by Martyn Shuttleworth (2009)
Often, one of the trickiest parts of designing and writing up any research paper is how to write a hypothesis.
The entire experiment and research revolves around the research hypothesis (H1) and the null hypothesis (H0), so making a mistake here could ruin the whole design.
Needless to say, it can all be a little intimidating, and many students find this to be the most difficult stage of the scientific method.
In fact, it is not as difficult as it looks, and if you have followed the steps of the scientific process and found an area of research and potential research problem, then you may already have a few ideas.
It is just about making sure that you are asking the right questions and wording your hypothesis statements correctly.
THE THREE-STEP PROCESS
Often, it is still quite difficult to isolate a testable hypothesis after all of the research and study. The best way is to adopt a three-step hypothesis; this will help you to narrow things down, and is the most foolproof guide to how to write a hypothesis.
Step one is to think of a general hypothesis, including everything that you have observed and reviewed during the information gathering stage of any research design. This stage is often called developing the research problem.
AN EXAMPLE OF HOW TO WRITE A HYPOTHESIS
A worker on a fish-farm notices that his trout seem have more fish lice in the summer, when the water levels are low, and wants to find out why. His research leads him to believe that the amount of oxygen is the reason – fish that are oxygen stressed tend to be more susceptible to disease and parasites.
He proposes a general hypothesis.
“Water levels affect the amount of lice suffered by rainbow trout.”
This is a good general hypothesis, but it gives no guide to how to design the research or experiment. The hypothesis must be refined to give a little direction.
“Rainbow trout suffer more lice when water levels are low.”
Now there is some directionality, but the hypothesis is not really testable, so the final stage is to design an experiment around which research can be designed, a testable hypothesis.
“Rainbow trout suffer more lice in low water conditions because there is less oxygen in the water.”
This is a testable hypothesis – he has established variables, and by measuring the amount of oxygen in the water, eliminating other controlled variables, such as temperature, he can see if there is a correlation against the number of lice on the fish.
This is an example of how a gradual focusing of research helps to define how to write a hypothesis.
THE NEXT STAGE – WHAT TO DO WITH THE HYPOTHESIS
Once you have your hypothesis, the next stage is to design the experiment, allowing a statistical analysis of data, and allowing you to test your hypothesis.
The statistical analysis will allow you to reject either the null or the alternative hypothesis. If the alternative is rejected, then you need to go back and refine the initial hypothesis or design a completely new research program.
This is part of the scientific process, striving for greater accuracy and developing ever more refined hypotheses.
Source: http://www.experiment-resources.com/how-to-write-a-hypothesis.html
Showing posts with label Thesis. Show all posts
Showing posts with label Thesis. Show all posts
Monday, April 26, 2010
NULL HYPOTHESIS
by Martyn Shuttleworth (2008)
The null hypothesis, H0, is an essential part of any research design, and is always tested, even indirectly.
The simplistic definition of the null is as the opposite of the alternative hypothesis, H1, although the principle is a little more complex than that.
The null hypothesis is a hypothesis which the researcher tries to disprove, reject or nullify.
The 'null' often refers to the common view of something, while the alternative hypothesis is what the researcher really think is the cause of a phenomenon.
An experiment conclusion always refers to the null, rejecting or accepting H0 rather than H1.
Despite this, many researchers neglect the null hypothesis when testing hypotheses, which is poor practice and can have adverse effects.
EXAMPLES OF THE NULL HYPOTHESIS
A researcher may postulate a hypothesis:
H1: Tomato plants exhibit a higher rate of growth when planted in compost rather than in soil.
And a null hypothesis:
H0: Tomato plants do not exhibit a higher rate of growth when planted in compost rather than soil.
It is important to carefully select the wording of the null, and ensure that it is as specific as possible. For example, the researcher might postulate a null hypothesis:
H0: Tomato plants show no difference in growth rates when planted in compost rather than soil.
There is a major flaw with this null hypothesis. If the plants actually grow more slowly in compost than in soil, an impasse is reached. H1 is not supported, but neither is H0, because there is a difference in growth rates.
If the null is rejected, with no alternative, the experiment may be invalid. This is the reason why science uses a battery of deductive and inductive processes to ensure that there are no flaws in the hypotheses.
Many scientists neglect the null, assuming that it is merely the opposite of the alternative, but it is good practice to spend a little time creating a sound hypothesis. It is not possible to change any hypothesis retrospectively, including H0.
SIGNIFICANCE TESTS
If significance tests generate 95% or 99% likelihood that the results do not fit the null hypothesis, then it is rejected, in favor of the alternative.
Otherwise, the null is accepted. These are the only correct assumptions, and it is incorrect to reject, or accept, H1.
Accepting the null hypothesis does not mean that it is true. It is still a hypothesis, and must conform to the principle of falsifiability, in the same way that rejecting the null does not prove the alternative.
PERCEIVED PROBLEMS WITH THE NULL
The major problem with the null hypothesis is that many researchers, and reviewers, see accepting the null as a failure of the experiment. This is very poor science, as accepting or rejecting any hypothesis is a positive result.
Even if the null is not refuted, the world of science has learned something new. Strictly speaking, the term ‘failure’, should only apply to errors in the experimental design, or incorrect initial assumptions.
DEVELOPMENT OF THE NULL
Up until the 1500's most people thought that the world was flat (At the time: The null hypothesis). Columbus challenged this idea with the alternative hypothesis: The world is round. Then most people thought that the earth was the center of the universe (The 'new' null hypothesis).
Copernicus had an alternative research hypothesis that the world actually circled around the sun, thus being the center of the universe. Eventually, people got convinced and accepted it as the null.
Later someone proposed an alternative hypothesis that the sun itself also circled around the something within the galaxy. This is how research works - the null hypothesis get's closer to the reality each time, even if it isn't correct, it is better than the last null hypothesis.
Source: http://www.experiment-resources.com/null-hypothesis.html
Citation:
Shuttleworth, Martyn (2008). Null Hypothesis. Retrieved [Date of Retrieval] from Experiment Resources: http://www.experiment-resources.com/null-hypothesis.html
The null hypothesis, H0, is an essential part of any research design, and is always tested, even indirectly.
The simplistic definition of the null is as the opposite of the alternative hypothesis, H1, although the principle is a little more complex than that.
The null hypothesis is a hypothesis which the researcher tries to disprove, reject or nullify.
The 'null' often refers to the common view of something, while the alternative hypothesis is what the researcher really think is the cause of a phenomenon.
An experiment conclusion always refers to the null, rejecting or accepting H0 rather than H1.
Despite this, many researchers neglect the null hypothesis when testing hypotheses, which is poor practice and can have adverse effects.
EXAMPLES OF THE NULL HYPOTHESIS
A researcher may postulate a hypothesis:
H1: Tomato plants exhibit a higher rate of growth when planted in compost rather than in soil.
And a null hypothesis:
H0: Tomato plants do not exhibit a higher rate of growth when planted in compost rather than soil.
It is important to carefully select the wording of the null, and ensure that it is as specific as possible. For example, the researcher might postulate a null hypothesis:
H0: Tomato plants show no difference in growth rates when planted in compost rather than soil.
There is a major flaw with this null hypothesis. If the plants actually grow more slowly in compost than in soil, an impasse is reached. H1 is not supported, but neither is H0, because there is a difference in growth rates.
If the null is rejected, with no alternative, the experiment may be invalid. This is the reason why science uses a battery of deductive and inductive processes to ensure that there are no flaws in the hypotheses.
Many scientists neglect the null, assuming that it is merely the opposite of the alternative, but it is good practice to spend a little time creating a sound hypothesis. It is not possible to change any hypothesis retrospectively, including H0.
SIGNIFICANCE TESTS
If significance tests generate 95% or 99% likelihood that the results do not fit the null hypothesis, then it is rejected, in favor of the alternative.
Otherwise, the null is accepted. These are the only correct assumptions, and it is incorrect to reject, or accept, H1.
Accepting the null hypothesis does not mean that it is true. It is still a hypothesis, and must conform to the principle of falsifiability, in the same way that rejecting the null does not prove the alternative.
PERCEIVED PROBLEMS WITH THE NULL
The major problem with the null hypothesis is that many researchers, and reviewers, see accepting the null as a failure of the experiment. This is very poor science, as accepting or rejecting any hypothesis is a positive result.
Even if the null is not refuted, the world of science has learned something new. Strictly speaking, the term ‘failure’, should only apply to errors in the experimental design, or incorrect initial assumptions.
DEVELOPMENT OF THE NULL
Up until the 1500's most people thought that the world was flat (At the time: The null hypothesis). Columbus challenged this idea with the alternative hypothesis: The world is round. Then most people thought that the earth was the center of the universe (The 'new' null hypothesis).
Copernicus had an alternative research hypothesis that the world actually circled around the sun, thus being the center of the universe. Eventually, people got convinced and accepted it as the null.
Later someone proposed an alternative hypothesis that the sun itself also circled around the something within the galaxy. This is how research works - the null hypothesis get's closer to the reality each time, even if it isn't correct, it is better than the last null hypothesis.
Source: http://www.experiment-resources.com/null-hypothesis.html
Citation:
Shuttleworth, Martyn (2008). Null Hypothesis. Retrieved [Date of Retrieval] from Experiment Resources: http://www.experiment-resources.com/null-hypothesis.html
What is a Research Hypothesis
by Martyn Shuttleworth (2008)
A research hypothesis is the statement created by a researcher when they speculate upon the outcome of a research or experiment.
Every true experimental design must have this statement at the core of its structure, as the ultimate aim of any experiment.
The hypothesis is generated via a number of means, but is usually the result of a process of inductive reasoning where observations lead to the formation of a theory. Scientists then use a large battery of deductive methods to arrive at a hypothesis that is testable, falsifiable and realistic.
The precursor to a hypothesis is a research problem, usually framed as a question. It might ask what, or why, something is happening.
For example, to use a topical subject, we might wonder why the stocks of cod in the North Atlantic are declining. The problem question might be ‘Why are the numbers of Cod in the North Atlantic declining?’
This is too broad a statement and is not testable by any reasonable scientific means. It is merely a tentative question arising from literature reviews and intuition. Many people would think that instinct and intuition are unscientific, but many of the greatest scientific leaps were a result of ‘hunches’.
The research hypothesis is a paring down of the problem into something testable and falsifiable. In the aforementioned example, a researcher might speculate that the decline in the fish stocks is due to prolonged over fishing. They must generate a realistic and testable hypothesis around which they can build the experiment.
This might be a question, a statement or an ‘If/Or’ statement. Some examples could be:
* Is over-fishing causing a decline in the stocks of Cod in the North Atlantic?
* Over-fishing affects the stocks of cod.
* If over-fishing is causing a decline in the numbers of Cod, reducing the amount of trawlers will increase cod stocks.
These are all acceptable statements and they all give the researcher a focus for constructing a research experiment. Science tends to formalize things and use the ‘If’ statement, measuring the effect that manipulating one variable has upon another, but the other forms are perfectly acceptable. An ideal research hypothesis should contain a prediction, which is why the more formal ones are favored.
A scientist who becomes fixated on proving a research hypothesis loses their impartiality and credibility. Statistical tests often uncover trends, but rarely give a clear-cut answer, with other factors often affecting the outcome and influencing the results.
Whilst gut instinct and logic tells us that fish stocks are affected by over fishing, it is not necessarily true and the researcher must consider that outcome. Perhaps environmental factors or pollution are causal effects influencing fish stocks.
A hypothesis must be testable, taking into account current knowledge and techniques, and be realistic. If the researcher does not have a multi-million dollar budget then there is no point in generating complicated hypotheses. A hypothesis must be verifiable by statistical and analytical means, to allow a verification or falsification.
In fact, a hypothesis is never proved, and it is better practice to use the terms ‘supported’ or ‘verified’. This means that the research showed that the evidence supported the hypothesis and further research is built upon that.
A research hypothesis, which stands the test of time, eventually becomes a theory, Source: http://www.experiment-resources.com/research-hypothesis.html
A research hypothesis is the statement created by a researcher when they speculate upon the outcome of a research or experiment.
Every true experimental design must have this statement at the core of its structure, as the ultimate aim of any experiment.
The hypothesis is generated via a number of means, but is usually the result of a process of inductive reasoning where observations lead to the formation of a theory. Scientists then use a large battery of deductive methods to arrive at a hypothesis that is testable, falsifiable and realistic.
The precursor to a hypothesis is a research problem, usually framed as a question. It might ask what, or why, something is happening.
For example, to use a topical subject, we might wonder why the stocks of cod in the North Atlantic are declining. The problem question might be ‘Why are the numbers of Cod in the North Atlantic declining?’
This is too broad a statement and is not testable by any reasonable scientific means. It is merely a tentative question arising from literature reviews and intuition. Many people would think that instinct and intuition are unscientific, but many of the greatest scientific leaps were a result of ‘hunches’.
The research hypothesis is a paring down of the problem into something testable and falsifiable. In the aforementioned example, a researcher might speculate that the decline in the fish stocks is due to prolonged over fishing. They must generate a realistic and testable hypothesis around which they can build the experiment.
This might be a question, a statement or an ‘If/Or’ statement. Some examples could be:
* Is over-fishing causing a decline in the stocks of Cod in the North Atlantic?
* Over-fishing affects the stocks of cod.
* If over-fishing is causing a decline in the numbers of Cod, reducing the amount of trawlers will increase cod stocks.
These are all acceptable statements and they all give the researcher a focus for constructing a research experiment. Science tends to formalize things and use the ‘If’ statement, measuring the effect that manipulating one variable has upon another, but the other forms are perfectly acceptable. An ideal research hypothesis should contain a prediction, which is why the more formal ones are favored.
A scientist who becomes fixated on proving a research hypothesis loses their impartiality and credibility. Statistical tests often uncover trends, but rarely give a clear-cut answer, with other factors often affecting the outcome and influencing the results.
Whilst gut instinct and logic tells us that fish stocks are affected by over fishing, it is not necessarily true and the researcher must consider that outcome. Perhaps environmental factors or pollution are causal effects influencing fish stocks.
A hypothesis must be testable, taking into account current knowledge and techniques, and be realistic. If the researcher does not have a multi-million dollar budget then there is no point in generating complicated hypotheses. A hypothesis must be verifiable by statistical and analytical means, to allow a verification or falsification.
In fact, a hypothesis is never proved, and it is better practice to use the terms ‘supported’ or ‘verified’. This means that the research showed that the evidence supported the hypothesis and further research is built upon that.
A research hypothesis, which stands the test of time, eventually becomes a theory, Source: http://www.experiment-resources.com/research-hypothesis.html
Friday, December 18, 2009
A suggested thesis structure
The list of contents and chapter headings below is appropriate for some theses. In some cases, one or two of them may be irrelevant. Results and Discussion are usually combined in several chapters of a thesis. Think about the plan of chapters and decide what is best to report your work. Then make a list, in point form, of what will go in each chapter. Try to make this rather detailed, so that you end up with a list of points that corresponds to subsections or even to the paragraphs of your thesis. At this stage, think hard about the logic of the presentation: within chapters, it is often possible to present the ideas in different order, and not all arrangements will be equally easy to follow. If you make a plan of each chapter and section before you sit down to write, the result will probably be clearer and easier to read. It will also be easier to write.
Copyright waiver
Your institution may have a form for this (UNSW does). In any case, this standard page gives the university library the right to publish the work, possibly by microfilm or other medium. (At UNSW, the Postgraduate Student Office will give you a thesis pack with various guide-lines and rules about thesis format. Make sure that you consult that for its formal requirements, as well as this rather informal guide.)
Declaration
Check the wording required by your institution, and whether there is a standard form. Many universities require something like: "I hereby declare that this submission is my own work and that, to the best of my knowledge and belief, it contains no material previously published or written by another person nor material which to a substantial extent has been accepted for the award of any other degree or diploma of the university or other institute of higher learning, except where due acknowledgment has been made in the text. (signature/name/date)"
Title page
This may vary among institutions, but as an example: Title/author/"A thesis submitted for the degree of Doctor of Philosophy in the Faculty of Science/The University of New South Wales"/date.
Abstract
Of all your thesis, this part will be the most widely published and most read because it will be published in Dissertation Abstracts International. It is best written towards the end, but not at the very last minute because you will probably need several drafts. It should be a distillation of the thesis: a concise description of the problem(s) addressed, your method of solving it/them, your results and conclusions. An abstract must be self-contained. Usually they do not contain references. When a reference is necessary, its details should be included in the text of the abstract. Check the word limit. Remember: even though it appears at the beginning, an abstract is not an introduction. It is a résumé of your thesis.
Acknowledgments
Most thesis authors put in a page of thanks to those who have helped them in matters scientific, and also indirectly by providing such essentials as food, education, genes, money, help, advice, friendship etc. If any of your work is collaborative, you should make it quite clear who did which sections.
Table of contents
The introduction starts on page 1, the earlier pages should have roman numerals. It helps to have the subheadings of each chapter, as well as the chapter titles. Remember that the thesis may be used as a reference in the lab, so it helps to be able to find things easily.
Introduction
What is the topic and why is it important? State the problem(s) as simply as you can. Remember that you have been working on this project for a few years, so you will be very close to it. Try to step back mentally and take a broader view of the problem. How does it fit into the broader world of your discipline?
Especially in the introduction, do not overestimate the reader's familiarity with your topic. You are writing for researchers in the general area, but not all of them need be specialists in your particular topic. It may help to imagine such a person---think of some researcher whom you might have met at a conference for your subject, but who was working in a different area. S/he is intelligent, has the same general background, but knows little of the literature or tricks that apply to your particular topic.
The introduction should be interesting. If you bore the reader here, then you are unlikely to revive his/her interest in the materials and methods section. For the first paragraph or two, tradition permits prose that is less dry than the scientific norm. If want to wax lyrical about your topic, here is the place to do it. Try to make the reader want to read the heavy bundle that has arrived uninvited on his/her desk. Go to the library and read several thesis introductions. Did any make you want to read on? Which ones were boring?
This section might go through several drafts to make it read well and logically, while keeping it short. For this section, I think that it is a good idea to ask someone who is not a specialist to read it and to comment. Is it an adequate introduction? Is it easy to follow? There is an argument for writing this section---or least making a major revision of it---towards the end of the thesis writing. Your introduction should tell where the thesis is going, and this may become clearer during the writing.
Literature review
Where did the problem come from? What is already known about this problem? What other methods have been tried to solve it?
Ideally, you will already have much of the hard work done, if you have been keeping up with the literature as you vowed to do three years ago, and if you have made notes about important papers over the years. If you have summarised those papers, then you have some good starting points for the review.
If you didn't keep your literature notes up to date, you can still do something useful: pass on the following advice to any beginning PhD students in your lab and tell them how useful this would have been to you. When you start reading about a topic, you should open a spread sheet file, or at least a word processor file, for your literature review. Of course you write down the title, authors, year, volume and pages. But you also write a summary (anything from a couple of sentences to a couple of pages, depending on the relevance). In other columns of the spread sheet, you can add key words (your own and theirs) and comments about its importance, relevance to you and its quality.
How many papers? How relevant do they have to be before you include them? Well, that is a matter of judgement. On the order of a hundred is reasonable, but it will depend on the field. You are the world expert on the (narrow) topic of your thesis: you must demonstrate this.
A political point: make sure that you do not omit relevant papers by researchers who are like to be your examiners, or by potential employers to whom you might be sending the thesis in the next year or two.
Middle chapters
In some theses, the middle chapters are the journal articles of which the student was major author. There are several disadvantages to this format.
One is that a thesis is both allowed and expected to have more detail than a journal article. For journal articles, one usually has to reduce the number of figures. In many cases, all of the interesting and relevant data can go in the thesis, and not just those which appeared in the journal. The degree of experimental detail is usually greater in a thesis. Relatively often a researcher requests a thesis in order to obtain more detail about how a study was performed.
Another disadvantage is that your journal articles may have some common material in the introduction and the "Materials and Methods" sections.
The exact structure in the middle chapters will vary among theses. In some theses, it is necessary to establish some theory, to describe the experimental techniques, then to report what was done on several different problems or different stages of the problem, and then finally to present a model or a new theory based on the new work. For such a thesis, the chapter headings might be: Theory, Materials and Methods, {first problem}, {second problem}, {third problem}, {proposed theory/model} and then the conclusion chapter. For other theses, it might be appropriate to discuss different techniques in different chapters, rather than to have a single Materials and Methods chapter.
Here follow some comments on the elements Materials and Methods, Theory, Results and discussion which may or may not correspond to thesis chapters.
Materials and Methods
This varies enormously from thesis to thesis, and may be absent in theoretical theses. It should be possible for a competent researcher to reproduce exactly what you have done by following your description. There is a good chance that this test will be applied: sometime after you have left, another researcher will want to do a similar experiment either with your gear, or on a new set-up in a foreign country. Please write for the benefit of that researcher.
In some theses, particularly multi-disciplinary or developmental ones, there may be more than one such chapter. In this case, the different disciplines should be indicated in the chapter titles.
Theory
When you are reporting theoretical work that is not original, you will usually need to include sufficient material to allow the reader to understand the arguments used and their physical bases. Sometimes you will be able to present the theory ab initio, but you should not reproduce two pages of algebra that the reader could find in a standard text. Do not include theory that you are not going to relate to the work you have done.
When writing this section, concentrate at least as much on the physical arguments as on the equations. What do the equations mean? What are the important cases?
When you are reporting your own theoretical work, you must include rather more detail, but you should consider moving lengthy derivations to appendices. Think too about the order and style of presentation: the order in which you did the work may not be the clearest presentation.
Suspense is not necessary in reporting science: you should tell the reader where you are going before you start.
Results and discussion
The results and discussion are very often combined in theses. This is sensible because of the length of a thesis: you may have several chapters of results and, if you wait till they are all presented before you begin discussion, the reader may have difficulty remembering what you are talking about. The division of Results and Discussion material into chapters is usually best done according to subject matter.
Make sure that you have described the conditions which obtained for each set of results. What was held constant? What were the other relevant parameters? Make sure too that you have used appropriate statistical analyses. Where applicable, show measurement errors and standard errors on the graphs. Use appropriate statistical tests.
Take care plotting graphs. The origin and intercepts are often important so, unless the ranges of your data make it impractical, the zeros of one or both scales should usually appear on the graph. You should show error bars on the data, unless the errors are very small. For single measurements, the bars should be your best estimate of the experimental errors in each coordinate. For multiple measurements these should include the standard error in the data. The errors in different data are often different, so, where this is the case, regressions and fits should be weighted (i.e. they should minimize the sum of squares of the differences weighted inversely as the size of the errors.) (A common failing in many simple software packages that draw graphs and do regressions is that they do not treat errors adequately. UNSW student Mike Johnston has written a plotting routine that plots data with error bars and performs weighted least square regressions. It is at http://www.phys.unsw.edu.au/3rdyearlab/graphing/graph.html). You can just 'paste' your data into the input and it generates a .ps file of the graph.
In most cases, your results need discussion. What do they mean? How do they fit into the existing body of knowledge? Are they consistent with current theories? Do they give new insights? Do they suggest new theories or mechanisms?
Try to distance yourself from your usual perspective and look at your work. Do not just ask yourself what it means in terms of the orthodoxy of your own research group, but also how other people in the field might see it. Does it have any implications that do not relate to the questions that you set out to answer?
Final chapter, references and appendices
Conclusions and suggestions for further work
Your abstract should include your conclusions in very brief form, because it must also include some other material. A summary of conclusions is usually longer than the final section of the abstract, and you have the space to be more explicit and more careful with qualifications. You might find it helpful to put your conclusions in point form.
It is often the case with scientific investigations that more questions than answers are produced. Does your work suggest any interesting further avenues? Are there ways in which your work could be improved by future workers? What are the practical implications of your work?
This chapter should usually be reasonably short---a few pages perhaps. As with the introduction, I think that it is a good idea to ask someone who is not a specialist to read this section and to comment.
References (See also under literature review)
It is tempting to omit the titles of the articles cited, and the university allows this, but think of all the times when you have seen a reference in a paper and gone to look it up only to find that it was not helpful after all.
Should you reference web sites and, if so, how? If you cite a journal article or book, the reader can go to a library and check that the cited document and check whether or not it says what you say it did. A web site may disappear, and it may have been updated or changed completely. So references to the web are usually less satisfactory. Nevertheless, there are some very useful and authoritative sources. So, if the rules of your institution permit it, it may be appropriate to cite web sites. (Be cautious, and don't overuse such citations. In particular, don't use a web citation where you could reasonably use a "hard" citation. Remember that your examiners are likely to be older and more conservative.) You should give the URL and also the date you downloaded it. If there is a date on the site itself (last updated on .....) you should included that, too.
Appendices
If there is material that should be in the thesis but which would break up the flow or bore the reader unbearably, include it as an appendix. Some things which are typically included in appendices are: important and original computer programs, data files that are too large to be represented simply in the results chapters, pictures or diagrams of results which are not important enough to keep in the main text.
Source: http://phys.unsw.edu.au/~jw/thesis.html
Copyright waiver
Your institution may have a form for this (UNSW does). In any case, this standard page gives the university library the right to publish the work, possibly by microfilm or other medium. (At UNSW, the Postgraduate Student Office will give you a thesis pack with various guide-lines and rules about thesis format. Make sure that you consult that for its formal requirements, as well as this rather informal guide.)
Declaration
Check the wording required by your institution, and whether there is a standard form. Many universities require something like: "I hereby declare that this submission is my own work and that, to the best of my knowledge and belief, it contains no material previously published or written by another person nor material which to a substantial extent has been accepted for the award of any other degree or diploma of the university or other institute of higher learning, except where due acknowledgment has been made in the text. (signature/name/date)"
Title page
This may vary among institutions, but as an example: Title/author/"A thesis submitted for the degree of Doctor of Philosophy in the Faculty of Science/The University of New South Wales"/date.
Abstract
Of all your thesis, this part will be the most widely published and most read because it will be published in Dissertation Abstracts International. It is best written towards the end, but not at the very last minute because you will probably need several drafts. It should be a distillation of the thesis: a concise description of the problem(s) addressed, your method of solving it/them, your results and conclusions. An abstract must be self-contained. Usually they do not contain references. When a reference is necessary, its details should be included in the text of the abstract. Check the word limit. Remember: even though it appears at the beginning, an abstract is not an introduction. It is a résumé of your thesis.
Acknowledgments
Most thesis authors put in a page of thanks to those who have helped them in matters scientific, and also indirectly by providing such essentials as food, education, genes, money, help, advice, friendship etc. If any of your work is collaborative, you should make it quite clear who did which sections.
Table of contents
The introduction starts on page 1, the earlier pages should have roman numerals. It helps to have the subheadings of each chapter, as well as the chapter titles. Remember that the thesis may be used as a reference in the lab, so it helps to be able to find things easily.
Introduction
What is the topic and why is it important? State the problem(s) as simply as you can. Remember that you have been working on this project for a few years, so you will be very close to it. Try to step back mentally and take a broader view of the problem. How does it fit into the broader world of your discipline?
Especially in the introduction, do not overestimate the reader's familiarity with your topic. You are writing for researchers in the general area, but not all of them need be specialists in your particular topic. It may help to imagine such a person---think of some researcher whom you might have met at a conference for your subject, but who was working in a different area. S/he is intelligent, has the same general background, but knows little of the literature or tricks that apply to your particular topic.
The introduction should be interesting. If you bore the reader here, then you are unlikely to revive his/her interest in the materials and methods section. For the first paragraph or two, tradition permits prose that is less dry than the scientific norm. If want to wax lyrical about your topic, here is the place to do it. Try to make the reader want to read the heavy bundle that has arrived uninvited on his/her desk. Go to the library and read several thesis introductions. Did any make you want to read on? Which ones were boring?
This section might go through several drafts to make it read well and logically, while keeping it short. For this section, I think that it is a good idea to ask someone who is not a specialist to read it and to comment. Is it an adequate introduction? Is it easy to follow? There is an argument for writing this section---or least making a major revision of it---towards the end of the thesis writing. Your introduction should tell where the thesis is going, and this may become clearer during the writing.
Literature review
Where did the problem come from? What is already known about this problem? What other methods have been tried to solve it?
Ideally, you will already have much of the hard work done, if you have been keeping up with the literature as you vowed to do three years ago, and if you have made notes about important papers over the years. If you have summarised those papers, then you have some good starting points for the review.
If you didn't keep your literature notes up to date, you can still do something useful: pass on the following advice to any beginning PhD students in your lab and tell them how useful this would have been to you. When you start reading about a topic, you should open a spread sheet file, or at least a word processor file, for your literature review. Of course you write down the title, authors, year, volume and pages. But you also write a summary (anything from a couple of sentences to a couple of pages, depending on the relevance). In other columns of the spread sheet, you can add key words (your own and theirs) and comments about its importance, relevance to you and its quality.
How many papers? How relevant do they have to be before you include them? Well, that is a matter of judgement. On the order of a hundred is reasonable, but it will depend on the field. You are the world expert on the (narrow) topic of your thesis: you must demonstrate this.
A political point: make sure that you do not omit relevant papers by researchers who are like to be your examiners, or by potential employers to whom you might be sending the thesis in the next year or two.
Middle chapters
In some theses, the middle chapters are the journal articles of which the student was major author. There are several disadvantages to this format.
One is that a thesis is both allowed and expected to have more detail than a journal article. For journal articles, one usually has to reduce the number of figures. In many cases, all of the interesting and relevant data can go in the thesis, and not just those which appeared in the journal. The degree of experimental detail is usually greater in a thesis. Relatively often a researcher requests a thesis in order to obtain more detail about how a study was performed.
Another disadvantage is that your journal articles may have some common material in the introduction and the "Materials and Methods" sections.
The exact structure in the middle chapters will vary among theses. In some theses, it is necessary to establish some theory, to describe the experimental techniques, then to report what was done on several different problems or different stages of the problem, and then finally to present a model or a new theory based on the new work. For such a thesis, the chapter headings might be: Theory, Materials and Methods, {first problem}, {second problem}, {third problem}, {proposed theory/model} and then the conclusion chapter. For other theses, it might be appropriate to discuss different techniques in different chapters, rather than to have a single Materials and Methods chapter.
Here follow some comments on the elements Materials and Methods, Theory, Results and discussion which may or may not correspond to thesis chapters.
Materials and Methods
This varies enormously from thesis to thesis, and may be absent in theoretical theses. It should be possible for a competent researcher to reproduce exactly what you have done by following your description. There is a good chance that this test will be applied: sometime after you have left, another researcher will want to do a similar experiment either with your gear, or on a new set-up in a foreign country. Please write for the benefit of that researcher.
In some theses, particularly multi-disciplinary or developmental ones, there may be more than one such chapter. In this case, the different disciplines should be indicated in the chapter titles.
Theory
When you are reporting theoretical work that is not original, you will usually need to include sufficient material to allow the reader to understand the arguments used and their physical bases. Sometimes you will be able to present the theory ab initio, but you should not reproduce two pages of algebra that the reader could find in a standard text. Do not include theory that you are not going to relate to the work you have done.
When writing this section, concentrate at least as much on the physical arguments as on the equations. What do the equations mean? What are the important cases?
When you are reporting your own theoretical work, you must include rather more detail, but you should consider moving lengthy derivations to appendices. Think too about the order and style of presentation: the order in which you did the work may not be the clearest presentation.
Suspense is not necessary in reporting science: you should tell the reader where you are going before you start.
Results and discussion
The results and discussion are very often combined in theses. This is sensible because of the length of a thesis: you may have several chapters of results and, if you wait till they are all presented before you begin discussion, the reader may have difficulty remembering what you are talking about. The division of Results and Discussion material into chapters is usually best done according to subject matter.
Make sure that you have described the conditions which obtained for each set of results. What was held constant? What were the other relevant parameters? Make sure too that you have used appropriate statistical analyses. Where applicable, show measurement errors and standard errors on the graphs. Use appropriate statistical tests.
Take care plotting graphs. The origin and intercepts are often important so, unless the ranges of your data make it impractical, the zeros of one or both scales should usually appear on the graph. You should show error bars on the data, unless the errors are very small. For single measurements, the bars should be your best estimate of the experimental errors in each coordinate. For multiple measurements these should include the standard error in the data. The errors in different data are often different, so, where this is the case, regressions and fits should be weighted (i.e. they should minimize the sum of squares of the differences weighted inversely as the size of the errors.) (A common failing in many simple software packages that draw graphs and do regressions is that they do not treat errors adequately. UNSW student Mike Johnston has written a plotting routine that plots data with error bars and performs weighted least square regressions. It is at http://www.phys.unsw.edu.au/3rdyearlab/graphing/graph.html). You can just 'paste' your data into the input and it generates a .ps file of the graph.
In most cases, your results need discussion. What do they mean? How do they fit into the existing body of knowledge? Are they consistent with current theories? Do they give new insights? Do they suggest new theories or mechanisms?
Try to distance yourself from your usual perspective and look at your work. Do not just ask yourself what it means in terms of the orthodoxy of your own research group, but also how other people in the field might see it. Does it have any implications that do not relate to the questions that you set out to answer?
Final chapter, references and appendices
Conclusions and suggestions for further work
Your abstract should include your conclusions in very brief form, because it must also include some other material. A summary of conclusions is usually longer than the final section of the abstract, and you have the space to be more explicit and more careful with qualifications. You might find it helpful to put your conclusions in point form.
It is often the case with scientific investigations that more questions than answers are produced. Does your work suggest any interesting further avenues? Are there ways in which your work could be improved by future workers? What are the practical implications of your work?
This chapter should usually be reasonably short---a few pages perhaps. As with the introduction, I think that it is a good idea to ask someone who is not a specialist to read this section and to comment.
References (See also under literature review)
It is tempting to omit the titles of the articles cited, and the university allows this, but think of all the times when you have seen a reference in a paper and gone to look it up only to find that it was not helpful after all.
Should you reference web sites and, if so, how? If you cite a journal article or book, the reader can go to a library and check that the cited document and check whether or not it says what you say it did. A web site may disappear, and it may have been updated or changed completely. So references to the web are usually less satisfactory. Nevertheless, there are some very useful and authoritative sources. So, if the rules of your institution permit it, it may be appropriate to cite web sites. (Be cautious, and don't overuse such citations. In particular, don't use a web citation where you could reasonably use a "hard" citation. Remember that your examiners are likely to be older and more conservative.) You should give the URL and also the date you downloaded it. If there is a date on the site itself (last updated on .....) you should included that, too.
Appendices
If there is material that should be in the thesis but which would break up the flow or bore the reader unbearably, include it as an appendix. Some things which are typically included in appendices are: important and original computer programs, data files that are too large to be represented simply in the results chapters, pictures or diagrams of results which are not important enough to keep in the main text.
Source: http://phys.unsw.edu.au/~jw/thesis.html
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