Practical & Teaching Resource: Genetic Databases

Preamble

One of the challenges I have found for teaching the new (2016) IBDP Biology syllabus is getting up to speed with the new content as expressed in the understandings, applications and skills sections of the syllabus. This has been particularly true when this new “content” implies an understanding of new technologies such as the huge rise in bioinformatics databases. To make matters worse, I am the only biology teacher in my school and I have been acutely aware of this when, stumbling across new requirements, I have had no one to bounce ideas off (or steal resources from! :))

So what do you do when you have new content that you have not taught before, that relies on an understanding of bioinformatic technology that wasn’t widely available, or covered on your masters in ecology eight years ago and you have no colleagues to help you? You go back to the drawing board…

When planning my course the year before I had shunned ordering the text book written by the chief examiner for the subject for my students on the grounds that it was too big and heavy. I had opted for a slimmer, light-weight textbook that was written by an old colleague. However, In preparation for times like this, I had purchased a copy for my own reference, not to teach from the textbook, you understand, but to refer to when I was unsure of exactly how much depth a topic needed going into (and therefore how much classtime to devote to it) or what the chief examiner had in mind when he wrote the course as part of the curriculum review committee.

While I applaud the move away from a list of learning statements as we had in the old syllabus, statements from the understandings section, like this one from topic 3.1 Genes:

The entire base sequence of human genes was sequenced in the Human Genome Project”

often leave me wondering how much time needs to be allocated to them. This is where having a copy of the chief examiners textbook comes in handy.

The Practical

Earlier this term I was teaching the IB Biology core topic 3 – Genetics and while planning came across the following statements:

3.1 S1: “Use of a database to determine differences in the base sequence of a gene in two species

3.2 S1 “Use of databases to identify the locus of a human gene and its polypeptide product”

These along with several other “application” statements in 3.1 an 3.2 left me slightly bamboozled as to how to approach teaching this, seeing as I had never used these kinds of databases in this way myself, and whats more I was left asking the question – aren’t the kinds of databases that these statements refer to way too complicated to expect 16-18 students to be able access?

Anyway, the instruction was there so I had to do something with it. In the end I referred to the Allott & Mindorf (2014) textbook along and the inthinking biology teacher resource website and combined and adapted two of their practicals to use in my classroom. The result is below:

  1. I designed a practical protocol worksheet which is available here, which could be printed out and handed to students. There is QR code which, when scanned, links to the following video.

Download (PDF, 70KB)

  1. I made the following video that takes students through the worksheet. They can be used together.

Reflections

The video and the activities together take about an hour or just over to complete and do count towards practical hours on the PSOW. I am hugely indebted to the work of Allott & Mindorff and David Faure at inthinking to be able to produce this. Students are able, if they have a mobile phone and QR scanner to link directly to the film and follow the instructions. Alternatively the video can be played on a projector. Students could also complete this as a homework task but this couldn’t then count as practical.

I think that the video and the activities could be broken up into smaller individual activities as I think this may help students to process exactly and clearly what they are doing. These databases can be complex to navigate and contain a lot of information which can be overwhelming for anybody who is new to this area.

While I personally like this part of the syllabus and think that there are some possible IA ideas here, especially when combined with evolutionary studies, I can’t help but think that this material is a bit too advanced for 16-19 year old students, particularly for SL students. It is fairly niche and I would be interested to know how many universities would cover this type of bioinformatic content in their first or second years.

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