Archive for September, 2009

On Revisionism

Thursday, September 17th, 2009

Today, I attempted to log into the Sanger computing cluster, and was presented with the following error message:

> ssh farm2-login
You don’t exist, go away!

I was somewhat taken aback by the snappy tone from a usually jovial machine. As much to reassure myself as anything, I enquire who the computer thinks I am.

> whoami
whoami: cannot find name for user ID 12722

I see, so the computer is claiming to not know who I am; that to it, I have ceased to exist, or have never existed. Given that I was in work yesterday, it is unfortunate that the computer would forget about me so rapidly.

I attempted to reassert my existence, and was met with this:

> su lj4
Sorry.

The resigned sadness of this message is haunting. The computer would be refusing to meet my eye, if it was able to do so in the first place.

I cannot help but feel that my machine has done something terrible, something that fills it with guilt and shame, something that it knows I cannot forgive. It greets me with shock and anger, then with denial, and then finally with a guilt-weary apology. What has happened? Should I be reassuring my machine? Growing angry with it? Or panicking blindly as the sense of unease and mounting horror rises sharply in my breast?

In the end, I go with turning it off and then on again.

Recombination in the X and Y Chromosomes

Monday, September 14th, 2009

ResearchBlogging.org

Rosser, Z., Balaresque, P., & Jobling, M. (2009). Gene Conversion between the X Chromosome and the Male-Specific Region of the Y Chromosome at a Translocation Hotspot The American Journal of Human Genetics, 85 (1), 130-134 DOI: 10.1016/j.ajhg.2009.06.009


There is new paper is out in American Journal of Human Genetics about how the X and Y chromosome might not be as separate as we think, and in fact might undergo regular recombination in certain regions (you can read a press release for the paper here).

Specifically, the paper is a resequencing study of the X and Y chromosome homologues PRKX and PRKY in around 60 individuals, looking for signatures of recombination. In summary; it is an interesting and well supported paper in as far as it goes, but it raises more questions about Y chromosome evolution than it answers
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Punishment, Praise and Regression to the Mean

Wednesday, September 9th, 2009

I am currently preparing a paper for publication, and the last author sent it out to a bunch of people for comments. A common complain was a discrepancy between the run times of the same algorithm in two different parts of the paper. I ran a number of algorithms 12 times each, and then later on in the paper I picked the fastest and re-ran it another 36 times; the average time taken for the fastest algorithm in the second set of runs was significantly slower than in the first. Two different people asked me to fix this, but it isn’t a mistake, it is of course regression to the mean.

Anyway, this inspired me to post a very interesting anecdote from the economist Daniel Kahneman, writing about punishment, praise and regression to the mean:

I had the most satisfying Eureka experience of my career while attempting to teach flight instructors that praise is more effective than punishment for promoting skill-learning. When I had finished my enthusiastic speech, one of the most seasoned instructors in the audience raised his hand and made his own short speech, which began by conceding that positive reinforcement might be good for the birds, but went on to deny that it was optimal for flight cadets. He said, “On many occasions I have praised flight cadets for clean execution of some aerobatic maneuver, and in general when they try it again, they do worse. On the other hand, I have often screamed at cadets for bad execution, and in general they do better the next time. So please don’t tell us that reinforcement works and punishment does not, because the opposite is the case.” This was a joyous moment, in which I understood an important truth about the world: because we tend to reward others when they do well and punish them when they do badly, and because there is regression to the mean, it is part of the human condition that we are statistically punished for rewarding others and rewarded for punishing them. I immediately arranged a demonstration in which each participant tossed two coins at a target behind his back, without any feedback. We measured the distances from the target and could see that those who had done best the first time had mostly deteriorated on their second try, and vice versa. But I knew that this demonstration would not undo the effects of lifelong exposure to a perverse contingency.

How Much Health Information Is In A Person’s Genome?

Friday, September 4th, 2009

How much information can we get from a genome scan? Many companies, such as 23andMe and deCODE Genetics sell genetic tests that allow you to determine parts of your DNA sequence: one selling point is that it can tell you how susceptible you are to various diseases. But how much can a genome really tell you?

In general, people say ‘not much’, and cite the importance of the environment, social, cultural factors, and our lack of knowledge of disease genetics: these are all valid and important points. But, can we put some figures on exactly how much a genome scan can tell us? Can we calculate exactly how much the average person’s predicted probability of getting a disease will change after they get their DNA scanned?

In this post, we will take three important diseases of decreasing rarity, and take all the genetic variants that are known to influence them. We will see exactly how much we expect this information to change someone’s likelihood of getting the disease.
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