Breaking laws

Black Coffee and Tea in White Cup is HotI have just got back from Liquids 2014, a conference in Lisbon. I thoroughly enjoyed it, and Lisbon was great – sunny, friendly and with great seafood. I will probably write a post or two on the best talks later, but now I want to talk about how I learnt of two scientists trying to reinvent thermodynamics.


Swift movement in shrink-to-fit genes

Circle Line Party getting pretty crowded (2540701648)The remarkable fact that people who work on understanding our DNA always mention in their talks is that we have about 1.5 m of DNA in the nucleus of each of cells, and these nuclei are only around 5 thousandths of a millimetre across. That is a lot of DNA in a small space. Stretched out the DNA is longer than some of us are tall, but this DNA is crammed into a space too small to see with the naked eye.


Monkeying around with HIV

Young Rhesus MacaqueI have just got back from co-organising a science workshop in Lausanne, Switzerland. It was great fun, I thoroughly enjoyed many of the talks. And as an organiser it made me happy to see the scientists enjoying the talks then realising that they can use these ideas in their own work. Some of the attendees who met at the meeting for the first time were even talking of teaming up and working together. If they do, it’ll put a smile on my face that I have helped that.


From the mushy zone to squishy cells

20140711_104433Today I am at conference on metals crystallisation, next
Friday I will be co-chairing a workshop on structure in living cells. These are two of four back-to-back conferences will be attending over the next two weeks. With this many conferences it is good to have variety. This one is near Egham in Surrey, the picture shows part of the venue.


Are less active chromosomes like WD40?

PLoSBiol3.5.Fig1bNucleus46ChromosomesWe all have 46 chromosomes worth of DNA in each of our cells. Each one is kind of a stringy object that is typically around a few micrometres across, and all 46 are squeezed into a cell nucleus that is itself maybe only 7 micrometres across. These chromosomes are surprisingly variable. Chromosome number 18 has maybe 250 genes on it, while number 19 has around 1,500 genes, despite being around the same size*. So chromosome 19 is a lot more active than 18, many more proteins are being made from its much larger number of genes.

It has been known for a long time that the chromosomes are not uniformly distributed in the nucleus. The active ones, the ones like chromosome 19 with many genes, tend to be nearer the centre, while the quieter ones are near the edge. You can see this in image and schematic at top left, the less active chromosome 18 is at the bottom near the right end, while the more active chromosome 19 is above it and so away from the edge. The image is a from a paper by Bolzer et al.


Don’t get too excited

YD LawWhat with high pressure penalties, last minute corners, etc, now is a good time to consider the Yerkes-Dodson Law. This is illustrated in the figure to the left. Basically it shows how difficult you find doing a task, e.g., taking a good penalty, is as a function of how much stress you are under/how much adrenalin is in your bloodstream. The y-axis says learning but is known to be more general than just learning.

For simple tasks (solid curve), the more adrenalin, the better, i.e., the more likely it is that you complete the simple task correctly. But for tasks where you have to think (see the dashed curve), it is not so simple. A bit of stress, a bit of adrenalin, helps, but too much hinders you, and the chance of you failing goes back up. There is an optimal level of pressure where you perform your best. Being half asleep is bad, but so is being panicked.


The Department where CDs never go out of fashion

CD autolev cropToday was the second of two back-to-back Open Days the University runs for prospective students. A-level students thinking of going to university in autumn 2015, and their parents, visit the university to learn about degrees and university life. Today we had about 350 to 400 visitors in the Department, and maybe a bit more than half than yesterday.


Direct from the Sun


As a scientist I guess I should stop and admire the beautiful natural world a bit more than I do. Too busy doing stuff most of the time, which is a poor excuse. Anyway, above is a picture of sunset over the river Seine in Paris. To the right you can see twin squarish towers, this is I think the Notre Dame cathedral.


A personal study of nucleation

I study nucleation, but mainly via modelling on a computer. The guy below, Harley Morenstein, took a more personal approach. Incidentally, if you are bored of the Vine looping just click on it.

Drinks like Diet Coke, lemonade etc, are carbonated, i.e., have carbon dioxide pumped into them under pressure to make them fizzy. If you carefully take the top off and are gentle with then (as opposed to giving them a shake) most of the carbon dioxide remains in the drink. This means that the amount of carbon dioxide dissolved in the water is actually above the solubility of carbon dioxide in water (at atmospheric pressure), and so this carbon dioxide wants out (technically speaking it is thermodynamically ‘downhill’ for the carbon dioxide to leave the water and go into the atmosphere).

The carbon dioxide comes out as bubbles and if the drink is not shaken these bubbles can find it hard to start to form. This initial step when a tiny bubble starts to form is called nucleation. If nucleation is not possible then this traps the carbon dioxide in the Diet Coke or whatever the drink is.

Until something comes along to make nucleation easier, like Mentos. Mentos are an American sweet, and for reasons nobody really understands, carbon dioxide bubbles nucleate like crazy on the surface of Mentos. So when the guy in the Mentos suit drops into the Diet Coke tub, bubbles of carbon dioxide nucleate like crazy, and you saw the result above.