ubuntu laptop with Ati radeon mobility X1300. X session not resuming correctly

I have this old HP nc6400 which is gradually deteriorating. However it is pretty good for browsing the web, and taking to places where it might get nicked.

Unfortunately, at some point recently, either due to it developing a hardware issue, or that a kernel package upgrade or the graphics module upgrade has introduced a bug, and now there is a screen colour depth issue when it resumes from suspend.

So if you boot up and open a browser. It seems fine and images look like this...;

However if you allow the screen to go to sleep, either by some timeout, or by closing the lid. Once the machine is disturbed from sleeping, it appears that there is a colour depth problem.

After it has resumed it looks like this;

During troubleshooting, someone asked that I should send them my xorg.conf file. However I've not seen an actual one on the filesystem for some time, and I understand that the config is generated on the fly by introspection of the hardware.

As there is no default or generated xorg.conf on my installation, I tried generating one out using the "# Xorg -configure" command. This should produce a file in the local directory containing those values introspected from the system.

Unfortunately I get a seg fault when running the command;

# Xorg -configure

However the file it generates still seems to work once I copied it to the /etc/X11 directory.

Basically it looks like X11 needs the xorg.conf file to properly resume from suspend.

Are our spooks distracted by social media?

It's obvious Media and politics had become distracted by social media. You know it, I know it, they know it.

But f**k it, its more interesting than the daily grind of traditional analysis. For example have you seen how thick a copy of the Sunday Times is these days, it's practically equivalent to a session at the gym just to lug it home from the newspaper shop of a morning.

Reading it cover to cover takes you right through to the next Sunday. A tweet is so much more succinct.

But more unpleasantly it seems that while our intelligence services were spending vast amounts of cash shovelling tweets, and pokes and pictures of fapping off yahoo webcam chats into their archive, that Russia was busy planning world war III

The basic failure of the intelligence services, is not so much that they were obviously collecting personal and private data on mass, but that in their fervour to establish and enable these dubious activities, they actually failed to do the job which they are there for.

If we are all killed in nuclear armageddeon, I've trained a cockroach to talk, it will say "I told you so" to anyone who manages to survive.

p.s. I'm joking, that was all a setup for the speaking cockroach joke.

Hard to concentrate after strenuous exercise?

Whenever I am doing regular training I noticed that if I do a solid session of exercise, particularly in the morning, that I feel badly spaced-out during the rest of the day. I used to do a bit of climbing, and I used to go in the late afternoon at the Mile End wall, but it basically meant that I would write-off any meaningful work during the rest of the evening.

So post-exercise, I could potter about and procrastinate, but anything requiring concentrated focused effort was almost impossible. I thought it odd that other people, such as those I climbed with, didn't experience similar degradation in concentration.

But since then I've noticed that some other people were reporting similar issues of loss of concentration on a cycling forum, so I googled for the issue, and it seems a common complaint;
"s5fskzfv" on Bike Forums said: "After a long workout I often have trouble concentrating. It's hard to describe exactly what the problem is, it's like if I have something I need to read, or something that takes thinking like balancing a checkbook, I just don't feel like doing it. Trying to concentrate feels uncomfortable to the point that I can't do it. I tend to do a lot of reading, if I didn't, I might not even notice the problem, it's sort of subtle. I'm not sure exactly what it is, maybe not enough sleep or low blood sugar? Usually by the next day I'm back to normal after a couple of meals and some sleep."
NaturalBeasting talking on Testosterone Nation made this post:
"It is extremely difficult for me to do critical thinking after a really ball-busting tough workout. I completely space out and can't focus.

This effect usually lasts for the remainder of that day and sometimes 1-2 days afterwards. (It affects my performance in school/work.)

If I don't workout for a week or so there's a dramatic difference in my mental capabilities.

It's been happening my entire life, despite good sleep, nutrition and overall health.

Anyone else experienced this?

And "strawberry" asked this question on yahoo Answers:

After doing my morning exercise I can't concentrate in lectures..will I just 'outgrow' this?

 I'm 22. I love my exercise. In my summer holidays (I'm at uni), I always start my day with a half-hour workout. But if I'm in the middle of a university term, I find that after doing my morning workout, I find it difficult to concentrate in lectures due to feeling tired from the workout.

So today, I did a short run and some weights, after a bit of a layoff, and right now I am feeling completely unable to work.

I've eaten a good breakfast since, so I don't think that low blood sugar is the issue. Unless its some sort of "hangover" effect. I don't feel tired right now, and I wouldn't be able to doze off, which is unusual for this time of day, whereas normally I could easily have an hours kip.

There are a few theories on the acute changes brought by exercise, both aerobic and muscular;

for example copper and zinc blood levels;

Elevated brain-derived neurotrophic factor levels;

This paper seems to suggest, that you benefit from CV fitness, but not from the exercise itself;
These findings suggest that cardiorespiratory fitness, but not acute aerobic exercise, may be beneficial to behavioral and neuroelectric indices of action monitoring following errors of commission by increasing top-down attentional control.

If anyone has got any suggestions on how to alleviate this problem, I am perfectly happy to try them out! (In the name of science)






How to make zotero format organizational creators correctly when fields are parsed from metadata.

I puzzled over this one for a while, and given the answer was fairly simple I thought it was worth a write-up.

When I generated my bibliography for an assignment I was writing, I noticed that Zotero has made a mess of the author credit in some references. For example:
Nutrition, C. for F. S. and A. (n.d.) ‘Laboratory Methods - BAM: Staphylococcus aureus’, WebContent, [online] Available from: http://www.fda.gov/Food/FoodScienceResearch/LaboratoryMethods/ucm071429.htm (Accessed 10 February 2014).
The credit should actually be to the institution named "Center for Food Safety and Applied Nutrition".

Research Log: rereading course text

I reread the Antibacterial Agents chapter from the course book;
Patrick, G. L. (2009) An Introduction to Medicinal Chemistry, New York, Oxford University Press.

They are cheeky little things, those bacteria.

I was particularly looking for articles from Medicinal Chemistry journals, however I found this one from the "one stop search" at the OU library;
Kalia, Vipin Chandra (2013) ‘Quorum sensing inhibitors: An overview’, Biotechnology Advances, 31(2), pp. 224–245.

It's quite a lot of reading,  but it seems pretty comprehensive for a review of the mechanisms.

Research Log: Cardiac Glycosides

I am currently researching Cardiac Glycosides, and need to keep a "research diary" for an OU module

The final 3 papers I chose were these;

Gayed, Bishoy A., O’Malley, Katherine J., Pilch, Jan and Wang, Zhou (2012) ‘Digoxin Inhibits Blood Vessel Density and HIF-1a Expression in Castration-Resistant C4-2 Xenograft Prostate Tumors’, CTS: Clinical & Translational Science, 5(1), pp. 39–42.

Jensen, Marie, Schmidt, Steffen, Fedosova, Natalya U., Mollenhauer, Jan and Jensen, Henrik H. (2011) ‘Synthesis and evaluation of cardiac glycoside mimics as potential anticancer drugs’, Bioorganic & Medicinal Chemistry, 19(7), pp. 2407–2417.

Slingerland, M., Cerella, C., Guchelaar, H. J., Diederich, M. and Gelderblom, H. (2013) ‘Cardiac glycosides in cancer therapy: from preclinical investigations towards clinical trials’, Investigational New Drugs, 31(4), pp. 1087–1094.

The paper by Gayed et al (2012) reports on an in-vivo experiment in which where tumour cells are grafted into adult male nude mice.

Jensen et al (2011) describe some novel synthetic cardiac glycoside compounds in a in-vitro cell line.

Slingerland, M. et al (2013) is a review article of the use of cardiac glycosides in anticancer medicinal chemistry.

statistically speaking... guardian writer is confused about statistics

This piece by guardian writer Barbara Ellen probably needs to be rechecked by their sub-editors for statistical correctness.

If you really think you're gay, guys, why not act on it?


The latest National Survey of Sexual Attitudes and Lifestyles revealed many things (from unplanned pregnancies to unreported sexual assaults), but also that there has been a 400% increase in (mainly younger) women, some fully lesbian, declaring same sex sexual experimentation – around 16%. By contrast, the number of men who'd had a same sex experience had only gone up 1% (to 7%) since 1991.

The data that Barbara Ellen is quoting appears to be this:

Percentage of the population who have ever had same-sex experience (people aged 16-44)



So I think there are two problems with the quoted statement above.

1) There has been a 300% increase in women declaring same sex experimentation.

The absolute increase of 4% to 16%, is 12%... and 12% is 300% of the 1991 figure of 4%.

2) Barbara is also comparing the change in the proportion (of women declaring same sex experimentation) as a percentage of the original 1990-91 value (which should be 300%), to the absolute change (of men declaring same sex experimentation), from 6% to 7%, which is 1%.

However these are not equivalent values. The correct comparison figure for men (of percentage change in proportion of population), to the 300% figure would be 16%, i.e.  

The change from 6% to 7% is a 16.66% increase, when looked at as a percentage change in the proportion.

So the correct way of describing that would be:

"also that there has been a 300% proportional increase of (mainly younger) women, some fully lesbian, declaring same sex sexual experimentation – around 16%. By contrast, the proportional change in percentage of men who'd had a same sex experience  was only 16.66% (to 7%) since 1991."

However, it would also be possible to look at both figures as absolute changes, and that would result in the following correct version:

"also that there has been a 12% absolute increase in (mainly younger) women, some fully lesbian, declaring same sex sexual experimentation – to around 16%. By contrast, the number of men who'd had a same sex experience had only gone up 1% (to 7%) since 1991."

I might be wrong about the interpretation, if I am using the wrong source data...