Geoff Coupe's Blog

Good Science

Wed, 08 Oct 2008 09:53:23 GMT

Having mentioned Ben Goldacre's book Bad Science in my previous entry, I just wanted to emphasise how good his book is. Really, you owe it to yourself to get a copy of this book to buff up your bullshit detector. The blurb on the back of the book puts it well:

Ben Goldacre masterfully dismantles the dodgy science behind some of the great drug trials, court cases and missed opportunities of our time, but he also goes further: out of the bullshit, he shows us the fascinating story of how we know what we know, and gives us the tools to uncover bad science for ourselves.

And it's funny, to boot.

Goldacre also has his own blog Bad Science, which is well worth keeping an eye on. I see that over the past few years, I've referred to things on his blog over 1,000 times. He's very good at what he does.

Statistics and Lies

Wed, 08 Oct 2008 09:39:56 GMT

I see from today’s Volkskrant that Lucia de Berk has at last won the right to a retrial of her case. De Berk is a nurse who was convicted in 2003 for the supposed four murders and three attempted murders of patients in her care.

The history of the case makes chilling reading, not because of anything that de Berk may have done, but because of the web of statistical “proof” that the prosecution used to put her behind bars. It is perfectly clear that the statistical evidence was deeply flawed from the start, but here we are in 2008, and she has spent almost six years in jail for “crimes” that never existed in the first case.

The judgement against her was based largely on the claim (from the prosecution’s statistician) that the chances of so many people dying on the wards where she was on shift were “one in 342 million to one against”. But, as Ben Goldacre makes clear in his excellent book Bad Science, the fundamental flaw about this claim is twofold. First, the data was selected to make the hypothesis, and then the prosecution’s statistician made a simple, rudimentary error: he combined individual statistical tests by multiplying p-values (the mathematical description of chance, or statistical significance). As Goldacre points out in respect of the first part of the claim:

A huge amount of corollary statistical information was almost completely ignored. In the three years before Lucia worked on the ward in question, there were seven deaths. In the three years that she did work on the ward, there were six deaths. Here’s a thought: it seems odd that the death rate should go down on a ward at the precise moment that a serial killer – on a killing spree – arrives. If Lucia killed them all, then there must have been no natural deaths on that ward at all in the whole of the three years that she worked there.

And in respect of the second flaw, Goldacre points out:

If you multiply p-values together, then harmless and probable incidents rapidly appear vanishingly unlikely. Let’s say you worked in twenty hospitals, each with a harmless incident pattern: say p=0.5. If you multiply those harmless p-values, of entirely chance findings, you end up with a final p-value of 0.5 to the power of twenty, which is p < 0.000001, which is extremely, very, highly, statistically significant. With this mathematical error, by his reasoning, if you change hospitals a lot, you automatically become a suspect. Have you worked in twenty hospitals? For God’s sake don’t tell the Dutch police if you have.

It’s a very cautionary tale of statistics gone horribly wrong, and very reminiscent of the Sally Clark case in the UK (which Goldacre also dissects). Clark was put on trial in 1999, and convicted, for murdering her two babies. At the trial, child expert Professor Sir Roy Meadows stated that the chance of two children in the same family dying of Sudden Infant Death Syndrome (SIDS) was “one in seventy-three million”. It was another case of statistics wielded in error, and Clark spent three years in jail (where she was targeted by other prisoners as a supposed baby-murderer) before her conviction was quashed by the Court of Appeal. She emerged a broken woman and died in March 2007. I fervently hope that that will not be the fate of Lucia de Berk.

Pot, Kettle, Black..

Tue, 07 Oct 2008 13:50:23 GMT

I think my irony meter has just exploded...

A Small Incentive

Mon, 06 Oct 2008 10:30:18 GMT

Justin, over at Chicken Yoghurt, has come up with a rather whizzo scheme to drive the FTSE share index back up again. It has a rather Ballardian whiff about it...

Know Your Human Rights

Fri, 03 Oct 2008 13:35:15 GMT

The Universal Declaration of Human Rights spelt out in animated form. Excellent.

The Universal Declaration of Human Rights from Seth Brau on Vimeo.

(hat tip to the Osocio Weblog)

A Really Bad Disney Movie...

Fri, 03 Oct 2008 12:03:58 GMT

... but we seem to be edging dangerously close to Head of Skate becoming a disastrous reality.

Oh, and this piece written by Matt Taibbi is like being in the front row at the Grand Guignol and being spattered by the blood and gore. The trouble is, there's a good chance that we won't be able to leave at the interval. A small sample:

So, sure, Barack Obama might be every bit as much a slick piece of imageering as Sarah Palin. The difference is in what the image represents. The Obama image represents tolerance, intelligence, education, patience with the notion of compromise and negotiation, and a willingness to stare ugly facts right in the face, all qualities we're actually going to need in government if we're going to get out of this huge mess we're in.

Here's what Sarah Palin represents: being a fat fucking pig who pins "Country First" buttons on his man titties and chants "U-S-A! U-S-A!" at the top of his lungs while his kids live off credit cards and Saudis buy up all the mortgages in Kansas.

The truly disgusting thing about Sarah Palin isn't that she's totally unqualified, or a religious zealot, or married to a secessionist, or unable to educate her own daughter about sex, or a fake conservative who raised taxes and horked up earmark millions every chance she got. No, the most disgusting thing about her is what she says about us: that you can ram us in the ass for eight solid years, and we'll not only thank you for your trouble, we'll sign you up for eight more years, if only you promise to stroke us in the right spot for a few hours around election time.

Go and read the whole thing - and weep, not just for America, but for the whole world.

Update: The ever-dependable Jonathan Raban has written an equally good piece on Palin for this month's London Review of Books. It delivers a cool, surgically-precise flensing of Palin in contrast to Taibbi's hatchet job.

The Placebo is God

Thu, 02 Oct 2008 16:56:53 GMT

Following hot on the heels of that august organ of journalism, the Daily Mail, today's Guardian also jumps on the bandwagon of the latest "let's all misinterpret the science" story. Yes, it's the "Religious belief can help relieve pain, say researchers". Well, well, what a surprise: it's the placebo effect of course. Yet another pronouncement from the department of the bleeding obvious, I would have thought.

People tend to underestimate the power of the placebo. As a cure for this debilitating condition, I recommend a simple remedy. Merely purchase a copy of Ben Goldacre's Bad Science and read chapter 5: The Placebo Effect. Instant relief and the realisation that "We are human, we are irrational, we have foibles, and the power of the mind over the body is greater than anything you have previously imagined".

So van Gogh Was Killed...

Wed, 01 Oct 2008 17:02:26 GMT

I don't know who this Christopher Howse person is, but he strikes me as being either a) an idiot or b) will write any old tosh for money. Either way, his piece in today's Telegraph leaves a particularly nasty taste in the mouth. He's not alone, today's Guardian has a letter from Dr. Charlie Gere informing us that there is no such thing as free speech. With friends like these, who needs enemies?

Ophelia is on hand to dismantle their apologia with the contempt that they deserve.

A Fair(y) Tale

Wed, 01 Oct 2008 16:16:19 GMT

Alright children, gather round and let uncle Geoff tell you all about the tale of Copyright and Fair Use. Once upon a time...

(hat tip to Nina Paley). Oh, and may I just say that I was pleased to see Sleeping Beauty in there. It may not have been reckoned as one of the great Disney films, but for my money the medieval style of the backgrounds achieved by Eyvind Earle were one of the great examples of the animated film.

A Victory for Common Sense

Wed, 01 Oct 2008 10:58:45 GMT

I see that a group of retired Gurkhas have won their court battle for the right to stay in Britain. As their lawyer says, it is a victory for common sense. It just strikes me as a slap in the face for them that the UK Home Office would let this come to having to be judged in a court of law.

Even now, the statement by Home Secretary Jacqui Smith as reported in the story hardly rings true as accepting that the men are owed a "moral debt of honour" (the judge's words) and that the "Home Office rules are unlawful. She still hedges with weasel words and phrases: "where there is a compelling case" and "honouring our commitment... by reviewing all cases...". Distasteful, Ms. Smith, distasteful.

The Astrobiology Rap

Wed, 01 Oct 2008 07:39:59 GMT

Rap music is not usually my cup of tea, but every once in a while a piece comes along that makes me sit up and listen. It happened with the Dawkins Rap a little while back. And now, here's the Astrobiology Rap by Oort Kuiper, a.k.a. Jonathan Chase, a postgraduate student.

(hat tip to SciencePunk)

Precisely

Mon, 29 Sep 2008 17:02:00 GMT

In today's Guardian, Philip Pullman reacts with some glee to the news that his book The Golden Compass (aka as The Northern Lights) is in the top five of the American Library Association's list of most-challenged books in 2007. In passing he makes what strikes me as a pretty profound and true statement about organised religion:

Religion, uncontaminated by power, can be the source of a great deal of private solace, artistic inspiration, and moral wisdom. But when it gets its hands on the levers of political or social authority, it goes rotten very quickly indeed. The rank stench of oppression wafts from every authoritarian church, chapel, temple, mosque, or synagogue – from every place of worship where the priests have the power to meddle in the social and intellectual lives of their flocks, from every presidential palace or prime ministerial office where civil leaders have to pander to religious ones.

My basic objection to religion is not that it isn't true; I like plenty of things that aren't true. It's that religion grants its adherents malign, intoxicating and morally corrosive sensations. Destroying intellectual freedom is always evil, but only religion makes doing evil feel quite so good.

There's something in what he says... Whether it's the Catholic church stoking the AIDS epidemic in Africa, or the Taleban gunning down policewomen in Afghanistan, organised religion and the levers of political power are a dangerous combination. Malalai Kakar has been killed by this potent cocktail. She won't be the last.

Round the Hurin

Sun, 28 Sep 2008 07:28:02 GMT

Henry Gee, over at his blog, The End of the Pier Show, pens a pastiche that views Tolkien's The Lord of the Rings through the lens of Round the Horne. British people of a certain age and sensibility (e.g. me) will find it irresistably funny. I can hear all the characters speaking the script as clear as a bell.

Segregation

Fri, 26 Sep 2008 19:13:18 GMT

The author and cartoonist Alison Bechdel blogs about the strange phenomenon of segregated drinking fountains in Indianapolis airport...

Proofs of God

Fri, 26 Sep 2008 19:06:46 GMT

Ontological, Teleological, Physiological... I can't help feeling that we need to add in Psychological in there somewhere as well...

Stampede

Fri, 26 Sep 2008 14:11:33 GMT

We had a bit of excitement this morning. First of all, we were woken up at 7 am by a maize harvester working the field that is ten yards away from the bedroom window. Then, while I was letting the dog out for his morning constitutional at 8, I became aware of a lot of shouting going on at the front of the house. The dog ran there barking, and I followed as quickly as I could. I was met by the sight of our neighbour's cows galloping back and forth in the garden and José, his partner, trying to round them up without too much success. She was trying to put them in the field next to us, but they had got away from her at the road crossing, and decided to make a dash for freedom.

She yelled at me to ring Herman, the farmer, to come and help, so I went inside and rang him, while watching the herd thunder past on the front lawn in the direction of the maize field. He arrived after a couple of minutes, and between us, and with the help of the men harvesting the maize, we managed to get the herd under control and into the field where it should have been.

There's a couple of fence posts damaged, and some of the borders look a bit the worse for wear, but it could have been a lot worse. The lawns are in a bit of a state, but they'll recover. The stampede has hopefully scared away the moles with a bit of luck. Never a dull moment...

Two Analyses of a Disaster

Fri, 26 Sep 2008 11:21:31 GMT

My understanding of economics is pretty basic. I can understand, and try to follow, the financial principles espoused by Mr. Micawber in Dickens' David Copperfield:

"Annual income twenty pounds, annual expenditure nineteen pounds nineteen and six, result happiness. Annual income twenty pounds, annual expenditure twenty pounds ought and six, result misery."

I really think that that is all one needs to know, anything more, it seems to me, gets closer to religion and blind faith. So I can't say that I'm much surprised by the current crisis in the financial markets.

In an attempt to understand the causes, I've been reading two analyses of the events. The first is an article in Edge written by Nassim Nicholas Taleb called The Fourth Quadrant. I will forgive him the air of "I told you so" that permeates the article, he's somewhat justified in having it. After all, it was he who wrote back in 2006:

The government-sponsored institution Fannie Mae, when I look at its risks, seems to be sitting on a barrel of dynamite, vulnerable to the slightest hiccup. But not to worry: their large staff of scientists deemed these events "unlikely."

However, his analysis goes into dizzying detail about statistical theory and how people misinterpret statistics and probabilities. I'll probably need to read the article several times before I can come closer to understanding what he is saying. But even after all that, I can't help feeling that he's shining the light of reason in the wrong place. That was brought home to me when I read John Carter Wood's article over at Obscene Desserts. Like me, John finds the workings of high finance rather mysterious. He quotes from an article in the New York Times:

The mortgages, with an average size of about $450,000, were Alt-A loans — the kind often referred to as liar loans, because lenders made them without the usual documentation to verify borrowers’ incomes or savings.

And then, without the benefit of graphs or statistics, John gets to the root of the matter:

Let's just pause here for a brief moment. Just for a measly few seconds.
Please just consider that last sentence, the one in which it is pointed out that lenders gave people mortgages worth an average of nearly a half-million dollars without even checking how much they earned or how much money they had?
Is this for real?
Because if it is, I can only say: What--please pardon my French (you know, I've been spending some time there)--the fuck?!

It seems to me to be all too easy to label the shenanigans on Wall Street and in other financial centres as “a crisis too complex for easy fixes”. John’s put his finger on it, the world’s economy is seemingly run by a bunch of greedy wankers. Micawber’s principles should never have been forgotten.

Managing Metadata

Thu, 25 Sep 2008 07:07:01 GMT

Metadata is “data about data”. While the term is used to cover a wide variety of fields, the one that most interests me is metadata used in digital images.

The most prevalent standard for digital image metadata is Exif, implemented in every digital camera. It’s metadata focused on technical information about the picture itself: camera shutter speed, exposure, etc. The standards of IPTC-IIM and XMP are focused on metadata about the subject of the photograph: topic, location, photographer, etc. IPTC-IIM is an earlier standard that has been in use by the press agencies since the 1980s - so there's a large installed base. However, it's not easily extensible. Enter XMP, which is XML-based, first created by Adobe Systems Inc. in 2001. In 2004, Adobe got together with the IPTC organisation and others to create the “IPTC Core” standard, an XML-based successor to IPTC-IIM.

Of course, as the old joke has it, “the great thing about standards is that there are so many to choose from”. What is worse, is that different manufacturers (of cameras, application software, operating system software) interpret the standards in subtly different ways so that the resulting implementations are often incompatible with each other.

This got to such a stage that in 2006, Microsoft proposed the setting up of a cross-industry working group to deal with the matter. As a result, the Metadata Working Group was created in 2007 by five founding members: Apple, Adobe, Canon, Microsoft and Nokia. In 2008, Sony joined the party. The goals are:

Preservation and seamless interoperability of digital image metadata.
Interoperability and availability to all applications, devices, and services.

Not before time, I hear you cry. Certainly I get very frustrated by the current lack of interoperability that exists.

Yesterday, at the bi-annual Photokina exhibition, the Metadata Working Group released version 1.0 of their Guidelines for Handling Image Metadata. In the Group’s own words, “this document describes how best to use existing standards such as Exif, IPTC, and XMP to address the key organizational metadata questions that most consumers have”.

I’ve only had time to quickly glance through the document, but it does seem to be a good effort to attempt to herd the bunch of cats that are software developers – many of them in their own companies.

It was with some irony that I noted this paragraph (page 32):

Hierarchical keywords are not covered. However it's well understood that this is an important use case even in the context of the consumer and will be added to future versions of this document. There are existing solutions available e.g. Adobe Bridge, Adobe Lightroom as well as Microsoft Expression Media and Windows Live Photo Gallery that have introduced hierarchical keyword workflows specific to their needs.

Irony, because it’s the way that Microsoft’s Windows Live Photo Gallery has currently implemented hierarchical keywords that is causing me some interoperability problems and frustration at the moment.

Oh well, back to herding cats…

Q.E.D.

Wed, 24 Sep 2008 17:32:32 GMT

Jesus and Mo explain the difference between a cult and a religion. I thought the difference was at least 1,400 years...

The Ghost of Miguel Servetus

Wed, 24 Sep 2008 08:06:48 GMT

An excellent and eloquent statement by Austin Dacey in yesterday's meeting of the Human Rights Council being held in Geneva.

Photo Album: Seasonal Landscape

Mon, 22 Sep 2008 18:18:09 GMT

Seasonal Landscape

050217-1406-39

050225-1446-01

050313-1131-03

050319-1454-15

050417-1205-57

050515-1333-55

050527-1400-47

050608-1135-55

050620-1422-32

050623-1510-56

More Photos...

Photo Album: Winter Landscapes

Sat, 12 Apr 2008 07:15:21 GMT

Winter Landscapes

20071219-1145-30

Photo Album: Seasonal Landscape 2

Fri, 21 Dec 2007 18:52:06 GMT

Seasonal Landscape 2

July 2006

November 2006

December 2006

January 2007

March 2007

April 2007

December 2007

Photo Album: The Boven Slinge River

Tue, 16 Oct 2007 07:23:48 GMT

The Boven Slinge River

20071014-1219-45

20071014-1232-21

20071014-1234-57

20071014-1254-13

20071014-1258-41

Photo Album: Woodpeckers

Tue, 25 Sep 2007 10:57:43 GMT

Woodpeckers

20070912-1716-18

20070912-1716-19

20070912-1716-21

20070912-1717-39

20070912-1717-56

Photo Album: Summer Day in Reeuwijk

Thu, 23 Jun 2005 19:54:14 GMT

Summer Day in Reeuwijk

Heron catching frog

Heron trying to eat frog

Heron still trying to eat frog

Coot Chick

Coot's nest with eggs

Coot defending its nest

Greylag Goose

Greylag Geese

Giant Hogweed

Swan and Cygnets

Photo Album: Spring Day 2

Tue, 26 Apr 2005 17:28:18 GMT

Spring Day 2

Rosemary blossom

Oystercatchers on the Rottemeer

Windmills by the Rottemeer

Cormorant Colony by the Rottemeer

Kestrel

Stork

With a bit of mint sauce - yum!

The Gravedigger's Cottage - literally

Road near Linschoten

Photo Album: Spring Day

Thu, 21 Apr 2005 15:33:44 GMT

Spring Day

Magnolia Blossom near Oudewater

Cherry Blossom in Gouda

Nesting swan and her mate

Don't get too close

Grebe feeding young

Grebes with young on their backs

Some exotic sheep

Photo Album: The Garden in Spring

Fri, 11 Feb 2005 18:18:42 GMT

The Garden in Spring

March 2001

March 2002

Sunrise over the garden

January 2004

More Photos...

Photo Album: Gouda and Reeuwijk

Sun, 06 Feb 2005 08:35:16 GMT

Gouda and Reeuwijk

Winter 2003

Stadhuis Gouda

Gouda

Reeuwijk scene

Gouda

Waaghuis Gouda

Stadhuis at Christmas

Winter 1984

Photo Album: Family

Sun, 06 Feb 2005 08:32:06 GMT

Family

Martin - my husband

Wedding Day

Summer 2003

On Snaefell - 2004

Art in The Hague

Dymchurch Beach

Wedding Day

Portrait by Mary Grooteman

Custom List: Slightly Bizarre

Mon, 15 Sep 2008 08:10:46 GMT

Slightly Bizarre

The Human Clock
Interesting take on a digital clock
The Book of Zogg
As with Borges I'm never sure what I'm reading...am I reading what he imagined or am I reading what he imagined he imagined? Or indeed to the third power am I reading what he imagined he imagined as imagined by a third party: an alien perhaps?
The Cremaster Cycle
Well, OK, this isn't 'slightly bizarre' but 'truly bizarre'. My excuse is that Cremaster 4 was filmed in the land of my birth.
And the Dish Ran Away with the Spoon
SF writer Paul DiFilippo has a wonderful story on SciFi.com called And the Dish Ran Away With the Spoon that\'s funny, dirty, and technologically prescient. (description by Cory Doctorow)
The Devil's Tramping Ground
Turn out the lights and turn up the sound...
The Genomic Dub Collective
A celebration of Darwin's Origin of Species realised through themedium of reggae music
The Annals of Improbable Research
Reports from the Haunted Wings of the Research Establishments ofthe World
Amaztype
What you get when you cross Web Services with Typography
The Tarot of Sneezing
Geshundheit!
Darth Vader's Blog
Someone had to do it, I suppose.
Master Yoda's Blog
Strangulated syntax for the masses
Swanksigns
Dedicated to the art of mocking public works
Jabberwacky
A chatbot - and contender for the Turing prize.
Teasmade.com
A website devoted to the Teasmade.
Camp Events at Gay Rodeos
Oh dearie me. Goat dressing? Sometimes I despair...
We Feel Fine
Is the Art? Science? Both?
Urinal.Net
The best place to piss away your time on the internet
The Radio Guy's Collection
Oddball and scary scientific stuff, and more...
Wordsplosion!
A site to grind one's teeth over if you're a grammar pedant.

Blog list: Blog list

Tue, 26 Aug 2008 16:08:49 GMT

Random Acts of Reality
A blog written by an emergency medical technician working for the London Ambulance Service
Language Log
Musings on Language
Coffee Corner
A colleague's Blog
A Nice Cup of Tea and a Sit Down
Mission statement: Well I think we should all sit down and havea nice cup of tea, and some biscuits, nice ones mind you. Oh and some cake would be nice as well. Lovely.
Apparently Nothing
A rather beautiful photoblog
Pepys' Diary
The diaries of Samuel Pepys done as a blog
Cooking for Engineers
Title says it all
The Passionate Cook
Cooking is like love. It should be entered into with abandon ornot at all.
WorldChanging
Models, Tools, and Ideas for Building a Bright Green Future
Chromasia
Another photoblog of stunning images
Opinionated About Dining
The name says it all
Shut Up you Fat Whiner!
Salam Pax, blogging from Baghdad
Operation Eden
A chronicle of what hurricane Katrina has done to people
Rachel from North London
A survivor of the London Bombing on 7th July 2005
Under Brian's Rock
Good writing here
An Experiment in Normality
More good writing
NHS Blog Doctor
Dr. Crippen documents how the NHS is going down the tubes
Alastair Appleton
BBC Presenter and off on another plane
Unspeak
Words are weapons
Obscene Desserts
Life, death, and many things in between
One Good Thing
Flea writes about her life. It's worth reading
Stephen Fry
One of Britain's National Treasures, with his equally great blog.
Ballardian
Looking at the world through the sensibilities of J. G. Ballard
Butterfliesandwheels
Fighting fashionable nonsense
Celebrating Sagan
Remembering Carl Sagan and his contributions to humanity
Sense About Science
Trying to combat pseudoscience and woo-woo
The Loom
Writings on Science and Evolution
Pharyngula
Blog of Paul Z. Myers, associate professor of biology at UMM
The Panda's Thumb
The virtual pub where patrons gather to discuss evolutionary theory, critique the claims of the antievolution movement, defend the integrity of both science and science education, and share good conversation.
The Richard Dawkins Foundation
A clear-thinking oasis
Ask The Atheists
A resource for people who are curious about atheism and to counter some misunderstandings about this way of looking at the world
I Blame the Patriarchy
being the blog of Twisty Faster, a gentleman farmer and spinsteraunt
GayUganda
A reminder that many kindred spirits live in a state of unease that is not of their doing, and some quite literally in fear for their lives.
Future Perfect
The collision between people, societies and technology

Custom List: HomePages

Fri, 11 Jan 2008 14:09:05 GMT

HomePages

Music List: Kate Bush

Thu, 10 Jan 2008 15:47:43 GMT

Kate Bush

Kate Bush: AerialAerial [UK] Disc 2
Kate Bush: Aerial TalAerial [UK] Disc 2
Kate Bush: An Architect's DreamAerial [UK] Disc 2
Kate Bush: BertieAerial [UK] Disc 1
Kate Bush: Coral RoomAerial [UK] Disc 1
Kate Bush: How To Be InvisibleAerial [UK] Disc 1
Kate Bush: JoanniAerial [UK] Disc 1
Kate Bush: King Of The MountainAerial [UK] Disc 1
Kate Bush: Mrs. BartolozziAerial [UK] Disc 1
Kate Bush: NocturnAerial [UK] Disc 2
Kate Bush: Painter's LinkAerial [UK] Disc 2
Kate Bush: PiAerial [UK] Disc 1
Kate Bush: PreludeAerial [UK] Disc 2
Kate Bush: PrologueAerial [UK] Disc 2
Kate Bush: Somewhere In BetweenAerial [UK] Disc 2
Kate Bush: SunsetAerial [UK] Disc 2