Thursday, 14 January 2010

Plagiarism: The art of referencing...

How do I reference a paper? If I reference a paper can I copy from 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. in need to reference the source. So, how do you reference?

There are many different styles of referencing. If you read papers from different journals and you will see a whole range of styles. On the degrees in the School of Biomedical Sciences we tend (unless you have been told otherwise) to use what is called the 'Harvard' style (please note: this may not be true in CMB3000 and CMB3001, please check your module study guides).

No matter what style is being used the approach and idea of referencing is the same. You write some facts/information in your work and you state from where that information came. 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).

And 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 put in the reference in the text and the bibliography, so that will have to be checked.

And 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 on the other-hand 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).

And in your bibliography (references at the end of your work) you would write:

  1. 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

For more details have a look at:

http://www.ncl.ac.uk/students/wdc/learning/conduct/references/
http://www.ncl.ac.uk/students/wdc/learning/conduct/citations/

If I reference a paper can I copy from it?

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

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

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

This is a possibly the most comment I receive from students when discussing plagiarised work. Just because you reference a paper does not mean you can copy from it.

If you have any questions about plagiarism and/or referencing please feel free to email me: n.j.morris@ncl.ac.uk.

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

At a really simple level plagiarism can be defined as copying, that is, you take the work of another person and pass it off as your own.

Plagiarism can be split in to four main types:

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

Text Plagiarism: This is the most easy to understand, and the most common form of plagiarism. Basically it is the copying of text from some source (a paper, text book, 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 text book or paper and pass it off as your own (this can also be viewed as 'idea' plagiarism as some one 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. Or put another way, it is like making one burger in McDonald's and selling it twice.

If you have any questions about plagiarism please feel free to email me: n.j.morris@ncl.ac.uk.

Wednesday, 13 January 2010

Single letter amino acid codes

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

The single letter amino acid codes are fairly easy to remember. In eleven cases it is just the first letter.

AAlaAlanine
CCysCysteine
GGlyGlycine
HHisHistidine
IIleIsoleucine
LLeuLeucine
MMetMethionine
PProProline
SSerSerine
TThrThreonine
VValValine

And in 9 cases it not:

DAspAspartate
EGluGlutamate
FPhePhenylalanine
KLysLysine
NAsnAsparagine
QGlnGlutamine
RArgArginine
WTrpTryptophan
YTyrTyrosine

For those of you who wish to test their knowledge of the single letter amino acid codes I have put together a little test (it gives random questions so you can try it as many times as you like), which can be found on the teaching website https://teaching.ncl.ac.uk/bms

CMB2002: PKA, PDE, HSL, cAMP, phosphorylation and perilipin

One of the questions I had during the CMB2002 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 perlipin. 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.

Hsl2

Figure 1: Regulation of lipolysis. Activation of a G-protein coupled receptor (GPCR) by a hormone (A) (e.g. glucagon) or catecolamine (e.g. epinephrine) causes an exchange of GTP for GDP on the α subunit of a heterotrimeric Gs protein. The active GTP bound α subunit activates adenylyl cylcase (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 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 catecolamine, or with insulin, or a combination of insulin and catecolamine you may see the type of result shown in figure 2. Basically, in the absences of insulin or a catecolamine cAMP levels are at a basal level. Upon the addition of a catecolamine 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 catecolamine the levels of cAMP may be higher than basal, but not as high as catecolamine only as PDE3B is active (see figure 2).

C amp

Figure 2: Hypothetical levels of cAMP upon ligand challenge. Stimulation of adipocytes with a catecolamine 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 catecolamine and insulin dampens the response of the catecolamine 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 on to 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.

Friday, 8 January 2010

Plagiarism: Making notes from papers during your projects

During your projects 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 note book, 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 have forgotten 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, 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.

If you have any questions on plagiarism please feel free to email me: n.j.morris@ncl.ac.uk.

CMB3000/CMB3001: Projects and Plagiarism

Over the next few weeks I will be putting out a series of posts on how to avoid plagiarism in your projects.

At Newcastle you have a number of pieces of work scanned for plagiarism during your degree. The aim of this scanning is not to catch you plagiarising, but to make sure you know how not to plagiarise. That is, in conjunction with the lecture on plagiarism, the scanning helps you know that you do not plagiarise, and that your 'academic practice' is good.

My aim through this process is to make sure everyone understands plagiarism, and the academic consequences of plagiarism, before they embark on their biggest piece of academic work, the project. The last thing I want to see is plagiarism occurring during the projects.

If you have any questions on plagiarism please feel free to email me: n.j.morris@ncl.ac.uk.

Wednesday, 6 January 2010

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 to 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 Calvert in a paper in 2010 reported:

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

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

And you wrote:

"The discovery of X in London by Smith in 1920, and the subsequent discoveries of Y by Jones in 1933 and Z by Brown 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 Calvert as your own. The correct way to report this would be:

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

That is, the inclusion of the reference of Calvert '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 plagiarism.