MS2B

I shall post the most recent (top of the page) and a defining post on this page for my undergraduate course Molecular Systems and Synthetic Biology (Locally known as MBB308). The archive can be found here and will remain available indefinitely.

Last Post

The module is over, well all bar the formal announcement of marks for this year's MBB 308 students, and so I thought I would reflect on its ups and downs, and prepare the way for next winter's course. Feedback from this module has always been a major driver for getting the right content and best the methods of assessment. MBB308 (Molecular Systems and Synthetic Biology, or MS2B for short) is intended to provide students with a rounded view of the inter-connected mechanisms that contribute to cell function, and with the critical thinking skills that are required to evaluate and contribute not only to the field of Synthetic Biology, but  are also essential for any future area of professional life. I take may lead in running this course from the sentiments expressed by Anne Isabella Thackeray Ritchie (the daughter of the prominent writer William Makepeace Thackeray)

‘He certainly doesn’t practise his precepts, but I suppose the Patron meant that if you give a man a fish he is hungry again in an hour. If you teach him to catch a fish you do him a good turn. But these very elementary principles are apt to clash with the leisure of the cultivated classes.’

This advice is usually expressed in the more direct form of words....
  

Give someone a fish, and you feed them for a day. 

Teach someone to fish, and you feed them for a lifetime

One of the major approaches to supporting communities in challenging situations, such as Malaria zones in sub-Saharan Africa, is to educate in this way. As students at school, teaching is often a mixture of this approach (teaching students to read, for example) and imparting information (learning the elements in the Periodic Table, for example). Both methods are known to work, but it is a balanced measure of both approaches  that is, in my experience, the most satisfactory approach; and as students progress through an undergraduate degree, I believe that teaching students to "metaphorically" fish should dominate. 

This approach to delivering a course does not always make MBB308 (or me) a popular choice for students, and a week into the course, I prepare myself for the regular cries of despair. [If you read my archive posts on this site, you will find the evidence!]. So how did this year's group of students feel about the 2016-2017 format? And importantly how will this influence the format of the course for next academic year? I should perhaps add for my main (USA and Russian) audience, that  course evaluation in the Department is standardised: every module is assessed a couple of days before the course ends. It is anonymous, and combines a series of semi-quantitative "grade boxes" with a free text comments space. In my own experience, the assessment is typically completed by over 80% of students, and the class  comprises an average of 70 final year Molecular Biology undergraduate students.

The most common feedback I receive from students, is that I should give out more fish! These students feel that this would enable them to become better anglers. Or, without recourse to an attempted, literary flourish: why don't you just deliver the content as formal lectures, and reduce the independent work, team work and student presentation sessions? In 2015-2016, I realised that despite providing a clearly written description of the teaching methods used in the course (in advance of the point at which students make their selection of final year courses), around one third of the class had never read it! On the one hand, this makes me field a little more justified in forging on regardless, but on the other hand, I know from experience, that the best courses "bring the students with you": especially the skeptics! Whilst I am happy for students to feel uncomfortable at the start of a course; I am not happy if they feel it wasn't worth it by the end! Unfortunately, it is not always possible to carry the crowd, and so I settle for a clear majority.

The second "complaint" that I often face, is that the course has an air of "vagueness". This is at the heart of feedback such as: "I am not sure I know how or what to revise for the exam". Or, "I don't feel that I have been prepared by MBB308 to answer some of the exam questions". The last point seems to relate to questions of the type:

"Using your knowledge of Biochemistry, how would you design a protein or RNA based Biosensor....pointing out the limitations in our current knowledge of these disciplines throughout your answer"

or

"Contemporary, experimental metabolomic data are sometimes difficult to reconcile with established ideas of metabolic pathways. Choose two pathways from the first half of your degree course (or your own reading) and critically discuss this statement" 

On a typical undergraduate Molecular Biology course, much of the core principles of the structure and function of proteins and nucleic acids is delivered in lectures and practicals by the end of the second year. The same would apply to aspects to catabolism, anabolism, gene regulation and cell signalling. If the method of delivery of these topics represents the approach that is "preferred" by students, it would seem rational for me to assume that the information (but not necessarily all of the details) remains at their fingertips. In my own experience, this is generally not the case. In contrast, can students taught to read at the age of 5/6 retain this ability? Generally, this is the case. At this point I shall rest my (many) case(s)! I do expect however, that students refresh their early years material as part of their commitment to studying. I don't think this is unreasonable?

Whilst these complaints crop up every year, they do not represent the majority view. However, sometimes there are just as many who embrace my approach, as there are who dislike it. In the end, this module represents one of many on our undergraduate courses in Molecular Biology (including Genetics, Biochemistry, Microbiology etc.) and I think one module delivered in this way is perfectly acceptable, even for those who prefer a more traditional, didactic approach. 

What will be different next year?

At this point last year, I decided to modify the content and the list of primary publications and reviews that students must use for their self-directed and team work tasks. I also reduced the number of team presentations from one to two and replaced a mini-literature review with an infographic assessment. This seems to have worked well, in terms of feedback (some concerns expressed by students over previous years have now been addressed, and these related mostly to the "stacking up" of coursework deadlines before Christmas). This year, I felt that the element of choice between a "Systems" OR a "Synthetic" presentation was more manageable, given the number of students choosing this module. With less presentations in the afternoon sessions we were all less rushed, and question time was more relaxed and thoughtful.

For next year, the content will be largely unaltered,with the exception of the usual introduction of new publications at the expense of some older ones (although a core of "high quality" foundational publications will remain on the list). However, the mode of assessment will change, particularly in respect of the examination. 

Currently, assessment comprises 40% course work (both group work and individual), next year it will be a fifty-fifty split and the format of the examination will shift from a compulsory set of 6 questions, to 2 compulsory question, 1 choice question, and you will also be expected to read through a primary publication in the field of Systems or Synthetic Biology, during the examination and condense the contents into a "structured abstract" complete with infographic. The duration of the examination will be accordingly increased to provide you with sufficient time to complete the examination questions. 

The reasons behind the changes

Whenever I receive student feedback from a course, or whenever I am assessing the quality of a candidate for promotion or appointment,  there are several phases that contribute to my reaction. Let's assume I am that candidate. A glowing report from students, with greater than 90% satisfaction and a string of positive comments gives me a very warm glow. Then I start to think, have I delivered a course that think will help them secure a good set of marks in the examination, or have I taught them something new? Have I stretched the brightest, ones and have I enlightened those who had some difficulties? A score of 90% might not be what I wanted after all....

Now let's assume I obtain a score of 60% satisfaction and a mixture of positive comments and some negative. Much more likely for me! What could I have improved on? Maybe this is what to expect from a course that stretches and brings new material to table? Let's be positive and try and extract any areas of criticism that I can work on and put right for next year. Or should I respond by making the assessment more recall based. After all, if I do want that job, or that promotion, I don't want to have to explain why 60% satisfaction is better than 90%! Or do I? Or should I expect senior staff to understand this?

And importantly, what level of responsibility do students have in making assessments of teachers and courses? And have you (as a student) discussed this with your colleagues? At University, I would expect a poor satisfaction rating and complaints if the content of course was factually incorrect, or was delivered in an unprofessional way. However, it is often only post-graduation when what seemed like a great course and a great lecturer, turns out to have been light entertainment and not a preparation for work or further study. I realise that feedback from you to us can become tedious, and I know you value constructive  criticism of your work. Feedback is a two way process and it requires careful thought: it should not be a reflex reaction, but rather a considered one. We will all then benefit from the process.

So why have I changed the exam paper in this way, specifically? During the course you are asked to provide two individual critical summaries of two published papers. You are also asked to carry this same task as a team, and then re-present your opinions in the form of a short class presentation. This is a key element of this course and I feel that the course work experience is somewhat different than completing the same exercise in a limited time. Since this "unseen" challenge is a common feature of many post graduate study and work challenges, I feel it needs assessing in both contexts. It is no different to a data handling assessment. I have reduced the number of other questions accordingly and introduced a choice element. The compulsory elements of the examination are generally answered less well than the course work, which is not uncommon, but they do "flush out" the extent of knowledge gaps in the year group: this is a vital piece of information for examiners and for me in addressing any problems year on year. I have also added a choice question. This is to reflect the significant amount of extra reading you are all doing and provides you with a vehicle to "shine". I believe these changes will improve the value students obtain from the module, as previous changes have done in the past.

And finally, I would like to thank all of the students who took the time to complete the self assessment forms and in particular those who emailed and spoke with me during the course. Your comments continue to inspire me to improve the course for the students who will follow in your footsteps. As educators we rely on a huge amount of good-will from those we teach: and I firmly believe that we should all put something back into the education system for the future of the wider community. Good luck with your other exams, courses and I hope MBB308 will serve you well in the future!

A Defining Post

Today was my first lecture for MS2B2 students on MBB308. On the whole it was a good start (from my perspective): plenty of students with a mathematical "bent" and some answers that were more sophisticated than I expected for a first lecture in the  module, at 9am. Also a good turnout, maybe 80%? It was also the case that more than 30% of students had selected the module without first looking at the content and method of delivery. My challenge is to keep as many on board under the circumstances, so I will once again refer you all to the earlier post on the pros and cons of taking MBB308. The aims and objectives and the MOLE site should clarify the module structure in terms of content, delivery and assessment.

PLEASE LET ME KNOW IF YOU NEED ANY FURTHER INFORMATION OR ADVICE!

A few logistical points from today's session.  

Assignment of groups and allocation of papers.

• The first step is to identify your group members, and I have updated the spread sheet after a few comments today.

• I have used the University course registration data base as my information source. Occasionally there are missing entries. Could you please let me know if you have been left off (in which case you wont receive my emails). Also if you decide to opt out, it would be good for me to know, so that I can make sure the group sizes are balanced for your colleagues.

• The tasks are as follows (thanks for the email queries today). Let's say you are student Bloggs in group B. You will complete 4 assignments:

1. An individual report on your allocated paper on Systems Biology (from the provided list).
2. A group presentation on either Systems (or Synthetic Biology) based on the allocated paper.
3. An individual report on your allocated paper on Systems Biology EITHER from the provided list or of your own choosing. 
4. An infographic, to communicate one aspect of either Systems Biology or  Synthetic  Biology (or both).

All assignments will appear on MOLE from 3pm today (8th November), together with the associated percentage marks.

Optional task. Anyone who wants to have a go at the question relating to the "volume" of the genome, please email me!

Feedback This is the first time I have had immediate feedback in this module! So of course I am in a state of shock! In a good way! First, I like the fact that some of you are already "stress-testing" perceived wisdom, and I would encourage you to approach revision in this way over the entire year: it will come across powerfully in finals answers.

Then a very nice question:  Is redundancy a driving force of evolution or is it caused because of evolution? Or indeed is it a bit of both? If we consider some examples of redundancy it might facilitate discussion. The gut microbe  Helicobacter pylori, cause of some ulcers, has over 10 restriction and modification systems, while some bacteria have 1 or 2; and some none at all, to combat bacteriophage invasion. In developmental genetics, the hox genes show redundancy, which often arises through gene duplication (apologies for the scary, figure!). Human cyclins E1 and E2 are functionally redundant: one or other (but not both) can be knocked out without loss of cell cycle progression, and mouse viability. I think I would suggest that redundancy enhances robustness and complexity and this must therefore be a driver of evolution. However, some gene duplications produce pseudo-genes. The question for me is whether we are sure enough that a "pseudo-gene" has no useful function, or are we not measuring the right thing. So I think I am mostly in favour of redundancy as a driver, but with the caveat that there may be cases where it is not.

Another question relates to the comment I made in my last post about Beadle and Tatum and the one gene one enzyme hypothesis. The question being did this misdirect many biologists? And in an (edited) response:

I feel that it did seem to have a knock-on effect in subsequent years... especially until the emergence of more modern technologies...leading to What effect that this has on our interpretation of systems biology? Was it the fact that they didn't foresee the grander picture which was later discovered? 

Another great question! In response I would say that I pointed out this particular "concept" since it typifies the reductionist approach and makes me (at least) think of isolated reactions in metabolic pathways. However, you are right. As new methods become available, we build on our ideas and ultimately we will end up with a "systems" way of thinking. And the reductionist experiments, if robust, should meet up with the systems analysis; which must also be presented as a robust model. On a final point, I think Beadle and Tatum did appreciate the big picture, but not everyone who followed in their foot-steps did?

Good luck with the critical evaluation of the papers!