipulative experiment)

Better Hypothesis

(manipulative experiment)

We hypothesized that Daphnia magna reared in warm water will have a greater sexual mating response.

(The dependent variable “sexual response” has not been defined enough to be able to make this hypothesis testable or falsifiable. In addition, no comparison has been specified— greater sexual mating response as compared to what?)

We hypothesized that Daphnia magna (STUDY ORGANISM) reared in warm water temperatures ranging from 25-28 °C (IND. VAR.) would produce greater (direction) numbers of male offspring and females carrying haploid egg sacs (DEPEND. VAR.) than D. magna reared in cooler water temperatures of 18-22°C.

If you are doing a systematic observation, your hypothesis presents a variable or set of variables that you predict are important for helping you characterize the system as a whole, or predict differences between components/areas of the system that help you explain how the system functions or changes over time.

Hypothesis that Needs Work

(systematic observation)

Better Hypothesis

(systematic observation)

We hypothesize that the frequency and extent of algal blooms in Lake Mendota over the last 10 years causes fish kills and imposes a human health risk.

(The variables “frequency and extent of algal blooms,” “fish kills” and “human health risk” have not been defined enough to be able to make this hypothesis testable or falsifiable. How do you measure algal blooms? Although implied, hypothesis should express predicted direction of expected results [e.g., higher frequency associated with greater kills]. Note that cause and effect cannot be implied without a controlled, manipulative experiment.)

We hypothesize that increasing (DIRECTION) cell densities of algae (VAR.) in Lake Mendota over the last 10 years is correlated with 1. increased numbers of dead fish (VAR.) washed up on Madison beaches and 2. increased numbers of reported hospital/clinical visits (VAR.) following full-body exposure to lake water.

Experimental Approach
: Briefly gives the reader a general sense of the experiment, the type of data it will yield, and the kind of conclusions you expect to obtain from the data. Do not confuse the experimental approach with the experimental protocol. The experimental protocol consists of the detailed step-by-step procedures and techniques used during the experiment that are to be reported in the Methods and Materials section.

Some Final Tips on Writing an Introduction

  • As you progress through the Biocore sequence, for instance, from organismal level of Biocore 301/302 to the cellular level in Biocore 303/304, we expect the contents of your “Introduction” paragraphs to reflect the level of your coursework and previous writing experience. For example, in Biocore 304 (Cell Biology Lab) biological rationale should draw upon assumptions we are making about cellular and biochemical processes.
  • Be Concise yet Specific: Remember to be concise and only include relevant information given your audience and your experimental design. As you write, keep asking, “Is this necessary information or is this irrelevant detail?” For example, if you are writing a paper claiming that a certain compound is a competitive inhibitor to the enzyme alkaline phosphatase and acts by binding to the active site, you need to explain (briefly) Michaelis-Menton kinetics and the meaning and significance of Km and Vmax. This explanation is not necessary if you are reporting the dependence of enzyme activity on pH because you do not need to measure Km and Vmax to get an estimate of enzyme activity.
  • Another example: if you are writing a paper reporting an increase in Daphnia magna heart rate upon exposure to caffeine you need not describe the reproductive cycle of magna unless it is germane to your results and discussion. Be specific and concrete, especially when making introductory or summary statements.

Where Do You Discuss Pilot Studies?
Many times it is important to do pilot studies to help you get familiar with your experimental system or to improve your experimental design. If your pilot study influences your biological rationale or hypothesis, you need to describe it in your Introduction. If your pilot study simply informs the logistics or techniques, but does not influence your rationale, then the description of your pilot study belongs in the Materials and Methods section. 


Introduction That Needs Work from an Intro Ecology Lab:

         Researchers studying global warming predict an increase in average global temperature of 1.3°C in the next 10 years (Seetwo 2003). (background info) Daphnia magna are small zooplankton that live in freshwater inland lakes. They are filter-feeding crustaceans with a transparent exoskeleton that allows easy observation of heart rate and digestive function. Thomas et al (2001) found that Daphnia heart rate increases significantly in higher water temperatures. (background info., not relevant or necessary) Daphnia are also thought to switch their mode of reproduction from asexual to sexual in response to extreme temperatures. (unreferenced background info) Gender is not mediated by genetics, but by the environment. Therefore, D. magna reproduction may be sensitive to increased temperatures resulting from global warming (maybe a question?) and may serve as a good environmental indicator for global climate change. (The latter part of this last sentence is an overzealous social justification for the experiment.)

         In this experiment we hypothesized that D. magna reared in warm water will switch from an asexual to a sexual mode of reproduction. (hypothesis) In order to prove this hypothesis correct we observed Daphnia grown in warm and cold water and counted the number of males observed after 10 days. (approach)


Background information

·       Good to recognize D. magna as a model organism from which some general conclusions can be made about the quality of the environment; however no attempt is made to connect increased lake temperatures and D. magna gender. Link early on to increase focus.

·       Connection to global warming is too far-reaching. First sentence gives impression that Global Warming is topic for this paper. Changes associated with global warming are not well known and therefore little can be concluded about use of D. magna as indicator species.

·       Information about heart rate is unnecessary because heart rate in not being tested in this experiment.


·       Rationale is missing; how is this study related to what we know about D. magna survivorship and reproduction as related to water temperature, and how will this experiment contribute to our knowledge of the system?

·       Think about the ecosystem in which this organism lives and the context. Under what conditions would D. magna be in a body of water with elevated temperatures?


·       Not falsifiable; variables need to be better defined (state temperatures or range tested rather than “warm” or “cold”) and predict direction and magnitude of change in number of males after 10 days.

·       It is unclear what comparison will be made or what the control is

·       What dependent variable will be measured to determine “switch” in mode of reproduction (what criteria are definitive for switch?)


·       Hypotheses cannot be “proven” correct. They are either supported or rejected.

Better Introduction
from an Intro Ecology Lab:

         Daphnia magna are small zooplankton found in freshwater inland lakes and are thought to switch their mode of reproduction from asexual to sexual in response to extreme temperatures (Mitchell 1999). Lakes containing D. magna have an average summer surface temperature of 20°C (Harper 1995) but may increase by more than 15% when expose to warm water effluent from power plants, paper mills, and chemical industry (Baker et al. 2000). (background info) Could an increase in lake temperature caused by industrial thermal pollution affect the survivorship and reproduction of D. magna? (study question)

         The sex of D. magna is mediated by the environment rather than genetics. Under optimal environmental conditions, D. magna populations consist of asexually reproducing females. When the environment shifts D. magna may be queued to reproduce sexually resulting in the production of male offspring and females carrying haploid eggs in sacs called ephippia (definition) (Mitchell 1999). (background info)

         The purpose of this laboratory study is to examine the effects of increased water temperature on D. magna survivorship and reproduction. This study will help us characterize the magnitude of environmental change required to induce the onset of the sexual life cycle in D. magna. (biological rationale) Because D. magna are known to be a sensitive environmental indicator species (Baker et al. 2000) and share similar structural and physiological features with many aquatic species, they serve as a good model for examining the effects of increasing water temperature on reproduction in a variety of aquatic invertebrates. (biological rationale)

         We hypothesized that D. magna (study organism) populations reared in water temperatures ranging from 24-26 °C (indep. Var) would have lower survivorship, higher [direction] male/female ratio among the offspring, and more female offspring carrying ephippia (depend. var) as compared with D. magna grown in water temperatures of 20-22°C. (hypothesis) To test this hypothesis we reared D. magna populations in tanks containing water at either 24 +/- 2°C or 20 +/- 2°C. Over 10 days, we monitored survivorship, determined the sex of the offspring, and counted the number of female offspring containing ephippia. (approach)


Background information

·       Opening paragraph provides good focus immediately. The study organism, gender switching response, and temperature influence are mentioned in the first sentence. Although it does a good job documenting average lake water temperature and changes due to industrial run-off, it fails to make an argument that the 15% increase in lake temperature could be considered “extreme” temperature change.

·       The study question is nicely embedded within relevant, well-cited background information. Alternatively, it could be stated as the first sentence in the introduction, or after all background information has been discussed before the hypothesis.


·       Good. Well-defined purpose for study; to examine the degree of environmental change necessary to induce the Daphnia sexual life

How will introductions be evaluated?
The following is part of the rubric we will be using to evaluate your papers.



0 = inadequate

(C, D or F)

1 = adequate


2 = good


3 = very good


4 = excellent



BIG PICTURE: Did the Intro convey why experiment was performed and what it was designed to test?


Introduction provides little to no relevant information. (This often results in a hypothesis that “comes out of nowhere.”)

Many key components are very weak or missing; those stated are unclear and/or are not stated concisely. Weak/missing components make it difficult to follow the rest of the paper.

e.g., background information is not focused on a specific question and minimal biological rationale is presented such that hypothesis isn’t entirely logical


Covers most key components but could be done much more logically, clearly, and/or concisely.

e.g., biological rationale not fully developed but still supports hypothesis. Remaining components are done reasonably well, though there is still room for improvement.

Concisely & clearly covers all but one key component (w/ exception of rationale; see left) OR clearly covers all key components but could be a little more concise and/or clear.

e.g., has done a reasonably nice job with the Intro but fails to state the approach OR has done a nice job with Intro but has also included some irrelevant background information


Clearly, concisely, & logically presents all key components: relevant & correctly cited background information, question, biological rationale, hypothesis, approach.