I've posted a brief article (On the gain of genes and gene function) over at Wonderful Life on two recent papers that reveal something of the rate and nature of gene duplication and diversification within the species of Drosophila.  This is by way of response to recent review article written by the prominent supporter of Intelligent Design creationism, Michael Behe.

The bearded rotund dude clad in red paid a visit a few days ago, leaving a selection of gifts, among them a Squeezebox Radio.  This is part of a range of wi-fi audio devices from Logitech - I already have one of the original Squeezeboxes, now renamed Squeezebox Classic.[caption id="" align="alignleft" width="268" caption="Squeezebox Radio (image via Logitech website)."][/caption]Each of these devices connects to a server system that serves audio streams, either from local audio files of from the internet.  In my case, I'm using a QNap NAS box as a server.  The software for this, Squeezebox Server, is available as a download for a variety of platforms, including Linux, OSX and Windows, as well as a perl tarball.  Squeezebox server supports multiple players, which need not be playing the same audio streams.  Squeezebox Server is open source, and supports a whole array of plugins.  My current set up consists of a Squeezebox Classic, the new Squeezebox Radio, and the iPad app SqueezePad which following a recent update now has the ability to use the iPad as a player.  In addition, one can emulate the players on one's computer using Squeezeslave.I intend to use the Squeezebox Radio to replace an ageing radio alarm clock.  Reviews suggest that it's a bit unreliable as an alarm clock when used to play internet radio feeds from the Logitech server.  In my case I'll be mostly streaming BBC radio via the iPlayer plugin.The Squeezebox Radio is principally operated by the buttons and knobs on the front panel, though some of the functionality can be accessed via Squeezebox Server.  A remote control is available separately along with the rechargeable battery pack (which bizarrely isn't included unless you've selected the device as part of a bundle).  So, in order of size:The colour monitor shows the status of the device.  It can be set to show a variety of information while playing or in standby: I've set this to show the time and date most of the time.  It can be a bit bright for use as a bedside radio, but this can be addressed by adjusting the brightness and the theme in use.The large knob isn't actually the volume, but the selecter used to scroll down configuration options and through the music files.  You push it to make a selection.  The on/off button, actually more of a standby button is bottom right, with the volume knowb bottom left.  There are several switches for 'Home', 'Back' and the like, which are used in navigating the menu system, along with conventional play, pause, ffwd etc functions.The six silver buttons (three either side of the display) are used to preset playlists and radio stations.In use, the thing was almost ridiculously easy to set up.  It quickly found my wireless network.  I had a brief pause while I figured out what my login details for the squeezenetwork were, but then the remaining setup was straightforward, including a download of a firmware update.Sound quality is pretty good for such a small device.  Setting the alarms is easiest using Squeezebox Server, but many of the things I've tweaked have had to be done through the devices interface itself.  This includes setting preset playlists, and setting the display brightness and theme.Does it work as an alarm clock?  Yes, no problems on the testing so far.  I have one or two worries about bandwidth when the server is doing backups, and I'll need to keep an eye on this.I'm really very pleased with the device - so far it's worked well, though of course it needs to b

A seasonal cartoon from xkcd...[caption id="" align="alignnone" width="551" caption="Incident"][/caption]Somebody must read all those logfiles...surely?

[caption id="" align="alignleft" width="220" caption="Captain Beefheart"][/caption]I see from the BBC news website that Don Van Vliet, aka Captain Beefheart, has died (Don Van Vliet, aka 'Captain Beefheart', dies aged 69).  Very sad news.  Although Van Vliet had retired from music back in the 1980s to concentrate on painting, his music has been a major part of my life since I first listened to Trout Mask Replica several decades ago.More obituaries:The Captain Beefheart Radar StationThe Guardian - Captain Beefheart, who has died aged 69, was provocative and unpredictableLA Weekly - Top 14 Reasons Why Captain Beefheart Was a True American GeniusA sad day indeed.  Here's an old video of the Magic Band playing 'Electricity'...

Not too much activity here on Flies&Bikes lately, mostly because I've been more active posting about intelligent design over at Wonderful Life, and grumbling about politics at Posterous.  Oh and the small matter of the day job.I just thought I'd point out the current status of voting intention, as revealed by YouGov polls.  I note the spike in LibDem popularity, back in the General Election campaign, when they were at the height of their campaign (including their stated intentions about Higher Education funding).  But look how their popularity has slipped since they took on the role of patsys for the Tories.

[caption id="attachment_1217" align="aligncenter" width="568" caption="Voting intentions 2005-2010"][/caption]Visit the site for more information (click on the image).

The Rev Dr Peter Hearty of the excellent 'Platitude of the Day' website is clearly concerned that former Archbish Carey is rather upset at the (supposed) continued victimisation of christians in the UK*.  He thinks we should send Christmas cards to the poor old soul.

It's been suggested that Lord Carey deserves a response to his Not Ashamed campaign. He's obviously feeling a bit down, what with all this Christian persecution that's going on. I think the idea of sending him a Season's Greetings card, perhaps with a picture of some jolly penguins or some reindeer on the front, is an excellent way of cheering the old chap up.

Click over to Platitude of the day for more...I think I may well just do the same...and I'm sure Lord Carey, ensconced in the House of Lords with the others who are there merely because they are senior figures of the Church of England will enjoy all those seasonal sentiments and images.*Of course, not everyone agrees that there is any persecution.  The Bishop of Croydon disagrees (Bishop bashes Christian persecution complex).

This is a listing of my favourite iPad apps:Dropbox - Absoutely invaluable for shifting files too and from the iPad; synchronise files between iPad and other computers; useful for collaborationsSqueezepad - Excellent and easy to use interface for Squeezebox Server.  Logitech's series of Squeezebox audio devices are really rather a nice way of managing and playing digital audio files.iAnnotate - read and annotate pdf files.  Aji Reader Service can be used to synchronise pdf files between Mac or PC and iAnnotate.  I use this to synch my pdf collection which I manage on the Linux and Mac notebooks using Mendeley.  Unfortunately the current version of the Mendeley iPhone/iPad app leaves quite a lot to be desired.iWork - three iWork applications have iPad versions: Pages, Numbers and KeynoteSkype -VOIP telephony via the iPad.  No video of course, but the rumoured second generation iPad may have video.  Works well on my WiFi model iPad.The Feed -Interfaces with Google Reader to help keep on top of your RSS feeds (I usually follow around 120 or more feeds).Tweetdeck - Not quite as full-featured as the desktop version, but still pretty good for emitting thoughts into the twitterverse.  Has a useful browser panel.Headspace - A kind of hybrid task manager, planning, to-do list app that is really quite versatile.  Three dimensional effects!Wolfram - Very useful if your web searches aim to pull out numerical analyses.  Reasonably good value when I got it on special offer, but I guess one could always access Wolfram Alpha via Safari.  A bit too focussed on American data.Notes Plus - very versatile note taking app, with diagrams and text.  No character recognition - for this try WritePad.  Works best with an iPad stylus.Quickoffice - read and edit MS Office documents.Penultimate - a neat and easy graphic note-taking app.  Works best with a stylus, otherwise you're finger-painting

The BBC reports that the UK ISP TalkTalk (also known as StalkStalk) is pressing on with its intrusive malware scanning system (Talk Talk to introduce controversial virus alert system).  However a better analysis can be read over at NoDPI (Update: StalkStalk, Time to Switch ISP).Essentially TalkTalk will visit every website visited by every TalkTalk customer, and investigate it for malware.  Essentially this is an exercise in recording customers' web activity, in many cases recording URLs containing personal information.  TalkTalk customers cannot opt-out of the URL stalking.  As NoDPI put it:

Yesterday, TalkTalk announced the forthcoming relaunch of their ‘anti-malware’ service. The same system was covertly tested on TalkTalk subscribers in June/July.[...]Every URL that you visit will be captured, and used to classify the web site that you visit. The technology is supplied by Chinese company Huawei, who are commercial partners with notorious spyware company Phorm, who in turn use technology supplied by malware hackers OCS Lab in Moscow.

TalkTalk customers are advised to read the NoDPI article and judge whether their privacy would be best served by leaving for a new ISP. Personally I left BT over their dalliance with the dreadful Phorm.See also

Related articles

• TalkTalk rapped for trial silence (bbc.co.uk)
• TalkTalk to launch controversial Virus Alerts system (v3.co.uk)
• ISP to test controversial alerts (bbc.co.uk)
• TalkTalk reprimanded over Malware trial (ghacks.net)

Techdirt's latest story on the ongoing saga of the Murdoch media paywall rounds up the apparent effect on the ability of the Murdoch media to break stories (How Murdoch's Paywalls Meant Some News It Broke Went Unnoticed & Uncredited | Techdirt) - no-one notices.This on top of falling advertiser revenues makes me wonder how long they plan to continue the paywall.  On the other hand, they've just moved The News of the World behind the paywall.I read a multitude of sites regularly - using the Feedly front-end to Google Reader - and I probably do so just as most web users do.  I'm what you might call a 'fly-by' reader - I follow links from feeds, twitter, other websites.  I don't read on line newspapers as I do (did) print newspapers, I read single articles.  Paywalls just mean I don't go to those sites, so when the NewsCorp paywall went up, I went elsewhere.I guess the big question for NewsCorp is whether paywall income compensates for the loss of advertiser revenue.

Buoyancy, fat and metabolism

In a previous stage of my research career, I spent a considerable amount of time screening a collection of recessive lethal Drosophila strains for abnormal mitotic phenotypes. I looked for such phenotypes in squash preparations from third instar larval brains, and to get the larvae out of the fly food, we often floated them out in salt solution.  So, while scanning through an alert of new publications in PLoS Genetics, one particular title popped out at me:

A Buoyancy-Based Screen of Drosophila Larvae for Fat- Storage Mutants Reveals a Role for Sir2 in Coupling Fat Storage to Nutrient Availability

One of my mantras in the lab is that if one can think of a suitable selection, one can find any kind of mutant phenotype. In this paper, the authors have used a seemingly trivial selection system to identify mutants with a phenotype of altered fat metabolism. You can see the selection in this figure (Panel A in Figure 1):[caption id="attachment_1189" align="alignleft" width="160" caption="Selecting mutant larvae by buoyancy"][/caption]The plastic cuvette is filled with 10% sucrose, and the larvae added and left to float or sink to equilibrium.  You can see the wild type larvae in the left cuvette mostly sink, while all the adp mutant larvae float.Clearly there's a difference in buoyant density between the two genotypes.  adp is a spontaneous mutation identified many years ago.  Somewhat oddly, the authors refer to adp as "a conserved anti-obesity gene first identified as a naturally-occurring mutation in Drosophila".  This sounds kind of odd to me.  The FlyBase record for adp describes it thus:

There is experimental evidence that it is involved in the biological process: lipid metabolic process; response to desiccation; negative regulation of sequestering of triglyceride.

Still, it clearly affects lipid deposition such that adp mutants mostly float in 10% sucrose, thereby demonstrating the efficacy of the selection.The authors used this buoyancy test to screen nearly 900 strains, each bearing transposon insertions, that represent about 500 distinct loci.  66 genes were identified by this assay as affecting body fat composition - some were previously characterised as having a function related to fat physiology, and about two thirds of the genes had mammalian orthologues.