Choir Stuff Part II

Last Fridays concert didn't go well - a lot of the male voices weren't able to come, and one of the two pieces we performed sounded very thin as a result. However, the second piece was hauntingly good, and apparently the audience was very impressed with us regardless.

Sunday went well. We scrapped one of the pieces during our practice on Saturday, to the relief of most people, and everything else sounded fantastic (in my opinion anyway!)

Just need to get through the mass this Sunday, and then I can get sick.

Only in South Africa

Will a world cup winning coach lose his job two weeks after winning the Cup. SARFU is made up of a bunch of morons who couldn't organise a piss-up in a brewery.

http://www.iol.co.za/index.php?set_id=6&click_id=4&art_id=nw20071031133542569C940466

I am so angry about the way the Jake White has been treated by the upper echelons of South African Rugby.

Radio Ga-Ga

I had a call yesterday from one of these advertising companies asking me about what radio stations I listen to. I’ve stopped listening to the radio almost completely in the last six or so months. I have close to 400 cd’s, and my iPod – this allows me to listen to the music I want to listen to, when I want to listen to it. Ironically the radio station I listen to most is the classical one, mainly because I’m more likely to hear Led Zeppelin or the Doors there (even if it classical versions!) then on the local contempary station.

So the guy asked me to listen to some clips and rate them as to whether I liked them or not. It was a case of No, no, no, no, no, maybe, no, no, no…. Out of 30 clips, I probably liked 2 or 3. Which pretty much sums up why I don’t listen to the radio any more. I’m young, single, have plenty of disposable cash, and yet there is no radio station that plays the music I want to listen to. The times that I do turn onto the local station they will play one of the big hits at least 20 times during that day, it will be mainly dance music, and the occasional classic hit. It gets a bit annoying.

So what would make me listen to the radio again? Simple, more rock, more classics including stuff from the 60s and 70s (the station only plays music from the 80s onwards), and fewer adverts. Which basically means I won’t be listening to the radio any time soon.

Choir stuff

Busy week for Choir. I sing in two choirs at the moment; one is the church one and one is a small chamber choir. The Chamber choir has gone through a rough patch in the last few years, we're on our fourth choir leader, and a lot of the older members have left for various reasons. Thankfully the current woman taking us is absolutely awesome and fantastic, and has been serious about recruiting. So we've gone from a group of about 15 with me being the youngest to a group of about 30, and with most of those being younger then me. It's fantastic to be in a choir that is so enthusiastic! However it's going to be a busy weekend. Normal practice tomorrow, singing at a carol concert on Friday (whose bright idea was it to schedule a carol concert the same evening as the Springbok ruby celebration at Montecasino??), an extended practice on Saturday, and another concert on Sunday!

Church choir isn't much better - we also have an extra practice on Saturday which I have to skip as it is at the same time as the other practice! We're singing at a big mass in two weeks time in a joint choir, with the members of the choir from one of the other services on a Sunday. There is much politics involved in that service - it could be an interesting mass!

It doesn't help that I can just feel a niggling cold sneaking up on me! I just need to survive the next two weeks though!

BookLog: Until Proven Innocent – Stuart Taylor and KC Johnson

This book covers the events of the attempted railroading of three young men accused of rape. Two of the men could prove that they were not at the house where the woman claimed she was raped, at the time of interest. Despite this they were all indicted. The prosecutor knew that at least one of them couldn’t have been involved, he knew that DNA evidence cleared them, he knew that the woman’s story had changed several times, and yet he proceeded with charges. The DA, Mike Nifong, has now seen his surname become a synonym for being railroaded. This case is a strong indictment of how power can corrupt any person.

The three men received no backing from their college, Duke University. They, and the rest of the lacrosse team, were presumed guilty in the absence of any evidence for their guilt.

It’s hard to tell who the authors have the most contempt for – Mr Nifong, or the staff and Duke who left three young men at the mercy of a corrupt DA.

This book is a must read, particularly for the last few chapters which discuss the way that racial and sexual politics have come to dominate higher education in the last few years. Living in a country where racial politics is a strong feature of life, this section really struck home for me. It would be really nice where the dominant feature of deciding guilt or innocence was not dependant on your race.

CDQuest: Radiohead - In Rainbows

OK, so this isn't strictly a cd (yet). Downloaded it (5 quid if you're asking), gave it a listen, and I like it. Need to have a couple more listens but first impressions are good.

Ruby World Cup Champions: South Africa

Nice one boys!

Here's to the next four years

CDQuest: Johnny Cash - American IV

I have a playlist on my iPod that covers songs that are guaranteed to make me cry. It includes older songs such as Danny Boy and Going Home, as well as some newer ones such as Sometimes you can't make it on your own by U2. This list also includes the heart breaking Hurt by Johnny Cash, arguably one of the best cover songs ever.

I first came across the music of Johnny Cash in the film "Walk the Line". I purchased his Greatest Hits, which contained Hurt. I've since purchased most of the American Recordings series, and finally managed to get my hands on American IV - The Man Come Round. I think I may be adding one or two more songs to my sob story playlist.

The album starts with The Man comes round, a song full of imagery from the book of Revelations. It continues with Hurt, and then Give my love to Rose. Other notable tear jerkers include covers of Simon and Garfunkels Bridge over Troubled Water, The Eagles Desperado, and the classic Danny Boy, finishing with We'll meet again. This album is sad, and yet there is always an element of hope. He had a good life, and at the end of it, it is not surprising that there is an element of sadness and acceptance of death in this album.

Rating: 9/10. Note to self, don't listen to this album while driving again - it's very difficult to drive when you can't see through the tears

Open Source, Open Access and OpenOffice

There was an interesting article at ZDnet today on QuickOffice

http://news.zdnet.co.uk/communications/0,1000000085,39290063,00.htm

Scrap that, the article wasn't so interesting, what was interesting was the comment by the chief executive at the end.

“Asked whether Quickoffice would at any point support OpenOffice's .odf format, a rival to .xml, the company's vice president of product management, Paul Moreton, claimed there "has not been a whole lot of demand" because, he suggested, most OpenOffice users saved their documents in a Microsoft format anyway.”

Now this is something that really irritates me. I work in a scientific environment, and the company as a whole is in the process of moving away from proprietary software to Open Source software. Our desktops will be moving onto Ubuntu Linux (http://www.ubuntu.com/), our word processing package will be OpenOffice.org (http://www.openoffice.org/), and as far as possible all software will be open source. Now, this is a very exciting move for me as a biological scientist. Most of the software I use has very good open source options, and much of the software has only been available on linux platforms. As such I have learnt a lot about linux in the last few years. Other people are not so excited and are incredibly sceptical; one of the biggests reasons for the scepticism is the need to publish.

A lot of journals are moving towards the open acess model (http://en.wikipedia.org/wiki/Open_access), however a significant proportion, particularly in the Chemistry realm are not. Invariably, all of these journals require submission in a proprietary format be it .doc or .pdf. This includes the Open Acess journals. I've emailed journals asking them whether they will consider submissions that come in .odf format, and the answer is always no, because we can convert to .doc. Quite frankly that isn't good enough. I want to be free to chose what software I use, to use the best software for the job, not to have to worry whether conversion errors are going to ruin my manuscript and hence my chances of publishing, and to be able to submit in an open format, that I know I will be able to access in ten, twenty or fifty years time. Relatedly, it puts an additional burden on scientists in third world countries. Why should they have to purchase expensive software to publish, when there is a suitable alternative that is far more cost effective. The open access journals will not be truly open until they realise this.

Oblivion - New official addon

http://www.elderscrolls.com/downloads/updates_plugins_fightersstronghold.html

After the strongholds for Mages, Thieves, Generic Evil People, and Paladin types, the one for straight fighters had to be inevitable I guess.

It's looking like my most recent Morrowind run through will be put on hold for a couple of days; this new mod actually looks pretty cool. That's the thing about Oblivion - it's so pretty, it sucks you in. Unfortunately it looks like this is the last official plugin, which will be a pity. It would have been nice to have a couple of expansion packs such as the Morrowind expansions Tribunal and Bloodmoon. Oh well.

CDQuest: Led Zeppelin - IV

Led Zeppelin IV, 1971. The album was actually untitled, but has conventially been referred to by IV. What can you say about an album that has Stairway to Heaven on it, arguably one of the greatest rock songs ever released. But that would be ignoring The Battle of Evermore, the Tolkien inspired epic, the hauntingly beautiful Going to California and the thematic Rock and Roll. I really don't think a better album has been released (although I'm still getting to Physical Graffiti, which contains my all time favourite Led Zeppelin song - Kashmir).

Actually there isn't really much more I can say. Great album. Love it, and I am now going to go and listen to it again.

Score - A decided 10/10. An album that really should be in everyone's collection.

BLAST problem

I have an interesting problem at work at the moment. The team have some novel enzymes which we are trying to characterise. Now we know the overall groups that these enzymes belong to - the problem is that the groups are very, very broad - specifically lipases and proteases. A quick search through BRENDA indicates a huge variety of lipases and proteases. So, I can do a BLAST and find the closest matches to our protein sequences. The problem is though, finding the closest match that has been characterised. The sheer amount of genome sequence data being generated is flooding the protein data banks at NCBI and EMBL. Having a characterised protein for comparison does help in determination of novelty, as well as possibly giving you a baseline to start at for characterisation of your protein

I have a few options - I can do the standard BLAST and check every single result for level of characterisation - this is not the prefered alternative.
I can start playing around with various databases - the optimal databases to BLAST against would be the BRENDA database, but I can't find an option to do this.
The SWISS-PROT database would also be an option, but I get very few hits, and no significant ones using this method.
Alternatively I can BLAST against the PDB database. This is the database for structural information, and almost by definition, any protein that has had it's structure determined is likely to be well characterised. However this is only appropriate for groups of enzymes and proteins that have a certain number of structures, which is not applicable to the vast number of proteins out there.
Using TrEMBL, and other annotated databases is another option, but again these tend to have a high noise to signal ratio for what I want.

Basically I need a database for BLAST that only contains characterised proteins that have been published, and I'm out of ideas as to where to get one!

Awards dinner

A few weeks ago our divisional head visited our site with one of the members of the comittee that runs the whole company. Our division is split over two sites, and the site where I work is very much seen as the poor relation. Anyway, the chief executive asked the divisional head to describe the work we do here, and what sort of research groups we have. The divisional head managed to mention four of the research groups, and two of the group leaders, completely forgetting about the group that I work in.

We had our annual awards dinner on Friday.

Our reseach group won five of the eleven awards. The group responsible for finance won three. No other research group at our site won anything. No other group won more then one.

We'll see if he forgets us again....

My day is ruined

EA is buying Bioware.

http://games.slashdot.org/article.pl?sid=07/10/11/2053228
and
http://kotaku.com/gaming/ea/ea-buys-bioware-pandemic-309937.php

I want to cry.


Although reading the /. comments I am particularly partial to HK47's response

Statement: Master, would you like to make a trip to EA headquarters? Clarification: For research purposes of course. Unrelated Query: Have you seen my blaster rifle?

(http://games.slashdot.org/comments.pl?sid=325631&threshold=1
&commentsort=0&mode=thread&cid=20947889)


Updated
Reaction from ArsTechnica
http://episteme.arstechnica.com/eve/forums/a/tpc/f/39309975/m/517006987831

CDQuest: Oleta Adams: Circle of One

In 1989 British band Tears for Fears released their album The Seeds of Love. One of the hits released of that album was Woman in Chains featuring Oleta Adams. While not a huge hit, it did lead to the start of Adam's successful solo career. There had been two albums released prior to Circle of One, but they were not commercially successful.

Circle of One was released in 1990, with it's biggest hit being Get Here which was a Top five hit in both the States and the UK, with the album going to No. 1 in the UK. The album was produced by the members of Tears for Fears, who also co-wrote some of the tracks on the album. Musically it's very much a laid-back, jazzy sound; perfect for background listening. It's not really a Tears for Fears sound. Highlights of the album include Get Here (unsurprisingly!), Circle of One, and I've got to sing my song. So, it's the perfect album to put on in the background and just chill out to. Probably 6.5 / 10 tending towards a 7. Not a fantastic album, but not one I regret buying.

CDQuest: The Quest for the perfect album

I love music. I spend way too much money on albums each month, which get ripped and stored. Consequently I have a lot of CD's sitting around gathering dust. However, the direness the local radio station has given me an incentive to start listening to CD's again on my drive to and from work. It's also a chance to start thinking about what are my top albums. There are a couple that immediately leap to mind such as Led Zeppelin IV and Physical Graffiti, as well as Pink Floyds Dark Side of the Moon. There are also some newer ones, U2 – How to dismantle an atomic bomb, and Joss Stone – Introducing. So let's get started.....

Girls and gaming

I came across an interesting link today (http://lookspring.co.uk/balancing-act) which discusses being a woman gamer.

So here is my confession for the day - I love my computer games. There are a couple of games that get installed almost by default on any computer of mine – Baldurs Gate II and Alpha Centauri, although the newest incarnation of Civilisation will probably join that list, and possibly, even with all it's faults, Oblivion.

So why do I love those games so much? Well in the case of Baldurs Gate, it was the story, it was the side plots, it was the fact that the game did vary depending on the type of character you played. I still find it very disapointing that there are so few games like that now, Jade Empire and the Knights of the Old Republic series being some notable exceptions. However they lack the one thing that really made BG for me, and that was the party interactions. Choosing my character for a run through, and choosing the associated party was always great fun. I have great hopes for Planewalker games run by Jason Compton and Westley Weimer, two of the most outstanding modders for BG2.

As for Alpha Centauri and the various incarnations of the Civilisation series – I dread to think how many months of my life I've wasted on those games. The “just one more turn” is so addictive, and they have to rank as some of the greatest games ever made. And yet, interestingly, I have never got into one of the biggest so-called “Female” games – The Sims. I've tried, and I just can not see what the attraction of it is. Shrug.

So what are irritations for me? Games that just won't run for starters. A prime example is a piece of shit I recently bought called Mage Knight: Apocalypse. Wouldn't work, kept trying to find a server. In the single player game. Not a mention of Net access required anywhere on the box or in the manual. A quick google revealed that it was trying to set up a local server. Details that should have been in the manual. So, yeah, one game that was quickly uninstalled.

Games that are unbeatable if you chose a poor character combination at the start. Titan Quest is a prime example. Went through the game reasonably easily, got to the final boss, couldn't even scratch him. Spending hours trying to defeat a boss character who your character can't even scratch is not fun, especially when in a fit of desperation you lower the difficulty level. Apparently I'd chosen a poor character combination. The final boss should be beatable by any character combination with some difficulty, without the player feeling as though they would rather walk over broken glass. Interestingly another game that got that wrong was the Sacred expansion pack. Sacred is an enjoyable Diablo-like romp which had a pretty well judged difficulty level, up to the point of the final boss of the expansion pack. Fortunately my character re-spawned right by the boss every time he died, so it was a case of hit, hit, die, respawn, hit, hit, die, respawn, etc. Not fun.

Another irritation is when the sequel to a game mucks up something that worked well in the previous game, such as in the Elder Scrolls. I loved Daggerfall, crashes, bugs and all. It was a game where you genuinely didn't have to follow the script. It had issues, but there was still an element of freedom to do what you wanted to do, and to make your character exactly what you wanted it to be. Morrowind was a fun game, but it suffered from two main weaknesses. Firstly there was no fast travel option, which meant you did a lot of trudging around, secondly when you had finished doing any of the guild story lines that was it, no more quests. Oblivion took a lot of the things from Morrowing and improved them, such as alchemy being a lot more intuitive, and bringing back the fast travel from Daggerfall. But it stuffed up the leveling, so whereas in Morrowind there were regions it wasn't worth visiting until you had levelled up quite a bit, in Oblivion you could beat the game at level 2, and it was often easier to do so. My other major irritation with Oblivion was that it was perfectly feasible for a pure fighter to become head of the Mages guild, and a pure mage that wouldn't know what to do with a sword could become head of the Fighters guild. Morrowind had the ranking system working very well, by linking your skill levels to your rank in the guild. But once you become head of the guild, that's it, there is nothing else to do.... Oh well, hopefully TES V will sort out some of these issues.

This has become bit of a monster post, so I'll expand on some of these themes later.

Nobel Prize in Medicine 2007

Capecchi, Evans and Smithies
for their discoveries of principles for introducing specific gene modifications in mice by the use of embryonic stem cells

http://nobelprize.org/nobel_prizes/medicine/laureates/2007/press.html

This year's Nobel Laureates have made a series of ground-breaking discoveries concerning embryonic stem cells and DNA recombination in mammals. Their discoveries led to the creation of an immensely powerful technology referred to as gene targeting in mice. It is now being applied to virtually all areas of biomedicine – from basic research to the development of new therapies.

Gene targeting is often used to inactivate single genes. Such gene "knockout" experiments have elucidated the roles of numerous genes in embryonic development, adult physiology, aging and disease. To date, more than ten thousand mouse genes (approximately half of the genes in the mammalian genome) have been knocked out. Ongoing international efforts will make "knockout mice" for all genes available within the near future.

With gene targeting it is now possible to produce almost any type of DNA modification in the mouse genome, allowing scientists to establish the roles of individual genes in health and disease. Gene targeting has already produced more than five hundred different mouse models of human disorders, including cardiovascular and neuro-degenerative diseases, diabetes and cancer.

Rugby World Cup

Interesting weekend for rugby. I was very sure that it would be an all Southern hemisphere pair of semi-finals. I was amazed that England beat Australia, but was stunned that the All Blacks lost - they had been looking very impressive, and practically unbeatable. So, England play France, and South Africa play Argentina (first time Argentina are in the RWC semi-finals). My prediction is a South Africa - France final, with South Africa edging France (hopefully!). However, I'm not very good at this prediction thing!

More music idiocy

Relatedly to the story that Sony lawyers think that copying your own cd's is stealing, comes this story from Scotland
http://news.bbc.co.uk/2/hi/uk_news/scotland/edinburgh_and_east/7029892.stm

Slashdot commentary
http://yro.slashdot.org/yro/07/10/07/2335244.shtml

So, making a copy of a cd is illegal, playing the radio in public is illegal.... What next?

Metagenomics: Introduction

Metagenomics is a new sub-section of genomics. At its essence it involves isolating genomic material from environmental sources, and using this to generate genomic libraries. The genomic material is generally DNA, but there is some work being done on isolating RNA, and using that to generate cDNA libraries. The big advantage of making metagenome libraries is that there is no need to have a culturable organism. The majority of micro-organisms are unculturable in the lab, making it difficult to investigate their functioning. Equally, the types of environments that have often been sampled (marine, mines, hot springs) tend to be "extreme" environments; the micro-organisms generally survive at extrememes of temperature and pH. The thought is that enzymes isolated from these bacteria will tend to be more applicable to industrial applications. Additionally, information from the various high throughput sequencing projects is starting to fill in gaps on "the tree of life"

The big disadvantage is that you are dealing with a mixed culture of organisms. So there is a variety of genetic material present, and identifying which organisms are present, and relating the gene sequence for interesting proteins back to an organism can be challenging.

However, this is a fascinating area of research, particularly with the advent of high throughput screening techniques, and high throughput sequencing techniques, both of which will be discussed in subsequent posts.

Immaculee Ilibagiza

I was at book club last night, and we watched an interview with Immaculee Ilibagiza, a survivor of the Rwandan genocide. She wrote a book called "Left to Tell", which I'm studiously avoiding as I know that it is harrowing reading. I had two thoughts though. We're facing a similar situation in Sudan at the moment - what is the most appropriate way to intervene? Just send in troops? Who sends in troops? With whose approval?

And secondly?

How can people you've grown up with, that you've known all your life, think that one day you're a friend, and the next day you're a cockroach? And how do you forgive them?

My criminal tendencies are showing

http://arstechnica.com/news.ars/post/20071002-sony-bmgs-chief-anti-piracy-lawyer-copying-music-you-own-is-stealing.html

Oh well, obviously I need to be downloading all the music I buy as well as having a copy on CD....

Except that I don't live in a country with a iTunes store, and the one music store that does forces you to use Internet Explorer, which is a deal breaker for me.
Except that I like music, and buy quite a lot on a monthly basis
Except that I have a 160 GB iPod with 98 % of the music on being music that I have bought on cd
Except that I don't like being told that I'm a thief because I buy music legally, and make a copy for my personal use on my iPod....

I guess I won't be buying any music from an artist released by Sony

106 books meme

So I saw this 106 book meme, and I thought it might be interesting to look at. I'm a fairly voracious reader, but getting new suggestions on reading material is always useful. Bold is read, italics is partially read

Jonathan Strange & Mr Norrell
Anna Karenina
Crime and Punishment
Catch-22
One Hundred Years of Solitude
Wuthering Heights
The Silmarillion
Life of Pi : a novel
The Name of the Rose
Don Quixote
Moby Dick
Ulysses
Madame Bovary
The Odyssey
Pride and Prejudice
Jane Eyre
The Tale of Two Cities
The Brothers Karamazov
Guns, Germs, and Steel: the fates of human societies
War and Peace
Vanity Fair
The Time Traveler’s Wife
The Iliad Emma
The Blind Assassin
The Kite Runner
Mrs. Dalloway
Great Expectations
American Gods
A Heartbreaking Work of Staggering Genius
Atlas Shrugged
Reading Lolita in Tehran : a memoir in books
Memoirs of a Geisha
Middlesex
Quicksilver
Wicked : the life and times of the wicked witch of the West
The Canterbury tales
The Historian : a novel
A Portrait of the Artist as a Young Man
Love in the Time of Cholera
Brave New World
The Fountainhead
Foucault’s Pendulum
Middlemarch
Frankenstein
The Count of Monte Cristo
Dracula
A Clockwork Orange
Anansi Boys
The Once and Future King
The Grapes of Wrath
The Poisonwood Bible : a novel
1984
Angels & Demons
The Inferno
The Satanic Verses
Sense and Sensibility
The Picture of Dorian Gray
Mansfield Park
One Flew Over the Cuckoo’s Nest
To the Lighthouse
Tess of the D’Urbervilles
Oliver Twist
Gulliver’s Travels
Les Misérables
The Corrections
The Amazing Adventures of Kavalier and Clay
The Curious Incident of the Dog in the Night-Time
Dune
The Prince
The Sound and the Fury
Angela’s Ashes : a memoir
The God of Small Things
A People’s History of the United States : 1492-present
Cryptonomicon Neverwhere A Confederacy of Dunces
A Short History of Nearly Everything
Dubliners
The Unbearable Lightness of Being
Beloved
Slaughterhouse-five
The Scarlet Letter
Eats, Shoots & Leaves
The Mists of Avalon
Oryx and Crake : a novel
Collapse : how societies choose to fail or succeed
Cloud Atlas
The Confusion
Lolita
Persuasion
Northanger Abbey
The Catcher in the Rye
On the Road
The Hunchback of Notre Dame
Freakonomics : a rogue economist explores the hidden side of everything
Zen and the Art of Motorcycle Maintenance : an inquiry into values
The Aeneid
Watership Down
Gravity’s Rainbow
The Hobbit
In Cold Blood : a true account of a multiple murder and its consequences
White Teeth
Treasure Island
David Copperfield
The Three Musketeers

Comments: I've read all the Austens, am surprised by a list that includes the Hobbit, and the Silmarillion but not the Lord of the Rings. I will never read anything by Dan Brown. All in all an interesting list, and one I'll come back to for future reading ideas.

Introduction

This is my musings on science, politics, music and literature. A little bit of everything. Somewhere to let me keep my thoughts on what interests me.