Glasgow, Venn-diagrams and The Festival

The Edinburgh Festival

In the spring, while trying to decide how to best prepare for my dissertation and the associated, short-prep-time trial-lecture, I had the great luck of being hunted down by one of the up and coming names in the functional genomics of hypertension. After my talk at the ESH meeting in Oslo, when I was heading directly to the air-port, Martin McBride ran me down to suggest that we should compare our data-sets. The result was that two weeks before my dissertation, just as the title of my trial-lecture had been announced, I went to Scotland for four days to work on something completely different.

Our data-set is from the mRNA expression profiling of old rats with hypertension and slow developing kidney damage, while his is from salt-challenged stroke prone spontaneously hypertensive rats that develop kidney damage very quickly. By combining these datasets we hoped to learn something about the common pathways for kidney damage in our different models.

With Martins, and the Glasgow group's great experience with these kind of things we managed to get our data into comparable formats in just under four days. The next step was actually comparing the changed genes. To do this we basically want to check which genes popped up in both of our sets, an onerous task but one greatly simplified by the use of Venn-diagrams (John Venn FRS, Symbolic Logic, 1881).


John Venn FRS

Basically you represent each data-set as an area, for example a circle, and by intersecting these you can illustrate the set of common items. We started with a simple online-tool that can make 2 to 4-way Venn diagrams. But soon progressed to running the comparisons in R with a little help from Glasgow statistician John McClure.


Venn-diagram

If you want more Venn-diagrams to look at you should visit Jessica Hagy at Indexed. Although, she has made a complete hash out of what makes baby Jesus cry.


Dog at The Festival

It was my first time in Scotland, so I made sure to try the black-pudding (innocuous), the haggis (spicy) and a number of local beer (nice). The most amazing timing was that I managed to be there during The Festival. It's a festival like many others, Edinburgh is completely full of tourists and local festival goers. The Scottish present it as The Festival, the one, the original, the only true festival of which all others are pale comparisons. In many ways they are right. It doesn't have the arranged feeling of many other festivals. The main happening is the Fringe, which is the thousands of performers that aren't part of the festival proper, but show up anyway.


The Fringe

Everyone should go, but since it is a popular thing, you need to book your hotel about a year in advance. If I only knew my schedule for next August, I would have booked mine already.

Fillet of horse sous vide

It has been kind of hectic lately, finishing the thesis, preparing for the dissertation, getting a mortgage for buying a new place to live in Sweden, working full time in the cardiology department and revising two papers.

Anyway, my fiancée got a job on Wednesday and by Friday we had outbid the competition for our dream-apartment. Or, a nice apartment anyway. So, today we were celebrating. She brought a Veuve Clicqout Ponsardin from the air-port and I went to the butcher's and got a slice of horse's fillet.


Horse is a dark, game-like, meat. Like any red meat it shouldn't be cooked to harshly, and this was so tender that I accidentally put my thumb through it when I was preparing it. So, cooking with care was the order of the day.

I have been reading a lot Cooking Issues since I was made aware of it. It is a fantastic cooking blog, especially if you are scientifically minded. Anyway, they do sous vide (eng. under vacuum) cooking, which is slow cooking with a twist. You vacuum-pack your uncooked food and then cook it in a water-bath at the desired temperature (58 centigrade for medium rare beef) for an hour or two.


First, I seared it quickly with salt and pepper.


Since I don't have a vacuum-pump at home I just packed it in a plastic bag with red onions and garlic, sucked all the air out, and put it in a pot with water in the oven. The goal temperature is 58 centigrade for medium rare. Sadly my cooking thermometer is broken and the oven temperature dial is not as accurate as I would wish. Thus, I checked the temperature the old fashioned way, 58 is hot enough to hurt, but not scalding. I put a small weight on top to keep it under. It was allowed to cook for about two hours. Then I seared it once more and served directly.


The temperature wasn't exact enough and we ended up with a medium cooked piece of meat. It was a very tender, fantastically juicy and tasty piece of meat though. Any time now, I am going to buy a proper heater/circulator like the Sous vide professional, which is made especially for cooking sous vide. It does look very much like your standard scientific water-bath heater/circulator and that is because it is. Although, they have a prettier, black, casing for the cooking variant.


If you have meat, you need potatoes. In this case a spring potatoe & melon salad. The sweetness works fantastically with the dark horse-meat and the champagne.


For a sauce I made a classic reduction of assorted vegetables and the juices pressed out of the meat during cooking. I reused the root-vegetables to make a purée, nothing much by itself, but adds a nice extra texture to the meal.


Here are the vegetables, the rosemary and the juniper-berries before they were transformed into stock with the help of some gin and a lot of water.


And there we are: Horse-fillet sous vide with mashed celeriac and turnip. A potato and melon salad, sauce and champagne. I served it with a little balsamic syrup to add some acidity.