Students, answer the question! (And other exam tips)

Every year when I mark exam scripts, I am surprised by the number of students that fail to recognise the single most important aspect of an exam answer: it should answer the question! Importantly, questions are rarely (if ever) "Write everything you know about subject X". If, therefore, your answer to a question related to X is to write everything you know about X, you are not demonstrating understanding - quite the opposite.

For example:

"Discuss the role of point mutations and duplications in the evolution of a protein family of your choice."

This does not mean:

"Write everything you know about point mutations and duplications and occasionally mention a protein family as an example when you can."

If you are not discussing the evolution of your protein family - or explicitly providing background material - you are not answering the question.

As a marker, I do not enjoy giving out bad marks. It is especially frustrating if the answer is long and most of what was written is right. Marks cannot be given for just being right, though. Otherwise, people could just write about whatever they wanted in an exam, which would defy the point somewhat.

The same advice applies to diagrams/figures. Don't just reproduce a figure from a lecture because it relates in some undefined way to the topic being examined. Draw a figure to illustrate a specific point. Better still, customise a figure from a lecture - or even create a totally new figure yourself - to illustrate a specific point. Then draw attention to that point by citing the figure at the appropriate point in the text. Don't just hope that I, as a marker, will make the right connection. Of course, I know how the figure connects to the topic/question - I set the question! I want to see whether you know! Unfortunately, unless given evidence to the contrary, I will have to assume that you do not.

Finally, please re-read your answer at make sure that, at the very least, sentences make sense. Exams are your opportunity to demonstrate what you know. Returning garbled nonsense is not a good way to do this. (Unless, of course, garbled nonsense is an accurate representation of what you know, in which case you have other problems!)

Science nay-sayers, why the rush?

I get annoyed at the repeated premature announcements that scientific breakthrough X or Y has not yielded the benefits it promised. This week's Nature Biotechnology, for example, features an editorial entitled "What happened to personalised medicine?" with the tag line:

"Personalized medicine falls a long way short of the predictive and preventative healthcare paradigm it once promised."

Notice the past tense? "It once promised." Personalised medicine as a concept has failed, apparently.

The article then says:

"In some respects, 2011 was a banner year for personalized medicine. Academic medical centers began to demonstrate the feasibility of routine clinical genotyping as a means of guiding treatment selection in oncology. The US Food and Drug Administration released its companion diagnostics draft guidance. Sanofi, Pfizer and AstraZeneca signed deals with Medco and WellPoint for access to their large databases of patient data. Cancer Research UK's Stratified Medicine Programme was launched to demonstrate how genetic tests can be used to match National Health Service cancer patients to treatments. And two new targeted oncology therapies, Roche/Genentech's Zelboraf and Pfizer's Xalkori, were approved in conjunction with companion diagnostics for BRAFV600E and structural variants of anaplastic lymphoma kinase (ALK), respectively.

All are no doubt important steps, but illustrative of a rather pedestrian form of progress in personalized care rather than a march to the future."

So, it's not that it's failing to deliver anything. It's just happening too slow. The same thing happened with the Human Genome Project (HGP). This was "completed" less than a decade ago but people have already proclaimed that it has failed to deliver because we haven't been overwhelmed with a deluge of new HGP-derived drugs. The average drug development time is 10-15 years, I think, and that's when you already understand a fair amount about the target. So, even if the genome project truly was "complete" then it is still unrealistic and unfair to have expected it to already have yielded dozens of new therapeutics, even if you ignore the fact that novel targets arising from the genome project are, by definition, going to start off with practically nothing known except the sequence.

Annotation is still ongoing but the current state is over three billion nucleotides, approx 21,000 high confidence protein-coding genes plus over 47,000 gene predictions. This is a lot of data to deal with and it is naive beyond belief to think that the "answers" are just going to magically fall out in a few years. Going back to personalised medicine, the current Ensembl release has over 45 million variants and even this is not enough data. To really make sense of the role of genetic variants, we need a lot more genomes from both patient and control populations, and these patient populations need to be sensibly stratified by, e.g. treatment response. Such data is beginning to come but it is still early days, plus we still don't really know how to analyse all this data.

Biology is flaming complicated and the more we learn, the more messy and complicated it gets. Expecting us to unlock the secrets of first "The Human Genome" and then human variability in a few years goes beyond naive or arrogant, it's ridiculous.

I'm a big believer in The Human Genome Project and it really has changed the world already, even if its "promise" in terms of new drugs etc. will take many more years to be realised. (And this realisation will probably come mostly from Academia rather tha pharma.) I'm also a big believer in the concept of personalised medicine - the tailoring of treatment to the individual based on their particular genetic background. The fact is, however, that whilst this is totally the right road to be heading down, it's going to be a very long and windy road, no doubt with a few wrong-turns and dead-ends along the way.

To be fair, the rest of the editorial does then raise some pertinent points about things that need to happen to facilitate our journey down the road towards personalised medicine. These include better incorporation of the human "microbiome" - in sheer numerical terms, we have far more bacterial cells, genes and proteins in our bodies that human ones - and increased incentives for pharma companies to develop diagnostics as well as treatments. I just wish that the whole thing hadn't been given such a negative spin from the outset. It seems that with live in a world where everything needs to be over-hyped initially and then over-criticised when it doesn't live up to the over-hyping. I say, stop that: it's silly.

21st Century Referencing

One of the new issues that I am beginning to see in undergraduate project work is uncertainty regarding how to cite various atypical sources. In my day [gets out pipe and smoking jacket], the most tricky source was a book section or occasional website. Now, though, it seems that podcasts and Youtube videos etc. are being added to list of legitimate and useful sources of information and opinion. Fortunately, help is at hand. The library staff at Anglia Ruskin University have made a really useful Harvard System of Referencing Guide [1] containing all manner of source types and the required information for citations thereof. This is the best website of this kind I have seen and well worth bookmarking if you have to deal with this stuff regularly.

1. Anglia Ruskin University, 2011. Harvard System of Referencing Guide. [online] Available at: <http://libweb.anglia.ac.uk/referencing/harvard.htm> [Accessed 14 January 2012].

Damn fine Dalmatian Dingač

Yesterday was the first tasting of the Year for the University of Southampton Wine Club. The tasting was "8 Dalmations":

"The 2012 inaugural wine tasting will bring back fond memories of summer warmth and sun-drenched picturesque shores of the south Adriatic Sea – and hopefully this setting can be recreated by tasting the wines typical of that region: Pelješac peninsula and Korčula Island. Already the ancient Greeks grew vine there and after a brief exile in established wine-making regions of the old and new world more and more wine-growers and makers return to Croatia, only to express their newly polished skills in exciting wines.

We will experience 3 white wines from the Korčula vinogorje (typical/registered region), a relatively green island with rolling hills, famous also for being the home of Marco Polo. In contrast, northern Pelješac is characterised by wind swept escarpments and small villages. Grapes barely survive what nature and the gods throws at them, but for the wine-lover the efforts of hard working small wine estates can be very rewarding, and we will taste 5 reds from the Pelješac vinogorje."

This was a great tasting that embodies all that is good about these events: good company, good nibbles and an interesting selection of wines that I would not normally have access to nor think about trying. (Too be honest, I had never heard of any of them!)

The stand-out discovery for me was my enjoyment of the Dingač red wines. We sampled two robust reds (14.3% and 15% vol!) and a dessert variety, and all three were very tasty. My personal favourite was the 2006 Matuško (right) but others favoured the 2004 Skaramuča (centre). They have an interesting flavour, with a lot more cherry versus the berries of the red wines that I normally go for. Sadly, I think they are only really available in Croatia but it is on my holiday destination wishlist, so I will just have to make a mental note and bide my time!

A flowchart for choosing your religion

I'm not sure where this originally came from but it's a classic! (I'm not rich and insane.)

A month (or so) with iPlan

At the end of November, our iPlan energy kit arrived. With one full month under our belt, I thought it timely to give an update.

Initial experiences were a bit mixed as the website was done for quite a while but, right from the outset, the ability to monitor energy usage was really useful and reminded me to switch off lighs etc. It was also interesting to see how much energy some of our light use. (Not surprisingly (but still disappointing), the worst offenders were the brightest, most useful ones!)

Less useful at this stage is the daily target. This started off at a fairly reasonable 8.0 kWh per day (although I'm not sure how this was determined) but went down dramatically when I switched to our predicted usage from Scottish & Southern Electric (SSE). You can see this on our monthly usage chart for December, below, where the target line drops sharply on the fourth:

This is clearly nonsense, as the only days that we meet are target are those that either or both of us are away and thus (practically) nothing is being used. (The big spikes caused by extra laundry each side of trips is also clearly visible!) Having contacted SSE, I have learnt that this prediction is based on meter readings and because our reading-before-last was a massive over-estimate, our last period's usage was practically nothing. It should, I am told, sort itself out with our next meter reading later this month. Time will tell. (I still think it is a bit silly that you cannot over-ride their estimate and set your own target; you can set it for a percentage under their prediction but not over.)

Fortunately, even though we can't set a sensible target, we can still feel good about ourselves with some of the other comparisons available, such as the "LikeMe" comparison with "similar homes". It's not clear how a "similar home" is defined but I suspect, given how well we appear to be doing, it does not include a comparison of the number of occupants. (Either that, or the average couple out there are big consumers!)

You can also compare your usage with all iPlan users, although I'm not really sure how much this tells you:

Still, it makes electricity billing more interesting!

Just 24 to go until a big round-number milestone

I love geeks! Happy cartoon 1111101000, xkcd!