Plagiarism: The art of referencing...

How do I reference a paper? If I reference a paper, can I copy it? "But that can't be plagiarised, I referenced the paper!!!"

These are all common questions and misconceptions about referencing.

Referencing a paper

You have read a paper and wish to report the facts and findings in your report/essay, etc., but you need to reference the source. So, how do you reference?

There are many different styles of referencing. If you read papers from different journals, you will see a whole range of styles, such as the Harvard and Vancouver styles, to name but two.

No matter what style is used, the approach and idea of referencing are the same. You write some facts/information in your work and state where that information came from. For example, you have read a paper on an amine oxidase found in adipocytes and in your essay, you wish to talk about the protein. So, the full reference of the paper you read would be:

Morris NJ, Ducret A, Aebersold R, Ross SA, Keller SR, and Lienhard GE. (1997) Membrane amine oxidase cloning and identification as a major protein in the adipocyte plasma membrane. J Biol Chem. 272(14):9388-92. - link

In your essay, you state that:

The first membrane-bound amine oxidase was discovered in 1997 and was found in adipocyte plasma membranes (Morris et al., 1997).

In your bibliography (references at the end of your work), you would write:

Morris NJ, Ducret A, Aebersold R, Ross SA, Keller SR, and Lienhard GE. (1997) Membrane amine oxidase cloning and identification as a major protein in the adipocyte plasma membrane. J Biol Chem. 272(14):9388-92

(By the way, please note that et al. should normally be in italics or underlined. Also, please note the full stop after the al. in et al.)

Now, depending on the referencing style you are using, there may be some rules governing how many authors you include in the references in the text and the bibliography, so that will have to be checked.

Finally, with 'names referencing,' there can be the problem of the same name publishing two papers in the same year. So, for example, imagine there were these two papers.

Morris NJ (2010) Everything you wanted to know about plagiarism. J. Plag. 123(10):992-999 

and

Morris NJ (2010) How to plagiarise and not get caught. J. Cheats 1(13):10-15

The way you would cite them in your text would be as (Morris, 2010a) and (Morris, 2010b), and in the bibliography as:

Morris NJ (2010a) Everything you wanted to know about plagiarism. J. Plag. 123(10):992-999
Morris NJ (2010b) How to plagiarise and not get caught. J. Cheats 1(13):10-15

If you were using a numbering style of referencing, it may look like this:

The first membrane-bound amine oxidase was discovered in 1997 and was found in adipocyte plasma membranes (12).

In your bibliography (references at the end of your work), you would write:

12. Morris NJ, Ducret A, Aebersold R, Ross SA, Keller SR, and Lienhard GE. (1997) Membrane amine oxidase cloning and identification as a major protein in the adipocyte plasma membrane. J Biol Chem. 272(14):9388-92

If I reference a paper, can I copy it?

No. Referencing does not mean you can copy the text from a paper. All referencing does is state where you got the data, idea, or hypothesis so that other scientists can check the facts, look up the method etc. Putting a reference in your text as a link on a webpage allows the reader to find additional information.

Referencing does 'protect' against ideas plagiarism because referencing the source states who originally had the idea and where it was published.

"But that can't be plagiarised, I referenced the paper!!!"

This is the most common comment I receive from students when discussing plagiarised work.

Just because you reference a paper does not mean you can copy from it.

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Plagiarism: What is plagiarism and how can I avoid it?

Plagiarism, a serious academic offense, is defined as the act of copying another person's work and presenting it as your own. The consequences of plagiarism can be severe, ranging from academic penalties to damage to one's professional reputation.

Plagiarism can be split into four main types:

1. ‘Text’ - copying text from a book, paper, document etc.
2. ‘Diagrams’ - copying a diagram
3. ‘Idea’ - passing off another person's idea as your own
4. ‘Auto’ - copying from yourself!

Text Plagiarism: This is the easiest to understand and the most common form of plagiarism. Basically, it is the copying of text from some source (a paper, textbook, fellow student, internet) into your own work and then passing it off as your own. It should be noted that adding a reference (i.e. stating from where you copied the text) is no 'protection' and doesn't mean you can copy. If you find yourself reaching for the copy and paste keys on the computer, then there is a good chance it will be plagiarism.

Diagram Plagiarism: This is where you copy a diagram or figure from a textbook or paper and pass it off as your own (this can also be viewed as 'idea' plagiarism as someone has thought long and hard about constructing (and drawing) the figure). You can 'protect' against diagram plagiarism by simply stating from where you got the figure (see later post for more details).

Idea Plagiarism: This, in my opinion, is the worst form of plagiarism, as you would be attempting to pass off the hard work and intellectual property of a fellow scientist as your own. You can write about the ideas and thoughts of other scientists, but YOU MUST STATE FROM WHERE YOU GOT THE IDEA. Basically, this is one of the reasons why we reference sources of information; you are stating who had the original idea and how they came by it. Effectively, by referencing, you are acknowledging the hard work of the other scientists.

Auto-Plagiarism: This form of plagiarism is the one most people have difficulty understanding. After all, how can you plagiarise yourself? You 'own' the work and the intellectual property! Well, basically, auto-plagiarism would occur if you handed in the same piece of work for two different assignments and got two lots of marks for it. Put another way, it is like making one burger at McDonald's and selling it twice.

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Single letter amino acid codes

The amino acids have single and three-letter codes, and these are worth learning for your degree.

Remembering the single-letter amino acid codes is a breeze. In most cases, it's just the first letter of the amino acid's name.

A	Ala	Alanine
C	Cys	Cysteine
G	Gly	Glycine
H	His	Histidine
I	Ile	Isoleucine
L	Leu	Leucine
M	Met	Methionine
P	Pro	Proline
S	Ser	Serine
T	Thr	Threonine
V	Val	Valine

However, in 9 cases it is not the first letter:

D	Asp	Aspartate
E	Glu	Glutamate
F	Phe	Phenylalanine
K	Lys	Lysine
N	Asn	Asparagine
Q	Gln	Glutamine
R	Arg	Arginine
W	Trp	Tryptophan
Y	Tyr	Tyrosine

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PKA, PDE, HSL, cAMP, phosphorylation and perilipin

One of the questions I had during a feedback session was on PKA, hormone-sensitive lipase (HSL), phosphorylation and perilipin, and how this all relates to the breakdown of triglycerides.

PKA phosphorylates HSL and perilipin. However, for PKA to do that it has to be active, that is, cAMP needs to be available to activate the kinase (see figure 1).

If the PDE is active it hydrolyses cAMP, this will reduce cAMP levels, and this will reduce the level of active PKA. Net result, less HSL phosphorylated, less perilipin phosphorylated, therefore less triglyceride broken down. That is, HSL has to be phosphorylated to be active and to remove the perilipin from blocking HSL access to the fat droplet in the adipocytes it also has to be phosphorylated.

Figure 1: Regulation of lipolysis. Activation of a G-protein coupled receptor (GPCR) by a hormone (A) (e.g. glucagon) or catecholamine (e.g. epinephrine) causes an exchange of GTP for GDP on the α subunit of a heterotrimeric G_s protein. The active GTP bound α subunit activates adenylyl cyclase (AC), which converts ATP to cAMP. cAMP activates protein kinase A (PKA), which in turn phosphorylates, and therefore activates, hormone-sensitive lipase (HSL), and phosphorylates perilipin and removes its 'block' on the fat droplet. Net result: increased lipolysis and hence the production of fatty acids and glycerol. The activation of the insulin receptor (IR) by insulin (I), via insulin receptor substrate (IRS) and a number of other proteins, results in the phosphorylation of protein kinase B (PKB), which in turn phosphorylates and activates phosphodiesterase 3B (PDE3B). The active PDE3B hydrolyses cAMP to AMP, and therefore effectively lowers intracellular cAMP levels, therefore reducing PKA activity. As phosphatases (P) are removing phosphates from HSL and perilipin there will be a decrease in phosphorylated HSL and perilipin as PKA is not replacing the phosphates. The net result is less HSL and perilipin is phosphorylated, so lipolysis is reduced.

If you were to examine the intracellular cAMP levels of adipocytes that been stimulated with a catecholamine, or with insulin, or a combination of insulin and catecholamine you may see the type of result shown in figure 2. Basically, in the absences of insulin or a catecholamine cAMP levels are at a basal level. Upon the addition of a catecholamine levels are raised 2 fold. If insulin alone is used then levels of cAMP are reduced below that of basal, and in the presence of insulin and catecholamine, the levels of cAMP may be higher than basal, but not as high as catecholamine only as PDE3B is active (see figure 2).

Figure 2: Hypothetical levels of cAMP upon ligand challenge. Stimulation of adipocytes with a catecholamine causes an increase in intracellular levels of cAMP. Stimulation of adipocytes with insulin causes cAMP levels to fall below basal levels as PDE3B is activated. The stimulation of the cells with catecholamine and insulin dampens the response of the catecholamine as PDE3B is activated by insulin.

What you have to remember is these systems are dynamic and in a state of equilibrium. cAMP is being made (adenylyl cyclase) and destroyed (PDEs). Kinases will be putting phosphates onto proteins, and phosphatases will be removing them. All that is happening is this equilibrium is being changed and pushed in one direction or the other, active or inactive, phosphorylated or not phosphorylated.

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Plagiarism: Making notes from papers during your research

When writing essays, you will read many papers and make lots of notes. During this process, you have to be careful, as there is the danger that you can accidentally copy material from a paper to your notes and then from your notes to your final write-up and, therefore, plagiarise.

When you are making notes from a paper for your own personal use there is no problem in copying from the paper to your notebook, word-for-word. At least that way, you know you have the information correct...

However, when you return to your notes some days or weeks later, you may forget you have copied word-for-word from the paper and think your notes are all your own work and, hence, can be used directly in your write-up. The result is that you plagiarise.

When you make your notes mark the notes that are 'word-for-word' in a way so that you know they are copied, so you don't inadvertently use them in your final write-up. Put the notes in inverted commas or underline them. Do something to make them stand out and help you remember that they are copied and, therefore, can't be used directly in your final work.

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Plagiarism: timelines and historical events from text books

Question: "Is it plagiarism to read a section in a book and rewrite it in your own words? It's hard to change the order around because it's in a timeline of events."

Answer:

This is a tough one...

Yes, it is plagiarism if you are copying word for word.

It could also be plagiarism if the timeline was a specific argument (i.e. it could be 'idea' plagiarism), as opposed to a historical report of events.

For example (assuming your own words):

11:05 John went to the pub
11:10 John ordered a pint
11:15 John sat down

would not be (in my opinion) plagiarism as you are reporting a series of events.

But, if Smith, in a paper in 2010, reported:

"1920 X was discovered by Brown in London
1933 Y was discovered by Jones in Paris
1977 Z was discovered by Green in Tokyo

This led to the discovery of A by Morris in 2010"

And you wrote:

"The discovery of X in London by Brown in 1920, and the subsequent discoveries of Y by Jones in 1933 and Z by Green in 1977, led to Morris discovering A in 2010."

Then, although that wouldn't be 'text' plagiarism, it would be 'idea' plagiarism as you are passing off the hard work and reading of Smith as your own. The correct way to report this would be:

"The discovery of X in London by Brown in 1920, and the subsequent discoveries of Y by Jones in 1933 and Z by Green in 1977, led to Morris discovering A in 2010 (Smith, 2010)."

That is, including Smith's reference 'protects' against an accusation of 'idea' plagiarism, and putting the 'findings' in your own words 'protects' against 'text' plagiarism.

Alternatively, if you have made the connection between the events yourself (i.e. you have done all the hard work of finding the original papers and making the connections), then it would not be plagiarism.

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