The importance of cell referencing in Excel spreadsheets...

Using Excel correctly in the lab is an important skill to develop, and students sometimes get this wrong by failing to correctly use cell referencing and instead "hardcoding" key numbers into the formulas they are using. The consequence of doing this is that if the student later changes any of the numbers, these changes will not cascade through the spreadsheet, and this can lead to errors.

The video below demonstrates the importance of cell referencing and why it should be used as opposed to "hardcoding"...

The key points are:

• When analysing scientific data, the only number that should be entered into the spreadsheet is the raw data
• All calculations being performed should reference cells (e.g. A2) used for the calculations and not contain numbers (e.g. the number from cell A2

So this means that cells should be:

And not...

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Video of Paramecium, C. elegans and Gram stained bacteria

The video below I put together from videos shot using the main teaching microscope during classes. The video shows Paramecium, C. elegans, and Gram-stained bacteria. Enjoy!

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End of a journey - no more blogging at Scitable

For the last three years I have been blogging over at Nature Scitable about bioscience elearning and today, after 143 posts, I have decided to stop.

I have two main reasons for stopping:

1. The pressure of day-to-day life as an academic. To much to do, too little time to do it.
2. I have never really got on with the blogging platform at Scitable as I find it old, slow and clunky, and these days I like to blog in Markdown (as I am doing here).

It has been fun posting over at Scitable as it has given me the excuse, and therefore the time, to every so often step back from my day-to-day work and think about teaching and what I could, and should, do differently.

The problem now is I need to find an outlet for these 'teaching thoughts' and so there may be an increase in pedagogical material on this blog from now on...

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E-mail - dark social media? I think not...

Yesterday evening, I had the privilege of engaging in a thought-provoking discussion with Alan Carr on the pervasive use of email in teaching and day-to-day communication.

I won't repeat my views and opinions via email here, but you can read them over at Scitable:

1. My hypothesis: e-mail is evil and deserves to die!
2. Problems with email….. I appear to have touched a nerve...
3. What is wrong with e-mail? Can it be fixed?
4. What is wrong with e-mail? Can it be fixed? - The Programmers
5. What is wrong with e-mail? Can it be fixed? - The Receiver and the dreaded FYI
6. What is wrong with e-mail? Can it be fixed? - The Receiver and meta-data
7. What is wrong with e-mail? Can it be fixed? - The Sender
8. What is wrong with e-mail? Can it be fixed? - My battle to get e-mail working again - some tips and suggestions

Needless to say, I am not a fan of email... (as you may be able to guess from some of the above post titles).

Despite being overseas, I was determined to share my perspective on why email is problematic. Alan, a staunch advocate of email, graciously invited me to his session at SpotOn London 2013. I prepared a compelling video, just in case our Skype connection failed, to underscore the severity of the email issue.

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Observing and genotyping C. elegans

I had a fun day yesterday doing the "C. elegans" practical, which is part of the first-year labs. In the practical, we got to look at live C. elegans and also set up some PCR reactions to genotype some wild-type and mutant C. elegans. It was all fun stuff.

Below is a movie we shot of the worms on the day of the practical and some stills from the microscopes.

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Fun and games with Paramecium

Last week we had our annual first-year 'paramecium practical'. The aims of the session were to familiarise the students with the microscopes and to also introduce unicellular organisms.

In the UK we order the paramecium for the practical from a local supplier. However, in Malaysia, despite 4 months of searching, I was unable to find a supplier. This left me with three options:

1. Don't do the practical
2. Find an alternative supplier
3. Culture my own…

I tried to find an alternative supplier (paramecium are used to feed baby fish), but none of the local pet stores stocked them - although I did get a rather nice bag of water fleas (Daphnia).

A bag of Water Flea - Daphnia

A Water Flea - Daphnia

Finally, I decided to culture them.

After a quick read around the Internet, I found a recipe for culture media and some advice on where to find paramecium.

The general advice for 'hunting' paramecium is to take water from close to the top or the edge of a pond. In the end, I took a sample of water from the surface, plus some material from the bottom of the pond. This was allowed to settle overnight (see photo below).

The culture media consisted of dog biscuits, and 4 or 5 cm² of lettuce leaf, in water.

Dog Biscuits

Lettuce Leaf

Water

Pond Water - a mixture of material from the bottom of the pond, and water from the surface and edge

Two culture bottles and a bottle of bond water

I set up three bottles, two culture media, and a bottle of pond water. These were left overnight.

And the next morning… The pond water had cleared, and the bottles with dog biscuits and lettuce were cloudy (the cloudiness was caused by bacteria growing) - these will be a food source for the paramecium.

One of the 'culture media' bottles was seeded with 20 ml of water from the top of the pond bottle, and the other with 20 ml of water collected near the vegetation at the bottom of the pond bottle.

Next morning - the three bottles…..

An examination of the pond water under a microscope revealed the presence of paramecium, but not that many.

There were also some other ciliates present…

Over the next 12 days, the cultures got progressively more cloudy and exceedingly smelly.

12 days after adding the pond water

Of the two culture bottles, the one seeded with water from the top of the pond bottle produced the best (most and largest) paramecium, and the best place to harvest the paramecium was from the top 5 - 10 mm of the bottle, and in particular the layer of 'scum' that had formed on the top of the water. Paramecium taken from elsewhere in the bottle tended to be smaller.

Movie

The movie below was shot during the practical.

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It is all in the name…. Why am I (not) Dr Nick?

In Malaysia, I am called Dr Nick.... And I couldn't understand why... Today, I found out.

In Malaysia, there are no family names, as in Morris, Smith, Jones etc. Your last name is your father's first name, so if my father's first name was Ian, then I would be Nick Ian. Hence, as I am Dr Nick Morris, this suggests that my father's first name was Morris, and Dr Morris would be my father!

This can get odd for a woman, as they would be Julie Ian, and so would Ms Ian if the European convention was followed.

Thanks to The Simpsons, Dr. Nick has a certain 'feeling' about it. You can read more about Dr. Nick of Simpson's fame on Wikipedia.

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