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.

Blog Bonus: Free flowchart to help you decide if something is plagiarised - download.

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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Blog Bonus: Free flowchart to help you decide if something is plagiarised - download.

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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Additional Resources

• 📗 - Biochemistry (Stryer) (affiliate link)
• 📗 - Principles of Biochemistry (Lehninger) (affiliate link)

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.

If you would like to support my blogging efforts, then please feel free to buy me a coffee at https://www.buymeacoffee.com/drnickm

Additional Resources

• 📗 - Biochemistry (Stryer) (affiliate link)
• 📗 - Principles of Biochemistry (Lehninger) (affiliate link)

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.

Blog Bonus: Free flowchart to help you decide if something is plagiarised - download.

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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Blog Bonus: Free flowchart to help you decide if something is plagiarised - download.

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."

Blog Bonus: Free flowchart to help you decide if something is plagiarised - download.

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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Blog Bonus: Free flowchart to help you decide if something is plagiarised - download.

Why did I get my standard deviation calculation wrong?

A number of the class members have asked why (or how) they calculated the standard deviation incorrectly in the assessment.

Having looked at the class answers it would appear that the main reason students got it wrong is because they were calculating the standard deviation of a POPULATION and not of a SAMPLE.

The equation for the standard deviation of a population (remember a population is ALL possible examples of a measurement/object and is something that is normally difficult to measure - think of the apple example in the lecture - as all examples can't be collected) is:

Equation for the standard deviation of a population

Whereas the standard deviation of a sample (which is what we had) is calculated by:

The equation for the standard deviation of a sample

Note that the real differences between the two equations are that in the calculation of the standard deviation of a population, we are using the true population mean (µ), whereas in the calculation of the standard deviation of a sample, we are using an estimate of the mean (x bar), plus in the calculation of the standard deviation of a sample we are using n - 1 (also called degrees of freedom) as this gives better estimate of the true standard deviation of a population (and we are working with a sample).

If you would like to support my blogging efforts, then please feel free to buy me a coffee at https://www.buymeacoffee.com/drnickm

Additional Resources

• 📗 - Maths and Chemistry Refresher for Life and Biomedical Scientists
• 📗 - Catchup Maths and Stats (affiliate link to the book)

How many molecules of X are there in a band on a Western Blot?

One of the questions I have often enjoyed setting in western blotting assessments, and that always seems to give problems, is...

"You have set up a western blot in which you wish to estimate the amount of GLUT4 per 3T3-L1 adipocyte (the cultured cell line used in the practical). You know that a 35 mm culture dish contains 2 million cells, and gives 1.5 mg total protein. You also have a recombinant stock of GLUT4 at 50 ng/ml. On your gel you load 15 µg of protein from the 3T3-L1 adipocytes and 1, 5, 10 and 20 µl of the GLUT4 stock. After probing with antibodies, you have a 55 kDa band in the 3T3-L1 adipocyte lane and in the GLUT4 stock lane. The band in the 3T3-L1 adipocyte sample has the same intensity of band as the 10 µl GLUT4 stock. How many molecules of GLUT4 are there per adipocyte?"

The chances are you are getting 'freaked out' by all the weird numbers flying around. The answer is to go back to basics.

For example:

If you had something with a molecular weight of 10, and you loaded 5 g on a lane, you would have 0.5 moles in that lane.

You know how many molecules there are in a mole (it is a constant that is the number of atoms in 12 g of carbon 12), so that constant multiplied by the number of moles would be the number of molecules in the lane.

Let's say one mole of something contains 100 molecules (which it doesn't; the real number is much, much bigger).

So, if you have 0.5 moles in the lane, you would have 50 molecules in that lane.

If you have another lane with a known number of cells in, say, 25, and that lane has the same intensity of staining as the lane containing 50 molecules, you could say that lane also has 50 molecules.
These 50 molecules came from 25 cells, so each cell must have 2 molecules.....

Now you can work it through with 'simple' numbers. All you need to do is to plug in the 'complicated' numbers in the question...

If you struggle with 'Science Maths' then you may like to look at Maths4Biosciences

If you would like to support my blogging efforts, then please feel free to buy me a coffee at https://www.buymeacoffee.com/drnickm

Additional Resources

• 📗 - Maths and Chemistry Refresher for Life and Biomedical Scientists
• 📗 - Catchup Chemistry (affiliate link to the book)
• 📗 - Catchup Maths and Stats (affiliate link to the book)